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Conserved domains on  [gi|850385791|ref|WP_048034937|]
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MULTISPECIES: ribonuclease R [Brevibacillus]

Protein Classification

ribonuclease R family protein( domain architecture ID 11426128)

ribonuclease R (RNaseR or RNR) family protein similar to RNR, a 3'-5' exoribonuclease that releases 5'-nucleoside monophosphates and is involved in maturation of structured RNAs

EC:  3.1.-.-
Gene Ontology:  GO:0003723|GO:0004527
PubMed:  25542646
SCOP:  3000135

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
VacB COG0557
Exoribonuclease R [Transcription];
2-712 0e+00

Exoribonuclease R [Transcription];


:

Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 1142.53  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791   2 EDQEKILAFMREQAYHPMTVRELEEAFGIKDSATFKELVKTLNALEASGEVIRTRANRYGVPEKMNLVRGRLQSHPKGFG 81
Cdd:COG0557    3 NSRETILAFLKEDAYKPLSKKELAKALGLKDEESREALKRRLRALEREGQLVKTRRGRYRLPEKLDLVEGRVRGHRDGFG 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  82 FVIPEtQGMEDVYVHANDMNGALHGDTVLVRVEKEAGGNRLEGQIIRIVERGMKQVVGTFKDETYYAFVIPDEKRLGKDI 161
Cdd:COG0557   83 FVIPD-DGEEDIFIPPRELNGALHGDRVLVRVTKEDRRGRPEGRVVEILERANTRVVGRFEKEKGFGFVVPDDKRLLQDI 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 162 FIPKEAYNGAVDGHKVVVNIVRYPEGRVNPEGEVVEILGHKNDPGVDILSIIRKFNLPEAFPDDVLEEAEAAPDEISEEE 241
Cdd:COG0557  162 FIPPDDLNGAKDGDLVVVEITRYPERRGPPEGRVVEVLGSPGDPGAEILIAIRKHGLPHEFPEEVLAEAEALPDEVPEAD 241

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 242 ISGRRDLRERMMVTIDGADAKDLDDAVSLERLPNGNVRLGVHIADVSYYVREKSQLDNEAYRRGTSVYLVDRVIPMLPHR 321
Cdd:COG0557  242 LKGRRDLRDLPLVTIDGEDAKDFDDAVSAEKLDNGGWRLGVHIADVSHYVRPGSALDREARKRGTSVYLPDRVIPMLPER 321

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 322 LSNGICSLNPQVDRLTISCDMEMDSSGNTVKYDIFLSVIRTDERMTYADVRSILEDKDEALTEKYSRLVPMFEDMKELAL 401
Cdd:COG0557  322 LSNGLCSLNPGEDRLAMSCEMEIDAKGEVVSYEFYRSVIRSDARLTYEEVQAILDGKDEELREEYADLVPMLEELYELAK 401

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 402 KLRKKRMQRGAIDFDFREAKIYVDEEGTPTEIGFRTRSIAEQIIEEFMLAANETVAEHFHWMKQPFMYRIHEDPNAEKLM 481
Cdd:COG0557  402 ILRKAREKRGAIDFDLPETKIILDEEGKPEDIVPRERNDAHKLIEEFMLLANEAVAEFLEKLKLPFLYRVHEEPDPEKLE 481

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 482 AFMEFITNFGYSIRGkGNSVHPRALQQLLEEVKGTPEEIIISTVMLRSMKQARYDAESLGHYGLSTEFYTHFTSPIRRYP 561
Cdd:COG0557  482 ALREFLANLGLKLKG-GDEPTPKDLQKLLEQVKGRPEEELLNTLLLRSMKQAVYSPENIGHFGLALEAYTHFTSPIRRYP 560

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 562 DLIVHRRIREWieLGNQISEKRLGYWAEQMPVIAEHASQRERLAVDAERETDDLKKAEFMLERVGEEFEGVISSVTSFGI 641
Cdd:COG0557  561 DLLVHRALKAY--LEGKRSPGLQEYLEEELEEIAEHCSETERRADEAERDVVDLKKAEYMKDRVGEEFEGVISGVTSFGL 638

                        650       660       670       680       690       700       710
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 850385791 642 FVELPNT-IEGLVHVSFLTDDYYHYHEKMFALVGERTGKQYRIGDVVEVRVANVNVDERTIDFEIVGMPKAG 712
Cdd:COG0557  639 FVELDELgVEGLVHVSSLGDDYYEYDERRQALVGERTGKRYRLGDRVEVRVVRVDLDRRQIDFELVEGGSEA 710
 
Name Accession Description Interval E-value
VacB COG0557
Exoribonuclease R [Transcription];
2-712 0e+00

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 1142.53  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791   2 EDQEKILAFMREQAYHPMTVRELEEAFGIKDSATFKELVKTLNALEASGEVIRTRANRYGVPEKMNLVRGRLQSHPKGFG 81
Cdd:COG0557    3 NSRETILAFLKEDAYKPLSKKELAKALGLKDEESREALKRRLRALEREGQLVKTRRGRYRLPEKLDLVEGRVRGHRDGFG 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  82 FVIPEtQGMEDVYVHANDMNGALHGDTVLVRVEKEAGGNRLEGQIIRIVERGMKQVVGTFKDETYYAFVIPDEKRLGKDI 161
Cdd:COG0557   83 FVIPD-DGEEDIFIPPRELNGALHGDRVLVRVTKEDRRGRPEGRVVEILERANTRVVGRFEKEKGFGFVVPDDKRLLQDI 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 162 FIPKEAYNGAVDGHKVVVNIVRYPEGRVNPEGEVVEILGHKNDPGVDILSIIRKFNLPEAFPDDVLEEAEAAPDEISEEE 241
Cdd:COG0557  162 FIPPDDLNGAKDGDLVVVEITRYPERRGPPEGRVVEVLGSPGDPGAEILIAIRKHGLPHEFPEEVLAEAEALPDEVPEAD 241

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 242 ISGRRDLRERMMVTIDGADAKDLDDAVSLERLPNGNVRLGVHIADVSYYVREKSQLDNEAYRRGTSVYLVDRVIPMLPHR 321
Cdd:COG0557  242 LKGRRDLRDLPLVTIDGEDAKDFDDAVSAEKLDNGGWRLGVHIADVSHYVRPGSALDREARKRGTSVYLPDRVIPMLPER 321

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 322 LSNGICSLNPQVDRLTISCDMEMDSSGNTVKYDIFLSVIRTDERMTYADVRSILEDKDEALTEKYSRLVPMFEDMKELAL 401
Cdd:COG0557  322 LSNGLCSLNPGEDRLAMSCEMEIDAKGEVVSYEFYRSVIRSDARLTYEEVQAILDGKDEELREEYADLVPMLEELYELAK 401

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 402 KLRKKRMQRGAIDFDFREAKIYVDEEGTPTEIGFRTRSIAEQIIEEFMLAANETVAEHFHWMKQPFMYRIHEDPNAEKLM 481
Cdd:COG0557  402 ILRKAREKRGAIDFDLPETKIILDEEGKPEDIVPRERNDAHKLIEEFMLLANEAVAEFLEKLKLPFLYRVHEEPDPEKLE 481

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 482 AFMEFITNFGYSIRGkGNSVHPRALQQLLEEVKGTPEEIIISTVMLRSMKQARYDAESLGHYGLSTEFYTHFTSPIRRYP 561
Cdd:COG0557  482 ALREFLANLGLKLKG-GDEPTPKDLQKLLEQVKGRPEEELLNTLLLRSMKQAVYSPENIGHFGLALEAYTHFTSPIRRYP 560

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 562 DLIVHRRIREWieLGNQISEKRLGYWAEQMPVIAEHASQRERLAVDAERETDDLKKAEFMLERVGEEFEGVISSVTSFGI 641
Cdd:COG0557  561 DLLVHRALKAY--LEGKRSPGLQEYLEEELEEIAEHCSETERRADEAERDVVDLKKAEYMKDRVGEEFEGVISGVTSFGL 638

                        650       660       670       680       690       700       710
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 850385791 642 FVELPNT-IEGLVHVSFLTDDYYHYHEKMFALVGERTGKQYRIGDVVEVRVANVNVDERTIDFEIVGMPKAG 712
Cdd:COG0557  639 FVELDELgVEGLVHVSSLGDDYYEYDERRQALVGERTGKRYRLGDRVEVRVVRVDLDRRQIDFELVEGGSEA 710
RNase_R TIGR02063
ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. ...
 1-706 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: 969.82  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791    1 MEDQEKILAFMREQAYHPMTVRELEEAFGIKDSATFKELVKTLNALEASGEVIRTRANRYGVPEKMNLVRGRLQSHPKGF 80
Cdd:TIGR02063   1 SPLRELILEFLKSKKGKPISLKELAKAFHLKGADEKKALRKRLRALEDDGLVKKNRRGLYALPESLKLVKGTVIAHRDGF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791   81 GFVIPETQGMEDVYVHANDMNGALHGDTVLVRV-EKEAGGNRLEGQIIRIVERGMKQVVGTFKDETYYAFVIPDEKRLGK 159
Cdd:TIGR02063  81 GFLRPEDDDEDDIFIPPRQMNGAMHGDRVLVRItGKPDGGDRFEARVIKILERANDQIVGTFYIENGIGFVIPDDKRIYL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  160 DIFIPKEAYNGAVDGHKVVVNIVRYPEGRVNPEGEVVEILGHKNDPGVDILSIIRKFNLPEAFPDDVLEEAEAAPDEISE 239
Cdd:TIGR02063 161 DIFIPPEQILGAEEGDKVLVEITKYPDRNRPAIGKVVEILGHADDPGIDILIIIRKHGIPYEFPEEVLDEAAKIPEEVPE 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  240 EEISGRRDLRERMMVTIDGADAKDLDDAVSLERLPNGNVRLGVHIADVSYYVREKSQLDNEAYRRGTSVYLVDRVIPMLP 319
Cdd:TIGR02063 241 EEIKGRKDLRDLPFVTIDGEDAKDFDDAVYVEKLKDGNYKLGVAIADVSHYVREGSALDKEALKRGTSVYLPDRVIPMLP 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  320 HRLSNGICSLNPQVDRLTISCDMEMDSSGNTVKYDIFLSVIRTDERMTYADVRSILEDKDeALTEKYSRLVPMFEDMKEL 399
Cdd:TIGR02063 321 ERLSNGICSLNPNEDRLTLSCEMEIDKKGRVKKYEFYEAVINSHARLTYNQVNDIIEGKD-ALDKKEPPLKEMLKNLFEL 399

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  400 ALKLRKKRMQRGAIDFDFREAKIYVDEEGTPTEIGFRTRSIAEQIIEEFMLAANETVAEHFHWMKQPFMYRIHEDPNAEK 479
Cdd:TIGR02063 400 YKILRKKRKKRGAIDFDSKEAKIILDENGKPIDIVPRERGDAHKLIEEFMIAANETVAEHLEKAKLPFIYRVHERPSEEK 479

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  480 LMAFMEFITNFGYSIRGKG-NSVHPRALQQLLEEVKGTPEEIIISTVMLRSMKQARYDAESLGHYGLSTEFYTHFTSPIR 558
Cdd:TIGR02063 480 LQNLREFLKTLGITLKGGTsDKPQPKDFQKLLEKVKGRPEEELINTVLLRSMQQAKYSPENIGHFGLALEYYTHFTSPIR 559

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  559 RYPDLIVHRRIREWIELG-NQISEKRLGYWAEQMPVIAEHASQRERLAVDAERETDDLKKAEFMLERVGEEFEGVISSVT 637
Cdd:TIGR02063 560 RYPDLIVHRLIKKALFGGeNTTTEKEREYLEAKLEEIAEHSSKTERRADEAERDVNDWKKAEYMSEKIGEEFEGVISGVT 639

                         650       660       670       680       690       700       710
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  638 SFGIFVELPN-TIEGLVHVSFLTDDYYHYHEKMFALVGERTGKQYRIGDVVEVRVANVNVDERTIDFEIV 706
Cdd:TIGR02063 640 SFGLFVELENnTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTGKIDFELV 709
PRK11642 PRK11642
ribonuclease R;
4-784 0e+00

ribonuclease R;


Pssm-ID: 236944 [Multi-domain]  Cd Length: 813  Bit Score: 547.03  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791   4 QEKILAFMREQAyHPMTVRELEEAFGIKDSATFKELVKTLNALEASGEVIRTRANRYGVPEKMNLVRGRLQSHPKGFGFV 83
Cdd:PRK11642  21 REFILEHLTKRE-KPASREELAVELNIEGEEQLEALRRRLRAMERDGQLVFTRRQCYALPERLDLLKGTVIGHRDGYGFL 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  84 IPETQgMEDVYVHANDMNGALHGDTVLVRVEKEAGGNRLEGQIIRIVERGMKQVVGTFKDETYYAFVIPDEKRLGKDIFI 163
Cdd:PRK11642 100 RVEGR-KDDLYLSSEQMKTCIHGDQVLAQPLGADRKGRREARIVRVLVPKTSQIVGRYFTDAGVGFVVPDDSRLSFDILI 178

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 164 PKEAYNGAVDGHKVVVNIVRYPEGRVNPEGEVVEILGHKNDPGVDILSIIRKFNLPEAFPDDVLEEAEAAPDEISEEEIS 243
Cdd:PRK11642 179 PPEQIMGARMGFVVVVELTQRPTRRTKAVGKIVEVLGDNMGTGMAVDIALRTHEIPYIWPQAVEQQVAGLKEEVPEEAKA 258

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 244 GRRDLRERMMVTIDGADAKDLDDAVSLERLPNGNVRLGVHIADVSYYVREKSQLDNEAYRRGTSVYLVDRVIPMLPHRLS 323
Cdd:PRK11642 259 GRVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPPTPLDREARNRGTSVYFPSQVVPMLPEVLS 338

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 324 NGICSLNPQVDRLTISCDMEMDSSGNTVKYDIFLSVIRTDERMTYADVRSILeDKDEALTEKYSRLVPMFEDMKELALKL 403
Cdd:PRK11642 339 NGLCSLNPQVDRLCMVCEMTISSKGRLTGYKFYEAVMSSHARLTYTKVWHIL-QGDQDLREQYAPLVKHLEELHNLYKVL 417

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 404 RKKRMQRGAIDFDFREAKIYVDEEGTPTEIGFRTRSIAEQIIEEFMLAANETVAEHFHWMKQPFMYRIHEDPNAEKLMAF 483
Cdd:PRK11642 418 DKAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFVEKAKEPALFRIHDKPSTEAITSF 497

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 484 MEFITNFGYSIRGkGNSVHPRALQQLLEEVKGTPEEIIISTVMLRSMKQARYDAESLGHYGLSTEFYTHFTSPIRRYPDL 563
Cdd:PRK11642 498 RSVLAELGLELPG-GNKPEPRDYAELLESVADRPDAEMLQTMLLRSMKQAIYDPENRGHFGLALQSYAHFTSPIRRYPDL 576

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 564 IVHRRIREWI--ELGNQISEKRLGYW---AEQMPVIAEHASQRERLAVDAERETDDLKKAEFMLERVGEEFEGVISSVTS 638
Cdd:PRK11642 577 SLHRAIKYLLakEQGHKGNTTETGGYhysMEEMLQLGQHCSMTERRADEATRDVADWLKCDFMLDQVGNVFKGVISSVTG 656

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 639 FGIFVELPNT-IEGLVHVSFLTDDYYHYHEKMFALVGERTGKQYRIGDVVEVRVANVNVDERTIDFEIVGM---PKAGFR 714
Cdd:PRK11642 657 FGFFVRLDDLfIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDERKIDFSLISSeraPRNVGK 736

                        730       740       750       760       770       780       790
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 850385791 715 GSRERTPRVIDGRGGDRKPTRGKQDRSRAGRADRPDRPDRQKDKKHPAEIRQKYKDR-RKAEGNKPPRRAG 784
Cdd:PRK11642 737 TAREKAKKGDAGKKGGKRRQVGKKVNFEPDSAFRGEKKAKPKAAKKDARKAKKPSAKtQKIAAATKAKRAA 807
RNB pfam00773
RNB domain; This domain is the catalytic domain of ribonuclease II.
 245-573 1.29e-133

RNB domain; This domain is the catalytic domain of ribonuclease II.


Pssm-ID: 459934 [Multi-domain]  Cd Length: 314  Bit Score: 400.51  E-value: 1.29e-133
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  245 RRDLRERMMVTIDGADAKDLDDAVSLERLPNGNVRLGVHIADVSYYVREKSQLDNEAYRRGTSVYLVDRVIPMLPHRLSN 324
Cdd:pfam00773   1 RKDLRDLPFITIDPADAKDLDDAISVEKLPNGGYRLGVHIADVSHYVPPGSPLDREARKRGTSVYLPDRVIPMLPEKLSN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  325 GICSLNPQVDRLTISCDMEMDSSGNTVKYDIFLSVIRTDERMTYADVRSILEDKDEALTEKysRLVPMFEDMKELALKLR 404
Cdd:pfam00773  81 DLCSLNPGEDRLALSVEITIDADGEVTSYEIYPSVIRSKARLTYEEVDDLLEGKDAEKDKP--DLAEDLRLLYELAKILR 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  405 KKRMQRGAIDFDFREAKIYVDEEGtPTEIGFRTRSIAEQIIEEFMLAANETVAEHFHWMKQPFMYRIHEDPNAEKLMAFM 484
Cdd:pfam00773 159 AKRLQRGALDLDTPENKLILDEEG-VIDILIQERTDAHSLIEEFMLLANEAVARHLQELGIPALYRVHPEPDLEKLNSLI 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  485 EFItnfgysirgkGNSVHPRALQQLLEEVKGtpEEIIISTVMLRSMKQARYDAESLGHYGLSTEFYTHFTSPIRRYPDLI 564
Cdd:pfam00773 238 KLL----------QLLPDDKGLSKSLEKIKD--DERLLSILLLRTMPRAEYSPEPLGHFGLGLDIYTHFTSPIRRYPDLI 305


                  ....*....
gi 850385791  565 VHRRIREWI 573
Cdd:pfam00773 306 VHRQLKALL 314
RNB smart00955
This domain is the catalytic domain of ribonuclease II;
245-573 1.37e-129

This domain is the catalytic domain of ribonuclease II;


Pssm-ID: 214935 [Multi-domain]  Cd Length: 286  Bit Score: 388.93  E-value: 1.37e-129
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791   245 RRDLRERMMVTIDGADAKDLDDAVSLERLPNGNVRLGVHIADVSYYVREKSQLDNEAYRRGTSVYLVDRVIPMLPHRLSN 324
Cdd:smart00955   1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLDNGGYRLGVHIADVSHYVKPGSALDREARKRGTSVYLPDRVIPMLPEELSN 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791   325 GICSLNPQVDRLTISCDMEMDSSGNTVK-YDIFLSVIRTDERMTYADVRSILEdkdealtekysrlvpmfedmkelalkl 403
Cdd:smart00955  81 GLCSLNPGEDRLALSVEMTLDADGGEILdYEFYRSVIRSKARLTYEEVDAILE--------------------------- 133

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791   404 rkkrmqrgaidfdfreaKIYVDEEGTPTEIGFRTRSIAEQIIEEFMLAANETVAEHFHWMKQPFMYRIHEDPNAEKLMAF 483
Cdd:smart00955 134 -----------------KIVLDEEGKIEDIVPRERNDAHSLVEEFMILANEAVARFLAKNGIPGLYRVHEGPDPEKLAEL 196

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791   484 M-EFITNFGYSIRGKGNsvhPRALQQLLEEVKGTPEEIIISTVMLRSMKQARYDAESLGHYGLSTEFYTHFTSPIRRYPD 562
Cdd:smart00955 197 LkEFLALLGLLLLGGDG---PKALAKLLEKIRDSPEERLLELLLLRSMPHAEYSVDNSGHFGLALDAYTHFTSPIRRYPD 273

                          330
                   ....*....|.
gi 850385791   563 LIVHRRIREWI 573
Cdd:smart00955 274 LIVHRQLKAAL 284
S1_RNase_R cd04471
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ...
 625-706 1.18e-41

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: 146.78  E-value: 1.18e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 625 VGEEFEGVISSVTSFGIFVELPN-TIEGLVHVSFLTDDYYHYHEKMFALVGERTGKQYRIGDVVEVRVANVNVDERTIDF 703
Cdd:cd04471    1 VGEEFDGVISGVTSFGLFVELDNlTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDF 80


                 ...
gi 850385791 704 EIV 706
Cdd:cd04471   81 ELV 83
 
Name Accession Description Interval E-value
VacB COG0557
Exoribonuclease R [Transcription];
2-712 0e+00

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 1142.53  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791   2 EDQEKILAFMREQAYHPMTVRELEEAFGIKDSATFKELVKTLNALEASGEVIRTRANRYGVPEKMNLVRGRLQSHPKGFG 81
Cdd:COG0557    3 NSRETILAFLKEDAYKPLSKKELAKALGLKDEESREALKRRLRALEREGQLVKTRRGRYRLPEKLDLVEGRVRGHRDGFG 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  82 FVIPEtQGMEDVYVHANDMNGALHGDTVLVRVEKEAGGNRLEGQIIRIVERGMKQVVGTFKDETYYAFVIPDEKRLGKDI 161
Cdd:COG0557   83 FVIPD-DGEEDIFIPPRELNGALHGDRVLVRVTKEDRRGRPEGRVVEILERANTRVVGRFEKEKGFGFVVPDDKRLLQDI 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 162 FIPKEAYNGAVDGHKVVVNIVRYPEGRVNPEGEVVEILGHKNDPGVDILSIIRKFNLPEAFPDDVLEEAEAAPDEISEEE 241
Cdd:COG0557  162 FIPPDDLNGAKDGDLVVVEITRYPERRGPPEGRVVEVLGSPGDPGAEILIAIRKHGLPHEFPEEVLAEAEALPDEVPEAD 241

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 242 ISGRRDLRERMMVTIDGADAKDLDDAVSLERLPNGNVRLGVHIADVSYYVREKSQLDNEAYRRGTSVYLVDRVIPMLPHR 321
Cdd:COG0557  242 LKGRRDLRDLPLVTIDGEDAKDFDDAVSAEKLDNGGWRLGVHIADVSHYVRPGSALDREARKRGTSVYLPDRVIPMLPER 321

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 322 LSNGICSLNPQVDRLTISCDMEMDSSGNTVKYDIFLSVIRTDERMTYADVRSILEDKDEALTEKYSRLVPMFEDMKELAL 401
Cdd:COG0557  322 LSNGLCSLNPGEDRLAMSCEMEIDAKGEVVSYEFYRSVIRSDARLTYEEVQAILDGKDEELREEYADLVPMLEELYELAK 401

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 402 KLRKKRMQRGAIDFDFREAKIYVDEEGTPTEIGFRTRSIAEQIIEEFMLAANETVAEHFHWMKQPFMYRIHEDPNAEKLM 481
Cdd:COG0557  402 ILRKAREKRGAIDFDLPETKIILDEEGKPEDIVPRERNDAHKLIEEFMLLANEAVAEFLEKLKLPFLYRVHEEPDPEKLE 481

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 482 AFMEFITNFGYSIRGkGNSVHPRALQQLLEEVKGTPEEIIISTVMLRSMKQARYDAESLGHYGLSTEFYTHFTSPIRRYP 561
Cdd:COG0557  482 ALREFLANLGLKLKG-GDEPTPKDLQKLLEQVKGRPEEELLNTLLLRSMKQAVYSPENIGHFGLALEAYTHFTSPIRRYP 560

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 562 DLIVHRRIREWieLGNQISEKRLGYWAEQMPVIAEHASQRERLAVDAERETDDLKKAEFMLERVGEEFEGVISSVTSFGI 641
Cdd:COG0557  561 DLLVHRALKAY--LEGKRSPGLQEYLEEELEEIAEHCSETERRADEAERDVVDLKKAEYMKDRVGEEFEGVISGVTSFGL 638

                        650       660       670       680       690       700       710
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 850385791 642 FVELPNT-IEGLVHVSFLTDDYYHYHEKMFALVGERTGKQYRIGDVVEVRVANVNVDERTIDFEIVGMPKAG 712
Cdd:COG0557  639 FVELDELgVEGLVHVSSLGDDYYEYDERRQALVGERTGKRYRLGDRVEVRVVRVDLDRRQIDFELVEGGSEA 710
RNase_R TIGR02063
ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. ...
 1-706 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: 969.82  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791    1 MEDQEKILAFMREQAYHPMTVRELEEAFGIKDSATFKELVKTLNALEASGEVIRTRANRYGVPEKMNLVRGRLQSHPKGF 80
Cdd:TIGR02063   1 SPLRELILEFLKSKKGKPISLKELAKAFHLKGADEKKALRKRLRALEDDGLVKKNRRGLYALPESLKLVKGTVIAHRDGF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791   81 GFVIPETQGMEDVYVHANDMNGALHGDTVLVRV-EKEAGGNRLEGQIIRIVERGMKQVVGTFKDETYYAFVIPDEKRLGK 159
Cdd:TIGR02063  81 GFLRPEDDDEDDIFIPPRQMNGAMHGDRVLVRItGKPDGGDRFEARVIKILERANDQIVGTFYIENGIGFVIPDDKRIYL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  160 DIFIPKEAYNGAVDGHKVVVNIVRYPEGRVNPEGEVVEILGHKNDPGVDILSIIRKFNLPEAFPDDVLEEAEAAPDEISE 239
Cdd:TIGR02063 161 DIFIPPEQILGAEEGDKVLVEITKYPDRNRPAIGKVVEILGHADDPGIDILIIIRKHGIPYEFPEEVLDEAAKIPEEVPE 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  240 EEISGRRDLRERMMVTIDGADAKDLDDAVSLERLPNGNVRLGVHIADVSYYVREKSQLDNEAYRRGTSVYLVDRVIPMLP 319
Cdd:TIGR02063 241 EEIKGRKDLRDLPFVTIDGEDAKDFDDAVYVEKLKDGNYKLGVAIADVSHYVREGSALDKEALKRGTSVYLPDRVIPMLP 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  320 HRLSNGICSLNPQVDRLTISCDMEMDSSGNTVKYDIFLSVIRTDERMTYADVRSILEDKDeALTEKYSRLVPMFEDMKEL 399
Cdd:TIGR02063 321 ERLSNGICSLNPNEDRLTLSCEMEIDKKGRVKKYEFYEAVINSHARLTYNQVNDIIEGKD-ALDKKEPPLKEMLKNLFEL 399

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  400 ALKLRKKRMQRGAIDFDFREAKIYVDEEGTPTEIGFRTRSIAEQIIEEFMLAANETVAEHFHWMKQPFMYRIHEDPNAEK 479
Cdd:TIGR02063 400 YKILRKKRKKRGAIDFDSKEAKIILDENGKPIDIVPRERGDAHKLIEEFMIAANETVAEHLEKAKLPFIYRVHERPSEEK 479

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  480 LMAFMEFITNFGYSIRGKG-NSVHPRALQQLLEEVKGTPEEIIISTVMLRSMKQARYDAESLGHYGLSTEFYTHFTSPIR 558
Cdd:TIGR02063 480 LQNLREFLKTLGITLKGGTsDKPQPKDFQKLLEKVKGRPEEELINTVLLRSMQQAKYSPENIGHFGLALEYYTHFTSPIR 559

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  559 RYPDLIVHRRIREWIELG-NQISEKRLGYWAEQMPVIAEHASQRERLAVDAERETDDLKKAEFMLERVGEEFEGVISSVT 637
Cdd:TIGR02063 560 RYPDLIVHRLIKKALFGGeNTTTEKEREYLEAKLEEIAEHSSKTERRADEAERDVNDWKKAEYMSEKIGEEFEGVISGVT 639

                         650       660       670       680       690       700       710
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  638 SFGIFVELPN-TIEGLVHVSFLTDDYYHYHEKMFALVGERTGKQYRIGDVVEVRVANVNVDERTIDFEIV 706
Cdd:TIGR02063 640 SFGLFVELENnTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTGKIDFELV 709
3_prime_RNase TIGR00358
VacB and RNase II family 3'-5' exoribonucleases; This model is defined to identify a pair of ...
 59-706 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: 755.78  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791   59 RYGVPEKMNLVRGRLQSHPKGFGFVIPETQGMEDVYVHANDMNGALHGDTVLVRVEKEAGGNRLEGQIIRIVERGMKQVV 138
Cdd:TIGR00358   7 KYALPEKDDLVKGVVKAHNKGFGFLRPDDDDKKDYFIPPPQMKKVMHGDLVEACPLSQPQRGRFEAEVERILEPALTRFV 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  139 GTFKDETYYAFVIPDEKRLGKDIFIPKEAY-NGAVDGHKVVVNIVRYPEGRVNPEGEVVEILGHKNDPGVDILSIIRKFN 217
Cdd:TIGR00358  87 GKFLGENDFGFVVPDDPRIYLDIIVPKASVkNELAEGDKVVVELTEYPLRRNLFYGEITQILGNNDDPLIPWWVTLARHE 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  218 LPEAFPDDVLEEAEAAPDEISEEEISGRRDLRERMMVTIDGADAKDLDDAVSLERLPNGNVRLGVHIADVSYYVREKSQL 297
Cdd:TIGR00358 167 IPFEFPDGVEQQAAKLQFDVDEQAKKYREDLTDLAFVTIDGADAKDLDDAVYVKKLPDGGWKLYVAIADVSYYVAENSPL 246

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  298 DNEAYRRGTSVYLVDRVIPMLPHRLSNGICSLNPQVDRLTISCDMEMDSSGNTVKYDIFLSVIRTDERMTYADVRSILED 377
Cdd:TIGR00358 247 DKEAKHRGFSVYLPGFVIPMLPEELSNGLCSLNPNEDRLVLVCEMTISAQGRITDNEFYPATIESKARLTYDKVNDWLEN 326

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  378 KDEaLTEKYSRLVPMFEDMKELALKLRKKRMQRGAIDFDFREAKIYVDEEGTPTEIGFRTRSIAEQIIEEFMLAANETVA 457
Cdd:TIGR00358 327 DDE-LQPEYETLVEQLKALHQLSQALGEWRHKRGLIDFEHPETKFIVDEEGRVIDIVAEVRRIAEKIIEEAMIVANICAA 405

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  458 EHFHWMKQPFMYRIHEDPNAEKLMAFMEFITNFGYSI-RGKGNSVHPRALQQLLEEVKGTPEEIIISTVMLRSMKQARYD 536
Cdd:TIGR00358 406 RFLHNHKVPGIYRVHPGPSKKKLQSLLEFLAELGLTLpGGNAENVTTLDGACWLREVKDRPEYEILVTRLLRSLSQAEYS 485

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  537 AESLGHYGLSTEFYTHFTSPIRRYPDLIVHRRIreWIELGNQISEKRLGYWAEQMPVIAEHASQRERLAVDAERETDDLK 616
Cdd:TIGR00358 486 PEPLGHFGLGLEHYAHFTSPIRRYPDLTNHRLI--KAVLAKEQTDTERYQPQDELLQIAEHCSDTERRARDAERDVADWL 563

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  617 KAEFMLERVGEEFEGVISSVTSFGIFVELP-NTIEGLVHVSFLTDDYYHYHEKMFALVGERTGKQYRIGDVVEVRVANVN 695
Cdd:TIGR00358 564 KCRYLLDKVGTEFSGEISSVTRFGMFVRLDdNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVN 643

                         650
                  ....*....|.
gi 850385791  696 VDERTIDFEIV 706
Cdd:TIGR00358 644 METRSIIFELV 654
PRK11642 PRK11642
ribonuclease R;
4-784 0e+00

ribonuclease R;


Pssm-ID: 236944 [Multi-domain]  Cd Length: 813  Bit Score: 547.03  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791   4 QEKILAFMREQAyHPMTVRELEEAFGIKDSATFKELVKTLNALEASGEVIRTRANRYGVPEKMNLVRGRLQSHPKGFGFV 83
Cdd:PRK11642  21 REFILEHLTKRE-KPASREELAVELNIEGEEQLEALRRRLRAMERDGQLVFTRRQCYALPERLDLLKGTVIGHRDGYGFL 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  84 IPETQgMEDVYVHANDMNGALHGDTVLVRVEKEAGGNRLEGQIIRIVERGMKQVVGTFKDETYYAFVIPDEKRLGKDIFI 163
Cdd:PRK11642 100 RVEGR-KDDLYLSSEQMKTCIHGDQVLAQPLGADRKGRREARIVRVLVPKTSQIVGRYFTDAGVGFVVPDDSRLSFDILI 178

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 164 PKEAYNGAVDGHKVVVNIVRYPEGRVNPEGEVVEILGHKNDPGVDILSIIRKFNLPEAFPDDVLEEAEAAPDEISEEEIS 243
Cdd:PRK11642 179 PPEQIMGARMGFVVVVELTQRPTRRTKAVGKIVEVLGDNMGTGMAVDIALRTHEIPYIWPQAVEQQVAGLKEEVPEEAKA 258

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 244 GRRDLRERMMVTIDGADAKDLDDAVSLERLPNGNVRLGVHIADVSYYVREKSQLDNEAYRRGTSVYLVDRVIPMLPHRLS 323
Cdd:PRK11642 259 GRVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPPTPLDREARNRGTSVYFPSQVVPMLPEVLS 338

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 324 NGICSLNPQVDRLTISCDMEMDSSGNTVKYDIFLSVIRTDERMTYADVRSILeDKDEALTEKYSRLVPMFEDMKELALKL 403
Cdd:PRK11642 339 NGLCSLNPQVDRLCMVCEMTISSKGRLTGYKFYEAVMSSHARLTYTKVWHIL-QGDQDLREQYAPLVKHLEELHNLYKVL 417

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 404 RKKRMQRGAIDFDFREAKIYVDEEGTPTEIGFRTRSIAEQIIEEFMLAANETVAEHFHWMKQPFMYRIHEDPNAEKLMAF 483
Cdd:PRK11642 418 DKAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFVEKAKEPALFRIHDKPSTEAITSF 497

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 484 MEFITNFGYSIRGkGNSVHPRALQQLLEEVKGTPEEIIISTVMLRSMKQARYDAESLGHYGLSTEFYTHFTSPIRRYPDL 563
Cdd:PRK11642 498 RSVLAELGLELPG-GNKPEPRDYAELLESVADRPDAEMLQTMLLRSMKQAIYDPENRGHFGLALQSYAHFTSPIRRYPDL 576

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 564 IVHRRIREWI--ELGNQISEKRLGYW---AEQMPVIAEHASQRERLAVDAERETDDLKKAEFMLERVGEEFEGVISSVTS 638
Cdd:PRK11642 577 SLHRAIKYLLakEQGHKGNTTETGGYhysMEEMLQLGQHCSMTERRADEATRDVADWLKCDFMLDQVGNVFKGVISSVTG 656

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 639 FGIFVELPNT-IEGLVHVSFLTDDYYHYHEKMFALVGERTGKQYRIGDVVEVRVANVNVDERTIDFEIVGM---PKAGFR 714
Cdd:PRK11642 657 FGFFVRLDDLfIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDERKIDFSLISSeraPRNVGK 736

                        730       740       750       760       770       780       790
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 850385791 715 GSRERTPRVIDGRGGDRKPTRGKQDRSRAGRADRPDRPDRQKDKKHPAEIRQKYKDR-RKAEGNKPPRRAG 784
Cdd:PRK11642 737 TAREKAKKGDAGKKGGKRRQVGKKVNFEPDSAFRGEKKAKPKAAKKDARKAKKPSAKtQKIAAATKAKRAA 807
RNB pfam00773
RNB domain; This domain is the catalytic domain of ribonuclease II.
 245-573 1.29e-133

RNB domain; This domain is the catalytic domain of ribonuclease II.


Pssm-ID: 459934 [Multi-domain]  Cd Length: 314  Bit Score: 400.51  E-value: 1.29e-133
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  245 RRDLRERMMVTIDGADAKDLDDAVSLERLPNGNVRLGVHIADVSYYVREKSQLDNEAYRRGTSVYLVDRVIPMLPHRLSN 324
Cdd:pfam00773   1 RKDLRDLPFITIDPADAKDLDDAISVEKLPNGGYRLGVHIADVSHYVPPGSPLDREARKRGTSVYLPDRVIPMLPEKLSN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  325 GICSLNPQVDRLTISCDMEMDSSGNTVKYDIFLSVIRTDERMTYADVRSILEDKDEALTEKysRLVPMFEDMKELALKLR 404
Cdd:pfam00773  81 DLCSLNPGEDRLALSVEITIDADGEVTSYEIYPSVIRSKARLTYEEVDDLLEGKDAEKDKP--DLAEDLRLLYELAKILR 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  405 KKRMQRGAIDFDFREAKIYVDEEGtPTEIGFRTRSIAEQIIEEFMLAANETVAEHFHWMKQPFMYRIHEDPNAEKLMAFM 484
Cdd:pfam00773 159 AKRLQRGALDLDTPENKLILDEEG-VIDILIQERTDAHSLIEEFMLLANEAVARHLQELGIPALYRVHPEPDLEKLNSLI 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  485 EFItnfgysirgkGNSVHPRALQQLLEEVKGtpEEIIISTVMLRSMKQARYDAESLGHYGLSTEFYTHFTSPIRRYPDLI 564
Cdd:pfam00773 238 KLL----------QLLPDDKGLSKSLEKIKD--DERLLSILLLRTMPRAEYSPEPLGHFGLGLDIYTHFTSPIRRYPDLI 305


                  ....*....
gi 850385791  565 VHRRIREWI 573
Cdd:pfam00773 306 VHRQLKALL 314
RNB smart00955
This domain is the catalytic domain of ribonuclease II;
245-573 1.37e-129

This domain is the catalytic domain of ribonuclease II;


Pssm-ID: 214935 [Multi-domain]  Cd Length: 286  Bit Score: 388.93  E-value: 1.37e-129
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791   245 RRDLRERMMVTIDGADAKDLDDAVSLERLPNGNVRLGVHIADVSYYVREKSQLDNEAYRRGTSVYLVDRVIPMLPHRLSN 324
Cdd:smart00955   1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLDNGGYRLGVHIADVSHYVKPGSALDREARKRGTSVYLPDRVIPMLPEELSN 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791   325 GICSLNPQVDRLTISCDMEMDSSGNTVK-YDIFLSVIRTDERMTYADVRSILEdkdealtekysrlvpmfedmkelalkl 403
Cdd:smart00955  81 GLCSLNPGEDRLALSVEMTLDADGGEILdYEFYRSVIRSKARLTYEEVDAILE--------------------------- 133

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791   404 rkkrmqrgaidfdfreaKIYVDEEGTPTEIGFRTRSIAEQIIEEFMLAANETVAEHFHWMKQPFMYRIHEDPNAEKLMAF 483
Cdd:smart00955 134 -----------------KIVLDEEGKIEDIVPRERNDAHSLVEEFMILANEAVARFLAKNGIPGLYRVHEGPDPEKLAEL 196

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791   484 M-EFITNFGYSIRGKGNsvhPRALQQLLEEVKGTPEEIIISTVMLRSMKQARYDAESLGHYGLSTEFYTHFTSPIRRYPD 562
Cdd:smart00955 197 LkEFLALLGLLLLGGDG---PKALAKLLEKIRDSPEERLLELLLLRSMPHAEYSVDNSGHFGLALDAYTHFTSPIRRYPD 273

                          330
                   ....*....|.
gi 850385791   563 LIVHRRIREWI 573
Cdd:smart00955 274 LIVHRQLKAAL 284
Rnb COG4776
Exoribonuclease II [Transcription];
69-701 4.40e-61

Exoribonuclease II [Transcription];


Pssm-ID: 443808 [Multi-domain]  Cd Length: 644  Bit Score: 218.57  E-value: 4.40e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  69 VRGRLQSHPKGFGFVipETQGMEDVYVHANDMNGALHGDTV--LVRVEKEaggnRLEGQIIRIVERGMKQVVG--TFKDE 144
Cdd:COG4776   22 VEGVVKATDKGFGFL--EVDDQKSYFIPPPQMKKVMHGDRIkaVIRTEKD----KESAEPETLIEPFLTRFVGrvQKKDG 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 145 tyYAFVIPDEKRLGKDIFIP-----KEAYNgavDGHKVVVNIVRYP-EGRVNPEGEVVEILGHKNDPGVDILSIIRKFNL 218
Cdd:COG4776   96 --RLFVVPDHPLIKDAIKARpkkglEEGLK---EGDWVVAELKRHPlKGDRGFFAEITEFIADADDPFAPWWVTLARHNL 170

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 219 PEAFPDDvleeaeAAPDEISEEEISgRRDLRERMMVTIDGADAKDLDDAVSLERLPNGNVRLGVHIADVSYYVREKSQLD 298
Cdd:COG4776  171 EREAPEG------DDEWELLDEGLE-REDLTALPFVTIDSESTEDMDDALYIEKLENGGWKLTVAIADPTAYIPEGSELD 243

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 299 NEAYRRGTSVYLVDRVIPMLPHRLSNGICSLNPQVDRLTISCDMEMDSSGNTV-KYDIFLSVIRTDERMTYADVRSILED 377
Cdd:COG4776  244 KEARQRAFTNYLPGFNIPMLPRELSDDLCSLKENEKRPALVCRVTIDADGSIGdDIEFFAAWIRSKAKLAYDNVSDWLEG 323

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 378 KDEaltekysrLVPMFED-------MKELALKLRKKRMQRGAIdfdFREAKIY---VDEEGTPTEIGFRTRSIAEQIIEE 447
Cdd:COG4776  324 KGE--------WQPENEEiaeqirlLHQFALARSQWRQQHALV---FKDRPDYrfeLDEKGNVLDIHAEPRRIANRIVEE 392

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 448 FMLAAN----ETVAEHFHWMkqpfMYRIHEDPNAEKLMAFMEFITNFGysIRGKGNSVHP----RALQQLLEEVKGTPEE 519
Cdd:COG4776  393 AMIAANicaaRVLREHLGFG----IFNVHSGFDPEKLEQAVELLAEHG--IEFDPEQLLTlegfCALRRELDAQPTSYLD 466

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 520 iiistVMLRSMKQ-ARYDAESLGHYGLSTEFYTHFTSPIRRYPDLIVHRRIREWI--ELGNQISEKrlgywaeqmpvIAE 596
Cdd:COG4776  467 -----SRLRRFQTfAEISTEPGPHFGLGLDAYATWTSPIRKYGDMVNHRLIKAVIlgQPAEKPDEE-----------LTE 530

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 597 HASQRERLAVDAERETDDLKKAEFMLERVGEE--FEGVISSVTSFGIFVELP-NTIEGLVHVSFLTDDyyhyheKMFALV 673
Cdd:COG4776  531 RLAERRRLNRMAERDVADWLYARYLKPKVGSGqvFTAEIIDINRGGLRVRLLeNGAVAFIPASFIHSV------RDELVC 604

                        650       660       670
                 ....*....|....*....|....*....|....*
gi 850385791 674 GERTG-------KQYRIGDVVEVRVANVNVDERTI 701
Cdd:COG4776  605 SQEEGtvyikgeVRYKLGDTIQVTLAEVREETRSI 639
PRK05054 PRK05054
exoribonuclease II; Provisional
 69-709 4.16e-48

exoribonuclease II; Provisional


Pssm-ID: 179920 [Multi-domain]  Cd Length: 644  Bit Score: 181.23  E-value: 4.16e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  69 VRGRLQSHPKGFGFVipETQGMEDVYVHANDMNGALHGDTV--LVRVEKEaggnRLEGQIIRIVERGMKQVVGT--FKDE 144
Cdd:PRK05054  22 VEGVVKATEKGFGFL--EVDAQKSYFIPPPQMKKVMHGDRIiaVIHTEKD----REIAEPEELIEPFLTRFVGRvqKKDD 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 145 TYyaFVIPDEKRLgKDiFIPKEAYNGAV----DGHKVVVNIVRYP-EGRVNPEGEVVEILGHKNDPGVDILSIIRKFNLP 219
Cdd:PRK05054  96 RL--SIVPDHPLL-KD-AIPCRAAKGLNhefkEGDWVVAELRRHPlKGDRGFYAEITQFITDADDHFAPWWVTLARHNLE 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 220 EAFPDDvleeaeAAPDEISEEEISgRRDLRERMMVTIDGADAKDLDDAVSLERLPNGNVRLGVHIADVSYYVREKSQLDN 299
Cdd:PRK05054 172 REAPAG------GVAWEMLDEGLE-REDLTALDFVTIDSASTEDMDDALYVEKLPDGGLQLTVAIADPTAYIAEGSKLDK 244

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 300 EAYRRGTSVYLVDRVIPMLPHRLSNGICSLNPQVDRLTISCDMEMDSSGN-TVKYDIFLSVIRTDERMTYADVRSILEDK 378
Cdd:PRK05054 245 AARQRAFTNYLPGFNIPMLPRELSDDLCSLRPNERRPALACRVTIDADGTiEDDIRFFAAWIESKAKLAYDNVSDWLENG 324

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 379 ------DEALTEKYSRLvpmfedmKELALKLRKKRMQRGAI-----DFDFReakiyVDEEGTPTEIGFRTRSIAEQIIEE 447
Cdd:PRK05054 325 gdwqpeSEAIAEQIRLL-------HQFCLARSEWRKQHALVfkdrpDYRFE-----LGEKGEVLDIVAEPRRIANRIVEE 392

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 448 FMLAAN----ETVAEHFHwmkqpF-MYRIHEDPNAEKLMAFMEFITNFGysirgkgnsvhpralqqlleeVKGTPEEI-- 520
Cdd:PRK05054 393 SMIAANicaaRVLRDKLG-----FgIYNVHSGFDPANAEQAVALLKEHG---------------------LHFDAEELlt 446

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 521 ------------IISTVML-----RSMKQARYDAESLGHYGLSTEFYTHFTSPIRRYPDLIVHRRIREWI---------- 573
Cdd:PRK05054 447 legfcklrreldAQPTGYLdsrirRFQSFAEISTEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIkgetaerpqd 526

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 574 ELGNQISEKRlgywaeqmpviaehasQRERLavdAERETDDLKKAEFMLERVGEE--FEGVISSVTSFGIFVEL-PNTIE 650
Cdd:PRK05054 527 EITVQLAERR----------------RLNRM---AERDVGDWLYARYLKDKAGTDtrFAAEIIDISRGGMRVRLlENGAV 587

                        650       660       670       680       690       700
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 850385791 651 GLVHVSFLTDDyyhyHEKM--------FALVGERTgkqYRIGDVVEVRVANVNVDERTidfeIVGMP 709
Cdd:PRK05054 588 AFIPASFLHAV----RDELvcnqengtVQIKGETV---YKLGDVIDVTLAEVRMETRS----IIARP 643
S1_RNase_R cd04471
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ...
 625-706 1.18e-41

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: 146.78  E-value: 1.18e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 625 VGEEFEGVISSVTSFGIFVELPN-TIEGLVHVSFLTDDYYHYHEKMFALVGERTGKQYRIGDVVEVRVANVNVDERTIDF 703
Cdd:cd04471    1 VGEEFDGVISGVTSFGLFVELDNlTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDF 80


                 ...
gi 850385791 704 EIV 706
Cdd:cd04471   81 ELV 83
CSD2 pfam17876
Cold shock domain; Crystallographic structure analysis of E. coli wild-type RNase II revealed ...
 149-223 1.15e-35

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: 129.43  E-value: 1.15e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 850385791  149 FVIPDEKRLGKDIFIPKEAYNGAVDGHKVVVNIVRYPEGRvNPEGEVVEILGHKNDPGVDILSIIRKFNLPEAFP 223
Cdd:pfam17876   1 FVVPDDKRIPQDIFIPKEDLKGAKDGDKVVVEITEYPDGK-NPEGKIVEVLGDPGDPGVEILSIIRKHGLPHEFP 74
OB_RNB pfam08206
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease ...
 71-129 7.39e-19

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: 80.66  E-value: 7.39e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 850385791   71 GRLQSHPKGFGFVIPETqGMEDVYVHANDMNGALHGDTVLVRVEKEAGGNRLEGQIIRI 129
Cdd:pfam08206   1 GTVRGHKKGFGFLIPDD-EEDDIFIPPNQMKKAMHGDRVLVRITKGDRRGRREGRIVRI 58
S1_RpoE cd04460
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 630-713 3.41e-14

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: 68.85  E-value: 3.41e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 630 EGVISSVTSFGIFVELpNTIEGLVHVSFLTDDYYHYHEKMFALVGERTGKQYRIGDVVEVRVANVNVDERTIdfeivGMP 709
Cdd:cd04460    4 EGEVVEVVDFGAFVRI-GPVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRP-----RES 77


                 ....
gi 850385791 710 KAGF 713
Cdd:cd04460   78 KIGL 81
PRK08563 PRK08563
DNA-directed RNA polymerase subunit E'; Provisional
 630-701 3.46e-13

DNA-directed RNA polymerase subunit E'; Provisional


Pssm-ID: 236289 [Multi-domain]  Cd Length: 187  Bit Score: 68.70  E-value: 3.46e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 850385791 630 EGVISSVTSFGIFVEL-PntIEGLVHVSFLTDDYYHYHEKMFALVGERTGKQYRIGDVVEVRVANVNVDERTI 701
Cdd:PRK08563  86 EGEVVEVVEFGAFVRIgP--VDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRP 156
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
624-705 7.62e-13

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 64.16  E-value: 7.62e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791   624 RVGEEFEGVISSVTSFGIFVELPNTIEGLVHVSFLTDDYyhyhekmfalvGERTGKQYRIGDVVEVRVANVNVDERTIDF 703
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKR-----------VKDPEEVLKVGDEVKVKVLSVDEEKGRIIL 69


                   ..
gi 850385791   704 EI 705
Cdd:smart00316  70 SL 71
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 624-705 3.00e-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: 59.61  E-value: 3.00e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  624 RVGEEFEGVISSVTSFGIFVELPNTIEGLVHVSFLTDDYYhyhekmfalvgERTGKQYRIGDVVEVRVANVNVDERTIDF 703
Cdd:pfam00575   2 EKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHV-----------EDPDEVIKVGDEVKVKVLKVDKDRRRIIL 70


                  ..
gi 850385791  704 EI 705
Cdd:pfam00575  71 SI 72
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 625-701 1.37e-10

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 64.80  E-value: 1.37e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 850385791 625 VGEEFEGVISSVTSFGIFVELPNTIEGLVHVSFLTddyyhyHEKmfalVGERTGKQYRIGDVVEVRVANVNVDERTI 701
Cdd:PRK06299 373 VGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDIS------WDK----KGEEAVELYKKGDEVEAVVLKVDVEKERI 439
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 70-130 4.34e-10

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: 56.07  E-value: 4.34e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 850385791    70 RGRLQSHPKGFGFVIPETQGmEDVYVHAN----DMNGALHGDTVLVRVEKEAGGNRLEGQIIRIV 130
Cdd:smart00357   1 TGVVKWFNKGFGFIRPDDGG-KDVFVHPSqiqgGLKSLREGDEVEFKVVSPEGGEKPEAENVVKL 64
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 626-701 4.88e-09

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: 53.39  E-value: 4.88e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 850385791 626 GEEFEGVISSVTSFGIFVELPNTIEGLVHVSFLTDDYYHyhekmfalvgeRTGKQYRIGDVVEVRVANVNVDERTI 701
Cdd:cd05685    1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVS-----------HPSDVVSVGDIVEVKVISIDEERGRI 65
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 624-701 1.41e-08

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 58.25  E-value: 1.41e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 850385791 624 RVGEEFEGVISSVTSFGIFVELPNTIEGLVHVSFLTDDYyhyhekmfalvGERTGKQYRIGDVVEVRVANVNVDERTI 701
Cdd:PRK06299 459 KKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDR-----------VEDATEVLKVGDEVEAKVINIDRKNRRI 525
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 626-701 1.70e-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: 51.73  E-value: 1.70e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 850385791 626 GEEFEGVISSVTSFGIFVELPNTIEGLVHVSFLTddyyhyhekmFALVGERTGKQYRIGDVVEVRVANVNVDERTI 701
Cdd:cd05690    1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDIS----------WTQRVRHPSEIYKKGQEVEAVVLNIDVERERI 66
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 629-701 4.02e-08

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: 50.46  E-value: 4.02e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 850385791 629 FEGVISSVTSFGIFVELPNTIEGLVHVSFLTDDYYHYHEKMFalvgertgkqyRIGDVVEVRVANVNVDERTI 701
Cdd:cd00164    1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVF-----------KVGDEVEVKVLEVDPEKGRI 62
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 625-701 4.04e-08

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


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 56.21  E-value: 4.04e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 850385791 625 VGEEFEGVISSVTSFGIFVELPNTIEGLVHVSFLTddyyhYHEKMfalvgERTGKQYRIGDVVEVRVANVNVDERTI 701
Cdd:COG0539  274 VGDVVKGKVTRLTDFGAFVELEPGVEGLVHISEMS-----WTKRV-----AHPSDVVKVGDEVEVKVLDIDPEERRI 340
OB_RNB pfam08206
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease ...
 147-198 5.87e-08

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: 49.84  E-value: 5.87e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 850385791  147 YAFVIPDEKrlGKDIFIPKEAYNGAVDGHKVVVNIVRYPEGRvNPEGEVVEI 198
Cdd:pfam08206  10 FGFLIPDDE--EDDIFIPPNQMKKAMHGDRVLVRITKGDRRG-RREGRIVRI 58
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 624-699 8.16e-08

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 51.72  E-value: 8.16e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 850385791 624 RVGEEFEGVISSVTSFGIFVELPNTIEGLVHVSFLTDDYyhyhekmfalVGERtgKQY-RIGDVVEVRVanVNVDER 699
Cdd:COG1098    4 EVGDIVEGKVTGITPFGAFVELPEGTTGLVHISEIADGY----------VKDI--NDYlKVGDEVKVKV--LSIDED 66
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 625-699 8.37e-08

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 55.83  E-value: 8.37e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 850385791 625 VGEEFEGVISSVTSFGIFVELPNTIEGLVHVSfltddyyhyhekmfALVGERTGK---QYRIGDVVEVRVanVNVDER 699
Cdd:PRK11824 621 VGEIYEGKVVRIVDFGAFVEILPGKDGLVHIS--------------EIADERVEKvedVLKEGDEVKVKV--LEIDKR 682
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 624-705 1.17e-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: 55.13  E-value: 1.17e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  624 RVGEEFEGVISSVTSFGIFVELPNTIEGLVHVSFLTDDYYHYHEKMfalvgertgkqYRIGDVVEVRVANVNVDERTIDF 703
Cdd:TIGR00717 445 KVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDE-----------IKVGDEVEAKVVDIDKKNRKVSL 513


                  ..
gi 850385791  704 EI 705
Cdd:TIGR00717 514 SV 515
PRK08582 PRK08582
RNA-binding protein S1;
625-775 5.34e-07

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 49.65  E-value: 5.34e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 625 VGEEFEGVISSVTSFGIFVELPNTIEGLVHVSFLTDDYY---HYHEKmfalvgertgkqyrIGDVVEVRVANVNVDERtI 701
Cdd:PRK08582   5 VGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVkdiNDHLK--------------VGDEVEVKVLNVEDDGK-I 69

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 850385791 702 DFEIvgmpkagfrgsrertprvidgrggdRKPTrgkqdrsragradrpDRPDRQKDKKHPAEIRQKYKDRRKAE 775
Cdd:PRK08582  70 GLSI-------------------------KKAK---------------DRPKRQHDRPRHEDNRGGGNDVAPKE 103
Pnp COG1185
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ...
 625-699 7.68e-07

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


Pssm-ID: 440798 [Multi-domain]  Cd Length: 686  Bit Score: 52.70  E-value: 7.68e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 850385791 625 VGEEFEGVISSVTSFGIFVELPNTIEGLVHVSFLTDdyyhyhekmfalvgERTGK---QYRIGDVVEVRVanVNVDER 699
Cdd:COG1185  616 VGEIYEGKVVRIMDFGAFVEILPGKDGLVHISELAD--------------ERVEKvedVLKEGDEVKVKV--LEIDDQ 677
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 626-699 1.00e-06

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: 46.89  E-value: 1.00e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 850385791 626 GEEFEGVISSVTSFGIFVELPNTIEGLVHVSFLTDDYYhyhekmfalvgeRTGKQY-RIGDVVEVRVANVNVDER 699
Cdd:cd05692    1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRV------------KDVKDVlKEGDKVKVKVLSIDARGR 63
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 626-700 2.30e-06

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: 45.61  E-value: 2.30e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 850385791 626 GEEFEGVISSVTSFGIFVELPNTIEGLVHVSFLTDDYYhyhekmfalvgERTGKQYRIGDVVEVRVANVNVDERT 700
Cdd:cd04472    1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERV-----------EKVEDVLKVGDEVKVKVIEVDDRGRI 64
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 625-703 2.45e-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: 45.78  E-value: 2.45e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 625 VGEEFEGVISSVTSFGIFVELPNT-IEGLVHVSFLTDDyyhyhekmfalVGERTGKQYRIGDVVEVRVANVNVDERTIDF 703
Cdd:cd05708    2 VGQKIDGTVRRVEDYGVFIDIDGTnVSGLCHKSEISDN-----------RVADASKLFRVGDKVRAKVLKIDAEKKRISL 70
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 581-705 3.56e-06

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 50.87  E-value: 3.56e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 581 EKRLGYWAEQMPVIAEHASQRERLAVdaERETDDLKKAEFMLERVGEEFEGVISSVTSFGIFVELPNTIEGLVHVSfltd 660
Cdd:PRK12269 710 ELEVGKEIECMVIECDPQARRIRLGV--KQLSDNPWQVFANAYGVGSTVEGEVSSVTDFGIFVRVPGGVEGLVRKQ---- 783

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 850385791 661 dyyHYHEKMFALVGERTgKQYRIGDVVEVRVANVNVDERTIDFEI 705
Cdd:PRK12269 784 ---HLVENRDGDPGEAL-RKYAVGDRVKAVIVDMNVKDRKVAFSV 824
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 625-701 5.22e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 49.49  E-value: 5.22e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 850385791 625 VGEEFEGVISSVTSFGIFVELPNTIEGLVHVSFLTDDYY-HYHEKMfalvgertgkqyRIGDVVEVRVANVNVDERTI 701
Cdd:PRK06676 277 EGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHIaTPSEVL------------EEGQEVKVKVLEVNEEEKRI 342
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 602-656 1.38e-05

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: 48.12  E-value: 1.38e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 850385791 602 ERLAVDAERETddlKKAEFM--LErVGEEFEGVISSVTSFGIFVELPNtIEGLVHVS 656
Cdd:COG0539  168 RRAVLEEEREE---KREELLekLE-EGDVVEGTVKNITDFGAFVDLGG-VDGLLHIS 219
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 626-701 2.83e-05

S1_Rrp5_repeat_hs5: 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 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 42.61  E-value: 2.83e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 850385791 626 GEEFEGVISSVTSFGIFVELPNTIEGLVHVSFLTDDYYHYHEkmfalvgertgKQYRIGDVVEVRVANVNVDERTI 701
Cdd:cd05697    1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPE-----------KKFKPGLKVKCRVLSVEPERKRL 65
S1_RecJ_like cd04473
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ...
 624-706 4.94e-05

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: 42.21  E-value: 4.94e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 624 RVGEEFEGVISSVTSFGIFVELPNTIEGLVHVSFLtddyyhyhekmfalvgertGKQYRIGDVVEVRVANVNvDERTIDF 703
Cdd:cd04473   15 EVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNL-------------------LRDYEVGDEVIVQVTDIP-ENGNIDL 74


                 ...
gi 850385791 704 EIV 706
Cdd:cd04473   75 IPV 77
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 624-697 5.17e-05

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: 42.19  E-value: 5.17e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 850385791 624 RVGEEFEGVISSVTSFGIFVELPNTIEGLVHVSFLTDDYYhyhekmfalvgERTGKQYRIGDVVEVRVANVNVD 697
Cdd:cd04461   13 KPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFV-----------TDPSFGFKKGQSVTAKVTSVDEE 75
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
613-697 5.27e-05

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 46.94  E-value: 5.27e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 613 DDLKKAEFM-----LE--RVGEEFEGVISSVTSFGIFVElpntI----EGLVHVSFLTDDYY-HYHEkmfaLVgertgkq 680
Cdd:COG2183  622 PEFKTPTFRegvlkIEdlKPGMILEGTVTNVTDFGAFVD----IgvhqDGLVHISQLSDRFVkDPRE----VV------- 686

                         90
                 ....*....|....*..
gi 850385791 681 yRIGDVVEVRVANVNVD 697
Cdd:COG2183  687 -KVGDIVKVKVLEVDLK 702
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 625-701 5.98e-05

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


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 46.65  E-value: 5.98e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 850385791  625 VGEEFEGVISSVTSFGIFVELPNTIEGLVHVS--FLTDDyyhyhekmfalvGERTGKQYRIGDVVEVRVANVNVDERTI 701
Cdd:TIGR00717 359 VGDRVTGKIKKITDFGAFVELEGGIDGLIHLSdiSWDKD------------GREADHLYKKGDEIEAVVLAVDKEKKRI 425
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 625-701 9.94e-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: 45.88  E-value: 9.94e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 850385791  625 VGEEFEGVISSVTSFGIFVELPNTIEGLVHVSFLTDDYYHYHEKmfalvgertgKQYRIGDVVEVRVANVNVDERTI 701
Cdd:TIGR00717 272 VGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHPS----------KVVKKGDEVEVMILDIDPERRRL 338
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 625-701 1.47e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 45.16  E-value: 1.47e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 850385791 625 VGEEFEGVISSVTSFGIFVELPNTIEGLVHVSFLTDDYYHYHekmfalvgerTGKQYRIGDVVEVRVANVNVDERTI 701
Cdd:PRK06299 286 VGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSWTKKNKH----------PSKVVSVGQEVEVMVLEIDEEKRRI 352
OB_Dis3 pfam17849
Dis3-like cold-shock domain 2 (CSD2); This domain has an OB fold and is found in the Dis3l2 ...
 147-212 2.32e-04

Dis3-like cold-shock domain 2 (CSD2); This domain has an OB fold and is found in the Dis3l2 protein. This domain along with CSD1 binds to RNA.


Pssm-ID: 436091 [Multi-domain]  Cd Length: 77  Bit Score: 40.29  E-value: 2.32e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 850385791  147 YAFVIPDEKRL----------GKDIFIPKEAYngavDGHKVVVNIVRYPEGRVNPEGEVVEILGHKNDPGVDILSI 212
Cdd:pfam17849   1 YVLFVPRDKRIpririptksaPEEFLENPEDL----EGKLFVVKIDDWPENSRYPLGHIVKVLGEIGDIETETEAI 72
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 626-701 3.42e-04

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: 39.87  E-value: 3.42e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 850385791 626 GEEFEGVISSVTSFGIFVELPNTIEGLVHVSFLTDDYYHYHekmfalvgerTGKQYRIGDVVEVRVANVNVDERTI 701
Cdd:cd05689    4 GTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIH----------PSKVVSLGDEVEVMVLDIDEERRRI 69
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 625-656 4.60e-04

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: 39.15  E-value: 4.60e-04
                         10        20        30
                 ....*....|....*....|....*....|..
gi 850385791 625 VGEEFEGVISSVTSFGIFVELpNTIEGLVHVS 656
Cdd:cd05688    1 EGDVVEGTVKSITDFGAFVDL-GGVDGLLHIS 31
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 599-705 5.89e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 42.94  E-value: 5.89e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 599 SQRErlAVDAERETddlKKAEFM--LErVGEEFEGVISSVTSFGIFVELpNTIEGLVHVSFLTddyyhyHEKMfalvgER 676
Cdd:PRK06676 170 SRRA--VVEEERAA---KKEELLssLK-EGDVVEGTVARLTDFGAFVDI-GGVDGLVHISELS------HERV-----EK 231

                         90       100
                 ....*....|....*....|....*....
gi 850385791 677 TGKQYRIGDVVEVRVANVNVDERTIDFEI 705
Cdd:PRK06676 232 PSEVVSVGQEVEVKVLSIDWETERISLSL 260
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
625-701 6.33e-04

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 43.40  E-value: 6.33e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 850385791 625 VGEEFEGVISSVTSFGIFVELPNTIEGLVHVSFLTDDYYhyhekmfalvgERTGKQYRIGDVVEVRVANVNVDERTI 701
Cdd:PRK00087 562 VGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRI-----------DKPEDVLSEGEEVKAKILEVDPEEKRI 627
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 626-656 8.07e-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: 38.76  E-value: 8.07e-04
                         10        20        30
                 ....*....|....*....|....*....|....
gi 850385791 626 GEEFEGVISSVTSFGIFVELPNTI---EGLVHVS 656
Cdd:cd05684    1 GKIYKGKVTSIMDFGCFVQLEGLKgrkEGLVHIS 34
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 621-778 8.85e-04

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 42.96  E-value: 8.85e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 621 MLERVGEEFEGV-ISSVTSFGIFVELPNTIEGLVHVSFLTDDYYHYHEKMFAlvgertgkqyrIGDVVEVRVANVNVDER 699
Cdd:PLN00207 749 MVPTVGDIYRNCeIKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFK-----------VGDRIDVKLIEVNDKGQ 817

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 850385791 700 TIDFEIVGMPKAgfrGSRERTPRVIDGRGGDRKPTRGKQDRSRAGRADRPDRPDRQKDkkhpAEIRQKYKDRRKAEGNK 778
Cdd:PLN00207 818 LRLSRRALLPEA---NSEKSSQKQQGGSTKDKAPQKKYVNTSSRPRRAAQAEKNSAEN----AAVPKKKDYKRATSGSK 889
rpsA PRK13806
30S ribosomal protein S1; Provisional
 609-659 1.25e-03

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 42.40  E-value: 1.25e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 850385791 609 ERETDDLKKAEFMLERVGEEFEGVISSVTSFGIFVELPNTIEGLVHVSFLT 659
Cdd:PRK13806 186 EREQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELS 236
S1_Rrp5_repeat_sc10 cd05706
S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 624-701 2.20e-03

S1_Rrp5_repeat_sc10: 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 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240211 [Multi-domain]  Cd Length: 73  Bit Score: 37.62  E-value: 2.20e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 850385791 624 RVGEEFEGVISSVTSFGIFVELPNTIEGLVHVSFLTDDYYHyhekmfALVGErtgkqYRIGDVVEVRVANVNVDERTI 701
Cdd:cd05706    2 KVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSE------ALPYK-----FKKNDIVRACVLSVDVPNKKI 68
CspC COG1278
Cold shock protein, CspA family [Transcription];
78-119 2.43e-03

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 37.10  E-value: 2.43e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 850385791  78 KGFGFVIPEtQGMEDVYVHANDMNGALH-----GDTVLVRVEKEAGG 119
Cdd:COG1278   13 KGFGFITPD-DGGEDVFVHISALQRSGFrtlreGQRVEFEVEQGDKG 58
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 611-701 3.04e-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: 40.87  E-value: 3.04e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791  611 ETDDLKKAEFMLERV--GEEFEGVISSVTSFGIFVELpNTIEGLVHVSfltdDYYHYHEKmfalvgeRTGKQYRIGDVVE 688
Cdd:TIGR00717 171 EEERSQAREELLENLkeGDVVKGVVKNITDFGAFVDL-GGVDGLLHIT----DMSWKRVK-------HPSEYVKVGQEVK 238

                          90
                  ....*....|...
gi 850385791  689 VRVANVNVDERTI 701
Cdd:TIGR00717 239 VKVIKFDKEKGRI 251
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 626-691 3.99e-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: 36.80  E-value: 3.99e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 850385791 626 GEEFEGVISSVTSFGIFVELPNTIEGLVHVSFLTDDYyhyhekmfaLVGERTGKQYRIGDVVEVRV 691
Cdd:cd05702    1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEW---------PDGKNPLSKFKIGQKIKARV 57
PRK08059 PRK08059
general stress protein 13; Validated
 625-723 4.05e-03

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 38.10  E-value: 4.05e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 625 VGEEFEGVISSVTSFGIFVELPNTIEGLVHVS-----FLTD--DYYHyhekmfalvgertgkqyrIGDVVEVRVANVNVD 697
Cdd:PRK08059   7 VGSVVTGKVTGIQPYGAFVALDEETQGLVHISeithgFVKDihDFLS------------------VGDEVKVKVLSVDEE 68

                         90       100
                 ....*....|....*....|....*.
gi 850385791 698 ERTIDFEIVGMPKAGFRGSRERTPRV 723
Cdd:PRK08059  69 KGKISLSIRATEEAPEAKRKKGKILI 94
rpsA PRK13806
30S ribosomal protein S1; Provisional
 625-701 4.89e-03

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 40.48  E-value: 4.89e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 850385791 625 VGEEFEGVISSVTSFGIFVELPNTIEGLVHVSFLTddyyhyHEKMFAlvgeRTGKQYRIGDVVEVRVANVNVDERTI 701
Cdd:PRK13806 292 AGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMS------WTRRVN----KPEDVVAPGDAVAVKIKDIDPAKRRI 358
PRK05807 PRK05807
RNA-binding protein S1;
621-662 6.63e-03

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 37.80  E-value: 6.63e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 850385791 621 MLERVGEEFEGVISSVTSFGIFVELPNTIeGLVHVSFLTDDY 662
Cdd:PRK05807   1 MTLKAGSILEGTVVNITNFGAFVEVEGKT-GLVHISEVADTY 41
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
598-701 8.51e-03

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 39.54  E-value: 8.51e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 850385791 598 ASQRERLAVDAERetddlKKAEFMLER-VGEEFEGVISSVTSFGIFVELpNTIEGLVHVSFLTddyYHYHEKmfalvger 676
Cdd:PRK00087 454 LSRKAILEEEKEK-----KKEETWNSLeEGDVVEGEVKRLTDFGAFVDI-GGVDGLLHVSEIS---WGRVEK-------- 516

                         90       100
                 ....*....|....*....|....*
gi 850385791 677 TGKQYRIGDVVEVRVANVNVDERTI 701
Cdd:PRK00087 517 PSDVLKVGDEIKVYILDIDKENKKL 541
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 610-656 9.97e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 39.38  E-value: 9.97e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 850385791 610 RETDDLKKAEFM--LErVGEEFEGVISSVTSFGIFVELpNTIEGLVHVS 656
Cdd:PRK06299 185 EEERAEEREELLenLE-EGQVVEGVVKNITDYGAFVDL-GGVDGLLHIT 231
 
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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