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Conserved domains on  [gi|349732166|ref|NP_001093345|]
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tRNA methyltransferase 2 homolog A S homeolog [Xenopus laevis]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TrmA COG2265
tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure ...
 189-600 3.11e-71

tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family is part of the Pathway/BioSystem: tRNA modification


:

Pssm-ID: 441866 [Multi-domain]  Cd Length: 377  Bit Score: 234.69  E-value: 3.11e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 189 WQ-VPYEEQLKIKEEecckVLKQLTKEIGVNNKPlmpwlfeqkqkynrlccPLERVIPSPIQTEYRNKSEFligyGVNRE 267
Cdd:COG2265   78 LQhLSYEAQLELKQR----VVREALERIGGLPEV-----------------EVEPIIGSPEPWGYRNRARL----SVRRT 132

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 268 DKTVgcRLSKYKGGTCAVVEPFDTINIPPVTKNVVKAFQEYIRSTpydvyspETYDGHWKQLTVRttrkgqvmaivyfnp 347
Cdd:COG2265  133 DGRL--RLGFYARGSHELVDIDECPLLDPALNALLPALRELLAEL-------GARRGELRHLVVR--------------- 188

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 348 qklpkevltelkaslsdyftkgsgkesgvtslyfveegqrksplledlpvehvAGDQYIYEDLLGLSFRISPHAFFQVNT 427
Cdd:COG2265  189 -----------------------------------------------------AGRDYLTERLGGLTFRISPGSFFQVNP 215

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 428 LAAEVLYSAIGDWAQLDQDTTVLDVCCGTGTIGISLAKKVKKVVGIELCQEAIADAKANAQLNNLDNVEFRCGKAEDIFP 507
Cdd:COG2265  216 EQAEALYAAALEWLDLTGGERVLDLYCGVGTFALPLARRAKKVIGVEIVPEAVEDARENARLNGLKNVEFVAGDLEEVLP 295

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 508 TLINSYTFpsPLAIVDPPRAGLHSKVIIAIRKAEhLKQLIYVSCNPKAamnnFV-DLcrapsNRVKGRPFRPIKALAVDL 586
Cdd:COG2265  296 ELLWGGRP--DVVVLDPPRAGAGPEVLEALAALG-PRRIVYVSCNPAT----LArDL-----ALLVEGGYRLEKVQPVDM 363

                        410
                 ....*....|....
gi 349732166 587 FPQTPHFELVILFE 600
Cdd:COG2265  364 FPHTHHVESVALLE 377
RRM_TRMT2A cd12439
RNA recognition motif (RRM) found in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and ...
 65-143 4.43e-46

RNA recognition motif (RRM) found in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins; This subfamily corresponds to the RRM of TRMT2A, also known as HpaII tiny fragments locus 9c protein (HTF9C), a novel cell cycle regulated protein. It is an independent biologic factor expressed in tumors associated with clinical outcome in HER2 expressing breast cancer. The function of TRMT2A remains unclear although by sequence homology it has a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), related to RNA methyltransferases.


:

Pssm-ID: 409873 [Multi-domain]  Cd Length: 79  Bit Score: 157.02  E-value: 4.43e-46
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 349732166  65 FTSEIFKVEIQNLPKYIGFNDLKKFLGKYGLNPHKIKLMKKQTFAFVTFKSEEERDKAMKVIHGVMWKNRPLSVRLAKP 143
Cdd:cd12439    1 FTSEIFKIEIKNLPKYIGFGQLKKFLQKLGLKPHKIKLIGRQTFAFVTFRNEEDRDKALKVLNGHKWKGKVLSAKLAKP 79
 
Name Accession Description Interval E-value
TrmA COG2265
tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure ...
 189-600 3.11e-71

tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 441866 [Multi-domain]  Cd Length: 377  Bit Score: 234.69  E-value: 3.11e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 189 WQ-VPYEEQLKIKEEecckVLKQLTKEIGVNNKPlmpwlfeqkqkynrlccPLERVIPSPIQTEYRNKSEFligyGVNRE 267
Cdd:COG2265   78 LQhLSYEAQLELKQR----VVREALERIGGLPEV-----------------EVEPIIGSPEPWGYRNRARL----SVRRT 132

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 268 DKTVgcRLSKYKGGTCAVVEPFDTINIPPVTKNVVKAFQEYIRSTpydvyspETYDGHWKQLTVRttrkgqvmaivyfnp 347
Cdd:COG2265  133 DGRL--RLGFYARGSHELVDIDECPLLDPALNALLPALRELLAEL-------GARRGELRHLVVR--------------- 188

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 348 qklpkevltelkaslsdyftkgsgkesgvtslyfveegqrksplledlpvehvAGDQYIYEDLLGLSFRISPHAFFQVNT 427
Cdd:COG2265  189 -----------------------------------------------------AGRDYLTERLGGLTFRISPGSFFQVNP 215

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 428 LAAEVLYSAIGDWAQLDQDTTVLDVCCGTGTIGISLAKKVKKVVGIELCQEAIADAKANAQLNNLDNVEFRCGKAEDIFP 507
Cdd:COG2265  216 EQAEALYAAALEWLDLTGGERVLDLYCGVGTFALPLARRAKKVIGVEIVPEAVEDARENARLNGLKNVEFVAGDLEEVLP 295

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 508 TLINSYTFpsPLAIVDPPRAGLHSKVIIAIRKAEhLKQLIYVSCNPKAamnnFV-DLcrapsNRVKGRPFRPIKALAVDL 586
Cdd:COG2265  296 ELLWGGRP--DVVVLDPPRAGAGPEVLEALAALG-PRRIVYVSCNPAT----LArDL-----ALLVEGGYRLEKVQPVDM 363

                        410
                 ....*....|....
gi 349732166 587 FPQTPHFELVILFE 600
Cdd:COG2265  364 FPHTHHVESVALLE 377
RRM_TRMT2A cd12439
RNA recognition motif (RRM) found in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and ...
 65-143 4.43e-46

RNA recognition motif (RRM) found in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins; This subfamily corresponds to the RRM of TRMT2A, also known as HpaII tiny fragments locus 9c protein (HTF9C), a novel cell cycle regulated protein. It is an independent biologic factor expressed in tumors associated with clinical outcome in HER2 expressing breast cancer. The function of TRMT2A remains unclear although by sequence homology it has a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), related to RNA methyltransferases.


Pssm-ID: 409873 [Multi-domain]  Cd Length: 79  Bit Score: 157.02  E-value: 4.43e-46
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 349732166  65 FTSEIFKVEIQNLPKYIGFNDLKKFLGKYGLNPHKIKLMKKQTFAFVTFKSEEERDKAMKVIHGVMWKNRPLSVRLAKP 143
Cdd:cd12439    1 FTSEIFKIEIKNLPKYIGFGQLKKFLQKLGLKPHKIKLIGRQTFAFVTFRNEEDRDKALKVLNGHKWKGKVLSAKLAKP 79
rumA TIGR00479
23S rRNA (uracil-5-)-methyltransferase RumA; This protein family was first proposed to be RNA ...
 189-594 3.81e-44

23S rRNA (uracil-5-)-methyltransferase RumA; This protein family was first proposed to be RNA methyltransferases by homology to the TrmA family. The member from E. coli has now been shown to act as the 23S RNA methyltransferase for the conserved U1939. The gene is now designated rumA and was previously designated ygcA. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 129571 [Multi-domain]  Cd Length: 431  Bit Score: 163.07  E-value: 3.81e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166  189 WQ-VPYEEQLKIKEEECCKVLKQLTKeigVNNKPLMPWLFEQKQKYNrlccplervipspiqteYRNKSEFLIGYgvnre 267
Cdd:TIGR00479  69 LQhLSYELQLRSKQQQVIALLERIGK---FVSEPIEDVPTIGDDPWG-----------------YRNKARLSLGR----- 123

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166  268 DKTVGCRLSKYKGGT--------CAVVEPFDTINIPPVTKNVVKafqeyirstpydvYSPETYDGHWKQLTVRT------ 333
Cdd:TIGR00479 124 SPSGQLQAGFYQKGShdivdvkqCPVQAPALNALLPKVRAILEN-------------FGASRYLEHKELGQARHgvlrig 190

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166  334 TRKGQVMAIVYFNPQKLP--KEVLTELKASLSDYFTKGSGKESGVTSLYFVEEgqrksplledlpVEHVAGDQYIYEDLL 411
Cdd:TIGR00479 191 RHTGELSSVDRTALERFPhkEELDLYLQPDSPDVKSICQNINPEKTNVIFGEE------------TEVIAGEMPIYDKSG 258

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166  412 GLSFRISPHAFFQVNTLAAEVLYSAIGDWAQLDQDTTVLDVCCGTGTIGISLAKKVKKVVGIELCQEAIADAKANAQLNN 491
Cdd:TIGR00479 259 DLSFTFSARDFIQVNSGQNEKLVDRALEWLELQGEERVLDAYCGMGTFTLPLAKQAKSVVGVEGVPESVEKAQQNAELNG 338

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166  492 LDNVEFRCGKAEDIFPTLINSYTFPSPLaIVDPPRAGLHSKVIIAIRKAEHlKQLIYVSCNPKAAMNNFVDLCRApsnrv 571
Cdd:TIGR00479 339 IANVTFYHGTLETVLPKQPWAGNGFDKV-LLDPPRKGCAAGVLRTIIKLKP-ERIVYVSCNPATLARDLEALCKA----- 411

                         410       420
                  ....*....|....*....|...
gi 349732166  572 kgrPFRPIKALAVDLFPQTPHFE 594
Cdd:TIGR00479 412 ---GYTIARVQPVDMFPHTGHVE 431
rumB PRK03522
23S rRNA (uracil(747)-C(5))-methyltransferase RlmC;
391-601 1.15e-27

23S rRNA (uracil(747)-C(5))-methyltransferase RlmC;


Pssm-ID: 235128 [Multi-domain]  Cd Length: 315  Bit Score: 113.81  E-value: 1.15e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 391 LLEDLP---V-------EHVA---GDQYIY--------EDLLGLSFRISPHAFFQVNTLAAEVLYSAIGDWAQLDQDTTV 449
Cdd:PRK03522  98 LQAQLPqlkVisvniqpVHMAileGEEEIFlteqqalpERFNGVPLFIRPQSFFQTNPAVAAQLYATARDWVRELPPRSM 177

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 450 LDVCCGTGTIGISLAKKVKKVVGIELCQEAIADAKANAQLNNLDNVEFRCGKAEDiFPTliNSYTFPSpLAIVDPPRAGl 529
Cdd:PRK03522 178 WDLFCGVGGFGLHCATPGMQLTGIEISAEAIACAKQSAAELGLTNVQFQALDSTQ-FAT--AQGEVPD-LVLVNPPRRG- 252

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 349732166 530 hskviIAIRKAEHLKQ-----LIYVSCNPKAAMNnfvDLCRAPSnrvkgrpFRPIKALAVDLFPQTPHFELVILFER 601
Cdd:PRK03522 253 -----IGKELCDYLSQmaprfILYSSCNAQTMAK---DLAHLPG-------YRIERVQLFDMFPHTAHYEVLTLLVR 314
tRNA_U5-meth_tr pfam05958
tRNA (Uracil-5-)-methyltransferase; This family consists of (Uracil-5-)-methyltransferases EC: ...
 393-601 1.05e-16

tRNA (Uracil-5-)-methyltransferase; This family consists of (Uracil-5-)-methyltransferases EC:2.1.1.35 from bacteria, archaea and eukaryotes. A 5-methyluridine (m(5)U) residue at position 54 is a conserved feature of bacterial and eukaryotic tRNAs. The methylation of U54 is catalyzed by the tRNA(m5U54)methyltransferase, which in Saccharomyces cerevisiae is encoded by the nonessential TRM2 gene. It is thought that tRNA modification enzymes might have a role in tRNA maturation not necessarily linked to their known catalytic activity.


Pssm-ID: 428692  Cd Length: 357  Bit Score: 82.10  E-value: 1.05e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166  393 EDLPVehvAGDQYIYEDLLGlSFrISPHAFFQVNTL--AAEVLYSAIGDwaqldqdttVLDVCCGTGTIGISLAKKVKKV 470
Cdd:pfam05958 161 ETLPV---AGREFIYRQVEN-SF-TQPNAAVNIKMLewACDVTQGSKGD---------LLELYCGNGNFSLALARNFRKV 226

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166  471 VGIELCQEAIADAKANAQLNNLDNVEFRCGKAEDI---------FPTL----INSYTFPSPLaiVDPPRAGLHSKVIIAI 537
Cdd:pfam05958 227 LATEIAKPSVAAAQYNIAANNIDNVQIIRMSAEEFtqamngvreFNRLkgidLKSYNCSTIF--VDPPRAGLDPETLKLV 304

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 349732166  538 RKAEhlkQLIYVSCNPKAAMNNFVDLCRapSNRVKgrpfrpiKALAVDLFPQTPHFELVILFER 601
Cdd:pfam05958 305 QAYP---RILYISCNPETLCANLEQLSK--THRVE-------RFALFDQFPYTHHMECGVLLEK 356
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 448-540 1.86e-12

S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).


Pssm-ID: 100107 [Multi-domain]  Cd Length: 107  Bit Score: 63.99  E-value: 1.86e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 448 TVLDVCCGTGTIGISLAK-KVKKVVGIELCQEAIADAKANAQLNNLDNVEFRCGKAEDIFPTLINSYTFpsplAIVDPP- 525
Cdd:cd02440    1 RVLDLGCGTGALALALASgPGARVTGVDISPVALELARKAAAALLADNVEVLKGDAEELPPEADESFDV----IISDPPl 76

                         90
                 ....*....|....*..
gi 349732166 526 --RAGLHSKVIIAIRKA 540
Cdd:cd02440   77 hhLVEDLARFLEEARRL 93
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
76-146 3.34e-10

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 56.64  E-value: 3.34e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 349732166  76 NLPKYIGFNDLKKFLGKYGlNPHKIKLMK-KQT-----FAFVTFKSEEERDKAMKVIHGVMWKNRPLSVRLAKPRAD 146
Cdd:COG0724    8 NLPYSVTEEDLRELFSEYG-EVTSVKLITdRETgrsrgFGFVEMPDDEEAQAAIEALNGAELMGRTLKVNEARPREE 83
RRM smart00360
RNA recognition motif;
74-138 1.28e-08

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 51.83  E-value: 1.28e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 349732166    74 IQNLPKYIGFNDLKKFLGKYGlNPHKIKLMKKQT------FAFVTFKSEEERDKAMKVIHGVMWKNRPLSV 138
Cdd:smart00360   4 VGNLPPDTTEEELRELFSKFG-KVESVRLVRDKEtgkskgFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 74-136 6.59e-07

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 46.84  E-value: 6.59e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 349732166   74 IQNLPKYIGFNDLKKFLGKYGLnPHKIKLMKKQT-----FAFVTFKSEEERDKAMKVIHGVMWKNRPL 136
Cdd:pfam00076   3 VGNLPPDTTEEDLKDLFSKFGP-IKSIRLVRDETgrskgFAFVEFEDEEDAEKAIEALNGKELGGREL 69
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 49-154 1.81e-05

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 47.88  E-value: 1.81e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166   49 ESKDKA-GIYRYIK--DDLFTSEifkveiqnlpkyigfnDLKKFLGKYGlNPHKIKLMKKQT-----FAFVTFKSEEERD 120
Cdd:TIGR01628 278 ERKMKAqGVNLYVKnlDDTVTDE----------------KLRELFSECG-EITSAKVMLDEKgvsrgFGFVCFSNPEEAN 340

                          90       100       110
                  ....*....|....*....|....*....|....
gi 349732166  121 KAMKVIHGVMWKNRPLSVRLAKPRADPIMQKRKQ 154
Cdd:TIGR01628 341 RAVTEMHGRMLGGKPLYVALAQRKEQRRAHLQDQ 374
 
Name Accession Description Interval E-value
TrmA COG2265
tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure ...
 189-600 3.11e-71

tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 441866 [Multi-domain]  Cd Length: 377  Bit Score: 234.69  E-value: 3.11e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 189 WQ-VPYEEQLKIKEEecckVLKQLTKEIGVNNKPlmpwlfeqkqkynrlccPLERVIPSPIQTEYRNKSEFligyGVNRE 267
Cdd:COG2265   78 LQhLSYEAQLELKQR----VVREALERIGGLPEV-----------------EVEPIIGSPEPWGYRNRARL----SVRRT 132

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 268 DKTVgcRLSKYKGGTCAVVEPFDTINIPPVTKNVVKAFQEYIRSTpydvyspETYDGHWKQLTVRttrkgqvmaivyfnp 347
Cdd:COG2265  133 DGRL--RLGFYARGSHELVDIDECPLLDPALNALLPALRELLAEL-------GARRGELRHLVVR--------------- 188

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 348 qklpkevltelkaslsdyftkgsgkesgvtslyfveegqrksplledlpvehvAGDQYIYEDLLGLSFRISPHAFFQVNT 427
Cdd:COG2265  189 -----------------------------------------------------AGRDYLTERLGGLTFRISPGSFFQVNP 215

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 428 LAAEVLYSAIGDWAQLDQDTTVLDVCCGTGTIGISLAKKVKKVVGIELCQEAIADAKANAQLNNLDNVEFRCGKAEDIFP 507
Cdd:COG2265  216 EQAEALYAAALEWLDLTGGERVLDLYCGVGTFALPLARRAKKVIGVEIVPEAVEDARENARLNGLKNVEFVAGDLEEVLP 295

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 508 TLINSYTFpsPLAIVDPPRAGLHSKVIIAIRKAEhLKQLIYVSCNPKAamnnFV-DLcrapsNRVKGRPFRPIKALAVDL 586
Cdd:COG2265  296 ELLWGGRP--DVVVLDPPRAGAGPEVLEALAALG-PRRIVYVSCNPAT----LArDL-----ALLVEGGYRLEKVQPVDM 363

                        410
                 ....*....|....
gi 349732166 587 FPQTPHFELVILFE 600
Cdd:COG2265  364 FPHTHHVESVALLE 377
RRM_TRMT2A cd12439
RNA recognition motif (RRM) found in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and ...
 65-143 4.43e-46

RNA recognition motif (RRM) found in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins; This subfamily corresponds to the RRM of TRMT2A, also known as HpaII tiny fragments locus 9c protein (HTF9C), a novel cell cycle regulated protein. It is an independent biologic factor expressed in tumors associated with clinical outcome in HER2 expressing breast cancer. The function of TRMT2A remains unclear although by sequence homology it has a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), related to RNA methyltransferases.


Pssm-ID: 409873 [Multi-domain]  Cd Length: 79  Bit Score: 157.02  E-value: 4.43e-46
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 349732166  65 FTSEIFKVEIQNLPKYIGFNDLKKFLGKYGLNPHKIKLMKKQTFAFVTFKSEEERDKAMKVIHGVMWKNRPLSVRLAKP 143
Cdd:cd12439    1 FTSEIFKIEIKNLPKYIGFGQLKKFLQKLGLKPHKIKLIGRQTFAFVTFRNEEDRDKALKVLNGHKWKGKVLSAKLAKP 79
rumA TIGR00479
23S rRNA (uracil-5-)-methyltransferase RumA; This protein family was first proposed to be RNA ...
 189-594 3.81e-44

23S rRNA (uracil-5-)-methyltransferase RumA; This protein family was first proposed to be RNA methyltransferases by homology to the TrmA family. The member from E. coli has now been shown to act as the 23S RNA methyltransferase for the conserved U1939. The gene is now designated rumA and was previously designated ygcA. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 129571 [Multi-domain]  Cd Length: 431  Bit Score: 163.07  E-value: 3.81e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166  189 WQ-VPYEEQLKIKEEECCKVLKQLTKeigVNNKPLMPWLFEQKQKYNrlccplervipspiqteYRNKSEFLIGYgvnre 267
Cdd:TIGR00479  69 LQhLSYELQLRSKQQQVIALLERIGK---FVSEPIEDVPTIGDDPWG-----------------YRNKARLSLGR----- 123

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166  268 DKTVGCRLSKYKGGT--------CAVVEPFDTINIPPVTKNVVKafqeyirstpydvYSPETYDGHWKQLTVRT------ 333
Cdd:TIGR00479 124 SPSGQLQAGFYQKGShdivdvkqCPVQAPALNALLPKVRAILEN-------------FGASRYLEHKELGQARHgvlrig 190

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166  334 TRKGQVMAIVYFNPQKLP--KEVLTELKASLSDYFTKGSGKESGVTSLYFVEEgqrksplledlpVEHVAGDQYIYEDLL 411
Cdd:TIGR00479 191 RHTGELSSVDRTALERFPhkEELDLYLQPDSPDVKSICQNINPEKTNVIFGEE------------TEVIAGEMPIYDKSG 258

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166  412 GLSFRISPHAFFQVNTLAAEVLYSAIGDWAQLDQDTTVLDVCCGTGTIGISLAKKVKKVVGIELCQEAIADAKANAQLNN 491
Cdd:TIGR00479 259 DLSFTFSARDFIQVNSGQNEKLVDRALEWLELQGEERVLDAYCGMGTFTLPLAKQAKSVVGVEGVPESVEKAQQNAELNG 338

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166  492 LDNVEFRCGKAEDIFPTLINSYTFPSPLaIVDPPRAGLHSKVIIAIRKAEHlKQLIYVSCNPKAAMNNFVDLCRApsnrv 571
Cdd:TIGR00479 339 IANVTFYHGTLETVLPKQPWAGNGFDKV-LLDPPRKGCAAGVLRTIIKLKP-ERIVYVSCNPATLARDLEALCKA----- 411

                         410       420
                  ....*....|....*....|...
gi 349732166  572 kgrPFRPIKALAVDLFPQTPHFE 594
Cdd:TIGR00479 412 ---GYTIARVQPVDMFPHTGHVE 431
rumB PRK03522
23S rRNA (uracil(747)-C(5))-methyltransferase RlmC;
391-601 1.15e-27

23S rRNA (uracil(747)-C(5))-methyltransferase RlmC;


Pssm-ID: 235128 [Multi-domain]  Cd Length: 315  Bit Score: 113.81  E-value: 1.15e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 391 LLEDLP---V-------EHVA---GDQYIY--------EDLLGLSFRISPHAFFQVNTLAAEVLYSAIGDWAQLDQDTTV 449
Cdd:PRK03522  98 LQAQLPqlkVisvniqpVHMAileGEEEIFlteqqalpERFNGVPLFIRPQSFFQTNPAVAAQLYATARDWVRELPPRSM 177

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 450 LDVCCGTGTIGISLAKKVKKVVGIELCQEAIADAKANAQLNNLDNVEFRCGKAEDiFPTliNSYTFPSpLAIVDPPRAGl 529
Cdd:PRK03522 178 WDLFCGVGGFGLHCATPGMQLTGIEISAEAIACAKQSAAELGLTNVQFQALDSTQ-FAT--AQGEVPD-LVLVNPPRRG- 252

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 349732166 530 hskviIAIRKAEHLKQ-----LIYVSCNPKAAMNnfvDLCRAPSnrvkgrpFRPIKALAVDLFPQTPHFELVILFER 601
Cdd:PRK03522 253 -----IGKELCDYLSQmaprfILYSSCNAQTMAK---DLAHLPG-------YRIERVQLFDMFPHTAHYEVLTLLVR 314
rumA PRK13168
23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD;
386-601 2.33e-22

23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD;


Pssm-ID: 237291 [Multi-domain]  Cd Length: 443  Bit Score: 100.23  E-value: 2.33e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 386 QRKSPLLEDLPVEHVAGDQYIYEDLlGLSFRISPHAFFQVNTLAAEVLYS-AIgDWAQLDQDTTVLDVCCGTGTIGISLA 464
Cdd:PRK13168 239 QPKGPDLVHLLGPADAQLSYYLPEF-GLRLAFSPRDFIQVNAQVNQKMVArAL-EWLDPQPGDRVLDLFCGLGNFTLPLA 316

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 465 KKVKKVVGIELCQEAIADAKANAQLNNLDNVEFRCGKAEDIFPTlinsytfpSPLA-------IVDPPRAGlhskviiAI 537
Cdd:PRK13168 317 RQAAEVVGVEGVEAMVERARENARRNGLDNVTFYHANLEEDFTD--------QPWAlggfdkvLLDPPRAG-------AA 381

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 349732166 538 RKAEHLKQL-----IYVSCNPkaamnnfVDLCRAPSNRVKGrPFRPIKALAVDLFPQTPHFELVILFER 601
Cdd:PRK13168 382 EVMQALAKLgpkriVYVSCNP-------ATLARDAGVLVEA-GYRLKRAGMLDMFPHTGHVESMALFER 442
tRNA_U5-meth_tr pfam05958
tRNA (Uracil-5-)-methyltransferase; This family consists of (Uracil-5-)-methyltransferases EC: ...
 393-601 1.05e-16

tRNA (Uracil-5-)-methyltransferase; This family consists of (Uracil-5-)-methyltransferases EC:2.1.1.35 from bacteria, archaea and eukaryotes. A 5-methyluridine (m(5)U) residue at position 54 is a conserved feature of bacterial and eukaryotic tRNAs. The methylation of U54 is catalyzed by the tRNA(m5U54)methyltransferase, which in Saccharomyces cerevisiae is encoded by the nonessential TRM2 gene. It is thought that tRNA modification enzymes might have a role in tRNA maturation not necessarily linked to their known catalytic activity.


Pssm-ID: 428692  Cd Length: 357  Bit Score: 82.10  E-value: 1.05e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166  393 EDLPVehvAGDQYIYEDLLGlSFrISPHAFFQVNTL--AAEVLYSAIGDwaqldqdttVLDVCCGTGTIGISLAKKVKKV 470
Cdd:pfam05958 161 ETLPV---AGREFIYRQVEN-SF-TQPNAAVNIKMLewACDVTQGSKGD---------LLELYCGNGNFSLALARNFRKV 226

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166  471 VGIELCQEAIADAKANAQLNNLDNVEFRCGKAEDI---------FPTL----INSYTFPSPLaiVDPPRAGLHSKVIIAI 537
Cdd:pfam05958 227 LATEIAKPSVAAAQYNIAANNIDNVQIIRMSAEEFtqamngvreFNRLkgidLKSYNCSTIF--VDPPRAGLDPETLKLV 304

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 349732166  538 RKAEhlkQLIYVSCNPKAAMNNFVDLCRapSNRVKgrpfrpiKALAVDLFPQTPHFELVILFER 601
Cdd:pfam05958 305 QAYP---RILYISCNPETLCANLEQLSK--THRVE-------RFALFDQFPYTHHMECGVLLEK 356
PRK09328 PRK09328
N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional
 391-500 6.82e-16

N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional


Pssm-ID: 236467 [Multi-domain]  Cd Length: 275  Bit Score: 78.28  E-value: 6.82e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 391 LLEDLPVEHVAGDQYIYedllGLSFRISPHAF---FQVNTLAAEVLysaigDWAQLDQDTTVLDVCCGTGTIGISLAKKV 467
Cdd:PRK09328  60 RAAGEPLQYILGEAEFW----GLDFKVSPGVLiprPETEELVEWAL-----EALLLKEPLRVLDLGTGSGAIALALAKER 130

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 349732166 468 K--KVVGIELCQEAIADAKANAQLNNLDNVEFRCG 500
Cdd:PRK09328 131 PdaEVTAVDISPEALAVARRNAKHGLGARVEFLQG 165
PRK05031 PRK05031
tRNA (uracil-5-)-methyltransferase; Validated
 391-601 1.00e-15

tRNA (uracil-5-)-methyltransferase; Validated


Pssm-ID: 235332  Cd Length: 362  Bit Score: 79.10  E-value: 1.00e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 391 LLEDLPVehvAGDQYIY---EDllglSFrISPHAFFQVNTL--AAEVLYSAIGDwaqldqdttVLDVCCGTGTIGISLAK 465
Cdd:PRK05031 164 VDERLPV---AGREFIYrqvEN----SF-TQPNAAVNEKMLewALDATKGSKGD---------LLELYCGNGNFTLALAR 226

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 466 KVKKVVGIELCQEAIADAKANAQLNNLDNVEFRCGKAEDI---------FPTL----INSYTFPSPLaiVDPPRAGLHSK 532
Cdd:PRK05031 227 NFRRVLATEISKPSVAAAQYNIAANGIDNVQIIRMSAEEFtqamngvreFNRLkgidLKSYNFSTIF--VDPPRAGLDDE 304

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 533 VIIAIRKAEhlkQLIYVSCNPKAAMNNFVDLCRapSNRvkgrpfrpIKALAV-DLFPQTPHFELVILFER 601
Cdd:PRK05031 305 TLKLVQAYE---RILYISCNPETLCENLETLSQ--THK--------VERFALfDQFPYTHHMECGVLLEK 361
HemK COG2890
Methylase of polypeptide chain release factors [Translation, ribosomal structure and ...
 396-506 2.20e-14

Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis];


Pssm-ID: 442135 [Multi-domain]  Cd Length: 282  Bit Score: 74.03  E-value: 2.20e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 396 PVEHVAGDQYIYedllGLSFRISPHAFfqV---NTlaaEVLYSAIGDWAQLDQDTTVLDVCCGTGTIGISLAKKVK--KV 470
Cdd:COG2890   69 PLAYILGEAEFY----GLEFKVDPGVL--IprpET---EELVELALALLPAGAPPRVLDLGTGSGAIALALAKERPdaRV 139

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 349732166 471 VGIELCQEAIADAKANAQLNNLDN-VEFRCGkaeDIF 506
Cdd:COG2890  140 TAVDISPDALAVARRNAERLGLEDrVRFLQG---DLF 173
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 448-540 1.86e-12

S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).


Pssm-ID: 100107 [Multi-domain]  Cd Length: 107  Bit Score: 63.99  E-value: 1.86e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 448 TVLDVCCGTGTIGISLAK-KVKKVVGIELCQEAIADAKANAQLNNLDNVEFRCGKAEDIFPTLINSYTFpsplAIVDPP- 525
Cdd:cd02440    1 RVLDLGCGTGALALALASgPGARVTGVDISPVALELARKAAAALLADNVEVLKGDAEELPPEADESFDV----IISDPPl 76

                         90
                 ....*....|....*..
gi 349732166 526 --RAGLHSKVIIAIRKA 540
Cdd:cd02440   77 hhLVEDLARFLEEARRL 93
Methyltransf_25 pfam13649
Methyltransferase domain; This family appears to be a methyltransferase domain.
 449-505 3.94e-12

Methyltransferase domain; This family appears to be a methyltransferase domain.


Pssm-ID: 463945 [Multi-domain]  Cd Length: 96  Bit Score: 62.58  E-value: 3.94e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 349732166  449 VLDVCCGTGTIGISLAKKVK-KVVGIELCQEAIADAKANAQLNNLdNVEFRCGKAEDI 505
Cdd:pfam13649   1 VLDLGCGTGRLTLALARRGGaRVTGVDLSPEMLERARERAAEAGL-NVEFVQGDAEDL 57
TrmN6 COG4123
tRNA1(Val) A37 N6-methylase TrmN6 [Translation, ribosomal structure and biogenesis]; tRNA1(Val) ...
 438-525 8.35e-12

tRNA1(Val) A37 N6-methylase TrmN6 [Translation, ribosomal structure and biogenesis]; tRNA1(Val) A37 N6-methylase TrmN6 is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 443299 [Multi-domain]  Cd Length: 238  Bit Score: 65.55  E-value: 8.35e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 438 GDWAQLDQDTTVLDVCCGTGTIGISLAKKVK--KVVGIELCQEAIADAKANAQLNNLDN-VEFRCGKAEDIFPTLI-NSY 513
Cdd:COG4123   30 AAFAPVKKGGRVLDLGTGTGVIALMLAQRSPgaRITGVEIQPEAAELARRNVALNGLEDrITVIHGDLKEFAAELPpGSF 109

                         90
                 ....*....|..
gi 349732166 514 TfpspLAIVDPP 525
Cdd:COG4123  110 D----LVVSNPP 117
SmtA COG0500
SAM-dependent methyltransferase [Secondary metabolites biosynthesis, transport and catabolism, ...
 441-507 1.00e-11

SAM-dependent methyltransferase [Secondary metabolites biosynthesis, transport and catabolism, General function prediction only];


Pssm-ID: 440266 [Multi-domain]  Cd Length: 199  Bit Score: 64.55  E-value: 1.00e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 349732166 441 AQLDQDTTVLDVCCGTGTIGISLAKKVK-KVVGIELCQEAIADAKANAQLNNLDNVEFRCGKAEDIFP 507
Cdd:COG0500   22 ERLPKGGRVLDLGCGTGRNLLALAARFGgRVIGIDLSPEAIALARARAAKAGLGNVEFLVADLAELDP 89
Methyltransf_31 pfam13847
Methyltransferase domain; This family appears to have methyltransferase activity.
 443-505 3.08e-11

Methyltransferase domain; This family appears to have methyltransferase activity.


Pssm-ID: 463998 [Multi-domain]  Cd Length: 150  Bit Score: 61.66  E-value: 3.08e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 349732166  443 LDQDTTVLDVCCGTGTIGISLAKKV---KKVVGIELCQEAIADAKANAQLNNLDNVEFRCGKAEDI 505
Cdd:pfam13847   1 IDKGMRVLDLGCGTGHLSFELAEELgpnAEVVGIDISEEAIEKARENAQKLGFDNVEFEQGDIEEL 66
UbiE COG2226
Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; ...
 433-507 6.11e-11

Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG is part of the Pathway/BioSystem: Biotin biosynthesis


Pssm-ID: 441828 [Multi-domain]  Cd Length: 143  Bit Score: 60.78  E-value: 6.11e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 349732166 433 LYSAIGDWAQLDQDTTVLDVCCGTGTIGISLAKKVKKVVGIELCQEAIADAKANAQLNNLdNVEFRCGKAEDI-FP 507
Cdd:COG2226   10 GREALLAALGLRPGARVLDLGCGTGRLALALAERGARVTGVDISPEMLELARERAAEAGL-NVEFVVGDAEDLpFP 84
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
76-146 3.34e-10

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 56.64  E-value: 3.34e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 349732166  76 NLPKYIGFNDLKKFLGKYGlNPHKIKLMK-KQT-----FAFVTFKSEEERDKAMKVIHGVMWKNRPLSVRLAKPRAD 146
Cdd:COG0724    8 NLPYSVTEEDLRELFSEYG-EVTSVKLITdRETgrsrgFGFVEMPDDEEAQAAIEALNGAELMGRTLKVNEARPREE 83
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 72-139 7.25e-10

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 55.37  E-value: 7.25e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 349732166  72 VEIQNLPKYIGFNDLKKFLGKYGlNPHKIKLMKKQT-----FAFVTFKSEEERDKAMKVIHGVMWKNRPLSVR 139
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELFSKFG-EVVSVRIVRDRDgkskgFAFVEFESPEDAEKALEALNGTELGGRPLKVS 72
RsmC COG2813
16S rRNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; 16S rRNA ...
 448-498 1.03e-09

16S rRNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; 16S rRNA G1207 methylase RsmC is part of the Pathway/BioSystem: 16S rRNA modification


Pssm-ID: 442062 [Multi-domain]  Cd Length: 191  Bit Score: 58.28  E-value: 1.03e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 349732166 448 TVLDVCCGTGTIGISLAKK--VKKVVGIELCQEAIADAKANAQLNNLDNVEFR 498
Cdd:COG2813   52 RVLDLGCGYGVIGLALAKRnpEARVTLVDVNARAVELARANAAANGLENVEVL 104
UbiG COG2227
2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme transport and ...
 441-505 1.73e-09

2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme transport and metabolism]; 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase is part of the Pathway/BioSystem: Ubiquinone biosynthesis


Pssm-ID: 441829 [Multi-domain]  Cd Length: 126  Bit Score: 56.18  E-value: 1.73e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 349732166 441 AQLDQDTTVLDVCCGTGTIGISLAKKVKKVVGIELCQEAIADAKANAQLNnldNVEFRCGKAEDI 505
Cdd:COG2227   20 RLLPAGGRVLDVGCGTGRLALALARRGADVTGVDISPEALEIARERAAEL---NVDFVQGDLEDL 81
MenG_MenH_UbiE TIGR01934
ubiquinone/menaquinone biosynthesis methyltransferases; This model represents a family of ...
 439-504 1.03e-08

ubiquinone/menaquinone biosynthesis methyltransferases; This model represents a family of methyltransferases involved in the biosynthesis of menaquinone and ubiqinone. Some members such as the UbiE enzyme from E. coli are believed to act in both pathways, while others may act in only the menaquinone pathway. These methyltransferases are members of the UbiE/CoQ family of methyltransferases (pfam01209) which also contains ubiquinone methyltransferases and other methyltransferases. Members of this clade include a wide distribution of bacteria and eukaryotes, but no archaea. An outgroup for this clade is provided by the phosphatidylethanolamine methyltransferase (EC 2.1.1.17) from Rhodobacter sphaeroides. Note that a number of non-orthologous genes which are members of pfam03737 have been erroneously annotated as MenG methyltransferases. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone]


Pssm-ID: 273884 [Multi-domain]  Cd Length: 223  Bit Score: 56.12  E-value: 1.03e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 349732166  439 DWAQLDQDTTVLDVCCGTGTIGISLAKKV---KKVVGIELCQEAIADAKANAQLNNldNVEFRCGKAED 504
Cdd:TIGR01934  33 KLIGVFKGQKVLDVACGTGDLAIELAKSApdrGKVTGVDFSSEMLEVAKKKSELPL--NIEFIQADAEA 99
RRM smart00360
RNA recognition motif;
74-138 1.28e-08

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 51.83  E-value: 1.28e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 349732166    74 IQNLPKYIGFNDLKKFLGKYGlNPHKIKLMKKQT------FAFVTFKSEEERDKAMKVIHGVMWKNRPLSV 138
Cdd:smart00360   4 VGNLPPDTTEEELRELFSKFG-KVESVRLVRDKEtgkskgFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
MTS pfam05175
Methyltransferase small domain; This domain is found in ribosomal RNA small subunit ...
 449-545 2.72e-08

Methyltransferase small domain; This domain is found in ribosomal RNA small subunit methyltransferase C as well as other methyltransferases.


Pssm-ID: 428349 [Multi-domain]  Cd Length: 170  Bit Score: 53.75  E-value: 2.72e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166  449 VLDVCCGTGTIGISLAKKVKK--VVGIELCQEAIADAKANAQLNNLDNVEFRcgkAEDIF-PTLINSYTFpsplaIV-DP 524
Cdd:pfam05175  35 VLDLGCGAGVLGAALAKESPDaeLTMVDINARALESARENLAANGLENGEVV---ASDVYsGVEDGKFDL-----IIsNP 106

                          90       100
                  ....*....|....*....|....*.
gi 349732166  525 P-RAGLHSKVIIA---IRKA-EHLKQ 545
Cdd:pfam05175 107 PfHAGLATTYNVAqrfIADAkRHLRP 132
COG2263 COG2263
Predicted RNA methylase [General function prediction only];
428-540 4.44e-08

Predicted RNA methylase [General function prediction only];


Pssm-ID: 441864 [Multi-domain]  Cd Length: 199  Bit Score: 53.75  E-value: 4.44e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 428 LAAEVLYSA--IGDWAqldqDTTVLDVCCGTGTIGI-SLAKKVKKVVGIELCQEAIADAKANAqLNNLDNVEFRCGKAED 504
Cdd:COG2263   30 LAAELLHLAylRGDIE----GKTVLDLGCGTGMLAIgAALLGAKKVVGVDIDPEALEIARENA-ERLGVRVDFIRADVTR 104

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 349732166 505 IfpTLINSYT-------FPSPLAIVDPP---RAGLHSKVIIAIRKA 540
Cdd:COG2263  105 I--PLGGSVDtvvmnppFGAQRRHADRPfleKALEIAAVIYSIHNA 148
ubiE PRK00216
bifunctional demethylmenaquinone methyltransferase/2-methoxy-6-polyprenyl-1,4-benzoquinol ...
 439-507 4.63e-08

bifunctional demethylmenaquinone methyltransferase/2-methoxy-6-polyprenyl-1,4-benzoquinol methylase UbiE;


Pssm-ID: 234689 [Multi-domain]  Cd Length: 239  Bit Score: 54.39  E-value: 4.63e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 349732166 439 DWAQLDQDTTVLDVCCGTGTIGISLAKKVKK---VVGIELCQE--AIADAKAnAQLNNLDNVEFRCGKAEDI-FP 507
Cdd:PRK00216  45 KWLGVRPGDKVLDLACGTGDLAIALAKAVGKtgeVVGLDFSEGmlAVGREKL-RDLGLSGNVEFVQGDAEALpFP 118
Cfa COG2230
Cyclopropane fatty-acyl-phospholipid synthase and related methyltransferases [Lipid transport ...
 429-508 5.48e-08

Cyclopropane fatty-acyl-phospholipid synthase and related methyltransferases [Lipid transport and metabolism];


Pssm-ID: 441831 [Multi-domain]  Cd Length: 158  Bit Score: 52.62  E-value: 5.48e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 429 AAEVLYSAIGDWAQLDQDTTVLDVCCGTGTIGISLAKKVK-KVVGIELCQEAIADAKANAQLNNL-DNVEFRCGKAEDIF 506
Cdd:COG2230   35 AQEAKLDLILRKLGLKPGMRVLDIGCGWGGLALYLARRYGvRVTGVTLSPEQLEYARERAAEAGLaDRVEVRLADYRDLP 114


                 ..
gi 349732166 507 PT 508
Cdd:COG2230  115 AD 116
Trm11 COG1041
tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]; tRNA G10 ...
 441-525 9.28e-08

tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]; tRNA G10 N-methylase Trm11 is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 440663 [Multi-domain]  Cd Length: 172  Bit Score: 52.26  E-value: 9.28e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 441 AQLDQDTTVLDVCCGTGTIGISLAKKVKKVVGIELCQEAIADAKANAQLNNLDNVEFRCGKAEDIfPTLINSYTfpspLA 520
Cdd:COG1041   22 AGAKEGDTVLDPFCGTGTILIEAGLLGRRVIGSDIDPKMVEGARENLEHYGYEDADVIRGDARDL-PLADESVD----AI 96


                 ....*
gi 349732166 521 IVDPP 525
Cdd:COG1041   97 VTDPP 101
PRK14968 PRK14968
putative methyltransferase; Provisional
 448-497 1.95e-07

putative methyltransferase; Provisional


Pssm-ID: 237872 [Multi-domain]  Cd Length: 188  Bit Score: 51.44  E-value: 1.95e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 349732166 448 TVLDVCCGTGTIGISLAKKVKKVVGIELCQEAIADAKANAQLNNLDN--VEF 497
Cdd:PRK14968  26 RVLEVGTGSGIVAIVAAKNGKKVVGVDINPYAVECAKCNAKLNNIRNngVEV 77
RRM2_RBM40_like cd12239
RNA recognition motif 2 (RRM2) found in RNA-binding protein 40 (RBM40) and similar proteins; ...
 74-141 1.95e-07

RNA recognition motif 2 (RRM2) found in RNA-binding protein 40 (RBM40) and similar proteins; This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear.


Pssm-ID: 409685 [Multi-domain]  Cd Length: 82  Bit Score: 48.76  E-value: 1.95e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 349732166  74 IQNLPKYIGFNDLKKFLGKY------GLNPHKIKLMKK-----QtfAFVTFKSEEERDKAMKVIHGVMWKNRPLSVRLA 141
Cdd:cd12239    6 VKNLSKRVSEKDLKYIFGRFvdssseEKNMFDIRLMTEgrmkgQ--AFITFPSEELAEKALNLTNGYVLHGKPMVVQFA 82
Tam COG4106
Trans-aconitate methyltransferase [Energy production and conversion];
445-507 2.18e-07

Trans-aconitate methyltransferase [Energy production and conversion];


Pssm-ID: 443282 [Multi-domain]  Cd Length: 100  Bit Score: 49.05  E-value: 2.18e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 349732166 445 QDTTVLDVCCGTGTIGISLAKKVK--KVVGIELCQEAIADAKAnaqlnNLDNVEFRCGKAEDIFP 507
Cdd:COG4106    1 PPRRVLDLGCGTGRLTALLAERFPgaRVTGVDLSPEMLARARA-----RLPNVRFVVADLRDLDP 60
RlmK COG1092
23S rRNA G2069 N7-methylase RlmK or C1962 C5-methylase RlmI [Translation, ribosomal structure ...
 441-593 2.53e-07

23S rRNA G2069 N7-methylase RlmK or C1962 C5-methylase RlmI [Translation, ribosomal structure and biogenesis]; 23S rRNA G2069 N7-methylase RlmK or C1962 C5-methylase RlmI is part of the Pathway/BioSystem: 23S rRNA modification


Pssm-ID: 440709 [Multi-domain]  Cd Length: 392  Bit Score: 53.26  E-value: 2.53e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 441 AQLDQDTTVLDVCCGTGTIGISLAKK-VKKVVGIELCQEAIADAKANAQLNNL-DNVEFRCGKAEDIFPTLINSY-TFps 517
Cdd:COG1092  212 AELAKGKRVLNLFSYTGGFSVHAAAGgAKSVTSVDLSATALEWAKENAALNGLdDRHEFVQADAFDWLRELAREGeRF-- 289

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 518 PLAIVDPP-----RAGLHSkviiAIRK--------AEHLKQ---LIYVSCNPKAAMNNFVDLCRAPSNRVkGRPFRPIKA 581
Cdd:COG1092  290 DLIILDPPafaksKKDLFD----AQRDykdlnrlaLKLLAPggiLVTSSCSRHFSLDLFLEILARAARDA-GRRVRIIER 364

                        170
                 ....*....|....
gi 349732166 582 L--AVDlFPQTPHF 593
Cdd:COG1092  365 LtqPPD-HPVLPAF 377
COG4976 COG4976
Predicted methyltransferase, contains TPR repeat [General function prediction only];
428-485 3.37e-07

Predicted methyltransferase, contains TPR repeat [General function prediction only];


Pssm-ID: 444001 [Multi-domain]  Cd Length: 181  Bit Score: 50.77  E-value: 3.37e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 349732166 428 LAAEVLYSAIGDWAQ-------LDQDTTVLDVCCGTGTIGISLAKKVKKVVGIELCQEAIADAKA 485
Cdd:COG4976   22 LVEDLGYEAPALLAEellarlpPGPFGRVLDLGCGTGLLGEALRPRGYRLTGVDLSEEMLAKARE 86
RRM3_Prp24 cd12298
RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
 71-140 3.59e-07

RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.


Pssm-ID: 409739 [Multi-domain]  Cd Length: 78  Bit Score: 48.03  E-value: 3.59e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 349732166  71 KVEIQNLPKYIGFNDLKKFLGKYGlNPHKIKLMKKQT---------FAFVTFKSEEERDKAMKvIHGVMWKNRPLSVRL 140
Cdd:cd12298    2 EIRVRNLDFELDEEALRGIFEKFG-EIESINIPKKQKnrkgrhnngFAFVTFEDADSAESALQ-LNGTLLDNRKISVSL 78
CobL COG2242
Precorrin-6B methylase 2 [Coenzyme transport and metabolism]; Precorrin-6B methylase 2 is part ...
 442-521 6.46e-07

Precorrin-6B methylase 2 [Coenzyme transport and metabolism]; Precorrin-6B methylase 2 is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis


Pssm-ID: 441843 [Multi-domain]  Cd Length: 403  Bit Score: 52.09  E-value: 6.46e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 442 QLDQDTTVLDVCCGTGTIGISLAKKVK--KVVGIELCQEAIADAKANAQLNNLDNVEFRCGKAEDIFPTLinsytfPSPL 519
Cdd:COG2242  244 ALRPGDVLWDIGAGSGSVSIEAARLAPggRVYAIERDPERAALIRANARRFGVPNVEVVEGEAPEALADL------PDPD 317


                 ..
gi 349732166 520 AI 521
Cdd:COG2242  318 AV 319
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 74-136 6.59e-07

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 46.84  E-value: 6.59e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 349732166   74 IQNLPKYIGFNDLKKFLGKYGLnPHKIKLMKKQT-----FAFVTFKSEEERDKAMKVIHGVMWKNRPL 136
Cdd:pfam00076   3 VGNLPPDTTEEDLKDLFSKFGP-IKSIRLVRDETgrskgFAFVEFEDEEDAEKAIEALNGKELGGREL 69
RRM1_RRT5 cd12409
RNA recognition motif 1 (RRM1) found in yeast regulator of rDNA transcription protein 5 (RRT5) ...
 71-143 3.29e-06

RNA recognition motif 1 (RRM1) found in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins; This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409843 [Multi-domain]  Cd Length: 84  Bit Score: 45.35  E-value: 3.29e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166  71 KVEIQNLPKYIGFNDLKKFLGKYG----LNP-HKIKLMKKQT-----FAFVTFKSEEERDKAMKVIHGVMWKNRPLSVRL 140
Cdd:cd12409    1 RVYISNLSYSTTEEELEELLKDYKpvsvLIPsYTVRGFRSRKhrplgIAYAEFSSVEEAEKVVKDLNGKVFKGRKLFVKL 80


                 ...
gi 349732166 141 AKP 143
Cdd:cd12409   81 HVP 83
PrmA COG2264
Ribosomal protein L11 methylase PrmA [Translation, ribosomal structure and biogenesis];
441-504 5.38e-06

Ribosomal protein L11 methylase PrmA [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441865 [Multi-domain]  Cd Length: 284  Bit Score: 48.63  E-value: 5.38e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 349732166 441 AQLDQDTTVLDVCCGTGTIGIsLAKK--VKKVVGIELCQEAIADAKANAQLNNL-DNVEFRCGKAED 504
Cdd:COG2264  144 KLLKPGKTVLDVGCGSGILAI-AAAKlgAKRVLAVDIDPVAVEAARENAELNGVeDRIEVVLGDLLE 209
RRM2_RBM28_like cd12414
RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 74-141 6.42e-06

RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409848 [Multi-domain]  Cd Length: 76  Bit Score: 44.46  E-value: 6.42e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 349732166  74 IQNLPKYIGFNDLKKFLGKYG--------LNPHKiklmKKQTFAFVTFKSEEERDKAMKVIHGVMWKNRPLSVRLA 141
Cdd:cd12414    4 VRNLPFKCTEDDLKKLFSKFGkvlevtipKKPDG----KLRGFAFVQFTNVADAAKAIKGMNGKKIKGRPVAVDWA 75
RRM_RBM18 cd12355
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; ...
 74-142 9.48e-06

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear.


Pssm-ID: 409791 [Multi-domain]  Cd Length: 80  Bit Score: 43.83  E-value: 9.48e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 349732166  74 IQNLPKYIGFNDLKKFLGKYG------LNPHKIKLMKKQT--FAFVTFKSEEERDKAMKVIHGVMWKNRPLSVRLAK 142
Cdd:cd12355    4 IGNLDPRLTEYHLLKLLSKYGkikkfdFLFHKTGPLKGQPrgYCFVTFETKEEAEKAIECLNGKLALGKKLVVRWAH 80
RRM_hnRNPH_ESRPs_RBM12_like cd12254
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein ...
 72-139 1.30e-05

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins; The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409699 [Multi-domain]  Cd Length: 73  Bit Score: 43.32  E-value: 1.30e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 349732166  72 VEIQNLPKYIGFNDLKKFLGKYGLNPHKIKLMKKQTF-----AFVTFKSEEERDKAMKVIHGVMwKNRPLSVR 139
Cdd:cd12254    2 VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGrptgeAYVEFASEEDAQRALRRHKGKM-GGRYIEVF 73
Cons_hypoth95 pfam03602
Conserved hypothetical protein 95;
440-549 1.31e-05

Conserved hypothetical protein 95;


Pssm-ID: 427391 [Multi-domain]  Cd Length: 179  Bit Score: 46.08  E-value: 1.31e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166  440 WAQLDQDTTVLDVCCGTGTIGI-SLAKKVKKVVGIELCQEAIADAKANAQLNNLDNVEFRcGKAEDIFPTLInSYTFPSP 518
Cdd:pfam03602  36 LAPYIEGARVLDLFAGSGALGLeALSRGAKRVTLVEKDKRAVQILKENLQLLGLPGAVLV-MDALLALLRLA-GKGPVFD 113

                          90       100       110
                  ....*....|....*....|....*....|....
gi 349732166  519 LAIVDPP-RAGLHSKVIIAIRKAEHLKQ--LIYV 549
Cdd:pfam03602 114 IVFLDPPyAKGLIEEVLDLLAEKGWLKPnaLIYV 147
Methyltransf_11 pfam08241
Methyltransferase domain; Members of this family are SAM dependent methyltransferases.
 450-507 1.44e-05

Methyltransferase domain; Members of this family are SAM dependent methyltransferases.


Pssm-ID: 462406 [Multi-domain]  Cd Length: 94  Bit Score: 43.81  E-value: 1.44e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 349732166  450 LDVCCGTGTIGISLAKKVKKVVGIELCQEAIADAKANAQlnnLDNVEFRCGKAEDI-FP 507
Cdd:pfam08241   1 LDVGCGTGLLTELLARLGARVTGVDISPEMLELAREKAP---REGLTFVVGDAEDLpFP 56
RsmD COG0742
16S rRNA G966 N2-methylase RsmD [Translation, ribosomal structure and biogenesis]; 16S rRNA ...
 445-549 1.51e-05

16S rRNA G966 N2-methylase RsmD [Translation, ribosomal structure and biogenesis]; 16S rRNA G966 N2-methylase RsmD is part of the Pathway/BioSystem: 16S rRNA modification


Pssm-ID: 440505 [Multi-domain]  Cd Length: 183  Bit Score: 45.84  E-value: 1.51e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 445 QDTTVLDVCCGTGTIGI-SL---AkkvKKVVGIELCQEAIADAKANAQ-LNNLDNVEFRCGKAEDIFPTLInsytfPSPL 519
Cdd:COG0742   41 EGARVLDLFAGSGALGLeALsrgA---ASVVFVEKDRKAAAVIRKNLEkLGLEDRARVIRGDALRFLKRLA-----GEPF 112

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 349732166 520 AIV--DPP-RAGLHSKVIIAIRKAEHLKQ--LIYV 549
Cdd:COG0742  113 DLVflDPPyAKGLLEKALELLAENGLLAPggLIVV 147
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 49-154 1.81e-05

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 47.88  E-value: 1.81e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166   49 ESKDKA-GIYRYIK--DDLFTSEifkveiqnlpkyigfnDLKKFLGKYGlNPHKIKLMKKQT-----FAFVTFKSEEERD 120
Cdd:TIGR01628 278 ERKMKAqGVNLYVKnlDDTVTDE----------------KLRELFSECG-EITSAKVMLDEKgvsrgFGFVCFSNPEEAN 340

                          90       100       110
                  ....*....|....*....|....*....|....
gi 349732166  121 KAMKVIHGVMWKNRPLSVRLAKPRADPIMQKRKQ 154
Cdd:TIGR01628 341 RAVTEMHGRMLGGKPLYVALAQRKEQRRAHLQDQ 374
RRM1_PSP1 cd12586
RNA recognition motif 1 (RRM1) found in vertebrate paraspeckle protein 1 (PSP1); This subgroup ...
 74-140 3.74e-05

RNA recognition motif 1 (RRM1) found in vertebrate paraspeckle protein 1 (PSP1); This subgroup corresponds to the RRM1 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently, however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus.


Pssm-ID: 409999 [Multi-domain]  Cd Length: 71  Bit Score: 42.21  E-value: 3.74e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 349732166  74 IQNLPKYIGFNDLKKFLGKYGlNPHKIKLMKKQTFAFVTFKSEEERDKAMKVIHGVMWKNRPLSVRL 140
Cdd:cd12586    6 VGNLPTDITEEDFKRLFERYG-EPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRF 71
arsM PRK11873
arsenite methyltransferase;
441-505 3.81e-05

arsenite methyltransferase;


Pssm-ID: 237007 [Multi-domain]  Cd Length: 272  Bit Score: 45.71  E-value: 3.81e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 349732166 441 AQLDQDTTVLDVCCGTGTIGISLAKKVK---KVVGIELCQEAIADAKANAQLNNLDNVEFRCGKAEDI 505
Cdd:PRK11873  73 AELKPGETVLDLGSGGGFDCFLAARRVGptgKVIGVDMTPEMLAKARANARKAGYTNVEFRLGEIEAL 140
RRM4_I_PABPs cd12381
RNA recognition motif 4 (RRM4) found in type I polyadenylate-binding proteins; This subfamily ...
 74-141 6.63e-05

RNA recognition motif 4 (RRM4) found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM4 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in theThe CD corresponds to the RRM. regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409815 [Multi-domain]  Cd Length: 79  Bit Score: 41.49  E-value: 6.63e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 349732166  74 IQNLPKYIGFNDLKKFLGKYGlNPHKIKLM-----KKQTFAFVTFKSEEERDKAMKVIHGVMWKNRPLSVRLA 141
Cdd:cd12381    6 VKNLDDTIDDEKLREEFSPFG-TITSAKVMtdeggRSKGFGFVCFSSPEEATKAVTEMNGRIIGGKPLYVALA 77
PRK08317 PRK08317
hypothetical protein; Provisional
 448-508 7.08e-05

hypothetical protein; Provisional


Pssm-ID: 181382 [Multi-domain]  Cd Length: 241  Bit Score: 44.54  E-value: 7.08e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 349732166 448 TVLDVCCGTGTIGISLAKKVK---KVVGIELCQEAIADAKaNAQLNNLDNVEFRCGKAEDI-FPT 508
Cdd:PRK08317  22 RVLDVGCGPGNDARELARRVGpegRVVGIDRSEAMLALAK-ERAAGLGPNVEFVRGDADGLpFPD 85
RRM1_MRD1 cd12565
RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 ...
 74-141 7.32e-05

RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409981 [Multi-domain]  Cd Length: 76  Bit Score: 41.39  E-value: 7.32e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 349732166  74 IQNLPKYIGFNDLKKFLGKYGLnPHKIKLMKKQT-----FAFVTFKSEEERDKAMKVIHGVMWKNRPLSVRLA 141
Cdd:cd12565    5 VKNLPKYVTEKRLKEHFSKKGE-ITDVKVMRTKDgksrrFGFIGFKSEEEAQKAVKYFNKTFIDTSKISVEFA 76
Trm5 COG2520
tRNA G37 N-methylase Trm5 [Translation, ribosomal structure and biogenesis]; tRNA G37 ...
 448-513 8.70e-05

tRNA G37 N-methylase Trm5 [Translation, ribosomal structure and biogenesis]; tRNA G37 N-methylase Trm5 is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 442010 [Multi-domain]  Cd Length: 333  Bit Score: 44.85  E-value: 8.70e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 349732166 448 TVLDVCCGTGTIGISLAKK-VKKVVGIELCQEAIADAKANAQLNNL-DNVEFRCGKAEDIFPTLINSY 513
Cdd:COG2520  183 RVLDMFAGVGPFSIPIAKRsGAKVVAIDINPDAVEYLKENIRLNKVeDRVTPILGDAREVAPELEGKA 250
RRM1_RBM28_like cd12413
RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 108-144 1.16e-04

RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409847 [Multi-domain]  Cd Length: 79  Bit Score: 41.04  E-value: 1.16e-04
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 349732166 108 FAFVTFKSEEERDKAMKVIHGVMWKNRPLSVRLAKPR 144
Cdd:cd12413   43 FGYVTFALAEDAQRALEEVKGKKFGGRKIKVELAKKK 79
RRM1_p54nrb_like cd12332
RNA recognition motif 1 (RRM1) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds ...
 76-139 1.40e-04

RNA recognition motif 1 (RRM1) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members.


Pssm-ID: 409769 [Multi-domain]  Cd Length: 71  Bit Score: 40.36  E-value: 1.40e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 349732166  76 NLPKYIGFNDLKKFLGKYGlNPHKIKLMKKQTFAFVTFKSEEERDKAMKVIHGVMWKNRPLSVR 139
Cdd:cd12332    8 NLPNDITEEEFKELFQKYG-EVSEVFLNKGKGFGFIRLDTRANAEAAKAELDGTPRKGRQLRVR 70
MenG_heptapren TIGR02752
demethylmenaquinone methyltransferase; MenG is a generic term for a methyltransferase that ...
 447-502 1.58e-04

demethylmenaquinone methyltransferase; MenG is a generic term for a methyltransferase that catalyzes the last step in menaquinone biosynthesis; the exact enzymatic activity differs for different MenG because the menaquinone differ in their prenoid side chains in different species. Members of this MenG protein family are 2-heptaprenyl-1,4-naphthoquinone methyltransferase, and are found together in operons with the two subunits of the heptaprenyl diphosphate synthase in Bacillus subtilis and related species. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone]


Pssm-ID: 131799  Cd Length: 231  Bit Score: 43.64  E-value: 1.58e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 349732166  447 TTVLDVCCGTGTIGISLAKKV---KKVVGIELCQEAIADAKANAQLNNLDNVEFRCGKA 502
Cdd:TIGR02752  47 TSALDVCCGTADWSIALAEAVgpeGHVIGLDFSENMLSVGRQKVKDAGLHNVELVHGNA 105
PCMT pfam01135
Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT);
392-500 1.83e-04

Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT);


Pssm-ID: 395902 [Multi-domain]  Cd Length: 205  Bit Score: 43.13  E-value: 1.83e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166  392 LEDLPVEHVAGD---QYIYEDllglsfriSPHAFFQVNTLAAEVLYSAIGDWAQLDQDTTVLDVCCGTGTIGISLAKKVK 468
Cdd:pfam01135  25 MLAVDREEFVPEsfkSYAYED--------IPLSIGYGQTISAPHMHAMMLELLELKPGMRVLEIGSGSGYLTACFARMVG 96

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 349732166  469 ---KVVGIELCQEAIADAKANAQLNNLDNVEFRCG 500
Cdd:pfam01135  97 evgRVVSIEHIPELVEIARRNLEKLGLENVIVVVG 131
hemK_fam TIGR00536
HemK family putative methylases; The gene hemK from E. coli was found to contribute to heme ...
 449-497 2.11e-04

HemK family putative methylases; The gene hemK from E. coli was found to contribute to heme biosynthesis and originally suggested to be protoporphyrinogen oxidase. Functional analysis of the nearest homolog in Saccharomyces cerevisiae, YNL063w, finds it is not protoporphyrinogen oxidase and sequence analysis suggests that HemK homologs have S-adenosyl-methionine-dependent methyltransferase activity (Medline 99237242). Homologs are found, usually in a single copy, in nearly all completed genomes, but varying somewhat in apparent domain architecture. Both E. coli and H. influenzae have two members rather than one. The members from the Mycoplasmas have an additional C-terminal domain. [Protein fate, Protein modification and repair]


Pssm-ID: 273125 [Multi-domain]  Cd Length: 284  Bit Score: 43.50  E-value: 2.11e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 349732166  449 VLDVCCGTGTIGISLAKKV--KKVVGIELCQEAIADAKANAQLNNL-DNVEF 497
Cdd:TIGR00536 118 ILDLGTGSGCIALALAYEFpnAEVIAVDISPDALAVAEENAEKNQLeHRVEF 169
RBD_RRM1_NPL3 cd12340
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; ...
 74-138 2.46e-04

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues.


Pssm-ID: 409777 [Multi-domain]  Cd Length: 69  Bit Score: 39.69  E-value: 2.46e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 349732166  74 IQNLPKYIGFNDLKKFLGKYGlNPHKIKLMKKQTFAFVTFKSEEERDKAMKVIHGVMWKNRPLSV 138
Cdd:cd12340    4 VRPFPPDTSESAIREIFSPYG-PVKEVKMLSDSNFAFVEFEELEDAIRAKDSVHGRVLNNEPLYV 67
prmA PRK00517
50S ribosomal protein L11 methyltransferase;
445-497 2.93e-04

50S ribosomal protein L11 methyltransferase;


Pssm-ID: 234786 [Multi-domain]  Cd Length: 250  Bit Score: 42.83  E-value: 2.93e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 349732166 445 QDTTVLDVCCGTGTIGISLAKK-VKKVVGIELCQEAIADAKANAQLNNLDNVEF 497
Cdd:PRK00517 119 PGKTVLDVGCGSGILAIAAAKLgAKKVLAVDIDPQAVEAARENAELNGVELNVY 172
RRM_NOL8 cd12226
RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This ...
 74-142 3.17e-04

RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells.


Pssm-ID: 409673 [Multi-domain]  Cd Length: 77  Bit Score: 39.48  E-value: 3.17e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 349732166  74 IQNLPKYIGFNDLKKFLGKYG----LNPHKIKLMKKQTFAFVTFK-SEEERDKAMKVIHGVMWKNRPLSVRLAK 142
Cdd:cd12226    4 VGGLSPSITEDDLERRFSRFGtvsdVEIIRKKDAPDRGFAYIDLRtSEAALQKCLSTLNGVKWKGSRLKIQLAK 77
Methyltransf_15 pfam09445
RNA cap guanine-N2 methyltransferase; RNA cap guanine-N2 methyltransferases such as ...
 447-518 4.53e-04

RNA cap guanine-N2 methyltransferase; RNA cap guanine-N2 methyltransferases such as Schizosaccharomyces pombe Tgs1 and Giardia lamblia Tgs2 catalyze methylation of the exocyclic N2 amine of 7-methylguanosine.


Pssm-ID: 370496  Cd Length: 165  Bit Score: 41.17  E-value: 4.53e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 349732166  447 TTVLDVCCGTGTIGISLAKKVKKVVGIELCQEAIADAKANAQL-NNLDNVEFRCGKAEDI-----FPTLINSYTFPSP 518
Cdd:pfam09445   2 TRILDVFCGGGGNTIQFANVFDSVISIDINLEHLACAQHNAEVyGVSDRIWLIHGDWFELlaklkFEKIKYDCVFASP 79
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
 71-141 4.89e-04

RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410187 [Multi-domain]  Cd Length: 76  Bit Score: 39.07  E-value: 4.89e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 349732166  71 KVEIQNLPKYIGFNDLKKFLGKYGlNPHKIKLMK-KQT-----FAFVTFKSEEERDKAMKVIHGVMWKNRPLSVRLA 141
Cdd:cd21608    1 KLYVGNLSWDTTEDDLRDLFSEFG-EVESAKVITdRETgrsrgFGFVTFSTAEAAEAAIDALNGKELDGRSIVVNEA 76
RRM1_RBM5_like cd12561
RNA recognition motif 1 (RRM1) found in RNA-binding protein 5 (RBM5) and similar proteins; ...
 76-130 5.10e-04

RNA recognition motif 1 (RRM1) found in RNA-binding protein 5 (RBM5) and similar proteins; This subgroup corresponds to the RRM1 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 409977 [Multi-domain]  Cd Length: 81  Bit Score: 39.27  E-value: 5.10e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 349732166  76 NLPKYIGFNDLKKFLGKYGLNPHKIKLMKKQT------FAFVTFKSEEERDKAMKVIHGVM 130
Cdd:cd12561    9 GLPLSVTEEDIRNALVSHGVQPKDVRLMRRKTtgasrgFAFVEFMSLEEATRWMEANQGKL 69
RRM_CNOT4 cd12438
RNA recognition motif (RRM) found in Eukaryotic CCR4-NOT transcription complex subunit 4 (NOT4) ...
 86-136 5.11e-04

RNA recognition motif (RRM) found in Eukaryotic CCR4-NOT transcription complex subunit 4 (NOT4) and similar proteins; This subfamily corresponds to the RRM of NOT4, also termed CCR4-associated factor 4, or E3 ubiquitin-protein ligase CNOT4, or potential transcriptional repressor NOT4Hp, a component of the CCR4-NOT complex, a global negative regulator of RNA polymerase II transcription. NOT4 functions as an ubiquitin-protein ligase (E3). It contains an N-terminal C4C4 type RING finger motif, followed by a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RING fingers may interact with a subset of ubiquitin-conjugating enzymes (E2s), including UbcH5B, and mediate protein-protein interactions. T


Pssm-ID: 409872 [Multi-domain]  Cd Length: 98  Bit Score: 39.43  E-value: 5.11e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 349732166  86 LKK--FLGKYGlNPHKIKLMKKQTF---------AFVTFKSEEERDKAMKVIHGVMWKNRPL 136
Cdd:cd12438   23 LKRpeYFGQYG-KIKKIVINRSTSYagsqgpsasAYVTYSRKEDALRAIQAVDGFVLDGRTL 83
sex-lethal TIGR01659
sex-lethal family splicing factor; This model describes the sex-lethal family of splicing ...
 74-142 5.53e-04

sex-lethal family splicing factor; This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).


Pssm-ID: 273740 [Multi-domain]  Cd Length: 346  Bit Score: 42.70  E-value: 5.53e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 349732166   74 IQNLPKYIGFNDLKKFLGKYGLNPHKIKLMKKQT-----FAFVTFKSEEERDKAMKVIHGVMWK--NRPLSVRLAK 142
Cdd:TIGR01659 198 VTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTgtprgVAFVRFNKREEAQEAISALNNVIPEggSQPLTVRLAE 273
RRM_SAFB_like cd12417
RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This ...
 74-138 5.95e-04

RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM.


Pssm-ID: 409851 [Multi-domain]  Cd Length: 74  Bit Score: 38.77  E-value: 5.95e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166  74 IQNLPKYIGFNDLKKFLGKYGL--NPHKIKLMK---KQTFAFVTFKSEEERDKAMKVIHGVMWKNRPLSV 138
Cdd:cd12417    4 ISGLSDTTKAADLKKIFSKYGKvvSAKVVTSARtpgSRCYGYVTMASVEEADLCIKSLNKTELHGRVITV 73
RRM1_RBM40_like cd12238
RNA recognition motif 1 (RRM1) found in RNA-binding protein 40 (RBM40) and similar proteins; ...
 74-138 6.42e-04

RNA recognition motif 1 (RRM1) found in RNA-binding protein 40 (RBM40) and similar proteins; This subfamily corresponds to the RRM1 of RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein), It serves as a bridging factor between the U11 and U12 snRNPs. It contains two repeats of RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions.


Pssm-ID: 409684 [Multi-domain]  Cd Length: 73  Bit Score: 38.77  E-value: 6.42e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 349732166  74 IQNLPKYIGFNDLKKFLGKYGLnpHKIKLM----KKQTFAFVTFKSEEERDKAMKVIHGVMWKNRPLSV 138
Cdd:cd12238    4 VRHLPPELSEDDKEDLLKHFGA--TSVRVMkrrgKLKHTAFATFDNEQAASKALSRLHQLKILGKRLVV 70
PrmA pfam06325
Ribosomal protein L11 methyltransferase (PrmA); This family consists of several Ribosomal ...
 441-494 8.63e-04

Ribosomal protein L11 methyltransferase (PrmA); This family consists of several Ribosomal protein L11 methyltransferase (EC:2.1.1.-) sequences.


Pssm-ID: 428888 [Multi-domain]  Cd Length: 294  Bit Score: 41.87  E-value: 8.63e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 349732166  441 AQLDQDTTVLDVCCGTGTIGISLAK-KVKKVVGIELCQEAIADAKANAQLNNLDN 494
Cdd:pfam06325 157 RLVKPGESVLDVGCGSGILAIAALKlGAKKVVGVDIDPVAVRAAKENAELNGVEA 211
RRM1_U1A_like cd12246
RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily ...
 74-142 9.84e-04

RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding.


Pssm-ID: 409692 [Multi-domain]  Cd Length: 78  Bit Score: 38.28  E-value: 9.84e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 349732166  74 IQNLPKYIGFNDLKK----FLGKYG----LNPHKIKLMKKQtfAFVTFKSEEERDKAMKVIHGVMWKNRPLSVRLAK 142
Cdd:cd12246    4 INNLNEKIKKDELKRslyaLFSQFGpvldIVASKSLKMRGQ--AFVVFKDVESATNALRALQGFPFYGKPMRIQYAK 78
Ubie_methyltran pfam01209
ubiE/COQ5 methyltransferase family;
448-505 1.18e-03

ubiE/COQ5 methyltransferase family;


Pssm-ID: 395966 [Multi-domain]  Cd Length: 228  Bit Score: 40.89  E-value: 1.18e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 349732166  448 TVLDVCCGTGTIGISLAKKVK---KVVGIELCQEAIADAKANAQLNNLDNVEFRCGKAEDI 505
Cdd:pfam01209  45 KFLDVAGGTGDWTFGLSDSAGssgKVVGLDINENMLKEGEKKAKEEGKYNIEFLQGNAEEL 105
RRM2_Hu_like cd12376
RNA recognition motif 2 (RRM2) found in the Hu proteins family, Drosophila sex-lethal (SXL), ...
 74-141 2.26e-03

RNA recognition motif 2 (RRM2) found in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins; This subfamily corresponds to the RRM2 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Also included in this subfamily is the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 240822 [Multi-domain]  Cd Length: 79  Bit Score: 37.22  E-value: 2.26e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 349732166  74 IQNLPKYIGFNDLKKFLGKYGLNPHKIKLMKKQT-----FAFVTFKSEEERDKAMKVIHGV--MWKNRPLSVRLA 141
Cdd:cd12376    5 VSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTgvsrgVGFIRFDKRIEAEEAIKGLNGQkpEGASEPITVKFA 79
RRM3_hnRNPR_like cd12251
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) ...
 74-143 2.34e-03

RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins; This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409697 [Multi-domain]  Cd Length: 72  Bit Score: 36.84  E-value: 2.34e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166  74 IQNLPKYIGFNDLKKFLGKYGlNPHKIKLMKKqtFAFVTFKSEEERDKAMKVIHGVMWKNRPLSVRLAKP 143
Cdd:cd12251    6 VRNLMLSTTEEKLRELFSEYG-KVERVKKIKD--YAFVHFEERDDAVKAMEEMNGKELEGSEIEVSLAKP 72
RRM1_RBM19 cd12564
RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19) and similar proteins; ...
 74-138 2.88e-03

RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19) and similar proteins; This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409980 [Multi-domain]  Cd Length: 76  Bit Score: 36.91  E-value: 2.88e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 349732166  74 IQNLPKYIGFNDLKKFLGKYG-LNPHKIKLMKK---QTFAFVTFKSEEERDKAMKVIHGVMWKNRPLSV 138
Cdd:cd12564    5 VKNLPSSITEDRLRKLFSAFGtITDVQLKYTKDgkfRRFGFVGFKSEEEAQKALKHFNNSFIDTSRITV 73
PRK13943 PRK13943
protein-L-isoaspartate O-methyltransferase; Provisional
 404-500 3.80e-03

protein-L-isoaspartate O-methyltransferase; Provisional


Pssm-ID: 237568 [Multi-domain]  Cd Length: 322  Bit Score: 39.83  E-value: 3.80e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166 404 QYIYEDLLGLSFRISPhaffQVNTLAAEVLYSAIGDWAQLDQDTTVLDVCCGTGTIGISLAKKVKK---VVGIELCQEAI 480
Cdd:PRK13943  43 SYVYEDIVLVSYDDGE----EYSTSSQPSLMALFMEWVGLDKGMRVLEIGGGTGYNAAVMSRVVGEkglVVSVEYSRKIC 118

                         90       100
                 ....*....|....*....|
gi 349732166 481 ADAKANAQLNNLDNVEFRCG 500
Cdd:PRK13943 119 EIAKRNVRRLGIENVIFVCG 138
PRK07580 PRK07580
Mg-protoporphyrin IX methyl transferase; Validated
 439-505 4.13e-03

Mg-protoporphyrin IX methyl transferase; Validated


Pssm-ID: 236059 [Multi-domain]  Cd Length: 230  Bit Score: 39.05  E-value: 4.13e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 349732166 439 DWAQLDQD---TTVLDVCCGTGTIGISLAKKVKKVVGIELCQEAIADAK--ANAQLNNlDNVEFRCGKAEDI 505
Cdd:PRK07580  54 SWLPADGDltgLRILDAGCGVGSLSIPLARRGAKVVASDISPQMVEEARerAPEAGLA-GNITFEVGDLESL 124
RRM1_RIM4_like cd12453
RNA recognition motif 1 (RRM1) found in yeast meiotic activator RIM4 and similar proteins; ...
 86-142 4.36e-03

RNA recognition motif 1 (RRM1) found in yeast meiotic activator RIM4 and similar proteins; This subfamily corresponds to the RRM1 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1.


Pssm-ID: 409887 [Multi-domain]  Cd Length: 86  Bit Score: 36.62  E-value: 4.36e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166  86 LKKFLGKYGLNPHkIKLMK---KQTFAFVTFKSEEERDKAMKVIHGVMWKNRPLSVRLAK 142
Cdd:cd12453   23 VTNHFSKWGELLN-VKVLKdwsNRPYAFVQYTNTEDAKNALVNGHNTLLDGRHLRVEKAK 81
RRM_SR140 cd12223
RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This ...
 66-143 5.43e-03

RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain).


Pssm-ID: 409670 [Multi-domain]  Cd Length: 84  Bit Score: 36.12  E-value: 5.43e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166  66 TSEIFkveIQNLPKYIGFNDLKKFLGKYGlnP-HKIKLM---------KKQTFAFVTFKSEEERDKAMKVIHGVMWKNRP 135
Cdd:cd12223    1 TTNLY---VGNLPPSVTEEVLLREFGRFG--PlASVKIMwprteeerrRNRNCGFVAFMSRADAERAMRELNGKDVMGYE 75


                 ....*...
gi 349732166 136 LSVRLAKP 143
Cdd:cd12223   76 LKLGWGKA 83
fkbM_fam TIGR01444
methyltransferase, FkbM family; Members of this family are characterized by two well-conserved ...
 448-520 5.75e-03

methyltransferase, FkbM family; Members of this family are characterized by two well-conserved short regions separated by a variable in both sequence and length. The first of the two regions is found in a large number of proteins outside this subfamily, a number of which have been characterized as methyltransferases. One member of the present family, FkbM, was shown to be required for a specific methylation in the biosynthesis of the immunosuppressant FK506 in Streptomyces strain MA6548.


Pssm-ID: 273628  Cd Length: 143  Bit Score: 37.68  E-value: 5.75e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 349732166  448 TVLDVCCGTGTIGISLAKKVK--KVVGIELCQEAIADAKANAQLNNLDNVEF-------RCGKAE-DIFPTLI-NSYTFP 516
Cdd:TIGR01444   1 VVIDVGANIGDTSLYFARKGAegRVIAFEPLPDAYEILEENVKLNNLPNVVLlnaavgdRDGELEfNVSDDDTgNSSLLP 80


                  ....
gi 349732166  517 SPLA 520
Cdd:TIGR01444  81 TPDA 84
cbiT PRK00377
cobalt-precorrin-6Y C(15)-methyltransferase; Provisional
 441-509 6.28e-03

cobalt-precorrin-6Y C(15)-methyltransferase; Provisional


Pssm-ID: 234740  Cd Length: 198  Bit Score: 38.24  E-value: 6.28e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 349732166 441 AQLDQDTTVLDVCCGTGTIGISLAKKV---KKVVGIELCQEAIADAKANAQ-LNNLDNVEFRCGKAEDIFPTL 509
Cdd:PRK00377  36 LRLRKGDMILDIGCGTGSVTVEASLLVgetGKVYAVDKDEKAINLTRRNAEkFGVLNNIVLIKGEAPEILFTI 108
RRM1_RAVER cd12388
RNA recognition motif 1 (RRM1) found in ribonucleoprotein PTB-binding raver-1, raver-2 and ...
 71-141 6.74e-03

RNA recognition motif 1 (RRM1) found in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins; This subfamily corresponds to the RRM1 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only.


Pssm-ID: 409822 [Multi-domain]  Cd Length: 70  Bit Score: 35.65  E-value: 6.74e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 349732166  71 KVEIQNLPKYIGFNDLKKFLGKYGLNphKIKLMKKQTFAFVTFKSEEERDKAMKVIHGVMWKNRPLSVRLA 141
Cdd:cd12388    1 RILVRNLPNDITAQEVHDLLADYGLK--YCHVDKAKGTAFVTLLNGEQAGTAILKFHQSSYRDRQLSVQLQ 69
RRM3_I_PABPs cd12380
RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This ...
 72-138 6.80e-03

RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409814 [Multi-domain]  Cd Length: 80  Bit Score: 36.00  E-value: 6.80e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 349732166  72 VEIQNLPKYIGFNDLKKFLGKYGlnphKI---KLMKKQT-----FAFVTFKSEEERDKAMKVIHGVMWKNRPLSV 138
Cdd:cd12380    4 VYVKNFGEDVDDDELKELFEKYG----KItsaKVMKDDSgkskgFGFVNFENHEAAQKAVEELNGKELNGKKLYV 74
PRK06202 PRK06202
hypothetical protein; Provisional
 444-499 9.20e-03

hypothetical protein; Provisional


Pssm-ID: 180466 [Multi-domain]  Cd Length: 232  Bit Score: 38.06  E-value: 9.20e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 349732166 444 DQDTTVLDVCCGTGTIGISLAKKVKK------VVGIELCQEAIADAKANAQlnnLDNVEFRC 499
Cdd:PRK06202  59 DRPLTLLDIGCGGGDLAIDLARWARRdglrleVTAIDPDPRAVAFARANPR---RPGVTFRQ 117
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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