NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|767914795|ref|XP_011531248|]
View 

S1 RNA-binding domain-containing protein 1 isoform X1 [Homo sapiens]

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

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Tex super family cl34417
Transcriptional accessory protein Tex/SPT6 [Transcription];
210-973 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: 600.47  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 210 MNWDMVQVLSERTNIEPWVCANIIRLFNDDNTIPFIIRYRKELINNLDADSLREVQQTLEELRAVAKKVHSTIQKIKKEG 289
Cdd:COG2183    1 MMMDIIQRIAQELGLRPKQVEAAVELLDEGATVPFIARYRKEATGGLDEVQLRTIEERLTYLRELEKRRETILKSIEEQG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 290 KMSECLLKAMLNCKTFEELEHVSAPYKTGSKgTKAQRARQLGLEGAARALLEKPgELSLLS----YIRPDvKGLSTLQDI 365
Cdd:COG2183   81 KLTPELKAKIEAADTKQELEDLYLPYKPKRR-TKATIAREKGLEPLADLLLAQP-TGDPEAeaakYINEE-KGVADVEAA 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 366 EIGVQHILADMIAKDKDTLDFIRNLCQKRHVcIQSslaKVSSKKVNEKDvdKFLLYQHFSCNIRNIHHHQILAINRGENL 445
Cdd:COG2183  158 LDGARDILAERISEDAELRGKLRELLWKEGV-LVS---KVKKGKEEEGA--KFRDYFDYSEPLKKIPSHRILALNRGEKE 231

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 446 KVLTVKVNI-SDGVKDEFCRWCIQNRWRPrsfARPELMKilynSLNDSFKRLIYPLLCREFRAKLTSDAEKESVMMFGRN 524
Cdd:COG2183  232 GVLKVKLEPdEEEAEAYIARRFIKDQGRP---ADEWLKE----AVRDAYKRLLAPSLERELRNELKEKAEEEAIKVFAEN 304

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 525 LRQLLLTSPVPGRTLMGVDPGYKHGCKLAIISPTSQILHTDVVYLHCGQGFRE--AEKIKTLLLNFNCSTVVIGNGTACR 602
Cdd:COG2183  305 LRDLLLAAPAGGKVVLGLDPGFRTGCKVAVVDETGKLLDTATIYPHPPQNKWEeaAKTLAALIKKYKVELIAIGNGTASR 384

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 603 ETEAYFADLImKNYFAPLDVVYCFEA----Y-------ESLP-----FRteSQVSIARRVQDPLAELVKIEPKHIGVGMY 666
Cdd:COG2183  385 ETEQFVAELI-KELDLKVQYVIVSEAgasvYsaselarEEFPdldvtVR--GAVSIARRLQDPLAELVKIDPKSIGVGQY 461

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 667 QHDVSQTLLKATLDSVVEECVSFVGVDINICSEVLLRHIAGLNANRAKNIIEWREKNGPFINREQLKKVKGLGPKSFQQC 746
Cdd:COG2183  462 QHDVNQKKLKRSLDAVVEDCVNAVGVDLNTASAPLLSYVSGLNPTLAKNIVAYRDENGAFKSRKELLKVPRLGPKAFEQA 541

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 747 AGFIRInqdyirtfcsqqtetsgqiqgvavtssadvevtneKQGKkksktavnvllkpNPLDQTCIHPESYDIAMRFLSS 826
Cdd:COG2183  542 AGFLRI-----------------------------------RDGD-------------NPLDNSAVHPESYPVVEKILKD 573

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 827 IGGTLYEV-GKPEMQQKINsflekegMEKIAERLqTTVHTLQVIIDGLSQPeSFDFRTDFDKPDFKRSIVCLEDLQIGTV 905
Cdd:COG2183  574 LGVSVKDLiGNKELLKKLD-------PEKYADEL-FGLPTLRDILKELEKP-GRDPRPEFKTPTFREGVLKIEDLKPGMI 644

                        730       740       750       760       770       780       790
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767914795 906 LTGKVENATLFGIFVDIGVGKSGLIPIrnvteAKLSKT---------KkrrslglgPGERVEVQVLNIDIPRSRITL 973
Cdd:COG2183  645 LEGTVTNVTDFGAFVDIGVHQDGLVHI-----SQLSDRfvkdprevvK--------VGDIVKVKVLEVDLKRKRISL 708
 
Name Accession Description Interval E-value
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
210-973 0e+00

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 600.47  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 210 MNWDMVQVLSERTNIEPWVCANIIRLFNDDNTIPFIIRYRKELINNLDADSLREVQQTLEELRAVAKKVHSTIQKIKKEG 289
Cdd:COG2183    1 MMMDIIQRIAQELGLRPKQVEAAVELLDEGATVPFIARYRKEATGGLDEVQLRTIEERLTYLRELEKRRETILKSIEEQG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 290 KMSECLLKAMLNCKTFEELEHVSAPYKTGSKgTKAQRARQLGLEGAARALLEKPgELSLLS----YIRPDvKGLSTLQDI 365
Cdd:COG2183   81 KLTPELKAKIEAADTKQELEDLYLPYKPKRR-TKATIAREKGLEPLADLLLAQP-TGDPEAeaakYINEE-KGVADVEAA 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 366 EIGVQHILADMIAKDKDTLDFIRNLCQKRHVcIQSslaKVSSKKVNEKDvdKFLLYQHFSCNIRNIHHHQILAINRGENL 445
Cdd:COG2183  158 LDGARDILAERISEDAELRGKLRELLWKEGV-LVS---KVKKGKEEEGA--KFRDYFDYSEPLKKIPSHRILALNRGEKE 231

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 446 KVLTVKVNI-SDGVKDEFCRWCIQNRWRPrsfARPELMKilynSLNDSFKRLIYPLLCREFRAKLTSDAEKESVMMFGRN 524
Cdd:COG2183  232 GVLKVKLEPdEEEAEAYIARRFIKDQGRP---ADEWLKE----AVRDAYKRLLAPSLERELRNELKEKAEEEAIKVFAEN 304

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 525 LRQLLLTSPVPGRTLMGVDPGYKHGCKLAIISPTSQILHTDVVYLHCGQGFRE--AEKIKTLLLNFNCSTVVIGNGTACR 602
Cdd:COG2183  305 LRDLLLAAPAGGKVVLGLDPGFRTGCKVAVVDETGKLLDTATIYPHPPQNKWEeaAKTLAALIKKYKVELIAIGNGTASR 384

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 603 ETEAYFADLImKNYFAPLDVVYCFEA----Y-------ESLP-----FRteSQVSIARRVQDPLAELVKIEPKHIGVGMY 666
Cdd:COG2183  385 ETEQFVAELI-KELDLKVQYVIVSEAgasvYsaselarEEFPdldvtVR--GAVSIARRLQDPLAELVKIDPKSIGVGQY 461

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 667 QHDVSQTLLKATLDSVVEECVSFVGVDINICSEVLLRHIAGLNANRAKNIIEWREKNGPFINREQLKKVKGLGPKSFQQC 746
Cdd:COG2183  462 QHDVNQKKLKRSLDAVVEDCVNAVGVDLNTASAPLLSYVSGLNPTLAKNIVAYRDENGAFKSRKELLKVPRLGPKAFEQA 541

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 747 AGFIRInqdyirtfcsqqtetsgqiqgvavtssadvevtneKQGKkksktavnvllkpNPLDQTCIHPESYDIAMRFLSS 826
Cdd:COG2183  542 AGFLRI-----------------------------------RDGD-------------NPLDNSAVHPESYPVVEKILKD 573

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 827 IGGTLYEV-GKPEMQQKINsflekegMEKIAERLqTTVHTLQVIIDGLSQPeSFDFRTDFDKPDFKRSIVCLEDLQIGTV 905
Cdd:COG2183  574 LGVSVKDLiGNKELLKKLD-------PEKYADEL-FGLPTLRDILKELEKP-GRDPRPEFKTPTFREGVLKIEDLKPGMI 644

                        730       740       750       760       770       780       790
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767914795 906 LTGKVENATLFGIFVDIGVGKSGLIPIrnvteAKLSKT---------KkrrslglgPGERVEVQVLNIDIPRSRITL 973
Cdd:COG2183  645 LEGTVTNVTDFGAFVDIGVHQDGLVHI-----SQLSDRfvkdprevvK--------VGDIVKVKVLEVDLKRKRISL 708
Tex_N pfam09371
Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss: ...
 218-400 9.02e-60

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: 202.25  E-value: 9.02e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795  218 LSERTNIEPWVCANIIRLFNDDNTIPFIIRYRKELINNLDADSLREVQQTLEELRAVAKKVHSTIQKIKKEGKMSECLLK 297
Cdd:pfam09371   1 IAEELGLKPKQVEATVKLLDEGNTVPFIARYRKEATGGLDEVQLREIEERLEYLRELEKRKETILKSIEEQGKLTDELKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795  298 AMLNCKTFEELEHVSAPYKTgSKGTKAQRARQLGLEGAARALLEKPGELSLL-SYIRPDvKGLSTLQDIEIGVQHILADM 376
Cdd:pfam09371  81 AIEAADTLTELEDLYLPYKP-KRRTKATIAREKGLEPLADAILAQPDPEEEAaKYINPE-KGVADVEEALAGARDIIAER 158

                         170       180
                  ....*....|....*....|....
gi 767914795  377 IAKDKDTLDFIRNLCQKRHVCIQS 400
Cdd:pfam09371 159 ISEDAELRKKLRELLWREGVIVSK 182
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 903-974 2.83e-25

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: 99.61  E-value: 2.83e-25
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767914795 903 GTVLTGKVENATLFGIFVDIGVGKSGLIPIRNVTEAKLSktkkRRSLGLGPGERVEVQVLNIDIPRSRITLD 974
Cdd:cd05685    1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVS----HPSDVVSVGDIVEVKVISIDEERGRISLS 68
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
 537-632 7.20e-16

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: 73.76  E-value: 7.20e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795   537 RTLMGVDPGyKHGCKLAIISPTSQILHTDVVYLHcGQGFREAEKIKTLLLNFNCSTVVIG-----NGTACRETEAYFADL 611
Cdd:smart00732   1 KRVLGLDPG-RKGIGVAVVDETGKLADPLEVIPR-TNKEADAARLKKLIKKYQPDLIVIGlplnmNGTASRETEEAFAEL 78

                           90       100
                   ....*....|....*....|.
gi 767914795   612 IMKNYfaPLDVVYCFEAYESL 632
Cdd:smart00732  79 LKERF--NLPVVLVDERLATV 97
TIGR00426 TIGR00426
competence protein ComEA helix-hairpin-helix repeat region; Members of the subfamily ...
 692-745 5.40e-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: 5.40e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 767914795  692 VDINICS-EVLLRHIAGLNANRAKNIIEWREKNGPFINREQLKKVKGLGPKSFQQ 745
Cdd:TIGR00426   8 VNINTATaEELQRAMNGVGLKKAEAIVSYREEYGPFKTVEDLKQVPGIGNSLVEK 62
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 897-975 2.00e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 54.50  E-value: 2.00e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767914795 897 LEDLQIGTVLTGKVENATLFGIFVDIGvGKSGLIPIrnvTEAKLSKTKKRRSLgLGPGERVEVQVLNIDIPRSRITLDL 975
Cdd:PRK06676 187 LSSLKEGDVVEGTVARLTDFGAFVDIG-GVDGLVHI---SELSHERVEKPSEV-VSVGQEVEVKVLSIDWETERISLSL 260
 
Name Accession Description Interval E-value
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
210-973 0e+00

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 600.47  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 210 MNWDMVQVLSERTNIEPWVCANIIRLFNDDNTIPFIIRYRKELINNLDADSLREVQQTLEELRAVAKKVHSTIQKIKKEG 289
Cdd:COG2183    1 MMMDIIQRIAQELGLRPKQVEAAVELLDEGATVPFIARYRKEATGGLDEVQLRTIEERLTYLRELEKRRETILKSIEEQG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 290 KMSECLLKAMLNCKTFEELEHVSAPYKTGSKgTKAQRARQLGLEGAARALLEKPgELSLLS----YIRPDvKGLSTLQDI 365
Cdd:COG2183   81 KLTPELKAKIEAADTKQELEDLYLPYKPKRR-TKATIAREKGLEPLADLLLAQP-TGDPEAeaakYINEE-KGVADVEAA 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 366 EIGVQHILADMIAKDKDTLDFIRNLCQKRHVcIQSslaKVSSKKVNEKDvdKFLLYQHFSCNIRNIHHHQILAINRGENL 445
Cdd:COG2183  158 LDGARDILAERISEDAELRGKLRELLWKEGV-LVS---KVKKGKEEEGA--KFRDYFDYSEPLKKIPSHRILALNRGEKE 231

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 446 KVLTVKVNI-SDGVKDEFCRWCIQNRWRPrsfARPELMKilynSLNDSFKRLIYPLLCREFRAKLTSDAEKESVMMFGRN 524
Cdd:COG2183  232 GVLKVKLEPdEEEAEAYIARRFIKDQGRP---ADEWLKE----AVRDAYKRLLAPSLERELRNELKEKAEEEAIKVFAEN 304

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 525 LRQLLLTSPVPGRTLMGVDPGYKHGCKLAIISPTSQILHTDVVYLHCGQGFRE--AEKIKTLLLNFNCSTVVIGNGTACR 602
Cdd:COG2183  305 LRDLLLAAPAGGKVVLGLDPGFRTGCKVAVVDETGKLLDTATIYPHPPQNKWEeaAKTLAALIKKYKVELIAIGNGTASR 384

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 603 ETEAYFADLImKNYFAPLDVVYCFEA----Y-------ESLP-----FRteSQVSIARRVQDPLAELVKIEPKHIGVGMY 666
Cdd:COG2183  385 ETEQFVAELI-KELDLKVQYVIVSEAgasvYsaselarEEFPdldvtVR--GAVSIARRLQDPLAELVKIDPKSIGVGQY 461

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 667 QHDVSQTLLKATLDSVVEECVSFVGVDINICSEVLLRHIAGLNANRAKNIIEWREKNGPFINREQLKKVKGLGPKSFQQC 746
Cdd:COG2183  462 QHDVNQKKLKRSLDAVVEDCVNAVGVDLNTASAPLLSYVSGLNPTLAKNIVAYRDENGAFKSRKELLKVPRLGPKAFEQA 541

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 747 AGFIRInqdyirtfcsqqtetsgqiqgvavtssadvevtneKQGKkksktavnvllkpNPLDQTCIHPESYDIAMRFLSS 826
Cdd:COG2183  542 AGFLRI-----------------------------------RDGD-------------NPLDNSAVHPESYPVVEKILKD 573

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 827 IGGTLYEV-GKPEMQQKINsflekegMEKIAERLqTTVHTLQVIIDGLSQPeSFDFRTDFDKPDFKRSIVCLEDLQIGTV 905
Cdd:COG2183  574 LGVSVKDLiGNKELLKKLD-------PEKYADEL-FGLPTLRDILKELEKP-GRDPRPEFKTPTFREGVLKIEDLKPGMI 644

                        730       740       750       760       770       780       790
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767914795 906 LTGKVENATLFGIFVDIGVGKSGLIPIrnvteAKLSKT---------KkrrslglgPGERVEVQVLNIDIPRSRITL 973
Cdd:COG2183  645 LEGTVTNVTDFGAFVDIGVHQDGLVHI-----SQLSDRfvkdprevvK--------VGDIVKVKVLEVDLKRKRISL 708
Tex_N pfam09371
Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss: ...
 218-400 9.02e-60

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: 202.25  E-value: 9.02e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795  218 LSERTNIEPWVCANIIRLFNDDNTIPFIIRYRKELINNLDADSLREVQQTLEELRAVAKKVHSTIQKIKKEGKMSECLLK 297
Cdd:pfam09371   1 IAEELGLKPKQVEATVKLLDEGNTVPFIARYRKEATGGLDEVQLREIEERLEYLRELEKRKETILKSIEEQGKLTDELKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795  298 AMLNCKTFEELEHVSAPYKTgSKGTKAQRARQLGLEGAARALLEKPGELSLL-SYIRPDvKGLSTLQDIEIGVQHILADM 376
Cdd:pfam09371  81 AIEAADTLTELEDLYLPYKP-KRRTKATIAREKGLEPLADAILAQPDPEEEAaKYINPE-KGVADVEEALAGARDIIAER 158

                         170       180
                  ....*....|....*....|....
gi 767914795  377 IAKDKDTLDFIRNLCQKRHVCIQS 400
Cdd:pfam09371 159 ISEDAELRKKLRELLWREGVIVSK 182
Tex_YqgF pfam16921
Tex protein YqgF-like domain; This is the YqgF-like domain of the bacterial Tex protein, which ...
 538-647 1.35e-33

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: 125.59  E-value: 1.35e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795  538 TLMGVDPGYKHGCKLAIISPTSQILHTDVVYLHCGQGFRE--AEKIKTLLLNFNCSTVVIGNGTACRETEAYFADLIMKN 615
Cdd:pfam16921   1 VVLGLDPGYRTGCKLAVVDETGKVLDTAVIYPHPPQNKVEeaKKKLKKLIKKYGVELIAIGNGTASRETEQFVAELIKEL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 767914795  616 yfaPLDVVYCF-------------EAYESLP-----FRteSQVSIARRVQ 647
Cdd:pfam16921  81 ---PLKVKYVIvseagasvysaseLAREEFPdldvsLR--GAVSIARRLQ 125
HHH_3 pfam12836
Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.
 689-750 1.70e-27

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


Pssm-ID: 463723 [Multi-domain]  Cd Length: 62  Bit Score: 105.64  E-value: 1.70e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767914795  689 FVGVDINICSEVLLRHIAGLNANRAKNIIEWREKNGPFINREQLKKVKGLGPKSFQQCAGFI 750
Cdd:pfam12836   1 AVGVDINTASAELLSRVPGLGPKLAKNIVEYREENGPFRSREDLLKVKGLGPKTFEQLAGFL 62
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 903-974 2.83e-25

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: 99.61  E-value: 2.83e-25
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767914795 903 GTVLTGKVENATLFGIFVDIGVGKSGLIPIRNVTEAKLSktkkRRSLGLGPGERVEVQVLNIDIPRSRITLD 974
Cdd:cd05685    1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVS----HPSDVVSVGDIVEVKVISIDEERGRISLS 68
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
 537-632 7.20e-16

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: 73.76  E-value: 7.20e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795   537 RTLMGVDPGyKHGCKLAIISPTSQILHTDVVYLHcGQGFREAEKIKTLLLNFNCSTVVIG-----NGTACRETEAYFADL 611
Cdd:smart00732   1 KRVLGLDPG-RKGIGVAVVDETGKLADPLEVIPR-TNKEADAARLKKLIKKYQPDLIVIGlplnmNGTASRETEEAFAEL 78

                           90       100
                   ....*....|....*....|.
gi 767914795   612 IMKNYfaPLDVVYCFEAYESL 632
Cdd:smart00732  79 LKERF--NLPVVLVDERLATV 97
ComEA COG1555
DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair]; ...
 692-758 3.20e-14

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


Pssm-ID: 441164 [Multi-domain]  Cd Length: 72  Bit Score: 68.35  E-value: 3.20e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767914795 692 VDINICSEVLLRHIAGLNANRAKNIIEWREKNGPFINREQLKKVKGLGPKSFQQcagfiriNQDYIR 758
Cdd:COG1555   13 VDINTATAEELQTLPGIGPKLAQRIVEYREKNGPFKSVEDLLEVKGIGPKTLEK-------LKPYLT 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
901-975 7.75e-12

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 61.47  E-value: 7.75e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767914795   901 QIGTVLTGKVENATLFGIFVDIGVGKSGLIPIRNVTEAKLSKTKKRrslgLGPGERVEVQVLNIDIPRSRITLDL 975
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEV----LKVGDEVKVKVLSVDEEKGRIILSL 71
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 903-973 2.73e-09

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: 54.21  E-value: 2.73e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767914795 903 GTVLTGKVENATLFGIFVDIGVGKSGLIPIRNVTEAKLSKTKKRrslgLGPGERVEVQVLNIDiPRSRITL 973
Cdd:cd05692    1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDV----LKEGDKVKVKVLSID-ARGRISL 66
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 902-973 1.36e-08

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: 52.25  E-value: 1.36e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767914795 902 IGTVLTGKVENATLFGIFVDIGvGKSGLIpirNVTEAKLSKTKKRRSLgLGPGERVEVQVLNIDIPRSRITL 973
Cdd:cd05688    1 EGDVVEGTVKSITDFGAFVDLG-GVDGLL---HISDMSWGRVKHPSEV-VNVGDEVEVKVLKIDKERKRISL 67
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 897-975 1.67e-08

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: 52.59  E-value: 1.67e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767914795 897 LEDLQIGTVLTGKVENATLFGIFVDIGVGKSGLIPIRNVTEAKLSKTKKrrslGLGPGERVEVQVLNIDIPRSRITLDL 975
Cdd:cd04461    9 FSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSF----GFKKGQSVTAKVTSVDEEKQRFLLSL 83
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 900-973 2.72e-08

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: 51.52  E-value: 2.72e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767914795  900 LQIGTVLTGKVENATLFGIFVDIGVGKSGLIPIRNVTeaklSKTKKRRSLGLGPGERVEVQVLNIDIPRSRITL 973
Cdd:pfam00575   1 PEKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELS----DDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIIL 70
TIGR00426 TIGR00426
competence protein ComEA helix-hairpin-helix repeat region; Members of the subfamily ...
 692-745 5.40e-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: 5.40e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 767914795  692 VDINICS-EVLLRHIAGLNANRAKNIIEWREKNGPFINREQLKKVKGLGPKSFQQ 745
Cdd:TIGR00426   8 VNINTATaEELQRAMNGVGLKKAEAIVSYREEYGPFKTVEDLKQVPGIGNSLVEK 62
HHH_9 pfam17674
HHH domain;
805-876 5.85e-08

HHH domain;


Pssm-ID: 465451 [Multi-domain]  Cd Length: 70  Bit Score: 50.61  E-value: 5.85e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767914795  805 NPLDQTCIHPESYDIAMRFLSSIGGTLYE-VGKPEMQQKINSflekegmEKIAERlqtTVH--TLQVIIDGLSQP 876
Cdd:pfam17674   1 NPLDNTAIHPESYPLAEKILKDLGLDLKDlIGNSALLKKLDP-------KKLAEE---EVGlpTLKDILEELAKP 65
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 897-973 9.02e-08

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: 55.44  E-value: 9.02e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767914795 897 LEDLQIGTVLTGKVENATLFGIFVDIGvGKSGLIPIrnvTEAKLSKTKKRRSLgLGPGERVEVQVLNIDIPRSRITL 973
Cdd:COG0539  184 LEKLEEGDVVEGTVKNITDFGAFVDLG-GVDGLLHI---SEISWGRVKHPSEV-LKVGDEVEVKVLKIDREKERISL 255
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 903-973 1.44e-07

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: 49.41  E-value: 1.44e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767914795 903 GTVLTGKVENATLFGIFVDIGVGKSGLIpirNVTEAKLSKTKKRRSLGLGPGERVEVQVLNIDIPRSRITL 973
Cdd:cd05690    1 GTVVSGKIKSITDFGIFVGLDGGIDGLV---HISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 898-973 1.71e-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: 54.28  E-value: 1.71e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767914795 898 EDLQIGTVLTGKVENATLFGIFVDIGVGKSGLIPIrnvTEakLSKTKKRRSLG--LGPGERVEVQVLNIDIPRSRITL 973
Cdd:COG0539  270 EKYPVGDVVKGKVTRLTDFGAFVELEPGVEGLVHI---SE--MSWTKRVAHPSdvVKVGDEVEVKVLDIDPEERRISL 342
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 897-975 2.00e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 54.50  E-value: 2.00e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767914795 897 LEDLQIGTVLTGKVENATLFGIFVDIGvGKSGLIPIrnvTEAKLSKTKKRRSLgLGPGERVEVQVLNIDIPRSRITLDL 975
Cdd:PRK06676 187 LSSLKEGDVVEGTVARLTDFGAFVDIG-GVDGLVHI---SELSHERVEKPSEV-VSVGQEVEVKVLSIDWETERISLSL 260
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 898-975 2.15e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 54.79  E-value: 2.15e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 898 EDLQIGTVLTGKVENATLFGIFVDIGVGKSGLIpirNVTEakLSKTKKRRSLG--LGPGERVEVQVLNIDIPRSRITLDL 975
Cdd:PRK06299 282 KKYPVGSKVKGKVTNITDYGAFVELEEGIEGLV---HVSE--MSWTKKNKHPSkvVSVGQEVEVMVLEIDEEKRRISLGL 356
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 906-973 2.90e-07

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: 48.53  E-value: 2.90e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767914795 906 LTGKVENATLFGIFVDIGVGKSGLIPIRNVTEAKLSKTKKRrslgLGPGERVEVQVLNIDIPRSRITL 973
Cdd:cd00164    1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEV----FKVGDEVEVKVLEVDPEKGRISL 64
HHH_7 pfam14635
Helix-hairpin-helix motif;
666-752 3.33e-07

Helix-hairpin-helix motif;


Pssm-ID: 291309  Cd Length: 104  Bit Score: 49.46  E-value: 3.33e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795  666 YQHDVSQTLLKATLDSVVEECVSFVGVDINIC-----SEVLLRHIAGLNANRAKNIIE-WREKNGPFINREQLKKVKGLG 739
Cdd:pfam14635  11 LQELLPKEELLKALETAFVDIVNLVGVDVNEAiankyEAAILPYIAGLGPRKADHLLKiLAANNGRLDNRSQLITKCIMG 90

                          90
                  ....*....|...
gi 767914795  740 PKSFQQCAGFIRI 752
Cdd:pfam14635  91 PKVFMNCAGFLII 103
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 901-973 3.62e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 54.01  E-value: 3.62e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767914795 901 QIGTVLTGKVENATLFGIFVDIGVGKSGLIPI------RNVTEAKlSKTKKrrslglgpGERVEVQVLNIDIPRSRITL 973
Cdd:PRK06299 372 PVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLsdiswdKKGEEAV-ELYKK--------GDEVEAVVLKVDVEKERISL 441
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 898-973 3.71e-07

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 50.18  E-value: 3.71e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767914795 898 EDLQIGTVLTGKVENATLFGIFVDIGVGKSGLIPIRNVTEaklSKTKKRRSLgLGPGERVEVQVLNIDiPRSRITL 973
Cdd:COG1098    1 MSIEVGDIVEGKVTGITPFGAFVELPEGTTGLVHISEIAD---GYVKDINDY-LKVGDEVKVKVLSID-EDGKISL 71
rpsA PRK13806
30S ribosomal protein S1; Provisional
 898-973 7.04e-07

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 52.80  E-value: 7.04e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767914795 898 EDLQIGTVLTGKVENATLFGIFVDIGVGKSGLIPirnvtEAKLSKTKKRRSL-GLGPGERVEVQVLNIDIPRSRITL 973
Cdd:PRK13806 375 ERFAPGTTVTGTVEKRAQFGLFVNLAPGVTGLLP-----ASVISRAGKPATYeKLKPGDSVTLVVEEIDTAKRKISL 446
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 897-978 1.84e-06

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: 51.66  E-value: 1.84e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795  897 LEDLQIGTVLTGKVENATLFGIFVDIGVGKSGLIPirnVTEAKLSKTKKRRSLGLGPGERVEVQVLNIDIPRSRITLDLI 976
Cdd:TIGR00717 267 EKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVH---VSEMSWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLK 343


                  ..
gi 767914795  977 RV 978
Cdd:TIGR00717 344 QC 345
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 903-973 3.10e-06

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: 45.65  E-value: 3.10e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767914795 903 GTVLTGKVENATLFGIFVDIGVGKSGLIpirNVTEAKLSKTKKRRSLGLGPGERVEVQVLNIDIPRSRITL 973
Cdd:cd05689    4 GTRLFGKVTNLTDYGCFVELEEGVEGLV---HVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISL 71
S1_RNase_E cd04453
S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential ...
 901-961 9.08e-06

S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain that is highly homologous to that of RNase E. RNase G not only shares sequence similarity with RNase E, but also functionally overlaps with RNase E. In Escherichia coli, RNase G is involved in the maturation of the 5' end of the 16S rRNA. RNase G plays a secondary role in mRNA decay.


Pssm-ID: 239900 [Multi-domain]  Cd Length: 88  Bit Score: 44.89  E-value: 9.08e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767914795 901 QIGTVLTGKVEN--ATLFGIFVDIGVGKSGLIPIRNVTEAKLSKTKKRRSLgLGPGERVEVQV 961
Cdd:cd04453    6 IVGNIYLGRVKKivPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKL-LKEGQEILVQV 67
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 898-973 1.99e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 47.95  E-value: 1.99e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767914795 898 EDLQIGTVLTGKVENATLFGIFVDIGVGKSGLIPIRNVTEAKLSKTKKRrslgLGPGERVEVQVLNIDIPRSRITL 973
Cdd:PRK06676 273 EKLPEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHIATPSEV----LEEGQEVKVKVLEVNEEEKRISL 344
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 903-975 2.61e-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: 43.09  E-value: 2.61e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767914795 903 GTVLTGKVENATLFGIFVDI-GVGKSGLIPIRNVTEAKlsktKKRRSLGLGPGERVEVQVLNIDIPRSRITLDL 975
Cdd:cd05708    3 GQKIDGTVRRVEDYGVFIDIdGTNVSGLCHKSEISDNR----VADASKLFRVGDKVRAKVLKIDAEKKRISLGL 72
rpsA PRK13806
30S ribosomal protein S1; Provisional
 898-975 3.07e-05

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 47.80  E-value: 3.07e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 898 EDLQIGTVLTGKVENATLFGIFVDIGVGKSGLIPIrnvteAKLSKTKKRRSLG--LGPGERVEVQVLNIDIPRSRITLDL 975
Cdd:PRK13806 288 DRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHV-----SEMSWTRRVNKPEdvVAPGDAVAVKIKDIDPAKRRISLSL 362
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 882-975 6.50e-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: 46.65  E-value: 6.50e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795  882 RTDFDKPDFKRSIVCLEDLQIGTVLTGKVENATLFGIFVDIGvGKSGLIPIRNVTEaklsKTKKRRSLGLGPGERVEVQV 961
Cdd:TIGR00717 167 RAYLEEERSQAREELLENLKEGDVVKGVVKNITDFGAFVDLG-GVDGLLHITDMSW----KRVKHPSEYVKVGQEVKVKV 241

                          90
                  ....*....|....
gi 767914795  962 LNIDIPRSRITLDL 975
Cdd:TIGR00717 242 IKFDKEKGRISLSL 255
PRK08582 PRK08582
RNA-binding protein S1;
900-965 1.05e-04

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 43.10  E-value: 1.05e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767914795 900 LQIGTVLTGKVENATLFGIFVDIGVGKSGLIPIRNVTEAKLSKTKKRRSLglgpGERVEVQVLNID 965
Cdd:PRK08582   3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKV----GDEVEVKVLNVE 64
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
898-978 1.20e-04

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 46.09  E-value: 1.20e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 898 EDLQIGTVLTGKVENATLFGIFVDIGVGKSGLIPIRNVTEAKLSKTKKRrslgLGPGERVEVQVLNIDIPRSRITLDLIR 977
Cdd:PRK00087 558 EKYPVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDV----LSEGEEVKAKILEVDPEEKRIRLSIKE 633


                 .
gi 767914795 978 V 978
Cdd:PRK00087 634 V 634
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 901-973 3.08e-04

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: 44.34  E-value: 3.08e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767914795  901 QIGTVLTGKVENATLFGIFVDIGVGKSGLIpirNVTEAKLSKTKKRRSLGLGPGERVEVQVLNIDIPRSRITL 973
Cdd:TIGR00717 358 PVGDRVTGKIKKITDFGAFVELEGGIDGLI---HLSDISWDKDGREADHLYKKGDEIEAVVLAVDKEKKRISL 427
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 897-973 3.39e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 44.38  E-value: 3.39e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767914795 897 LEDLQIGTVLTGKVENATLFGIFVDIGVGKSGLIPIRNVTEAKLSKTKKRrslgLGPGERVEVQVLNIDIPRSRITL 973
Cdd:PRK06299 455 AKKHKKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEV----LKVGDEVEAKVINIDRKNRRISL 527
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
897-979 3.47e-04

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 44.55  E-value: 3.47e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 897 LEDLQIGTVLTGKVENATLFGIFVDIGvGKSGLIPIRNVTEAKLSKTkkrrSLGLGPGERVEVQVLNIDIPRSRITLDLI 976
Cdd:PRK00087 472 WNSLEEGDVVEGEVKRLTDFGAFVDIG-GVDGLLHVSEISWGRVEKP----SDVLKVGDEIKVYILDIDKENKKLSLSLK 546


                 ...
gi 767914795 977 RVL 979
Cdd:PRK00087 547 KLL 549
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 891-973 3.82e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 44.38  E-value: 3.82e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 891 KRSIVcLEDLQIGTVLTGKVENATLFGIFVDIGvGKSGLIPIRNVTEAKLSKTKKRRSLglgpGERVEVQVLNIDIPRSR 970
Cdd:PRK06299 191 EREEL-LENLEEGQVVEGVVKNITDYGAFVDLG-GVDGLLHITDISWKRVNHPSEVVNV----GDEVKVKVLKFDKEKKR 264


                 ...
gi 767914795 971 ITL 973
Cdd:PRK06299 265 VSL 267
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 893-979 4.00e-04

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 44.27  E-value: 4.00e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 893 SIVclEDLQIGTVLTGKVENATLFGIFVDIGVGKSGLIPIRNVTEAKLSKTKKRrslgLGPGERVEVQVLNIDiPRSRIT 972
Cdd:PRK11824 614 GIT--AEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDV----LKEGDEVKVKVLEID-KRGRIR 686


                 ....*..
gi 767914795 973 LDLIRVL 979
Cdd:PRK11824 687 LSRKAVL 693
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 901-975 8.97e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 43.11  E-value: 8.97e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767914795 901 QIGTVLTGKVENATLFGIFVDIGVGKSGLIPIRNVTEAKLSKTKKRrslgLGPGERVEVQVLNIDIPRSRITLDL 975
Cdd:PRK07899 292 AIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQV----VQVGDEVFVKVIDIDLERRRISLSL 362
PRK08059 PRK08059
general stress protein 13; Validated
 896-975 1.13e-03

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 40.03  E-value: 1.13e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 896 CLEDLQIGTVLTGKVENATLFGIFVDIGVGKSGLIPIRNVTEAKLSKTKKRRSLglgpGERVEVQVLNIDIPRSRITLDL 975
Cdd:PRK08059   1 MMSQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSV----GDEVKVKVLSVDEEKGKISLSI 76
rpsA PRK13806
30S ribosomal protein S1; Provisional
 897-965 2.70e-03

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 41.25  E-value: 2.70e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767914795 897 LEDLQIGTVLTGKVENATLFGIFVDIGVGKSGLIPIRNVTEAKLSKTKKRRSlglgPGERVEVQVLNID 965
Cdd:PRK13806 197 METVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVS----VGDTVRVKVLGIE 261
S1_RecJ_like cd04473
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ...
 897-976 3.03e-03

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: 37.20  E-value: 3.03e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767914795 897 LEDLQIGTVLTGKVENATLFGIFVDIGVGKSGLIPIRNVTEAklsktkkrrslgLGPGERVEVQVlnIDIPRSRiTLDLI 976
Cdd:cd04473   11 MEDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLRD------------YEVGDEVIVQV--TDIPENG-NIDLI 75
S1_RPS1_repeat_ec1_hs1 cd05687
S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 903-965 6.02e-03

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: 36.35  E-value: 6.02e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767914795 903 GTVLTGKVENATLFGIFVDIGVGKSGLIPIRNVTEAKLSKTKKrrslGLGPGERVEVQVLNID 965
Cdd:cd05687    1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGED----EVKVGDEVEVYVLRVE 59
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 897-973 7.60e-03

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: 39.64  E-value: 7.60e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767914795 897 LEDLQIGTVLTGKVENATLFGIFVDIGVGKSGLIPIRNVTEAKLSKTKKrrslglgPGERVEVQVLNIDIPRSRITL 973
Cdd:COG0539   13 LKELKEGDIVKGTVVSIDDDEVLVDIGYKSEGIIPLSEFSDEPGELEVK-------VGDEVEVYVEKVEDGEGEIVL 82
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH