Psyllid ID: psy13107

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
MFYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQPGQGFVVYPVKYRAIVFRPFKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFAIGTLMDDYLGL
cEEEEEEEEEEEEccccccccHHHHHHHHHHHHHccEEEccEEEEEEEEEEcccccEEEEcccccEEEEEEEEEEEEEEccccEEEEEEEEEccccEEEEEcccEEEEcccccccccEEEcccccEEEEEcccEEEEccccEEEEEEEEEEEcccccEEEEEEccccccc
cEEEEEEEEEEEEcHHHccccHHHHHHHHHHHHHccccccccEEEEEEEEEEEccccEEEccccEEEEEEEEEEEEEEccccEEEEEEEEEEcccEEEEEEccccEEEEEcccccccEEccccccccEEEccccEEEEcccEEEEEEEEEEEcccccEEEEEEccccccc
MFYHISLEHEillhpryfgpqlyETVKQKLYSevegtctgkYGFVIAVTTIDsigagliqpgqgfvvypvkyraivfrpfkGEVLDAVVTQVNKVgmfaeigplscfishhsiptdmqfcpnsnpvcyksvhgevviqeddEIRLKIVgtrvdasgIFAIGTLMDDYLGL
MFYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQPGQGFVVYPVKYRAIVFRPFKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVgtrvdasgifaigtlmddylgl
MFYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQPGQGFVVYPVKYRAIVFRPFKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFAIGTLMDDYLGL
*FYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQPGQGFVVYPVKYRAIVFRPFKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFAIGTLMDDYL**
MFYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQPGQGFVVYPVKYRAIVFRPFKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFAIGTLMDDYLGL
MFYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQPGQGFVVYPVKYRAIVFRPFKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFAIGTLMDDYLGL
MFYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQPGQGFVVYPVKYRAIVFRPFKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFAIGTLMDDYLGL
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MFYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQPGQGFVVYPVKYRAIVFRPFKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFAIGTLMDDYLGL
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 ?
Query170 2.2.26 [Sep-21-2011]
Q7ZW41172 DNA-directed RNA polymera yes N/A 1.0 0.988 0.829 5e-81
P62489172 DNA-directed RNA polymera yes N/A 1.0 0.988 0.817 2e-80
P62488172 DNA-directed RNA polymera yes N/A 1.0 0.988 0.817 2e-80
P62487172 DNA-directed RNA polymera yes N/A 1.0 0.988 0.817 2e-80
Q5E9B8172 DNA-directed RNA polymera yes N/A 1.0 0.988 0.817 2e-80
P46279176 DNA-directed RNA polymera yes N/A 0.994 0.960 0.582 4e-54
P38421176 DNA-directed RNA polymera yes N/A 0.994 0.960 0.570 4e-53
Q54P04172 DNA-directed RNA polymera yes N/A 1.0 0.988 0.535 2e-51
O14459172 DNA-directed RNA polymera yes N/A 0.976 0.965 0.523 6e-46
P34087171 DNA-directed RNA polymera yes N/A 0.982 0.976 0.432 1e-33
>sp|Q7ZW41|RPB7_DANRE DNA-directed RNA polymerase II subunit RPB7 OS=Danio rerio GN=polr2g PE=2 SV=1 Back     alignment and function desciption
 Score =  299 bits (766), Expect = 5e-81,   Method: Compositional matrix adjust.
 Identities = 141/170 (82%), Positives = 159/170 (93%)

Query: 1   MFYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQ 60
           MFYHISLEHEILLHPRYFGP L  TVKQKL++EVEGTCTGKYGFVIAVTTID+IGAG+IQ
Sbjct: 1   MFYHISLEHEILLHPRYFGPNLLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGVIQ 60

Query: 61  PGQGFVVYPVKYRAIVFRPFKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFC 120
           PG+GFV+YPVKY+AIVFRPFKGEV+DAVVTQVNKVG+F EIGP+SCFIS HSIP++M+F 
Sbjct: 61  PGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFD 120

Query: 121 PNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFAIGTLMDDYLGL 170
           PNSNP CYK+V  +VVIQ+DDEIRLKIVGTRVD + IFAIG+LMDDYLGL
Sbjct: 121 PNSNPPCYKTVDEDVVIQQDDEIRLKIVGTRVDKNDIFAIGSLMDDYLGL 170
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.
Danio rerio (taxid: 7955)
>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|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|P46279|RPB7_SOYBN DNA-directed RNA polymerase II subunit RPB7 OS=Glycine max PE=2 SV=1 Back     alignment and function description
>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|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|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 ?
Query170
242005679 3311 mixed-lineage leukemia protein, mll, put 0.976 0.050 0.921 8e-88
307201488179 DNA-directed RNA polymerase II subunit R 0.994 0.944 0.887 2e-85
383865506173 PREDICTED: DNA-directed RNA polymerase I 1.0 0.982 0.894 3e-85
340711605173 PREDICTED: DNA-directed RNA polymerase I 1.0 0.982 0.894 3e-85
357630895173 putative mixed-lineage leukemia protein, 1.0 0.982 0.9 6e-85
328789158173 PREDICTED: DNA-directed RNA polymerase I 1.0 0.982 0.888 7e-85
307183360249 DNA-directed RNA polymerase II subunit R 0.988 0.674 0.892 2e-84
219879810173 RNA polymerase II subunit 7 [Nasonia vit 1.0 0.982 0.888 2e-84
332024088267 DNA-directed RNA polymerase II subunit R 0.982 0.625 0.892 1e-83
170030019173 DNA-directed RNA polymerase II 19 kDa po 1.0 0.982 0.894 1e-83
>gi|242005679|ref|XP_002423690.1| mixed-lineage leukemia protein, mll, putative [Pediculus humanus corporis] gi|212506866|gb|EEB10952.1| mixed-lineage leukemia protein, mll, putative [Pediculus humanus corporis] Back     alignment and taxonomy information
 Score =  327 bits (839), Expect = 8e-88,   Method: Composition-based stats.
 Identities = 153/166 (92%), Positives = 156/166 (93%)

Query: 5   ISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQPGQG 64
           ISLEHEILLHPRYFGPQL ETVKQKLY+EVEGTCTGKYGFVIAVT ID+IGAGLI PGQG
Sbjct: 3   ISLEHEILLHPRYFGPQLLETVKQKLYAEVEGTCTGKYGFVIAVTLIDNIGAGLILPGQG 62

Query: 65  FVVYPVKYRAIVFRPFKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFCPNSN 124
           FVVYPVKYRAIVFRPFKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIP DMQFCPN N
Sbjct: 63  FVVYPVKYRAIVFRPFKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPADMQFCPNFN 122

Query: 125 PVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFAIGTLMDDYLGL 170
           P CYKS   +VVIQ DDEIRLKIVGTRVDASGIFAIGTLMDDYLGL
Sbjct: 123 PPCYKSKDEDVVIQADDEIRLKIVGTRVDASGIFAIGTLMDDYLGL 168

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|307201488|gb|EFN81256.1| DNA-directed RNA polymerase II subunit RPB7 [Harpegnathos saltator] Back     alignment and taxonomy information
>gi|383865506|ref|XP_003708214.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB7-like [Megachile rotundata] Back     alignment and taxonomy information
>gi|340711605|ref|XP_003394365.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB7-like [Bombus terrestris] gi|350416078|ref|XP_003490834.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB7-like [Bombus impatiens] Back     alignment and taxonomy information
>gi|357630895|gb|EHJ78714.1| putative mixed-lineage leukemia protein, mll [Danaus plexippus] Back     alignment and taxonomy information
>gi|328789158|ref|XP_624976.2| PREDICTED: DNA-directed RNA polymerase II subunit RPB7-like [Apis mellifera] gi|380030530|ref|XP_003698899.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB7-like [Apis florea] Back     alignment and taxonomy information
>gi|307183360|gb|EFN70218.1| DNA-directed RNA polymerase II subunit RPB7 [Camponotus floridanus] Back     alignment and taxonomy information
>gi|219879810|ref|NP_001137380.1| RNA polymerase II subunit 7 [Nasonia vitripennis] Back     alignment and taxonomy information
>gi|332024088|gb|EGI64305.1| DNA-directed RNA polymerase II subunit RPB7 [Acromyrmex echinatior] Back     alignment and taxonomy information
>gi|170030019|ref|XP_001842888.1| DNA-directed RNA polymerase II 19 kDa polypeptide [Culex quinquefasciatus] gi|167865348|gb|EDS28731.1| DNA-directed RNA polymerase II 19 kDa polypeptide [Culex quinquefasciatus] 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 ?
Query170
FB|FBgn0051155173 Rpb7 "Rpb7" [Drosophila melano 1.0 0.982 0.882 4.2e-79
ZFIN|ZDB-GENE-030131-2808172 polr2gl "polymerase (RNA) II ( 1.0 0.988 0.829 2.1e-75
UNIPROTKB|Q5E9B8172 POLR2G "DNA-directed RNA polym 1.0 0.988 0.817 5.7e-75
UNIPROTKB|P62487172 POLR2G "DNA-directed RNA polym 1.0 0.988 0.817 5.7e-75
UNIPROTKB|I3LJZ9172 POLR2G "Uncharacterized protei 1.0 0.988 0.817 5.7e-75
MGI|MGI:1914960172 Polr2g "polymerase (RNA) II (D 1.0 0.988 0.817 5.7e-75
RGD|621284172 Polr2g "polymerase (RNA) II (D 1.0 0.988 0.817 5.7e-75
WB|WBGene00021845197 rpb-7 [Caenorhabditis elegans 1.0 0.862 0.729 1.5e-67
TAIR|locus:2168514176 NRPB7 [Arabidopsis thaliana (t 0.994 0.960 0.570 2.2e-50
DICTYBASE|DDB_G0284891172 rpb7 "DNA-directed RNA polymer 1.0 0.988 0.535 2.3e-48
FB|FBgn0051155 Rpb7 "Rpb7" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
 Score = 795 (284.9 bits), Expect = 4.2e-79, P = 4.2e-79
 Identities = 150/170 (88%), Positives = 158/170 (92%)

Query:     1 MFYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQ 60
             MFYHISLE EILLHPRYFGPQL ETVKQKLYSEVEGTCTGKYGFVIAVTTID IG+G+IQ
Sbjct:     1 MFYHISLEQEILLHPRYFGPQLLETVKQKLYSEVEGTCTGKYGFVIAVTTIDQIGSGVIQ 60

Query:    61 PGQGFVVYPVKYRAIVFRPFKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFC 120
             PGQGFVVYPVKY+AIVFRPFKGEVLDAVV Q+NKVGMFAEIGPLSCFISHHSIP DMQFC
Sbjct:    61 PGQGFVVYPVKYKAIVFRPFKGEVLDAVVKQINKVGMFAEIGPLSCFISHHSIPADMQFC 120

Query:   121 PNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFAIGTLMDDYLGL 170
             PN NP CYKS   +VVI  +D+IRLKIVGTRVDA+GIFAIGTLMDDYLGL
Sbjct:   121 PNGNPPCYKSKDEDVVISGEDKIRLKIVGTRVDATGIFAIGTLMDDYLGL 170
GO:0006366 "transcription from RNA polymerase II promoter" evidence=ISS
GO:0005665 "DNA-directed RNA polymerase II, core complex" evidence=ISS;IPI
GO:0003899 "DNA-directed RNA polymerase activity" evidence=ISS
GO:0005515 "protein binding" evidence=IPI
GO:0003723 "RNA binding" evidence=IEA
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
RGD|621284 Polr2g "polymerase (RNA) II (DNA directed) polypeptide G" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
WB|WBGene00021845 rpb-7 [Caenorhabditis elegans (taxid:6239)] Back     alignment and assigned GO terms
TAIR|locus:2168514 NRPB7 [Arabidopsis thaliana (taxid:3702)] 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

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) ?
P38421RPB7_ARATHNo assigned EC number0.57050.99410.9602yesN/A
O14459RPB7_SCHPONo assigned EC number0.52320.97640.9651yesN/A
P46279RPB7_SOYBNNo assigned EC number0.58230.99410.9602yesN/A
Q54P04RPB7_DICDINo assigned EC number0.53521.00.9883yesN/A
P62488RPB7_MOUSENo assigned EC number0.81761.00.9883yesN/A
P62489RPB7_RATNo assigned EC number0.81761.00.9883yesN/A
Q7ZW41RPB7_DANRENo assigned EC number0.82941.00.9883yesN/A
P34087RPB7_YEASTNo assigned EC number0.43270.98230.9766yesN/A
Q5E9B8RPB7_BOVINNo assigned EC number0.81761.00.9883yesN/A
P62487RPB7_HUMANNo assigned EC number0.81761.00.9883yesN/A
P39466RPOE_SULAC2, ., 7, ., 7, ., 60.24700.98820.9180yesN/A
Q57840RPOE1_METJA2, ., 7, ., 7, ., 60.27560.90.8181yesN/A

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query170
PTZ00162176 PTZ00162, PTZ00162, DNA-directed RNA polymerase II 1e-71
cd0446288 cd04462, S1_RNAPII_Rpb7, S1_RNAPII_Rpb7: Eukaryoti 1e-47
COG1095183 COG1095, RPB7, DNA-directed RNA polymerase, subuni 1e-46
cd0432980 cd04329, RNAP_II_Rpb7_N, RNAP_II_Rpb7_N: Rpb7, N-t 2e-42
PRK08563187 PRK08563, PRK08563, DNA-directed RNA polymerase su 5e-22
pfam0387670 pfam03876, SHS2_Rpb7-N, SHS2 domain found in N ter 6e-20
TIGR00448179 TIGR00448, rpoE, DNA-directed RNA polymerase (rpoE 2e-17
cd0065580 cd00655, RNAP_Rpb7_N_like, RNAP_Rpb7_N_like: This 1e-15
cd0433180 cd04331, RNAP_E_N, RNAP_E_N: RpoE, N-terminal ribo 1e-11
pfam0057574 pfam00575, S1, S1 RNA binding domain 2e-08
cd0433080 cd04330, RNAP_III_Rpc25_N, RNAP_III_Rpc25_N: Rpc25 2e-07
>gnl|CDD|240298 PTZ00162, PTZ00162, DNA-directed RNA polymerase II subunit 7; Provisional Back     alignment and domain information 
 Score =  213 bits (544), Expect = 1e-71
 Identities = 79/169 (46%), Positives = 108/169 (63%)

Query: 1   MFYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQ 60
           MF+ + L   + L P   GP+  + ++  L S+VEG CT KYG+VI V  I     G +Q
Sbjct: 1   MFFVVELWKNVSLKPSQLGPRYQQIIEDMLRSQVEGQCTRKYGYVICVIRIIHNEPGRVQ 60

Query: 61  PGQGFVVYPVKYRAIVFRPFKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFC 120
            G G +V  VKY+AIVF+PFK EVLDA+VT VNK+G FA+ GPL  F+S  +IP D  + 
Sbjct: 61  DGTGMIVVNVKYQAIVFKPFKDEVLDAIVTDVNKLGFFAQAGPLKAFVSRSAIPPDFVYD 120

Query: 121 PNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFAIGTLMDDYLG 169
            +S   CY S  G++ I+ + E+RL++ G R DAS +FAI T+  DYLG
Sbjct: 121 SDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASNLFAIATINSDYLG 169

Length = 176
>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|224020 COG1095, RPB7, DNA-directed RNA polymerase, subunit E' [Transcription] Back     alignment and domain information
>gnl|CDD|239821 cd04329, RNAP_II_Rpb7_N, RNAP_II_Rpb7_N: Rpb7, N-terminal ribonucleoprotein (RNP) domain Back     alignment and domain information
>gnl|CDD|236289 PRK08563, PRK08563, DNA-directed RNA polymerase subunit E'; Provisional 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|129540 TIGR00448, rpoE, DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form 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
>gnl|CDD|216000 pfam00575, S1, S1 RNA binding domain Back     alignment and domain information
>gnl|CDD|239822 cd04330, RNAP_III_Rpc25_N, RNAP_III_Rpc25_N: Rpc25, 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 170
PTZ00162176 DNA-directed RNA polymerase II subunit 7; Provisio 100.0
COG1095183 RPB7 DNA-directed RNA polymerase, subunit E' [Tran 100.0
TIGR00448179 rpoE DNA-directed RNA polymerase (rpoE), archaeal 100.0
KOG3297|consensus202 100.0
PRK08563187 DNA-directed RNA polymerase subunit E'; Provisiona 100.0
KOG3298|consensus170 100.0
cd0433080 RNAP_III_Rpc25_N RNAP_III_Rpc25_N: Rpc25, N-termin 99.93
cd0446288 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly 99.93
cd0065580 RNAP_Rpb7_N_like RNAP_Rpb7_N_like: This conserved 99.92
cd0432980 RNAP_II_Rpb7_N RNAP_II_Rpb7_N: Rpb7, N-terminal ri 99.92
cd0433180 RNAP_E_N RNAP_E_N: RpoE, N-terminal ribonucleoprot 99.92
PF08292122 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; I 99.91
PF0387670 SHS2_Rpb7-N: SHS2 domain found in N terminus of Rp 99.76
cd0432889 RNAP_I_Rpa43_N RNAP_I_Rpa43_N: Rpa43, N-terminal r 99.65
cd0446099 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. 99.55
cd0447183 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai 99.44
KOG4134|consensus253 99.4
PF0057574 S1: S1 RNA binding domain; InterPro: IPR003029 Rib 99.31
PRK11642813 exoribonuclease R; Provisional 99.31
cd0568673 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom 99.27
cd0569870 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp 99.2
cd0570574 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a 99.2
cd0569069 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p 99.2
cd0569769 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t 99.2
PLN00207891 polyribonucleotide nucleotidyltransferase; Provisi 99.19
TIGR00358654 3_prime_RNase VacB and RNase II family 3'-5' exori 99.19
cd0570673 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a 99.19
TIGR02063709 RNase_R ribonuclease R. This family consists of an 99.19
TIGR03591684 polynuc_phos polyribonucleotide nucleotidyltransfe 99.19
cd0446183 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp 99.17
cd0570768 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a 99.15
TIGR02696719 pppGpp_PNP guanosine pentaphosphate synthetase I/p 99.15
cd0568972 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p 99.14
cd0570877 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a 99.14
PRK08582139 hypothetical protein; Provisional 99.13
COG1098129 VacB Predicted RNA binding protein (contains ribos 99.11
cd0569671 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t 99.09
cd0445276 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr 99.09
cd0578986 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. 99.08
COG0539 541 RpsA Ribosomal protein S1 [Translation, ribosomal 99.07
PRK11824693 polynucleotide phosphorylase/polyadenylase; Provis 99.06
cd0570373 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R 99.05
cd0568568 S1_Tex S1_Tex: The C-terminal S1 domain of a trans 99.04
cd0568868 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p 99.04
cd0568479 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal 99.03
cd0445482 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA- 99.02
COG1185692 Pnp Polyribonucleotide nucleotidyltransferase (pol 99.01
cd0569269 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p 99.01
cd0569173 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p 99.0
PRK07252120 hypothetical protein; Provisional 99.0
PRK05807136 hypothetical protein; Provisional 98.98
cd0570472 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a 98.92
cd0447268 S1_PNPase S1_PNPase: Polynucleotide phosphorylase 98.92
smart0031672 S1 Ribosomal protein S1-like RNA-binding domain. 98.92
cd0569474 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp 98.92
PRK08059123 general stress protein 13; Validated 98.92
cd0569566 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t 98.91
PRK07400318 30S ribosomal protein S1; Reviewed 98.89
cd0568770 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib 98.86
PRK12269863 bifunctional cytidylate kinase/ribosomal protein S 98.85
cd0445388 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik 98.84
PTZ00248 319 eukaryotic translation initiation factor 2 subunit 98.8
PRK07899 486 rpsA 30S ribosomal protein S1; Reviewed 98.8
cd0446567 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib 98.79
PRK05054644 exoribonuclease II; Provisional 98.78
cd0447377 S1_RecJ_like S1_RecJ_like: The S1 domain of the ar 98.77
cd0570270 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R 98.73
TIGR02062639 RNase_B exoribonuclease II. This family consists o 98.69
COG0557706 VacB Exoribonuclease R [Transcription] 98.69
cd0445567 S1_NusA S1_NusA: N-utilizing substance A protein ( 98.67
PRK03987 262 translation initiation factor IF-2 subunit alpha; 98.65
COG0539 541 RpsA Ribosomal protein S1 [Translation, ribosomal 98.64
cd0016465 S1_like S1_like: Ribosomal protein S1-like RNA-bin 98.59
PRK04163235 exosome complex RNA-binding protein Rrp4; Provisio 98.59
PHA0294588 interferon resistance protein; Provisional 98.58
cd05693100 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp 98.58
COG2183780 Tex Transcriptional accessory protein [Transcripti 98.57
PRK09521189 exosome complex RNA-binding protein Csl4; Provisio 98.55
PRK13806 491 rpsA 30S ribosomal protein S1; Provisional 98.49
PRK13806491 rpsA 30S ribosomal protein S1; Provisional 98.48
PRK07899 486 rpsA 30S ribosomal protein S1; Reviewed 98.47
PRK06676 390 rpsA 30S ribosomal protein S1; Reviewed 98.43
PRK12269 863 bifunctional cytidylate kinase/ribosomal protein S 98.39
PRK07400 318 30S ribosomal protein S1; Reviewed 98.32
PRK06299 565 rpsA 30S ribosomal protein S1; Reviewed 98.31
TIGR00717516 rpsA ribosomal protein S1. This model provides tru 98.31
PRK06299 565 rpsA 30S ribosomal protein S1; Reviewed 98.28
PRK06676390 rpsA 30S ribosomal protein S1; Reviewed 98.24
TIGR00717516 rpsA ribosomal protein S1. This model provides tru 98.24
PRK09202 470 nusA transcription elongation factor NusA; Validat 98.23
COG1093 269 SUI2 Translation initiation factor 2, alpha subuni 98.2
PRK12327 362 nusA transcription elongation factor NusA; Provisi 98.19
PRK00087647 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 98.17
PRK00087647 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 98.14
cd0579086 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai 98.11
cd0579192 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. 98.11
TIGR01953 341 NusA transcription termination factor NusA. This m 97.97
PF03293160 Pox_RNA_pol: Poxvirus DNA-directed RNA polymerase, 97.96
KOG1067|consensus760 97.7
COG1097239 RRP4 RNA-binding protein Rrp4 and related proteins 97.54
TIGR00757 414 RNaseEG ribonuclease, Rne/Rng family. The C-termin 97.48
PRK12328 374 nusA transcription elongation factor NusA; Provisi 97.44
PF1350961 S1_2: S1 domain; PDB: 3GO5_A. 97.18
PF1044782 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I 96.99
COG1096188 Predicted RNA-binding protein (consists of S1 doma 96.85
PRK12329 449 nusA transcription elongation factor NusA; Provisi 96.75
KOG1070|consensus 1710 96.67
cd0569972 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t 96.55
PRK11712 489 ribonuclease G; Provisional 96.18
PRK10811 1068 rne ribonuclease E; Reviewed 95.98
KOG1070|consensus 1710 95.22
COG1107 715 Archaea-specific RecJ-like exonuclease, contains D 95.04
KOG3409|consensus193 94.01
PF0031366 CSD: 'Cold-shock' DNA-binding domain; InterPro: IP 93.71
KOG1004|consensus230 93.61
COG2996287 Predicted RNA-bindining protein (contains S1 and H 93.44
PHA0285886 EIF2a-like PKR inhibitor; Provisional 93.43
PF10246104 MRP-S35: Mitochondrial ribosomal protein MRP-S35; 93.24
COG4776645 Rnb Exoribonuclease II [Transcription] 92.49
PRK1546370 cold shock-like protein CspF; Provisional 90.17
COG1530 487 CafA Ribonucleases G and E [Translation, ribosomal 89.87
PF0707661 DUF1344: Protein of unknown function (DUF1344); In 89.69
PRK1546470 cold shock-like protein CspH; Provisional 89.45
PRK0989070 cold shock protein CspG; Provisional 87.62
PRK1094369 cold shock-like protein CspC; Provisional 86.84
PRK0950769 cspE cold shock protein CspE; Reviewed 86.43
PRK1035470 RNA chaperone/anti-terminator; Provisional 84.61
COG2996 287 Predicted RNA-bindining protein (contains S1 and H 84.58
PRK1244287 translation initiation factor IF-1; Reviewed 84.58
PRK0993774 stationary phase/starvation inducible regulatory p 83.74
PRK1499873 cold shock-like protein CspD; Provisional 80.02
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional Back     alignment and domain information 
Probab=100.00  E-value=1.7e-53  Score=321.59  Aligned_cols=170  Identities=46%  Similarity=0.826  Sum_probs=166.7

Q ss_pred             CeEEEEEEEEEEEcCCCCCCCHHHHHHHHHHhhhcceEeCCeeEEEEEceeceeCCeeEecCCCceEEeEEEEEEEeecC
Q psy13107          1 MFYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQPGQGFVVYPVKYRAIVFRPF   80 (170)
Q Consensus         1 Mf~~~~~~~~i~i~P~~l~~~~~~~i~~~l~~~~~gk~~~~~G~~i~i~~i~~~~~g~I~~~~g~~~~~v~f~~i~f~p~   80 (170)
                      ||++++++|+|+|||++|++++.+++.++|+++|+||+.++.|+||+++||.++++|+|.+|||+++|+|+|+|++|+|+
T Consensus         1 MF~~~~l~d~v~i~P~~f~~~~~~~i~~~L~~~~egkv~~~~GliV~v~di~~i~~G~I~~gdG~~~~~V~FraivFrPf   80 (176)
T PTZ00162          1 MFFVVELWKNVSLKPSQLGPRYQQIIEDMLRSQVEGQCTRKYGYVICVIRIIHNEPGRVQDGTGMIVVNVKYQAIVFKPF   80 (176)
T ss_pred             CcEEEEEEEEEEECHHHcCccHHHHHHHHHHHHHCCCCcCcccEEEEEEEeeEecCCEEEcCCCCEEEEEEEEEEEEecC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCEEEEEEEEEecccEEEEecCeeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceEEE
Q psy13107         81 KGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFAI  160 (170)
Q Consensus        81 ~gev~~g~V~~i~~~Gifv~lg~~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~~i  160 (170)
                      +||+++|+|++++++|+|+++||+++|||.++||+++.||++++.|+|.+++++.+++.|+.||+||.+++++.+.++++
T Consensus        81 ~gEVv~g~V~~v~~~G~~v~~Gp~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~~~~i  160 (176)
T PTZ00162         81 KDEVLDAIVTDVNKLGFFAQAGPLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASNLFAI  160 (176)
T ss_pred             CCCEEEEEEEEEecceEEEEeeCeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCCCcEEE
Confidence            99999999999999999999999999999999999999999999999997777899999999999999999999999999


Q ss_pred             EEecCCCCCC
Q psy13107        161 GTLMDDYLGL  170 (170)
Q Consensus       161 g~~~~~~LG~  170 (170)
                      |||++||||+
T Consensus       161 ~T~~~~~LG~  170 (176)
T PTZ00162        161 ATINSDYLGP  170 (176)
T ss_pred             EEecCCCcCc
Confidence            9999999997

>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription] Back     alignment and domain information
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form Back     alignment and domain information
>KOG3297|consensus Back     alignment and domain information
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional Back     alignment and domain information
>KOG3298|consensus 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
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 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
>cd04329 RNAP_II_Rpb7_N RNAP_II_Rpb7_N: Rpb7, N-terminal ribonucleoprotein (RNP) domain Back     alignment and domain information
>cd04331 RNAP_E_N RNAP_E_N: RpoE, N-terminal ribonucleoprotein (RNP) domain 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
>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
>cd04328 RNAP_I_Rpa43_N RNAP_I_Rpa43_N: Rpa43, N-terminal ribonucleoprotein (RNP) domain Back     alignment and domain information
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain Back     alignment and domain information
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain Back     alignment and domain information
>KOG4134|consensus 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
>PRK11642 exoribonuclease R; Provisional Back     alignment and domain information
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain 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
>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
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain 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
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional Back     alignment and domain information
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases 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
>TIGR02063 RNase_R ribonuclease R Back     alignment and domain information
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase 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
>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
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase Back     alignment and domain information
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain 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
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>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
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain Back     alignment and domain information
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional Back     alignment and domain information
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>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
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain 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
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain Back     alignment and domain information
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>PRK07252 hypothetical protein; Provisional Back     alignment and domain information
>PRK05807 hypothetical protein; Provisional 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
>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
>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
>PRK08059 general stress protein 13; Validated 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
>PRK07400 30S ribosomal protein S1; Reviewed 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
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional 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
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional Back     alignment and domain information
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed 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
>PRK05054 exoribonuclease II; 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
>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
>TIGR02062 RNase_B exoribonuclease II Back     alignment and domain information
>COG0557 VacB Exoribonuclease R [Transcription] 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
>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
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain Back     alignment and domain information
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional Back     alignment and domain information
>PHA02945 interferon resistance protein; Provisional 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
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional 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
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed 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
>PRK07400 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
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK06676 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
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK12327 nusA transcription elongation factor NusA; Provisional Back     alignment and domain information
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed Back     alignment and domain information
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed Back     alignment and domain information
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain Back     alignment and domain information
>cd05791 S1_CSL4 S1_CSL4: CSL4, 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
>KOG1067|consensus 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
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family Back     alignment and domain information
>PRK12328 nusA transcription elongation factor NusA; Provisional Back     alignment and domain information
>PF13509 S1_2: S1 domain; PDB: 3GO5_A 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
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK12329 nusA transcription elongation factor NusA; Provisional Back     alignment and domain information
>KOG1070|consensus 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
>PRK11712 ribonuclease G; Provisional Back     alignment and domain information
>PRK10811 rne ribonuclease E; Reviewed Back     alignment and domain information
>KOG1070|consensus 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
>KOG3409|consensus 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
>KOG1004|consensus Back     alignment and domain information
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only] Back     alignment and domain information
>PHA02858 EIF2a-like PKR inhibitor; Provisional 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
>COG4776 Rnb Exoribonuclease II [Transcription] Back     alignment and domain information
>PRK15463 cold shock-like protein CspF; Provisional Back     alignment and domain information
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length Back     alignment and domain information
>PRK15464 cold shock-like protein CspH; Provisional Back     alignment and domain information
>PRK09890 cold shock protein CspG; Provisional Back     alignment and domain information
>PRK10943 cold shock-like protein CspC; Provisional Back     alignment and domain information
>PRK09507 cspE cold shock protein CspE; Reviewed Back     alignment and domain information
>PRK10354 RNA chaperone/anti-terminator; Provisional Back     alignment and domain information
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only] Back     alignment and domain information
>PRK12442 translation initiation factor IF-1; Reviewed Back     alignment and domain information
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional Back     alignment and domain information
>PRK14998 cold shock-like protein CspD; Provisional 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 ?
Query170
2c35_B172 Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii L 1e-81
3h0g_G172 Rna Polymerase Ii From Schizosaccharomyces Pombe Le 6e-47
2b8k_G215 12-Subunit Rna Polymerase Ii Length = 215 6e-35
1nt9_G171 Complete 12-Subunit Rna Polymerase Ii Length = 171 1e-34
1go3_E187 Structure Of An Archeal Homolog Of The Eukaryotic R 5e-11
3ayh_B203 Crystal Structure Of The C1725 SUBCOMPLEX FROM S. P 2e-08
2y0s_E180 Crystal Structure Of Sulfolobus Shibatae Rna Polyme 1e-05
2pmz_E180 Archaeal Rna Polymerase From Sulfolobus Solfataricu 1e-05
2waq_E180 The Complete Structure Of The Archaeal 13-Subunit D 1e-05
2ckz_B218 X-Ray Structure Of Rna Polymerase Iii Subcomplex C1 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 =  298 bits (762), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 139/170 (81%), Positives = 159/170 (93%)
Query: 1   MFYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQ 60
           MFYHISLEHEILLHPRYFGP L  TVKQKL++EVEGTCTGKYGFVIAVTTID+IGAG+IQ
Sbjct: 1   MFYHISLEHEILLHPRYFGPNLLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGVIQ 60
Query: 61  PGQGFVVYPVKYRAIVFRPFKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFC 120
           PG+GFV+YPVKY+AIVFRPFKGEV+DAVVTQVNKVG+F EIGP+SCFIS HSIP++M+F 
Sbjct: 61  PGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFD 120
Query: 121 PNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFAIGTLMDDYLGL 170
           PNSNP CYK++  ++VIQ+DDEIRLKIVGTRVD + IFAIG+LMDDYLGL
Sbjct: 121 PNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIFAIGSLMDDYLGL 170
>pdb|3H0G|G Chain G, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 172 Back     alignment and structure
>pdb|2B8K|G Chain G, 12-Subunit Rna Polymerase Ii Length = 215 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
>pdb|2Y0S|E Chain E, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In P21 Space Group Length = 180 Back     alignment and structure
>pdb|2PMZ|E Chain E, Archaeal Rna Polymerase From Sulfolobus Solfataricus Length = 180 Back     alignment and structure
>pdb|2WAQ|E Chain E, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 180 Back     alignment and structure
>pdb|2CKZ|B Chain B, X-Ray Structure Of Rna Polymerase Iii Subcomplex C17-C25. Length = 218 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 ?
Query170
2c35_B172 Human RPB7, DNA-directed RNA polymerase II 19 kDa 5e-61
1y14_B171 B16, RPB7, DNA-directed RNA polymerase II 19 kDa p 4e-58
2b8k_G215 B16, DNA-directed RNA polymerase II 19 kDa polypep 1e-56
3h0g_G172 DNA-directed RNA polymerase II subunit RPB7; trans 2e-52
4ayb_E180 DNA-directed RNA polymerase; transferase, multi-su 6e-52
1go3_E187 DNA-directed RNA polymerase subunit E; transferase 4e-50
2ckz_B218 C25, DNA-directed RNA polymerase III 25 KD polypep 2e-49
3ayh_B203 DNA-directed RNA polymerase III subunit RPC8; tran 1e-44
2rf4_A214 DNA-directed RNA polymerase I subunit RPA4; transf 1e-20
>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 =  185 bits (472), Expect = 5e-61
 Identities = 139/170 (81%), Positives = 159/170 (93%)

Query: 1   MFYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQ 60
           MFYHISLEHEILLHPRYFGP L  TVKQKL++EVEGTCTGKYGFVIAVTTID+IGAG+IQ
Sbjct: 1   MFYHISLEHEILLHPRYFGPNLLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGVIQ 60

Query: 61  PGQGFVVYPVKYRAIVFRPFKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFC 120
           PG+GFV+YPVKY+AIVFRPFKGEV+DAVVTQVNKVG+F EIGP+SCFIS HSIP++M+F 
Sbjct: 61  PGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFD 120

Query: 121 PNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFAIGTLMDDYLGL 170
           PNSNP CYK++  ++VIQ+DDEIRLKIVGTRVD + IFAIG+LMDDYLGL
Sbjct: 121 PNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIFAIGSLMDDYLGL 170
>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
>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
>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
>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
>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
>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A {Schizosaccharomyces pombe} Length = 203 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} Length = 214 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query170
3h0g_G172 DNA-directed RNA polymerase II subunit RPB7; trans 100.0
3ayh_B203 DNA-directed RNA polymerase III subunit RPC8; tran 100.0
2ckz_B218 C25, DNA-directed RNA polymerase III 25 KD polypep 100.0
2c35_B172 Human RPB7, DNA-directed RNA polymerase II 19 kDa 100.0
4ayb_E180 DNA-directed RNA polymerase; transferase, multi-su 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
1go3_E187 DNA-directed RNA polymerase subunit E; transferase 100.0
2rf4_A214 DNA-directed RNA polymerase I subunit RPA4; transf 99.98
4aid_A726 Polyribonucleotide nucleotidyltransferase; transfe 99.34
2k52_A80 Uncharacterized protein MJ1198; metal-binding, zin 99.3
1kl9_A182 Eukaryotic translation initiation factor 2 subuni; 99.26
1luz_A88 Protein K3, protein K2; stranded anti-parallel bet 99.26
3cdi_A723 Polynucleotide phosphorylase; mRNA turnover, RNAse 99.26
2khi_A115 30S ribosomal protein S1; acetylation, phosphoprot 99.24
2k4k_A130 GSP13, general stress protein 13; cytoplasm, stres 99.23
2a19_A175 EIF-2- alpha, eukaryotic translation initiation fa 99.22
2eqs_A103 ATP-dependent RNA helicase DHX8; S1 domain, OB-fol 99.21
2cqo_A119 Nucleolar protein of 40 kDa; S1 domain, OB-fold, s 99.21
2khj_A109 30S ribosomal protein S1; OB fold, acetylation, ph 99.14
1wi5_A119 RRP5 protein homolog; S1 domain, OB-fold, structur 99.12
2id0_A644 Exoribonuclease 2; RNAse, exonuclease, hydrolyase, 98.99
3aev_A 275 Translation initiation factor 2 subunit alpha; pro 98.98
1e3p_A757 Guanosine pentaphosphate synthetase; polyribonucle 98.94
1q8k_A 308 Eukaryotic translation initiation factor 2 subunit 98.93
2nn6_I209 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, 98.91
3bzc_A785 TEX; helix-turn-helix, helix-hairpin-helix, S1 dom 98.82
3m7n_A179 Putative uncharacterized protein AF_0206; exosome, 98.81
3psi_A 1219 Transcription elongation factor SPT6; nucleus; 3.3 98.78
2wp8_J977 Exosome complex exonuclease DIS3; nucleus, hydrola 98.73
3cw2_C 266 Translation initiation factor 2 subunit alpha; AIF 98.73
2vnu_D760 Exosome complex exonuclease RRP44; hydrolase-RNA c 98.72
2je6_I251 RRP4, exosome complex RNA-binding protein 1; nucle 98.7
2ba0_A229 Archeal exosome RNA binding protein RRP4; RNAse PH 98.69
3psf_A1030 Transcription elongation factor SPT6; nucleus; 2.5 98.64
2z0s_A235 Probable exosome complex RNA-binding protein 1; al 98.63
3go5_A285 Multidomain protein with S1 RNA-binding domains; s 98.53
2ja9_A175 Exosome complex exonuclease RRP40; RNA-binding pro 98.52
2nn6_H 308 Exosome complex exonuclease RRP4; RNA, exosome, PM 98.33
2bh8_A101 1B11; transcription, molecular evolution, unique a 98.31
1hh2_P 344 NUSA, N utilization substance protein A; transcrip 98.23
1k0r_A 366 NUSA; two component arrangement, S1 domain, two K- 97.92
2bx2_L 517 Ribonuclease E, RNAse E; RNA-binding, RNA turnover 97.9
3go5_A 285 Multidomain protein with S1 RNA-binding domains; s 97.87
2asb_A 251 Transcription elongation protein NUSA; protein-RNA 97.75
2nn6_G289 Exosome complex exonuclease RRP40; RNA, exosome, P 97.16
2r7d_A469 Ribonuclease II family protein; structural genomic 95.33
2bh8_A101 1B11; transcription, molecular evolution, unique a 95.18
1wfq_A89 UNR protein; beta-barrel, translational regulation 91.64
1h95_A79 CSD, Y-box binding protein; translation factor, tr 90.84
2yty_A88 Cold shock domain-containing protein E1; cell-free 90.53
3i2z_B71 RNA chaperone, negative regulator of CSPA transcri 90.01
3cam_A67 Cold-shock domain family protein; cold shock prote 87.26
3aqq_A147 Calcium-regulated heat stable protein 1; compact b 85.14
1c9o_A66 CSPB, cold-shock protein; beta barrel, homodimer, 84.82
1g6p_A66 Cold shock protein TMCSP; greek-KEY, beta barrel, 83.29
2ytx_A97 Cold shock domain-containing protein E1; cell-free 83.15
3a0j_A73 Cold shock protein; OB-fold, cytoplasm, transcript 80.12
>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure
Probab=100.00  E-value=1.2e-49  Score=299.45  Aligned_cols=168  Identities=51%  Similarity=0.956  Sum_probs=159.9

Q ss_pred             CeEEEEEEE-EEEEcCCCCCCCHHHHHHHHHHhhhcceEeCCeeEEEEEc--eeceeCCeeEecCCCceEEeEEEEEEEe
Q psy13107          1 MFYHISLEH-EILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVT--TIDSIGAGLIQPGQGFVVYPVKYRAIVF   77 (170)
Q Consensus         1 Mf~~~~~~~-~i~i~P~~l~~~~~~~i~~~l~~~~~gk~~~~~G~~i~i~--~i~~~~~g~I~~~~g~~~~~v~f~~i~f   77 (170)
                      ||++.+|+| +|++||++|++++++++..+|+++|+|+|+++.|+||+++  ||.++++|+|.++||+++++|+|++++|
T Consensus         1 Mf~l~~l~d~~i~ipp~~~~~~~~~~i~~~l~~~~~g~vi~~~G~~I~i~~idi~~i~~G~I~~gdg~~~~~v~f~~ivf   80 (172)
T 3h0g_G            1 MPFFLKELSLTISLHPSYFGPRMQDYLKAKLLADVEGTCSGQYGYIICVLDSNTIDIDKGRVVPGQGFAEFEVKYRAVLW   80 (172)
T ss_dssp             --CEEEEEEEEEECCGGGCTTTHHHHHHHHHHHHHTTCEETTTEEEEEECTTTSEEECCCEECTTTCCEEEEEEEEEEEE
T ss_pred             CeEEEEEecCeEEeCHHHhCccHHHHHHHHHHHHhCCcCcCCccEEEEEEeeeeeEeeCCEEECCCCcEEEEEEEEEeee
Confidence            999999999 9999999999999999999999999999999999999999  9999999999999999999999999999


Q ss_pred             ecCCCCEEEEEEEEEecccEEEEecCeeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCce
Q psy13107         78 RPFKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGI  157 (170)
Q Consensus        78 ~p~~gev~~g~V~~i~~~Gifv~lg~~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i  157 (170)
                      +|++||+++|+|++++++|+||++++++||||.|+|+++|.||++++.|+|  ++++..++.||+|||||.+++.+++++
T Consensus        81 ~p~~Gev~~G~V~~v~~fG~FV~l~~~~glVh~s~l~~~~~~d~~~~~~~~--~~~~~~~~~Gd~VrvkV~~vd~~~~~~  158 (172)
T 3h0g_G           81 RPFRGEVVDAIVTTVNKMGFFANIGPLNVFVSSHLVPPDMKFDPTANPPNY--SGEDQVIEKGSNVRLKIVGTRTDATEI  158 (172)
T ss_dssp             CCCTTCEEECCCCEEETTEEECCBTTBCCEEEGGGSCTTCCCBSSSSSCBE--ESSSCEECSSCCEEEEEEEEEESSSCE
T ss_pred             ccCCCCEEEEEEEEEEcceEEEEeCCeEEEEEHHHCCCccccCcccccceE--ecCCcEECCCCEEEEEEEEEECCCCCc
Confidence            999999999999999999999999999999999999877999998777888  455679999999999999999999999


Q ss_pred             EEEEEecCCCCCC
Q psy13107        158 FAIGTLMDDYLGL  170 (170)
Q Consensus       158 ~~ig~~~~~~LG~  170 (170)
                      .+||||++|||||
T Consensus       159 ~~Igtm~~~~LG~  171 (172)
T 3h0g_G          159 FAIATMKEDYLGV  171 (172)
T ss_dssp             EEEEECCSTTCEE
T ss_pred             eEEEEcCCCCCCC
Confidence            9999999999996
>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A {Schizosaccharomyces pombe} 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
>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
>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
>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
>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
>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
>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A 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
>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
>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A Back     alignment and structure
>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Back     alignment and structure
>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis} 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
>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
>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} 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
>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
>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
>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
>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
>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
>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
>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
>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae} 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
>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
>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
>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
>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae} 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
>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
>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
>2bh8_A 1B11; transcription, molecular evolution, unique architecture, transcription regulation, phosphorylation; 1.9A {Escherichia coli} Back     alignment and structure
>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A Back     alignment and structure
>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 Back     alignment and structure
>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
>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
>1wfq_A UNR protein; beta-barrel, translational regulation, RNA chaperone, RNA/DN binding, QB fold, greek-KEY topology, structur genomics; NMR {Homo sapiens} SCOP: b.40.4.5 Back     alignment and structure
>1h95_A CSD, Y-box binding protein; translation factor, transcription factor, OB-fold, 5- stranded anti-parallel beta-barrel, single stranded DNA binding; NMR {Homo sapiens} SCOP: b.40.4.5 Back     alignment and structure
>2yty_A Cold shock domain-containing protein E1; cell-free protein synthesis, beta-barrel, translational REGU RNA chaperone, RNA/DNA binding, QB fold; NMR {Homo sapiens} Back     alignment and structure
>3i2z_B RNA chaperone, negative regulator of CSPA transcription; beta barrel, DNA binding protein/transcription, cytoplasm, gene regulation; 1.10A {Salmonella typhimurium} SCOP: b.40.4.5 PDB: 2l15_A 1mjc_A 3mef_A Back     alignment and structure
>3cam_A Cold-shock domain family protein; cold shock protein, chain SWAP, STRU genomics, oxford protein production facility, OPPF, gene RE; 2.60A {Neisseria meningitidis MC58} Back     alignment and structure
>3aqq_A Calcium-regulated heat stable protein 1; compact beta-barrel, cold shock domain, ssDNA binding, DNA B protein; 2.80A {Homo sapiens} Back     alignment and structure
>1c9o_A CSPB, cold-shock protein; beta barrel, homodimer, transcription; 1.17A {Bacillus caldolyticus} SCOP: b.40.4.5 PDB: 2hax_A 1hz9_A 1hzb_A 1i5f_A 1hza_A 1hzc_A 3pf4_A 1csq_A 1nmf_A 1nmg_A 1csp_A 2f52_A 2es2_A 3pf5_A 2i5m_X 2i5l_X Back     alignment and structure
>1g6p_A Cold shock protein TMCSP; greek-KEY, beta barrel, OB-fold, structural genomics; NMR {Thermotoga maritima} SCOP: b.40.4.5 Back     alignment and structure
>2ytx_A Cold shock domain-containing protein E1; cell-free protein synthesis, beta-barrel, translational REGU RNA chaperone, RNA/DNA binding, QB fold; NMR {Homo sapiens} Back     alignment and structure
>3a0j_A Cold shock protein; OB-fold, cytoplasm, transcription, structural genomics, NPPSFA; 1.65A {Thermus thermophilus} 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 170
d2c35b277 d.230.1.1 (B:1-77) N-terminal, heterodimerisation 7e-29
d1y14b280 d.230.1.1 (B:1-80) N-terminal, heterodimerisation 4e-28
d1y14b191 b.40.4.5 (B:81-171) C-terminal domain of RNA polym 2e-27
d2c35b194 b.40.4.5 (B:78-171) C-terminal domain of RNA polym 3e-27
d1go3e278 d.230.1.1 (E:1-78) N-terminal, heterodimerisation 1e-26
d1go3e1106 b.40.4.5 (E:79-184) C-terminal domain of RNA polym 3e-07
d3bzka494 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas ae 6e-04
>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

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: Human (Homo sapiens) [TaxId: 9606]

 Score = 99.7 bits (249), Expect = 7e-29
 Identities = 67/77 (87%), Positives = 74/77 (96%)

Query: 1  MFYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQ 60
          MFYHISLEHEILLHPRYFGP L  TVKQKL++EVEGTCTGKYGFVIAVTTID+IGAG+IQ
Sbjct: 1  MFYHISLEHEILLHPRYFGPNLLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGVIQ 60

Query: 61 PGQGFVVYPVKYRAIVF 77
          PG+GFV+YPVKY+AIVF
Sbjct: 61 PGRGFVLYPVKYKAIVF 77
>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
>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
>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
>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
>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
>d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]} Length = 94 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 ?
Query170
d2c35b194 C-terminal domain of RNA polymerase II subunit RBP 99.97
d1y14b191 C-terminal domain of RNA polymerase II subunit RBP 99.96
d1go3e278 N-terminal, heterodimerisation domain of RBP7 (Rpo 99.92
d2c35b277 N-terminal, heterodimerisation domain of RBP7 (Rpo 99.91
d1y14b280 N-terminal, heterodimerisation domain of RBP7 (Rpo 99.9
d1go3e1106 C-terminal domain of RNA polymerase II subunit RBP 99.83
d2ix0a387 Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5 99.61
d2ba0a183 S1-domain of exosome complex RNA-binding protein 1 99.48
d2z0sa188 S1-domain of exosome complex RNA-binding protein 1 99.42
d2je6i187 S1-domain of exosome complex RNA-binding protein 1 99.42
d1kl9a286 Eukaryotic initiation factor 2alpha, eIF2alpha, N- 99.37
d1sroa_76 S1 RNA-binding domain of polyribonucleotide phosph 99.31
d2ahob284 Eukaryotic initiation factor 2alpha, eIF2alpha, N- 99.29
d3bzka494 Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287] 99.16
d2nn6h195 S1-domain of Ribosomal RNA-processing protein 4, R 99.13
d1e3pa262 S1 RNA-binding domain of polyribonucleotide phosph 98.88
d1wi5a_119 S1-domain of RRP5 protein homolog (PDCD11, KIAA018 98.84
d2nn6g188 S1-domain of exosome component 3 (RRP40) {Human (H 98.78
d1hh2p172 S1 domain of NusA {Thermotoga maritima [TaxId: 233 98.61
d2ja9a190 S1-domain of exosome component 3 (RRP40) {Saccharo 98.39
d2nn6i1125 Exosome component 1, EXOSC1 {Human (Homo sapiens) 97.94
d2asba176 S1 domain of NusA {Mycobacterium tuberculosis [Tax 97.67
d1smxa_87 S1-domain of Ribonuclease E {Escherichia coli [Tax 97.49
d2vnud288 Exosome complex exonuclease RRP44 {Saccharomyces c 94.68
d1mjca_69 Major cold shock protein {Escherichia coli [TaxId: 93.03
d1h95a_79 Y-box protein 1 cold shock domain (YB1-CSD) {Human 92.6
d1c9oa_66 Major cold shock protein {Bacillus caldolyticus [T 91.48
d1g6pa_66 Major cold shock protein {Thermotoga maritima [Tax 88.01
d1wfqa_89 Cold shock domain protein E1 (UNR) {Human (Homo sa 86.9
d1k3ra171 Hypothetical protein MTH1 (MT0001), insert domain 84.63
>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=99.97  E-value=9.7e-31  Score=176.61  Aligned_cols=93  Identities=77%  Similarity=1.303  Sum_probs=90.2

Q ss_pred             ecCCCCEEEEEEEEEecccEEEEecCeeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCce
Q psy13107         78 RPFKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGI  157 (170)
Q Consensus        78 ~p~~gev~~g~V~~i~~~Gifv~lg~~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i  157 (170)
                      ||++||+++|+|++++++|+|+++|++++|||.++||+|+.|+.+++.|+|.+++++..|++||.|||||.+++++++++
T Consensus         1 rPf~Gev~~g~V~~v~~~G~fv~lg~~~~~v~~~~l~~d~~y~~~~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~~~I   80 (94)
T d2c35b1           1 RPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDI   80 (94)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEETTEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEETTEE
T ss_pred             CCCCCCEEEEEEEEEEeeEEEEEecCceEEEEhhhcCcceeecccccceEEEcccceEEEeCCCEEEEEEEEEecCcCcc
Confidence            79999999999999999999999999999999999999988888888899999999999999999999999999999999


Q ss_pred             EEEEEecCCCCCC
Q psy13107        158 FAIGTLMDDYLGL  170 (170)
Q Consensus       158 ~~ig~~~~~~LG~  170 (170)
                      +|+|+|++||||+
T Consensus        81 ~~igt~~~d~LG~   93 (94)
T d2c35b1          81 FAIGSLMDDYLGL   93 (94)
T ss_dssp             EEEEECCSTTCEE
T ss_pred             eEEEEccCCCccc
Confidence            9999999999996
>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
>d2ix0a3 b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]} 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
>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
>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
>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
>d1sroa_ b.40.4.5 (A:) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Escherichia coli [TaxId: 562]} 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
>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
>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
>d1wi5a_ b.40.4.5 (A:) S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2nn6g1 b.40.4.5 (G:107-194) S1-domain of exosome component 3 (RRP40) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1hh2p1 b.40.4.5 (P:127-198) S1 domain of NusA {Thermotoga maritima [TaxId: 2336]} 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
>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
>d2vnud2 b.40.4.5 (D:911-998) Exosome complex exonuclease RRP44 {Saccharomyces cerevisiae [TaxId: 4932]} Back     information, alignment and structure
>d1mjca_ b.40.4.5 (A:) Major cold shock protein {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1h95a_ b.40.4.5 (A:) Y-box protein 1 cold shock domain (YB1-CSD) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1c9oa_ b.40.4.5 (A:) Major cold shock protein {Bacillus caldolyticus [TaxId: 1394]} Back     information, alignment and structure
>d1g6pa_ b.40.4.5 (A:) Major cold shock protein {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1wfqa_ b.40.4.5 (A:) Cold shock domain protein E1 (UNR) {Human (Homo sapiens) [TaxId: 9606]} 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