Citrus Sinensis ID: 037872

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------
MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVSSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSDLNFTLSDLLKTSFRANFDHSKKNKK
cccccccccHHHHHHHHHHHHccccccccccEEEEEccccccHHHHHHHHHHcccccccccccEEcHHHHHHHHHccccccccccHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHccccHHHHHHccc
cccccccccHHHHHHHHHHHHHHHccccccEEEEEEccccccHHHHHHHHHHHcccccccccHHcHHHHHHHHccccccccccccHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHccccHHHcccccc
mvnrsyvprmedLIPIVIKYVNSRLGPGEIAIFVAhnarrfdvpflAKEFsrcsmnipdnwrfldTLPLARELMKQNGSVSSKTSLQALREYfgiplegsahraMSDVNSLASILERITSDLNFTLSDLLKTSFranfdhskknkk
mvnrsyvprmedlIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVSSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSDLNFTLSDLLktsfranfdhskknkk
MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVSSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSDLNFTLSDLLKTSFRANFDHSKKNKK
*******PRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLAREL************LQALREYFGIPLEGSAHRAMSDVNSLASILERITSDLNFTLSDLLKTSF************
*****YVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVSSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSDLNFTLSD******************
MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMK********TSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSDLNFTLSDLLKTSFRANF********
**N*SYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVSSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSDLNFTLSDLLKTSFRAN*********
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiii
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MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSVSSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSDLNFTLSDLLKTSFRANFDHSKKNKK
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 ?
Query146 2.2.26 [Sep-21-2011]
Q08I43313 3'-5' exonuclease eri1 OS yes no 0.486 0.226 0.3 0.0005
Q8CP71 902 Probable ATP-dependent he yes no 0.527 0.085 0.369 0.0006
Q5HP88 902 Probable ATP-dependent he yes no 0.527 0.085 0.369 0.0006
>sp|Q08I43|ERI1_SCHPO 3'-5' exonuclease eri1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=eri1 PE=1 SV=1 Back     alignment and function desciption
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 45/80 (56%), Gaps = 9/80 (11%)

Query: 45  FLAKEFSRCSMNIPDNW---RFLDTLPLARELMKQNGSVSSKTSLQALREYFGIPLEGSA 101
           FLAK+F    M IPD W    F+D     +++ +       +T++  + E++G+  EGS 
Sbjct: 210 FLAKQFKYDKMPIPD-WIKGPFVDIRSFYKDVYR-----VPRTNINGMLEHWGLQFEGSE 263

Query: 102 HRAMSDVNSLASILERITSD 121
           HR + D  +L+ I++++ S+
Sbjct: 264 HRGIDDARNLSRIVKKMCSE 283
RNA exonuclease that acts as a negative regulator of RNA interference (RNAi). Acts by degrading the 3'-overhangs of double-stranded short interfering RNAs (siRNAs). Represses the accumulation of heterochromatic siRNAs leading to negative regulation of the RNAi-mediated heterochromoatin assembly. Also involved in rRNA biogenesis, trimming the 5.8S ribosomal RNA (rRNA) from a slightly longer pre-5.8S RNA in the cytoplasm.
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)
EC: 3EC: .EC: 1EC: .EC: -EC: .EC: -
>sp|Q8CP71|DING_STAES Probable ATP-dependent helicase DinG homolog OS=Staphylococcus epidermidis (strain ATCC 12228) GN=dinG PE=3 SV=1 Back     alignment and function description
>sp|Q5HP88|DING_STAEQ Probable ATP-dependent helicase DinG homolog OS=Staphylococcus epidermidis (strain ATCC 35984 / RP62A) GN=dinG PE=3 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 ?
Query146
356572944 329 PREDICTED: DNA polymerase III polC-type- 1.0 0.443 0.623 1e-43
147814790 340 hypothetical protein VITISV_042394 [Viti 1.0 0.429 0.564 2e-39
225450649 337 PREDICTED: DNA polymerase III polC-type- 1.0 0.433 0.557 4e-39
296089746 332 unnamed protein product [Vitis vinifera] 1.0 0.439 0.557 5e-39
356505791 329 PREDICTED: DNA polymerase III polC-type- 0.917 0.407 0.634 2e-38
357511765 332 DNA polymerase III polC-type [Medicago t 0.993 0.436 0.541 2e-37
449435615 327 PREDICTED: DNA polymerase III PolC-type- 0.917 0.409 0.567 5e-37
449517739 334 PREDICTED: DNA polymerase III PolC-type- 0.917 0.401 0.559 3e-36
255542840 334 exonuclease, putative [Ricinus communis] 0.993 0.434 0.541 3e-36
356533554 332 PREDICTED: DNA polymerase III polC-type- 1.0 0.439 0.523 2e-35
>gi|356572944|ref|XP_003554625.1| PREDICTED: DNA polymerase III polC-type-like [Glycine max] Back     alignment and taxonomy information
 Score =  181 bits (458), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 91/146 (62%), Positives = 109/146 (74%)

Query: 1   MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDN 60
           MVN+  VPRMEDLIPI+++YV SR  PG   IFVAHNAR FDVPF+  E  R S+ IP N
Sbjct: 182 MVNKPGVPRMEDLIPILLQYVRSREKPGGDVIFVAHNARCFDVPFIINELRRYSVEIPPN 241

Query: 61  WRFLDTLPLARELMKQNGSVSSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITS 120
           W FLDTLPLAREL+K  G+  S TSL ALR+ +GI ++GSAHRAM DVN+L+ IL R+TS
Sbjct: 242 WLFLDTLPLARELIKSGGTTLSSTSLAALRDLYGIKVDGSAHRAMVDVNALSLILSRLTS 301

Query: 121 DLNFTLSDLLKTSFRANFDHSKKNKK 146
           DL  TLSDL+K SF  +   + KNKK
Sbjct: 302 DLKLTLSDLVKKSFTESDIINSKNKK 327

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|147814790|emb|CAN74413.1| hypothetical protein VITISV_042394 [Vitis vinifera] Back     alignment and taxonomy information
>gi|225450649|ref|XP_002282861.1| PREDICTED: DNA polymerase III polC-type-like isoform 2 [Vitis vinifera] gi|225450651|ref|XP_002282855.1| PREDICTED: DNA polymerase III polC-type-like isoform 1 [Vitis vinifera] Back     alignment and taxonomy information
>gi|296089746|emb|CBI39565.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|356505791|ref|XP_003521673.1| PREDICTED: DNA polymerase III polC-type-like [Glycine max] Back     alignment and taxonomy information
>gi|357511765|ref|XP_003626171.1| DNA polymerase III polC-type [Medicago truncatula] gi|355501186|gb|AES82389.1| DNA polymerase III polC-type [Medicago truncatula] Back     alignment and taxonomy information
>gi|449435615|ref|XP_004135590.1| PREDICTED: DNA polymerase III PolC-type-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|449517739|ref|XP_004165902.1| PREDICTED: DNA polymerase III PolC-type-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|255542840|ref|XP_002512483.1| exonuclease, putative [Ricinus communis] gi|223548444|gb|EEF49935.1| exonuclease, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|356533554|ref|XP_003535328.1| PREDICTED: DNA polymerase III polC-type-like [Glycine max] 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 ?
Query146
TAIR|locus:2148453316 DPD1 "defective in pollen orga 0.993 0.458 0.5 3.3e-31
ZFIN|ZDB-GENE-110411-9235 si:ch1073-296i8.2 "si:ch1073-2 0.609 0.378 0.357 3.7e-08
TIGR_CMR|CJE_0502233 CJE_0502 "exonuclease, DNA pol 0.698 0.437 0.310 5.3e-06
TIGR_CMR|BA_3672 315 BA_3672 "DNA polymerase III, e 0.691 0.320 0.275 1.3e-05
UNIPROTKB|Q74DD3181 GSU1383 "3'-to-5' exonuclease, 0.534 0.430 0.388 4.2e-05
TIGR_CMR|GSU_1383181 GSU_1383 "exonuclease" [Geobac 0.534 0.430 0.388 4.2e-05
UNIPROTKB|Q10384 645 MT2247 "Uncharacterized protei 0.856 0.193 0.265 0.00025
POMBASE|SPBC30B4.08313 eri1 "double-strand siRNA ribo 0.486 0.226 0.3 0.00099
TAIR|locus:2148453 DPD1 "defective in pollen organelle DNA degradation1" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 343 (125.8 bits), Expect = 3.3e-31, P = 3.3e-31
 Identities = 75/150 (50%), Positives = 97/150 (64%)

Query:     1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDN 60
             MV R  VPRME+LIPI ++YV SR  PG   + VAHN + FD  FL  EF+RCS  IP N
Sbjct:   167 MVCRPEVPRMEELIPIFLRYVESRQKPGGYVMLVAHNGKSFDFQFLINEFNRCSYEIPHN 226

Query:    61 WRFLDTLPLARELMKQ-NGSVSSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERIT 119
             W  LD+LPLARE MK    +V   +SL+AL +Y+ +  EG AHRA+SDV  L+ + +++T
Sbjct:   227 WLLLDSLPLARENMKSVEPTVKLSSSLEALADYYSLTREGDAHRALSDVLLLSKVFQKLT 286

Query:   120 SDLNFTLSDLLKTSFRANFDHSK---KNKK 146
              DL  +LSDL+     A+ D S    KNKK
Sbjct:   287 IDLKLSLSDLVLRCHTAS-DISAAMAKNKK 315
GO:0003676 "nucleic acid binding" evidence=IEA
GO:0004527 "exonuclease activity" evidence=IEA;ISS;IDA
GO:0005622 "intracellular" evidence=IEA;ISS
GO:0000738 "DNA catabolic process, exonucleolytic" evidence=IMP
GO:0005739 "mitochondrion" evidence=IDA
GO:0009536 "plastid" evidence=IDA
ZFIN|ZDB-GENE-110411-9 si:ch1073-296i8.2 "si:ch1073-296i8.2" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
TIGR_CMR|CJE_0502 CJE_0502 "exonuclease, DNA polymerase III, epsilon subunit family" [Campylobacter jejuni RM1221 (taxid:195099)] Back     alignment and assigned GO terms
TIGR_CMR|BA_3672 BA_3672 "DNA polymerase III, epsilon subunit, putative" [Bacillus anthracis str. Ames (taxid:198094)] Back     alignment and assigned GO terms
UNIPROTKB|Q74DD3 GSU1383 "3'-to-5' exonuclease, putative" [Geobacter sulfurreducens PCA (taxid:243231)] Back     alignment and assigned GO terms
TIGR_CMR|GSU_1383 GSU_1383 "exonuclease" [Geobacter sulfurreducens PCA (taxid:243231)] Back     alignment and assigned GO terms
UNIPROTKB|Q10384 MT2247 "Uncharacterized protein Rv2191/MT2247" [Mycobacterium tuberculosis (taxid:1773)] Back     alignment and assigned GO terms
POMBASE|SPBC30B4.08 eri1 "double-strand siRNA ribonuclease Eri1" [Schizosaccharomyces pombe (taxid:4896)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

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

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

Prediction LevelEC numberConfidence of Prediction
3rd Layer2.7.7LOW CONFIDENCE prediction!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
grail3.0133007201
hypothetical protein (147 aa)
(Populus trichocarpa)
Predicted Functional Partners:
 
Sorry, there are no predicted associations at the current settings.
 

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 ?
Query146
smart00479169 smart00479, EXOIII, exonuclease domain in DNA-poly 2e-18
cd06127159 cd06127, DEDDh, DEDDh 3'-5' exonuclease domain fam 5e-18
PRK06309232 PRK06309, PRK06309, DNA polymerase III subunit eps 7e-15
PRK07883 557 PRK07883, PRK07883, hypothetical protein; Validate 5e-12
COG0847243 COG0847, DnaQ, DNA polymerase III, epsilon subunit 1e-11
PRK08517257 PRK08517, PRK08517, DNA polymerase III subunit eps 5e-11
PRK00448 1437 PRK00448, polC, DNA polymerase III PolC; Validated 3e-10
pfam00929161 pfam00929, RNase_T, Exonuclease 1e-09
cd06136177 cd06136, TREX1_2, DEDDh 3'-5' exonuclease domain o 1e-09
PRK06310250 PRK06310, PRK06310, DNA polymerase III subunit eps 2e-09
TIGR01407 850 TIGR01407, dinG_rel, DnaQ family exonuclease/DinG 6e-09
cd06131167 cd06131, DNA_pol_III_epsilon_Ecoli_like, DEDDh 3'- 3e-08
TIGR01406225 TIGR01406, dnaQ_proteo, DNA polymerase III, epsilo 3e-08
TIGR01405 1213 TIGR01405, polC_Gram_pos, DNA polymerase III, alph 7e-08
cd06130156 cd06130, DNA_pol_III_epsilon_like, an uncharacteri 8e-08
COG2176 1444 COG2176, PolC, DNA polymerase III, alpha subunit ( 1e-07
PRK06807 313 PRK06807, PRK06807, DNA polymerase III subunit eps 1e-07
PRK08074 928 PRK08074, PRK08074, bifunctional ATP-dependent DNA 6e-07
PRK06063 313 PRK06063, PRK06063, DNA polymerase III subunit eps 7e-07
PRK05711240 PRK05711, PRK05711, DNA polymerase III subunit eps 1e-06
cd06133176 cd06133, ERI-1_3'hExo_like, DEDDh 3'-5' exonucleas 9e-06
PRK07740244 PRK07740, PRK07740, hypothetical protein; Provisio 2e-05
TIGR00573217 TIGR00573, dnaq, exonuclease, DNA polymerase III, 9e-05
>gnl|CDD|214685 smart00479, EXOIII, exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases Back     alignment and domain information 
 Score = 76.6 bits (189), Expect = 2e-18
 Identities = 31/115 (26%), Positives = 53/115 (46%), Gaps = 11/115 (9%)

Query: 8   PRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTL 67
           P  E+++  +++++  R       I VA N+  FD+ FL  E  R  +  P     +DTL
Sbjct: 65  PTFEEVLEELLEFLRGR-------ILVAGNSAHFDLRFLKLEHPRLGIKQPPKLPVIDTL 117

Query: 68  PLARELMKQNGSVSSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSDL 122
            LAR           K SL+ L +   + +   AHRA+ D  + A + +++   L
Sbjct: 118 KLARATN----PGLPKYSLKKLAKRLLLEVIQRAHRALDDARATAKLFKKLLERL 168

Length = 169
>gnl|CDD|176648 cd06127, DEDDh, DEDDh 3'-5' exonuclease domain family Back     alignment and domain information
>gnl|CDD|180524 PRK06309, PRK06309, DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>gnl|CDD|236123 PRK07883, PRK07883, hypothetical protein; Validated Back     alignment and domain information
>gnl|CDD|223916 COG0847, DnaQ, DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|236281 PRK08517, PRK08517, DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>gnl|CDD|234767 PRK00448, polC, DNA polymerase III PolC; Validated Back     alignment and domain information
>gnl|CDD|216200 pfam00929, RNase_T, Exonuclease Back     alignment and domain information
>gnl|CDD|99839 cd06136, TREX1_2, DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins Back     alignment and domain information
>gnl|CDD|180525 PRK06310, PRK06310, DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>gnl|CDD|233398 TIGR01407, dinG_rel, DnaQ family exonuclease/DinG family helicase, putative Back     alignment and domain information
>gnl|CDD|99835 cd06131, DNA_pol_III_epsilon_Ecoli_like, DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins Back     alignment and domain information
>gnl|CDD|130473 TIGR01406, dnaQ_proteo, DNA polymerase III, epsilon subunit, Proteobacterial Back     alignment and domain information
>gnl|CDD|233397 TIGR01405, polC_Gram_pos, DNA polymerase III, alpha chain, Gram-positive type Back     alignment and domain information
>gnl|CDD|99834 cd06130, DNA_pol_III_epsilon_like, an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III Back     alignment and domain information
>gnl|CDD|225087 COG2176, PolC, DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|235864 PRK06807, PRK06807, DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>gnl|CDD|236148 PRK08074, PRK08074, bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>gnl|CDD|180377 PRK06063, PRK06063, DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>gnl|CDD|235574 PRK05711, PRK05711, DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>gnl|CDD|99836 cd06133, ERI-1_3'hExo_like, DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins Back     alignment and domain information
>gnl|CDD|236085 PRK07740, PRK07740, hypothetical protein; Provisional Back     alignment and domain information
>gnl|CDD|129663 TIGR00573, dnaq, exonuclease, DNA polymerase III, epsilon subunit family Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 146
PRK08517257 DNA polymerase III subunit epsilon; Provisional 99.91
PRK06195 309 DNA polymerase III subunit epsilon; Validated 99.88
PRK06063 313 DNA polymerase III subunit epsilon; Provisional 99.88
PRK06309232 DNA polymerase III subunit epsilon; Validated 99.88
TIGR01406225 dnaQ_proteo DNA polymerase III, epsilon subunit, P 99.88
PRK09146239 DNA polymerase III subunit epsilon; Validated 99.88
PRK05711240 DNA polymerase III subunit epsilon; Provisional 99.87
COG2176 1444 PolC DNA polymerase III, alpha subunit (gram-posit 99.86
PRK06310250 DNA polymerase III subunit epsilon; Validated 99.86
PRK07748207 sporulation inhibitor KapD; Provisional 99.86
cd06131167 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonucl 99.86
cd06130156 DNA_pol_III_epsilon_like an uncharacterized bacter 99.86
TIGR00573217 dnaq exonuclease, DNA polymerase III, epsilon subu 99.85
PRK07740244 hypothetical protein; Provisional 99.85
PRK07942232 DNA polymerase III subunit epsilon; Provisional 99.85
PRK06807 313 DNA polymerase III subunit epsilon; Validated 99.85
PRK07883 557 hypothetical protein; Validated 99.84
TIGR01298200 RNaseT ribonuclease T. in gamma-subdivision Proteo 99.83
cd06134189 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. 99.83
PRK05168211 ribonuclease T; Provisional 99.83
smart00479169 EXOIII exonuclease domain in DNA-polymerase alpha 99.83
PRK08074 928 bifunctional ATP-dependent DNA helicase/DNA polyme 99.82
PRK07246 820 bifunctional ATP-dependent DNA helicase/DNA polyme 99.81
PRK06722281 exonuclease; Provisional 99.81
TIGR01405 1213 polC_Gram_pos DNA polymerase III, alpha chain, Gra 99.8
TIGR01407 850 dinG_rel DnaQ family exonuclease/DinG family helic 99.8
PRK09145202 DNA polymerase III subunit epsilon; Validated 99.8
cd06136177 TREX1_2 DEDDh 3'-5' exonuclease domain of three pr 99.8
PRK07983219 exodeoxyribonuclease X; Provisional 99.78
cd06133176 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain o 99.77
cd06138183 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain o 99.77
cd06127159 DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh 99.76
PRK07247195 DNA polymerase III subunit epsilon; Validated 99.76
PRK05601 377 DNA polymerase III subunit epsilon; Validated 99.75
PRK00448 1437 polC DNA polymerase III PolC; Validated 99.74
cd06145150 REX1_like DEDDh 3'-5' exonuclease domain of RNA ex 99.74
cd06144152 REX4_like DEDDh 3'-5' exonuclease domain of RNA ex 99.73
cd06149157 ISG20 DEDDh 3'-5' exonuclease domain of Interferon 99.72
COG0847243 DnaQ DNA polymerase III, epsilon subunit and relat 99.7
cd06137161 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the 99.66
PTZ00315 582 2'-phosphotransferase; Provisional 99.65
PRK09182294 DNA polymerase III subunit epsilon; Validated 99.62
PF00929164 RNase_T: Exonuclease; InterPro: IPR013520 This ent 99.59
cd06135173 Orn DEDDh 3'-5' exonuclease domain of oligoribonuc 99.58
COG5018210 KapD Inhibitor of the KinA pathway to sporulation, 99.53
PRK11779 476 sbcB exonuclease I; Provisional 99.52
KOG0542280 consensus Predicted exonuclease [Replication, reco 99.49
PRK05359181 oligoribonuclease; Provisional 99.49
cd05782208 DNA_polB_like1_exo Uncharacterized bacterial subgr 99.25
PF10108209 DNA_pol_B_exo2: Predicted 3'-5' exonuclease relate 99.25
cd05160199 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain 99.15
cd05781188 DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of 99.05
cd05785207 DNA_polB_like2_exo Uncharacterized bacterial subgr 99.05
cd05780195 DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease dom 98.99
cd05779204 DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domai 98.92
cd0612596 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonucleas 98.76
cd05783204 DNA_polB_B1_exo DEDDy 3'-5' exonuclease domain of 98.66
KOG4793318 consensus Three prime repair exonuclease [Replicat 98.65
cd05784193 DNA_polB_II_exo DEDDy 3'-5' exonuclease domain of 98.61
COG2925 475 SbcB Exonuclease I [DNA replication, recombination 98.6
cd06139193 DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease 98.59
cd05777230 DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain 98.58
PF13482164 RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A 98.49
cd06143174 PAN2_exo DEDDh 3'-5' exonuclease domain of the euk 98.45
KOG2249280 consensus 3'-5' exonuclease [Replication, recombin 98.44
cd05776234 DNA_polB_alpha_exo inactive DEDDy 3'-5' exonucleas 98.37
PRK05762 786 DNA polymerase II; Reviewed 98.34
PRK05755 880 DNA polymerase I; Provisional 98.3
KOG4793318 consensus Three prime repair exonuclease [Replicat 98.23
PF04857262 CAF1: CAF1 family ribonuclease; InterPro: IPR00694 98.05
cd05778231 DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease 98.01
COG3359278 Predicted exonuclease [DNA replication, recombinat 97.97
PHA02528 881 43 DNA polymerase; Provisional 97.87
PF01612176 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR00 97.86
KOG0304239 consensus mRNA deadenylase subunit [RNA processing 97.84
cd06146193 mut-7_like_exo DEDDy 3'-5' exonuclease domain of C 97.8
PTZ00166 1054 DNA polymerase delta catalytic subunit; Provisiona 97.8
PHA02524 498 43A DNA polymerase subunit A; Provisional 97.78
smart00486 471 POLBc DNA polymerase type-B family. DNA polymerase 97.68
cd00007155 35EXOc 3'-5' exonuclease. The 35EXOc domain is res 97.61
PRK05761 787 DNA polymerase I; Reviewed 97.5
PF03104325 DNA_pol_B_exo1: DNA polymerase family B, exonuclea 97.46
cd06129161 RNaseD_like DEDDy 3'-5' exonuclease domain of RNas 97.34
PRK10829 373 ribonuclease D; Provisional 97.25
COG0417 792 PolB DNA polymerase elongation subunit (family B) 97.22
cd06141170 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and 97.22
smart00474172 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proo 97.06
COG1949184 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA 97.01
KOG1798 2173 consensus DNA polymerase epsilon, catalytic subuni 96.98
TIGR00592 1172 pol2 DNA polymerase (pol2). This family is based o 96.95
PHA02570220 dexA exonuclease; Provisional 96.91
KOG3242208 consensus Oligoribonuclease (3'->5' exoribonucleas 96.78
COG0349 361 Rnd Ribonuclease D [Translation, ribosomal structu 96.68
TIGR00593 887 pola DNA polymerase I. This family is based on the 96.45
cd06142178 RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribon 96.41
TIGR01388 367 rnd ribonuclease D. This model describes ribonucle 96.15
cd06140178 DNA_polA_I_Bacillus_like_exo inactive DEDDy 3'-5' 96.12
TIGR03491457 RecB family nuclease, putative, TM0106 family. Mem 95.94
COG5228299 POP2 mRNA deadenylase subunit [RNA processing and 95.93
cd06148197 Egl_like_exo DEDDy 3'-5' exonuclease domain of Dro 95.91
KOG2248380 consensus 3'-5' exonuclease [Replication, recombin 95.71
PHA03036 1004 DNA polymerase; Provisional 95.58
KOG3657 1075 consensus Mitochondrial DNA polymerase gamma, cata 94.73
KOG12751118 consensus PAB-dependent poly(A) ribonuclease, subu 94.45
KOG0969 1066 consensus DNA polymerase delta, catalytic subunit 94.11
cd09018150 DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease 92.81
cd06147192 Rrp6p_like_exo DEDDy 3'-5' exonuclease domain of y 92.76
COG0749 593 PolA DNA polymerase I - 3'-5' exonuclease and poly 90.2
PHA02563 630 DNA polymerase; Provisional 87.34
>PRK08517 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information 
Probab=99.91  E-value=1.7e-23  Score=160.23  Aligned_cols=127  Identities=27%  Similarity=0.386  Sum_probs=111.9

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCCcceeecHHHHHHHHhhCCCC
Q 037872            1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDNWRFLDTLPLARELMKQNGSV   80 (146)
Q Consensus         1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~~~~iDt~~l~~~~~~~~~~~   80 (146)
                      ||.  ++|+|.+|+.+|.+|+++       .++||||+ +||++||.+++.+++.+.... +++||+.+++..++.    
T Consensus       127 ~l~--~ap~~~evl~~f~~fl~~-------~v~VaHNa-~FD~~fL~~~l~r~g~~~~~~-~~ldtl~la~~~~~~----  191 (257)
T PRK08517        127 DLE--NAPSLKEVLEEFRLFLGD-------SVFVAHNV-NFDYNFISRSLEEIGLGPLLN-RKLCTIDLAKRTIES----  191 (257)
T ss_pred             HHc--CCCCHHHHHHHHHHHHCC-------CeEEEECH-HHHHHHHHHHHHHcCCCCCCC-CcEehHHHHHHHccC----
Confidence            466  899999999999999975       69999999 999999999999999876544 789999999988753    


Q ss_pred             CCCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHhhhh---cCHHHHHHhhcccccccccCC
Q 037872           81 SSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSDLN---FTLSDLLKTSFRANFDHSKKN  144 (146)
Q Consensus        81 ~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~~~---~~~~~l~~~~~~~~~~~~~~~  144 (146)
                       .+++|+++++++|++.+ .+|+|++||.+|++||..++.++.   .++.+|++-+-++..+.++++
T Consensus       192 -~~~~L~~L~~~lgi~~~-~~HrAl~DA~ata~ll~~ll~~~~~~~~t~~~L~~~~k~~~~~~~~~~  256 (257)
T PRK08517        192 -PRYGLSFLKELLGIEIE-VHHRAYADALAAYEIFKICLLNLPSYIKTTEDLIDFSKTAKTLKKKKP  256 (257)
T ss_pred             -CCCCHHHHHHHcCcCCC-CCCChHHHHHHHHHHHHHHHHHhHHhhcCHHHHHHHhhhcccccCCCC
Confidence             57899999999999988 599999999999999999998875   488999988888888877665

>PRK06195 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK06063 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>PRK06309 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial Back     alignment and domain information
>PRK09146 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK05711 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK06310 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK07748 sporulation inhibitor KapD; Provisional Back     alignment and domain information
>cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins Back     alignment and domain information
>cd06130 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III Back     alignment and domain information
>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family Back     alignment and domain information
>PRK07740 hypothetical protein; Provisional Back     alignment and domain information
>PRK07942 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>PRK06807 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK07883 hypothetical protein; Validated Back     alignment and domain information
>TIGR01298 RNaseT ribonuclease T Back     alignment and domain information
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T Back     alignment and domain information
>PRK05168 ribonuclease T; Provisional Back     alignment and domain information
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases Back     alignment and domain information
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK06722 exonuclease; Provisional Back     alignment and domain information
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type Back     alignment and domain information
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative Back     alignment and domain information
>PRK09145 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins Back     alignment and domain information
>PRK07983 exodeoxyribonuclease X; Provisional Back     alignment and domain information
>cd06133 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins Back     alignment and domain information
>cd06138 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins Back     alignment and domain information
>cd06127 DEDDh DEDDh 3'-5' exonuclease domain family Back     alignment and domain information
>PRK07247 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK05601 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK00448 polC DNA polymerase III PolC; Validated Back     alignment and domain information
>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins Back     alignment and domain information
>cd06144 REX4_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins Back     alignment and domain information
>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins Back     alignment and domain information
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair] Back     alignment and domain information
>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins Back     alignment and domain information
>PTZ00315 2'-phosphotransferase; Provisional Back     alignment and domain information
>PRK09182 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PF00929 RNase_T: Exonuclease; InterPro: IPR013520 This entry includes a variety of exonuclease proteins, such as ribonuclease T [] and the epsilon subunit of DNA polymerase III Back     alignment and domain information
>cd06135 Orn DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins Back     alignment and domain information
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only] Back     alignment and domain information
>PRK11779 sbcB exonuclease I; Provisional Back     alignment and domain information
>KOG0542 consensus Predicted exonuclease [Replication, recombination and repair] Back     alignment and domain information
>PRK05359 oligoribonuclease; Provisional Back     alignment and domain information
>cd05782 DNA_polB_like1_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases Back     alignment and domain information
>PF10108 DNA_pol_B_exo2: Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; InterPro: IPR019288 This entry represents various prokaryotic 3'-5' exonucleases and hypothetical proteins Back     alignment and domain information
>cd05160 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain of family-B DNA polymerases Back     alignment and domain information
>cd05781 DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases Back     alignment and domain information
>cd05785 DNA_polB_like2_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases Back     alignment and domain information
>cd05780 DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases Back     alignment and domain information
>cd05779 DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase Back     alignment and domain information
>cd06125 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily Back     alignment and domain information
>cd05783 DNA_polB_B1_exo DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases Back     alignment and domain information
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair] Back     alignment and domain information
>cd05784 DNA_polB_II_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases Back     alignment and domain information
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair] Back     alignment and domain information
>cd06139 DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases Back     alignment and domain information
>cd05777 DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase Back     alignment and domain information
>PF13482 RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A 2AJQ_F 1T8E_A 1T7P_A 1SKR_A 1X9W_A 1TK8_A 1TK0_A 1SL2_A Back     alignment and domain information
>cd06143 PAN2_exo DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2 Back     alignment and domain information
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair] Back     alignment and domain information
>cd05776 DNA_polB_alpha_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase Back     alignment and domain information
>PRK05762 DNA polymerase II; Reviewed Back     alignment and domain information
>PRK05755 DNA polymerase I; Provisional Back     alignment and domain information
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair] Back     alignment and domain information
>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation Back     alignment and domain information
>cd05778 DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase Back     alignment and domain information
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair] Back     alignment and domain information
>PHA02528 43 DNA polymerase; Provisional Back     alignment and domain information
>PF01612 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR002562 This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides Back     alignment and domain information
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification] Back     alignment and domain information
>cd06146 mut-7_like_exo DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins Back     alignment and domain information
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional Back     alignment and domain information
>PHA02524 43A DNA polymerase subunit A; Provisional Back     alignment and domain information
>smart00486 POLBc DNA polymerase type-B family Back     alignment and domain information
>cd00007 35EXOc 3'-5' exonuclease Back     alignment and domain information
>PRK05761 DNA polymerase I; Reviewed Back     alignment and domain information
>PF03104 DNA_pol_B_exo1: DNA polymerase family B, exonuclease domain Several related DNA polymerases were too dissimilar to be included Back     alignment and domain information
>cd06129 RNaseD_like DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins Back     alignment and domain information
>PRK10829 ribonuclease D; Provisional Back     alignment and domain information
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair] Back     alignment and domain information
>cd06141 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and similar proteins Back     alignment and domain information
>smart00474 35EXOc 3'-5' exonuclease Back     alignment and domain information
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification] Back     alignment and domain information
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair] Back     alignment and domain information
>TIGR00592 pol2 DNA polymerase (pol2) Back     alignment and domain information
>PHA02570 dexA exonuclease; Provisional Back     alignment and domain information
>KOG3242 consensus Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification] Back     alignment and domain information
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>TIGR00593 pola DNA polymerase I Back     alignment and domain information
>cd06142 RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins Back     alignment and domain information
>TIGR01388 rnd ribonuclease D Back     alignment and domain information
>cd06140 DNA_polA_I_Bacillus_like_exo inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases Back     alignment and domain information
>TIGR03491 RecB family nuclease, putative, TM0106 family Back     alignment and domain information
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification] Back     alignment and domain information
>cd06148 Egl_like_exo DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins Back     alignment and domain information
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair] Back     alignment and domain information
>PHA03036 DNA polymerase; Provisional Back     alignment and domain information
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair] Back     alignment and domain information
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair] Back     alignment and domain information
>KOG0969 consensus DNA polymerase delta, catalytic subunit [Replication, recombination and repair] Back     alignment and domain information
>cd09018 DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins Back     alignment and domain information
>cd06147 Rrp6p_like_exo DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins Back     alignment and domain information
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair] Back     alignment and domain information
>PHA02563 DNA polymerase; Provisional Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query146
1y97_A238 Three prime repair exonuclease 2; TREX2, hydrolase 1e-30
3mxm_B242 Three prime repair exonuclease 1; RNAse H-like fol 1e-24
3u3y_B314 Three prime repair exonuclease 1; RNAse H fold, 3' 2e-22
2p1j_A186 POLIII, DNA polymerase III POLC-type; structural g 2e-20
2f96_A224 Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolas 5e-15
3v9w_A235 Ribonuclease T; DEDD nucleases family, EXO-nucleas 3e-13
1zbh_A299 3'-5' exonuclease ERI1; histone mRNA 3'-END-specif 6e-11
1w0h_A204 3'-5' exonuclease ERI1; nuclease domain, hydrolase 2e-10
3cg7_A308 CRN-4, cell death-related nuclease 4; hydrolase, a 5e-10
1zbu_A349 ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; 9e-10
2xri_A224 ERI1 exoribonuclease 3; hydrolase, metal binding; 1e-09
2gui_A194 DNA polymerase III epsilon subunit; DNA polymerase 2e-08
>1y97_A Three prime repair exonuclease 2; TREX2, hydrolase; 2.50A {Homo sapiens} SCOP: c.55.3.5 Length = 238 Back     alignment and structure
 Score =  109 bits (273), Expect = 1e-30
 Identities = 31/127 (24%), Positives = 49/127 (38%), Gaps = 7/127 (5%)

Query: 1   MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDN 60
            + R      +  +   ++   SR         VAHN   +D P L  E  R    +P +
Sbjct: 86  GLARCRKAGFDGAVVRTLQAFLSRQAGP--ICLVAHNGFDYDFPLLCAELRRLGARLPRD 143

Query: 61  WRFLDTLPLARELMKQNGSVSSKT-----SLQALREYFGIPLEGSAHRAMSDVNSLASIL 115
              LDTLP  R L + +   +        SL +L   +      +AH A  DV++L  I 
Sbjct: 144 TVCLDTLPALRGLDRAHSHGTRARGRQGYSLGSLFHRYFRAEPSAAHSAEGDVHTLLLIF 203

Query: 116 ERITSDL 122
               ++L
Sbjct: 204 LHRAAEL 210
>3mxm_B Three prime repair exonuclease 1; RNAse H-like fold, polyproline type II helix, hydrolase-DNA; HET: DNA; 1.75A {Mus musculus} PDB: 3mxj_B 2ioc_B 3mxi_B* 3b6o_A* 2o4g_A* 3b6p_A* 2o4i_A 2oa8_A Length = 242 Back     alignment and structure
>3u3y_B Three prime repair exonuclease 1; RNAse H fold, 3' exonuclease, homodimer, hydrolase-DNA compl; HET: BU1; 2.28A {Mus musculus} PDB: 3u6f_B* Length = 314 Back     alignment and structure
>2p1j_A POLIII, DNA polymerase III POLC-type; structural genomics, exonuclease, PSI-2, protein structure initiative; HET: DNA; 2.50A {Thermotoga maritima MSB8} Length = 186 Back     alignment and structure
>2f96_A Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolase, SAD, PS protein structure initiative, midwest center for structural genomics; 2.09A {Pseudomonas aeruginosa} SCOP: c.55.3.5 Length = 224 Back     alignment and structure
>3v9w_A Ribonuclease T; DEDD nucleases family, EXO-nucleases, hydrolase-DNA complex; HET: DNA; 1.70A {Escherichia coli} PDB: 3ngy_A 3v9u_A* 3ngz_A* 3va3_A* 3v9z_A* 3nh0_A 3nh2_A 3nh1_A* 3v9s_A* 3v9x_A* 3va0_A* 2is3_A Length = 235 Back     alignment and structure
>1zbh_A 3'-5' exonuclease ERI1; histone mRNA 3'-END-specific recognition, structures of 3'- exonuclease and ITS RNA complex, hydrolase/RNA complex; HET: AMP; 3.00A {Homo sapiens} Length = 299 Back     alignment and structure
>1w0h_A 3'-5' exonuclease ERI1; nuclease domain, hydrolase; HET: AMP; 1.59A {Homo sapiens} SCOP: c.55.3.5 Length = 204 Back     alignment and structure
>3cg7_A CRN-4, cell death-related nuclease 4; hydrolase, apoptosis, 3'-5' exonuclease, deddh; 2.50A {Caenorhabditis elegans} PDB: 3cm5_A 3cm6_A Length = 308 Back     alignment and structure
>1zbu_A ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; HET: AMP; 3.00A {Homo sapiens} Length = 349 Back     alignment and structure
>2xri_A ERI1 exoribonuclease 3; hydrolase, metal binding; 2.15A {Homo sapiens} Length = 224 Back     alignment and structure
>2gui_A DNA polymerase III epsilon subunit; DNA polymerase proofreading domain, transferase; HET: DNA U5P; 1.60A {Escherichia coli} SCOP: c.55.3.5 PDB: 1j54_A* 1j53_A* 2ido_A* 2xy8_A* Length = 194 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query146
1w0h_A204 3'-5' exonuclease ERI1; nuclease domain, hydrolase 99.88
2gui_A194 DNA polymerase III epsilon subunit; DNA polymerase 99.87
2p1j_A186 POLIII, DNA polymerase III POLC-type; structural g 99.86
1zbh_A299 3'-5' exonuclease ERI1; histone mRNA 3'-END-specif 99.84
3mxm_B242 Three prime repair exonuclease 1; RNAse H-like fol 99.84
2f96_A224 Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolas 99.84
1y97_A238 Three prime repair exonuclease 2; TREX2, hydrolase 99.83
3u3y_B314 Three prime repair exonuclease 1; RNAse H fold, 3' 99.82
1zbu_A349 ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; 99.82
3v9w_A235 Ribonuclease T; DEDD nucleases family, EXO-nucleas 99.81
2xri_A224 ERI1 exoribonuclease 3; hydrolase, metal binding; 99.78
3cg7_A308 CRN-4, cell death-related nuclease 4; hydrolase, a 99.78
1wlj_A189 Interferon stimulated gene 20KDA; exoribonuclease, 99.72
2qxf_A 482 Exodeoxyribonuclease I; alpha-beta domain, DNAQ su 99.72
3tr8_A186 Oligoribonuclease; transcription, hydrolase; 2.50A 99.69
2igi_A180 Oligoribonuclease; RNAse, exoribonuclease, exonucl 99.67
2gbz_A194 Oligoribonuclease; ORN, deddh, structural genomics 99.59
2kfn_A 605 Klenow fragment of DNA polymerase I; complex (poly 98.8
1noy_A388 Protein (DNA polymerase (E.C.2.7.7.7)); exonucleas 98.5
1qht_A 775 Protein (DNA polymerase); archaea, hyperthermostab 98.49
3iay_A 919 DNA polymerase delta catalytic subunit; protein-DN 98.29
4gmj_B285 CCR4-NOT transcription complex subunit 7; mRNA dec 98.22
3k59_A 786 POL II, DNA polymerase II; protein-DNA complex, DN 98.22
1x9m_A 698 DNA polymerase; DNA ploymerase, N-2-acetylaminoflu 98.19
2gv9_A 1193 DNA polymerase; polymerase alpha fold, transferase 98.13
3d45_A507 Poly(A)-specific ribonuclease PARN; CAP analogue, 98.08
2d5r_A252 CCR4-NOT transcription complex subunit 7; poly(A) 97.98
3qex_A 903 DNA polymerase, GP43; difluorotoluene nucleoside; 97.98
1uoc_A289 POP2; hydrolase, DEDD nuclease, mRNA degradation, 97.9
1s5j_A 847 DNA polymerase I; replication, disulfide bonds, tr 97.85
2a1r_A430 Poly(A)-specific ribonuclease PARN; DEDD, nuclease 97.84
4hec_A190 Putative uncharacterized protein; ssgcid, structur 97.84
2p51_A333 SPCC18.06C protein; DEDD nuclease fold, hydrolase, 97.81
4dfk_A 540 DNA polymerase I, thermostable; DNA polymerase, tr 97.72
1vk0_A206 Hypothetical protein; homohexamer, AT5G06450, stru 97.4
3pv8_A 592 DNA polymerase I; DNA polymerase I, protein-DNA co 97.31
1yt3_A 375 Ribonuclease D, RNAse D; exoribonuclease, exonucle 97.08
3saf_A 428 Exosome component 10; exoribonuclease, RNA exosome 96.92
2e6m_A208 Werner syndrome ATP-dependent helicase homolog; AP 96.8
2hbj_A 410 Exosome complex exonuclease RRP6; RNA metabolism, 96.8
2py5_A 575 DNA polymerase; protein-DNA complex, replication, 96.64
3cym_A 440 Uncharacterized protein BAD_0989; structural genom 94.94
3ikm_A 1172 DNA polymerase subunit gamma-1; human mitochondria 93.9
1bgx_T 832 TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhi 80.92
>1w0h_A 3'-5' exonuclease ERI1; nuclease domain, hydrolase; HET: AMP; 1.59A {Homo sapiens} SCOP: c.55.3.5 Back     alignment and structure
Probab=99.88  E-value=2.6e-22  Score=147.11  Aligned_cols=117  Identities=17%  Similarity=0.261  Sum_probs=97.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHH-HHHHHHHHcCCCCCCC-cceeecHHHHHHHHhhCC
Q 037872            1 MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVP-FLAKEFSRCSMNIPDN-WRFLDTLPLARELMKQNG   78 (146)
Q Consensus         1 mv~~~~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~-~L~~~~~~~~~~~~~~-~~~iDt~~l~~~~~~~~~   78 (146)
                      ||+  ++|+|.+|+.+|.+|+.+.....+..++||||+ +||++ ||++++.+++++.|.. ..++||+.+++.+++.  
T Consensus        78 ~l~--~~~~~~~v~~~~~~~l~~~~~~~~~~~lv~hn~-~fD~~~~L~~~~~~~~~~~p~~~~~~~dt~~l~~~~~~~--  152 (204)
T 1w0h_A           78 QVD--RADTFPQVLKKVIDWMKLKELGTKYKYSLLTDG-SWDMSKFLNIQCQLSRLKYPPFAKKWINIRKSYGNFYKV--  152 (204)
T ss_dssp             HHH--TSBCHHHHHHHHHHHHHHTTBTTTBCEEEEESS-TTTTHHHHHHHHHHHTCCCCGGGSEEEEHHHHHHHHHTC--
T ss_pred             HHh--CCCCHHHHHHHHHHHHHhcCCCCCCcEEEEEEC-cchHHHHHHHHHHHhCCCCcccccceEEHHHHHHHHhCC--
Confidence            355  789999999999999987421122347999999 99997 9999999999887642 2799999999988863  


Q ss_pred             CCCCCCcHHHHHHHhCCCCCCCCCchHHHHHHHHHHHHHHHhhhh
Q 037872           79 SVSSKTSLQALREYFGIPLEGSAHRAMSDVNSLASILERITSDLN  123 (146)
Q Consensus        79 ~~~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~~~  123 (146)
                       +..+++|.+++++||++.++.+|+|++||.+|++||.++++++.
T Consensus       153 -~~~~~~L~~l~~~~gi~~~~~~H~Al~Da~~ta~l~~~l~~~~~  196 (204)
T 1w0h_A          153 -PRSQTKLTIMLEKLGMDYDGRPHCGLDDSKNIARIAVRMLQDGC  196 (204)
T ss_dssp             -CGGGCSHHHHHHHTTCCCCSCTTCHHHHHHHHHHHHHHHHHTTC
T ss_pred             -CCccchHHHHHHHcCCCCCCCccCcHHHHHHHHHHHHHHHHCCC
Confidence             12468999999999999986689999999999999999998764
>2gui_A DNA polymerase III epsilon subunit; DNA polymerase proofreading domain, transferase; HET: DNA U5P; 1.60A {Escherichia coli} SCOP: c.55.3.5 PDB: 1j54_A* 1j53_A* 2ido_A* 2xy8_A* Back     alignment and structure
>2p1j_A POLIII, DNA polymerase III POLC-type; structural genomics, exonuclease, PSI-2, protein structure initiative; HET: DNA; 2.50A {Thermotoga maritima MSB8} Back     alignment and structure
>1zbh_A 3'-5' exonuclease ERI1; histone mRNA 3'-END-specific recognition, structures of 3'- exonuclease and ITS RNA complex, hydrolase/RNA complex; HET: AMP; 3.00A {Homo sapiens} Back     alignment and structure
>3mxm_B Three prime repair exonuclease 1; RNAse H-like fold, polyproline type II helix, hydrolase-DNA; HET: DNA; 1.75A {Mus musculus} SCOP: c.55.3.5 PDB: 3mxj_B 2ioc_B 3mxi_B* 3b6o_A* 2o4g_A* 3b6p_A* 2o4i_A 2oa8_A Back     alignment and structure
>2f96_A Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolase, SAD, PS protein structure initiative, midwest center for structural genomics; 2.09A {Pseudomonas aeruginosa} SCOP: c.55.3.5 Back     alignment and structure
>1y97_A Three prime repair exonuclease 2; TREX2, hydrolase; 2.50A {Homo sapiens} SCOP: c.55.3.5 Back     alignment and structure
>3u3y_B Three prime repair exonuclease 1; RNAse H fold, 3' exonuclease, homodimer, hydrolase-DNA compl; HET: BU1; 2.28A {Mus musculus} PDB: 3u6f_B* Back     alignment and structure
>1zbu_A ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; HET: AMP; 3.00A {Homo sapiens} Back     alignment and structure
>3v9w_A Ribonuclease T; DEDD nucleases family, EXO-nucleases, hydrolase-DNA complex; HET: DNA; 1.70A {Escherichia coli} PDB: 3ngy_A 3v9u_A* 3ngz_A* 3va3_A* 3v9z_A* 3nh0_A 3nh2_A 3nh1_A* 3v9s_A* 3v9x_A* 3va0_A* 2is3_A Back     alignment and structure
>2xri_A ERI1 exoribonuclease 3; hydrolase, metal binding; 2.15A {Homo sapiens} Back     alignment and structure
>3cg7_A CRN-4, cell death-related nuclease 4; hydrolase, apoptosis, 3'-5' exonuclease, deddh; 2.50A {Caenorhabditis elegans} PDB: 3cm5_A 3cm6_A Back     alignment and structure
>1wlj_A Interferon stimulated gene 20KDA; exoribonuclease, hydrolase; HET: U5P; 1.90A {Homo sapiens} SCOP: c.55.3.5 Back     alignment and structure
>2qxf_A Exodeoxyribonuclease I; alpha-beta domain, DNAQ superfamily, SH3-like domain, produc structure, DNA damage, DNA repair, exonuclease; HET: TMP; 1.50A {Escherichia coli} SCOP: c.55.3.5 PDB: 1fxx_A* 3c94_A 3c95_A 3hl8_A* 3hp9_A* Back     alignment and structure
>3tr8_A Oligoribonuclease; transcription, hydrolase; 2.50A {Coxiella burnetii} Back     alignment and structure
>2igi_A Oligoribonuclease; RNAse, exoribonuclease, exonuclease, hydrolase, mRNA decay; 1.70A {Escherichia coli} SCOP: c.55.3.5 PDB: 1yta_A 1j9a_A Back     alignment and structure
>2gbz_A Oligoribonuclease; ORN, deddh, structural genomics, hydrolase; 2.30A {Xanthomonas campestris PV} Back     alignment and structure
>2kfn_A Klenow fragment of DNA polymerase I; complex (polymerase/DNA), exonuclease, transferase, transferase/DNA complex; HET: US1; 2.03A {Escherichia coli} SCOP: c.55.3.5 e.8.1.1 PDB: 1d9f_A* 1d9d_A* 1krp_A* 1ksp_A* 1qsl_A* 1kfs_A* 2kfz_A* 2kzm_A* 2kzz_A* 1dpi_A* 1kfd_A* 1kln_A* 1d8y_A* Back     alignment and structure
>1noy_A Protein (DNA polymerase (E.C.2.7.7.7)); exonuclease, DNA-binding, complex (nucleotidyltransferase/DNA); HET: DNA; 2.20A {Enterobacteria phage T4} SCOP: c.55.3.5 PDB: 1noz_A* Back     alignment and structure
>1qht_A Protein (DNA polymerase); archaea, hyperthermostable, family B polymer alpha family polymerase, transferase; 2.10A {Thermococcus SP} SCOP: c.55.3.5 e.8.1.1 PDB: 1tgo_A 2xhb_A* 2vwj_A* 2vwk_A* 1wns_A* 1wn7_A 1qqc_A* 4ahc_A* 4ail_C* 3a2f_A* 2jgu_A* 1d5a_A Back     alignment and structure
>3iay_A DNA polymerase delta catalytic subunit; protein-DNA complex, DNA replication, DNA-BI DNA-directed DNA polymerase, exonuclease, hydrolase; HET: DNA DOC DCP; 2.00A {Saccharomyces cerevisiae} Back     alignment and structure
>4gmj_B CCR4-NOT transcription complex subunit 7; mRNA decay, deadenylase, RNA bindin; HET: GOL; 2.70A {Homo sapiens} Back     alignment and structure
>3k59_A POL II, DNA polymerase II; protein-DNA complex, DNA damage, DNA repair, DNA-binding; HET: DNA DOC DCP; 1.92A {Escherichia coli} PDB: 3k57_A* 3k58_A* 3k5l_A* 3k5m_A* 3k5n_A* 3k5o_A* 3maq_A* 1q8i_A* Back     alignment and structure
>1x9m_A DNA polymerase; DNA ploymerase, N-2-acetylaminofluorene, replication block, mutagenesis, transferase/electron transport/DNA complex; HET: DNA 2DT 8FG; 2.10A {Enterobacteria phage T7} SCOP: c.55.3.5 e.8.1.1 PDB: 1skr_A* 1skw_A* 1sl0_A* 1sks_A* 1sl2_A* 1t7p_A* 1t8e_A* 1tk0_A* 1tk5_A* 1tk8_A* 1tkd_A* 1sl1_A* 1x9s_A* 1x9w_A* 1zyq_A* 2ajq_A* Back     alignment and structure
>2gv9_A DNA polymerase; polymerase alpha fold, transferase; HET: DNA; 2.68A {Human herpesvirus 1} PDB: 1dml_B* Back     alignment and structure
>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus} Back     alignment and structure
>2d5r_A CCR4-NOT transcription complex subunit 7; poly(A) deadenylase, antiproliferative protein, transcription; 2.50A {Homo sapiens} SCOP: c.55.3.9 Back     alignment and structure
>3qex_A DNA polymerase, GP43; difluorotoluene nucleoside; HET: DNA DOC DGT; 1.73A {Enterobacteria phage RB69} PDB: 3qei_A* 3qer_A* 3qes_A* 3qet_A* 3qep_A* 3qew_A* 3qev_A* 3s9h_A* 3sq0_A* 4dtn_A* 4dto_A* 4dtp_A* 4dtr_A* 4dts_A* 4dtu_A* 4dtx_A* 4e3s_A* 4fjm_A* 4fjl_A* 3spz_A* ... Back     alignment and structure
>1uoc_A POP2; hydrolase, DEDD nuclease, mRNA degradation, poly(A) tail, transcription regulation, repressor, phosphorylation.; 2.3A {Saccharomyces cerevisiae} SCOP: c.55.3.9 Back     alignment and structure
>1s5j_A DNA polymerase I; replication, disulfide bonds, transferase; HET: DNA; 2.40A {Sulfolobus solfataricus} SCOP: c.55.3.5 e.8.1.1 Back     alignment and structure
>2a1r_A Poly(A)-specific ribonuclease PARN; DEDD, nuclease domain, hydrolase-RNA complex; 2.60A {Homo sapiens} PDB: 2a1s_A Back     alignment and structure
>4hec_A Putative uncharacterized protein; ssgcid, structural genomics, SEA structural genomics center for infectious disease, unknown; 1.80A {Mycobacterium tuberculosis} Back     alignment and structure
>2p51_A SPCC18.06C protein; DEDD nuclease fold, hydrolase, gene regulation; 1.40A {Schizosaccharomyces pombe} PDB: 3g0z_A 3g10_A Back     alignment and structure
>4dfk_A DNA polymerase I, thermostable; DNA polymerase, transferase-DNA complex; HET: DNA DOC 0L5; 1.65A {Thermus aquaticus} PDB: 1jxe_A* 3ktq_A* 3lwl_A* 3lwm_A* 3m8s_A* 3m8r_A* 3oju_A* 3rr7_A* 3rr8_A* 3rrg_A* 3ojs_A* 3rtv_A* 3sv3_A* 3sv4_A* 3syz_A* 3sz2_A* 3t3f_A* 4df4_A* 4df8_A* 4dfj_A* ... Back     alignment and structure
>1vk0_A Hypothetical protein; homohexamer, AT5G06450, struc genomics, protein structure initiative, center for eukaryot structural genomics, CESG; 2.10A {Arabidopsis thaliana} SCOP: c.55.3.5 PDB: 2q3s_A Back     alignment and structure
>3pv8_A DNA polymerase I; DNA polymerase I, protein-DNA complex, thymine-adenine, CLOS conformation; HET: DNA 2DT D3T; 1.52A {Geobacillus kaustophilus} PDB: 3px0_A* 3px4_A* 3px6_A* 3thv_A* 3ti0_A* 4dse_A* 4dsf_A* 4ds4_A* 4dqp_A* 4dqi_A* 4ds5_A* 4e0d_A* 4dqr_A* 4dqq_A* 3tan_A* 3tap_A* 3taq_A* 3tar_A* 4dqs_A* 3hp6_A* ... Back     alignment and structure
>1yt3_A Ribonuclease D, RNAse D; exoribonuclease, exonuclease, hydrolase, tRNA processing, hydrolase,translation; 1.60A {Escherichia coli} SCOP: a.60.8.3 a.60.8.3 c.55.3.5 Back     alignment and structure
>3saf_A Exosome component 10; exoribonuclease, RNA exosome, hydrolase; 2.50A {Homo sapiens} PDB: 3sag_A 3sah_A 2cpr_A Back     alignment and structure
>2e6m_A Werner syndrome ATP-dependent helicase homolog; APO form, hydrolase; 2.00A {Mus musculus} PDB: 2e6l_A 2fby_A 2fbv_A 2fbx_A 2fbt_A 2fc0_A* Back     alignment and structure
>2hbj_A Exosome complex exonuclease RRP6; RNA metabolism, RNA surveillance, RNA processing, hydrolase, gene regulation; 2.10A {Saccharomyces cerevisiae} SCOP: a.60.8.4 c.55.3.5 PDB: 2hbk_A 2hbl_A* 2hbm_A* Back     alignment and structure
>2py5_A DNA polymerase; protein-DNA complex, replication, transferase/DNA complex; HET: DNA; 1.60A {Bacillus phage PHI29} SCOP: c.55.3.5 e.8.1.1 PDB: 1xhz_A* 1xhx_A* 2ex3_A* 1xi1_A* 2pyj_A* 2pyl_A* 2pzs_A* Back     alignment and structure
>3cym_A Uncharacterized protein BAD_0989; structural genomics, unknown function; 2.10A {Bifidobacterium adolescentis atcc 1570ORGANISM_TAXID} Back     alignment and structure
>3ikm_A DNA polymerase subunit gamma-1; human mitochondrial DNA polymerase, disease mutation, DNA replication, DNA-binding, DNA-directed DNA polymerase; HET: DNA; 3.24A {Homo sapiens} Back     alignment and structure
>1bgx_T TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhibition, helix-coil dynamics, inhibitor design, complex (polymerase/inhibitor); 2.30A {Thermus aquaticus} SCOP: a.60.7.1 c.120.1.2 c.55.3.5 e.8.1.1 PDB: 1cmw_A 1tau_A* 1taq_A* Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

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

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 146
d1y97a1228 c.55.3.5 (A:1-228) Three prime repair exonuclease 3e-12
d1w0ha_200 c.55.3.5 (A:) Exonuclease ERI1 {Human (Homo sapien 5e-11
d3b6oa1226 c.55.3.5 (A:9-234) Three prime repair exonuclease 7e-09
d2guia1174 c.55.3.5 (A:7-180) N-terminal exonuclease domain o 2e-07
d2f96a1202 c.55.3.5 (A:19-220) Ribonuclease T {Pseudomonas ae 3e-05
d2igia1180 c.55.3.5 (A:1-180) Oligoribonuclease {Escherichia 5e-04
>d1y97a1 c.55.3.5 (A:1-228) Three prime repair exonuclease 2, TREX2 {Human (Homo sapiens) [TaxId: 9606]} Length = 228 Back     information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: DnaQ-like 3'-5' exonuclease
domain: Three prime repair exonuclease 2, TREX2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.6 bits (143), Expect = 3e-12
 Identities = 30/128 (23%), Positives = 44/128 (34%), Gaps = 9/128 (7%)

Query: 1   MVNRSYVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDN 60
            + R      +  +   ++   SR         VAHN   +D P L  E  R    +P +
Sbjct: 84  GLARCRKAGFDGAVVRTLQAFLSRQAGP--ICLVAHNGFDYDFPLLCAELRRLGARLPRD 141

Query: 61  WRFLDTLPLAREL------MKQNGSVSSKTSLQALREYFGIPLEGSAHRAMSDVNSLASI 114
              LDTLP  R L        +       +       YF       AH A  DV++L  I
Sbjct: 142 TVCLDTLPALRGLDRAHSHGTRARGRQGYSLGSLFHRYFRAEPSA-AHSAEGDVHTLLLI 200

Query: 115 LERITSDL 122
                ++L
Sbjct: 201 FLHRAAEL 208
>d1w0ha_ c.55.3.5 (A:) Exonuclease ERI1 {Human (Homo sapiens) [TaxId: 9606]} Length = 200 Back     information, alignment and structure
>d3b6oa1 c.55.3.5 (A:9-234) Three prime repair exonuclease 1, TREX1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 226 Back     information, alignment and structure
>d2guia1 c.55.3.5 (A:7-180) N-terminal exonuclease domain of the epsilon subunit of DNA polymerase III {Escherichia coli [TaxId: 562]} Length = 174 Back     information, alignment and structure
>d2f96a1 c.55.3.5 (A:19-220) Ribonuclease T {Pseudomonas aeruginosa [TaxId: 287]} Length = 202 Back     information, alignment and structure
>d2igia1 c.55.3.5 (A:1-180) Oligoribonuclease {Escherichia coli [TaxId: 562]} Length = 180 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 ?
Query146
d2guia1174 N-terminal exonuclease domain of the epsilon subun 99.75
d1w0ha_200 Exonuclease ERI1 {Human (Homo sapiens) [TaxId: 960 99.75
d3b6oa1226 Three prime repair exonuclease 1, TREX1 {Mouse (Mu 99.74
d1wlja_173 Interferon-stimulated gene 20 kDa protein, ISG20 { 99.71
d1y97a1228 Three prime repair exonuclease 2, TREX2 {Human (Ho 99.69
d2qxfa1 467 Exonuclease I {Escherichia coli K12 (Escherichia c 99.45
d2f96a1202 Ribonuclease T {Pseudomonas aeruginosa [TaxId: 287 99.38
d2igia1180 Oligoribonuclease {Escherichia coli [TaxId: 562]} 98.76
d1tgoa1347 Exonuclease domain of family B DNA polymerases {Ar 98.64
d2d5ra1252 CCR4-NOT transcription complex subunit 7, CAF1 {Hu 98.52
d1q8ia1388 Exonuclease domain of family B DNA polymerases {Es 98.28
d1x9ma1204 Exonuclease domain of T7 DNA polymerase {Bacteriop 98.19
d1s5ja1410 Exonuclease domain of family B DNA polymerases {Su 98.06
d2hhva1171 Exonuclease domain of prokaryotic DNA polymerase { 97.97
d1yt3a3193 Ribonuclease D, catalytic domain {Escherichia coli 97.88
d1noya_372 Exonuclease domain of family B DNA polymerases {Ba 97.78
d1kfsa1195 Exonuclease domain of prokaryotic DNA polymerase { 97.73
d2hbka2292 Exosome complex exonuclease RRP6 {Baker's yeast (S 97.66
d1ih7a1375 Exonuclease domain of family B DNA polymerases {Ba 97.62
d1uoca_286 Pop2 RNase D domain {Baker's yeast (Saccharomyces 97.62
d1vk0a_206 Hypothetical protein AT5G06450 {Thale-cress (Arabi 97.53
d2py5a1183 Exonuclease domain of phi29 DNA polymerase {Bacter 94.84
>d2guia1 c.55.3.5 (A:7-180) N-terminal exonuclease domain of the epsilon subunit of DNA polymerase III {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: DnaQ-like 3'-5' exonuclease
domain: N-terminal exonuclease domain of the epsilon subunit of DNA polymerase III
species: Escherichia coli [TaxId: 562]

Probab=99.75  E-value=2.3e-18  Score=120.17  Aligned_cols=101  Identities=30%  Similarity=0.470  Sum_probs=88.1

Q ss_pred             CCCCHHHHHHHHHHHHhcccCCCCCcEEEEeCCCCCCHHHHHHHHHHcCCCCCCC---cceeecHHHHHHHHhhCCCCCC
Q 037872            6 YVPRMEDLIPIVIKYVNSRLGPGEIAIFVAHNARRFDVPFLAKEFSRCSMNIPDN---WRFLDTLPLARELMKQNGSVSS   82 (146)
Q Consensus         6 ~ap~f~ev~~~~~~~l~~~~~~~~~~~lVahN~~~FD~~~L~~~~~~~~~~~~~~---~~~iDt~~l~~~~~~~~~~~~~   82 (146)
                      ++|++.+++.+|.+|+++       ..+|+||. .||..++...+.+++...+..   +.++|++.+++.+++.     .
T Consensus        69 ~~~~~~~~~~~~~~~~~~-------~~~v~~~~-~~d~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~-----~  135 (174)
T d2guia1          69 DKPTFAEVADEFMDYIRG-------AELVIHNA-AFDIGFMDYEFSLLKRDIPKTNTFCKVTDSLAVARKMFPG-----K  135 (174)
T ss_dssp             TSCCHHHHHHHHHHHHTT-------SEEEETTH-HHHHHHHHHHHHHTCSCCCCGGGTSEEEEHHHHHHHHSTT-----S
T ss_pred             cchhHHHHHHHHHHhcCC-------CeEEEeec-chhhHHHHHHHHHhCCCCCCcccccchhhHHHHHHHHcCC-----C
Confidence            789999999999999986       58999999 999999999999988765432   3678999999998763     5


Q ss_pred             CCcHHHHHHHhCCCCCC-CCCchHHHHHHHHHHHHHHH
Q 037872           83 KTSLQALREYFGIPLEG-SAHRAMSDVNSLASILERIT  119 (146)
Q Consensus        83 ~~~L~~l~~~~gi~~~~-~~H~Al~Da~~ta~l~~~l~  119 (146)
                      .++|..++++||++.++ ++|+|++||.+|++||.+|+
T Consensus       136 ~~~L~~l~~~~~~~~~~~~~H~Al~Da~~ta~v~~~l~  173 (174)
T d2guia1         136 RNSLDALCARYEIDNSKRTLHGALLDAQILAEVYLAMT  173 (174)
T ss_dssp             CCSHHHHHHHTTCCCTTCSSCCHHHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHcCCCCCCCCCcCHHHHHHHHHHHHHHHc
Confidence            68999999999997653 48999999999999999985
>d1w0ha_ c.55.3.5 (A:) Exonuclease ERI1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d3b6oa1 c.55.3.5 (A:9-234) Three prime repair exonuclease 1, TREX1 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1wlja_ c.55.3.5 (A:) Interferon-stimulated gene 20 kDa protein, ISG20 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1y97a1 c.55.3.5 (A:1-228) Three prime repair exonuclease 2, TREX2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2qxfa1 c.55.3.5 (A:8-474) Exonuclease I {Escherichia coli K12 (Escherichia coli K-12) [TaxId: 83333]} Back     information, alignment and structure
>d2f96a1 c.55.3.5 (A:19-220) Ribonuclease T {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure
>d2igia1 c.55.3.5 (A:1-180) Oligoribonuclease {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1tgoa1 c.55.3.5 (A:1-347) Exonuclease domain of family B DNA polymerases {Archaeon Thermococcus gorgonarius [TaxId: 71997]} Back     information, alignment and structure
>d2d5ra1 c.55.3.9 (A:11-262) CCR4-NOT transcription complex subunit 7, CAF1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1q8ia1 c.55.3.5 (A:2-389) Exonuclease domain of family B DNA polymerases {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1x9ma1 c.55.3.5 (A:1-210) Exonuclease domain of T7 DNA polymerase {Bacteriophage T7 [TaxId: 10760]} Back     information, alignment and structure
>d1s5ja1 c.55.3.5 (A:40-449) Exonuclease domain of family B DNA polymerases {Sulfolobus solfataricus [TaxId: 2287]} Back     information, alignment and structure
>d2hhva1 c.55.3.5 (A:298-468) Exonuclease domain of prokaryotic DNA polymerase {Bacillus stearothermophilus, newly identified strain as yet unnamed [TaxId: 1422]} Back     information, alignment and structure
>d1yt3a3 c.55.3.5 (A:1-193) Ribonuclease D, catalytic domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1noya_ c.55.3.5 (A:) Exonuclease domain of family B DNA polymerases {Bacteriophage T4 [TaxId: 10665]} Back     information, alignment and structure
>d1kfsa1 c.55.3.5 (A:324-518) Exonuclease domain of prokaryotic DNA polymerase {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2hbka2 c.55.3.5 (A:129-420) Exosome complex exonuclease RRP6 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1ih7a1 c.55.3.5 (A:1-375) Exonuclease domain of family B DNA polymerases {Bacteriophage RB69 [TaxId: 12353]} Back     information, alignment and structure
>d1uoca_ c.55.3.9 (A:) Pop2 RNase D domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1vk0a_ c.55.3.5 (A:) Hypothetical protein AT5G06450 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]} Back     information, alignment and structure
>d2py5a1 c.55.3.5 (A:5-187) Exonuclease domain of phi29 DNA polymerase {Bacteriophage phi-29 [TaxId: 10756]} Back     information, alignment and structure