Citrus Sinensis ID: 030170

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--
MFLKVKLPWNVVVPAENLDAKGPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTLENIGEGRVRENTGEVLFPVVFSGITFKIFRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEAEREFQALVSLEGDFLGPVSCENPLD
cEEEEEEcEEEEEcccccccccccHHHHHHHHHHHHHHccEEcccEEEEEEEEEEccccccEEEEccccEEEEEEEEEEEEEEEcccEEEEEEEEEEEcEEEEEEccccEEEEccccccccccccccccEEEcccccccccccEEEEEEEEEEEEcccccEEEEEEEccccccccccccccc
cEEEEEEEEEEEEccHHcccccccHHHHHHHHHHHHHcccccccccEEEEEEEEEEEccccEEEccccEEEEEEEEEEEEEEcccccEEEEEEEEEcccEEEEEEccccEEEEEcccccccEEcccccccccccccEEEEcccEEEEEEEEEEEcccccccEEEEEEccccccccccccccc
mflkvklpwnvvvpaenldakgpmlQRSIVVRLLDDFARRKATKDLGYFLAVTTLenigegrvrentgevlfpvvfsgitfkifrgevldGTVHKVLKHgvflkcgpveniyltcskmpdyryvqaenpvflseknpkiekdVVVRVIVIGTKWLEAEREFQALVSLEgdflgpvscenpld
mflkvklpwnvvvpaenldakgpmlqRSIVVRLLDDFARRKATKDLGYFLAVTTlenigegrvrentgeVLFPVVFSGITFKIFRGEVLDGTVHKVLKhgvflkcgpVENIYLTCSKMPDYRYVQAENPvflseknpkiekdvvVRVIVIGTKWLEAEREFQALVslegdflgpvscenpld
MFLKVKLPWNVVVPAENLDAKGPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTLENIGEGRVRENTGEVLFPVVFSGITFKIFRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEAEREFQALVSLEGDFLGPVSCENPLD
**LKVKLPWNVVVPAENLDAKGPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTLENIGEGRVRENTGEVLFPVVFSGITFKIFRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEAEREFQALVSLEGDFLGPV*******
MFLKVKLPWNVVVPAENLDAKGPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTLENIGEGRVRENTGEVLFPVVFSGITFKIFRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEAEREFQALVSLEGDFLGPVSC*****
MFLKVKLPWNVVVPAENLDAKGPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTLENIGEGRVRENTGEVLFPVVFSGITFKIFRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEAEREFQALVSLEGDFLGPVSCENPLD
MFLKVKLPWNVVVPAENLDAKGPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTLENIGEGRVRENTGEVLFPVVFSGITFKIFRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEAEREFQALVSLEGDFLGPVS******
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MFLKVKLPWNVVVPAENLDAKGPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTLENIGEGRVRENTGEVLFPVVFSGITFKIFRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEAEREFQALVSLEGDFLGPVSCENPLD
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 ?
Query182 2.2.26 [Sep-21-2011]
P46279176 DNA-directed RNA polymera no no 0.928 0.960 0.325 2e-15
P38421176 DNA-directed RNA polymera no no 0.829 0.857 0.331 1e-13
P62489172 DNA-directed RNA polymera yes no 0.934 0.988 0.292 2e-12
P62488172 DNA-directed RNA polymera yes no 0.934 0.988 0.292 2e-12
P62487172 DNA-directed RNA polymera yes no 0.934 0.988 0.292 2e-12
Q54P04172 DNA-directed RNA polymera yes no 0.824 0.872 0.337 2e-12
Q5E9B8172 DNA-directed RNA polymera yes no 0.934 0.988 0.292 2e-12
Q7ZW41172 DNA-directed RNA polymera yes no 0.934 0.988 0.292 2e-12
O14459172 DNA-directed RNA polymera yes no 0.813 0.860 0.303 4e-10
P34087171 DNA-directed RNA polymera yes no 0.923 0.982 0.275 1e-09
>sp|P46279|RPB7_SOYBN DNA-directed RNA polymerase II subunit RPB7 OS=Glycine max PE=2 SV=1 Back     alignment and function desciption
 Score = 82.0 bits (201), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 58/178 (32%), Positives = 102/178 (57%), Gaps = 9/178 (5%)

Query: 1   MFLKVKLPWNVVVPAENLDAKGPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTLENIGE 60
           MF  + L  N+ +        G  L+ ++V +L+ D      +   G+ +AVT +ENIG+
Sbjct: 1   MFFHIVLERNMQLHPRYF---GRNLRDNLVSKLMKD-VEGTCSGRHGFVVAVTGIENIGK 56

Query: 61  GRVRENTGEVLFPVVFSGITFKIFRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMP- 119
           G +R+ TG V FPV +  + F+ F+GE+L+  V  V K G F + GPV+ I+++   +P 
Sbjct: 57  GLIRDGTGFVTFPVKYQCVVFRPFKGEILEAVVTMVNKMGFFAEAGPVQ-IFVSNHLIPD 115

Query: 120 DYRYVQAENPVF-LSEKNPKIEKDVVVRVIVIGTKWLEAEREFQALVSLEGDFLGPVS 176
           D  +   + P +  S+ + KI+KD  VR+ +IGT+ ++A   F  + +++ DFLG ++
Sbjct: 116 DMEFQSGDMPNYTTSDGSVKIQKDSEVRLKIIGTR-VDATEIF-CIGTIKDDFLGVIN 171
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB7 is part of a subcomplex with RPB4 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA.
Glycine max (taxid: 3847)
>sp|P38421|RPB7_ARATH DNA-directed RNA polymerase II subunit RPB7 OS=Arabidopsis thaliana GN=RPB19 PE=1 SV=1 Back     alignment and function description
>sp|P62489|RPB7_RAT DNA-directed RNA polymerase II subunit RPB7 OS=Rattus norvegicus GN=Polr2g PE=2 SV=1 Back     alignment and function description
>sp|P62488|RPB7_MOUSE DNA-directed RNA polymerase II subunit RPB7 OS=Mus musculus GN=Polr2g PE=2 SV=1 Back     alignment and function description
>sp|P62487|RPB7_HUMAN DNA-directed RNA polymerase II subunit RPB7 OS=Homo sapiens GN=POLR2G PE=1 SV=1 Back     alignment and function description
>sp|Q54P04|RPB7_DICDI DNA-directed RNA polymerase II subunit rpb7 OS=Dictyostelium discoideum GN=polr2g PE=3 SV=1 Back     alignment and function description
>sp|Q5E9B8|RPB7_BOVIN DNA-directed RNA polymerase II subunit RPB7 OS=Bos taurus GN=POLR2G PE=2 SV=1 Back     alignment and function description
>sp|Q7ZW41|RPB7_DANRE DNA-directed RNA polymerase II subunit RPB7 OS=Danio rerio GN=polr2g PE=2 SV=1 Back     alignment and function description
>sp|O14459|RPB7_SCHPO DNA-directed RNA polymerase II subunit rpb7 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpb7 PE=1 SV=1 Back     alignment and function description
>sp|P34087|RPB7_YEAST DNA-directed RNA polymerase II subunit RPB7 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPB7 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 ?
Query182
224102153176 predicted protein [Populus trichocarpa] 0.967 1.0 0.823 2e-82
255563208176 DNA-directed RNA polymerase II 19 kD pol 0.967 1.0 0.801 1e-80
449465372175 PREDICTED: DNA-directed RNA polymerase I 0.961 1.0 0.823 5e-80
297737162242 unnamed protein product [Vitis vinifera] 0.967 0.727 0.795 2e-79
225432916177 PREDICTED: DNA-directed RNA polymerase I 0.967 0.994 0.795 5e-79
118487294176 unknown [Populus trichocarpa] 0.967 1.0 0.789 4e-78
224107923193 predicted protein [Populus trichocarpa] 0.967 0.911 0.789 4e-78
297800772178 RNA polymerase Rpb7 N-terminal domain-co 0.978 1.0 0.685 8e-73
42566796178 DNA-directed RNA polymerase II subunit G 0.978 1.0 0.674 3e-72
388498028180 unknown [Medicago truncatula] 0.983 0.994 0.698 2e-71
>gi|224102153|ref|XP_002312568.1| predicted protein [Populus trichocarpa] gi|222852388|gb|EEE89935.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  310 bits (794), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 145/176 (82%), Positives = 166/176 (94%)

Query: 1   MFLKVKLPWNVVVPAENLDAKGPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTLENIGE 60
           MFLKV+LPWNV++PAENLDAKG MLQRSIVVRLLDDFA++ ATKDLGY+LAV+TLE+IGE
Sbjct: 1   MFLKVQLPWNVIIPAENLDAKGLMLQRSIVVRLLDDFAKKGATKDLGYYLAVSTLESIGE 60

Query: 61  GRVRENTGEVLFPVVFSGITFKIFRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPD 120
           G+VR++TG+VLFPVVFSGITFKIFRGE+LDG VHKVLKHGV L+CGP+ENIYL+C KMPD
Sbjct: 61  GKVRQHTGDVLFPVVFSGITFKIFRGEILDGIVHKVLKHGVLLRCGPIENIYLSCMKMPD 120

Query: 121 YRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEAEREFQALVSLEGDFLGPVS 176
           YRYV  ENPVFL++K  KIEKDVVVR +V+GTKWLEAEREFQALVSLEGD+LGPVS
Sbjct: 121 YRYVPGENPVFLNDKTSKIEKDVVVRFVVLGTKWLEAEREFQALVSLEGDYLGPVS 176

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|255563208|ref|XP_002522607.1| DNA-directed RNA polymerase II 19 kD polypeptide rpb7, putative [Ricinus communis] gi|223538083|gb|EEF39694.1| DNA-directed RNA polymerase II 19 kD polypeptide rpb7, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|449465372|ref|XP_004150402.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB7-like [Cucumis sativus] gi|449522228|ref|XP_004168129.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB7-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|297737162|emb|CBI26363.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|225432916|ref|XP_002284221.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB7 [Vitis vinifera] gi|147822056|emb|CAN61549.1| hypothetical protein VITISV_043525 [Vitis vinifera] Back     alignment and taxonomy information
>gi|118487294|gb|ABK95475.1| unknown [Populus trichocarpa] Back     alignment and taxonomy information
>gi|224107923|ref|XP_002314654.1| predicted protein [Populus trichocarpa] gi|222863694|gb|EEF00825.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|297800772|ref|XP_002868270.1| RNA polymerase Rpb7 N-terminal domain-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297314106|gb|EFH44529.1| RNA polymerase Rpb7 N-terminal domain-containing protein [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|42566796|ref|NP_193202.2| DNA-directed RNA polymerase II subunit G [Arabidopsis thaliana] gi|149944323|gb|ABR46204.1| At4g14660 [Arabidopsis thaliana] gi|332658072|gb|AEE83472.1| DNA-directed RNA polymerase II subunit G [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|388498028|gb|AFK37080.1| unknown [Medicago truncatula] 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 ?
Query182
TAIR|locus:2130060178 NRPE7 [Arabidopsis thaliana (t 0.978 1.0 0.674 4.4e-68
TAIR|locus:2084573174 NRPD7 [Arabidopsis thaliana (t 0.950 0.994 0.568 9.2e-52
TAIR|locus:2168514176 NRPB7 [Arabidopsis thaliana (t 0.829 0.857 0.331 4.1e-17
WB|WBGene00021845197 rpb-7 [Caenorhabditis elegans 0.846 0.781 0.327 2.3e-16
DICTYBASE|DDB_G0284891172 rpb7 "DNA-directed RNA polymer 0.824 0.872 0.337 1.3e-15
ZFIN|ZDB-GENE-030131-2808172 polr2gl "polymerase (RNA) II ( 0.829 0.877 0.310 1.6e-15
UNIPROTKB|Q5E9B8172 POLR2G "DNA-directed RNA polym 0.829 0.877 0.310 2e-15
UNIPROTKB|P62487172 POLR2G "DNA-directed RNA polym 0.829 0.877 0.310 2e-15
UNIPROTKB|I3LJZ9172 POLR2G "Uncharacterized protei 0.829 0.877 0.310 2e-15
MGI|MGI:1914960172 Polr2g "polymerase (RNA) II (D 0.829 0.877 0.310 2e-15
TAIR|locus:2130060 NRPE7 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 691 (248.3 bits), Expect = 4.4e-68, P = 4.4e-68
 Identities = 120/178 (67%), Positives = 159/178 (89%)

Query:     1 MFLKVKLPWNVVVPAENLDAKGPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTLENIGE 60
             MFLKV+LPWNV++PAEN+DAKG ML+R+I+V LL+ FA +KATK+LGY++AVTTL+ IGE
Sbjct:     1 MFLKVQLPWNVMIPAENMDAKGLMLKRAILVELLEAFASKKATKELGYYVAVTTLDKIGE 60

Query:    61 GRVRENTGEVLFPVVFSGITFKIFRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPD 120
             G++RE+TGEVLFPV+FSG+TFKIF+GE++ G VHKVLKHGVF++CGP+EN+YL+ +KMPD
Sbjct:    61 GKIREHTGEVLFPVMFSGMTFKIFKGEIIHGVVHKVLKHGVFMRCGPIENVYLSYTKMPD 120

Query:   121 YRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEAEREFQALVSLEGDFLGPVSCE 178
             Y+Y+  ENP+F++EK  +I+ +  VRV+VIG KW+E EREFQAL SLEGD+LGP+S E
Sbjct:   121 YKYIPGENPIFMNEKTSRIQVETTVRVVVIGIKWMEVEREFQALASLEGDYLGPLSEE 178
GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA;ISS
GO:0005634 "nucleus" evidence=ISM
GO:0006351 "transcription, DNA-dependent" evidence=IEA;ISS
GO:0000419 "DNA-directed RNA polymerase V complex" evidence=IPI
TAIR|locus:2084573 NRPD7 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2168514 NRPB7 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
WB|WBGene00021845 rpb-7 [Caenorhabditis elegans (taxid:6239)] Back     alignment and assigned GO terms
DICTYBASE|DDB_G0284891 rpb7 "DNA-directed RNA polymerase II subunit 7" [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-030131-2808 polr2gl "polymerase (RNA) II (DNA directed) polypeptide G-like" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
UNIPROTKB|Q5E9B8 POLR2G "DNA-directed RNA polymerase II subunit RPB7" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|P62487 POLR2G "DNA-directed RNA polymerase II subunit RPB7" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|I3LJZ9 POLR2G "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
MGI|MGI:1914960 Polr2g "polymerase (RNA) II (DNA directed) polypeptide G" [Mus musculus (taxid:10090)] 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

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
O14459RPB7_SCHPONo assigned EC number0.30320.81310.8604yesno
Q54P04RPB7_DICDINo assigned EC number0.33750.82410.8720yesno

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

Fail to connect to STRING server

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 ?
Query182
cd0432980 cd04329, RNAP_II_Rpb7_N, RNAP_II_Rpb7_N: Rpb7, N-t 7e-26
PTZ00162176 PTZ00162, PTZ00162, DNA-directed RNA polymerase II 9e-24
COG1095183 COG1095, RPB7, DNA-directed RNA polymerase, subuni 2e-20
TIGR00448179 TIGR00448, rpoE, DNA-directed RNA polymerase (rpoE 7e-14
PRK08563187 PRK08563, PRK08563, DNA-directed RNA polymerase su 2e-13
cd0446288 cd04462, S1_RNAPII_Rpb7, S1_RNAPII_Rpb7: Eukaryoti 4e-12
pfam0387670 pfam03876, SHS2_Rpb7-N, SHS2 domain found in N ter 2e-09
cd0065580 cd00655, RNAP_Rpb7_N_like, RNAP_Rpb7_N_like: This 3e-05
cd0433180 cd04331, RNAP_E_N, RNAP_E_N: RpoE, N-terminal ribo 8e-05
>gnl|CDD|239821 cd04329, RNAP_II_Rpb7_N, RNAP_II_Rpb7_N: Rpb7, N-terminal ribonucleoprotein (RNP) domain Back     alignment and domain information 
 Score = 94.2 bits (235), Expect = 7e-26
 Identities = 30/84 (35%), Positives = 48/84 (57%), Gaps = 4/84 (4%)

Query: 2  FLKVKLPWNVVVPAENLDAKGPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTLENIGEG 61
          F K++L  N+++        GP L+  +  +LL++      T D GY +AVT +++IGEG
Sbjct: 1  FFKIELEHNILLHPS---YFGPNLKEYLEQKLLEEVEGTC-TGDYGYIIAVTDIDDIGEG 56

Query: 62 RVRENTGEVLFPVVFSGITFKIFR 85
          ++   TG V FPV +  I FK F+
Sbjct: 57 KILPGTGSVEFPVKYKAIVFKPFK 80

Rpb7 is a subunit of eukaryotic RNA polymerase (RNAP) II that is homologous to Rpc25 of RNAP III, RpoE of archaeal RNAP, and Rpa43 of eukaryotic RNAP I. Rpb7 heterodimerizes with Rpb4 and this heterodimer binds the 10-subunit core of RNAP II, forming part of the floor of the DNA-binding cleft. Rpb7 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain, both of which bind single-stranded RNA. Rpb7 is thought to interact with the nascent RNA strand as it exits the RNAP II complex during transcription elongation. The Rpb7/Rpb4 heterodimer is also thought to serve as an upstream interface between the C-terminal domain of Rpb1 and the transcription factor IIB (TFIIB), recruiting pol II to the pol II promoter. Length = 80
>gnl|CDD|240298 PTZ00162, PTZ00162, DNA-directed RNA polymerase II subunit 7; Provisional Back     alignment and domain information
>gnl|CDD|224020 COG1095, RPB7, DNA-directed RNA polymerase, subunit E' [Transcription] Back     alignment and domain information
>gnl|CDD|129540 TIGR00448, rpoE, DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form Back     alignment and domain information
>gnl|CDD|236289 PRK08563, PRK08563, DNA-directed RNA polymerase subunit E'; Provisional Back     alignment and domain information
>gnl|CDD|239909 cd04462, S1_RNAPII_Rpb7, S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain Back     alignment and domain information
>gnl|CDD|202794 pfam03876, SHS2_Rpb7-N, SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 Back     alignment and domain information
>gnl|CDD|238354 cd00655, RNAP_Rpb7_N_like, RNAP_Rpb7_N_like: This conserved domain represents the N-terminal ribonucleoprotein (RNP) domain of the Rpb7 subunit of eukaryotic RNA polymerase (RNAP) II and its homologs, Rpa43 of eukaryotic RNAP I, Rpc25 of eukaryotic RNAP III, and RpoE (subunit E) of archaeal RNAP Back     alignment and domain information
>gnl|CDD|239823 cd04331, RNAP_E_N, RNAP_E_N: RpoE, N-terminal ribonucleoprotein (RNP) domain Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 182
TIGR00448179 rpoE DNA-directed RNA polymerase (rpoE), archaeal 100.0
COG1095183 RPB7 DNA-directed RNA polymerase, subunit E' [Tran 100.0
KOG3297202 consensus DNA-directed RNA polymerase subunit E' [ 100.0
PTZ00162176 DNA-directed RNA polymerase II subunit 7; Provisio 100.0
PRK08563187 DNA-directed RNA polymerase subunit E'; Provisiona 100.0
KOG3298170 consensus DNA-directed RNA polymerase subunit E' [ 100.0
PF08292122 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; I 99.93
cd0433080 RNAP_III_Rpc25_N RNAP_III_Rpc25_N: Rpc25, N-termin 99.91
cd0432980 RNAP_II_Rpb7_N RNAP_II_Rpb7_N: Rpb7, N-terminal ri 99.9
cd0065580 RNAP_Rpb7_N_like RNAP_Rpb7_N_like: This conserved 99.9
cd0433180 RNAP_E_N RNAP_E_N: RpoE, N-terminal ribonucleoprot 99.9
cd0446288 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly 99.84
PF0387670 SHS2_Rpb7-N: SHS2 domain found in N terminus of Rp 99.69
cd0446099 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. 99.61
cd0432889 RNAP_I_Rpa43_N RNAP_I_Rpa43_N: Rpa43, N-terminal r 99.5
cd0447183 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai 99.33
COG0539 541 RpsA Ribosomal protein S1 [Translation, ribosomal 99.26
PRK11642813 exoribonuclease R; Provisional 99.22
PF0057574 S1: S1 RNA binding domain; InterPro: IPR003029 Rib 99.21
cd0568673 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom 99.21
COG1098129 VacB Predicted RNA binding protein (contains ribos 99.11
cd0570574 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a 99.09
TIGR02063709 RNase_R ribonuclease R. This family consists of an 99.09
cd0569671 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t 99.09
TIGR00358654 3_prime_RNase VacB and RNase II family 3'-5' exori 99.06
cd0569769 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t 99.05
cd0578986 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. 99.05
cd0570673 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a 99.05
cd0570877 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a 99.05
PRK08582139 hypothetical protein; Provisional 99.05
cd0569870 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp 99.04
cd0446183 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp 99.03
cd0445276 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr 99.02
cd0569069 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p 99.02
cd0568972 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p 98.99
cd0570768 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a 98.98
cd0568479 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal 98.98
cd0570472 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a 98.95
PRK07252120 hypothetical protein; Provisional 98.95
cd0445482 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA- 98.94
cd0570373 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R 98.93
PRK05807136 hypothetical protein; Provisional 98.91
cd0568868 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p 98.89
cd0569269 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p 98.88
cd0568568 S1_Tex S1_Tex: The C-terminal S1 domain of a trans 98.87
cd0569173 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p 98.87
cd0445388 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik 98.84
PLN00207891 polyribonucleotide nucleotidyltransferase; Provisi 98.83
PTZ00248 319 eukaryotic translation initiation factor 2 subunit 98.8
COG0539 541 RpsA Ribosomal protein S1 [Translation, ribosomal 98.79
TIGR03591684 polynuc_phos polyribonucleotide nucleotidyltransfe 98.78
PRK08059123 general stress protein 13; Validated 98.76
cd0569474 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp 98.75
PRK07899 486 rpsA 30S ribosomal protein S1; Reviewed 98.75
cd0569566 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t 98.75
cd0447268 S1_PNPase S1_PNPase: Polynucleotide phosphorylase 98.75
smart0031672 S1 Ribosomal protein S1-like RNA-binding domain. 98.75
cd0568770 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib 98.74
PRK04163235 exosome complex RNA-binding protein Rrp4; Provisio 98.72
PRK07400318 30S ribosomal protein S1; Reviewed 98.68
COG0557706 VacB Exoribonuclease R [Transcription] 98.67
PRK05054644 exoribonuclease II; Provisional 98.64
cd0570270 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R 98.6
TIGR02696719 pppGpp_PNP guanosine pentaphosphate synthetase I/p 98.6
PRK03987 262 translation initiation factor IF-2 subunit alpha; 98.59
PRK09521189 exosome complex RNA-binding protein Csl4; Provisio 98.58
cd0447377 S1_RecJ_like S1_RecJ_like: The S1 domain of the ar 98.58
PRK11824693 polynucleotide phosphorylase/polyadenylase; Provis 98.53
cd0446567 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib 98.52
cd0445567 S1_NusA S1_NusA: N-utilizing substance A protein ( 98.49
TIGR02062639 RNase_B exoribonuclease II. This family consists o 98.44
PRK13806491 rpsA 30S ribosomal protein S1; Provisional 98.44
PRK13806 491 rpsA 30S ribosomal protein S1; Provisional 98.43
PHA0294588 interferon resistance protein; Provisional 98.43
PRK07899 486 rpsA 30S ribosomal protein S1; Reviewed 98.4
cd05693100 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp 98.39
COG2183780 Tex Transcriptional accessory protein [Transcripti 98.36
COG1185692 Pnp Polyribonucleotide nucleotidyltransferase (pol 98.35
cd0016465 S1_like S1_like: Ribosomal protein S1-like RNA-bin 98.34
PRK06676 390 rpsA 30S ribosomal protein S1; Reviewed 98.33
PRK12269 863 bifunctional cytidylate kinase/ribosomal protein S 98.27
cd0579192 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. 98.24
PRK12269863 bifunctional cytidylate kinase/ribosomal protein S 98.23
PRK06299 565 rpsA 30S ribosomal protein S1; Reviewed 98.23
PRK06676390 rpsA 30S ribosomal protein S1; Reviewed 98.21
PRK06299 565 rpsA 30S ribosomal protein S1; Reviewed 98.16
TIGR00717516 rpsA ribosomal protein S1. This model provides tru 98.15
PRK09202 470 nusA transcription elongation factor NusA; Validat 98.13
TIGR00717516 rpsA ribosomal protein S1. This model provides tru 98.13
PRK00087647 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 98.12
KOG4134253 consensus DNA-dependent RNA polymerase I [Transcri 98.11
COG1093 269 SUI2 Translation initiation factor 2, alpha subuni 98.08
PRK07400 318 30S ribosomal protein S1; Reviewed 98.06
PRK00087647 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 98.01
PRK12327 362 nusA transcription elongation factor NusA; Provisi 97.86
COG1097239 RRP4 RNA-binding protein Rrp4 and related proteins 97.85
cd0579086 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai 97.77
TIGR01953 341 NusA transcription termination factor NusA. This m 97.7
PF03293160 Pox_RNA_pol: Poxvirus DNA-directed RNA polymerase, 97.44
PRK12328 374 nusA transcription elongation factor NusA; Provisi 97.35
TIGR00757 414 RNaseEG ribonuclease, Rne/Rng family. The C-termin 97.34
COG1096188 Predicted RNA-binding protein (consists of S1 doma 96.88
PF1044782 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I 96.81
KOG1067760 consensus Predicted RNA-binding polyribonucleotide 96.8
PRK12329 449 nusA transcription elongation factor NusA; Provisi 96.76
COG1107 715 Archaea-specific RecJ-like exonuclease, contains D 95.75
PRK11712 489 ribonuclease G; Provisional 95.6
PHA0285886 EIF2a-like PKR inhibitor; Provisional 95.32
KOG1070 1710 consensus rRNA processing protein Rrp5 [RNA proces 95.24
PRK10811 1068 rne ribonuclease E; Reviewed 94.85
PF1350961 S1_2: S1 domain; PDB: 3GO5_A. 94.68
KOG3409193 consensus Exosomal 3'-5' exoribonuclease complex, 94.52
cd0569972 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t 92.5
COG1530 487 CafA Ribonucleases G and E [Translation, ribosomal 92.18
PF10246104 MRP-S35: Mitochondrial ribosomal protein MRP-S35; 91.92
KOG1004230 consensus Exosomal 3'-5' exoribonuclease complex s 91.78
KOG1070 1710 consensus rRNA processing protein Rrp5 [RNA proces 91.64
COG2996287 Predicted RNA-bindining protein (contains S1 and H 88.12
KOG2916 304 consensus Translation initiation factor 2, alpha s 83.81
PF0031366 CSD: 'Cold-shock' DNA-binding domain; InterPro: IP 81.97
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form Back     alignment and domain information 
Probab=100.00  E-value=1.3e-47  Score=299.71  Aligned_cols=176  Identities=22%  Similarity=0.436  Sum_probs=161.1

Q ss_pred             CeEEEEeceeEEEcCCCCCCCCCChHHHHHHHHHHhHhcCeeeCCccEEEEEEeeeeeCceEEecCCCceEEEEEEEEEE
Q 030170            1 MFLKVKLPWNVVVPAENLDAKGPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTLENIGEGRVRENTGEVLFPVVFSGIT   80 (182)
Q Consensus         1 MF~~~~l~d~v~i~P~~l~~~~~~~~~~i~~~l~~~~~~~k~~~~~G~~v~i~~i~~~~~g~i~~~~g~~~~~v~fk~~~   80 (182)
                      ||++++++|+|+|||++|++   ++++++.++|+++| +||+++++|+||+++++.++++|+|.||||+++++|+|+|++
T Consensus         1 Mf~~~~l~d~v~i~P~~~~~---~~~~~i~~~l~~~~-~gk~~~~~G~~i~v~di~~i~~g~i~~gdG~~~~~V~f~~i~   76 (179)
T TIGR00448         1 MYILSKIADTVRIPPDQFGE---DLEEVITHQLNEKF-EGRLDKNVGLCITIYDIEDIGEGKVIPGDGSAYHNVTFRALV   76 (179)
T ss_pred             CeEEEEEeeEEEECHHHhCc---cHHHHHHHHHHHHh-cCcCcCCcCEEEEEEEeEEecCCEEECCCCCEEEEEEEEEEE
Confidence            99999999999999999998   89999999998887 799999999999999999999999999999999999999999


Q ss_pred             eeecCCCEEEEEEEEEecceEEEEecCcceEEEcCCcCCCceeecC-CCcEEEcCCCceEcCCCeEEEEEEEEEeccc-c
Q 030170           81 FKIFRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPDYRYVQA-ENPVFLSEKNPKIEKDVVVRVIVIGTKWLEA-E  158 (182)
Q Consensus        81 f~p~~gEv~~g~V~~v~~~Gifv~lg~~~gl~~~s~~~~d~~~~~~-~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~-~  158 (182)
                      |+|++||+++|+|++++++|+|+++||++|++|+++++++++.+++ +..|.|.+...+|+.||.|||||.++++.++ .
T Consensus        77 f~p~~gEvv~G~V~~v~~~GifV~lg~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~  156 (179)
T TIGR00448        77 FKPELGEIVEGEVIEIVEFGAFVSLGPFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRP  156 (179)
T ss_pred             EeccCCCEEEEEEEEEEeeEEEEEeCCceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCC
Confidence            9999999999999999999999999999999999999999876665 4556665444799999999999999998654 2


Q ss_pred             cceEEEEeccCCCccccCCCCC
Q 030170          159 REFQALVSLEGDFLGPVSCENP  180 (182)
Q Consensus       159 ~~~~i~gs~~~~gLG~i~w~~~  180 (182)
                      ....+.+||+++|||++.|+++
T Consensus       157 ~~~~I~lt~k~~~LG~~~w~~~  178 (179)
T TIGR00448       157 EGSKIGLTMRQPLLGKLEWIEE  178 (179)
T ss_pred             CcceEEEEeccCcCCccccccc
Confidence            3446899999999999999975

This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription] Back     alignment and domain information
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription] Back     alignment and domain information
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional Back     alignment and domain information
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional Back     alignment and domain information
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription] Back     alignment and domain information
>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit Back     alignment and domain information
>cd04330 RNAP_III_Rpc25_N RNAP_III_Rpc25_N: Rpc25, N-terminal ribonucleoprotein (RNP) domain Back     alignment and domain information
>cd04329 RNAP_II_Rpb7_N RNAP_II_Rpb7_N: Rpb7, N-terminal ribonucleoprotein (RNP) domain Back     alignment and domain information
>cd00655 RNAP_Rpb7_N_like RNAP_Rpb7_N_like: This conserved domain represents the N-terminal ribonucleoprotein (RNP) domain of the Rpb7 subunit of eukaryotic RNA polymerase (RNAP) II and its homologs, Rpa43 of eukaryotic RNAP I, Rpc25 of eukaryotic RNAP III, and RpoE (subunit E) of archaeal RNAP Back     alignment and domain information
>cd04331 RNAP_E_N RNAP_E_N: RpoE, N-terminal ribonucleoprotein (RNP) domain 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
>PF03876 SHS2_Rpb7-N: SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397; InterPro: IPR005576 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core Back     alignment and domain information
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain Back     alignment and domain information
>cd04328 RNAP_I_Rpa43_N RNAP_I_Rpa43_N: Rpa43, N-terminal ribonucleoprotein (RNP) domain Back     alignment and domain information
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain Back     alignment and domain information
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK11642 exoribonuclease R; Provisional 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
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis] 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
>TIGR02063 RNase_R ribonuclease R 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
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases 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
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding 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
>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
>PRK08582 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
>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
>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
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain 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
>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
>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
>PRK07252 hypothetical protein; Provisional Back     alignment and domain information
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain 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
>PRK05807 hypothetical protein; Provisional Back     alignment and domain information
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) 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
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) 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
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional Back     alignment and domain information
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional Back     alignment and domain information
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase Back     alignment and domain information
>PRK08059 general stress protein 13; Validated 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
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed 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
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain 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
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional Back     alignment and domain information
>PRK07400 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>COG0557 VacB Exoribonuclease R [Transcription] Back     alignment and domain information
>PRK05054 exoribonuclease II; 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
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase Back     alignment and domain information
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated Back     alignment and domain information
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional 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
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional 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
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain Back     alignment and domain information
>TIGR02062 RNase_B exoribonuclease II Back     alignment and domain information
>PRK13806 rpsA 30S ribosomal protein S1; Provisional Back     alignment and domain information
>PRK13806 rpsA 30S ribosomal protein S1; Provisional Back     alignment and domain information
>PHA02945 interferon resistance protein; Provisional Back     alignment and domain information
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed 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
>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
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain Back     alignment and domain information
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional Back     alignment and domain information
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain Back     alignment and domain information
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional Back     alignment and domain information
>PRK06299 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
>TIGR00717 rpsA ribosomal protein S1 Back     alignment and domain information
>PRK09202 nusA transcription elongation factor NusA; Validated 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
>KOG4134 consensus DNA-dependent RNA polymerase I [Transcription] 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
>PRK07400 30S ribosomal protein S1; Reviewed 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
>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
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain Back     alignment and domain information
>TIGR01953 NusA transcription termination factor NusA Back     alignment and domain information
>PF03293 Pox_RNA_pol: Poxvirus DNA-directed RNA polymerase, 18 kD subunit; InterPro: IPR004973 DNA-directed RNA polymerases 2 Back     alignment and domain information
>PRK12328 nusA transcription elongation factor NusA; Provisional Back     alignment and domain information
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family Back     alignment and domain information
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis] 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
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only] Back     alignment and domain information
>PRK12329 nusA transcription elongation factor NusA; Provisional Back     alignment and domain information
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK11712 ribonuclease G; Provisional Back     alignment and domain information
>PHA02858 EIF2a-like PKR inhibitor; Provisional Back     alignment and domain information
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification] Back     alignment and domain information
>PRK10811 rne ribonuclease E; Reviewed Back     alignment and domain information
>PF13509 S1_2: S1 domain; PDB: 3GO5_A 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
>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
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>KOG1070 consensus rRNA processing protein Rrp5 [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
>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate [] 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 ?
Query182
2c35_B172 Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii L 1e-13
2b8k_G215 12-Subunit Rna Polymerase Ii Length = 215 1e-11
3h0g_G172 Rna Polymerase Ii From Schizosaccharomyces Pombe Le 3e-11
1nt9_G171 Complete 12-Subunit Rna Polymerase Ii Length = 171 1e-10
1go3_E187 Structure Of An Archeal Homolog Of The Eukaryotic R 2e-08
3ayh_B203 Crystal Structure Of The C1725 SUBCOMPLEX FROM S. P 7e-04
>pdb|2C35|B Chain B, Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii Length = 172 Back     alignment and structure 
Iteration: 1

 Score = 72.4 bits (176), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 52/178 (29%), Positives = 91/178 (51%), Gaps = 8/178 (4%)
Query: 1   MFLKVKLPWNVVVPAENLDAKGPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTLENIGE 60
           MF  + L   +++        GP L  ++  +L  +      T   G+ +AVTT++NIG 
Sbjct: 1   MFYHISLEHEILLHPRYF---GPNLLNTVKQKLFTE-VEGTCTGKYGFVIAVTTIDNIGA 56
Query: 61  GRVRENTGEVLFPVVFSGITFKIFRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPD 120
           G ++   G VL+PV +  I F+ F+GEV+D  V +V K G+F + GP+       S   +
Sbjct: 57  GVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSE 116
Query: 121 YRYVQAENPVFLS--EKNPKIEKDVVVRVIVIGTKWLEAEREFQALVSLEGDFLGPVS 176
             +    NP      +++  I++D  +R+ ++GT+    + +  A+ SL  D+LG VS
Sbjct: 117 MEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRV--DKNDIFAIGSLMDDYLGLVS 172
>pdb|2B8K|G Chain G, 12-Subunit Rna Polymerase Ii Length = 215 Back     alignment and structure
>pdb|3H0G|G Chain G, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 172 Back     alignment and structure
>pdb|1NT9|G Chain G, Complete 12-Subunit Rna Polymerase Ii Length = 171 Back     alignment and structure
>pdb|1GO3|E Chain E, Structure Of An Archeal Homolog Of The Eukaryotic Rna Polymerase Ii Rpb4RPB7 COMPLEX Length = 187 Back     alignment and structure
>pdb|3AYH|B Chain B, Crystal Structure Of The C1725 SUBCOMPLEX FROM S. POMBE RNA Polymerase Iii Length = 203 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 ?
Query182
2c35_B172 Human RPB7, DNA-directed RNA polymerase II 19 kDa 2e-35
4ayb_E180 DNA-directed RNA polymerase; transferase, multi-su 2e-35
1go3_E187 DNA-directed RNA polymerase subunit E; transferase 7e-34
1y14_B171 B16, RPB7, DNA-directed RNA polymerase II 19 kDa p 2e-33
3h0g_G172 DNA-directed RNA polymerase II subunit RPB7; trans 1e-32
3ayh_B203 DNA-directed RNA polymerase III subunit RPC8; tran 4e-32
2b8k_G215 B16, DNA-directed RNA polymerase II 19 kDa polypep 5e-32
2ckz_B218 C25, DNA-directed RNA polymerase III 25 KD polypep 6e-32
>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 Length = 172 Back     alignment and structure
 Score =  121 bits (305), Expect = 2e-35
 Identities = 52/178 (29%), Positives = 89/178 (50%), Gaps = 8/178 (4%)

Query: 1   MFLKVKLPWNVVVPAENLDAKGPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTLENIGE 60
           MF  + L   +++        GP L  ++  +L  +      T   G+ +AVTT++NIG 
Sbjct: 1   MFYHISLEHEILLHPRYF---GPNLLNTVKQKLFTEVEG-TCTGKYGFVIAVTTIDNIGA 56

Query: 61  GRVRENTGEVLFPVVFSGITFKIFRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPD 120
           G ++   G VL+PV +  I F+ F+GEV+D  V +V K G+F + GP+       S   +
Sbjct: 57  GVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSE 116

Query: 121 YRYVQAENPVFLSEKNPK--IEKDVVVRVIVIGTKWLEAEREFQALVSLEGDFLGPVS 176
             +    NP      +    I++D  +R+ ++GT+    + +  A+ SL  D+LG VS
Sbjct: 117 MEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRV--DKNDIFAIGSLMDDYLGLVS 172
>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 Length = 180 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 Length = 187 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* ... Length = 171 Back     alignment and structure
>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 172 Back     alignment and structure
>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A {Schizosaccharomyces pombe} Length = 203 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 Length = 215 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} Length = 218 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query182
2ckz_B218 C25, DNA-directed RNA polymerase III 25 KD polypep 100.0
3ayh_B203 DNA-directed RNA polymerase III subunit RPC8; tran 100.0
4ayb_E180 DNA-directed RNA polymerase; transferase, multi-su 100.0
3h0g_G172 DNA-directed RNA polymerase II subunit RPB7; trans 100.0
1go3_E187 DNA-directed RNA polymerase subunit E; transferase 100.0
2c35_B172 Human RPB7, DNA-directed RNA polymerase II 19 kDa 100.0
1y14_B171 B16, RPB7, DNA-directed RNA polymerase II 19 kDa p 100.0
2b8k_G215 B16, DNA-directed RNA polymerase II 19 kDa polypep 100.0
2rf4_A214 DNA-directed RNA polymerase I subunit RPA4; transf 99.94
1luz_A88 Protein K3, protein K2; stranded anti-parallel bet 99.32
2k52_A80 Uncharacterized protein MJ1198; metal-binding, zin 99.28
1kl9_A182 Eukaryotic translation initiation factor 2 subuni; 99.27
2khi_A115 30S ribosomal protein S1; acetylation, phosphoprot 99.26
2cqo_A119 Nucleolar protein of 40 kDa; S1 domain, OB-fold, s 99.24
2a19_A175 EIF-2- alpha, eukaryotic translation initiation fa 99.24
2eqs_A103 ATP-dependent RNA helicase DHX8; S1 domain, OB-fol 99.2
2k4k_A130 GSP13, general stress protein 13; cytoplasm, stres 99.17
1wi5_A119 RRP5 protein homolog; S1 domain, OB-fold, structur 99.12
2khj_A109 30S ribosomal protein S1; OB fold, acetylation, ph 99.12
3cdi_A723 Polynucleotide phosphorylase; mRNA turnover, RNAse 98.98
3aev_A 275 Translation initiation factor 2 subunit alpha; pro 98.98
2nn6_I209 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, 98.97
1q8k_A 308 Eukaryotic translation initiation factor 2 subunit 98.96
4aid_A726 Polyribonucleotide nucleotidyltransferase; transfe 98.92
2id0_A644 Exoribonuclease 2; RNAse, exonuclease, hydrolyase, 98.88
2je6_I251 RRP4, exosome complex RNA-binding protein 1; nucle 98.84
2ba0_A229 Archeal exosome RNA binding protein RRP4; RNAse PH 98.78
3m7n_A179 Putative uncharacterized protein AF_0206; exosome, 98.76
2z0s_A235 Probable exosome complex RNA-binding protein 1; al 98.73
2wp8_J977 Exosome complex exonuclease DIS3; nucleus, hydrola 98.73
3bzc_A785 TEX; helix-turn-helix, helix-hairpin-helix, S1 dom 98.71
1e3p_A757 Guanosine pentaphosphate synthetase; polyribonucle 98.69
3cw2_C 266 Translation initiation factor 2 subunit alpha; AIF 98.69
3psi_A 1219 Transcription elongation factor SPT6; nucleus; 3.3 98.68
2vnu_D760 Exosome complex exonuclease RRP44; hydrolase-RNA c 98.6
3psf_A1030 Transcription elongation factor SPT6; nucleus; 2.5 98.51
3go5_A285 Multidomain protein with S1 RNA-binding domains; s 98.43
2ja9_A175 Exosome complex exonuclease RRP40; RNA-binding pro 98.43
2bh8_A101 1B11; transcription, molecular evolution, unique a 98.37
2nn6_H 308 Exosome complex exonuclease RRP4; RNA, exosome, PM 98.35
1hh2_P 344 NUSA, N utilization substance protein A; transcrip 98.2
2bx2_L 517 Ribonuclease E, RNAse E; RNA-binding, RNA turnover 97.89
1k0r_A 366 NUSA; two component arrangement, S1 domain, two K- 97.87
3go5_A 285 Multidomain protein with S1 RNA-binding domains; s 97.86
2asb_A 251 Transcription elongation protein NUSA; protein-RNA 97.66
2nn6_G289 Exosome complex exonuclease RRP40; RNA, exosome, P 97.19
2r7d_A469 Ribonuclease II family protein; structural genomic 94.83
2bh8_A101 1B11; transcription, molecular evolution, unique a 93.03
>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
Probab=100.00  E-value=8.4e-51  Score=324.94  Aligned_cols=176  Identities=20%  Similarity=0.343  Sum_probs=160.7

Q ss_pred             CeEEEEeceeEEEcCCCCCCCCCChHHHHHHHHHHhHhcCeeeCCccEEEEEEeeeeeCceEEecCCCceEEEEEEEEEE
Q 030170            1 MFLKVKLPWNVVVPAENLDAKGPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTLENIGEGRVRENTGEVLFPVVFSGIT   80 (182)
Q Consensus         1 MF~~~~l~d~v~i~P~~l~~~~~~~~~~i~~~l~~~~~~~k~~~~~G~~v~i~~i~~~~~g~i~~~~g~~~~~v~fk~~~   80 (182)
                      ||++++++|+|+|||++|++   +++++|.++|.++| +||+++++|+||+++++.++++|+|.+|||.++++|.|+|++
T Consensus         1 MF~l~~l~d~V~I~P~~f~~---~l~~~i~~~L~~ky-egkv~~~~Gl~I~v~di~~i~eG~I~~GdG~~~~~V~fk~~~   76 (218)
T 2ckz_B            1 MFILSKIADLVRIPPDQFHR---DTISAITHQLNNKF-ANKIIPNVGLCITIYDLLTVEEGQLKPGDGSSYINVTFRAVV   76 (218)
T ss_dssp             CEEEEEEEEEEEECGGGTTS---CHHHHHHHHHHHHH-TTEEETTTEEEEEEEEEEEECCCEECSSSSCEEEEEEEEEEE
T ss_pred             CeEEEEEEEEEEECHHHcCc---hHHHHHHHHHHHHh-cCcCcCCccEEEEEEEeeeccCcEEeCCCCCEEEEEEEEEEE
Confidence            99999999999999999988   89999998888877 899999999999999999999999999999999999999999


Q ss_pred             eeecCCCEEEEEEEEEecceEEEEe-cCcceEEEcCCcCCCceeecCCCc-EEEc--CCC-ceEcCCCeEEEEEEEEEec
Q 030170           81 FKIFRGEVLDGTVHKVLKHGVFLKC-GPVENIYLTCSKMPDYRYVQAENP-VFLS--EKN-PKIEKDVVVRVIVIGTKWL  155 (182)
Q Consensus        81 f~p~~gEv~~g~V~~v~~~Gifv~l-g~~~gl~~~s~~~~d~~~~~~~~~-~~~~--~~~-~~~~~Gd~VrvrV~~v~~~  155 (182)
                      |+|++||+++|+|++++++|+||++ |+++|++|++++++|++.++++++ |.|.  +++ ++|++||.|||||.++++.
T Consensus        77 f~p~vGEv~~G~Is~Vt~fGifVeL~g~~eglv~~s~l~~d~~~fd~~~~~~vg~~~e~t~~~~~~Gd~VrvrV~~v~~~  156 (218)
T 2ckz_B           77 FKPFLGEIVTGWISKCTAEGIKVSLLGIFDDIFIPQNMLFEGCYYTPEESAWIWPMDEETKLYFDVNEKIRFRIEREVFV  156 (218)
T ss_dssp             ECCCTTCEEEEEEEEEETTEEEEECTTSCCCEEEETTTSCTTCEEETTTTEEEEECC--CEEEECTTCEEEEEEEEEEEC
T ss_pred             ecCCCCCEEEEEEEEEccCcEEEEccCccceEEEcHHHCCCCcEEcCcCceEEeeccccCCcEEcCCCEEEEEEEEEEcc
Confidence            9999999999999999999999999 899999999999999877776555 5553  333 6999999999999999997


Q ss_pred             cc--------------------------------ccceEEEEeccCCCccccCCCCC
Q 030170          156 EA--------------------------------EREFQALVSLEGDFLGPVSCENP  180 (182)
Q Consensus       156 ~~--------------------------------~~~~~i~gs~~~~gLG~i~w~~~  180 (182)
                      ++                                .+||.++|||+++|||+++||.-
T Consensus       157 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~i~gs~~~~GLG~~~ww~~  213 (218)
T 2ckz_B          157 DVKPKSPKERELEERAQLENEIEGKNEETPQNEKPPAYALLGSCQTDGMGLVSWWEH  213 (218)
T ss_dssp             CCCC-------------------------------CSEEEEEECCSTTCEEGGGCC-
T ss_pred             cCCCCCccccccccccccccccccccccccccCCCCCeEEEEEecCCCCchhhhhhc
Confidence            63                                13899999999999999999964
>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A {Schizosaccharomyces pombe} 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
>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} 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
>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
>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
>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
>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
>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii} 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
>2khi_A 30S ribosomal protein S1; 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
>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
>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
>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis} 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
>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} 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
>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
>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
>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
>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A 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
>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
>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
>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
>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
>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae} 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
>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
>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
>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae} 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
>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {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
>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
>2bh8_A 1B11; transcription, molecular evolution, unique architecture, transcription regulation, phosphorylation; 1.9A {Escherichia coli} 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
>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
>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
>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
>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
>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
>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
>2r7d_A Ribonuclease II family protein; structural genomics, PSI-2, structure initiative, northeast structural genomics consort NESG; 1.80A {Deinococcus radiodurans R1} SCOP: b.40.4.5 b.40.4.16 PDB: 2r7f_A Back     alignment and structure
>2bh8_A 1B11; transcription, molecular evolution, unique architecture, transcription regulation, phosphorylation; 1.9A {Escherichia coli} 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 182
d1go3e278 d.230.1.1 (E:1-78) N-terminal, heterodimerisation 1e-14
d2c35b277 d.230.1.1 (B:1-77) N-terminal, heterodimerisation 2e-14
d2c35b194 b.40.4.5 (B:78-171) C-terminal domain of RNA polym 4e-14
d1y14b191 b.40.4.5 (B:81-171) C-terminal domain of RNA polym 2e-12
d1y14b280 d.230.1.1 (B:1-80) N-terminal, heterodimerisation 5e-12
d1go3e1106 b.40.4.5 (E:79-184) C-terminal domain of RNA polym 2e-04
>d1go3e2 d.230.1.1 (E:1-78) N-terminal, heterodimerisation domain of RBP7 (RpoE) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 78 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Dodecin subunit-like
superfamily: N-terminal, heterodimerisation domain of RBP7 (RpoE)
family: N-terminal, heterodimerisation domain of RBP7 (RpoE)
domain: N-terminal, heterodimerisation domain of RBP7 (RpoE)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score = 63.9 bits (156), Expect = 1e-14
 Identities = 22/81 (27%), Positives = 43/81 (53%), Gaps = 4/81 (4%)

Query: 1  MFLKVKLPWNVVVPAENLDAKGPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTLENIGE 60
          M+  +++   V VP E     G  L+ ++   L++ +   +  KD+G+ L++  +++IGE
Sbjct: 1  MYKILEIADVVKVPPEEF---GKDLKETVKKILMEKYEG-RLDKDVGFVLSIVDVKDIGE 56

Query: 61 GRVRENTGEVLFPVVFSGITF 81
          G+V    G    PVVF  + +
Sbjct: 57 GKVVHGDGSAYHPVVFETLVY 77
>d2c35b2 d.230.1.1 (B:1-77) N-terminal, heterodimerisation domain of RBP7 (RpoE) {Human (Homo sapiens) [TaxId: 9606]} Length = 77 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]} Length = 94 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]} Length = 91 Back     information, alignment and structure
>d1y14b2 d.230.1.1 (B:1-80) N-terminal, heterodimerisation domain of RBP7 (RpoE) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 80 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]} Length = 106 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 ?
Query182
d2c35b194 C-terminal domain of RNA polymerase II subunit RBP 99.94
d1y14b191 C-terminal domain of RNA polymerase II subunit RBP 99.93
d1go3e278 N-terminal, heterodimerisation domain of RBP7 (Rpo 99.9
d2c35b277 N-terminal, heterodimerisation domain of RBP7 (Rpo 99.88
d1y14b280 N-terminal, heterodimerisation domain of RBP7 (Rpo 99.87
d1go3e1106 C-terminal domain of RNA polymerase II subunit RBP 99.82
d2je6i187 S1-domain of exosome complex RNA-binding protein 1 99.48
d2ix0a387 Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5 99.47
d2z0sa188 S1-domain of exosome complex RNA-binding protein 1 99.44
d2ba0a183 S1-domain of exosome complex RNA-binding protein 1 99.44
d1kl9a286 Eukaryotic initiation factor 2alpha, eIF2alpha, N- 99.3
d2ahob284 Eukaryotic initiation factor 2alpha, eIF2alpha, N- 99.27
d1sroa_76 S1 RNA-binding domain of polyribonucleotide phosph 99.25
d2nn6h195 S1-domain of Ribosomal RNA-processing protein 4, R 99.2
d3bzka494 Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287] 99.07
d1e3pa262 S1 RNA-binding domain of polyribonucleotide phosph 98.88
d2nn6g188 S1-domain of exosome component 3 (RRP40) {Human (H 98.82
d1wi5a_119 S1-domain of RRP5 protein homolog (PDCD11, KIAA018 98.77
d2ja9a190 S1-domain of exosome component 3 (RRP40) {Saccharo 98.64
d1hh2p172 S1 domain of NusA {Thermotoga maritima [TaxId: 233 98.51
d2nn6i1125 Exosome component 1, EXOSC1 {Human (Homo sapiens) 97.98
d2asba176 S1 domain of NusA {Mycobacterium tuberculosis [Tax 97.53
d1smxa_87 S1-domain of Ribonuclease E {Escherichia coli [Tax 96.9
d1k3ra171 Hypothetical protein MTH1 (MT0001), insert domain 90.91
d2vnud288 Exosome complex exonuclease RRP44 {Saccharomyces c 89.52
>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
class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.94  E-value=3.4e-26  Score=158.56  Aligned_cols=92  Identities=29%  Similarity=0.459  Sum_probs=81.3

Q ss_pred             eecCCCEEEEEEEEEecceEEEEecCcceEEEcCCcCCCceeecCCCcEEE-cCCC-ceEcCCCeEEEEEEEEEeccccc
Q 030170           82 KIFRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPDYRYVQAENPVFL-SEKN-PKIEKDVVVRVIVIGTKWLEAER  159 (182)
Q Consensus        82 ~p~~gEv~~g~V~~v~~~Gifv~lg~~~gl~~~s~~~~d~~~~~~~~~~~~-~~~~-~~~~~Gd~VrvrV~~v~~~~~~~  159 (182)
                      |||+||+++|+|++++++|+||++|++++++|.+++++++.|..+++.|.| ++++ ..|+.||.|||||.++++++  .
T Consensus         1 rPf~Gev~~g~V~~v~~~G~fv~lg~~~~~v~~~~l~~d~~y~~~~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~--~   78 (94)
T d2c35b1           1 RPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDK--N   78 (94)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEETTEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEET--T
T ss_pred             CCCCCCEEEEEEEEEEeeEEEEEecCceEEEEhhhcCcceeecccccceEEEcccceEEEeCCCEEEEEEEEEecCc--C
Confidence            799999999999999999999999999999999999998866656566555 4444 69999999999999999975  4


Q ss_pred             ceEEEEeccCCCcccc
Q 030170          160 EFQALVSLEGDFLGPV  175 (182)
Q Consensus       160 ~~~i~gs~~~~gLG~i  175 (182)
                      .++++|+|++||||+|
T Consensus        79 ~I~~igt~~~d~LG~i   94 (94)
T d2c35b1          79 DIFAIGSLMDDYLGLV   94 (94)
T ss_dssp             EEEEEEECCSTTCEEC
T ss_pred             cceEEEEccCCCcccC
Confidence            7789999999999986
>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
>d1go3e2 d.230.1.1 (E:1-78) N-terminal, heterodimerisation domain of RBP7 (RpoE) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
>d2c35b2 d.230.1.1 (B:1-77) N-terminal, heterodimerisation domain of RBP7 (RpoE) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1y14b2 d.230.1.1 (B:1-80) N-terminal, heterodimerisation domain of RBP7 (RpoE) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} 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
>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
>d2ix0a3 b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]} 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
>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
>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
>d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]} 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
>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
>d1wi5a_ b.40.4.5 (A:) S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) {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
>d1hh2p1 b.40.4.5 (P:127-198) S1 domain of NusA {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d2nn6i1 b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {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
>d1smxa_ b.40.4.5 (A:) S1-domain of Ribonuclease E {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1k3ra1 b.40.4.10 (A:93-163) Hypothetical protein MTH1 (MT0001), insert domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Back     information, alignment and structure
>d2vnud2 b.40.4.5 (D:911-998) Exosome complex exonuclease RRP44 {Saccharomyces cerevisiae [TaxId: 4932]} Back     information, alignment and structure