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Conserved domains on  [gi|17511129|ref|NP_491362|]
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S1 motif domain-containing protein [Caenorhabditis elegans]

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];
27-742 2.78e-126

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: 392.85  E-value: 2.78e-126
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129  27 ELN--STQAQRLVSLFKNGCETAYIARYRGDVHGYLAPEKIRKAMEAYVDAKNLNNKVSSAISTVTAkvagaQEKIivTE 104
Cdd:COG2183  12 ELGlrPKQVEAAVELLDEGATVPFIARYRKEATGGLDEVQLRTIEERLTYLRELEKRRETILKSIEE-----QGKL--TP 84

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129 105 ----RFKRCEEFDEVTDI-----SKeystgtRKTKANIARALGLEPPAQSILDGNFVDFKSLLS---NGLKTVKDVEEHL 172
Cdd:COG2183  85 elkaKIEAADTKQELEDLylpykPK------RRTKATIAREKGLEPLADLLLAQPTGDPEAEAAkyiNEEKGVADVEAAL 158

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129 173 K----IcLADLINRDEEVRKvsaNI-DILKKECRVSAKLSREAEknrkdlEKRGIIEKYKNFiGEKWNaeDIRDHTVSAL 247
Cdd:COG2183 159 DgardI-LAERISEDAELRG---KLrELLWKEGVLVSKVKKGKE------EEGAKFRDYFDY-SEPLK--KIPSHRILAL 225

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129 248 NKGFDEGIITWKIECEFNDA------KYIHPFSRKSvyfgmKNFYQEALAYSIKNYFIPRIERKMANHLKDKAKDRSIVL 321
Cdd:COG2183 226 NRGEKEGVLKVKLEPDEEEAeayiarRFIKDQGRPA-----DEWLKEAVRDAYKRLLAPSLERELRNELKEKAEEEAIKV 300

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129 322 FGENVDQLLSQEGIRDKFVIALDPG-RSKIKTAFLKPTGEVVDMSSfsIYGT----RFDGGgvdlLKKWSQQTERKDI-V 395
Cdd:COG2183 301 FAENLRDLLLAAPAGGKVVLGLDPGfRTGCKVAVVDETGKLLDTAT--IYPHppqnKWEEA----AKTLAALIKKYKVeL 374

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129 396 FAIGNGTNTYNTQIAVSDMINSNvfpkEINVSYCIVPEHGASKYSCTPSAIEEFGEnAEITEISAVSIGRRLIDPMSEYV 475
Cdd:COG2183 375 IAIGNGTASRETEQFVAELIKEL----DLKVQYVIVSEAGASVYSASELAREEFPD-LDVTVRGAVSIARRLQDPLAELV 449

                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129 476 KIEPQHLGKGQYQLSVDPKKLNESLLNVVRDRVSFNGVDLNTASKNLLQRINGLNEKTAKEIVQYREQNGRFRSRAELKE 555
Cdd:COG2183 450 KIDPKSIGVGQYQHDVNQKKLKRSLDAVVEDCVNAVGVDLNTASAPLLSYVSGLNPTLAKNIVAYRDENGAFKSRKELLK 529

                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129 556 VKGIGALTFQQCAGFLtvsRPDDAEdgppkkkfkksstskewNPFDETIVHPDDYRTGESLLGKLNVSIEDITG---RIK 632
Cdd:COG2183 530 VPRLGPKAFEQAAGFL---RIRDGD-----------------NPLDNSAVHPESYPVVEKILKDLGVSVKDLIGnkeLLK 589

                       650       660       670       680       690       700       710       720
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129 633 SFSISRLTAEEAKVLNL---LQNLtlktkMKP---------PPPLRTKVGQIRDLAEGQRFTGTVSNKTDFGVFIDIGVG 700
Cdd:COG2183 590 KLDPEKYADELFGLPTLrdiLKEL-----EKPgrdprpefkTPTFREGVLKIEDLKPGMILEGTVTNVTDFGAFVDIGVH 664

                       730       740       750       760       770
                ....*....|....*....|....*....|....*....|....*....|....
gi 17511129 701 QDGLAHISH-----FKDghyslmlP----SVNDSVEVV---IDKIRedGKISLS 742
Cdd:COG2183 665 QDGLVHISQlsdrfVKD-------PrevvKVGDIVKVKvleVDLKR--KRISLS 709
 
Name Accession Description Interval E-value
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
27-742 2.78e-126

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 392.85  E-value: 2.78e-126
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129  27 ELN--STQAQRLVSLFKNGCETAYIARYRGDVHGYLAPEKIRKAMEAYVDAKNLNNKVSSAISTVTAkvagaQEKIivTE 104
Cdd:COG2183  12 ELGlrPKQVEAAVELLDEGATVPFIARYRKEATGGLDEVQLRTIEERLTYLRELEKRRETILKSIEE-----QGKL--TP 84

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129 105 ----RFKRCEEFDEVTDI-----SKeystgtRKTKANIARALGLEPPAQSILDGNFVDFKSLLS---NGLKTVKDVEEHL 172
Cdd:COG2183  85 elkaKIEAADTKQELEDLylpykPK------RRTKATIAREKGLEPLADLLLAQPTGDPEAEAAkyiNEEKGVADVEAAL 158

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129 173 K----IcLADLINRDEEVRKvsaNI-DILKKECRVSAKLSREAEknrkdlEKRGIIEKYKNFiGEKWNaeDIRDHTVSAL 247
Cdd:COG2183 159 DgardI-LAERISEDAELRG---KLrELLWKEGVLVSKVKKGKE------EEGAKFRDYFDY-SEPLK--KIPSHRILAL 225

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129 248 NKGFDEGIITWKIECEFNDA------KYIHPFSRKSvyfgmKNFYQEALAYSIKNYFIPRIERKMANHLKDKAKDRSIVL 321
Cdd:COG2183 226 NRGEKEGVLKVKLEPDEEEAeayiarRFIKDQGRPA-----DEWLKEAVRDAYKRLLAPSLERELRNELKEKAEEEAIKV 300

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129 322 FGENVDQLLSQEGIRDKFVIALDPG-RSKIKTAFLKPTGEVVDMSSfsIYGT----RFDGGgvdlLKKWSQQTERKDI-V 395
Cdd:COG2183 301 FAENLRDLLLAAPAGGKVVLGLDPGfRTGCKVAVVDETGKLLDTAT--IYPHppqnKWEEA----AKTLAALIKKYKVeL 374

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129 396 FAIGNGTNTYNTQIAVSDMINSNvfpkEINVSYCIVPEHGASKYSCTPSAIEEFGEnAEITEISAVSIGRRLIDPMSEYV 475
Cdd:COG2183 375 IAIGNGTASRETEQFVAELIKEL----DLKVQYVIVSEAGASVYSASELAREEFPD-LDVTVRGAVSIARRLQDPLAELV 449

                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129 476 KIEPQHLGKGQYQLSVDPKKLNESLLNVVRDRVSFNGVDLNTASKNLLQRINGLNEKTAKEIVQYREQNGRFRSRAELKE 555
Cdd:COG2183 450 KIDPKSIGVGQYQHDVNQKKLKRSLDAVVEDCVNAVGVDLNTASAPLLSYVSGLNPTLAKNIVAYRDENGAFKSRKELLK 529

                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129 556 VKGIGALTFQQCAGFLtvsRPDDAEdgppkkkfkksstskewNPFDETIVHPDDYRTGESLLGKLNVSIEDITG---RIK 632
Cdd:COG2183 530 VPRLGPKAFEQAAGFL---RIRDGD-----------------NPLDNSAVHPESYPVVEKILKDLGVSVKDLIGnkeLLK 589

                       650       660       670       680       690       700       710       720
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129 633 SFSISRLTAEEAKVLNL---LQNLtlktkMKP---------PPPLRTKVGQIRDLAEGQRFTGTVSNKTDFGVFIDIGVG 700
Cdd:COG2183 590 KLDPEKYADELFGLPTLrdiLKEL-----EKPgrdprpefkTPTFREGVLKIEDLKPGMILEGTVTNVTDFGAFVDIGVH 664

                       730       740       750       760       770
                ....*....|....*....|....*....|....*....|....*....|....
gi 17511129 701 QDGLAHISH-----FKDghyslmlP----SVNDSVEVV---IDKIRedGKISLS 742
Cdd:COG2183 665 QDGLVHISQlsdrfVKD-------PrevvKVGDIVKVKvleVDLKR--KRISLS 709
Tex_N pfam09371
Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss: ...
 21-206 3.29e-33

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: 125.98  E-value: 3.29e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129    21 IHKEVHeLNSTQAQRLVSLFKNGCETAYIARYRGDVHGYLAPEKIRKAMEAYVDAKNLNNKVSSAISTVTakvagAQEK- 99
Cdd:pfam09371   1 IAEELG-LKPKQVEATVKLLDEGNTVPFIARYRKEATGGLDEVQLREIEERLEYLRELEKRKETILKSIE-----EQGKl 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129   100 -IIVTERFKRCEEFDEVTDISKEYSTgTRKTKANIARALGLEPPAQSILDGN--------FVDFKsllsNGLKTVKDVEE 170
Cdd:pfam09371  75 tDELKAAIEAADTLTELEDLYLPYKP-KRRTKATIAREKGLEPLADAILAQPdpeeeaakYINPE----KGVADVEEALA 149

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 17511129   171 HLKICLADLINRDEEVRKVSANidILKKECRVSAKL 206
Cdd:pfam09371 150 GARDIIAERISEDAELRKKLRE--LLWREGVIVSKV 183
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 678-742 7.08e-23

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: 92.30  E-value: 7.08e-23
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17511129 678 GQRFTGTVSNKTDFGVFIDIGVGQDGLAHISHFKDGHYS--LMLPSVNDSVEVVIDKIRED-GKISLS 742
Cdd:cd05685   1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVShpSDVVSVGDIVEVKVISIDEErGRISLS 68
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
 338-440 1.05e-15

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: 72.98  E-value: 1.05e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129    338 KFVIALDPGRSKIKTAFLKPTGEVVDMssFSIYGTRFDGGGVDLLKKWSQqtERKDIVFAIG-----NGTNTYNTQIAVS 412
Cdd:smart00732   1 KRVLGLDPGRKGIGVAVVDETGKLADP--LEVIPRTNKEADAARLKKLIK--KYQPDLIVIGlplnmNGTASRETEEAFA 76

                           90       100
                   ....*....|....*....|....*...
gi 17511129    413 DMINsnvfpKEINVSYCIVPEHGASKYS 440
Cdd:smart00732  77 ELLK-----ERFNLPVVLVDERLATVYA 99
comE TIGR01259
comEA protein; This model describes the ComEA protein in bacteria. The com E locus is ...
 445-573 2.27e-12

comEA protein; This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation. [Cellular processes, DNA transformation]


Pssm-ID: 213597 [Multi-domain]  Cd Length: 120  Bit Score: 64.54  E-value: 2.27e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129   445 AIEEFGENAEITEISAVSIGRRLIDPMSEYVkiepqhlgkgqyqlsvdPKKLNE--SLLNVVRDRVSFNGVDLNTASKNL 522
Cdd:TIGR01259   7 AIEKAGGFTEQADGLSVNLAGKLMDEMFVYV-----------------PMKGEEavSQQGTQSSAGKLAAVNINAASLEE 69

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 17511129   523 LQRINGLNEKTAKEIVQYREQNGRFRSRAELKEVKGIGALTFQQCAGFLTV 573
Cdd:TIGR01259  70 LQALPGIGPAKAKAIIEYREENGAFKSVDDLTKVSGIGEKSLEKLKDYATV 120
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 621-743 3.60e-10

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 63.53  E-value: 3.60e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129  621 NVSIEDiTGRIKSFSISRLTAEEAKvlNLLQNLTlktkmkpppplrtkvgqiRDLAEGQRFTGTVSNKTDFGVFIDIGVG 700
Cdd:PRK11824 586 KIDIED-DGTVKIAATDGEAAEAAK--ERIEGIT------------------AEPEVGEIYEGKVVRIVDFGAFVEILPG 644

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 17511129  701 QDGLAHISHFKDGHYS-----LmlpSVNDSVEVVIDKIREDGKISLSP 743
Cdd:PRK11824 645 KDGLVHISEIADERVEkvedvL---KEGDEVKVKVLEIDKRGRIRLSR 689
 
Name Accession Description Interval E-value
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
27-742 2.78e-126

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 392.85  E-value: 2.78e-126
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129  27 ELN--STQAQRLVSLFKNGCETAYIARYRGDVHGYLAPEKIRKAMEAYVDAKNLNNKVSSAISTVTAkvagaQEKIivTE 104
Cdd:COG2183  12 ELGlrPKQVEAAVELLDEGATVPFIARYRKEATGGLDEVQLRTIEERLTYLRELEKRRETILKSIEE-----QGKL--TP 84

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129 105 ----RFKRCEEFDEVTDI-----SKeystgtRKTKANIARALGLEPPAQSILDGNFVDFKSLLS---NGLKTVKDVEEHL 172
Cdd:COG2183  85 elkaKIEAADTKQELEDLylpykPK------RRTKATIAREKGLEPLADLLLAQPTGDPEAEAAkyiNEEKGVADVEAAL 158

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129 173 K----IcLADLINRDEEVRKvsaNI-DILKKECRVSAKLSREAEknrkdlEKRGIIEKYKNFiGEKWNaeDIRDHTVSAL 247
Cdd:COG2183 159 DgardI-LAERISEDAELRG---KLrELLWKEGVLVSKVKKGKE------EEGAKFRDYFDY-SEPLK--KIPSHRILAL 225

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129 248 NKGFDEGIITWKIECEFNDA------KYIHPFSRKSvyfgmKNFYQEALAYSIKNYFIPRIERKMANHLKDKAKDRSIVL 321
Cdd:COG2183 226 NRGEKEGVLKVKLEPDEEEAeayiarRFIKDQGRPA-----DEWLKEAVRDAYKRLLAPSLERELRNELKEKAEEEAIKV 300

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129 322 FGENVDQLLSQEGIRDKFVIALDPG-RSKIKTAFLKPTGEVVDMSSfsIYGT----RFDGGgvdlLKKWSQQTERKDI-V 395
Cdd:COG2183 301 FAENLRDLLLAAPAGGKVVLGLDPGfRTGCKVAVVDETGKLLDTAT--IYPHppqnKWEEA----AKTLAALIKKYKVeL 374

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129 396 FAIGNGTNTYNTQIAVSDMINSNvfpkEINVSYCIVPEHGASKYSCTPSAIEEFGEnAEITEISAVSIGRRLIDPMSEYV 475
Cdd:COG2183 375 IAIGNGTASRETEQFVAELIKEL----DLKVQYVIVSEAGASVYSASELAREEFPD-LDVTVRGAVSIARRLQDPLAELV 449

                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129 476 KIEPQHLGKGQYQLSVDPKKLNESLLNVVRDRVSFNGVDLNTASKNLLQRINGLNEKTAKEIVQYREQNGRFRSRAELKE 555
Cdd:COG2183 450 KIDPKSIGVGQYQHDVNQKKLKRSLDAVVEDCVNAVGVDLNTASAPLLSYVSGLNPTLAKNIVAYRDENGAFKSRKELLK 529

                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129 556 VKGIGALTFQQCAGFLtvsRPDDAEdgppkkkfkksstskewNPFDETIVHPDDYRTGESLLGKLNVSIEDITG---RIK 632
Cdd:COG2183 530 VPRLGPKAFEQAAGFL---RIRDGD-----------------NPLDNSAVHPESYPVVEKILKDLGVSVKDLIGnkeLLK 589

                       650       660       670       680       690       700       710       720
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129 633 SFSISRLTAEEAKVLNL---LQNLtlktkMKP---------PPPLRTKVGQIRDLAEGQRFTGTVSNKTDFGVFIDIGVG 700
Cdd:COG2183 590 KLDPEKYADELFGLPTLrdiLKEL-----EKPgrdprpefkTPTFREGVLKIEDLKPGMILEGTVTNVTDFGAFVDIGVH 664

                       730       740       750       760       770
                ....*....|....*....|....*....|....*....|....*....|....
gi 17511129 701 QDGLAHISH-----FKDghyslmlP----SVNDSVEVV---IDKIRedGKISLS 742
Cdd:COG2183 665 QDGLVHISQlsdrfVKD-------PrevvKVGDIVKVKvleVDLKR--KRISLS 709
Tex_N pfam09371
Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss: ...
 21-206 3.29e-33

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: 125.98  E-value: 3.29e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129    21 IHKEVHeLNSTQAQRLVSLFKNGCETAYIARYRGDVHGYLAPEKIRKAMEAYVDAKNLNNKVSSAISTVTakvagAQEK- 99
Cdd:pfam09371   1 IAEELG-LKPKQVEATVKLLDEGNTVPFIARYRKEATGGLDEVQLREIEERLEYLRELEKRKETILKSIE-----EQGKl 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129   100 -IIVTERFKRCEEFDEVTDISKEYSTgTRKTKANIARALGLEPPAQSILDGN--------FVDFKsllsNGLKTVKDVEE 170
Cdd:pfam09371  75 tDELKAAIEAADTLTELEDLYLPYKP-KRRTKATIAREKGLEPLADAILAQPdpeeeaakYINPE----KGVADVEEALA 149

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 17511129   171 HLKICLADLINRDEEVRKVSANidILKKECRVSAKL 206
Cdd:pfam09371 150 GARDIIAERISEDAELRKKLRE--LLWREGVIVSKV 183
HHH_3 pfam12836
Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.
 510-571 1.46e-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: 1.46e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17511129   510 FNGVDLNTASKNLLQRINGLNEKTAKEIVQYREQNGRFRSRAELKEVKGIGALTFQQCAGFL 571
Cdd:pfam12836   1 AVGVDINTASAELLSRVPGLGPKLAKNIVEYREENGPFRSREDLLKVKGLGPKTFEQLAGFL 62
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 678-742 7.08e-23

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: 92.30  E-value: 7.08e-23
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17511129 678 GQRFTGTVSNKTDFGVFIDIGVGQDGLAHISHFKDGHYS--LMLPSVNDSVEVVIDKIRED-GKISLS 742
Cdd:cd05685   1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVShpSDVVSVGDIVEVKVISIDEErGRISLS 68
Tex_YqgF pfam16921
Tex protein YqgF-like domain; This is the YqgF-like domain of the bacterial Tex protein, which ...
 340-467 2.77e-19

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: 84.37  E-value: 2.77e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129   340 VIALDPG-RSKIKTAFLKPTGEVVDmsSFSIYGTRFDGGGVDLLKKWSQQTERKDI-VFAIGNGTNTYNTQIAVSDMINS 417
Cdd:pfam16921   2 VLGLDPGyRTGCKLAVVDETGKVLD--TAVIYPHPPQNKVEEAKKKLKKLIKKYGVeLIAIGNGTASRETEQFVAELIKE 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 17511129   418 NvfpkEINVSYCIVPEHGASKYSCTPSAIEEFgENAEITEISAVSIGRRL 467
Cdd:pfam16921  80 L----PLKVKYVIVSEAGASVYSASELAREEF-PDLDVSLRGAVSIARRL 124
ComEA COG1555
DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair]; ...
 513-572 3.05e-18

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


Pssm-ID: 441164 [Multi-domain]  Cd Length: 72  Bit Score: 79.52  E-value: 3.05e-18
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129 513 VDLNTASKNLLQRINGLNEKTAKEIVQYREQNGRFRSRAELKEVKGIGALTFQQCAGFLT 572
Cdd:COG1555  13 VDINTATAEELQTLPGIGPKLAQRIVEYREKNGPFKSVEDLLEVKGIGPKTLEKLKPYLT 72
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
 338-440 1.05e-15

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: 72.98  E-value: 1.05e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129    338 KFVIALDPGRSKIKTAFLKPTGEVVDMssFSIYGTRFDGGGVDLLKKWSQqtERKDIVFAIG-----NGTNTYNTQIAVS 412
Cdd:smart00732   1 KRVLGLDPGRKGIGVAVVDETGKLADP--LEVIPRTNKEADAARLKKLIK--KYQPDLIVIGlplnmNGTASRETEEAFA 76

                           90       100
                   ....*....|....*....|....*...
gi 17511129    413 DMINsnvfpKEINVSYCIVPEHGASKYS 440
Cdd:smart00732  77 ELLK-----ERFNLPVVLVDERLATVYA 99
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 675-742 7.26e-13

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: 70.46  E-value: 7.26e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17511129 675 LAEGQRFTGTVSNKTDFGVFIDIGvGQDGLAHI---SHFKDGHYSLMLpSVNDSVEVVIDKI-REDGKISLS 742
Cdd:COG0539 187 LEEGDVVEGTVKNITDFGAFVDLG-GVDGLLHIseiSWGRVKHPSEVL-KVGDEVEVKVLKIdREKERISLS 256
comE TIGR01259
comEA protein; This model describes the ComEA protein in bacteria. The com E locus is ...
 445-573 2.27e-12

comEA protein; This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation. [Cellular processes, DNA transformation]


Pssm-ID: 213597 [Multi-domain]  Cd Length: 120  Bit Score: 64.54  E-value: 2.27e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129   445 AIEEFGENAEITEISAVSIGRRLIDPMSEYVkiepqhlgkgqyqlsvdPKKLNE--SLLNVVRDRVSFNGVDLNTASKNL 522
Cdd:TIGR01259   7 AIEKAGGFTEQADGLSVNLAGKLMDEMFVYV-----------------PMKGEEavSQQGTQSSAGKLAAVNINAASLEE 69

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 17511129   523 LQRINGLNEKTAKEIVQYREQNGRFRSRAELKEVKGIGALTFQQCAGFLTV 573
Cdd:TIGR01259  70 LQALPGIGPAKAKAIIEYREENGAFKSVDDLTKVSGIGEKSLEKLKDYATV 120
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 677-742 4.55e-12

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: 61.88  E-value: 4.55e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129 677 EGQRFTGTVSNKTDFGVFIDIGvGQDGLAHISHFKDG---HYSLMLpSVNDSVEVVIDKI-REDGKISLS 742
Cdd:cd05688   1 EGDVVEGTVKSITDFGAFVDLG-GVDGLLHISDMSWGrvkHPSEVV-NVGDEVEVKVLKIdKERKRISLG 68
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
677-742 1.14e-11

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 60.70  E-value: 1.14e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17511129    677 EGQRFTGTVSNKTDFGVFIDIGVGQDGLAHISHFKDGHYSLMLPS--VNDSVEVVIDKI-REDGKISLS 742
Cdd:smart00316   2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVlkVGDEVKVKVLSVdEEKGRIILS 70
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 674-742 1.77e-10

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 59.04  E-value: 1.77e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 17511129 674 DLAEGQRFTGTVSNKTDFGVFIDIGVGQDGLAHISHF-----KDGHYSLmlpSVNDSVEVVIDKIREDGKISLS 742
Cdd:COG1098   2 SIEVGDIVEGKVTGITPFGAFVELPEGTTGLVHISEIadgyvKDINDYL---KVGDEVKVKVLSIDEDGKISLS 72
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 621-743 3.60e-10

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 63.53  E-value: 3.60e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129  621 NVSIEDiTGRIKSFSISRLTAEEAKvlNLLQNLTlktkmkpppplrtkvgqiRDLAEGQRFTGTVSNKTDFGVFIDIGVG 700
Cdd:PRK11824 586 KIDIED-DGTVKIAATDGEAAEAAK--ERIEGIT------------------AEPEVGEIYEGKVVRIVDFGAFVEILPG 644

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 17511129  701 QDGLAHISHFKDGHYS-----LmlpSVNDSVEVVIDKIREDGKISLSP 743
Cdd:PRK11824 645 KDGLVHISEIADERVEkvedvL---KEGDEVKVKVLEIDKRGRIRLSR 689
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 675-742 9.39e-10

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 61.43  E-value: 9.39e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17511129  675 LAEGQRFTGTVSNKTDFGVFIDIGvGQDGLAHIS---HFKDGHYSLMLpSVNDSVEVVIDKI-REDGKISLS 742
Cdd:PRK06676 190 LKEGDVVEGTVARLTDFGAFVDIG-GVDGLVHISelsHERVEKPSEVV-SVGQEVEVKVLSIdWETERISLS 259
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 675-742 9.53e-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: 55.37  E-value: 9.53e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 17511129   675 LAEGQRFTGTVSNKTDFGVFIDIGVGQDGLAHISHFKDGHY--SLMLPSVNDSVEVVIDKIRED-GKISLS 742
Cdd:pfam00575   1 PEKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVedPDEVIKVGDEVKVKVLKVDKDrRRIILS 71
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 673-742 1.62e-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: 1.62e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 17511129 673 RDLAEGQRFTGTVSNKTDFGVFIDIGVGQDGLAHISHF----KDGHYSLMLpSVNDSVEVVIDKI-REDGKISLS 742
Cdd:COG0539 270 EKYPVGDVVKGKVTRLTDFGAFVELEPGVEGLVHISEMswtkRVAHPSDVV-KVGDEVEVKVLDIdPEERRISLS 343
TIGR00426 TIGR00426
competence protein ComEA helix-hairpin-helix repeat region; Members of the subfamily ...
 513-573 3.75e-09

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: 53.40  E-value: 3.75e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17511129   513 VDLNTASKNLLQR-INGLNEKTAKEIVQYREQNGRFRSRAELKEVKGIGALTFQQCAGFLTV 573
Cdd:TIGR00426   8 VNINTATAEELQRaMNGVGLKKAEAIVSYREEYGPFKTVEDLKQVPGIGNSLVEKNLAVITL 69
Pnp COG1185
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ...
 622-742 5.76e-09

Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440798 [Multi-domain]  Cd Length: 686  Bit Score: 59.63  E-value: 5.76e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129 622 VSIEDiTGRIKSFSISRLTAEEAKvlNLLQNLTlktkmkpppplrtkvgqiRDLAEGQRFTGTVSNKTDFGVFIDIGVGQ 701
Cdd:COG1185 582 IDIED-DGTVKIAATDGEAAEKAI--ERIEGIT------------------AEPEVGEIYEGKVVRIMDFGAFVEILPGK 640

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*..
gi 17511129 702 DGLAHISHFKDGHyslmLPSVND------SVEVVIDKIREDGKISLS 742
Cdd:COG1185 641 DGLVHISELADER----VEKVEDvlkegdEVKVKVLEIDDQGRIKLS 683
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 675-742 6.86e-09

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 59.02  E-value: 6.86e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17511129  675 LAEGQRFTGTVSNKTDFGVFIDIGvGQDGLAHI---SHFKDGHYSLMLpSVNDSVEVVIDKI-REDGKISLS 742
Cdd:PRK06299 199 LEEGQVVEGVVKNITDYGAFVDLG-GVDGLLHItdiSWKRVNHPSEVV-NVGDEVKVKVLKFdKEKKRVSLG 268
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 681-742 9.00e-09

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: 52.38  E-value: 9.00e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 17511129 681 FTGTVSNKTDFGVFIDIGVGQDGLAHISHFKDGHYSLMLP--SVNDSVEVVIDKI-REDGKISLS 742
Cdd:cd00164   1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEvfKVGDEVEVKVLEVdPEKGRISLS 65
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 678-742 2.45e-08

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: 51.13  E-value: 2.45e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129 678 GQRFTGTVSNKTDFGVFIDIGVGQDGLAHIS-----HFKDGHYSLmlpSVNDSVEVVIDKIREDGKISLS 742
Cdd:cd05692   1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISqiahkRVKDVKDVL---KEGDKVKVKVLSIDARGRISLS 67
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 676-742 2.48e-08

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: 51.56  E-value: 2.48e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 17511129 676 AEGQRFTGTVSNKTDFGVFIDI-GVGQDGLAHISHFKDGHYS--LMLPSVNDSVEVVIDKIRED-GKISLS 742
Cdd:cd05708   1 KVGQKIDGTVRRVEDYGVFIDIdGTNVSGLCHKSEISDNRVAdaSKLFRVGDKVRAKVLKIDAEkKRISLG 71
PRK08582 PRK08582
RNA-binding protein S1;
678-742 2.72e-08

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 53.11  E-value: 2.72e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129  678 GQRFTGTVSNKTDFGVFIDIGVGQDGLAHIS-----HFKDGHYSLmlpSVNDSVEVVIDKIREDGKISLS 742
Cdd:PRK08582   6 GSKLQGKVTGITNFGAFVELPEGKTGLVHISevadnYVKDINDHL---KVGDEVEVKVLNVEDDGKIGLS 72
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 678-742 4.65e-08

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: 50.23  E-value: 4.65e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17511129 678 GQRFTGTVSNKTDFGVFIDIGVGQDGLAHISHFKDGHyslmLPSVNDSVEV-------VIDkIREDGKISLS 742
Cdd:cd04472   1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDER----VEKVEDVLKVgdevkvkVIE-VDDRGRISLS 67
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 673-742 6.63e-08

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 55.94  E-value: 6.63e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 17511129  673 RDLAEGQRFTGTVSNKTDFGVFIDIGVGQDGLAHISHF----KDGHYSLMLpSVNDSVEVVIDKI-REDGKISLS 742
Cdd:PRK06299 282 KKYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMswtkKNKHPSKVV-SVGQEVEVMVLEIdEEKRRISLG 355
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
675-742 9.16e-08

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 55.72  E-value: 9.16e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17511129  675 LAEGQRFTGTVSNKTDFGVFIDIGvGQDGLAH---ISHFKDGHYSLMLpSVNDSVEVVIDKI-REDGKISLS 742
Cdd:PRK00087 475 LEEGDVVEGEVKRLTDFGAFVDIG-GVDGLLHvseISWGRVEKPSDVL-KVGDEIKVYILDIdKENKKLSLS 544
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 677-742 1.53e-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: 54.74  E-value: 1.53e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 17511129   677 EGQRFTGTVSNKTDFGVFIDIGVGQDGLAHISHF----KDGHYSLMLpSVNDSVEVVIDKIRED-GKISLS 742
Cdd:TIGR00717 272 VGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMswvkKNSHPSKVV-KKGDEVEVMILDIDPErRRLSLG 341
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 677-742 3.27e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 53.63  E-value: 3.27e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129  677 EGQRFTGTVSNKTDFGVFIDIGVGQDGLAH---ISHFKDGHYSLMLPSVNDSVEVVIDKI-REDGKISLS 742
Cdd:PRK06299 373 VGDVVEGKVKNITDFGAFVGLEGGIDGLVHlsdISWDKKGEEAVELYKKGDEVEAVVLKVdVEKERISLG 442
COG1107 COG1107
Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [Replication, ...
 672-744 9.23e-07

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: 52.15  E-value: 9.23e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 17511129 672 IRDLAEGQRFTGTVSNKTDFGVFIDIGVGQDGLAHISHFkDGHYslmlpSVNDSVEVVIDKIREDGKISLSPV 744
Cdd:COG1107  34 PDDLEPGRYYRGTVDGVADFGVFVDLNDHVTGLLHRSEL-DQDW-----EVGDEVFVQVKEVRDNGNVDLGWV 100
S1_RecJ_like cd04473
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ...
 671-744 1.10e-06

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: 46.83  E-value: 1.10e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 17511129 671 QIRDLAEGQRFTGTVSNKTDFGVFIDIGVGQDGLAHIShfkdghYSLMLPSVNDSVEVVIDKIREDGKISLSPV 744
Cdd:cd04473  10 TMEDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRS------NLLRDYEVGDEVIVQVTDIPENGNIDLIPV 77
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 677-741 1.29e-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: 46.42  E-value: 1.29e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129 677 EGQRFTGTVSNKTDFGVFIDIGVGQDGLAHISHF----KDGHYSLMLpSVNDSVEVVIDKIREDG-KISL 741
Cdd:cd05689   3 EGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMdwtnKNIHPSKVV-SLGDEVEVMVLDIDEERrRISL 71
PRK05807 PRK05807
RNA-binding protein S1;
675-742 2.04e-06

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 47.82  E-value: 2.04e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 17511129  675 LAEGQRFTGTVSNKTDFGVFIDIGvGQDGLAHIS-----HFKDGHYSLmlpSVNDSVEVVIDKIREDGKISLS 742
Cdd:PRK05807   3 LKAGSILEGTVVNITNFGAFVEVE-GKTGLVHISevadtYVKDIREHL---KEQDKVKVKVISIDDNGKISLS 71
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 672-742 4.30e-06

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: 49.66  E-value: 4.30e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17511129 672 IRDLAEGQRFTGTVSNKTDFGVFIDIGVGQDGLAHISHFKDGHYSLMLpSVNDSVEVVIDKIR-EDGKISLS 742
Cdd:COG0539  13 LKELKEGDIVKGTVVSIDDDEVLVDIGYKSEGIIPLSEFSDEPGELEV-KVGDEVEVYVEKVEdGEGEIVLS 83
S1_RNase_R cd04471
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ...
 678-744 5.14e-06

S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.


Pssm-ID: 239917 [Multi-domain]  Cd Length: 83  Bit Score: 45.08  E-value: 5.14e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129 678 GQRFTGTVSNKTDFGVFI---DIGVgqDGLAHISHFKDGHY-----SLMLP--------SVNDSVEVVIDKI-REDGKIS 740
Cdd:cd04471   2 GEEFDGVISGVTSFGLFVeldNLTV--EGLVHVSTLGDDYYefdeeNHALVgertgkvfRLGDKVKVRVVRVdLDRRKID 79


                ....
gi 17511129 741 LSPV 744
Cdd:cd04471  80 FELV 83
HHH_7 pfam14635
Helix-hairpin-helix motif;
487-574 1.00e-05

Helix-hairpin-helix motif;


Pssm-ID: 291309  Cd Length: 104  Bit Score: 44.84  E-value: 1.00e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129   487 YQLSVDPKKLNESLLNVVRDRVSFNGVDLNTA-----SKNLLQRINGLNEKTAKEIVQYREQ-NGRFRSRAELKEVKGIG 560
Cdd:pfam14635  11 LQELLPKEELLKALETAFVDIVNLVGVDVNEAiankyEAAILPYIAGLGPRKADHLLKILAAnNGRLDNRSQLITKCIMG 90

                          90
                  ....*....|....
gi 17511129   561 ALTFQQCAGFLTVS 574
Cdd:pfam14635  91 PKVFMNCAGFLIID 104
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 675-743 1.17e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 48.33  E-value: 1.17e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 17511129  675 LAEGQRFTGTVSNKTDFGVFIDIGVGQDGLAHISHFKD---GHYSLMLpSVNDSVEV-VIDKIREDGKISLSP 743
Cdd:PRK06676 275 LPEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHkhiATPSEVL-EEGQEVKVkVLEVNEEEKRISLSI 346
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 675-742 4.67e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 45.95  E-value: 4.67e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 17511129  675 LAEGQRFTGTVSNKTDFGVFIDIGvGQDGLAHISHFKDGH----YSLMlpSVNDSVEV-VIDKIREDGKISLS 742
Cdd:PRK07400 194 LEVGEVVVGTVRGIKPYGAFIDIG-GVSGLLHISEISHEHietpHSVF--NVNDEMKVmIIDLDAERGRISLS 263
HHH_9 pfam17674
HHH domain;
598-644 6.61e-05

HHH domain;


Pssm-ID: 465451 [Multi-domain]  Cd Length: 70  Bit Score: 41.37  E-value: 6.61e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 17511129   598 NPFDETIVHPDDYRTGESLLGKLNVSIEDITG---RIKSFSISRLTAEEA 644
Cdd:pfam17674   1 NPLDNTAIHPESYPLAEKILKDLGLDLKDLIGnsaLLKKLDPKKLAEEEV 50
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 678-742 1.05e-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: 45.50  E-value: 1.05e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17511129   678 GQRFTGTVSNKTDFGVFIDIGVGQDGLAH---ISHFKDGHYSLMLPSVNDSVEVVIDKI-REDGKISLS 742
Cdd:TIGR00717 360 GDRVTGKIKKITDFGAFVELEGGIDGLIHlsdISWDKDGREADHLYKKGDEIEAVVLAVdKEKKRISLG 428
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 678-741 1.07e-04

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: 40.94  E-value: 1.07e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17511129 678 GQRFTGTVSNKTDFGVFIDIGVGQDGLAHISHF---KDGHYSLMLPSVNDSVEVVIDKI-REDGKISL 741
Cdd:cd05690   1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDIswtQRVRHPSEIYKKGQEVEAVVLNIdVERERISL 68
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 675-742 1.09e-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: 45.50  E-value: 1.09e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17511129   675 LAEGQRFTGTVSNKTDFGVFIDIGvGQDGLAHI---SHFKDGHYSLMLpSVNDSVEVVIDKI-REDGKISLS 742
Cdd:TIGR00717 185 LKEGDVVKGVVKNITDFGAFVDLG-GVDGLLHItdmSWKRVKHPSEYV-KVGQEVKVKVIKFdKEKGRISLS 254
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 678-742 1.48e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 45.16  E-value: 1.48e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17511129  678 GQRFTGTVSNKTDFGVFIDIGVGQDGLAHISHFKDGHYSLMLPSVN--DSVEVVIDKI-REDGKISLS 742
Cdd:PRK06299 461 GSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKvgDEVEAKVINIdRKNRRISLS 528
rpsA PRK13806
30S ribosomal protein S1; Provisional
 675-742 3.55e-04

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 43.94  E-value: 3.55e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17511129  675 LAEGQRFTGTVSNKTDFGVFIDIGVGQDGLAHI---SHFKDGHYSLMLPSVNDSVEVVIDKIREDGK-ISLS 742
Cdd:PRK13806 290 LKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVsemSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRrISLS 361
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 678-742 5.33e-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: 39.14  E-value: 5.33e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17511129 678 GQRFTGTVSNKTDFGVFIDI---GVGQDGLAHIS----HFKDGHYSLMLpSVNDSVEVVIDKIrEDGKISLS 742
Cdd:cd05684   1 GKIYKGKVTSIMDFGCFVQLeglKGRKEGLVHISqlsfEGRVANPSDVV-KRGQKVKVKVISI-QNGKISLS 70
rpsA PRK13806
30S ribosomal protein S1; Provisional
 676-744 5.42e-04

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 43.17  E-value: 5.42e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17511129  676 AEGQRFTGTVSNKTDFGVFIDIGVGQDGLAHISHFKDGHYSLMLPSVN--DSVEVVIDKIR-EDGKISLSPV 744
Cdd:PRK13806 378 APGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAGKPATYEKLKpgDSVTLVVEEIDtAKRKISLAPA 449
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 674-742 6.11e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 43.23  E-value: 6.11e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17511129  674 DLAEGQRFTGTVSNKTDFGVFIDIGVGQDGLAHISHFKDGHYSLmLPSVNDSVEVVIDKIR-EDGKISLS 742
Cdd:PRK06299  27 ETREGSIVKGTVVAIDKDYVLVDVGLKSEGRIPLEEFKNEQGEL-EVKVGDEVEVYVERIEdGFGETVLS 95
PRK08059 PRK08059
general stress protein 13; Validated
 678-742 7.95e-04

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 40.03  E-value: 7.95e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 17511129  678 GQRFTGTVSNKTDFGVFIDIGVGQDGLAHISHF-----KDGHYSLmlpSVNDSVEV-VIDKIREDGKISLS 742
Cdd:PRK08059   8 GSVVTGKVTGIQPYGAFVALDEETQGLVHISEIthgfvKDIHDFL---SVGDEVKVkVLSVDEEKGKISLS 75
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
677-742 1.08e-03

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 42.24  E-value: 1.08e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 17511129  677 EGQRFTGTVSNKTDFGVFIDIGVGQDGLAHISHFKDGHYSlmLP----SVNDSVEVVIDKI-REDGKISLS 742
Cdd:PRK00087 562 VGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRID--KPedvlSEGEEVKAKILEVdPEEKRIRLS 630
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 673-742 1.43e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 41.95  E-value: 1.43e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 17511129  673 RDLAEGQRFTGTVSNKTDFGVFIDIGVGQDGLAHISHFKDGHysLMLP----SVNDSVEV-VIDKIREDGKISLS 742
Cdd:PRK07899 289 RTHAIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERH--VEVPeqvvQVGDEVFVkVIDIDLERRRISLS 361
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 675-742 4.09e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 40.41  E-value: 4.09e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 17511129  675 LAEGQRFTGTVSNKTDFGVFIDIGvGQDGLAHISHFKDGHysLMLPS----VNDSVEV-VIDKIREDGKISLS 742
Cdd:PRK07899 206 LQKGQVRKGVVSSIVNFGAFVDLG-GVDGLVHVSELSWKH--IDHPSevveVGQEVTVeVLDVDMDRERVSLS 275
VacB COG0557
Exoribonuclease R [Transcription];
678-715 5.49e-03

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 40.09  E-value: 5.49e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 17511129 678 GQRFTGTVSNKTDFGVFI---DIGVgqDGLAHISHFKDGHY 715
Cdd:COG0557 623 GEEFEGVISGVTSFGLFVeldELGV--EGLVHVSSLGDDYY 661
 
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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