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Conserved domains on  [gi|62484314|ref|NP_651070|]
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uncharacterized protein Dmel_CG31156 [Drosophila melanogaster]

Protein Classification

Tex family protein( domain architecture ID 1000117)

Tex (toxin expression) family protein is an RNA-binding transcriptional accessory protein; includes two functional domains, an N-terminal domain which may be a transcriptional factor, and a C-terminal S1 RNA-binding domain

Gene Ontology:  GO:0003729|GO:0003676
PubMed:  17242308|8755871

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
Tex super family cl34417
Transcriptional accessory protein Tex/SPT6 [Transcription];
184-932 0e+00

Transcriptional accessory protein Tex/SPT6 [Transcription];


The actual alignment was detected with superfamily member COG2183:

Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 603.94  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314 184 NIDELLAETESIQPQAARNIVKLFEDENTIPFICRYRRDL---VDHIApdrLRDIRNTYTEIVDLRKRAENIIGKLQREN 260
Cdd:COG2183   4 DIIQRIAQELGLRPKQVEAAVELLDEGATVPFIARYRKEAtggLDEVQ---LRTIEERLTYLRELEKRRETILKSIEEQG 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314 261 IMTPEIREELMCAKSNEELEFLYAPYKPASKgTLAERAKALGLQVYADCLLygSAPKVNLSEI----VDRRNEaLATEAL 336
Cdd:COG2183  81 KLTPELKAKIEAADTKQELEDLYLPYKPKRR-TKATIAREKGLEPLADLLL--AQPTGDPEAEaakyINEEKG-VADVEA 156

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314 337 VMSGICQIIIHNISKNTNVLEEIRR-LQNvhRVFLKCSKTkeaksskssssskassskgsnqnADKKLDSSKFENYFNFQ 415
Cdd:COG2183 157 ALDGARDILAERISEDAELRGKLRElLWK--EGVLVSKVK-----------------------KGKEEEGAKFRDYFDYS 211

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314 416 GDVKTIKPYQMLAINRGEKHKWLSVKIETND-----YLKRdlmRYITDQymnqglQYPLRREVfTKSLEECYAKKLQPLM 490
Cdd:COG2183 212 EPLKKIPSHRILALNRGEKEGVLKVKLEPDEeeaeaYIAR---RFIKDQ------GRPADEWL-KEAVRDAYKRLLAPSL 281

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314 491 CRQIRAALKEKGTKAAIDVFAKNLKQLLLISPLKGERILGIDPGFINGCKLALISETADVLYTGVIYPHGAMSNKRAAEQ 570
Cdd:COG2183 282 ERELRNELKEKAEEEAIKVFAENLRDLLLAAPAGGKVVLGLDPGFRTGCKVAVVDETGKLLDTATIYPHPPQNKWEEAAK 361

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314 571 KLVQLLSDHNCKIIGLGNGTACRETEHwltgmFHAGVLD--SRIIRYSIVNENGASIYSCSNVAAKEFPKMDTNERSAVS 648
Cdd:COG2183 362 TLAALIKKYKVELIAIGNGTASRETEQ-----FVAELIKelDLKVQYVIVSEAGASVYSASELAREEFPDLDVTVRGAVS 436

                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314 649 IARRLNDPLSEYVKIEPRHLGVGMYQHDVPEKILTASLNDVVSECVSYVGVDLNTASLSVLKHIAGLSEKKAEKIIEHRT 728
Cdd:COG2183 437 IARRLQDPLAELVKIDPKSIGVGQYQHDVNQKKLKRSLDAVVEDCVNAVGVDLNTASAPLLSYVSGLNPTLAKNIVAYRD 516

                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314 729 QKGPFKTRKDLLSVRSIGEKSFVQCAGFVRIeprsVGGQlqNPLDCTWVHPESYNVVESIVGECDLKLSDV-GKAAFIAS 807
Cdd:COG2183 517 ENGAFKSRKELLKVPRLGPKAFEQAAGFLRI----RDGD--NPLDNSAVHPESYPVVEKILKDLGVSVKDLiGNKELLKK 590

                       650       660       670       680       690       700       710       720
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314 808 I--KQFASSQ---PNLDRIAKqhklpmerlefllvalqrELLQ---DYRADLdKRPLFKQGLTRLDDLSMGEVVTGAVTN 879
Cdd:COG2183 591 LdpEKYADELfglPTLRDILK------------------ELEKpgrDPRPEF-KTPTFREGVLKIEDLKPGMILEGTVTN 651

                       730       740       750       760       770       780
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 62484314 880 VTQFGAFVDVGVERNGLIHNSNMNNS-------QLSVGDRIVASVVKVDLKRR--QLELRLE 932
Cdd:COG2183 652 VTDFGAFVDIGVHQDGLVHISQLSDRfvkdpreVVKVGDIVKVKVLEVDLKRKriSLSMKLD 713
 
Name Accession Description Interval E-value
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
184-932 0e+00

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 603.94  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314 184 NIDELLAETESIQPQAARNIVKLFEDENTIPFICRYRRDL---VDHIApdrLRDIRNTYTEIVDLRKRAENIIGKLQREN 260
Cdd:COG2183   4 DIIQRIAQELGLRPKQVEAAVELLDEGATVPFIARYRKEAtggLDEVQ---LRTIEERLTYLRELEKRRETILKSIEEQG 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314 261 IMTPEIREELMCAKSNEELEFLYAPYKPASKgTLAERAKALGLQVYADCLLygSAPKVNLSEI----VDRRNEaLATEAL 336
Cdd:COG2183  81 KLTPELKAKIEAADTKQELEDLYLPYKPKRR-TKATIAREKGLEPLADLLL--AQPTGDPEAEaakyINEEKG-VADVEA 156

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314 337 VMSGICQIIIHNISKNTNVLEEIRR-LQNvhRVFLKCSKTkeaksskssssskassskgsnqnADKKLDSSKFENYFNFQ 415
Cdd:COG2183 157 ALDGARDILAERISEDAELRGKLRElLWK--EGVLVSKVK-----------------------KGKEEEGAKFRDYFDYS 211

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314 416 GDVKTIKPYQMLAINRGEKHKWLSVKIETND-----YLKRdlmRYITDQymnqglQYPLRREVfTKSLEECYAKKLQPLM 490
Cdd:COG2183 212 EPLKKIPSHRILALNRGEKEGVLKVKLEPDEeeaeaYIAR---RFIKDQ------GRPADEWL-KEAVRDAYKRLLAPSL 281

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314 491 CRQIRAALKEKGTKAAIDVFAKNLKQLLLISPLKGERILGIDPGFINGCKLALISETADVLYTGVIYPHGAMSNKRAAEQ 570
Cdd:COG2183 282 ERELRNELKEKAEEEAIKVFAENLRDLLLAAPAGGKVVLGLDPGFRTGCKVAVVDETGKLLDTATIYPHPPQNKWEEAAK 361

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314 571 KLVQLLSDHNCKIIGLGNGTACRETEHwltgmFHAGVLD--SRIIRYSIVNENGASIYSCSNVAAKEFPKMDTNERSAVS 648
Cdd:COG2183 362 TLAALIKKYKVELIAIGNGTASRETEQ-----FVAELIKelDLKVQYVIVSEAGASVYSASELAREEFPDLDVTVRGAVS 436

                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314 649 IARRLNDPLSEYVKIEPRHLGVGMYQHDVPEKILTASLNDVVSECVSYVGVDLNTASLSVLKHIAGLSEKKAEKIIEHRT 728
Cdd:COG2183 437 IARRLQDPLAELVKIDPKSIGVGQYQHDVNQKKLKRSLDAVVEDCVNAVGVDLNTASAPLLSYVSGLNPTLAKNIVAYRD 516

                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314 729 QKGPFKTRKDLLSVRSIGEKSFVQCAGFVRIeprsVGGQlqNPLDCTWVHPESYNVVESIVGECDLKLSDV-GKAAFIAS 807
Cdd:COG2183 517 ENGAFKSRKELLKVPRLGPKAFEQAAGFLRI----RDGD--NPLDNSAVHPESYPVVEKILKDLGVSVKDLiGNKELLKK 590

                       650       660       670       680       690       700       710       720
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314 808 I--KQFASSQ---PNLDRIAKqhklpmerlefllvalqrELLQ---DYRADLdKRPLFKQGLTRLDDLSMGEVVTGAVTN 879
Cdd:COG2183 591 LdpEKYADELfglPTLRDILK------------------ELEKpgrDPRPEF-KTPTFREGVLKIEDLKPGMILEGTVTN 651

                       730       740       750       760       770       780
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 62484314 880 VTQFGAFVDVGVERNGLIHNSNMNNS-------QLSVGDRIVASVVKVDLKRR--QLELRLE 932
Cdd:COG2183 652 VTDFGAFVDIGVHQDGLVHISQLSDRfvkdpreVVKVGDIVKVKVLEVDLKRKriSLSMKLD 713
Tex_YqgF pfam16921
Tex protein YqgF-like domain; This is the YqgF-like domain of the bacterial Tex protein, which ...
 527-653 8.60e-53

Tex protein YqgF-like domain; This is the YqgF-like domain of the bacterial Tex protein, which is involved in transcriptional processes.


Pssm-ID: 465314  Cd Length: 125  Bit Score: 179.90  E-value: 8.60e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314   527 RILGIDPGFINGCKLALISETADVLYTGVIYPHGAMSNKRAAEQKLVQLLSDHNCKIIGLGNGTACRETEHWLTGMFHAG 606
Cdd:pfam16921   1 VVLGLDPGYRTGCKLAVVDETGKVLDTAVIYPHPPQNKVEEAKKKLKKLIKKYGVELIAIGNGTASRETEQFVAELIKEL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 62484314   607 VLDsriIRYSIVNENGASIYSCSNVAAKEFPKMDTNERSAVSIARRL 653
Cdd:pfam16921  81 PLK---VKYVIVSEAGASVYSASELAREEFPDLDVSLRGAVSIARRL 124
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 870-930 1.12e-21

S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.


Pssm-ID: 240190 [Multi-domain]  Cd Length: 68  Bit Score: 89.21  E-value: 1.12e-21
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 62484314 870 GEVVTGAVTNVTQFGAFVDVGVERNGLIHNSNMNNS-------QLSVGDRIVASVVKVDLKRRQLELR 930
Cdd:cd05685   1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRfvshpsdVVSVGDIVEVKVISIDEERGRISLS 68
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
 527-627 1.76e-17

Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative to RuvC in most bacteria, and could be the principal holliday junction resolvases in low-GC Gram-positive bacteria. In Spt6p orthologues, the catalytic residues are substituted indicating that they lack enzymatic functions.


Pssm-ID: 128971  Cd Length: 99  Bit Score: 78.38  E-value: 1.76e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314    527 RILGIDPGfINGCKLALISETADVLYTGVIYPHGamsNKRAAEQKLVQLLSDHNCKIIGLG-----NGTACRETEHWLTG 601
Cdd:smart00732   2 RVLGLDPG-RKGIGVAVVDETGKLADPLEVIPRT---NKEADAARLKKLIKKYQPDLIVIGlplnmNGTASRETEEAFAE 77

                           90       100
                   ....*....|....*....|....*.
gi 62484314    602 MFHagvlDSRIIRYSIVNENGASIYS 627
Cdd:smart00732  78 LLK----ERFNLPVVLVDERLATVYA 99
TIGR00426 TIGR00426
competence protein ComEA helix-hairpin-helix repeat region; Members of the subfamily ...
 699-750 5.60e-08

competence protein ComEA helix-hairpin-helix repeat region; Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model. [Cellular processes, DNA transformation]


Pssm-ID: 129520 [Multi-domain]  Cd Length: 69  Bit Score: 50.70  E-value: 5.60e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 62484314   699 VDLNTASLSVL-KHIAGLSEKKAEKIIEHRTQKGPFKTRKDLLSVRSIGEKSF 750
Cdd:TIGR00426   8 VNINTATAEELqRAMNGVGLKKAEAIVSYREEYGPFKTVEDLKQVPGIGNSLV 60
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 864-935 1.32e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 54.88  E-value: 1.32e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314  864 LDDLSMGEVVTGAVTNVTQFGAFVDVG-VErnGLIHNSNMNNSQ-------LSVGDRIVASVVKVDLKRRQLELRLENML 935
Cdd:PRK06676 187 LSSLKEGDVVEGTVARLTDFGAFVDIGgVD--GLVHISELSHERvekpsevVSVGQEVEVKVLSIDWETERISLSLKDTL 264
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 870-928 5.75e-06

CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a family of full-length homologs of RNA-binding proteins from the Firmicutes with a single copy of the S1 domain. Several members of the family have been characterized as general stress proteins, and the most recently characterized, CvfD, was shown to act as a post-transcriptional regulator.


Pssm-ID: 468553 [Multi-domain]  Cd Length: 113  Bit Score: 46.27  E-value: 5.75e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62484314  870 GEVVTGAVTNVTQFGAFVDVGVERNGLIHNS--------NMNNsQLSVGDRIVASVVKVD-------LKRRQLE 928
Cdd:NF040579   4 GDIVEGKVTGIQPYGAFVALDEHTQGLIHISeikhgyvkDIND-FLKVGQEVKVKVLDIDeytgkisLSLRALE 76
 
Name Accession Description Interval E-value
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
184-932 0e+00

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 603.94  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314 184 NIDELLAETESIQPQAARNIVKLFEDENTIPFICRYRRDL---VDHIApdrLRDIRNTYTEIVDLRKRAENIIGKLQREN 260
Cdd:COG2183   4 DIIQRIAQELGLRPKQVEAAVELLDEGATVPFIARYRKEAtggLDEVQ---LRTIEERLTYLRELEKRRETILKSIEEQG 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314 261 IMTPEIREELMCAKSNEELEFLYAPYKPASKgTLAERAKALGLQVYADCLLygSAPKVNLSEI----VDRRNEaLATEAL 336
Cdd:COG2183  81 KLTPELKAKIEAADTKQELEDLYLPYKPKRR-TKATIAREKGLEPLADLLL--AQPTGDPEAEaakyINEEKG-VADVEA 156

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314 337 VMSGICQIIIHNISKNTNVLEEIRR-LQNvhRVFLKCSKTkeaksskssssskassskgsnqnADKKLDSSKFENYFNFQ 415
Cdd:COG2183 157 ALDGARDILAERISEDAELRGKLRElLWK--EGVLVSKVK-----------------------KGKEEEGAKFRDYFDYS 211

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314 416 GDVKTIKPYQMLAINRGEKHKWLSVKIETND-----YLKRdlmRYITDQymnqglQYPLRREVfTKSLEECYAKKLQPLM 490
Cdd:COG2183 212 EPLKKIPSHRILALNRGEKEGVLKVKLEPDEeeaeaYIAR---RFIKDQ------GRPADEWL-KEAVRDAYKRLLAPSL 281

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314 491 CRQIRAALKEKGTKAAIDVFAKNLKQLLLISPLKGERILGIDPGFINGCKLALISETADVLYTGVIYPHGAMSNKRAAEQ 570
Cdd:COG2183 282 ERELRNELKEKAEEEAIKVFAENLRDLLLAAPAGGKVVLGLDPGFRTGCKVAVVDETGKLLDTATIYPHPPQNKWEEAAK 361

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314 571 KLVQLLSDHNCKIIGLGNGTACRETEHwltgmFHAGVLD--SRIIRYSIVNENGASIYSCSNVAAKEFPKMDTNERSAVS 648
Cdd:COG2183 362 TLAALIKKYKVELIAIGNGTASRETEQ-----FVAELIKelDLKVQYVIVSEAGASVYSASELAREEFPDLDVTVRGAVS 436

                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314 649 IARRLNDPLSEYVKIEPRHLGVGMYQHDVPEKILTASLNDVVSECVSYVGVDLNTASLSVLKHIAGLSEKKAEKIIEHRT 728
Cdd:COG2183 437 IARRLQDPLAELVKIDPKSIGVGQYQHDVNQKKLKRSLDAVVEDCVNAVGVDLNTASAPLLSYVSGLNPTLAKNIVAYRD 516

                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314 729 QKGPFKTRKDLLSVRSIGEKSFVQCAGFVRIeprsVGGQlqNPLDCTWVHPESYNVVESIVGECDLKLSDV-GKAAFIAS 807
Cdd:COG2183 517 ENGAFKSRKELLKVPRLGPKAFEQAAGFLRI----RDGD--NPLDNSAVHPESYPVVEKILKDLGVSVKDLiGNKELLKK 590

                       650       660       670       680       690       700       710       720
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314 808 I--KQFASSQ---PNLDRIAKqhklpmerlefllvalqrELLQ---DYRADLdKRPLFKQGLTRLDDLSMGEVVTGAVTN 879
Cdd:COG2183 591 LdpEKYADELfglPTLRDILK------------------ELEKpgrDPRPEF-KTPTFREGVLKIEDLKPGMILEGTVTN 651

                       730       740       750       760       770       780
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 62484314 880 VTQFGAFVDVGVERNGLIHNSNMNNS-------QLSVGDRIVASVVKVDLKRR--QLELRLE 932
Cdd:COG2183 652 VTDFGAFVDIGVHQDGLVHISQLSDRfvkdpreVVKVGDIVKVKVLEVDLKRKriSLSMKLD 713
Tex_YqgF pfam16921
Tex protein YqgF-like domain; This is the YqgF-like domain of the bacterial Tex protein, which ...
 527-653 8.60e-53

Tex protein YqgF-like domain; This is the YqgF-like domain of the bacterial Tex protein, which is involved in transcriptional processes.


Pssm-ID: 465314  Cd Length: 125  Bit Score: 179.90  E-value: 8.60e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314   527 RILGIDPGFINGCKLALISETADVLYTGVIYPHGAMSNKRAAEQKLVQLLSDHNCKIIGLGNGTACRETEHWLTGMFHAG 606
Cdd:pfam16921   1 VVLGLDPGYRTGCKLAVVDETGKVLDTAVIYPHPPQNKVEEAKKKLKKLIKKYGVELIAIGNGTASRETEQFVAELIKEL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 62484314   607 VLDsriIRYSIVNENGASIYSCSNVAAKEFPKMDTNERSAVSIARRL 653
Cdd:pfam16921  81 PLK---VKYVIVSEAGASVYSASELAREEFPDLDVSLRGAVSIARRL 124
Tex_N pfam09371
Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss: ...
 189-362 8.48e-47

Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss:Q45388. This protein defines a novel family of prokaryotic transcriptional accessory factors.


Pssm-ID: 462777  Cd Length: 183  Bit Score: 165.27  E-value: 8.48e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314   189 LAETESIQPQAARNIVKLFEDENTIPFICRYRRDLVDHIAPDRLRDIRNTYTEIVDLRKRAENIIGKLQRENIMTPEIRE 268
Cdd:pfam09371   1 IAEELGLKPKQVEATVKLLDEGNTVPFIARYRKEATGGLDEVQLREIEERLEYLRELEKRKETILKSIEEQGKLTDELKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314   269 ELMCAKSNEELEFLYAPYKPaSKGTLAERAKALGLQVYADCLLYGSAPKVNLSEIVDRRNE-ALATEALvmSGICQIIIH 347
Cdd:pfam09371  81 AIEAADTLTELEDLYLPYKP-KRRTKATIAREKGLEPLADAILAQPDPEEEAAKYINPEKGvADVEEAL--AGARDIIAE 157

                         170
                  ....*....|....*
gi 62484314   348 NISKNTNVLEEIRRL 362
Cdd:pfam09371 158 RISEDAELRKKLREL 172
HHH_3 pfam12836
Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.
 697-757 2.96e-25

Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.


Pssm-ID: 463723 [Multi-domain]  Cd Length: 62  Bit Score: 99.48  E-value: 2.96e-25
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 62484314   697 VGVDLNTASLSVLKHIAGLSEKKAEKIIEHRTQKGPFKTRKDLLSVRSIGEKSFVQCAGFV 757
Cdd:pfam12836   2 VGVDINTASAELLSRVPGLGPKLAKNIVEYREENGPFRSREDLLKVKGLGPKTFEQLAGFL 62
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 870-930 1.12e-21

S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.


Pssm-ID: 240190 [Multi-domain]  Cd Length: 68  Bit Score: 89.21  E-value: 1.12e-21
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 62484314 870 GEVVTGAVTNVTQFGAFVDVGVERNGLIHNSNMNNS-------QLSVGDRIVASVVKVDLKRRQLELR 930
Cdd:cd05685   1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRfvshpsdVVSVGDIVEVKVISIDEERGRISLS 68
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
 527-627 1.76e-17

Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative to RuvC in most bacteria, and could be the principal holliday junction resolvases in low-GC Gram-positive bacteria. In Spt6p orthologues, the catalytic residues are substituted indicating that they lack enzymatic functions.


Pssm-ID: 128971  Cd Length: 99  Bit Score: 78.38  E-value: 1.76e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314    527 RILGIDPGfINGCKLALISETADVLYTGVIYPHGamsNKRAAEQKLVQLLSDHNCKIIGLG-----NGTACRETEHWLTG 601
Cdd:smart00732   2 RVLGLDPG-RKGIGVAVVDETGKLADPLEVIPRT---NKEADAARLKKLIKKYQPDLIVIGlplnmNGTASRETEEAFAE 77

                           90       100
                   ....*....|....*....|....*.
gi 62484314    602 MFHagvlDSRIIRYSIVNENGASIYS 627
Cdd:smart00732  78 LLK----ERFNLPVVLVDERLATVYA 99
ComEA COG1555
DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair]; ...
 699-750 6.50e-14

DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair];


Pssm-ID: 441164 [Multi-domain]  Cd Length: 72  Bit Score: 67.58  E-value: 6.50e-14
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 62484314 699 VDLNTASLSVLKHIAGLSEKKAEKIIEHRTQKGPFKTRKDLLSVRSIGEKSF 750
Cdd:COG1555  13 VDINTATAEELQTLPGIGPKLAQRIVEYREKNGPFKSVEDLLEVKGIGPKTL 64
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
870-931 2.09e-12

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 63.01  E-value: 2.09e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 62484314    870 GEVVTGAVTNVTQFGAFVDVGVERNGLIHNSNM-------NNSQLSVGDRIVASVVKVDLKRRQLELRL 931
Cdd:smart00316   3 GDVVEGTVTEITPGGAFVDLGNGVEGLIPISELsdkrvkdPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 870-929 2.06e-10

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 57.30  E-value: 2.06e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 62484314   870 GEVVTGAVTNVTQFGAFVDVGVERNGLIHNSNM-------NNSQLSVGDRIVASVVKVDLKRRQLEL 929
Cdd:pfam00575   4 GDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELsddhvedPDEVIKVGDEVKVKVLKVDKDRRRIIL 70
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 870-929 1.56e-09

S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240193 [Multi-domain]  Cd Length: 68  Bit Score: 54.94  E-value: 1.56e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 62484314 870 GEVVTGAVTNVTQFGAFVDVGVErNGLIHNSNMNNSQ-------LSVGDRIVASVVKVDLKRRQLEL 929
Cdd:cd05688   2 GDVVEGTVKSITDFGAFVDLGGV-DGLLHISDMSWGRvkhpsevVNVGDEVEVKVLKIDKERKRISL 67
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 870-929 2.27e-09

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 60.06  E-value: 2.27e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314 870 GEVVTGAVTNVTQFGAFVDV--GVErnGLIHNSNMNNSQ--------LSVGDRIVASVVKVDLKRRQLEL 929
Cdd:COG0539 275 GDVVKGKVTRLTDFGAFVELepGVE--GLVHISEMSWTKrvahpsdvVKVGDEVEVKVLDIDPEERRISL 342
HHH_7 pfam14635
Helix-hairpin-helix motif;
664-759 9.13e-09

Helix-hairpin-helix motif;


Pssm-ID: 291309  Cd Length: 104  Bit Score: 53.70  E-value: 9.13e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314   664 EPRHLGVGMYQHDVPEKILTASLNDVVSECVSYVGVDLNTA-----SLSVLKHIAGLSEKKAEKIIEHRTQ-KGPFKTRK 737
Cdd:pfam14635   2 DILSLSFHPLQELLPKEELLKALETAFVDIVNLVGVDVNEAiankyEAAILPYIAGLGPRKADHLLKILAAnNGRLDNRS 81

                          90       100
                  ....*....|....*....|..
gi 62484314   738 DLLSVRSIGEKSFVQCAGFVRI 759
Cdd:pfam14635  82 QLITKCIMGPKVFMNCAGFLII 103
S1_RecJ_like cd04473
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ...
 864-924 9.27e-09

S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.


Pssm-ID: 239919 [Multi-domain]  Cd Length: 77  Bit Score: 52.99  E-value: 9.27e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 62484314 864 LDDLSMGEVVTGAVTNVTQFGAFVDVGVERNGLIHNSNMNNsQLSVGDRIVASVVKVDLKR 924
Cdd:cd04473  11 MEDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLR-DYEVGDEVIVQVTDIPENG 70
TIGR00426 TIGR00426
competence protein ComEA helix-hairpin-helix repeat region; Members of the subfamily ...
 699-750 5.60e-08

competence protein ComEA helix-hairpin-helix repeat region; Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model. [Cellular processes, DNA transformation]


Pssm-ID: 129520 [Multi-domain]  Cd Length: 69  Bit Score: 50.70  E-value: 5.60e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 62484314   699 VDLNTASLSVL-KHIAGLSEKKAEKIIEHRTQKGPFKTRKDLLSVRSIGEKSF 750
Cdd:TIGR00426   8 VNINTATAEELqRAMNGVGLKKAEAIVSYREEYGPFKTVEDLKQVPGIGNSLV 60
HHH_9 pfam17674
HHH domain;
770-815 1.27e-07

HHH domain;


Pssm-ID: 465451 [Multi-domain]  Cd Length: 70  Bit Score: 49.46  E-value: 1.27e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 62484314   770 NPLDCTWVHPESYNVVESIVGECDLKLSD-VGKAAFIASI--KQFASSQ 815
Cdd:pfam17674   1 NPLDNTAIHPESYPLAEKILKDLGLDLKDlIGNSALLKKLdpKKLAEEE 49
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 864-935 1.32e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 54.88  E-value: 1.32e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314  864 LDDLSMGEVVTGAVTNVTQFGAFVDVG-VErnGLIHNSNMNNSQ-------LSVGDRIVASVVKVDLKRRQLELRLENML 935
Cdd:PRK06676 187 LSSLKEGDVVEGTVARLTDFGAFVDIGgVD--GLVHISELSHERvekpsevVSVGQEVEVKVLSIDWETERISLSLKDTL 264
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 864-924 1.47e-07

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 54.67  E-value: 1.47e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 62484314 864 LDDLSMGEVVTGAVTNVTQFGAFVDV-GVErnGLIHNSNMNNSQ-------LSVGDRIVASVVKVDLKR 924
Cdd:COG0539 184 LEKLEEGDVVEGTVKNITDFGAFVDLgGVD--GLLHISEISWGRvkhpsevLKVGDEVEVKVLKIDREK 250
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
837-935 1.51e-07

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 55.34  E-value: 1.51e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314  837 VALQRELLQDYRADLDKRplfkqgltRLDDLSMGEVVTGAVTNVTQFGAFVDV-GVErnGLIHNSNMNNSQ-------LS 908
Cdd:PRK00087 453 VLSRKAILEEEKEKKKEE--------TWNSLEEGDVVEGEVKRLTDFGAFVDIgGVD--GLLHVSEISWGRvekpsdvLK 522

                         90       100
                 ....*....|....*....|....*..
gi 62484314  909 VGDRIVASVVKVDLKRRQLELRLENML 935
Cdd:PRK00087 523 VGDEIKVYILDIDKENKKLSLSLKKLL 549
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 864-931 3.07e-07

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 53.97  E-value: 3.07e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 62484314   864 LDDLSMGEVVTGAVTNVTQFGAFVDV--GVErnGLIHNSNMN--------NSQLSVGDRIVASVVKVDLKRRQLELRL 931
Cdd:TIGR00717 267 EKKFPVGDKITGRVTNLTDYGVFVEIeeGIE--GLVHVSEMSwvkknshpSKVVKKGDEVEVMILDIDPERRRLSLGL 342
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 868-931 3.23e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 53.89  E-value: 3.23e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 62484314  868 SMGEVVTGAVTNVTQFGAFVDV--GVErnGLIHNSNMNNSQL-------SVGDRIVASVVKVDLKRRQLELRL 931
Cdd:PRK07899 292 AIGQIVPGKVTKLVPFGAFVRVeeGIE--GLVHISELAERHVevpeqvvQVGDEVFVKVIDIDLERRRISLSL 362
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 870-929 3.66e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 54.01  E-value: 3.66e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314  870 GEVVTGAVTNVTQFGAFVDV--GVErnGLIHNSNM----NNSQ----LSVGDRIVASVVKVDLKRRQLEL 929
Cdd:PRK06299 287 GSKVKGKVTNITDYGAFVELeeGIE--GLVHVSEMswtkKNKHpskvVSVGQEVEVMVLEIDEEKRRISL 354
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 870-925 7.64e-07

S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240197 [Multi-domain]  Cd Length: 69  Bit Score: 47.28  E-value: 7.64e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 62484314 870 GEVVTGAVTNVTQFGAFVDVGVERNGLIHNSNMNNSQ-------LSVGDRIVASVVKVDLKRR 925
Cdd:cd05692   1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRvkdvkdvLKEGDKVKVKVLSIDARGR 63
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 873-929 1.06e-06

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 46.60  E-value: 1.06e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62484314 873 VTGAVTNVTQFGAFVDVGVERNGLIHNSNMNNSQ-------LSVGDRIVASVVKVDLKRRQLEL 929
Cdd:cd00164   1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFvkdpsevFKVGDEVEVKVLEVDPEKGRISL 64
rpsA PRK13806
30S ribosomal protein S1; Provisional
 865-931 1.09e-06

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 52.42  E-value: 1.09e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 62484314  865 DDLSMGEVVTGAVTNVTQFGAFVDV--GVErnGLIHNSNMNNSQ--------LSVGDRIVASVVKVDLKRRQLELRL 931
Cdd:PRK13806 288 DRLKAGDKVTGKVVRLAPFGAFVEIlpGIE--GLVHVSEMSWTRrvnkpedvVAPGDAVAVKIKDIDPAKRRISLSL 362
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 870-929 1.09e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 52.47  E-value: 1.09e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 62484314  870 GEVVTGAVTNVTQFGAFVDVGVERNGLIHNSNMN-------NSQLSVGDRIVASVVKVDLKRRQLEL 929
Cdd:PRK06299 461 GSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSrdrvedaTEVLKVGDEVEAKVINIDRKNRRISL 527
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 870-929 1.62e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 51.70  E-value: 1.62e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314  870 GEVVTGAVTNVTQFGAFV--DVGVErnGLIHNSNMN--------NSQLSVGDRIVASVVKVDLKRRQLEL 929
Cdd:PRK06299 374 GDVVEGKVKNITDFGAFVglEGGID--GLVHLSDISwdkkgeeaVELYKKGDEVEAVVLKVDVEKERISL 441
PRK08059 PRK08059
general stress protein 13; Validated
 870-931 2.59e-06

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 47.35  E-value: 2.59e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 62484314  870 GEVVTGAVTNVTQFGAFVDVGVERNGLIHNSNMN-------NSQLSVGDRIVASVVKVDLKRRQLELRL 931
Cdd:PRK08059   8 GSVVTGKVTGIQPYGAFVALDEETQGLVHISEIThgfvkdiHDFLSVGDEVKVKVLSVDEEKGKISLSI 76
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 870-921 2.72e-06

Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only];


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 47.48  E-value: 2.72e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 62484314 870 GEVVTGAVTNVTQFGAFVDVGVERNGLIHNSNMNNS-------QLSVGDRIVASVVKVD 921
Cdd:COG1098   6 GDIVEGKVTGITPFGAFVELPEGTTGLVHISEIADGyvkdindYLKVGDEVKVKVLSID 64
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 864-929 2.87e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 50.93  E-value: 2.87e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62484314  864 LDDLSMGEVVTGAVTNVTQFGAFVDV-GVErnGLIHNSNM------NNSQ-LSVGDRIVASVVKVDLKRRQLEL 929
Cdd:PRK06299 196 LENLEEGQVVEGVVKNITDYGAFVDLgGVD--GLLHITDIswkrvnHPSEvVNVGDEVKVKVLKFDKEKKRVSL 267
COG1107 COG1107
Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [Replication, ...
 862-917 3.57e-06

Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [Replication, recombination and repair];


Pssm-ID: 440724 [Multi-domain]  Cd Length: 626  Bit Score: 50.99  E-value: 3.57e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 62484314 862 TRLDDLSMGEVVTGAVTNVTQFGAFVDVGVERNGLIHNSNMnNSQLSVGDRIVASV 917
Cdd:COG1107  32 CTPDDLEPGRYYRGTVDGVADFGVFVDLNDHVTGLLHRSEL-DQDWEVGDEVFVQV 86
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 870-929 4.75e-06

S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240195 [Multi-domain]  Cd Length: 69  Bit Score: 45.18  E-value: 4.75e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 62484314 870 GEVVTGAVTNVTQFGAFVDVGVERNGLIHNSNMNNSQ--------LSVGDRIVASVVKVDLKRRQLEL 929
Cdd:cd05690   1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQrvrhpseiYKKGQEVEAVVLNIDVERERISL 68
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 870-928 5.75e-06

CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a family of full-length homologs of RNA-binding proteins from the Firmicutes with a single copy of the S1 domain. Several members of the family have been characterized as general stress proteins, and the most recently characterized, CvfD, was shown to act as a post-transcriptional regulator.


Pssm-ID: 468553 [Multi-domain]  Cd Length: 113  Bit Score: 46.27  E-value: 5.75e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62484314  870 GEVVTGAVTNVTQFGAFVDVGVERNGLIHNS--------NMNNsQLSVGDRIVASVVKVD-------LKRRQLE 928
Cdd:NF040579   4 GDIVEGKVTGIQPYGAFVALDEHTQGLIHISeikhgyvkDIND-FLKVGQEVKVKVLDIDeytgkisLSLRALE 76
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 870-931 1.22e-05

S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240213 [Multi-domain]  Cd Length: 77  Bit Score: 44.24  E-value: 1.22e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314 870 GEVVTGAVTNVTQFGAFVDV-GVERNGLIHNSNMNNS-------QLSVGDRIVASVVKVDLKRRQLELRL 931
Cdd:cd05708   3 GQKIDGTVRRVEDYGVFIDIdGTNVSGLCHKSEISDNrvadaskLFRVGDKVRAKVLKIDAEKKRISLGL 72
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 870-929 2.35e-05

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 48.19  E-value: 2.35e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 62484314   870 GEVVTGAVTNVTQFGAFVDV--GVErnGLIHNSNMNN-------SQLSVGDRIVASVVKVDLKRRQLEL 929
Cdd:TIGR00717 447 GSVVKGKVTEIKDFGAFVELpgGVE--GLIRNSELSEnrdedktDEIKVGDEVEAKVVDIDKKNRKVSL 513
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 870-929 4.00e-05

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 47.42  E-value: 4.00e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 62484314   870 GEVVTGAVTNVTQFGAFVDVGVERNGLIHNSNMN--------NSQLSVGDRIVASVVKVDLKRRQLEL 929
Cdd:TIGR00717 360 GDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISwdkdgreaDHLYKKGDEIEAVVLAVDKEKKRISL 427
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 870-929 4.23e-05

S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240194 [Multi-domain]  Cd Length: 72  Bit Score: 42.56  E-value: 4.23e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314 870 GEVVTGAVTNVTQFGAFVDV--GVErnGLIH-------NSNMNNSQL-SVGDRIVASVVKVDLKRRQLEL 929
Cdd:cd05689   4 GTRLFGKVTNLTDYGCFVELeeGVE--GLVHvsemdwtNKNIHPSKVvSLGDEVEVMVLDIDEERRRISL 71
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 864-931 4.43e-05

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 47.04  E-value: 4.43e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 62484314   864 LDDLSMGEVVTGAVTNVTQFGAFVDVGVERnGLIHNSNM------NNSQ-LSVGDRIVASVVKVDLKRRQLELRL 931
Cdd:TIGR00717 182 LENLKEGDVVKGVVKNITDFGAFVDLGGVD-GLLHITDMswkrvkHPSEyVKVGQEVKVKVIKFDKEKGRISLSL 255
rpsA PRK13806
30S ribosomal protein S1; Provisional
 836-931 6.18e-05

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 46.64  E-value: 6.18e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314  836 LVALQRELLQDYRADldkrplfkQGLTRLDDLSMGEVVTGAVTNVTQFGAFVDV--GVErnGLIHNSNMNNSQ------- 906
Cdd:PRK13806 177 IVVSRRALLEREQKE--------ALEAFMETVKEGDVVEGTVTRLAPFGAFVELapGVE--GMVHISELSWSRvqkadea 246

                         90       100
                 ....*....|....*....|....*
gi 62484314  907 LSVGDRIVASVVKVDLKRRQLELRL 931
Cdd:PRK13806 247 VSVGDTVRVKVLGIERAKKGKGLRI 271
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 870-929 6.65e-05

S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.


Pssm-ID: 239918 [Multi-domain]  Cd Length: 68  Bit Score: 41.76  E-value: 6.65e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 62484314 870 GEVVTGAVTNVTQFGAFVDVGVERNGLIHNSNMNNSQ-------LSVGDRIVASVVKVDlKRRQLEL 929
Cdd:cd04472   1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERvekvedvLKVGDEVKVKVIEVD-DRGRISL 66
PRK08563 PRK08563
DNA-directed RNA polymerase subunit E'; Provisional
 869-925 6.74e-05

DNA-directed RNA polymerase subunit E'; Provisional


Pssm-ID: 236289 [Multi-domain]  Cd Length: 187  Bit Score: 44.82  E-value: 6.74e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 62484314  869 MGEVVTGAVTNVTQFGAFVDVGVeRNGLIHNS-----NMN----NSQ---------LSVGDRIVASVVKVDLKRR 925
Cdd:PRK08563  81 LQEVVEGEVVEVVEFGAFVRIGP-VDGLLHISqimddYISydpkNGRligkeskrvLKVGDVVRARIVAVSLKER 154
S1_pNO40 cd05686
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ...
 869-925 6.87e-05

S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.


Pssm-ID: 240191 [Multi-domain]  Cd Length: 73  Bit Score: 42.08  E-value: 6.87e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 62484314 869 MGEVVTGAVTNVTQFGAFVDV-GVERNGLIHNSNMNNSQ-------LSVGDRIVASVVKVDLKRR 925
Cdd:cd05686   3 LYQIFKGEVASVTEYGAFVKIpGCRKQGLVHKSHMSSCRvddpsevVDVGEKVWVKVIGREMKDK 67
PRK08582 PRK08582
RNA-binding protein S1;
870-921 1.91e-04

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 42.33  E-value: 1.91e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 62484314  870 GEVVTGAVTNVTQFGAFVDVGVERNGLIHNSNMN-------NSQLSVGDRIVASVVKVD 921
Cdd:PRK08582   6 GSKLQGKVTGITNFGAFVELPEGKTGLVHISEVAdnyvkdiNDHLKVGDEVEVKVLNVE 64
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 865-929 2.36e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 44.48  E-value: 2.36e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62484314  865 DDLSMGEVVTGAVTNVTQFGAFVDV--GVErnGLIHNSNMNNSQ-------LSVGDRIVASVVKVDLKRRQLEL 929
Cdd:PRK06676 273 EKLPEGDVIEGTVKRLTDFGAFVEVlpGVE--GLVHISQISHKHiatpsevLEEGQEVKVKVLEVNEEEKRISL 344
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 870-923 2.89e-04

S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.


Pssm-ID: 240189 [Multi-domain]  Cd Length: 79  Bit Score: 40.30  E-value: 2.89e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 62484314 870 GEVVTGAVTNVTQFGAFVDV-GVERN--GLIHnsnmnNSQLSVGDRI--VASVVKVDLK 923
Cdd:cd05684   1 GKIYKGKVTSIMDFGCFVQLeGLKGRkeGLVH-----ISQLSFEGRVanPSDVVKRGQK 54
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 832-948 3.75e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 43.63  E-value: 3.75e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62484314  832 LEFLLVALQR-ELLQDYRADLDKRplfkqgltRLDDLSMGEVVTGAVTNVTQFGAFVDVGvERNGLIHNSNMN------- 903
Cdd:PRK07400 166 LKFLEVDEERnRLVLSHRRALVER--------KMNRLEVGEVVVGTVRGIKPYGAFIDIG-GVSGLLHISEIShehietp 236

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 62484314  904 NSQLSVGDRIVASVVKVDLKR-------RQLELRLENMLMETDTSFKfKAED 948
Cdd:PRK07400 237 HSVFNVNDEMKVMIIDLDAERgrislstKQLEPEPGDMLKDPQKVFD-KAEE 287
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 864-931 3.85e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 44.26  E-value: 3.85e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62484314  864 LDDLSMGEVVTGAVTNVTQFGAFVDV-GVErnGLIHNSNMN-------NSQLSVGDRIVASVVKVDLKRRQLELRL 931
Cdd:PRK07899 203 LNQLQKGQVRKGVVSSIVNFGAFVDLgGVD--GLVHVSELSwkhidhpSEVVEVGQEVTVEVLDVDMDRERVSLSL 276
PRK05807 PRK05807
RNA-binding protein S1;
867-921 5.03e-04

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 41.27  E-value: 5.03e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 62484314  867 LSMGEVVTGAVTNVTQFGAFVDVGvERNGLIHNSNMNNS-------QLSVGDRIVASVVKVD 921
Cdd:PRK05807   3 LKAGSILEGTVVNITNFGAFVEVE-GKTGLVHISEVADTyvkdireHLKEQDKVKVKVISID 63
S1_RPS1_repeat_ec1_hs1 cd05687
S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 870-929 5.78e-04

S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240192 [Multi-domain]  Cd Length: 70  Bit Score: 39.05  E-value: 5.78e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 62484314 870 GEVVTGAVTNVTQFGAFVDVGVERNGLI--------HNSNMNNSqLSVGDRIVASVVKVDLKRRQLEL 929
Cdd:cd05687   1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIpisefsddPIENGEDE-VKVGDEVEVYVLRVEDEEGNVVL 67
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 870-925 5.84e-04

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 43.88  E-value: 5.84e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 62484314  870 GEVVTGAVTNVTQFGAFVDV--GVErnGLIHNSNMNN-------SQLSVGDRIVASVVKVDLKRR 925
Cdd:PRK11824 622 GEIYEGKVVRIVDFGAFVEIlpGKD--GLVHISEIADervekveDVLKEGDEVKVKVLEIDKRGR 684
S1_RpoE cd04460
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 871-925 7.93e-04

S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.


Pssm-ID: 239907 [Multi-domain]  Cd Length: 99  Bit Score: 39.58  E-value: 7.93e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62484314 871 EVVTGAVTNVTQFGAFVDVG-VErnGLIHNSNM---------NNSQ---------LSVGDRIVASVVKVDLKRR 925
Cdd:cd04460   1 EVVEGEVVEVVDFGAFVRIGpVD--GLLHISQImddyisydpKNKRligeetkrvLKVGDVVRARIVAVSLKER 72
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 870-931 1.15e-03

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 41.73  E-value: 1.15e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 62484314  870 GEVVTGAVTNVTQFGAFVDV----GVErnGLIHNSNMNNS-------QLSVGDRIVASVVKVDLKRRQLELRL 931
Cdd:PRK03987   9 GELVVGTVKEVKDFGAFVTLdeypGKE--GFIHISEVASGwvknirdHVKEGQKVVCKVIRVDPRKGHIDLSL 79
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
870-921 2.82e-03

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 41.47  E-value: 2.82e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 62484314  870 GEVVTGAVTNVTQFGAFVDV--GVErnGLIHNSNMNNSQ-------LSVGDRIVASVVKVD 921
Cdd:PRK00087 563 GSIVLGKVVRIAPFGAFVELepGVD--GLVHISQISWKRidkpedvLSEGEEVKAKILEVD 621
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 870-931 3.79e-03

S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to complete the initiation complex, which is competent to begin translation. The IF2a subunit is a major site of control of the translation initiation process, via phosphorylation of a specific serine residue. This alpha subunit is well conserved in eukaryotes and archaea but is not present in bacteria. IF2 is a cold-shock-inducible protein.


Pssm-ID: 239899 [Multi-domain]  Cd Length: 76  Bit Score: 37.18  E-value: 3.79e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 62484314 870 GEVVTGAVTNVTQFGAFVDV----GVErnGLIHNSNMN-------NSQLSVGDRIVASVVKVDLKRRQLELRL 931
Cdd:cd04452   4 GELVVVTVKSIADMGAYVSLleygNIE--GMILLSELSrrrirsiRKLVKVGRKEVVKVIRVDKEKGYIDLSK 74
YqgF pfam14639
Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to ...
 617-663 4.06e-03

Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to the E.coli RuvC but its putative catalytic site lacks the carboxylate side chains critical for coordinating magnesium ions that mediate phosphodiester bond-cleavage


Pssm-ID: 258777  Cd Length: 150  Bit Score: 38.69  E-value: 4.06e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 62484314   617 IVNENGASIYSCSNVAAKEFPKMDTNERSAVSIARRLNDPLSEYVKI 663
Cdd:pfam14639 103 LVDDEVAILYQNSKRAEAEFPDYPPLLRYCVALARYIQDPLLEYAQV 149
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 861-931 4.79e-03

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 36.80  E-value: 4.79e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 62484314 861 LTRLDDLSMGEVVTGAVTNVTQFGAFVDVGVERNGLIHNSNM---NNSQLS----VGDRIVASVVKVDLKRRQLELRL 931
Cdd:cd04461   6 PTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYIsdeFVTDPSfgfkKGQSVTAKVTSVDEEKQRFLLSL 83
 
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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