Citrus Sinensis ID: 028346

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
MVVKEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGKLVYCISKYDLNIILFYSFWIFCILQIASNIISFITLFKFS
ccccccccEEEEcccEEcccccEEEcccEEEEccccEEEEEEEEEEEEccccccccccccEEEEEcccccccccccccEEEEEEEEEccccEEEEEEEEccEEcccccEEEEEccccccccccHHHHHcccccccEEEEEEEEccccccEEEEEEccccEEEEEEcccccEEEEEEccEEEEcccHHHHHHHHHHHHHccEEEEEEEEcc
cccccccccEEEccccccccccccccccEEEEEEccEEEEEEEEEEEEEcccccccccccEEEEEcccccccccccccEEEEEEEEEcccEEEEEEEEEcccccccccEEEEEEccccccccccEEEEEccccccEEEEEEEEccccccEEEEccccccEEEEEEcccccccEEcccccccEEEEEccEEEEEEEEccccEEEEEEEEcc
MVVKEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGllrtlspppdspdqrptvevtghkahgpvpepgSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIirqqdvrateidkvdmhlsfrpgdIVRASVLSLGDARAYFLSTAKndlgvvsaestagKLVYCISKYDLNIILFYSFWIFCILQIASNIISFITLFKFS
mvvkeeemvlvtpgevlgkateVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGhkahgpvpepgsvVIARVTKVMTRMASADIMCVGAKSVrekfsgiirqqdvrateidkvdmhlsfrpgDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGKLVYCISKYDLNIILFYSFWIFCILQIASNIISFITLFKFS
MVVKEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGKLVYCISKYDLNIILFYSFWIFCILQIASNIISFITLFKFS
********VLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLR******************************SVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGKLVYCISKYDLNIILFYSFWIFCILQIASNIISFITLFK**
******E***VTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPP*******************PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIR*Q******IDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGKLVYCISKYDLNIILFYSFWIFCILQIASNIISFITLFKFS
********VLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSP*************TGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGKLVYCISKYDLNIILFYSFWIFCILQIASNIISFITLFKFS
*******MVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGKLVYCISKYDLNIILFYSFWIFCILQIASNIISFITLFKFS
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ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiii
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MVVKEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGKLVYCISKYDLNIILFYSFWIFCILQIASNIISFITLFKFS
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

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query210 2.2.26 [Sep-21-2011]
Q9Y3B2195 Exosome complex component yes no 0.719 0.774 0.417 1e-24
Q9DAA6195 Exosome complex component yes no 0.719 0.774 0.417 1e-24
O59821181 Exosome complex component yes no 0.704 0.817 0.406 8e-24
P53859292 Exosome complex component yes no 0.576 0.414 0.350 1e-16
>sp|Q9Y3B2|EXOS1_HUMAN Exosome complex component CSL4 OS=Homo sapiens GN=EXOSC1 PE=1 SV=1 Back     alignment and function desciption
 Score =  113 bits (282), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 66/158 (41%), Positives = 94/158 (59%), Gaps = 7/158 (4%)

Query: 13  PGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGP 72
           PGE L    E   G G Y    +G +++SL G L   S         P V V        
Sbjct: 10  PGERLCNLEEGSPGSGTYT--RHGYIFSSLAGCLMKSS----ENGALPVVSVVRETESQL 63

Query: 73  VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFR 132
           +P+ G++V  +V+ + +R A   I+ VG+  ++  F G IR++DVRATE DKV+++ SFR
Sbjct: 64  LPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFR 123

Query: 133 PGDIVRASVLSLGDARA-YFLSTAKNDLGVVSAESTAG 169
           PGDIV A V+SLGDA++ Y L+TA+N+LGVV A S +G
Sbjct: 124 PGDIVLAKVISLGDAQSNYLLTTAENELGVVVAHSESG 161
Non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding 'pervasive' transcripts, such as antisense RNA species and promoter-upstream transcripts (PROMPTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. The RNA exosome may be involved in Ig class switch recombination (CSR) and/or Ig variable region somatic hypermutation (SHM) by targeting AICDA deamination activity to transcribed dsDNA substrates. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and specifically degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3' untranslated regions, and in RNA surveillance pathways, preventing translation of aberrant mRNAs. It seems to be involved in degradation of histone mRNA. The catalytic inactive RNA exosome core complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes. EXOSC1 as peripheral part of the Exo-9 complex stabilizes the hexameric ring of RNase PH-domain subunits through contacts with EXOSC6 and EXOSC8.
Homo sapiens (taxid: 9606)
>sp|Q9DAA6|EXOS1_MOUSE Exosome complex component CSL4 OS=Mus musculus GN=Exosc1 PE=2 SV=1 Back     alignment and function description
>sp|O59821|CSL4_SCHPO Exosome complex component csl4 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=csl4 PE=3 SV=2 Back     alignment and function description
>sp|P53859|CSL4_YEAST Exosome complex component CSL4 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=CSL4 PE=1 SV=1 Back     alignment and function description

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 ?
Query210
255634132189 unknown [Glycine max] 0.861 0.957 0.762 7e-73
224125764199 predicted protein [Populus trichocarpa] 0.857 0.904 0.760 2e-72
363814479197 uncharacterized protein LOC100796154 [Gl 0.861 0.918 0.756 5e-72
357441291 1109 Ammonium transporter [Medicago truncatul 0.857 0.162 0.738 2e-71
255562013 593 conserved hypothetical protein [Ricinus 0.866 0.306 0.755 4e-71
225430615200 PREDICTED: exosome complex component CSL 0.876 0.92 0.733 7e-70
297805862191 hypothetical protein ARALYDRAFT_494089 [ 0.823 0.905 0.725 1e-65
42568189191 exosome complex component CSL4 [Arabidop 0.823 0.905 0.72 4e-65
449453260196 PREDICTED: exosome complex component CSL 0.833 0.892 0.717 5e-64
226531832199 3-5 exoribonuclease CSL4 [Zea mays] gi|1 0.823 0.869 0.668 2e-58
>gi|255634132|gb|ACU17429.1| unknown [Glycine max] Back     alignment and taxonomy information
 Score =  278 bits (712), Expect = 7e-73,   Method: Compositional matrix adjust.
 Identities = 138/181 (76%), Positives = 153/181 (84%)

Query: 4   KEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVE 63
           +E+E V+VTPGEVLG+ ++VKAG+GAY A HN  VYASLTG   T+ P PDS D RPTVE
Sbjct: 3   EEKEAVMVTPGEVLGRTSDVKAGRGAYAALHNNTVYASLTGFRHTVPPAPDSSDLRPTVE 62

Query: 64  VTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEID 123
           VTGHKAHGPVP+PGSVVIARVTKVM R ASADIMCVG KSVREKF+GIIRQQDVRATEID
Sbjct: 63  VTGHKAHGPVPQPGSVVIARVTKVMARSASADIMCVGPKSVREKFTGIIRQQDVRATEID 122

Query: 124 KVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGKLVYCISKYDLNII 183
           KVDMHLSF PGDIVRA VLSLGDARAYFLSTAKN+LGVVSAES AG  +  +S  ++   
Sbjct: 123 KVDMHLSFHPGDIVRALVLSLGDARAYFLSTAKNELGVVSAESIAGATMVPVSWTEMQCP 182

Query: 184 L 184
           L
Sbjct: 183 L 183

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|224125764|ref|XP_002319669.1| predicted protein [Populus trichocarpa] gi|118483759|gb|ABK93772.1| unknown [Populus trichocarpa] gi|222858045|gb|EEE95592.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|363814479|ref|NP_001242874.1| uncharacterized protein LOC100796154 [Glycine max] gi|255640712|gb|ACU20640.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|357441291|ref|XP_003590923.1| Ammonium transporter [Medicago truncatula] gi|355479971|gb|AES61174.1| Ammonium transporter [Medicago truncatula] Back     alignment and taxonomy information
>gi|255562013|ref|XP_002522015.1| conserved hypothetical protein [Ricinus communis] gi|223538819|gb|EEF40419.1| conserved hypothetical protein [Ricinus communis] Back     alignment and taxonomy information
>gi|225430615|ref|XP_002266663.1| PREDICTED: exosome complex component CSL4 [Vitis vinifera] gi|296085148|emb|CBI28643.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|297805862|ref|XP_002870815.1| hypothetical protein ARALYDRAFT_494089 [Arabidopsis lyrata subsp. lyrata] gi|297316651|gb|EFH47074.1| hypothetical protein ARALYDRAFT_494089 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|42568189|ref|NP_568559.2| exosome complex component CSL4 [Arabidopsis thaliana] gi|124301132|gb|ABN04818.1| At5g38890 [Arabidopsis thaliana] gi|222423301|dbj|BAH19626.1| AT5G38890 [Arabidopsis thaliana] gi|332006986|gb|AED94369.1| exosome complex component CSL4 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|449453260|ref|XP_004144376.1| PREDICTED: exosome complex component CSL4-like [Cucumis sativus] gi|449515303|ref|XP_004164689.1| PREDICTED: exosome complex component CSL4-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|226531832|ref|NP_001148354.1| 3-5 exoribonuclease CSL4 [Zea mays] gi|195618352|gb|ACG31006.1| 3-5 exoribonuclease CSL4 [Zea mays] gi|223975657|gb|ACN32016.1| unknown [Zea mays] gi|413939469|gb|AFW74020.1| 3-5 exoribonuclease CSL4 [Zea mays] 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 ?
Query210
TAIR|locus:2152297191 AT5G38890 [Arabidopsis thalian 0.785 0.863 0.748 5.5e-61
UNIPROTKB|G4ML19213 MGG_08628 "3'-5' exoribonuclea 0.557 0.549 0.483 5.3e-30
ZFIN|ZDB-GENE-080926-3194 exosc1 "exosome component 1" [ 0.771 0.835 0.409 3.2e-26
ASPGD|ASPL0000007077246 AN11250 [Emericella nidulans ( 0.333 0.284 0.514 2.2e-25
UNIPROTKB|Q5E9E9195 EXOSC1 "Uncharacterized protei 0.752 0.810 0.412 3.6e-25
UNIPROTKB|Q9Y3B2195 EXOSC1 "Exosome complex compon 0.719 0.774 0.424 3.6e-25
UNIPROTKB|E2RT56207 EXOSC1 "Uncharacterized protei 0.752 0.763 0.412 4.6e-25
MGI|MGI:1913833195 Exosc1 "exosome component 1" [ 0.752 0.810 0.418 4.6e-25
UNIPROTKB|F1S8Y4196 EXOSC1 "Uncharacterized protei 0.752 0.806 0.409 5.3e-24
POMBASE|SPCC1840.11181 csl4 "exosome subunit Csl4 (pr 0.704 0.817 0.406 8.7e-24
TAIR|locus:2152297 AT5G38890 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 624 (224.7 bits), Expect = 5.5e-61, P = 5.5e-61
 Identities = 125/167 (74%), Positives = 144/167 (86%)

Query:    10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKA 69
             LVTPG+V+GKATE KAGKGAYV  ++  +YASLTG  R +SP P+S DQR  VEVTGHKA
Sbjct:     5 LVTPGDVIGKATEFKAGKGAYV--NDATIYASLTGTCRIVSPLPESIDQRAIVEVTGHKA 62

Query:    70 HGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHL 129
             HGP+PE GSVVIARVTKVMT+MA+ DI+CVG+K+VRE F+G+IRQQDVRATEIDKVDMH 
Sbjct:    63 HGPIPETGSVVIARVTKVMTKMAAVDILCVGSKAVRENFAGVIRQQDVRATEIDKVDMHQ 122

Query:   130 SFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAESTAGKLVYCIS 176
             SF  GDIVRA VLSLGDARAY+LSTAKN+LGVVSAES AG+ +  IS
Sbjct:   123 SFHAGDIVRAMVLSLGDARAYYLSTAKNELGVVSAESAAGETMVPIS 169
GO:0003723 "RNA binding" evidence=IEA
GO:0005634 "nucleus" evidence=ISM
GO:0008150 "biological_process" evidence=ND
GO:0006626 "protein targeting to mitochondrion" evidence=RCA
UNIPROTKB|G4ML19 MGG_08628 "3'-5' exoribonuclease CSL4" [Magnaporthe oryzae 70-15 (taxid:242507)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-080926-3 exosc1 "exosome component 1" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
ASPGD|ASPL0000007077 AN11250 [Emericella nidulans (taxid:162425)] Back     alignment and assigned GO terms
UNIPROTKB|Q5E9E9 EXOSC1 "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|Q9Y3B2 EXOSC1 "Exosome complex component CSL4" [Homo sapiens (taxid:9606)] 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
POMBASE|SPCC1840.11 csl4 "exosome subunit Csl4 (predicted)" [Schizosaccharomyces pombe (taxid:4896)] 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 Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
grail3.0016041401
SubName- Full=Putative uncharacterized protein; (199 aa)
(Populus trichocarpa)
Predicted Functional Partners:
estExt_fgenesh4_pm.C_LG_XIV0164
hypothetical protein (241 aa)
  ••••• 0.950
eugene3.00031704
hypothetical protein (320 aa)
  ••••• 0.926
estExt_Genewise1_v1.C_LG_XII0359
SubName- Full=Putative uncharacterized protein; (242 aa)
   •••• 0.901
estExt_fgenesh4_pm.C_LG_XIV0472
hypothetical protein (288 aa)
  ••••• 0.882
estExt_fgenesh4_pg.C_LG_III0702
hypothetical protein (935 aa)
   •••• 0.793
gw1.I.838.1
hypothetical protein (302 aa)
  ••••• 0.735
gw1.IX.3706.1
annotation not avaliable (298 aa)
  ••••• 0.730
gw1.XVIII.1197.1
hypothetical protein (232 aa)
   •••• 0.671
eugene3.00060466
hypothetical protein (318 aa)
  ••••• 0.644
estExt_Genewise1_v1.C_LG_XVIII2468
hypothetical protein (213 aa)
•       0.638

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query210
cd0579192 cd05791, S1_CSL4, S1_CSL4: CSL4, S1-like RNA-bindi 6e-43
pfam1044772 pfam10447, EXOSC1, Exosome component EXOSC1/CSL4 8e-33
COG1096188 COG1096, COG1096, Predicted RNA-binding protein (c 8e-24
PRK09521189 PRK09521, PRK09521, exosome complex RNA-binding pr 7e-15
cd0445482 cd04454, S1_Rrp4_like, S1_Rrp4_like: Rrp4-like, S1 7e-12
pfam1438239 pfam14382, ECR1_N, Exosome complex exonuclease RRP 7e-09
COG1097239 COG1097, RRP4, RNA-binding protein Rrp4 and relate 4e-05
PRK04163235 PRK04163, PRK04163, exosome complex RNA-binding pr 4e-05
>gnl|CDD|240217 cd05791, S1_CSL4, S1_CSL4: CSL4, S1-like RNA-binding domain Back     alignment and domain information 
 Score =  138 bits (351), Expect = 6e-43
 Identities = 55/91 (60%), Positives = 75/91 (82%)

Query: 72  PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSF 131
            +P+ GS+VIARVT++  R A  DI+CVG + ++E F G+IR++D+RATE DKV+M+  F
Sbjct: 2   VLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCF 61

Query: 132 RPGDIVRASVLSLGDARAYFLSTAKNDLGVV 162
           RPGDIVRA V+SLGDA +Y+LSTA+N+LGVV
Sbjct: 62  RPGDIVRAKVISLGDASSYYLSTAENELGVV 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|239901 cd04454, S1_Rrp4_like, S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain 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|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

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 210
COG1096188 Predicted RNA-binding protein (consists of S1 doma 100.0
PRK09521189 exosome complex RNA-binding protein Csl4; Provisio 100.0
KOG3409193 consensus Exosomal 3'-5' exoribonuclease complex, 100.0
PRK04163235 exosome complex RNA-binding protein Rrp4; Provisio 99.98
COG1097239 RRP4 RNA-binding protein Rrp4 and related proteins 99.96
KOG3013301 consensus Exosomal 3'-5' exoribonuclease complex, 99.95
cd0579192 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. 99.95
PF1044782 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I 99.87
cd0445482 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA- 99.77
KOG1004230 consensus Exosomal 3'-5' exoribonuclease complex s 99.69
cd0578986 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. 99.65
cd0579086 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai 99.59
PF1438239 ECR1_N: Exosome complex exonuclease RRP4 N-termina 99.37
COG1098129 VacB Predicted RNA binding protein (contains ribos 99.35
cd0570472 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a 99.33
cd0568770 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib 99.22
cd0570673 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a 99.15
cd0569173 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p 99.13
cd0570574 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a 99.13
cd0445276 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr 99.1
PRK08582139 hypothetical protein; Provisional 99.09
cd0570270 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R 99.06
cd05693100 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp 99.05
cd0570373 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R 99.04
cd0569269 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p 99.04
cd0568673 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom 99.02
PF0057574 S1: S1 RNA binding domain; InterPro: IPR003029 Rib 99.02
cd0570768 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a 99.01
cd0570877 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a 99.0
PRK07252120 hypothetical protein; Provisional 98.96
PRK05807136 hypothetical protein; Provisional 98.96
cd0569870 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp 98.96
PTZ00248 319 eukaryotic translation initiation factor 2 subunit 98.92
smart0031672 S1 Ribosomal protein S1-like RNA-binding domain. 98.92
PRK08059123 general stress protein 13; Validated 98.91
cd0569671 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t 98.86
cd0446183 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp 98.85
cd0569769 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t 98.85
PRK03987 262 translation initiation factor IF-2 subunit alpha; 98.84
COG0539 541 RpsA Ribosomal protein S1 [Translation, ribosomal 98.82
cd0569474 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp 98.78
cd0568868 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p 98.76
cd0569566 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t 98.76
cd0447268 S1_PNPase S1_PNPase: Polynucleotide phosphorylase 98.75
cd0568568 S1_Tex S1_Tex: The C-terminal S1 domain of a trans 98.74
cd0445388 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik 98.69
PRK11824693 polynucleotide phosphorylase/polyadenylase; Provis 98.69
PHA0294588 interferon resistance protein; Provisional 98.65
COG1093 269 SUI2 Translation initiation factor 2, alpha subuni 98.63
PRK08563187 DNA-directed RNA polymerase subunit E'; Provisiona 98.62
PRK07400318 30S ribosomal protein S1; Reviewed 98.61
cd0568479 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal 98.6
cd0569069 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p 98.58
TIGR00448179 rpoE DNA-directed RNA polymerase (rpoE), archaeal 98.57
cd0446099 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. 98.55
TIGR02696719 pppGpp_PNP guanosine pentaphosphate synthetase I/p 98.52
TIGR03591684 polynuc_phos polyribonucleotide nucleotidyltransfe 98.47
cd0016465 S1_like S1_like: Ribosomal protein S1-like RNA-bin 98.47
PRK07400 318 30S ribosomal protein S1; Reviewed 98.43
cd0568972 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p 98.43
cd0445567 S1_NusA S1_NusA: N-utilizing substance A protein ( 98.42
PRK13806491 rpsA 30S ribosomal protein S1; Provisional 98.41
COG1095183 RPB7 DNA-directed RNA polymerase, subunit E' [Tran 98.4
cd0447377 S1_RecJ_like S1_RecJ_like: The S1 domain of the ar 98.38
cd0446567 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib 98.35
COG0539 541 RpsA Ribosomal protein S1 [Translation, ribosomal 98.34
PRK13806 491 rpsA 30S ribosomal protein S1; Provisional 98.31
PRK07899 486 rpsA 30S ribosomal protein S1; Reviewed 98.3
PLN00207891 polyribonucleotide nucleotidyltransferase; Provisi 98.28
PRK07899 486 rpsA 30S ribosomal protein S1; Reviewed 98.28
PRK06299565 rpsA 30S ribosomal protein S1; Reviewed 98.25
PRK12269 863 bifunctional cytidylate kinase/ribosomal protein S 98.25
PRK06676390 rpsA 30S ribosomal protein S1; Reviewed 98.22
PRK06676390 rpsA 30S ribosomal protein S1; Reviewed 98.2
PRK06299 565 rpsA 30S ribosomal protein S1; Reviewed 98.17
cd0447183 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai 98.16
PRK00087647 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 98.1
TIGR00717516 rpsA ribosomal protein S1. This model provides tru 98.09
PTZ00162176 DNA-directed RNA polymerase II subunit 7; Provisio 98.04
PRK12269863 bifunctional cytidylate kinase/ribosomal protein S 98.02
TIGR00717 516 rpsA ribosomal protein S1. This model provides tru 97.95
PRK00087 647 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 97.94
COG2183780 Tex Transcriptional accessory protein [Transcripti 97.93
COG1185692 Pnp Polyribonucleotide nucleotidyltransferase (pol 97.67
PRK09202 470 nusA transcription elongation factor NusA; Validat 97.64
PRK12327 362 nusA transcription elongation factor NusA; Provisi 97.51
TIGR01953341 NusA transcription termination factor NusA. This m 97.49
cd0446288 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly 97.36
PHA0285886 EIF2a-like PKR inhibitor; Provisional 97.23
TIGR00757 414 RNaseEG ribonuclease, Rne/Rng family. The C-termin 96.97
TIGR02063709 RNase_R ribonuclease R. This family consists of an 96.83
PRK12328 374 nusA transcription elongation factor NusA; Provisi 96.64
KOG1070 1710 consensus rRNA processing protein Rrp5 [RNA proces 96.62
PRK12329 449 nusA transcription elongation factor NusA; Provisi 96.54
PRK11642813 exoribonuclease R; Provisional 96.52
KOG1070 1710 consensus rRNA processing protein Rrp5 [RNA proces 96.46
TIGR00358654 3_prime_RNase VacB and RNase II family 3'-5' exori 96.13
cd0569972 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t 95.87
KOG1067760 consensus Predicted RNA-binding polyribonucleotide 95.59
KOG1856 1299 consensus Transcription elongation factor SPT6 [RN 95.52
COG2996287 Predicted RNA-bindining protein (contains S1 and H 95.46
KOG2916 304 consensus Translation initiation factor 2, alpha s 95.25
PRK11712 489 ribonuclease G; Provisional 94.81
PRK10811 1068 rne ribonuclease E; Reviewed 94.57
COG1571421 Predicted DNA-binding protein containing a Zn-ribb 92.73
PF1350961 S1_2: S1 domain; PDB: 3GO5_A. 91.86
KOG3298170 consensus DNA-directed RNA polymerase subunit E' [ 91.68
PF0929732 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon do 90.5
PF0101681 Ribosomal_L27: Ribosomal L27 protein; InterPro: IP 89.42
smart0065944 RPOLCX RNA polymerase subunit CX. present in RNA p 89.15
CHL0012186 rpl27 ribosomal protein L27; Reviewed 89.1
PRK05054644 exoribonuclease II; Provisional 88.28
PRK0543582 rpmA 50S ribosomal protein L27; Validated 88.18
PF0775424 DUF1610: Domain of unknown function (DUF1610); Int 86.64
COG1530 487 CafA Ribonucleases G and E [Translation, ribosomal 85.05
PF0749778 Rho_RNA_bind: Rho termination factor, RNA-binding 83.85
TIGR0006283 L27 ribosomal protein L27. Eubacterial, chloroplas 83.25
COG0557706 VacB Exoribonuclease R [Transcription] 82.82
PF0360432 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa 82.5
PF01959354 DHQS: 3-dehydroquinate synthase (EC 4.6.1.3); Inte 80.57
>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=1.1e-44  Score=296.69  Aligned_cols=169  Identities=31%  Similarity=0.394  Sum_probs=158.7

Q ss_pred             CCceEEecCCccCCCCCeeeCCcEEEeCCeeEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEE
Q 028346            6 EEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVT   85 (210)
Q Consensus         6 ~~~~iV~PGd~l~~~ee~~~G~GtY~~~g~~~I~Asv~G~v~~~~~~~~~d~~~~~i~V~p~~~~~y~p~vGDiViG~V~   85 (210)
                      .++.+|+|||.|+..|||+||.|||+++|+  |+|+.+|.+.+       |++++.++|.|.+..+.+|+.||+|+|+|+
T Consensus         3 ~~g~~v~PGd~~a~~EE~~~G~gt~~~~g~--i~Aa~~G~~~~-------d~~n~~~~V~p~~~~~~~~K~GdiV~grV~   73 (188)
T COG1096           3 KDGTFVLPGDVLAVIEEFLPGEGTYEEGGE--IRAAATGVVRR-------DDKNRVISVKPGKKTPPLPKGGDIVYGRVT   73 (188)
T ss_pred             ccCcEEcCcceeeeeeeeecCCCeEeECCE--EEEeecccEEE-------cccceEEEeccCCCCCCCCCCCCEEEEEEe
Confidence            367789999999999999999999999999  99999999999       667889999999876889999999999999


Q ss_pred             EEecCeEEEEEeeecccc--ccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCCcceEEEeecCCceeeE
Q 028346           86 KVMTRMASADIMCVGAKS--VREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVS  163 (210)
Q Consensus        86 ~v~~~~a~V~I~~v~~~~--l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~~~~~LSt~~~~LGVv~  163 (210)
                      +++.+.|.|+|.++++..  +..++.|.||+||++..+..  +++++|++||+|+|+|+|.+  .++.|||++++||||+
T Consensus        74 ~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~--~~~d~f~~GDivrA~Vis~~--~~~~Lst~~~dlGVI~  149 (188)
T COG1096          74 DVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVE--KLSDAFRIGDIVRARVISTG--DPIQLSTKGNDLGVIY  149 (188)
T ss_pred             eccceEEEEEEEEEecccccCCCCceeeEEEEeccccccc--ccccccccccEEEEEEEecC--CCeEEEecCCcceEEE
Confidence            999999999999999954  88899999999999998887  89999999999999999987  4799999999999999


Q ss_pred             EEc-CCCCeeEEcccceEEecccchh
Q 028346          164 AES-TAGKLVYCISKYDLNIILFYSF  188 (210)
Q Consensus       164 a~~-~~G~~m~~~~~~~l~C~~~~~~  188 (210)
                      |+| +||++|.+ .|++|.||+|+..
T Consensus       150 A~CsrC~~~L~~-~~~~l~Cp~Cg~t  174 (188)
T COG1096         150 ARCSRCRAPLVK-KGNMLKCPNCGNT  174 (188)
T ss_pred             EEccCCCcceEE-cCcEEECCCCCCE
Confidence            999 99999999 8899999999864

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional Back     alignment and domain information
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis] 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
>KOG3013 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification] Back     alignment and domain information
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain 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
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain Back     alignment and domain information
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 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
>PF14382 ECR1_N: Exosome complex exonuclease RRP4 N-terminal region; PDB: 2NN6_I 3M7N_C 2BA1_A 3M85_C 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
>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
>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
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain 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
>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
>PRK08582 hypothetical protein; Provisional 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
>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
>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
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain 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
>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
>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
>PRK07252 hypothetical protein; 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
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional Back     alignment and domain information
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain Back     alignment and domain information
>PRK08059 general stress protein 13; Validated 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
>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
>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
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated Back     alignment and domain information
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis] 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
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain 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
>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
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain Back     alignment and domain information
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional Back     alignment and domain information
>PHA02945 interferon resistance protein; Provisional 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
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional Back     alignment and domain information
>PRK07400 30S ribosomal protein S1; Reviewed 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
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form Back     alignment and domain information
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain Back     alignment and domain information
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase Back     alignment and domain information
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase Back     alignment and domain information
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain 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
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain Back     alignment and domain information
>PRK13806 rpsA 30S ribosomal protein S1; Provisional Back     alignment and domain information
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription] 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
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK13806 rpsA 30S ribosomal protein S1; Provisional Back     alignment and domain information
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional Back     alignment and domain information
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional Back     alignment and domain information
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain 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
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional Back     alignment and domain information
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional Back     alignment and domain information
>TIGR00717 rpsA ribosomal protein S1 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
>COG2183 Tex Transcriptional accessory protein [Transcription] Back     alignment and domain information
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK09202 nusA transcription elongation factor NusA; Validated Back     alignment and domain information
>PRK12327 nusA transcription elongation factor NusA; 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
>PHA02858 EIF2a-like PKR inhibitor; Provisional Back     alignment and domain information
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family Back     alignment and domain information
>TIGR02063 RNase_R ribonuclease R Back     alignment and domain information
>PRK12328 nusA transcription elongation factor NusA; Provisional Back     alignment and domain information
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification] Back     alignment and domain information
>PRK12329 nusA transcription elongation factor NusA; Provisional Back     alignment and domain information
>PRK11642 exoribonuclease R; Provisional Back     alignment and domain information
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification] Back     alignment and domain information
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases 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
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only] Back     alignment and domain information
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification] Back     alignment and domain information
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only] Back     alignment and domain information
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK11712 ribonuclease G; Provisional Back     alignment and domain information
>PRK10811 rne ribonuclease E; Reviewed Back     alignment and domain information
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only] Back     alignment and domain information
>PF13509 S1_2: S1 domain; PDB: 3GO5_A Back     alignment and domain information
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription] 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
>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
>smart00659 RPOLCX RNA polymerase subunit CX Back     alignment and domain information
>CHL00121 rpl27 ribosomal protein L27; Reviewed Back     alignment and domain information
>PRK05054 exoribonuclease II; Provisional Back     alignment and domain information
>PRK05435 rpmA 50S ribosomal protein L27; Validated 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
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PF07497 Rho_RNA_bind: Rho termination factor, RNA-binding domain; InterPro: IPR011113 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts Back     alignment and domain information
>TIGR00062 L27 ribosomal protein L27 Back     alignment and domain information
>COG0557 VacB Exoribonuclease R [Transcription] Back     alignment and domain information
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates Back     alignment and domain information
>PF01959 DHQS: 3-dehydroquinate synthase (EC 4 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 ?
Query210
2nn6_I209 Structure Of The Human Rna Exosome Composed Of Rrp4 1e-25
4ifd_I301 Crystal Structure Of An 11-subunit Eukaryotic Exoso 1e-17
>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 =  112 bits (281), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 66/158 (41%), Positives = 94/158 (59%), Gaps = 7/158 (4%)
Query: 13  PGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGP 72
           PGE L    E   G G Y    +G +++SL G L   S         P V V        
Sbjct: 24  PGERLCNLEEGSPGSGTYT--RHGYIFSSLAGCLMKSS----ENGALPVVSVVRETESQL 77
Query: 73  VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFR 132
           +P+ G++V  +V+ + +R A   I+ VG+  ++  F G IR++DVRATE DKV+++ SFR
Sbjct: 78  LPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFR 137
Query: 133 PGDIVRASVLSLGDARA-YFLSTAKNDLGVVSAESTAG 169
           PGDIV A V+SLGDA++ Y L+TA+N+LGVV A S +G
Sbjct: 138 PGDIVLAKVISLGDAQSNYLLTTAENELGVVVAHSESG 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 ?
Query210
2nn6_I209 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, 4e-46
3m7n_A179 Putative uncharacterized protein AF_0206; exosome, 2e-30
2nn6_H308 Exosome complex exonuclease RRP4; RNA, exosome, PM 1e-23
2je6_I251 RRP4, exosome complex RNA-binding protein 1; nucle 2e-22
2z0s_A235 Probable exosome complex RNA-binding protein 1; al 2e-15
2ba0_A229 Archeal exosome RNA binding protein RRP4; RNAse PH 1e-13
>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 =  150 bits (381), Expect = 4e-46
 Identities = 67/168 (39%), Positives = 95/168 (56%), Gaps = 7/168 (4%)

Query: 10  LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKA 69
              PGE L    E   G G Y    +G +++SL G L             P V V     
Sbjct: 21  YCIPGERLCNLEEGSPGSGTYT--RHGYIFSSLAGCLMK----SSENGALPVVSVVRETE 74

Query: 70  HGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHL 129
              +P+ G++V  +V+ + +R A   I+ VG+  ++  F G IR++DVRATE DKV+++ 
Sbjct: 75  SQLLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYK 134

Query: 130 SFRPGDIVRASVLSLGDAR-AYFLSTAKNDLGVVSAESTAGKLVYCIS 176
           SFRPGDIV A V+SLGDA+  Y L+TA+N+LGVV A S +G  +  IS
Sbjct: 135 SFRPGDIVLAKVISLGDAQSNYLLTTAENELGVVVAHSESGIQMVPIS 182
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query210
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 99.97
2je6_I251 RRP4, exosome complex RNA-binding protein 1; nucle 99.97
2z0s_A235 Probable exosome complex RNA-binding protein 1; al 99.97
2nn6_G289 Exosome complex exonuclease RRP40; RNA, exosome, P 99.96
2ja9_A175 Exosome complex exonuclease RRP40; RNA-binding pro 99.75
2k52_A80 Uncharacterized protein MJ1198; metal-binding, zin 99.2
2k4k_A130 GSP13, general stress protein 13; cytoplasm, stres 99.18
2khi_A115 30S ribosomal protein S1; acetylation, phosphoprot 99.16
2khj_A109 30S ribosomal protein S1; OB fold, acetylation, ph 99.13
1kl9_A182 Eukaryotic translation initiation factor 2 subuni; 99.12
2eqs_A103 ATP-dependent RNA helicase DHX8; S1 domain, OB-fol 99.12
2a19_A175 EIF-2- alpha, eukaryotic translation initiation fa 99.11
2cqo_A119 Nucleolar protein of 40 kDa; S1 domain, OB-fold, s 99.08
1go3_E187 DNA-directed RNA polymerase subunit E; transferase 99.01
1luz_A88 Protein K3, protein K2; stranded anti-parallel bet 98.99
3aev_A 275 Translation initiation factor 2 subunit alpha; pro 98.95
4ayb_E180 DNA-directed RNA polymerase; transferase, multi-su 98.89
1wi5_A119 RRP5 protein homolog; S1 domain, OB-fold, structur 98.88
1q8k_A 308 Eukaryotic translation initiation factor 2 subunit 98.87
3cw2_C 266 Translation initiation factor 2 subunit alpha; AIF 98.78
2c35_B172 Human RPB7, DNA-directed RNA polymerase II 19 kDa 98.68
1y14_B171 B16, RPB7, DNA-directed RNA polymerase II 19 kDa p 98.6
3go5_A285 Multidomain protein with S1 RNA-binding domains; s 98.53
3h0g_G172 DNA-directed RNA polymerase II subunit RPB7; trans 98.48
4aid_A726 Polyribonucleotide nucleotidyltransferase; transfe 98.48
3psi_A 1219 Transcription elongation factor SPT6; nucleus; 3.3 98.47
2b8k_G215 B16, DNA-directed RNA polymerase II 19 kDa polypep 98.45
3psf_A1030 Transcription elongation factor SPT6; nucleus; 2.5 98.29
3cdi_A723 Polynucleotide phosphorylase; mRNA turnover, RNAse 98.25
3bzc_A785 TEX; helix-turn-helix, helix-hairpin-helix, S1 dom 98.22
3ayh_B203 DNA-directed RNA polymerase III subunit RPC8; tran 98.16
1e3p_A757 Guanosine pentaphosphate synthetase; polyribonucle 98.12
1hh2_P344 NUSA, N utilization substance protein A; transcrip 98.02
2asb_A 251 Transcription elongation protein NUSA; protein-RNA 97.98
1k0r_A 366 NUSA; two component arrangement, S1 domain, two K- 97.77
2bx2_L 517 Ribonuclease E, RNAse E; RNA-binding, RNA turnover 97.49
2ckz_B218 C25, DNA-directed RNA polymerase III 25 KD polypep 97.43
3go5_A285 Multidomain protein with S1 RNA-binding domains; s 97.25
2bh8_A101 1B11; transcription, molecular evolution, unique a 96.32
2id0_A644 Exoribonuclease 2; RNAse, exonuclease, hydrolyase, 96.2
3d0f_A106 Penicillin-binding 1 transmembrane protein MRCA; B 95.46
2vnu_D760 Exosome complex exonuclease RRP44; hydrolase-RNA c 95.29
2wp8_J977 Exosome complex exonuclease DIS3; nucleus, hydrola 94.86
2rf4_A214 DNA-directed RNA polymerase I subunit RPA4; transf 89.77
3v2d_085 50S ribosomal protein L27; ribosome associated inh 89.2
3r8s_W76 50S ribosomal protein L27; protein biosynthesis, R 85.9
2zjr_T91 50S ribosomal protein L27; ribosome, large ribosom 85.89
3h0g_L63 DNA-directed RNA polymerases I, II, and III subuni 81.35
>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=5.8e-45  Score=299.53  Aligned_cols=162  Identities=21%  Similarity=0.287  Sum_probs=151.2

Q ss_pred             ceEEecCCccCCCCCeeeCCcEEEeCCeeEEEEeEeeeEEEcCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEE
Q 028346            8 MVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKV   87 (210)
Q Consensus         8 ~~iV~PGd~l~~~ee~~~G~GtY~~~g~~~I~Asv~G~v~~~~~~~~~d~~~~~i~V~p~~~~~y~p~vGDiViG~V~~v   87 (210)
                      |++|+|||.|+..++|.+|+|||.++|+  |+||++|.+++         +++.++|+|.++++|.|+ ||+|+|+|+++
T Consensus         1 m~iV~PGd~l~~~~~~~~G~Gty~~~~~--i~as~~G~v~~---------~~~~v~V~~~~~~~y~p~-GdiV~G~V~~V   68 (179)
T 3m7n_A            1 MRFVMPGDRIGSAEEYVKGEGVYEEGGE--LFAAVAGKLII---------KDRVAKVESISPIPEIVK-GDVVLGRVVDL   68 (179)
T ss_dssp             CCEECTTCEEEETTTSEECTTEEEETTE--EEESSSEEEEE---------ETTEEEEEESSCCCCCCT-TCEEEEEEEEE
T ss_pred             CeEEcCCCCCCCCCCEeccCCEEEeCCE--EEEEEEEEEEE---------eCCEEEEEECCCCcccCC-CCEEEEEEEEE
Confidence            4789999999998999999999999999  99999999998         357999999987789999 99999999999


Q ss_pred             ecCeEEEEEeee--ccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCCcceEEEeecCCceeeEEE
Q 028346           88 MTRMASADIMCV--GAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDARAYFLSTAKNDLGVVSAE  165 (210)
Q Consensus        88 ~~~~a~V~I~~v--~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~~~~~LSt~~~~LGVv~a~  165 (210)
                      ++++|+|+|.++  +++++..+++|+||+||+++++.+  +++++|++||+|+|+|++    +++.|||++++||||+|+
T Consensus        69 ~~~ga~V~I~~v~~~~~~~~~~~~Gll~isei~~~~~~--~~~~~~~~GD~V~akVi~----~~i~LS~k~~~lGvv~a~  142 (179)
T 3m7n_A           69 RNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVK--EISEAVGYLDILKARVIG----DNLRLSTKEEEMGVLRAL  142 (179)
T ss_dssp             CSSEEEEEEEEETTCCSCCTTCEEEEEEGGGTTSSCCS--SGGGTCCTTCEEEEEEEE----TTTEEECCSTTCEEEECB
T ss_pred             eCCcEEEEEccccCcccccccCeeEEEEHHHcCcchhh--CHhhcCCCCCEEEEEEEC----CeEEEEEecCCCCEEEec
Confidence            999999999998  556777899999999999988776  899999999999999998    579999999999999999


Q ss_pred             c-CCCCeeEEcccceEEecccchh
Q 028346          166 S-TAGKLVYCISKYDLNIILFYSF  188 (210)
Q Consensus       166 ~-~~G~~m~~~~~~~l~C~~~~~~  188 (210)
                      | +||.+|+|.+ ++|+||+|+..
T Consensus       143 ~~~~g~~m~~~~-~~~~cp~~g~~  165 (179)
T 3m7n_A          143 CSNCKTEMVREG-DILKCPECGRV  165 (179)
T ss_dssp             CTTTCCBCEECS-SSEECSSSCCE
T ss_pred             ccccCCceEECC-CEEECCCCCCE
Confidence            9 9999999999 89999999875
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure
>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A Back     alignment and structure
>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae} 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
>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
>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A {Schizosaccharomyces pombe} 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
>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
>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
>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
>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
>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
>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
>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
>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
>2vnu_D Exosome complex exonuclease RRP44; hydrolase-RNA complex, RNA degradation, RNA-binding, RNA Pro; HET: 1PE; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 Back     alignment and structure
>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae} Back     alignment and structure
>2rf4_A DNA-directed RNA polymerase I subunit RPA4; transferase DNA/RNA, DNA-binding, phosphorylation, POL I, POLI, rpoli, nuclear protein; 3.10A {Saccharomyces cerevisiae} 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
>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
>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
>3h0g_L DNA-directed RNA polymerases I, II, and III subunit rpabc4; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} 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 210
d2nn6i1125 b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {H 2e-35
d2nn6h195 b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-pro 1e-06
d2nn6i255 b.84.4.2 (I:6-60) Exosome component 1, EXOSC1 {Hum 2e-05
d2je6i187 b.40.4.5 (I:66-152) S1-domain of exosome complex R 0.003
d2je6i259 b.84.4.2 (I:7-65) Exosome complex RNA-binding prot 0.004
>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 =  119 bits (300), Expect = 2e-35
 Identities = 51/105 (48%), Positives = 75/105 (71%), Gaps = 1/105 (0%)

Query: 73  VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFR 132
           +P+ G++V  +V+ + +R A   I+ VG+  ++  F G IR++DVRATE DKV+++ SFR
Sbjct: 4   LPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFR 63

Query: 133 PGDIVRASVLSLGDAR-AYFLSTAKNDLGVVSAESTAGKLVYCIS 176
           PGDIV A V+SLGDA+  Y L+TA+N+LGVV A S +G  +  IS
Sbjct: 64  PGDIVLAKVISLGDAQSNYLLTTAENELGVVVAHSESGIQMVPIS 108
>d2nn6h1 b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]} Length = 95 Back     information, alignment and structure
>d2nn6i2 b.84.4.2 (I:6-60) Exosome component 1, EXOSC1 {Human (Homo sapiens) [TaxId: 9606]} Length = 55 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]} Length = 87 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 ?
Query210
d2nn6i1125 Exosome component 1, EXOSC1 {Human (Homo sapiens) 100.0
d2nn6h195 S1-domain of Ribosomal RNA-processing protein 4, R 99.77
d2je6i187 S1-domain of exosome complex RNA-binding protein 1 99.74
d2z0sa188 S1-domain of exosome complex RNA-binding protein 1 99.73
d2nn6g188 S1-domain of exosome component 3 (RRP40) {Human (H 99.72
d2ja9a190 S1-domain of exosome component 3 (RRP40) {Saccharo 99.72
d2ba0a183 S1-domain of exosome complex RNA-binding protein 1 99.71
d2ba0a251 Exosome complex RNA-binding protein 1, ECR1 {Archa 99.46
d2nn6h248 Ribosomal RNA-processing protein 4, RRP4 {Human (H 99.4
d2nn6i255 Exosome component 1, EXOSC1 {Human (Homo sapiens) 99.37
d1sroa_76 S1 RNA-binding domain of polyribonucleotide phosph 99.35
d1kl9a286 Eukaryotic initiation factor 2alpha, eIF2alpha, N- 99.35
d2je6i259 Exosome complex RNA-binding protein 1, ECR1 {Sulfo 99.32
d2ahob284 Eukaryotic initiation factor 2alpha, eIF2alpha, N- 99.31
d3bzka494 Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287] 99.17
d1go3e1106 C-terminal domain of RNA polymerase II subunit RBP 98.96
d1wi5a_119 S1-domain of RRP5 protein homolog (PDCD11, KIAA018 98.96
d1y14b191 C-terminal domain of RNA polymerase II subunit RBP 98.71
d2c35b194 C-terminal domain of RNA polymerase II subunit RBP 98.63
d1e3pa262 S1 RNA-binding domain of polyribonucleotide phosph 98.36
d1hh2p172 S1 domain of NusA {Thermotoga maritima [TaxId: 233 98.36
d2asba176 S1 domain of NusA {Mycobacterium tuberculosis [Tax 97.66
d1smxa_87 S1-domain of Ribonuclease E {Escherichia coli [Tax 96.92
d2ix0a387 Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5 96.76
d2nn6g291 Ribosomal RNA-processing protein 40, RRP40 {Human 96.69
d1v8qa_66 Ribosomal protein L27 {Thermus thermophilus [TaxId 94.78
d2zjrt184 Ribosomal protein L27 {Deinococcus radiodurans [Ta 94.13
d1vk6a429 NADH pyrophosphatase intervening domain {Escherich 87.43
d1e1oa1143 Lysyl-tRNA synthetase (LysRS) {Escherichia coli, g 81.63
d2akla238 Hypothetical protein PA0128, N-terminal domain {Ps 81.0
>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=2.4e-38  Score=244.68  Aligned_cols=118  Identities=43%  Similarity=0.659  Sum_probs=113.3

Q ss_pred             CCCCCCCCEEEEEEEEEecCeEEEEEeeeccccccCceeEEEeccccccccccccccCCCCCCCCEEEEEEEEeCCCc-c
Q 028346           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRQQDVRATEIDKVDMHLSFRPGDIVRASVLSLGDAR-A  149 (210)
Q Consensus        71 ~y~p~vGDiViG~V~~v~~~~a~V~I~~v~~~~l~~~~~Gii~~s~v~~~~~d~~~~~~~~~~GDiV~AkV~s~~d~~-~  149 (210)
                      +|+|++||+|+|+|+++++++|.|+|++++++++..+|.|++|.+|+|+++.|+.+|+++|++||+|+|||+|+++.+ +
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            589999999999999999999999999999999999999999999999999999999999999999999999998764 5


Q ss_pred             eEEEeecCCceeeEEEcCCCCeeEEcccceEEecccchh
Q 028346          150 YFLSTAKNDLGVVSAESTAGKLVYCISKYDLNIILFYSF  188 (210)
Q Consensus       150 ~~LSt~~~~LGVv~a~~~~G~~m~~~~~~~l~C~~~~~~  188 (210)
                      |+|||+++|||||+|+|.+|++|+|.+|++|+||+|+..
T Consensus        82 ~~Lst~~~~LGVv~A~c~~g~~m~~~~~~~m~cp~~g~~  120 (125)
T d2nn6i1          82 YLLTTAENELGVVVAHSESGIQMVPISWCEMQCPKTHTK  120 (125)
T ss_dssp             EEEECCSSSCEECCCBCSSSCBCEEEETTEEECTTTTCC
T ss_pred             EEEEecCCCcEEEEEECCCCCEeEeecCCEEECCCCCCe
Confidence            999999999999999998899999999999999999975
>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
>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
>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
>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
>d2nn6i2 b.84.4.2 (I:6-60) Exosome component 1, EXOSC1 {Human (Homo sapiens) [TaxId: 9606]} 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
>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
>d2je6i2 b.84.4.2 (I:7-65) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} 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
>d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]} 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
>d1wi5a_ b.40.4.5 (A:) S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) {Human (Homo sapiens) [TaxId: 9606]} 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
>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
>d1hh2p1 b.40.4.5 (P:127-198) S1 domain of NusA {Thermotoga maritima [TaxId: 2336]} 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
>d1smxa_ b.40.4.5 (A:) S1-domain of Ribonuclease E {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2ix0a3 b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]} 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
>d1v8qa_ b.84.4.1 (A:) Ribosomal protein L27 {Thermus thermophilus [TaxId: 274]} 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
>d1vk6a4 g.41.14.1 (A:97-125) NADH pyrophosphatase intervening domain {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
>d2akla2 g.41.3.5 (A:3-40) Hypothetical protein PA0128, N-terminal domain {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure