Psyllid ID: psy6276

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-
MSNPPICIPGQRICQLDSDIVGGRGTYVRQGYLYSTLAGTVSINKHVEDNKEVSVIEVSSYKKEVIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILARLPLKELHSYQLSTAENELGVVIALSEAASLFRSSEKLTNDIEFLKQEKLKLYEELSSSQKENEILRQTTGDLEVRLMQMNEVKGEMEFKIKELNKKNQSESKLSDTIRELNEENIGLKQKVELQEAENQLIQTTKNE
cccccEEEcccccccccccEEccccEEEEccEEEEEEEEEEEEEcccccccEEEEEEEEcccccccccccccEEEEEEEEEcccEEEEEEEEEccEEcccccccccccccccccHHHHHHHHHccccccEEEEEEcccccccEEEEEEcccccEEEEEcccccEEEccccEEEcccccEEEEEEccccccccHHHHHHHHHHcccEEEEEEEcEEEccHHHHHHHHHHHHcccccHHHHHHHHHHHHHccccccccHHHHHHHHHHccccc
cccccEEEcccccccccccccccccEEEEccEEEEEEEEEEEEccccccccccEEEEEEcccccccccccccEEEEEEEEEcccEEEEEEEEEcccccccccEEEEEEccccccccccEEEEEccccccEEEEEEEEcccccEEEEccccccEEEEEEcccccccccccccccccHHccEEEEcHHHHccccccccEEEEcccccccEEEEEEEEEcccEEEEEHHHHcccccHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHcccc
msnppicipgqricqldsdivggrgtyvRQGYLYSTLAGTVSINkhvednkeVSVIEVSSYkkevivptpgdVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRateidriemykcyrpgdiilarlplkelHSYQLSTAENELGVVIALSEAASLFRSSEKLTNDIEFLKQEKLKLYEELSSSQKENEILRQTTGDLEVRLMQMNEVKGEMEFKIKELNkknqseskLSDTIRELNEENIGLKQKVELQEAENQLIQTTKNE
msnppicipgqricQLDSDIVGGRGTYVRQGYLYSTLAGTVSINKHVEDNKEVSvievssykkevivPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRAllrrenvrateidriemykcyrPGDIILARLPLKELHSYQLSTAENELGVVIALSEAASlfrssekltndIEFLKQEKLKLYEelsssqkeneilrqtTGDLEVRLMQMNEVKGEMEFKIkelnkknqsesklsDTIRELNEENiglkqkvelqeaenqliqttkne
MSNPPICIPGQRICQLDSDIVGGRGTYVRQGYLYSTLAGTVSINKHVEDNKEVSVIEVSSYKKEVIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILARLPLKELHSYQLSTAENELGVVIALSEAASLFRSSEKLTNDIEFlkqeklklyeelsssqkeNEILRQTTGDLEVRLMQMNEVKGEMEFKIKELNKKNQSESKLSDTIRELNEENIGLKQKVELQEAENQLIQTTKNE
*****ICIPGQRICQLDSDIVGGRGTYVRQGYLYSTLAGTVSINKHVEDNKEVSVIEVSSYKKEVIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILARLPLKELHSYQLSTAENELGVVIALSEAASLFRSSEKLTNDIEFLKQ*******************************************************************************************
**NPPICIPGQRICQLDSDIVGGRGTYVRQGYLYSTLAGTVSINKHVEDNKEVSVIEVSSYKKEVIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILARLPLKELHSYQLSTAENELGVVIALSEAASLFRSSEKLTNDIEFLKQEKLKLYEELSSSQKENEILRQTTGDLEVRLMQMNEVKGEMEF************SKLSDTIRELNEENIGLKQKVELQEAENQ*I******
MSNPPICIPGQRICQLDSDIVGGRGTYVRQGYLYSTLAGTVSINKHVEDNKEVSVIEVSSYKKEVIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILARLPLKELHSYQLSTAENELGVVIALSEAASLFRSSEKLTNDIEFLKQEKLKLYEELSSSQKENEILRQTTGDLEVRLMQMNEVKGEMEFKIKELN*********SDTIRELNEENIGLKQKVELQEAENQLIQTTKNE
***PPICIPGQRICQLDSDIVGGRGTYVRQGYLYSTLAGTVSINKHVEDNKEVSVIEVSSYKKEVIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILARLPLKELHSYQLSTAENELGVVIALSEAASLFRSSEKLTNDIEFLKQEKLKLYEELSSSQKENEILRQTTGDLEVRLMQMNEVKGEMEFKIKELNKKNQSESKLSDTIRELNEENIGLKQKVELQEAENQLIQT****
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
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MSNPPICIPGQRICQLDSDIVGGRGTYVRQGYLYSTLAGTVSINKHVEDNKEVSVIEVSSYKKEVIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILARLPLKELHSYQLSTAENELGVVIALSExxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxNEILRQTTGDLEVRxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxNQLIQTTKNE
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query271
91084271196 PREDICTED: similar to Csl4 CG6249-PA [Tr 0.594 0.821 0.548 3e-44
322789867217 hypothetical protein SINV_14459 [Solenop 0.575 0.718 0.527 3e-43
332018459200 3'-5' exoribonuclease CSL4-like protein 0.557 0.755 0.570 3e-43
156538385198 PREDICTED: exosome complex component CSL 0.568 0.777 0.553 5e-43
240848929195 exosomal core protein Csl4 [Acyrthosipho 0.575 0.8 0.534 2e-42
307203861197 3'-5' exoribonuclease CSL4-like protein 0.557 0.766 0.532 5e-41
170033758213 exosomal 3'-5' exoribonuclease complex s 0.553 0.704 0.529 6e-41
499003164216 PREDICTED: exosome complex component CSL 0.553 0.694 0.541 8e-41
478254874231 hypothetical protein YQE_08423, partial 0.560 0.658 0.541 6e-40
242013917208 conserved hypothetical protein [Pediculu 0.560 0.730 0.512 1e-39
>gi|91084271|ref|XP_971155.1| PREDICTED: similar to Csl4 CG6249-PA [Tribolium castaneum] gi|270008798|gb|EFA05246.1| hypothetical protein TcasGA2_TC015397 [Tribolium castaneum] Back     alignment and taxonomy information
 Score =  184 bits (468), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 91/166 (54%), Positives = 119/166 (71%), Gaps = 5/166 (3%)

Query: 1   MSNPPICIPGQRICQLDSDIVGGRGTYVRQGYLYSTLAGTVSINKHVEDNKEVSVIEVSS 60
           MS+P +C+PGQR+C  D   V G+GTY R GY+Y+TLAG V I    +DN  V +IEV S
Sbjct: 1   MSSPLVCLPGQRLCLSDPSHVSGQGTYERGGYIYATLAGVVDIVP--KDN--VQIIEVRS 56

Query: 61  YKKEVIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIE 120
             +E +VP+ GD+VTA+I  + Q  CK ++  VG+  L R +R +LR+E+VRATE DR+E
Sbjct: 57  SGQETLVPSQGDIVTAQIHTITQQFCKCYIKCVGDKVLGRQYRGILRKEDVRATEKDRVE 116

Query: 121 MYKCYRPGDIILAR-LPLKELHSYQLSTAENELGVVIALSEAASLF 165
           +YK +RPGD+ILAR LP+ E H+YQLSTAENELGVV A SE   L 
Sbjct: 117 IYKSFRPGDVILARVLPITEAHTYQLSTAENELGVVTAHSEHGGLM 162

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|322789867|gb|EFZ15014.1| hypothetical protein SINV_14459 [Solenopsis invicta] Back     alignment and taxonomy information
>gi|332018459|gb|EGI59049.1| 3'-5' exoribonuclease CSL4-like protein [Acromyrmex echinatior] Back     alignment and taxonomy information
>gi|156538385|ref|XP_001605472.1| PREDICTED: exosome complex component CSL4-like [Nasonia vitripennis] Back     alignment and taxonomy information
>gi|240848929|ref|NP_001155702.1| exosomal core protein Csl4 [Acyrthosiphon pisum] gi|239799438|dbj|BAH70639.1| ACYPI007328 [Acyrthosiphon pisum] Back     alignment and taxonomy information
>gi|307203861|gb|EFN82797.1| 3'-5' exoribonuclease CSL4-like protein [Harpegnathos saltator] Back     alignment and taxonomy information
>gi|170033758|ref|XP_001844743.1| exosomal 3'-5' exoribonuclease complex subunit ski4 [Culex quinquefasciatus] gi|167874820|gb|EDS38203.1| exosomal 3'-5' exoribonuclease complex subunit ski4 [Culex quinquefasciatus] Back     alignment and taxonomy information
>gi|499003164|ref|XP_004535019.1| PREDICTED: exosome complex component CSL4-like [Ceratitis capitata] Back     alignment and taxonomy information
>gi|478254874|gb|ENN75110.1| hypothetical protein YQE_08423, partial [Dendroctonus ponderosae] Back     alignment and taxonomy information
>gi|242013917|ref|XP_002427645.1| conserved hypothetical protein [Pediculus humanus corporis] gi|212512075|gb|EEB14907.1| conserved hypothetical protein [Pediculus humanus corporis] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query271
ZFIN|ZDB-GENE-080926-3194 exosc1 "exosome component 1" [ 0.586 0.819 0.436 1.8e-32
UNIPROTKB|Q5E9E9195 EXOSC1 "Uncharacterized protei 0.568 0.789 0.432 1.3e-31
UNIPROTKB|E2RT56207 EXOSC1 "Uncharacterized protei 0.568 0.743 0.432 1.3e-31
MGI|MGI:1913833195 Exosc1 "exosome component 1" [ 0.568 0.789 0.432 1.6e-31
UNIPROTKB|F1S8Y4196 EXOSC1 "Uncharacterized protei 0.568 0.785 0.435 1.1e-30
UNIPROTKB|Q9Y3B2195 EXOSC1 "Exosome complex compon 0.568 0.789 0.419 1.8e-30
FB|FBgn0032346204 Csl4 "Csl4" [Drosophila melano 0.546 0.725 0.431 7.9e-30
UNIPROTKB|B1AMU3170 EXOSC1 "Exosome complex compon 0.309 0.494 0.476 5.8e-27
UNIPROTKB|B1AMU4178 EXOSC1 "Exosome complex compon 0.512 0.780 0.375 9e-22
DICTYBASE|DDB_G0285377156 DDB_G0285377 "3'-5' exoribonuc 0.483 0.839 0.368 1.5e-21
ZFIN|ZDB-GENE-080926-3 exosc1 "exosome component 1" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
 Score = 355 (130.0 bits), Expect = 1.8e-32, P = 1.8e-32
 Identities = 72/165 (43%), Positives = 112/165 (67%)

Query:     1 MSNPPICIPGQRICQLDSDIVGGRGTYVRQGYLYSTLAGTVSINKHVEDNKEVSVIEVSS 60
             MS   +C+PG+R+C  + D + G GTY+R GY++++LAG V + K+  + +E+ VI V  
Sbjct:     1 MSPMKLCVPGERLCSTE-DCIPGTGTYLRHGYIFASLAGYV-LRKN--EGEELPVISVVR 56

Query:    61 YKKEVIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIE 120
               +  ++P  G +VT ++ ++     K H++ VG+T L   FR  +RRE+VRATE D++E
Sbjct:    57 ETEAQLLPDVGAIVTCKVTSINPRFAKVHILYVGSTPLKDRFRGTIRREDVRATEKDKVE 116

Query:   121 MYKCYRPGDIILAR-LPLKELHS-YQLSTAENELGVVIALSEAAS 163
              YK +RPGDI+LA+ + L ++ S Y L+TAENELGVV+A SEA +
Sbjct:   117 TYKSFRPGDIVLAKVISLGDVQSNYLLTTAENELGVVVAHSEAGA 161
GO:0000178 "exosome (RNase complex)" evidence=IEA
GO:0003723 "RNA binding" evidence=IEA
GO:0005730 "nucleolus" evidence=ISS
UNIPROTKB|Q5E9E9 EXOSC1 "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|E2RT56 EXOSC1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
MGI|MGI:1913833 Exosc1 "exosome component 1" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|F1S8Y4 EXOSC1 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|Q9Y3B2 EXOSC1 "Exosome complex component CSL4" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
FB|FBgn0032346 Csl4 "Csl4" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
UNIPROTKB|B1AMU3 EXOSC1 "Exosome complex component CSL4" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|B1AMU4 EXOSC1 "Exosome complex component CSL4" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
DICTYBASE|DDB_G0285377 DDB_G0285377 "3'-5' exoribonuclease CSL4 homolog" [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query271
cd0579192 cd05791, S1_CSL4, S1_CSL4: CSL4, S1-like RNA-bindi 3e-34
pfam1044772 pfam10447, EXOSC1, Exosome component EXOSC1/CSL4 8e-26
COG1096188 COG1096, COG1096, Predicted RNA-binding protein (c 4e-18
PRK09521189 PRK09521, PRK09521, exosome complex RNA-binding pr 1e-13
pfam1438239 pfam14382, ECR1_N, Exosome complex exonuclease RRP 5e-11
cd0445482 cd04454, S1_Rrp4_like, S1_Rrp4_like: Rrp4-like, S1 2e-09
COG1097239 COG1097, RRP4, RNA-binding protein Rrp4 and relate 3e-07
PRK04163235 PRK04163, PRK04163, exosome complex RNA-binding pr 3e-04
TIGR04211198 TIGR04211, SH3_and_anchor, SH3 domain protein 6e-04
COG1196 1163 COG1196, Smc, Chromosome segregation ATPases [Cell 0.004
>gnl|CDD|240217 cd05791, S1_CSL4, S1_CSL4: CSL4, S1-like RNA-binding domain Back     alignment and domain information 
 Score =  118 bits (299), Expect = 3e-34
 Identities = 43/92 (46%), Positives = 64/92 (69%), Gaps = 1/92 (1%)

Query: 65  VIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKC 124
           +++P  G +V AR+  +     K  ++ VG   L  +FR ++R+E++RATE D++EMYKC
Sbjct: 1   LVLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKC 60

Query: 125 YRPGDIILAR-LPLKELHSYQLSTAENELGVV 155
           +RPGDI+ A+ + L +  SY LSTAENELGVV
Sbjct: 61  FRPGDIVRAKVISLGDASSYYLSTAENELGVV 92

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure". Length = 92
>gnl|CDD|192591 pfam10447, EXOSC1, Exosome component EXOSC1/CSL4 Back     alignment and domain information
>gnl|CDD|224021 COG1096, COG1096, Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|236547 PRK09521, PRK09521, exosome complex RNA-binding protein Csl4; Provisional Back     alignment and domain information
>gnl|CDD|206550 pfam14382, ECR1_N, Exosome complex exonuclease RRP4 N-terminal region Back     alignment and domain information
>gnl|CDD|239901 cd04454, S1_Rrp4_like, S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain Back     alignment and domain information
>gnl|CDD|224022 COG1097, RRP4, RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|235233 PRK04163, PRK04163, exosome complex RNA-binding protein Rrp4; Provisional Back     alignment and domain information
>gnl|CDD|234501 TIGR04211, SH3_and_anchor, SH3 domain protein Back     alignment and domain information
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning] Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 271
COG1096188 Predicted RNA-binding protein (consists of S1 doma 100.0
KOG3409|consensus193 100.0
PRK09521189 exosome complex RNA-binding protein Csl4; Provisio 100.0
PRK04163235 exosome complex RNA-binding protein Rrp4; Provisio 100.0
COG1097239 RRP4 RNA-binding protein Rrp4 and related proteins 100.0
cd0579192 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. 99.94
KOG3013|consensus301 99.94
PF1044782 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I 99.87
KOG1004|consensus230 99.79
cd0445482 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA- 99.65
cd0579086 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai 99.5
cd0578986 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. 99.43
PF1438239 ECR1_N: Exosome complex exonuclease RRP4 N-termina 99.34
cd0570472 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a 98.67
cd0568770 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib 98.62
cd0570270 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R 98.51
cd0445276 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr 98.49
cd05693100 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp 98.45
cd0569173 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p 98.43
cd0570673 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a 98.38
cd0570574 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a 98.31
cd0569269 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p 98.3
COG1098129 VacB Predicted RNA binding protein (contains ribos 98.3
cd0570877 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a 98.25
cd0570768 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a 98.22
smart0031672 S1 Ribosomal protein S1-like RNA-binding domain. 98.2
PRK08582139 hypothetical protein; Provisional 98.19
cd0570373 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R 98.17
PF0057574 S1: S1 RNA binding domain; InterPro: IPR003029 Rib 98.15
cd0568673 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom 98.11
PRK08059123 general stress protein 13; Validated 98.1
PRK07252120 hypothetical protein; Provisional 98.05
PRK03987262 translation initiation factor IF-2 subunit alpha; 98.01
PRK08563187 DNA-directed RNA polymerase subunit E'; Provisiona 98.01
PRK05807136 hypothetical protein; Provisional 98.0
cd0569870 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp 97.99
cd0568868 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p 97.92
cd0446183 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp 97.8
TIGR00448179 rpoE DNA-directed RNA polymerase (rpoE), archaeal 97.8
cd0447268 S1_PNPase S1_PNPase: Polynucleotide phosphorylase 97.79
cd0568568 S1_Tex S1_Tex: The C-terminal S1 domain of a trans 97.77
PTZ00248 319 eukaryotic translation initiation factor 2 subunit 97.75
PRK11824693 polynucleotide phosphorylase/polyadenylase; Provis 97.75
cd0569566 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t 97.74
cd0569769 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t 97.73
cd0569474 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp 97.66
cd0446099 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. 97.59
cd0445388 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik 97.58
PRK07400318 30S ribosomal protein S1; Reviewed 97.55
TIGR03591684 polynuc_phos polyribonucleotide nucleotidyltransfe 97.53
COG0539 541 RpsA Ribosomal protein S1 [Translation, ribosomal 97.48
cd0569671 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t 97.42
COG1095183 RPB7 DNA-directed RNA polymerase, subunit E' [Tran 97.39
cd0016465 S1_like S1_like: Ribosomal protein S1-like RNA-bin 97.38
COG1093269 SUI2 Translation initiation factor 2, alpha subuni 97.38
cd0445567 S1_NusA S1_NusA: N-utilizing substance A protein ( 97.36
PHA0294588 interferon resistance protein; Provisional 97.28
TIGR02696719 pppGpp_PNP guanosine pentaphosphate synthetase I/p 97.18
cd0569069 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p 97.17
cd0447377 S1_RecJ_like S1_RecJ_like: The S1 domain of the ar 97.14
cd0568479 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal 97.11
PRK07400318 30S ribosomal protein S1; Reviewed 97.09
cd0568972 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p 96.94
cd0446567 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib 96.81
PTZ00162176 DNA-directed RNA polymerase II subunit 7; Provisio 96.8
PRK06299565 rpsA 30S ribosomal protein S1; Reviewed 96.8
PRK13806491 rpsA 30S ribosomal protein S1; Provisional 96.78
PRK06676390 rpsA 30S ribosomal protein S1; Reviewed 96.69
PRK07899 486 rpsA 30S ribosomal protein S1; Reviewed 96.68
PRK06676390 rpsA 30S ribosomal protein S1; Reviewed 96.65
PRK13806491 rpsA 30S ribosomal protein S1; Provisional 96.55
PRK06299565 rpsA 30S ribosomal protein S1; Reviewed 96.51
PRK09202 470 nusA transcription elongation factor NusA; Validat 96.44
PRK07899486 rpsA 30S ribosomal protein S1; Reviewed 96.41
PRK12269863 bifunctional cytidylate kinase/ribosomal protein S 96.32
PRK00087647 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 96.32
TIGR00717516 rpsA ribosomal protein S1. This model provides tru 96.26
PLN00207891 polyribonucleotide nucleotidyltransferase; Provisi 96.23
PRK00087647 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 96.18
PRK12327362 nusA transcription elongation factor NusA; Provisi 96.15
cd0447183 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai 96.13
TIGR00717516 rpsA ribosomal protein S1. This model provides tru 96.07
COG0539541 RpsA Ribosomal protein S1 [Translation, ribosomal 95.99
PRK12269863 bifunctional cytidylate kinase/ribosomal protein S 95.9
TIGR01953341 NusA transcription termination factor NusA. This m 95.83
cd0446288 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly 94.64
PRK12329 449 nusA transcription elongation factor NusA; Provisi 94.34
PRK12328374 nusA transcription elongation factor NusA; Provisi 94.18
PF0101681 Ribosomal_L27: Ribosomal L27 protein; InterPro: IP 93.25
TIGR00757 414 RNaseEG ribonuclease, Rne/Rng family. The C-termin 92.9
KOG1070|consensus 1710 92.54
CHL0012186 rpl27 ribosomal protein L27; Reviewed 92.51
COG2183780 Tex Transcriptional accessory protein [Transcripti 92.34
PRK0543582 rpmA 50S ribosomal protein L27; Validated 92.3
COG1185692 Pnp Polyribonucleotide nucleotidyltransferase (pol 89.52
cd0569972 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t 89.14
KOG1070|consensus 1710 88.42
TIGR0006283 L27 ribosomal protein L27. Eubacterial, chloroplas 85.65
KOG1856|consensus 1299 83.29
TIGR02063709 RNase_R ribonuclease R. This family consists of an 82.39
PRK11712 489 ribonuclease G; Provisional 82.09
PF0929732 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon do 81.83
PRK11642813 exoribonuclease R; Provisional 81.69
PF0775424 DUF1610: Domain of unknown function (DUF1610); Int 80.34
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information 
Probab=100.00  E-value=1e-44  Score=315.53  Aligned_cols=179  Identities=24%  Similarity=0.356  Sum_probs=167.1

Q ss_pred             CCCeEecCCcccCCCCCeeeCCCEEEeCCEEEEEEeeEEEEeccccCCCcceEEEEeeCCCccccCCCCCEEEEEEEEEe
Q psy6276           3 NPPICIPGQRICQLDSDIVGGRGTYVRQGYLYSTLAGTVSINKHVEDNKEVSVIEVSSYKKEVIVPTPGDVVTARIMAVQ   82 (271)
Q Consensus         3 ~~~iVlPGD~L~~~eE~~~~G~GtY~~~g~I~ASv~G~v~i~~~~~~~~~~~~I~V~P~~~~~yiP~vGDIVIGrVt~V~   82 (271)
                      ++.+|+|||.|+..|| |++|.|||+++|.|+|+.+|.+.+|.      ++++++|.|.+..+.+|+.||+|+|+|+++.
T Consensus         4 ~g~~v~PGd~~a~~EE-~~~G~gt~~~~g~i~Aa~~G~~~~d~------~n~~~~V~p~~~~~~~~K~GdiV~grV~~v~   76 (188)
T COG1096           4 DGTFVLPGDVLAVIEE-FLPGEGTYEEGGEIRAAATGVVRRDD------KNRVISVKPGKKTPPLPKGGDIVYGRVTDVR   76 (188)
T ss_pred             cCcEEcCcceeeeeee-eecCCCeEeECCEEEEeecccEEEcc------cceEEEeccCCCCCCCCCCCCEEEEEEeecc
Confidence            3589999999999999 99999999999999999999999998      7899999998666999999999999999999


Q ss_pred             cceEEEEEeeecCc--ccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCCCceeeeeccCCCeeEEEEc
Q psy6276          83 QHLCKAHVISVGNT--ALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKELHSYQLSTAENELGVVIALS  159 (271)
Q Consensus        83 ~~~a~VdI~~v~~~--~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~~~~~LST~~~eLGVV~A~c  159 (271)
                      .+.|.|+|.++++.  .+..++.|.||+|+++...  ..+++++|+|||||+|+ +|++  .+|.|||++++||||+|+|
T Consensus        77 ~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~--~~~~~d~f~~GDivrA~Vis~~--~~~~Lst~~~dlGVI~A~C  152 (188)
T COG1096          77 EQRALVRIVGVEGKERELATSGAADIHVSQVRDGY--VEKLSDAFRIGDIVRARVISTG--DPIQLSTKGNDLGVIYARC  152 (188)
T ss_pred             ceEEEEEEEEEecccccCCCCceeeEEEEeccccc--ccccccccccccEEEEEEEecC--CCeEEEecCCcceEEEEEc
Confidence            99999999999994  4889999999999998754  45788999999999999 9987  5799999999999999999


Q ss_pred             -cCCCeeEeccCccCchhhhhhhhhhhHHHhccc
Q psy6276         160 -EAASLFRSSEKLTNDIEFLKQEKLKLYEELSSS  192 (271)
Q Consensus       160 -~cG~~Mvp~s~~~~c~~~~~~e~rKla~~~~s~  192 (271)
                       +||.+|++.+..++||+|+.+|+||+|.++.+.
T Consensus       153 srC~~~L~~~~~~l~Cp~Cg~tEkRKia~~y~~~  186 (188)
T COG1096         153 SRCRAPLVKKGNMLKCPNCGNTEKRKIAKDYGKV  186 (188)
T ss_pred             cCCCcceEEcCcEEECCCCCCEEeeeeccccccc
Confidence             999999998899999999999999999997553

>KOG3409|consensus Back     alignment and domain information
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional Back     alignment and domain information
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional Back     alignment and domain information
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain Back     alignment and domain information
>KOG3013|consensus Back     alignment and domain information
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions [] Back     alignment and domain information
>KOG1004|consensus Back     alignment and domain information
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain Back     alignment and domain information
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain Back     alignment and domain information
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain Back     alignment and domain information
>PF14382 ECR1_N: Exosome complex exonuclease RRP4 N-terminal region; PDB: 2NN6_I 3M7N_C 2BA1_A 3M85_C Back     alignment and domain information
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain Back     alignment and domain information
>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain Back     alignment and domain information
>PRK08582 hypothetical protein; Provisional Back     alignment and domain information
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain Back     alignment and domain information
>PRK08059 general stress protein 13; Validated Back     alignment and domain information
>PRK07252 hypothetical protein; Provisional Back     alignment and domain information
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated Back     alignment and domain information
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional Back     alignment and domain information
>PRK05807 hypothetical protein; Provisional Back     alignment and domain information
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains Back     alignment and domain information
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form Back     alignment and domain information
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain Back     alignment and domain information
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa Back     alignment and domain information
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional Back     alignment and domain information
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional Back     alignment and domain information
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain Back     alignment and domain information
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain Back     alignment and domain information
>PRK07400 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase Back     alignment and domain information
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription] Back     alignment and domain information
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain Back     alignment and domain information
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain Back     alignment and domain information
>PHA02945 interferon resistance protein; Provisional Back     alignment and domain information
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase Back     alignment and domain information
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease Back     alignment and domain information
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide Back     alignment and domain information
>PRK07400 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional Back     alignment and domain information
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK13806 rpsA 30S ribosomal protein S1; Provisional Back     alignment and domain information
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK13806 rpsA 30S ribosomal protein S1; Provisional Back     alignment and domain information
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK09202 nusA transcription elongation factor NusA; Validated Back     alignment and domain information
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional Back     alignment and domain information
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed Back     alignment and domain information
>TIGR00717 rpsA ribosomal protein S1 Back     alignment and domain information
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional Back     alignment and domain information
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed Back     alignment and domain information
>PRK12327 nusA transcription elongation factor NusA; Provisional Back     alignment and domain information
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain Back     alignment and domain information
>TIGR00717 rpsA ribosomal protein S1 Back     alignment and domain information
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional Back     alignment and domain information
>TIGR01953 NusA transcription termination factor NusA Back     alignment and domain information
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain Back     alignment and domain information
>PRK12329 nusA transcription elongation factor NusA; Provisional Back     alignment and domain information
>PRK12328 nusA transcription elongation factor NusA; Provisional Back     alignment and domain information
>PF01016 Ribosomal_L27: Ribosomal L27 protein; InterPro: IPR001684 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family Back     alignment and domain information
>KOG1070|consensus Back     alignment and domain information
>CHL00121 rpl27 ribosomal protein L27; Reviewed Back     alignment and domain information
>COG2183 Tex Transcriptional accessory protein [Transcription] Back     alignment and domain information
>PRK05435 rpmA 50S ribosomal protein L27; Validated Back     alignment and domain information
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>KOG1070|consensus Back     alignment and domain information
>TIGR00062 L27 ribosomal protein L27 Back     alignment and domain information
>KOG1856|consensus Back     alignment and domain information
>TIGR02063 RNase_R ribonuclease R Back     alignment and domain information
>PRK11712 ribonuclease G; Provisional Back     alignment and domain information
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains Back     alignment and domain information
>PRK11642 exoribonuclease R; Provisional Back     alignment and domain information
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query271
2nn6_I209 Structure Of The Human Rna Exosome Composed Of Rrp4 1e-31
4ifd_I301 Crystal Structure Of An 11-subunit Eukaryotic Exoso 3e-11
>pdb|2NN6|I Chain I, Structure Of The Human Rna Exosome Composed Of Rrp41, Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40 Length = 209 Back     alignment and structure 
Iteration: 1

 Score =  133 bits (334), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 68/163 (41%), Positives = 106/163 (65%), Gaps = 8/163 (4%)
Query: 4   PPI--CIPGQRICQLDSDIVGGRGTYVRQGYLYSTLAGTVSINKHVEDNKEVSVIEVSSY 61
           PP+  CIPG+R+C L+     G GTY R GY++S+LAG +  +    +N  + V+ V   
Sbjct: 17  PPVRYCIPGERLCNLEEG-SPGSGTYTRHGYIFSSLAGCLMKS---SENGALPVVSVVRE 72
Query: 62  KKEVIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEM 121
            +  ++P  G +VT ++ ++     K H++ VG+  L  +FR  +R+E+VRATE D++E+
Sbjct: 73  TESQLLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEI 132
Query: 122 YKCYRPGDIILAR-LPLKELHS-YQLSTAENELGVVIALSEAA 162
           YK +RPGDI+LA+ + L +  S Y L+TAENELGVV+A SE+ 
Sbjct: 133 YKSFRPGDIVLAKVISLGDAQSNYLLTTAENELGVVVAHSESG 175
>pdb|4IFD|I Chain I, Crystal Structure Of An 11-subunit Eukaryotic Exosome Complex Bound To Rna Length = 301 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query271
2nn6_I209 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, 6e-43
3m7n_A179 Putative uncharacterized protein AF_0206; exosome, 5e-27
2nn6_H308 Exosome complex exonuclease RRP4; RNA, exosome, PM 3e-24
2je6_I251 RRP4, exosome complex RNA-binding protein 1; nucle 8e-18
2z0s_A235 Probable exosome complex RNA-binding protein 1; al 1e-15
2ba0_A229 Archeal exosome RNA binding protein RRP4; RNAse PH 1e-14
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-10
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-05
2dfs_A1080 Myosin-5A; myosin-V, inhibited state, cryoelectron 4e-06
2nn6_G289 Exosome complex exonuclease RRP40; RNA, exosome, P 2e-04
>2nn6_I 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 Length = 209 Back     alignment and structure
 Score =  144 bits (365), Expect = 6e-43
 Identities = 65/164 (39%), Positives = 103/164 (62%), Gaps = 7/164 (4%)

Query: 1   MSNPP-ICIPGQRICQLDSDIVGGRGTYVRQGYLYSTLAGTVSINKHVEDNKEVSVIEVS 59
           M+ P   CIPG+R+C    +   G GTY R GY++S+LAG +  +    +N  + V+ V 
Sbjct: 15  MAPPVRYCIPGERLCN-LEEGSPGSGTYTRHGYIFSSLAGCLMKS---SENGALPVVSVV 70

Query: 60  SYKKEVIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRI 119
              +  ++P  G +VT ++ ++     K H++ VG+  L  +FR  +R+E+VRATE D++
Sbjct: 71  RETESQLLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKV 130

Query: 120 EMYKCYRPGDIILARL--PLKELHSYQLSTAENELGVVIALSEA 161
           E+YK +RPGDI+LA++        +Y L+TAENELGVV+A SE+
Sbjct: 131 EIYKSFRPGDIVLAKVISLGDAQSNYLLTTAENELGVVVAHSES 174
>3m7n_A Putative uncharacterized protein AF_0206; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_A 3m85_A Length = 179 Back     alignment and structure
>2nn6_H Exosome complex exonuclease RRP4; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 d.51.1.1 Length = 308 Back     alignment and structure
>2je6_I RRP4, exosome complex RNA-binding protein 1; nuclease, hydrolase, exonuclease, phosphorolytic, exoribonuclease, RNA degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus} SCOP: b.40.4.5 b.84.4.2 d.51.1.1 PDB: 2jea_I* 2jeb_I* 3l7z_C Length = 251 Back     alignment and structure
>2z0s_A Probable exosome complex RNA-binding protein 1; alpha/beta protein, cytoplasm, structural genomics, NPPSFA; 3.20A {Aeropyrum pernix} SCOP: b.40.4.5 d.51.1.1 Length = 235 Back     alignment and structure
>2ba0_A Archeal exosome RNA binding protein RRP4; RNAse PH, RNA degradation, exoribonuclease, S1domain, KH domain, archaeal; 2.70A {Archaeoglobus fulgidus} SCOP: b.40.4.5 b.84.4.2 d.51.1.1 Length = 229 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080 Back     alignment and structure
>2nn6_G Exosome complex exonuclease RRP40; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 d.51.1.1 Length = 289 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query271
3m7n_A179 Putative uncharacterized protein AF_0206; exosome, 100.0
2nn6_I209 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, 100.0
2nn6_H308 Exosome complex exonuclease RRP4; RNA, exosome, PM 100.0
2ba0_A229 Archeal exosome RNA binding protein RRP4; RNAse PH 100.0
2z0s_A235 Probable exosome complex RNA-binding protein 1; al 100.0
2je6_I251 RRP4, exosome complex RNA-binding protein 1; nucle 100.0
2nn6_G289 Exosome complex exonuclease RRP40; RNA, exosome, P 100.0
2ja9_A175 Exosome complex exonuclease RRP40; RNA-binding pro 99.83
2k52_A80 Uncharacterized protein MJ1198; metal-binding, zin 98.52
2k4k_A130 GSP13, general stress protein 13; cytoplasm, stres 98.39
1go3_E187 DNA-directed RNA polymerase subunit E; transferase 98.34
2khi_A115 30S ribosomal protein S1; acetylation, phosphoprot 98.34
2khj_A109 30S ribosomal protein S1; OB fold, acetylation, ph 98.33
2cqo_A119 Nucleolar protein of 40 kDa; S1 domain, OB-fold, s 98.3
1kl9_A182 Eukaryotic translation initiation factor 2 subuni; 98.28
2eqs_A103 ATP-dependent RNA helicase DHX8; S1 domain, OB-fol 98.27
2a19_A175 EIF-2- alpha, eukaryotic translation initiation fa 98.17
3aev_A275 Translation initiation factor 2 subunit alpha; pro 98.02
1wi5_A119 RRP5 protein homolog; S1 domain, OB-fold, structur 98.0
4ayb_E180 DNA-directed RNA polymerase; transferase, multi-su 97.97
1luz_A88 Protein K3, protein K2; stranded anti-parallel bet 97.91
2c35_B172 Human RPB7, DNA-directed RNA polymerase II 19 kDa 97.86
1q8k_A308 Eukaryotic translation initiation factor 2 subunit 97.81
3cw2_C266 Translation initiation factor 2 subunit alpha; AIF 97.75
1y14_B171 B16, RPB7, DNA-directed RNA polymerase II 19 kDa p 97.48
3h0g_G172 DNA-directed RNA polymerase II subunit RPB7; trans 97.31
2b8k_G215 B16, DNA-directed RNA polymerase II 19 kDa polypep 97.1
3ayh_B203 DNA-directed RNA polymerase III subunit RPC8; tran 97.04
3go5_A285 Multidomain protein with S1 RNA-binding domains; s 97.03
4aid_A726 Polyribonucleotide nucleotidyltransferase; transfe 96.96
2asb_A251 Transcription elongation protein NUSA; protein-RNA 96.79
3psi_A 1219 Transcription elongation factor SPT6; nucleus; 3.3 96.72
1hh2_P344 NUSA, N utilization substance protein A; transcrip 96.64
1k0r_A366 NUSA; two component arrangement, S1 domain, two K- 96.36
3psf_A1030 Transcription elongation factor SPT6; nucleus; 2.5 96.35
3cdi_A723 Polynucleotide phosphorylase; mRNA turnover, RNAse 96.08
3bzc_A785 TEX; helix-turn-helix, helix-hairpin-helix, S1 dom 95.97
2ckz_B218 C25, DNA-directed RNA polymerase III 25 KD polypep 95.72
1e3p_A757 Guanosine pentaphosphate synthetase; polyribonucle 95.62
2bx2_L 517 Ribonuclease E, RNAse E; RNA-binding, RNA turnover 94.16
3d0f_A106 Penicillin-binding 1 transmembrane protein MRCA; B 92.75
3v2d_085 50S ribosomal protein L27; ribosome associated inh 92.47
3go5_A285 Multidomain protein with S1 RNA-binding domains; s 92.43
2zjr_T91 50S ribosomal protein L27; ribosome, large ribosom 90.91
3r8s_W76 50S ribosomal protein L27; protein biosynthesis, R 90.45
2bh8_A101 1B11; transcription, molecular evolution, unique a 85.12
2id0_A644 Exoribonuclease 2; RNAse, exonuclease, hydrolyase, 80.28
>3m7n_A Putative uncharacterized protein AF_0206; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_A 3m85_A Back     alignment and structure
Probab=100.00  E-value=1.1e-44  Score=313.80  Aligned_cols=172  Identities=27%  Similarity=0.347  Sum_probs=159.9

Q ss_pred             CeEecCCcccCCCCCeeeCCCEEEeCCEEEEEEeeEEEEeccccCCCcceEEEEeeCCCccccCCCCCEEEEEEEEEecc
Q psy6276           5 PICIPGQRICQLDSDIVGGRGTYVRQGYLYSTLAGTVSINKHVEDNKEVSVIEVSSYKKEVIVPTPGDVVTARIMAVQQH   84 (271)
Q Consensus         5 ~iVlPGD~L~~~eE~~~~G~GtY~~~g~I~ASv~G~v~i~~~~~~~~~~~~I~V~P~~~~~yiP~vGDIVIGrVt~V~~~   84 (271)
                      ++|+|||.|+..++ |.+|+|||.++|.||||++|.+.+.+        ++++|+|....+|+|+ ||+|+|+|++|.+.
T Consensus         2 ~iV~PGd~l~~~~~-~~~G~Gty~~~~~i~as~~G~v~~~~--------~~v~V~~~~~~~y~p~-GdiV~G~V~~V~~~   71 (179)
T 3m7n_A            2 RFVMPGDRIGSAEE-YVKGEGVYEEGGELFAAVAGKLIIKD--------RVAKVESISPIPEIVK-GDVVLGRVVDLRNS   71 (179)
T ss_dssp             CEECTTCEEEETTT-SEECTTEEEETTEEEESSSEEEEEET--------TEEEEEESSCCCCCCT-TCEEEEEEEEECSS
T ss_pred             eEEcCCCCCCCCCC-EeccCCEEEeCCEEEEEEEEEEEEeC--------CEEEEEECCCCcccCC-CCEEEEEEEEEeCC
Confidence            69999999999888 99999999999999999999999865        7999999755679999 99999999999999


Q ss_pred             eEEEEEeee--cCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCCCceeeeeccCCCeeEEEEc-c
Q psy6276          85 LCKAHVISV--GNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKELHSYQLSTAENELGVVIALS-E  160 (271)
Q Consensus        85 ~a~VdI~~v--~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~~~~~LST~~~eLGVV~A~c-~  160 (271)
                      .|+|+|.++  +.+++..++.|+||++|++.++.  .+|+++|++||+|+|+ ++    +.+.|||++++||||+|.| +
T Consensus        72 ga~V~I~~v~~~~~~~~~~~~Gll~isei~~~~~--~~~~~~~~~GD~V~akVi~----~~i~LS~k~~~lGvv~a~~~~  145 (179)
T 3m7n_A           72 IALIEVSSKKGENRGPSNRGIGILHVSNVDEGYV--KEISEAVGYLDILKARVIG----DNLRLSTKEEEMGVLRALCSN  145 (179)
T ss_dssp             EEEEEEEEETTCCSCCTTCEEEEEEGGGTTSSCC--SSGGGTCCTTCEEEEEEEE----TTTEEECCSTTCEEEECBCTT
T ss_pred             cEEEEEccccCcccccccCeeEEEEHHHcCcchh--hCHhhcCCCCCEEEEEEEC----CeEEEEEecCCCCEEEecccc
Confidence            999999998  55677789999999999987654  4899999999999999 88    5799999999999999999 8


Q ss_pred             CCCeeEeccCccCchhhhhhhhhhhHHHhccc
Q psy6276         161 AASLFRSSEKLTNDIEFLKQEKLKLYEELSSS  192 (271)
Q Consensus       161 cG~~Mvp~s~~~~c~~~~~~e~rKla~~~~s~  192 (271)
                      ||++|+|.|..++||+|+..|.||+|++++..
T Consensus       146 ~g~~m~~~~~~~~cp~~g~~e~RKva~~y~~~  177 (179)
T 3m7n_A          146 CKTEMVREGDILKCPECGRVEKRKISTDYGKG  177 (179)
T ss_dssp             TCCBCEECSSSEECSSSCCEECCCBCTTTTTT
T ss_pred             cCCceEECCCEEECCCCCCEEEEecccccccc
Confidence            99999999999999999999999999998765
>2nn6_I 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 Back     alignment and structure
>2nn6_H Exosome complex exonuclease RRP4; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 d.51.1.1 Back     alignment and structure
>2ba0_A Archeal exosome RNA binding protein RRP4; RNAse PH, RNA degradation, exoribonuclease, S1domain, KH domain, archaeal; 2.70A {Archaeoglobus fulgidus} SCOP: b.40.4.5 b.84.4.2 d.51.1.1 Back     alignment and structure
>2z0s_A Probable exosome complex RNA-binding protein 1; alpha/beta protein, cytoplasm, structural genomics, NPPSFA; 3.20A {Aeropyrum pernix} SCOP: b.40.4.5 d.51.1.1 Back     alignment and structure
>2je6_I RRP4, exosome complex RNA-binding protein 1; nuclease, hydrolase, exonuclease, phosphorolytic, exoribonuclease, RNA degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus} SCOP: b.40.4.5 b.84.4.2 d.51.1.1 PDB: 2jea_I* 2jeb_I* 3l7z_C Back     alignment and structure
>2nn6_G Exosome complex exonuclease RRP40; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 d.51.1.1 Back     alignment and structure
>2ja9_A Exosome complex exonuclease RRP40; RNA-binding protein, RNA, S1 domain, KH domain, hydrolase, RNA-binding, nuclear protein; 2.20A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.51.1.1 Back     alignment and structure
>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii} Back     alignment and structure
>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis} Back     alignment and structure
>1go3_E DNA-directed RNA polymerase subunit E; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} SCOP: b.40.4.5 d.230.1.1 Back     alignment and structure
>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Back     alignment and structure
>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Back     alignment and structure
>2cqo_A Nucleolar protein of 40 kDa; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>1kl9_A Eukaryotic translation initiation factor 2 subuni; OB fold, helical domain; 1.90A {Homo sapiens} SCOP: a.60.14.1 b.40.4.5 Back     alignment and structure
>2eqs_A ATP-dependent RNA helicase DHX8; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2a19_A EIF-2- alpha, eukaryotic translation initiation factor 2 alpha; transferase, protein biosynthesis, protein synthesis transferase complex; HET: TPO ANP; 2.50A {Saccharomyces cerevisiae} PDB: 2a1a_A* 1q46_A Back     alignment and structure
>3aev_A Translation initiation factor 2 subunit alpha; proteins-rRNA complex, 16S rRNA, RNA-binding; 2.80A {Pyrococcus horikoshii} PDB: 1yz6_A Back     alignment and structure
>1wi5_A RRP5 protein homolog; S1 domain, OB-fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: b.40.4.5 Back     alignment and structure
>4ayb_E DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_E 4b1o_E 4b1p_T 2waq_E 2wb1_E 2pmz_E 3hkz_E Back     alignment and structure
>1luz_A Protein K3, protein K2; stranded anti-parallel beta barrel, viral protein; 1.80A {Vaccinia virus} SCOP: b.40.4.5 Back     alignment and structure
>2c35_B Human RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transcription, nucleotidyltransferase; 2.70A {Homo sapiens} SCOP: b.40.4.5 d.230.1.1 Back     alignment and structure
>1q8k_A Eukaryotic translation initiation factor 2 subunit 1; NMR {Homo sapiens} SCOP: a.60.14.1 b.40.4.5 d.58.51.1 Back     alignment and structure
>3cw2_C Translation initiation factor 2 subunit alpha; AIF2, intact AIF2, initiation factor 2 alpha subunit, initiation factor 2 beta subunit; 2.80A {Sulfolobus solfataricus} PDB: 2aho_B 3v11_B* Back     alignment and structure
>1y14_B B16, RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transferase; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1 PDB: 1nt9_G 1wcm_G 1pqv_G 1y1v_G 1y1w_G 1y1y_G 1y77_G* 2b63_G* 2ja5_G* 2ja6_G* 2ja7_G* 2ja8_G* 2r7z_G 2r92_G 2r93_G 2vum_G* 3fki_G 3h3v_H 3hou_G* 3hov_G* ... Back     alignment and structure
>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure
>2b8k_G B16, DNA-directed RNA polymerase II 19 kDa polypeptide; DNA-dependent RNA polymerase, cellular RNA polymerase; 4.15A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1 Back     alignment and structure
>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A {Schizosaccharomyces pombe} Back     alignment and structure
>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae} Back     alignment and structure
>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A Back     alignment and structure
>2asb_A Transcription elongation protein NUSA; protein-RNA complex, transcription/RNA complex; 1.50A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 PDB: 2atw_A Back     alignment and structure
>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae} Back     alignment and structure
>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A Back     alignment and structure
>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 Back     alignment and structure
>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae} Back     alignment and structure
>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A Back     alignment and structure
>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} SCOP: a.60.2.6 a.60.2.6 a.294.1.1 b.40.4.5 c.55.3.13 PDB: 3bzk_A 2oce_A Back     alignment and structure
>2ckz_B C25, DNA-directed RNA polymerase III 25 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae} Back     alignment and structure
>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A Back     alignment and structure
>2bx2_L Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonu nuclease; 2.85A {Escherichia coli} PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_A Back     alignment and structure
>3d0f_A Penicillin-binding 1 transmembrane protein MRCA; BIG_1156.2, STR genomics, PSI-2, protein structure initiative; 1.64A {Nitrosomonas europaea atcc 19718} Back     alignment and structure
>3v2d_0 50S ribosomal protein L27; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 2hgj_Z 2hgq_Z 2hgu_Z 2j01_0 2j03_0 2jl6_0 2jl8_0 2wdi_0 2wdj_0 2wdl_0 2wdn_0 2wh2_0 2wh4_0 2wrj_0 2wrl_0 2wro_0 2wrr_0 2x9s_0 2x9u_0 2xg0_0 ... Back     alignment and structure
>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae} Back     alignment and structure
>2zjr_T 50S ribosomal protein L27; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: b.84.4.1 PDB: 1nwx_U* 1nwy_U* 1sm1_U* 1xbp_U* 1y69_U 1yl3_3 2b66_0 2b9n_0 2b9p_0 2zjp_T* 2zjq_T 1nkw_U 3cf5_T* 3dll_T* 3pio_T* 3pip_T* 1pnu_U 1pny_U 1vor_X 1vou_X ... Back     alignment and structure
>3r8s_W 50S ribosomal protein L27; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 3j19_W 2qam_W* 1p85_U 1p86_U 2awb_W 2gya_U 2gyc_U 2aw4_W 2i2v_W 2j28_W 2i2t_W* 2qao_W* 2qba_W* 2qbc_W* 2qbe_W 2qbg_W 2qbi_W* 2qbk_W* 2qov_W 2qox_W ... Back     alignment and structure
>2bh8_A 1B11; transcription, molecular evolution, unique architecture, transcription regulation, phosphorylation; 1.9A {Escherichia coli} Back     alignment and structure
>2id0_A Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR family, hydrolase; 2.35A {Escherichia coli} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 PDB: 2ix0_A* 2ix1_A Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 271
d2nn6i1125 b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {H 8e-29
d2nn6i255 b.84.4.2 (I:6-60) Exosome component 1, EXOSC1 {Hum 2e-12
d2nn6h248 b.84.4.2 (H:25-72) Ribosomal RNA-processing protei 2e-05
d2ba0a251 b.84.4.2 (A:2-52) Exosome complex RNA-binding prot 3e-05
d2je6i259 b.84.4.2 (I:7-65) Exosome complex RNA-binding prot 2e-04
>d2nn6i1 b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {Human (Homo sapiens) [TaxId: 9606]} Length = 125 Back     information, alignment and structure

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exosome component 1, EXOSC1
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  104 bits (260), Expect = 8e-29
 Identities = 45/98 (45%), Positives = 70/98 (71%), Gaps = 2/98 (2%)

Query: 66  IVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCY 125
           ++P  G +VT ++ ++     K H++ VG+  L  +FR  +R+E+VRATE D++E+YK +
Sbjct: 3   LLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSF 62

Query: 126 RPGDIILAR-LPLKELHS-YQLSTAENELGVVIALSEA 161
           RPGDI+LA+ + L +  S Y L+TAENELGVV+A SE+
Sbjct: 63  RPGDIVLAKVISLGDAQSNYLLTTAENELGVVVAHSES 100
>d2nn6i2 b.84.4.2 (I:6-60) Exosome component 1, EXOSC1 {Human (Homo sapiens) [TaxId: 9606]} Length = 55 Back     information, alignment and structure
>d2nn6h2 b.84.4.2 (H:25-72) Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]} Length = 48 Back     information, alignment and structure
>d2ba0a2 b.84.4.2 (A:2-52) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 51 Back     information, alignment and structure
>d2je6i2 b.84.4.2 (I:7-65) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 59 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

Original result of HHsearch against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query271
d2nn6i1125 Exosome component 1, EXOSC1 {Human (Homo sapiens) 100.0
d2nn6h195 S1-domain of Ribosomal RNA-processing protein 4, R 99.68
d2nn6g188 S1-domain of exosome component 3 (RRP40) {Human (H 99.59
d2ja9a190 S1-domain of exosome component 3 (RRP40) {Saccharo 99.57
d2je6i187 S1-domain of exosome complex RNA-binding protein 1 99.5
d2z0sa188 S1-domain of exosome complex RNA-binding protein 1 99.5
d2ba0a183 S1-domain of exosome complex RNA-binding protein 1 99.45
d2ba0a251 Exosome complex RNA-binding protein 1, ECR1 {Archa 99.39
d2nn6h248 Ribosomal RNA-processing protein 4, RRP4 {Human (H 99.35
d2je6i259 Exosome complex RNA-binding protein 1, ECR1 {Sulfo 99.3
d2nn6i255 Exosome component 1, EXOSC1 {Human (Homo sapiens) 99.29
d1kl9a286 Eukaryotic initiation factor 2alpha, eIF2alpha, N- 98.66
d2ahob284 Eukaryotic initiation factor 2alpha, eIF2alpha, N- 98.59
d1sroa_76 S1 RNA-binding domain of polyribonucleotide phosph 98.52
d3bzka494 Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287] 98.18
d1wi5a_119 S1-domain of RRP5 protein homolog (PDCD11, KIAA018 98.05
d1go3e1106 C-terminal domain of RNA polymerase II subunit RBP 97.92
d1y14b191 C-terminal domain of RNA polymerase II subunit RBP 97.83
d2c35b194 C-terminal domain of RNA polymerase II subunit RBP 97.73
d1hh2p172 S1 domain of NusA {Thermotoga maritima [TaxId: 233 97.59
d2nn6g380 Ribosomal RNA-processing protein 40, RRP40 {Human 96.89
d2asba176 S1 domain of NusA {Mycobacterium tuberculosis [Tax 96.06
d1v8qa_66 Ribosomal protein L27 {Thermus thermophilus [TaxId 96.02
d2nn6g291 Ribosomal RNA-processing protein 40, RRP40 {Human 95.9
d1e3pa262 S1 RNA-binding domain of polyribonucleotide phosph 95.74
d2zjrt184 Ribosomal protein L27 {Deinococcus radiodurans [Ta 95.64
d2ja9a285 Ribosomal RNA-processing protein 40, RRP40 {Saccha 92.43
d1smxa_87 S1-domain of Ribonuclease E {Escherichia coli [Tax 90.91
d1e1oa1143 Lysyl-tRNA synthetase (LysRS) {Escherichia coli, g 81.35
>d2nn6i1 b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exosome component 1, EXOSC1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=5.3e-38  Score=256.64  Aligned_cols=121  Identities=38%  Similarity=0.638  Sum_probs=116.5

Q ss_pred             cccCCCCCEEEEEEEEEecceEEEEEeeecCcccCCceeeEEeccccccchhhhHhhhcCCCCCCEEEEE-EecCCCC-c
Q psy6276          65 VIVPTPGDVVTARIMAVQQHLCKAHVISVGNTALSRTFRALLRRENVRATEIDRIEMYKCYRPGDIILAR-LPLKELH-S  142 (271)
Q Consensus        65 ~yiP~vGDIVIGrVt~V~~~~a~VdI~~v~~~~L~~~f~GiLr~sdvr~te~d~~~m~~~f~~GDIV~Ak-iS~~d~~-~  142 (271)
                      +|+|++||+|+|+|+++++++|.|+|+++++.++..+|.|++|.+|+|+++.|+.+|+++|+|||||+|| +|+++.. +
T Consensus         2 ~~vP~vGDiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~g~i~~~dvr~te~d~~~m~~~fr~GDiV~A~Vis~~~~~~~   81 (125)
T d2nn6i1           2 QLLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSN   81 (125)
T ss_dssp             CCCCCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEEEEEETTTTE
T ss_pred             CcCCCCCCEEEEEEEEecCCEEEEEEeEecCcccccCccccccHHHcccchhhhhhHHHhcCCCCEEEEEEEEccCCCcc
Confidence            6899999999999999999999999999999999999999999999999999999999999999999999 9998875 5


Q ss_pred             eeeeeccCCCeeEEEEccCCCeeEeccC-ccCchhhhhhhhhhh
Q psy6276         143 YQLSTAENELGVVIALSEAASLFRSSEK-LTNDIEFLKQEKLKL  185 (271)
Q Consensus       143 ~~LST~~~eLGVV~A~c~cG~~Mvp~s~-~~~c~~~~~~e~rKl  185 (271)
                      |+|||++++||||+|+|.||++|+|.+| .+.||+|+..|+||+
T Consensus        82 ~~Lst~~~~LGVv~A~c~~g~~m~~~~~~~m~cp~~g~~E~RKV  125 (125)
T d2nn6i1          82 YLLTTAENELGVVVAHSESGIQMVPISWCEMQCPKTHTKEFRKV  125 (125)
T ss_dssp             EEEECCSSSCEECCCBCSSSCBCEEEETTEEECTTTTCCBCCCC
T ss_pred             EEEEecCCCcEEEEEECCCCCEeEeecCCEEECCCCCCeeccCC
Confidence            9999999999999999999999999997 699999999999996
>d2nn6h1 b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2nn6g1 b.40.4.5 (G:107-194) S1-domain of exosome component 3 (RRP40) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2ja9a1 b.40.4.5 (A:62-151) S1-domain of exosome component 3 (RRP40) {Saccharomyces cerevisiae [TaxId: 4932]} Back     information, alignment and structure
>d2je6i1 b.40.4.5 (I:66-152) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Back     information, alignment and structure
>d2z0sa1 b.40.4.5 (A:60-147) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} Back     information, alignment and structure
>d2ba0a1 b.40.4.5 (A:53-135) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d2ba0a2 b.84.4.2 (A:2-52) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d2nn6h2 b.84.4.2 (H:25-72) Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2je6i2 b.84.4.2 (I:7-65) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Back     information, alignment and structure
>d2nn6i2 b.84.4.2 (I:6-60) Exosome component 1, EXOSC1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1kl9a2 b.40.4.5 (A:3-88) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2ahob2 b.40.4.5 (B:1-84) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Sulfolobus solfataricus [TaxId: 2287]} Back     information, alignment and structure
>d1sroa_ b.40.4.5 (A:) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure
>d1wi5a_ b.40.4.5 (A:) S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1go3e1 b.40.4.5 (E:79-184) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
>d1y14b1 b.40.4.5 (B:81-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d2c35b1 b.40.4.5 (B:78-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1hh2p1 b.40.4.5 (P:127-198) S1 domain of NusA {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d2nn6g3 d.51.1.1 (G:195-274) Ribosomal RNA-processing protein 40, RRP40 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2asba1 b.40.4.5 (A:108-183) S1 domain of NusA {Mycobacterium tuberculosis [TaxId: 1773]} Back     information, alignment and structure
>d1v8qa_ b.84.4.1 (A:) Ribosomal protein L27 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d2nn6g2 b.84.4.2 (G:16-106) Ribosomal RNA-processing protein 40, RRP40 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1e3pa2 b.40.4.5 (A:656-717) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Streptomyces antibioticus [TaxId: 1890]} Back     information, alignment and structure
>d2zjrt1 b.84.4.1 (T:2-85) Ribosomal protein L27 {Deinococcus radiodurans [TaxId: 1299]} Back     information, alignment and structure
>d2ja9a2 d.51.1.1 (A:152-236) Ribosomal RNA-processing protein 40, RRP40 {Saccharomyces cerevisiae [TaxId: 4932]} Back     information, alignment and structure
>d1smxa_ b.40.4.5 (A:) S1-domain of Ribonuclease E {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1e1oa1 b.40.4.1 (A:11-153) Lysyl-tRNA synthetase (LysRS) {Escherichia coli, gene lysU [TaxId: 562]} Back     information, alignment and structure