|
Name |
Accession |
Description |
Interval |
E-value |
| VacB |
COG0557 |
Exoribonuclease R [Transcription]; |
4-722 |
0e+00 |
|
Exoribonuclease R [Transcription];
Pssm-ID: 440323 [Multi-domain] Cd Length: 711 Bit Score: 942.61 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 4 NDLKNQIENVLRTYPDNVFTVEKIADVLRSHGSAAFKLIVQELASLERDKVAVVTEDGKFQLNPDKQQLSGIFHANDKGF 83
Cdd:COG0557 2 ENSRETILAFLKEDAYKPLSKKELAKALGLKDEESREALKRRLRALEREGQLVKTRRGRYRLPEKLDLVEGRVRGHRDGF 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 84 GFVTYDENAPDAYIAPDNTMNALNGDTVEmeiVRPAQPGSDRGPEGKVTKIAEHKYTRVVGPFEKTdddkGYIGQLTLND 163
Cdd:COG0557 82 GFVIPDDGEEDIFIPPRELNGALHGDRVL---VRVTKEDRRGRPEGRVVEILERANTRVVGRFEKE----KGFGFVVPDD 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 164 KKIAKYKFYINDVGLKPTPGEVITAQITEYPSTKHPdyMVGIADEVIGSVDDPGIDILQIVYAHDIPAEFPEDVIQAADA 243
Cdd:COG0557 155 KRLLQDIFIPPDDLNGAKDGDLVVVEITRYPERRGP--PEGRVVEVLGSPGDPGAEILIAIRKHGLPHEFPEEVLAEAEA 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 244 IPDHVTEAEKIGREDITDQDLVTIDGESSKDLDDAVTAWKLPNGNYHLGVHIADVSHYVQPGSAIDKEAFRRGTSVYLTD 323
Cdd:COG0557 233 LPDEVPEADLKGRRDLRDLPLVTIDGEDAKDFDDAVSAEKLDNGGWRLGVHIADVSHYVRPGSALDREARKRGTSVYLPD 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 324 RVIPMLPRRLSNGICSLNEGELRLCMSCEMEIDPSGNIIKHRIHPSLMRSTARMTYTAVNNILESHDQKTMDRYDKLVPM 403
Cdd:COG0557 313 RVIPMLPERLSNGLCSLNPGEDRLAMSCEMEIDAKGEVVSYEFYRSVIRSDARLTYEEVQAILDGKDEELREEYADLVPM 392
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 404 FETMGELHKILYKHRKARGAIDFDDNEAEIIVDDKGHPIDIKLRVRGTAERMIESFMLAANETVAKHYYEKHVPFIYRVH 483
Cdd:COG0557 393 LEELYELAKILRKAREKRGAIDFDLPETKIILDEEGKPEDIVPRERNDAHKLIEEFMLLANEAVAEFLEKLKLPFLYRVH 472
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 484 ETPDADRIRTFFETLTAFGINVKGDPEhVTPKTLQNVLKKVAGKPEEMMVSVMLLRSLKQARYADQSLGHFGLAAPFYTH 563
Cdd:COG0557 473 EEPDPEKLEALREFLANLGLKLKGGDE-PTPKDLQKLLEQVKGRPEEELLNTLLLRSMKQAVYSPENIGHFGLALEAYTH 551
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 564 FTSPIRRYPDTMVHRLIHYYQDNGINDETKKRYANVLDEIATTTSQYERRAVDAERDTDSMKKAEYMNDHIGEEFDGVVS 643
Cdd:COG0557 552 FTSPIRRYPDLLVHRALKAYLEGKRSPGLQEYLEEELEEIAEHCSETERRADEAERDVVDLKKAEYMKDRVGEEFEGVIS 631
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 644 SVMKFGLFIELPNT-VEGLVHISRMNDDYYQYVEQFMALVGRNTRRTYKMGQAIRVKVVNVDVKQSAVDFDIVDPEKTPQ 722
Cdd:COG0557 632 GVTSFGLFVELDELgVEGLVHVSSLGDDYYEYDERRQALVGERTGKRYRLGDRVEVRVVRVDLDRRQIDFELVEGGSEAP 711
|
|
| RNase_R |
TIGR02063 |
ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. ... |
5-715 |
0e+00 |
|
ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans. [Transcription, Degradation of RNA]
Pssm-ID: 273947 [Multi-domain] Cd Length: 709 Bit Score: 830.76 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 5 DLKNQIENVLRTYPDNVFTVEKIADVLRSHGSAAFKLIVQELASLERDKVAVVTEDGKFQLNPDKQQLSGIFHANDKGFG 84
Cdd:TIGR02063 2 PLRELILEFLKSKKGKPISLKELAKAFHLKGADEKKALRKRLRALEDDGLVKKNRRGLYALPESLKLVKGTVIAHRDGFG 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 85 FV-TYDENAPDAYIAPDNTMNALNGDTVEMEIVRPAQPGSDRgpEGKVTKIAEHKYTRVVGPFEKTDDdkgyIGQLTLND 163
Cdd:TIGR02063 82 FLrPEDDDEDDIFIPPRQMNGAMHGDRVLVRITGKPDGGDRF--EARVIKILERANDQIVGTFYIENG----IGFVIPDD 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 164 KKIAkYKFYIND-VGLKPTPGEVITAQITEYPSTKHPdyMVGIADEVIGSVDDPGIDILQIVYAHDIPAEFPEDVIQAAD 242
Cdd:TIGR02063 156 KRIY-LDIFIPPeQILGAEEGDKVLVEITKYPDRNRP--AIGKVVEILGHADDPGIDILIIIRKHGIPYEFPEEVLDEAA 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 243 AIPDHVTEAEKIGREDITDQDLVTIDGESSKDLDDAVTAWKLPNGNYHLGVHIADVSHYVQPGSAIDKEAFRRGTSVYLT 322
Cdd:TIGR02063 233 KIPEEVPEEEIKGRKDLRDLPFVTIDGEDAKDFDDAVYVEKLKDGNYKLGVAIADVSHYVREGSALDKEALKRGTSVYLP 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 323 DRVIPMLPRRLSNGICSLNEGELRLCMSCEMEIDPSGNIIKHRIHPSLMRSTARMTYTAVNNILEShDQKTMDRYDKLVP 402
Cdd:TIGR02063 313 DRVIPMLPERLSNGICSLNPNEDRLTLSCEMEIDKKGRVKKYEFYEAVINSHARLTYNQVNDIIEG-KDALDKKEPPLKE 391
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 403 MFETMGELHKILYKHRKARGAIDFDDNEAEIIVDDKGHPIDIKLRVRGTAERMIESFMLAANETVAKHYYEKHVPFIYRV 482
Cdd:TIGR02063 392 MLKNLFELYKILRKKRKKRGAIDFDSKEAKIILDENGKPIDIVPRERGDAHKLIEEFMIAANETVAEHLEKAKLPFIYRV 471
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 483 HETPDADRIRTFFETLTAFGINVKG-DPEHVTPKTLQNVLKKVAGKPEEMMVSVMLLRSLKQARYADQSLGHFGLAAPFY 561
Cdd:TIGR02063 472 HERPSEEKLQNLREFLKTLGITLKGgTSDKPQPKDFQKLLEKVKGRPEEELINTVLLRSMQQAKYSPENIGHFGLALEYY 551
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 562 THFTSPIRRYPDTMVHRLIHYY---QDNGINDETKKRYANVLDEIATTTSQYERRAVDAERDTDSMKKAEYMNDHIGEEF 638
Cdd:TIGR02063 552 THFTSPIRRYPDLIVHRLIKKAlfgGENTTTEKEREYLEAKLEEIAEHSSKTERRADEAERDVNDWKKAEYMSEKIGEEF 631
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 503493450 639 DGVVSSVMKFGLFIELPN-TVEGLVHISRMNDDYYQYVEQFMALVGRNTRRTYKMGQAIRVKVVNVDVKQSAVDFDIV 715
Cdd:TIGR02063 632 EGVISGVTSFGLFVELENnTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTGKIDFELV 709
|
|
| 3_prime_RNase |
TIGR00358 |
VacB and RNase II family 3'-5' exoribonucleases; This model is defined to identify a pair of ... |
62-715 |
0e+00 |
|
VacB and RNase II family 3'-5' exoribonucleases; This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases. [Transcription, Degradation of RNA]
Pssm-ID: 273033 [Multi-domain] Cd Length: 654 Bit Score: 603.63 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 62 KFQLNPDKQQLSGIFHANDKGFGFVTYDENAPDAYIAPDNTMN-ALNGDTVEmeiVRPAQPGSDRGPEGKVTKIAEHKYT 140
Cdd:TIGR00358 7 KYALPEKDDLVKGVVKAHNKGFGFLRPDDDDKKDYFIPPPQMKkVMHGDLVE---ACPLSQPQRGRFEAEVERILEPALT 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 141 RVVGPFeKTDDDKGYIgqlTLNDKKIAKYKFYINDVGLKP-TPGEVITAQITEYPSTKhpDYMVGIADEVIGSVDDPGID 219
Cdd:TIGR00358 84 RFVGKF-LGENDFGFV---VPDDPRIYLDIIVPKASVKNElAEGDKVVVELTEYPLRR--NLFYGEITQILGNNDDPLIP 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 220 ILQIVYAHDIPAEFPEDVIQAADAIPDHVTEAEKIGREDITDQDLVTIDGESSKDLDDAVTAWKLPNGNYHLGVHIADVS 299
Cdd:TIGR00358 158 WWVTLARHEIPFEFPDGVEQQAAKLQFDVDEQAKKYREDLTDLAFVTIDGADAKDLDDAVYVKKLPDGGWKLYVAIADVS 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 300 HYVQPGSAIDKEAFRRGTSVYLTDRVIPMLPRRLSNGICSLNEGELRLCMSCEMEIDPSGNIIKHRIHPSLMRSTARMTY 379
Cdd:TIGR00358 238 YYVAENSPLDKEAKHRGFSVYLPGFVIPMLPEELSNGLCSLNPNEDRLVLVCEMTISAQGRITDNEFYPATIESKARLTY 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 380 TAVNNILEShDQKTMDRYDKLVPMFETMGELHKILYKHRKARGAIDFDDNEAEIIVDDKGHPIDIKLRVRGTAERMIESF 459
Cdd:TIGR00358 318 DKVNDWLEN-DDELQPEYETLVEQLKALHQLSQALGEWRHKRGLIDFEHPETKFIVDEEGRVIDIVAEVRRIAEKIIEEA 396
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 460 MLAANETVAKHYYEKHVPFIYRVHETPDADRIRTFFETLTAFGI-NVKGDPEHVTPKTLQNVLKKVAGKPEEMMVSVMLL 538
Cdd:TIGR00358 397 MIVANICAARFLHNHKVPGIYRVHPGPSKKKLQSLLEFLAELGLtLPGGNAENVTTLDGACWLREVKDRPEYEILVTRLL 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 539 RSLKQARYADQSLGHFGLAAPFYTHFTSPIRRYPDTMVHRLIHYYQDNGINDETKKRYANVLDEIATTTSQYERRAVDAE 618
Cdd:TIGR00358 477 RSLSQAEYSPEPLGHFGLGLEHYAHFTSPIRRYPDLTNHRLIKAVLAKEQTDTERYQPQDELLQIAEHCSDTERRARDAE 556
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 619 RDTDSMKKAEYMNDHIGEEFDGVVSSVMKFGLFIELP-NTVEGLVHISRMNDDYYQYVEQFMALVGRNTRRTYKMGQAIR 697
Cdd:TIGR00358 557 RDVADWLKCRYLLDKVGTEFSGEISSVTRFGMFVRLDdNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVT 636
|
650
....*....|....*...
gi 503493450 698 VKVVNVDVKQSAVDFDIV 715
Cdd:TIGR00358 637 VKLTEVNMETRSIIFELV 654
|
|
| RNB |
smart00955 |
This domain is the catalytic domain of ribonuclease II; |
256-583 |
2.87e-131 |
|
This domain is the catalytic domain of ribonuclease II;
Pssm-ID: 214935 [Multi-domain] Cd Length: 286 Bit Score: 391.25 E-value: 2.87e-131
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 256 REDITDQDLVTIDGESSKDLDDAVTAWKLPNGNYHLGVHIADVSHYVQPGSAIDKEAFRRGTSVYLTDRVIPMLPRRLSN 335
Cdd:smart00955 1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLDNGGYRLGVHIADVSHYVKPGSALDREARKRGTSVYLPDRVIPMLPEELSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 336 GICSLNEGELRLCMSCEMEIDPSG-NIIKHRIHPSLMRSTARMTYTAVNNILEshdqktmdrydklvpmfetmgelhkil 414
Cdd:smart00955 81 GLCSLNPGEDRLALSVEMTLDADGgEILDYEFYRSVIRSKARLTYEEVDAILE--------------------------- 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 415 ykhrkargaidfddneaEIIVDDKGHPIDIKLRVRGTAERMIESFMLAANETVAKHYYEKHVPFIYRVHETPDADRIRTF 494
Cdd:smart00955 134 -----------------KIVLDEEGKIEDIVPRERNDAHSLVEEFMILANEAVARFLAKNGIPGLYRVHEGPDPEKLAEL 196
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 495 F-ETLTAFGINVKGDPehvTPKTLQNVLKKVAGKPEEMMVSVMLLRSLKQARYADQSLGHFGLAAPFYTHFTSPIRRYPD 573
Cdd:smart00955 197 LkEFLALLGLLLLGGD---GPKALAKLLEKIRDSPEERLLELLLLRSMPHAEYSVDNSGHFGLALDAYTHFTSPIRRYPD 273
|
330
....*....|
gi 503493450 574 TMVHRLIHYY 583
Cdd:smart00955 274 LIVHRQLKAA 283
|
|
| RNB |
pfam00773 |
RNB domain; This domain is the catalytic domain of ribonuclease II. |
256-581 |
7.57e-131 |
|
RNB domain; This domain is the catalytic domain of ribonuclease II.
Pssm-ID: 459934 [Multi-domain] Cd Length: 314 Bit Score: 391.26 E-value: 7.57e-131
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 256 REDITDQDLVTIDGESSKDLDDAVTAWKLPNGNYHLGVHIADVSHYVQPGSAIDKEAFRRGTSVYLTDRVIPMLPRRLSN 335
Cdd:pfam00773 1 RKDLRDLPFITIDPADAKDLDDAISVEKLPNGGYRLGVHIADVSHYVPPGSPLDREARKRGTSVYLPDRVIPMLPEKLSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 336 GICSLNEGELRLCMSCEMEIDPSGNIIKHRIHPSLMRSTARMTYTAVNNILESHDQKtmDRYDKLVPMFETMGELHKILY 415
Cdd:pfam00773 81 DLCSLNPGEDRLALSVEITIDADGEVTSYEIYPSVIRSKARLTYEEVDDLLEGKDAE--KDKPDLAEDLRLLYELAKILR 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 416 KHRKARGAIDFDDNEAEIIVDDKGhPIDIKLRVRGTAERMIESFMLAANETVAKHYYEKHVPFIYRVHETPDADRIRTFF 495
Cdd:pfam00773 159 AKRLQRGALDLDTPENKLILDEEG-VIDILIQERTDAHSLIEEFMLLANEAVARHLQELGIPALYRVHPEPDLEKLNSLI 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 496 ETLTafginvkgdpEHVTPKTLQNVLKKVAGkpEEMMVSVMLLRSLKQARYADQSLGHFGLAAPFYTHFTSPIRRYPDTM 575
Cdd:pfam00773 238 KLLQ----------LLPDDKGLSKSLEKIKD--DERLLSILLLRTMPRAEYSPEPLGHFGLGLDIYTHFTSPIRRYPDLI 305
|
....*.
gi 503493450 576 VHRLIH 581
Cdd:pfam00773 306 VHRQLK 311
|
|
| PRK11642 |
PRK11642 |
ribonuclease R; |
25-722 |
5.00e-128 |
|
ribonuclease R;
Pssm-ID: 236944 [Multi-domain] Cd Length: 813 Bit Score: 401.43 E-value: 5.00e-128
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 25 EKIADVLRSHGSAAFKLIVQELASLERDKVAVVTEDGKFQLNPDKQQLSGIFHANDKGFGFVTYDENAPDAYIAPDNTMN 104
Cdd:PRK11642 38 EELAVELNIEGEEQLEALRRRLRAMERDGQLVFTRRQCYALPERLDLLKGTVIGHRDGYGFLRVEGRKDDLYLSSEQMKT 117
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 105 ALNGDTVEmeivrpAQP-GSDRG--PEGKVTKIAEHKYTRVVGPFeKTDDDKGYIgqlTLNDKKIAkykFYIndvgLKPT 181
Cdd:PRK11642 118 CIHGDQVL------AQPlGADRKgrREARIVRVLVPKTSQIVGRY-FTDAGVGFV---VPDDSRLS---FDI----LIPP 180
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 182 P-------GEVITAQITEYPS--TKhpdyMVGIADEVIGSVDDPGIDILQIVYAHDIPAEFPEDVIQAADAIPDHVTEAE 252
Cdd:PRK11642 181 EqimgarmGFVVVVELTQRPTrrTK----AVGKIVEVLGDNMGTGMAVDIALRTHEIPYIWPQAVEQQVAGLKEEVPEEA 256
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 253 KIGREDITDQDLVTIDGESSKDLDDAVTAWKLPNGNYHLGVHIADVSHYVQPGSAIDKEAFRRGTSVYLTDRVIPMLPRR 332
Cdd:PRK11642 257 KAGRVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPPTPLDREARNRGTSVYFPSQVVPMLPEV 336
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 333 LSNGICSLNEGELRLCMSCEMEIDPSGNIIKHRIHPSLMRSTARMTYTAVNNILEShDQKTMDRYDKLVPMFETMGELHK 412
Cdd:PRK11642 337 LSNGLCSLNPQVDRLCMVCEMTISSKGRLTGYKFYEAVMSSHARLTYTKVWHILQG-DQDLREQYAPLVKHLEELHNLYK 415
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 413 ILYKHRKARGAIDFDDNEAEIIVDDKGHPIDIKLRVRGTAERMIESFMLAANETVAKHYYEKHVPFIYRVHETPDADRIR 492
Cdd:PRK11642 416 VLDKAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFVEKAKEPALFRIHDKPSTEAIT 495
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 493 TFFETLTAFGINVKGD--PEhvtPKTLQNVLKKVAGKPEEMMVSVMLLRSLKQARYADQSLGHFGLAAPFYTHFTSPIRR 570
Cdd:PRK11642 496 SFRSVLAELGLELPGGnkPE---PRDYAELLESVADRPDAEMLQTMLLRSMKQAIYDPENRGHFGLALQSYAHFTSPIRR 572
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 571 YPDTMVHRLIHYY--QDNGINDETKKR--YANVLDE---IATTTSQYERRAVDAERDTDSMKKAEYMNDHIGEEFDGVVS 643
Cdd:PRK11642 573 YPDLSLHRAIKYLlaKEQGHKGNTTETggYHYSMEEmlqLGQHCSMTERRADEATRDVADWLKCDFMLDQVGNVFKGVIS 652
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 644 SVMKFGLFIELPNT-VEGLVHISRMNDDYYQYVEQFMALVGRNTRRTYKMGQAIRVKVVNVDVKQSAVDFDIVDPEKTPQ 722
Cdd:PRK11642 653 SVTGFGFFVRLDDLfIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDERKIDFSLISSERAPR 732
|
|
| Rnb |
COG4776 |
Exoribonuclease II [Transcription]; |
63-710 |
1.08e-63 |
|
Exoribonuclease II [Transcription];
Pssm-ID: 443808 [Multi-domain] Cd Length: 644 Bit Score: 224.73 E-value: 1.08e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 63 FQLNPD----KQQL-------SGIFHANDKGFGFVTYDeNAPDAYIAPDNTMNALNGDTVEMEIvrpaqpgsdRGPEGKv 131
Cdd:COG4776 2 FQNNPLlaqlKQQLheqtprvEGVVKATDKGFGFLEVD-DQKSYFIPPPQMKKVMHGDRIKAVI---------RTEKDK- 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 132 tKIAEHkyTRVVGPFEKTdddkgYIGQLTLNDKK---IAKYKfYINDVgLKPTPGEVITAQITE-----YPSTKHP---- 199
Cdd:COG4776 71 -ESAEP--ETLIEPFLTR-----FVGRVQKKDGRlfvVPDHP-LIKDA-IKARPKKGLEEGLKEgdwvvAELKRHPlkgd 140
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 200 DYMVGIADEVIGSVDDPGIDILQIVYAHDIPAEFPEDviqaadaiPDHVT-EAEKIGREDITDQDLVTIDGESSKDLDDA 278
Cdd:COG4776 141 RGFFAEITEFIADADDPFAPWWVTLARHNLEREAPEG--------DDEWElLDEGLEREDLTALPFVTIDSESTEDMDDA 212
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 279 VTAWKLPNGNYHLGVHIADVSHYVQPGSAIDKEAFRRGTSVYLTDRVIPMLPRRLSNGICSLNEGELRLCMSCEMEIDPS 358
Cdd:COG4776 213 LYIEKLENGGWKLTVAIADPTAYIPEGSELDKEARQRAFTNYLPGFNIPMLPRELSDDLCSLKENEKRPALVCRVTIDAD 292
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 359 GNII-KHRIHPSLMRSTARMTYTAVNNILESHDQKTmdrydklvPMFETMGELHKILYKHRKARG------AIDFDDN-E 430
Cdd:COG4776 293 GSIGdDIEFFAAWIRSKAKLAYDNVSDWLEGKGEWQ--------PENEEIAEQIRLLHQFALARSqwrqqhALVFKDRpD 364
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 431 AEIIVDDKGHPIDIKLRVRGTAERMIESFMLAANETVAKhYYEKHVPF-IYRVHETPDADRIRTFFETLTAFGINVkgDP 509
Cdd:COG4776 365 YRFELDEKGNVLDIHAEPRRIANRIVEEAMIAANICAAR-VLREHLGFgIFNVHSGFDPEKLEQAVELLAEHGIEF--DP 441
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 510 EHVTpkTLQ---NVLKKVAGKPEEMMVSvmLLRslKQARYAD---QSLGHFGLAAPFYTHFTSPIRRYPDTMVHRLIhyy 583
Cdd:COG4776 442 EQLL--TLEgfcALRRELDAQPTSYLDS--RLR--RFQTFAEistEPGPHFGLGLDAYATWTSPIRKYGDMVNHRLI--- 512
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 584 qdngindetkKRY-----ANVLDEIATTTSQYERRAVD-AERDTDSMKKAEYMNDHIGEE--FDGVVSSVMKFGL----- 650
Cdd:COG4776 513 ----------KAVilgqpAEKPDEELTERLAERRRLNRmAERDVADWLYARYLKPKVGSGqvFTAEIIDINRGGLrvrll 582
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 503493450 651 ------FIELP-----------NTVEGLVHIsrmnddyyqyveqfmalvgrNTRRTYKMGQAIRVKVVNVDVKQSAV 710
Cdd:COG4776 583 engavaFIPASfihsvrdelvcSQEEGTVYI--------------------KGEVRYKLGDTIQVTLAEVREETRSI 639
|
|
| PRK05054 |
PRK05054 |
exoribonuclease II; Provisional |
63-703 |
7.29e-54 |
|
exoribonuclease II; Provisional
Pssm-ID: 179920 [Multi-domain] Cd Length: 644 Bit Score: 197.41 E-value: 7.29e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 63 FQLNPD----KQQL-------SGIFHANDKGFGFVTYDenAPDAY-IAPDNTMNALNGDTV--------EMEIVRPAQ-- 120
Cdd:PRK05054 2 FQDNPLlaqlKQQLhsqtprvEGVVKATEKGFGFLEVD--AQKSYfIPPPQMKKVMHGDRIiavihtekDREIAEPEEli 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 121 -PGSDRgpegkvtkiaehkytrvvgpfektdddkgYIGQLTLNDKK---IAKYKFyINDV-------GLKPTPGE---VI 186
Cdd:PRK05054 80 ePFLTR-----------------------------FVGRVQKKDDRlsiVPDHPL-LKDAipcraakGLNHEFKEgdwVV 129
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 187 --------------TAQITEYpstkhpdymvgIADEvigsvDDPGIDILQIVYAHDIPAEFPEdvIQAADAIPDhvteaE 252
Cdd:PRK05054 130 aelrrhplkgdrgfYAEITQF-----------ITDA-----DDHFAPWWVTLARHNLEREAPA--GGVAWEMLD-----E 186
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 253 KIGREDITDQDLVTIDGESSKDLDDAVTAWKLPNGNYHLGVHIADVSHYVQPGSAIDKEAFRRGTSVYLTDRVIPMLPRR 332
Cdd:PRK05054 187 GLEREDLTALDFVTIDSASTEDMDDALYVEKLPDGGLQLTVAIADPTAYIAEGSKLDKAARQRAFTNYLPGFNIPMLPRE 266
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 333 LSNGICSLNEGELRLCMSCEMEIDPSGNII-KHRIHPSLMRSTARMTYTAVNNILESHDQKtmdrydklVPMFETMGELH 411
Cdd:PRK05054 267 LSDDLCSLRPNERRPALACRVTIDADGTIEdDIRFFAAWIESKAKLAYDNVSDWLENGGDW--------QPESEAIAEQI 338
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 412 KILYKHRKARG------AIDFDDN-EAEIIVDDKGHPIDIKLRVRGTAERMIESFMLAANeTVAKHYYEKHVPF-IYRVH 483
Cdd:PRK05054 339 RLLHQFCLARSewrkqhALVFKDRpDYRFELGEKGEVLDIVAEPRRIANRIVEESMIAAN-ICAARVLRDKLGFgIYNVH 417
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 484 ETPDADRIRTFFETLTAFGINVkgDPEHVTpkTLQN--VLKKVAGKPEEMMVSVMLLRSLKQARYADQSLGHFGLAAPFY 561
Cdd:PRK05054 418 SGFDPANAEQAVALLKEHGLHF--DAEELL--TLEGfcKLRRELDAQPTGYLDSRIRRFQSFAEISTEPGPHFGLGLEAY 493
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 562 THFTSPIRRYPDTMVHRLIHYYqdngINDETKKRYA-NVLDEIAtttsqyERRAVD--AERDTDSMKKAEYMNDHIGEE- 637
Cdd:PRK05054 494 ATWTSPIRKYGDMINHRLLKAV----IKGETAERPQdEITVQLA------ERRRLNrmAERDVGDWLYARYLKDKAGTDt 563
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 638 -FDGVVSSVMKFGL-----------FIELP-----------NTVEGLVHIsrmnddyyqyveqfmalvgrNTRRTYKMGQ 694
Cdd:PRK05054 564 rFAAEIIDISRGGMrvrllengavaFIPASflhavrdelvcNQENGTVQI--------------------KGETVYKLGD 623
|
....*....
gi 503493450 695 AIRVKVVNV 703
Cdd:PRK05054 624 VIDVTLAEV 632
|
|
| S1_RNase_R |
cd04471 |
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ... |
634-715 |
1.17e-34 |
|
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: 126.75 E-value: 1.17e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 634 IGEEFDGVVSSVMKFGLFIELPN-TVEGLVHISRMNDDYYQYVEQFMALVGRNTRRTYKMGQAIRVKVVNVDVKQSAVDF 712
Cdd:cd04471 1 VGEEFDGVISGVTSFGLFVELDNlTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDF 80
|
...
gi 503493450 713 DIV 715
Cdd:cd04471 81 ELV 83
|
|
| S1 |
smart00316 |
Ribosomal protein S1-like RNA-binding domain; |
634-706 |
5.92e-13 |
|
Ribosomal protein S1-like RNA-binding domain;
Pssm-ID: 197648 [Multi-domain] Cd Length: 72 Bit Score: 64.55 E-value: 5.92e-13
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 503493450 634 IGEEFDGVVSSVMKFGLFIELPNTVEGLVHISRMNDDYyqyveqfmalvGRNTRRTYKMGQAIRVKVVNVDVK 706
Cdd:smart00316 2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKR-----------VKDPEEVLKVGDEVKVKVLSVDEE 63
|
|
| CSD2 |
pfam17876 |
Cold shock domain; Crystallographic structure analysis of E. coli wild-type RNase II revealed ... |
163-234 |
3.66e-12 |
|
Cold shock domain; Crystallographic structure analysis of E. coli wild-type RNase II revealed that the amino-terminal region starts with an alpha-helix followed by two consecutive five-stranded anti-parallel beta-barrels, identified as cold-shock domains (CSD1 and CSD2). This entry relates to CSD2 which lacks the typical sequence motifs RNPI and RNPII but contributes to RNA binding.
Pssm-ID: 465546 [Multi-domain] Cd Length: 74 Bit Score: 62.41 E-value: 3.66e-12
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 503493450 163 DKKIaKYKFYINDVGLK-PTPGEVITAQITEYPSTKHPdymVGIADEVIGSVDDPGIDILQIVYAHDIPAEFP 234
Cdd:pfam17876 6 DKRI-PQDIFIPKEDLKgAKDGDKVVVEITEYPDGKNP---EGKIVEVLGDPGDPGVEILSIIRKHGLPHEFP 74
|
|
| OB_RNB |
pfam08206 |
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease ... |
74-134 |
1.14e-11 |
|
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.
Pssm-ID: 429863 [Multi-domain] Cd Length: 58 Bit Score: 60.24 E-value: 1.14e-11
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 503493450 74 GIFHANDKGFGFVTYDENAPDAYIAPDNTMNALNGDTVemeIVRPAQPGSDRGPEGKVTKI 134
Cdd:pfam08206 1 GTVRGHKKGFGFLIPDDEEDDIFIPPNQMKKAMHGDRV---LVRITKGDRRGRREGRIVRI 58
|
|
| PRK11824 |
PRK11824 |
polynucleotide phosphorylase/polyadenylase; Provisional |
620-704 |
3.08e-11 |
|
polynucleotide phosphorylase/polyadenylase; Provisional
Pssm-ID: 236995 [Multi-domain] Cd Length: 693 Bit Score: 67.00 E-value: 3.08e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 620 DTDSMKKA-EYMND-----HIGEEFDGVVSSVMKFGLFIELPNTVEGLVHISRMNDDYYQYVEQFmalvgrntrrtYKMG 693
Cdd:PRK11824 601 DGEAAEAAkERIEGitaepEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDV-----------LKEG 669
|
90
....*....|.
gi 503493450 694 QAIRVKVVNVD 704
Cdd:PRK11824 670 DEVKVKVLEID 680
|
|
| PRK08563 |
PRK08563 |
DNA-directed RNA polymerase subunit E'; Provisional |
634-703 |
3.27e-11 |
|
DNA-directed RNA polymerase subunit E'; Provisional
Pssm-ID: 236289 [Multi-domain] Cd Length: 187 Bit Score: 62.92 E-value: 3.27e-11
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 503493450 634 IGEEFDGVVSSVMKFGLFIEL-PntVEGLVHISRMNDDYYQYVEQFMALVGRNTRRTYKMGQAIRVKVVNV 703
Cdd:PRK08563 81 LQEVVEGEVVEVVEFGAFVRIgP--VDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAV 149
|
|
| S1_RpoE |
cd04460 |
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ... |
639-706 |
3.92e-11 |
|
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Pssm-ID: 239907 [Multi-domain] Cd Length: 99 Bit Score: 59.99 E-value: 3.92e-11
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 503493450 639 DGVVSSVMKFGLFIELpNTVEGLVHISRMNDDYYQYVEQFMALVGRNTRRTYKMGQAIRVKVVNVDVK 706
Cdd:cd04460 4 EGEVVEVVDFGAFVRI-GPVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLK 70
|
|
| S1 |
pfam00575 |
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ... |
634-714 |
4.06e-11 |
|
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: 59.22 E-value: 4.06e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 634 IGEEFDGVVSSVMKFGLFIELPNTVEGLVHISRMNDDYYQYVEqfmalvgrntrRTYKMGQAIRVKVVNVDVKQSAVDFD 713
Cdd:pfam00575 3 KGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPD-----------EVIKVGDEVKVKVLKVDKDRRRIILS 71
|
.
gi 503493450 714 I 714
Cdd:pfam00575 72 I 72
|
|
| YabR |
COG1098 |
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ... |
634-704 |
1.03e-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: 59.81 E-value: 1.03e-10
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 503493450 634 IGEEFDGVVSSVMKFGLFIELPNTVEGLVHISRMNDDYYQYVEQFMalvgrntrrtyKMGQAIRVKVVNVD 704
Cdd:COG1098 5 VGDIVEGKVTGITPFGAFVELPEGTTGLVHISEIADGYVKDINDYL-----------KVGDEVKVKVLSID 64
|
|
| S1_PNPase |
cd04472 |
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ... |
635-706 |
2.02e-10 |
|
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: 57.17 E-value: 2.02e-10
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 503493450 635 GEEFDGVVSSVMKFGLFIELPNTVEGLVHISRMNDDYYQYVEQFmalvgrntrrtYKMGQAIRVKVVNVDVK 706
Cdd:cd04472 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDV-----------LKVGDEVKVKVIEVDDR 61
|
|
| S1_RPS1_repeat_hs4 |
cd05692 |
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
640-704 |
1.18e-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: 54.98 E-value: 1.18e-09
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 503493450 640 GVVSSVMKFGLFIELPNTVEGLVHISRMNDDYYQYVEQFMalvgrntrrtyKMGQAIRVKVVNVD 704
Cdd:cd05692 6 GTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVL-----------KEGDKVKVKVLSID 59
|
|
| S1_like |
cd00164 |
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ... |
638-707 |
4.20e-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: 53.15 E-value: 4.20e-09
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 638 FDGVVSSVMKFGLFIELPNTVEGLVHISRMNDDYYqyveqfmalvgRNTRRTYKMGQAIRVKVVNVDVKQ 707
Cdd:cd00164 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFV-----------KDPSEVFKVGDEVEVKVLEVDPEK 59
|
|
| PRK08582 |
PRK08582 |
RNA-binding protein S1; |
630-704 |
6.83e-08 |
|
RNA-binding protein S1;
Pssm-ID: 236305 [Multi-domain] Cd Length: 139 Bit Score: 51.96 E-value: 6.83e-08
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 503493450 630 MNDHIGEEFDGVVSSVMKFGLFIELPNTVEGLVHISRMNDDYYQYVEQFMalvgrntrrtyKMGQAIRVKVVNVD 704
Cdd:PRK08582 1 MSIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHL-----------KVGDEVEVKVLNVE 64
|
|
| S1_RPS1_repeat_ec5 |
cd05690 |
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
635-707 |
8.05e-08 |
|
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: 49.80 E-value: 8.05e-08
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 503493450 635 GEEFDGVVSSVMKFGLFIELPNTVEGLVHISRMNddYYQYVEQfmalvgrnTRRTYKMGQAIRVKVVNVDVKQ 707
Cdd:cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDIS--WTQRVRH--------PSEIYKKGQEVEAVVLNIDVER 63
|
|
| RpsA |
COG0539 |
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
633-704 |
5.96e-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: 52.35 E-value: 5.96e-07
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 503493450 633 HIGEEFDGVVSSVMKFGLFIELPNTVEGLVHISRMndDYYQYVeqfmalvgRNTRRTYKMGQAIRVKVVNVD 704
Cdd:COG0539 273 PVGDVVKGKVTRLTDFGAFVELEPGVEGLVHISEM--SWTKRV--------AHPSDVVKVGDEVEVKVLDID 334
|
|
| RpsA |
COG0539 |
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
612-704 |
1.08e-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: 51.58 E-value: 1.08e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 612 RRAV-DAERDTdsmKKAEYMND-HIGEEFDGVVSSVMKFGLFIELPNtVEGLVHISRMNddyYQYVEqfmalvgrNTRRT 689
Cdd:COG0539 168 RRAVlEEEREE---KREELLEKlEEGDVVEGTVKNITDFGAFVDLGG-VDGLLHISEIS---WGRVK--------HPSEV 232
|
90
....*....|....*
gi 503493450 690 YKMGQAIRVKVVNVD 704
Cdd:COG0539 233 LKVGDEVEVKVLKID 247
|
|
| S1_Rrp5_repeat_sc12 |
cd05708 |
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ... |
633-712 |
1.27e-06 |
|
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: 46.55 E-value: 1.27e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 633 HIGEEFDGVVSSVMKFGLFIELPNT-VEGLVHISRMNDDyyqyveqfmalVGRNTRRTYKMGQAIRVKVVNVDVKQSAVD 711
Cdd:cd05708 1 KVGQKIDGTVRRVEDYGVFIDIDGTnVSGLCHKSEISDN-----------RVADASKLFRVGDKVRAKVLKIDAEKKRIS 69
|
.
gi 503493450 712 F 712
Cdd:cd05708 70 L 70
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
640-714 |
1.57e-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: 1.57e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 503493450 640 GVVSSVMKFGLFIELPNTVEGLVHISRMNDDYYQYVEqfmalvgrntrRTYKMGQAIRVKVVNVDVKQSAVDFDI 714
Cdd:TIGR00717 452 GKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKT-----------DEIKVGDEVEAKVVDIDKKNRKVSLSV 515
|
|
| S1_Rrp5_repeat_hs8_sc7 |
cd04461 |
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ... |
633-707 |
2.01e-06 |
|
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: 46.43 E-value: 2.01e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 503493450 633 HIGEEFDGVVSSVMKFGLFIELPNTVEGLVHISRMNDDYYqyveqfmalvgRNTRRTYKMGQAIRVKVVNVDVKQ 707
Cdd:cd04461 13 KPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFV-----------TDPSFGFKKGQSVTAKVTSVDEEK 76
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
634-706 |
3.58e-06 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 50.55 E-value: 3.58e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 503493450 634 IGEEFDGVVSSVMKFGLFIELPNTVEGLVHISrmnddyyqyvEQFMALVGRNTRRTYKMGQAIRVKVVNVDVK 706
Cdd:PRK06299 373 VGDVVEGKVKNITDFGAFVGLEGGIDGLVHLS----------DISWDKKGEEAVELYKKGDEVEAVVLKVDVE 435
|
|
| rpsA |
PRK06676 |
30S ribosomal protein S1; Reviewed |
612-721 |
7.59e-06 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 49.10 E-value: 7.59e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 612 RRAV-DAERDtdSMKKAEYMNDHIGEEFDGVVSSVMKFGLFIELpNTVEGLVHISRMNddyYQYVEQFMALVgrntrrty 690
Cdd:PRK06676 171 RRAVvEEERA--AKKEELLSSLKEGDVVEGTVARLTDFGAFVDI-GGVDGLVHISELS---HERVEKPSEVV-------- 236
|
90 100 110
....*....|....*....|....*....|.
gi 503493450 691 KMGQAIRVKVVNVDVKQSAVDFDIVDPEKTP 721
Cdd:PRK06676 237 SVGQEVEVKVLSIDWETERISLSLKDTLPGP 267
|
|
| rpsA |
PRK06676 |
30S ribosomal protein S1; Reviewed |
633-725 |
8.73e-06 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 48.72 E-value: 8.73e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 633 HIGEEFDGVVSSVMKFGLFIELPNTVEGLVHISRMNDDYYQyveqfmalvgrNTRRTYKMGQAIRVKVVNVDVKQSAVDF 712
Cdd:PRK06676 276 PEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHIA-----------TPSEVLEEGQEVKVKVLEVNEEEKRISL 344
|
90
....*....|...
gi 503493450 713 DIVDPEKTPQSNM 725
Cdd:PRK06676 345 SIKALEEAPAEEE 357
|
|
| S1_RPS1_repeat_ec3 |
cd05688 |
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
634-704 |
1.03e-05 |
|
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: 43.77 E-value: 1.03e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 503493450 634 IGEEFDGVVSSVMKFGLFIELpNTVEGLVHISRMNddyYQYVeqfmalvgRNTRRTYKMGQAIRVKVVNVD 704
Cdd:cd05688 1 EGDVVEGTVKSITDFGAFVDL-GGVDGLLHISDMS---WGRV--------KHPSEVVNVGDEVEVKVLKID 59
|
|
| S1_Tex |
cd05685 |
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ... |
635-706 |
1.29e-05 |
|
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: 43.38 E-value: 1.29e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 503493450 635 GEEFDGVVSSVMKFGLFIELPNTVEGLVHISRMNDdyyQYVEQFMALVgrntrrtyKMGQAIRVKVVNVDVK 706
Cdd:cd05685 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMAD---RFVSHPSDVV--------SVGDIVEVKVISIDEE 61
|
|
| S1_DHX8_helicase |
cd05684 |
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ... |
635-667 |
1.98e-05 |
|
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: 43.38 E-value: 1.98e-05
10 20 30
....*....|....*....|....*....|....*.
gi 503493450 635 GEEFDGVVSSVMKFGLFIELPNT---VEGLVHISRM 667
Cdd:cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLkgrKEGLVHISQL 36
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
612-704 |
3.66e-05 |
|
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]
Pssm-ID: 273232 [Multi-domain] Cd Length: 516 Bit Score: 47.04 E-value: 3.66e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 612 RRAVDAERDtdSMKKAEYMND-HIGEEFDGVVSSVMKFGLFIELpNTVEGLVHISRMNddyYQYVeqfmalvgRNTRRTY 690
Cdd:TIGR00717 166 RRAYLEEER--SQAREELLENlKEGDVVKGVVKNITDFGAFVDL-GGVDGLLHITDMS---WKRV--------KHPSEYV 231
|
90
....*....|....
gi 503493450 691 KMGQAIRVKVVNVD 704
Cdd:TIGR00717 232 KVGQEVKVKVIKFD 245
|
|
| PRK12269 |
PRK12269 |
bifunctional cytidylate kinase/ribosomal protein S1; Provisional |
634-728 |
5.24e-05 |
|
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Pssm-ID: 105491 [Multi-domain] Cd Length: 863 Bit Score: 47.01 E-value: 5.24e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 634 IGEEFDGVVSSVMKFGLFIELPNTVEGLVHISRMnddyyqyVEQFMALVGRNTRRtYKMGQAIRVKVVNVDVKQSAVDFD 713
Cdd:PRK12269 752 VGSTVEGEVSSVTDFGIFVRVPGGVEGLVRKQHL-------VENRDGDPGEALRK-YAVGDRVKAVIVDMNVKDRKVAFS 823
|
90
....*....|....*
gi 503493450 714 IVDPEKTPQSNMLPK 728
Cdd:PRK12269 824 VRDYQRKVQRDELSR 838
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
628-706 |
5.51e-05 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 46.70 E-value: 5.51e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 628 EYMNDH-IGEEFDGVVSSVMKFGLFIELPNTVEGLVHISRMNDDyyqYVEQfmalvgrnTRRTYKMGQAIRVKVVNVDVK 706
Cdd:PRK06299 453 EFAKKHkKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRD---RVED--------ATEVLKVGDEVEAKVINIDRK 521
|
|
| Tex |
COG2183 |
Transcriptional accessory protein Tex/SPT6 [Transcription]; |
619-706 |
8.26e-05 |
|
Transcriptional accessory protein Tex/SPT6 [Transcription];
Pssm-ID: 441786 [Multi-domain] Cd Length: 719 Bit Score: 46.17 E-value: 8.26e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 619 RDT-DSMKKAEY------MND-HIGEEFDGVVSSVMKFGLFIELPNTVEGLVHISRMNDdyyQYVEQFMALVgrntrrty 690
Cdd:COG2183 618 RDPrPEFKTPTFregvlkIEDlKPGMILEGTVTNVTDFGAFVDIGVHQDGLVHISQLSD---RFVKDPREVV-------- 686
|
90
....*....|....*.
gi 503493450 691 KMGQAIRVKVVNVDVK 706
Cdd:COG2183 687 KVGDIVKVKVLEVDLK 702
|
|
| PRK00087 |
PRK00087 |
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; |
633-704 |
1.12e-04 |
|
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
Pssm-ID: 234623 [Multi-domain] Cd Length: 647 Bit Score: 45.71 E-value: 1.12e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 503493450 633 HIGEEFDGVVSSVMKFGLFIELPNTVEGLVHISRMNDdyyqyveqfmalvGR--NTRRTYKMGQAIRVKVVNVD 704
Cdd:PRK00087 561 PVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISW-------------KRidKPEDVLSEGEEVKAKILEVD 621
|
|
| PRK00087 |
PRK00087 |
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; |
588-704 |
1.50e-04 |
|
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
Pssm-ID: 234623 [Multi-domain] Cd Length: 647 Bit Score: 45.32 E-value: 1.50e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 588 INDETKKRYANVLDEIATTTSQYERRAvdaERDTDSMKKaeymndhiGEEFDGVVSSVMKFGLFIELpNTVEGLVHISRM 667
Cdd:PRK00087 442 IEFNRKRRKKVVLSRKAILEEEKEKKK---EETWNSLEE--------GDVVEGEVKRLTDFGAFVDI-GGVDGLLHVSEI 509
|
90 100 110
....*....|....*....|....*....|....*..
gi 503493450 668 NddyYQYVEQFMALVgrntrrtyKMGQAIRVKVVNVD 704
Cdd:PRK00087 510 S---WGRVEKPSDVL--------KVGDEIKVYILDID 535
|
|
| PRK07252 |
PRK07252 |
S1 RNA-binding domain-containing protein; |
634-704 |
4.19e-04 |
|
S1 RNA-binding domain-containing protein;
Pssm-ID: 180908 [Multi-domain] Cd Length: 120 Bit Score: 40.84 E-value: 4.19e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 503493450 634 IGEEFDGVVSSVMKFGLFIELPNTVEGLVHISRMNDDYYQyveqfmalvgrNTRRTYKMGQAIRVKVVNVD 704
Cdd:PRK07252 3 IGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFID-----------NIHQLLKVGEEVLVQVVDFD 62
|
|
| rpsA |
PRK07899 |
30S ribosomal protein S1; Reviewed |
634-704 |
4.82e-04 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 236126 [Multi-domain] Cd Length: 486 Bit Score: 43.49 E-value: 4.82e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 503493450 634 IGEEFDGVVSSVMKFGLFIELPNTVEGLVHISRMNDDYYQYVEQFMalvgrntrrtyKMGQAIRVKVVNVD 704
Cdd:PRK07899 293 IGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVV-----------QVGDEVFVKVIDID 352
|
|
| rpsA |
PRK13806 |
30S ribosomal protein S1; Provisional |
612-711 |
6.32e-04 |
|
30S ribosomal protein S1; Provisional
Pssm-ID: 237516 [Multi-domain] Cd Length: 491 Bit Score: 43.17 E-value: 6.32e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 612 RRAVDAERDTDSMKKAEYMNDhiGEEFDGVVSSVMKFGLFIELPNTVEGLVHISRMNddyYQYVEQFMALVgrntrrtyK 691
Cdd:PRK13806 182 RALLEREQKEALEAFMETVKE--GDVVEGTVTRLAPFGAFVELAPGVEGMVHISELS---WSRVQKADEAV--------S 248
|
90 100 110
....*....|....*....|....*....|...
gi 503493450 692 MGQAIRVKVVNVD-------------VKQSAVD 711
Cdd:PRK13806 249 VGDTVRVKVLGIErakkgkglrislsIKQAGGD 281
|
|
| rpsA |
PRK13806 |
30S ribosomal protein S1; Provisional |
632-725 |
7.31e-04 |
|
30S ribosomal protein S1; Provisional
Pssm-ID: 237516 [Multi-domain] Cd Length: 491 Bit Score: 42.79 E-value: 7.31e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 632 DHIGEEFD------GVVSSVMKFGLFIELPNTVEGLVHISRMNddyyqyveqfmalvgrNTRRTYK------MGQAIRVK 699
Cdd:PRK13806 284 DTVGDRLKagdkvtGKVVRLAPFGAFVEILPGIEGLVHVSEMS----------------WTRRVNKpedvvaPGDAVAVK 347
|
90 100
....*....|....*....|....*.
gi 503493450 700 VVNVDVKQSAVDFDIVDPEKTPQSNM 725
Cdd:PRK13806 348 IKDIDPAKRRISLSLRDAEGDPWADV 373
|
|
| RRM2_Hrp1p |
cd12330 |
RNA recognition motif 2 (RRM2) found in yeast nuclear polyadenylated RNA-binding protein 4 ... |
81-121 |
9.86e-04 |
|
RNA recognition motif 2 (RRM2) found in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins; This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway; it binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y.
Pssm-ID: 409767 [Multi-domain] Cd Length: 78 Bit Score: 38.46 E-value: 9.86e-04
10 20 30 40
....*....|....*....|....*....|....*....|..
gi 503493450 81 KGFGFVTYD-ENAPDAYIApdNTMNALNGDTVEmeiVRPAQP 121
Cdd:cd12330 41 RGFGFVTFDsESAVEKVLS--KGFHELGGKKVE---VKRATP 77
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
635-706 |
1.12e-03 |
|
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: 42.41 E-value: 1.12e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 503493450 635 GEEFDGVVSSVMKFGLFIELPNTVEGLVHISRmnddyyqyveqfMALVGRNT--RRTYKMGQAIRVKVVNVDVK 706
Cdd:TIGR00717 273 GDKITGRVTNLTDYGVFVEIEEGIEGLVHVSE------------MSWVKKNShpSKVVKKGDEVEVMILDIDPE 334
|
|
| PRK05807 |
PRK05807 |
RNA-binding protein S1; |
630-704 |
1.50e-03 |
|
RNA-binding protein S1;
Pssm-ID: 235614 [Multi-domain] Cd Length: 136 Bit Score: 39.34 E-value: 1.50e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 503493450 630 MNDHIGEEFDGVVSSVMKFGLFIELPNTVeGLVHISRMNDDYYqyveqfmalvgRNTRRTYKMGQAIRVKVVNVD 704
Cdd:PRK05807 1 MTLKAGSILEGTVVNITNFGAFVEVEGKT-GLVHISEVADTYV-----------KDIREHLKEQDKVKVKVISID 63
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
633-667 |
2.56e-03 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 41.30 E-value: 2.56e-03
10 20 30
....*....|....*....|....*....|....*
gi 503493450 633 HIGEEFDGVVSSVMKFGLFIELPNTVEGLVHISRM 667
Cdd:PRK06299 285 PVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEM 319
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
612-704 |
2.88e-03 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 40.92 E-value: 2.88e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 612 RRAV-DAERdtdSMKKAEYMND-HIGEEFDGVVSSVMKFGLFIELpNTVEGLVHISRMNddyYQYVeqfmalvgRNTRRT 689
Cdd:PRK06299 180 RRAVlEEER---AEEREELLENlEEGQVVEGVVKNITDYGAFVDL-GGVDGLLHITDIS---WKRV--------NHPSEV 244
|
90
....*....|....*
gi 503493450 690 YKMGQAIRVKVVNVD 704
Cdd:PRK06299 245 VNVGDEVKVKVLKFD 259
|
|
| S1_RecJ_like |
cd04473 |
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ... |
634-671 |
4.59e-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: 36.43 E-value: 4.59e-03
10 20 30
....*....|....*....|....*....|....*...
gi 503493450 634 IGEEFDGVVSSVMKFGLFIELPNTVEGLVHISRMNDDY 671
Cdd:cd04473 16 VGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLRDY 53
|
|
| S1_Rrp5_repeat_hs11_sc8 |
cd05702 |
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ... |
635-701 |
5.92e-03 |
|
S1_Rrp5_repeat_hs11_sc8: 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 H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Pssm-ID: 240207 [Multi-domain] Cd Length: 70 Bit Score: 36.03 E-value: 5.92e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 503493450 635 GEEFDGVVSSVMKFGLFIELPNTVEGLVHISRMNDDYYQyveqfmalvGRNTRRTYKMGQAIRVKVV 701
Cdd:cd05702 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPD---------GKNPLSKFKIGQKIKARVI 58
|
|
| PRK08059 |
PRK08059 |
general stress protein 13; Validated |
634-704 |
6.45e-03 |
|
general stress protein 13; Validated
Pssm-ID: 181215 [Multi-domain] Cd Length: 123 Bit Score: 37.33 E-value: 6.45e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 503493450 634 IGEEFDGVVSSVMKFGLFIELPNTVEGLVHISRMNDDYYQYVEQFMalvgrntrrtyKMGQAIRVKVVNVD 704
Cdd:PRK08059 7 VGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFL-----------SVGDEVKVKVLSVD 66
|
|
| PRK12269 |
PRK12269 |
bifunctional cytidylate kinase/ribosomal protein S1; Provisional |
591-721 |
7.54e-03 |
|
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Pssm-ID: 105491 [Multi-domain] Cd Length: 863 Bit Score: 39.70 E-value: 7.54e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 591 ETKKRYANvlDEIATTTSQY-ERRAVDAerdtdsmkKAEYMND-HIGEEFDGVVSSVMKFGLFIELpNTVEGLVHISRMN 668
Cdd:PRK12269 458 QSKQHRGN--DNIVINRRRYlEERARQA--------REEFFNSvHIEDSVSGVVKSFTSFGAFIDL-GGFDGLLHVNDMS 526
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|...
gi 503493450 669 DDYYQYVEQFMalvgrntrrtyKMGQAIRVKVVNVDVKQSAVDFDIVDPEKTP 721
Cdd:PRK12269 527 WGHVARPREFV-----------KKGQTIELKVIRLDQAEKRINLSLKHFQPDP 568
|
|
| rpsA |
PRK07899 |
30S ribosomal protein S1; Reviewed |
621-704 |
7.72e-03 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 236126 [Multi-domain] Cd Length: 486 Bit Score: 39.64 E-value: 7.72e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 621 TDSMKKAEYMND-HIGEEFDGVVSSVMKFGLFIELpNTVEGLVHISRMNddyYQYVEQFMALVgrntrrtyKMGQAIRVK 699
Cdd:PRK07899 194 TQSEVRSEFLNQlQKGQVRKGVVSSIVNFGAFVDL-GGVDGLVHVSELS---WKHIDHPSEVV--------EVGQEVTVE 261
|
....*
gi 503493450 700 VVNVD 704
Cdd:PRK07899 262 VLDVD 266
|
|
| CSP |
smart00357 |
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ... |
80-135 |
8.72e-03 |
|
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Pssm-ID: 214633 [Multi-domain] Cd Length: 64 Bit Score: 35.27 E-value: 8.72e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|
gi 503493450 80 DKGFGFVTYDENAPDAYIAP----DNTMNALNGDTVEMEIVrpaQPGSDRGPEGKVTKIA 135
Cdd:smart00357 8 NKGFGFIRPDDGGKDVFVHPsqiqGGLKSLREGDEVEFKVV---SPEGGEKPEAENVVKL 64
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|
| |
