Citrus Sinensis ID: 023843

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270------
MGSEETKKHPKTHLQLNPNWAQLQLKVKSNGLNKSSKHTKNPESETHNSILGKRKERLEAESDGSKPSPLTPINDDFSLTDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEGRILVGHALHNDLKALLLTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEHCPIDDARAAMLLYMKNRKQWEKSVKDQTRLEQKQKNRKPKKKPKLKDAAIVKAAVTAS
cccccccccccccccccccHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEEEEccccccEEEEEEEEcccccEEEEEccccccccccccccccccccccccccccHHHHHHHHHHHccccEEEEEccHHHHHHHccccccccEEEcccccccccccccccHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccHHccccccc
cccccccccccccccccccHHHHHHHHHccccccccccccccccccccHHcccccccccccccccccccccccccccccccEEEEEcEEcccccccccEEEEEEEEEccccEEEEEEEcccccEEEEEEEEccccHHHHHccccHHHHHHHHHHHHcccEEEEccHHHHHHHHHccccccccccccccccHHccccccHHHHHHHHHHHcccHcccccccHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccHHHHEEEcccEccc
mgseetkkhpkthlqlnpnwAQLQLKVKsnglnksskhtknpesethnSILGKRKErleaesdgskpspltpinddfsltDVVAMDCEmvgisqgnksaLGRVSLVNKWGNLIYDEFVRPLERVVDfrtrisgirprdlrkakdfpTVQKKVAELIEGRILVGHALHNDLKALLLTHSkkdlrdtseyqpflnrnGRSKALRHLAAEILAVEiqngehcpiDDARAAMLLYMKNRKQWEKSVKDQTRLEQkqknrkpkkkpklkdAAIVKAAVTAS
mgseetkkhpkthlqlnpnwAQLQLKVKSNGLnksskhtknpesethnsilgkRKERLEaesdgskpspltpindDFSLTDVVAMDCEMVGisqgnksalgRVSLVNKWGNLIydefvrplervvdfrtrisgirprdlrkakdfptVQKKVAELIEGRILVGHALHNDLKALLLTHskkdlrdtseyqpflnrngRSKALRHLAAEILAVeiqngehcPIDDARAAMLLYMKNRKQWeksvkdqtrleqkqknrkpkkkpklkdaaivkaavtas
MGSEETKKHPKTHLQLNPNWAQLQLKVKSNGLNKSSKHTKNPESETHNSILGKRKERLEAESDGSKPSPLTPINDDFSLTDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEGRILVGHALHNDLKALLLTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEHCPIDDARAAMLLYMKNRKQWEKSVKDQTRLEqkqknrkpkkkpklkDAAIVKAAVTAS
***************************************************************************DFSLTDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEGRILVGHALHNDLKALLLTHSK********YQPFLNRNGRSKALRHLAAEILAVEIQNGEHCPIDDARAAMLLYMKN******************************************
*****************************************************************************SLTDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEGRILVGHALHNDLKALLLTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEHCPIDDARAAMLLYMKNRKQW**************************************
************HLQLNPNWAQLQLKVKSNGL*****************ILGKRKER**********SPLTPINDDFSLTDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEGRILVGHALHNDLKALLLTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEHCPIDDARAAMLLYMKNRKQ*****************************AIVKAAVTAS
*****************P***********************************************************SLTDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEGRILVGHALHNDLKALLLTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEHCPIDDARAAMLLYMKNRKQWEKSVKDQ*******************************
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MGSEETKKHPKTHLQLNPNWAQLQLKVKSNGLNKSSKHTKNPESETHNSILGKRKERLEAESDGSKPSPLTPINDDFSLTDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEGRILVGHALHNDLKALLLTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEHCPIDDARAAMLLYMKNRKQWEKSVKDQTRLEQKQKNRKPKKKPKLKDAAIVKAAVTAS
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 ?
Query276 2.2.26 [Sep-21-2011]
Q91560421 RNA exonuclease 4 OS=Xeno N/A no 0.597 0.391 0.526 2e-48
Q6DEW6414 RNA exonuclease 4 OS=Xeno yes no 0.655 0.437 0.497 1e-47
Q9GZR2422 RNA exonuclease 4 OS=Homo yes no 0.615 0.402 0.5 2e-47
Q6PAQ4432 RNA exonuclease 4 OS=Mus yes no 0.601 0.384 0.494 4e-47
Q6BIK6272 RNA exonuclease 4 OS=Deba yes no 0.612 0.621 0.458 8e-44
Q08237289 RNA exonuclease 4 OS=Sacc yes no 0.615 0.588 0.491 1e-43
Q4WHF8310 RNA exonuclease 4 OS=Neos yes no 0.572 0.509 0.503 6e-41
Q4IEV5319 RNA exonuclease 4 OS=Gibb yes no 0.605 0.523 0.467 4e-40
Q6CMT3294 RNA exonuclease 4 OS=Kluy yes no 0.572 0.537 0.484 8e-40
Q4PER6375 RNA exonuclease 4 OS=Usti N/A no 0.605 0.445 0.461 2e-39
>sp|Q91560|REXO4_XENLA RNA exonuclease 4 OS=Xenopus laevis GN=rexo4 PE=2 SV=2 Back     alignment and function desciption
 Score =  192 bits (488), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 89/169 (52%), Positives = 122/169 (72%), Gaps = 4/169 (2%)

Query: 78  SLTDVVAMDCEMVGISQ-GNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRP 136
            LT  VAMDCEMVG+   G +S L RVS+VN +G  +YD++V+P ERV D+RT +SGIRP
Sbjct: 230 GLTRTVAMDCEMVGVGMDGEESILARVSIVNLFGKCVYDKYVKPTERVTDYRTAVSGIRP 289

Query: 137 RDLRKAKDFPTVQKKVAELIEGRILVGHALHNDLKALLLTHSKKDLRDTSEYQPFLN--R 194
            D++K + F  VQK+V+E++ GR LVGHA+HNDLK L L H KK +RDT +Y+PF    +
Sbjct: 290 EDVKKGEPFKVVQKEVSEILRGRTLVGHAVHNDLKILFLDHPKKAIRDTQKYKPFKQKVK 349

Query: 195 NGRSKALRHLAAEILAVEIQNGEHCPIDDARAAMLLYMKNRKQWEKSVK 243
           +GR  +L+ L  +IL V++Q GEHC + DA+AAM LY   +K WE ++K
Sbjct: 350 SGRP-SLKLLCEKILNVKVQTGEHCSVQDAQAAMRLYTMEKKSWEVAIK 397

Xenopus laevis (taxid: 8355)
EC: 3EC: .EC: 1EC: .EC: -EC: .EC: -
>sp|Q6DEW6|REXO4_XENTR RNA exonuclease 4 OS=Xenopus tropicalis GN=rexo4 PE=2 SV=1 Back     alignment and function description
>sp|Q9GZR2|REXO4_HUMAN RNA exonuclease 4 OS=Homo sapiens GN=REXO4 PE=1 SV=2 Back     alignment and function description
>sp|Q6PAQ4|REXO4_MOUSE RNA exonuclease 4 OS=Mus musculus GN=Rexo4 PE=2 SV=2 Back     alignment and function description
>sp|Q6BIK6|REXO4_DEBHA RNA exonuclease 4 OS=Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / JCM 1990 / NBRC 0083 / IGC 2968) GN=REX4 PE=3 SV=2 Back     alignment and function description
>sp|Q08237|REXO4_YEAST RNA exonuclease 4 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=REX4 PE=1 SV=1 Back     alignment and function description
>sp|Q4WHF8|REXO4_ASPFU RNA exonuclease 4 OS=Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) GN=rex4 PE=3 SV=1 Back     alignment and function description
>sp|Q4IEV5|REXO4_GIBZE RNA exonuclease 4 OS=Gibberella zeae (strain PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084) GN=REX4 PE=3 SV=1 Back     alignment and function description
>sp|Q6CMT3|REXO4_KLULA RNA exonuclease 4 OS=Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) GN=REX4 PE=3 SV=1 Back     alignment and function description
>sp|Q4PER6|REXO4_USTMA RNA exonuclease 4 OS=Ustilago maydis (strain 521 / FGSC 9021) GN=REX4 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 ?
Query276
224061284274 predicted protein [Populus trichocarpa] 0.923 0.930 0.684 2e-97
356542307266 PREDICTED: RNA exonuclease 4-like [Glyci 0.865 0.898 0.721 1e-95
356549691266 PREDICTED: RNA exonuclease 4-like [Glyci 0.865 0.898 0.721 2e-95
255635044237 unknown [Glycine max] 0.855 0.995 0.722 1e-94
302142939295 unnamed protein product [Vitis vinifera] 1.0 0.935 0.667 4e-94
225461580277 PREDICTED: RNA exonuclease 4-like [Vitis 1.0 0.996 0.667 5e-94
18400624275 exonuclease-like protein [Arabidopsis th 0.836 0.84 0.719 3e-93
297830060301 hypothetical protein ARALYDRAFT_318283 [ 0.884 0.810 0.656 1e-92
307135939265 RNA exonuclease [Cucumis melo subsp. mel 0.865 0.901 0.692 1e-91
255554662299 RNA exonuclease, putative [Ricinus commu 0.844 0.779 0.736 2e-90
>gi|224061284|ref|XP_002300407.1| predicted protein [Populus trichocarpa] gi|222847665|gb|EEE85212.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  361 bits (926), Expect = 2e-97,   Method: Compositional matrix adjust.
 Identities = 180/263 (68%), Positives = 211/263 (80%), Gaps = 8/263 (3%)

Query: 1   MGSEETKKHPKTH---LQLNPNWAQLQLKVKSNGLNKSSKHTKNPESETHNSILGKRKER 57
           MGSEE KK        L +NPNWAQLQ  ++ +G    S+  K   +ET +SILGKRKER
Sbjct: 1   MGSEEQKKKNPKKKQKLPINPNWAQLQQTLQIHG----SRRPKTSNTETQDSILGKRKER 56

Query: 58  LEAESDGSKPSPLTPINDDFSLTDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEF 117
            +AESD S+ +PL P NDDFS+TD +AMDCEMVG+ QGN+SALGRV+LVN+WGN++YDEF
Sbjct: 57  PDAESDKSQINPLIPTNDDFSVTDAIAMDCEMVGVGQGNRSALGRVTLVNQWGNVLYDEF 116

Query: 118 VRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEGRILVGHALHNDLKALLLTH 177
           VRP+ERV DFRT+ISGIRPRDLRKA+DF T QKKVA LI+GRILVGHAL NDLKALLL H
Sbjct: 117 VRPVERVADFRTQISGIRPRDLRKARDFSTAQKKVAVLIKGRILVGHALSNDLKALLLGH 176

Query: 178 SKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEHCPIDDARAAMLLYMKNRKQ 237
            KKDLRDTSEYQPFL +  R KALRHLAAE L  +IQ+GEHCPI+DARAAMLLY +N+K+
Sbjct: 177 PKKDLRDTSEYQPFL-KGRRRKALRHLAAEFLGAKIQSGEHCPIEDARAAMLLYQRNKKE 235

Query: 238 WEKSVKDQTRLEQKQKNRKPKKK 260
           WEKS++DQ RL QKQ  R  K K
Sbjct: 236 WEKSIRDQMRLRQKQNKRNQKGK 258

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|356542307|ref|XP_003539610.1| PREDICTED: RNA exonuclease 4-like [Glycine max] Back     alignment and taxonomy information
>gi|356549691|ref|XP_003543225.1| PREDICTED: RNA exonuclease 4-like [Glycine max] Back     alignment and taxonomy information
>gi|255635044|gb|ACU17880.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|302142939|emb|CBI20234.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|225461580|ref|XP_002282870.1| PREDICTED: RNA exonuclease 4-like [Vitis vinifera] Back     alignment and taxonomy information
>gi|18400624|ref|NP_566499.1| exonuclease-like protein [Arabidopsis thaliana] gi|21593535|gb|AAM65502.1| exonuclease, putative [Arabidopsis thaliana] gi|90186238|gb|ABD91495.1| At3g15080 [Arabidopsis thaliana] gi|110737668|dbj|BAF00773.1| putative exonuclease [Arabidopsis thaliana] gi|195971099|gb|ACG60894.1| exonuclease domain-containing protein [Arabidopsis thaliana] gi|332642093|gb|AEE75614.1| exonuclease-like protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|297830060|ref|XP_002882912.1| hypothetical protein ARALYDRAFT_318283 [Arabidopsis lyrata subsp. lyrata] gi|297328752|gb|EFH59171.1| hypothetical protein ARALYDRAFT_318283 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|307135939|gb|ADN33800.1| RNA exonuclease [Cucumis melo subsp. melo] Back     alignment and taxonomy information
>gi|255554662|ref|XP_002518369.1| RNA exonuclease, putative [Ricinus communis] gi|223542464|gb|EEF44005.1| RNA exonuclease, putative [Ricinus communis] 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 ?
Query276
TAIR|locus:2086320275 AT3G15080 [Arabidopsis thalian 0.876 0.88 0.693 5.3e-88
UNIPROTKB|H9KZR7379 H9KZR7 "Uncharacterized protei 0.710 0.517 0.492 5.3e-49
ZFIN|ZDB-GENE-120215-216418 si:ch73-209e20.4 "si:ch73-209e 0.597 0.394 0.550 1.4e-48
MGI|MGI:2684957432 Rexo4 "REX4, RNA exonuclease 4 0.601 0.384 0.494 2e-47
UNIPROTKB|F1N5B5402 REXO4 "Uncharacterized protein 0.702 0.482 0.455 2.9e-46
UNIPROTKB|F1NQP7414 Gga.48606 "Uncharacterized pro 0.710 0.473 0.492 6.2e-46
RGD|1306220409 Rexo4 "REX4, RNA exonuclease 4 0.655 0.442 0.443 2e-45
UNIPROTKB|F1PBR5411 REXO4 "Uncharacterized protein 0.702 0.472 0.46 9.1e-45
UNIPROTKB|Q9GZR2422 REXO4 "RNA exonuclease 4" [Hom 0.677 0.443 0.476 1.9e-44
ASPGD|ASPL0000065793299 AN10955 [Emericella nidulans ( 0.572 0.528 0.521 2.3e-44
TAIR|locus:2086320 AT3G15080 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 879 (314.5 bits), Expect = 5.3e-88, P = 5.3e-88
 Identities = 174/251 (69%), Positives = 204/251 (81%)

Query:     3 SEETKKHPKTHL-----QLNPNWAQLQLKVKSNGLNKSSKHTKNPESETHNSILGKRKER 57
             S + K+ PK  +     QLNPNW+ LQ K+KS+    + K + NPE+ +  SILGKRKER
Sbjct:     2 SSDLKRKPKKKITPKPVQLNPNWSLLQQKLKSDSHGNTRK-SSNPENPS--SILGKRKER 58

Query:    58 LEAESDGSKPSPLTPINDDFSLTDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEF 117
              ++E D  K +PL P+NDD SLTD VAMDCEMVG+SQG KSALGRV+LVNKWGN++YDEF
Sbjct:    59 PDSEVDVPKINPLAPVNDDSSLTDEVAMDCEMVGVSQGTKSALGRVTLVNKWGNVLYDEF 118

Query:   118 VRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEGRILVGHALHNDLKALLLTH 177
             VRP+E VVDFRT ISGIRPRDLRKAKDF   Q KVAELI+G+ILVGHALHNDLKALLLTH
Sbjct:   119 VRPVEHVVDFRTSISGIRPRDLRKAKDFRVAQTKVAELIKGKILVGHALHNDLKALLLTH 178

Query:   178 SKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEHCPIDDARAAMLLYMKNRKQ 237
              KKD+RDT EYQPFL    R K+L+HLA+EIL  +IQNGEHCPIDDARAAM+LY KNRK+
Sbjct:   179 PKKDIRDTGEYQPFLKGKTR-KSLKHLASEILGADIQNGEHCPIDDARAAMMLYQKNRKE 237

Query:   238 WEKSVKDQTRL 248
             WEK+VKDQTR+
Sbjct:   238 WEKTVKDQTRM 248
GO:0003676 "nucleic acid binding" evidence=IEA
GO:0004527 "exonuclease activity" evidence=IEA;ISS
GO:0005622 "intracellular" evidence=IEA;ISS
GO:0005737 "cytoplasm" evidence=ISM
GO:0009165 "nucleotide biosynthetic process" evidence=RCA
UNIPROTKB|H9KZR7 H9KZR7 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-120215-216 si:ch73-209e20.4 "si:ch73-209e20.4" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
MGI|MGI:2684957 Rexo4 "REX4, RNA exonuclease 4 homolog (S. cerevisiae)" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|F1N5B5 REXO4 "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|F1NQP7 Gga.48606 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
RGD|1306220 Rexo4 "REX4, RNA exonuclease 4 homolog (S. cerevisiae)" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|F1PBR5 REXO4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|Q9GZR2 REXO4 "RNA exonuclease 4" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
ASPGD|ASPL0000065793 AN10955 [Emericella nidulans (taxid:162425)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

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

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query276
cd06144152 cd06144, REX4_like, DEDDh 3'-5' exonuclease domain 7e-88
cd06149157 cd06149, ISG20, DEDDh 3'-5' exonuclease domain of 1e-46
cd06145150 cd06145, REX1_like, DEDDh 3'-5' exonuclease domain 3e-45
smart00479169 smart00479, EXOIII, exonuclease domain in DNA-poly 1e-37
cd06137161 cd06137, DEDDh_RNase, DEDDh 3'-5' exonuclease doma 5e-28
pfam00929161 pfam00929, RNase_T, Exonuclease 2e-25
cd06143174 cd06143, PAN2_exo, DEDDh 3'-5' exonuclease domain 3e-23
cd06127159 cd06127, DEDDh, DEDDh 3'-5' exonuclease domain fam 4e-11
COG0847243 COG0847, DnaQ, DNA polymerase III, epsilon subunit 5e-08
cd06130156 cd06130, DNA_pol_III_epsilon_like, an uncharacteri 1e-07
COG2176 1444 COG2176, PolC, DNA polymerase III, alpha subunit ( 7e-07
TIGR01405 1213 TIGR01405, polC_Gram_pos, DNA polymerase III, alph 9e-07
cd06133176 cd06133, ERI-1_3'hExo_like, DEDDh 3'-5' exonucleas 2e-05
PRK07246 820 PRK07246, PRK07246, bifunctional ATP-dependent DNA 0.001
PRK00448 1437 PRK00448, polC, DNA polymerase III PolC; Validated 0.002
>gnl|CDD|99847 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 
 Score =  257 bits (660), Expect = 7e-88
 Identities = 88/151 (58%), Positives = 115/151 (76%), Gaps = 2/151 (1%)

Query: 83  VAMDCEMVGI-SQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRK 141
           VA+DCEMVG+   G++SAL RVS+VN+ GN++YD +V+P E V D+RT +SGIRP  L+ 
Sbjct: 1   VALDCEMVGVGPDGSESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKD 60

Query: 142 AKDFPTVQKKVAELIEGRILVGHALHNDLKALLLTHSKKDLRDTSEYQPFLNRN-GRSKA 200
           A DF  VQKKVAEL++GRILVGHAL NDLK L L H KK +RDTS+Y+P      G+S +
Sbjct: 61  APDFEEVQKKVAELLKGRILVGHALKNDLKVLKLDHPKKLIRDTSKYKPLRKTAKGKSPS 120

Query: 201 LRHLAAEILAVEIQNGEHCPIDDARAAMLLY 231
           L+ LA ++L ++IQ GEH  ++DARAAM LY
Sbjct: 121 LKKLAKQLLGLDIQEGEHSSVEDARAAMRLY 151

This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherchia coli RNase T. Length = 152
>gnl|CDD|99852 cd06149, ISG20, DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins Back     alignment and domain information
>gnl|CDD|99848 cd06145, REX1_like, DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins Back     alignment and domain information
>gnl|CDD|214685 smart00479, EXOIII, exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases Back     alignment and domain information
>gnl|CDD|99840 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
>gnl|CDD|216200 pfam00929, RNase_T, Exonuclease Back     alignment and domain information
>gnl|CDD|99846 cd06143, PAN2_exo, DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2 Back     alignment and domain information
>gnl|CDD|176648 cd06127, DEDDh, DEDDh 3'-5' exonuclease domain family 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|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|233397 TIGR01405, polC_Gram_pos, DNA polymerase III, alpha chain, Gram-positive type 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|180905 PRK07246, PRK07246, bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>gnl|CDD|234767 PRK00448, polC, DNA polymerase III PolC; Validated Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 276
KOG2249280 consensus 3'-5' exonuclease [Replication, recombin 100.0
cd06144152 REX4_like DEDDh 3'-5' exonuclease domain of RNA ex 100.0
cd06149157 ISG20 DEDDh 3'-5' exonuclease domain of Interferon 99.98
cd06145150 REX1_like DEDDh 3'-5' exonuclease domain of RNA ex 99.98
cd06143174 PAN2_exo DEDDh 3'-5' exonuclease domain of the euk 99.98
cd06137161 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the 99.97
cd06130156 DNA_pol_III_epsilon_like an uncharacterized bacter 99.96
PRK07740244 hypothetical protein; Provisional 99.96
TIGR01406225 dnaQ_proteo DNA polymerase III, epsilon subunit, P 99.96
PRK05711240 DNA polymerase III subunit epsilon; Provisional 99.96
PRK07247195 DNA polymerase III subunit epsilon; Validated 99.96
PRK08517257 DNA polymerase III subunit epsilon; Provisional 99.95
PRK06195 309 DNA polymerase III subunit epsilon; Validated 99.95
PRK06807 313 DNA polymerase III subunit epsilon; Validated 99.95
PRK09146239 DNA polymerase III subunit epsilon; Validated 99.95
PRK06063313 DNA polymerase III subunit epsilon; Provisional 99.95
cd06131167 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonucl 99.95
PRK06310250 DNA polymerase III subunit epsilon; Validated 99.95
TIGR00573217 dnaq exonuclease, DNA polymerase III, epsilon subu 99.95
PRK07748207 sporulation inhibitor KapD; Provisional 99.95
PRK06309232 DNA polymerase III subunit epsilon; Validated 99.95
smart00479169 EXOIII exonuclease domain in DNA-polymerase alpha 99.95
PRK07983219 exodeoxyribonuclease X; Provisional 99.95
PRK09145202 DNA polymerase III subunit epsilon; Validated 99.94
PRK07942232 DNA polymerase III subunit epsilon; Provisional 99.94
PRK06722281 exonuclease; Provisional 99.94
PRK07883 557 hypothetical protein; Validated 99.94
PRK07246 820 bifunctional ATP-dependent DNA helicase/DNA polyme 99.93
cd06134189 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. 99.93
PRK05168211 ribonuclease T; Provisional 99.93
COG2176 1444 PolC DNA polymerase III, alpha subunit (gram-posit 99.93
TIGR01298200 RNaseT ribonuclease T. in gamma-subdivision Proteo 99.93
PRK08074 928 bifunctional ATP-dependent DNA helicase/DNA polyme 99.93
cd06133176 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain o 99.93
cd06136177 TREX1_2 DEDDh 3'-5' exonuclease domain of three pr 99.93
TIGR01405 1213 polC_Gram_pos DNA polymerase III, alpha chain, Gra 99.92
TIGR01407 850 dinG_rel DnaQ family exonuclease/DinG family helic 99.92
PRK05601377 DNA polymerase III subunit epsilon; Validated 99.92
cd06127159 DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh 99.92
KOG2248380 consensus 3'-5' exonuclease [Replication, recombin 99.91
PRK09182294 DNA polymerase III subunit epsilon; Validated 99.91
PF00929164 RNase_T: Exonuclease; InterPro: IPR013520 This ent 99.9
PTZ00315 582 2'-phosphotransferase; Provisional 99.9
cd06138183 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain o 99.9
COG0847243 DnaQ DNA polymerase III, epsilon subunit and relat 99.89
PRK11779 476 sbcB exonuclease I; Provisional 99.88
PRK00448 1437 polC DNA polymerase III PolC; Validated 99.87
PRK05359181 oligoribonuclease; Provisional 99.86
cd06135173 Orn DEDDh 3'-5' exonuclease domain of oligoribonuc 99.85
KOG0542280 consensus Predicted exonuclease [Replication, reco 99.63
KOG12751118 consensus PAB-dependent poly(A) ribonuclease, subu 99.62
COG2925 475 SbcB Exonuclease I [DNA replication, recombination 99.59
KOG3242208 consensus Oligoribonuclease (3'->5' exoribonucleas 99.58
COG5018210 KapD Inhibitor of the KinA pathway to sporulation, 99.52
COG1949184 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA 99.47
cd06139193 DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease 99.15
cd05160199 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain 99.03
PF01612176 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR00 99.01
PRK05755 880 DNA polymerase I; Provisional 98.88
COG0349 361 Rnd Ribonuclease D [Translation, ribosomal structu 98.77
cd06129161 RNaseD_like DEDDy 3'-5' exonuclease domain of RNas 98.57
PRK10829 373 ribonuclease D; Provisional 98.54
cd06141170 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and 98.53
cd06146193 mut-7_like_exo DEDDy 3'-5' exonuclease domain of C 98.51
cd00007155 35EXOc 3'-5' exonuclease. The 35EXOc domain is res 98.48
cd06148197 Egl_like_exo DEDDy 3'-5' exonuclease domain of Dro 98.48
PF04857262 CAF1: CAF1 family ribonuclease; InterPro: IPR00694 98.43
cd0612596 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonucleas 98.41
TIGR01388 367 rnd ribonuclease D. This model describes ribonucle 98.39
PF13482164 RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A 98.37
cd06140178 DNA_polA_I_Bacillus_like_exo inactive DEDDy 3'-5' 98.3
cd05780195 DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease dom 98.25
smart00474172 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proo 98.24
cd05781188 DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of 98.12
cd06142178 RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribon 98.12
COG0749 593 PolA DNA polymerase I - 3'-5' exonuclease and poly 98.03
PF10108209 DNA_pol_B_exo2: Predicted 3'-5' exonuclease relate 97.87
KOG0304239 consensus mRNA deadenylase subunit [RNA processing 97.75
cd05785207 DNA_polB_like2_exo Uncharacterized bacterial subgr 97.73
cd06147192 Rrp6p_like_exo DEDDy 3'-5' exonuclease domain of y 97.73
cd05779204 DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domai 97.7
cd05777230 DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain 97.65
cd09018150 DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease 97.61
KOG4793318 consensus Three prime repair exonuclease [Replicat 97.6
cd05783204 DNA_polB_B1_exo DEDDy 3'-5' exonuclease domain of 97.58
cd05784193 DNA_polB_II_exo DEDDy 3'-5' exonuclease domain of 97.57
cd05782208 DNA_polB_like1_exo Uncharacterized bacterial subgr 97.43
PTZ00166 1054 DNA polymerase delta catalytic subunit; Provisiona 97.29
TIGR00593 887 pola DNA polymerase I. This family is based on the 97.06
PHA02528 881 43 DNA polymerase; Provisional 96.97
cd05778231 DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease 96.86
PRK05762 786 DNA polymerase II; Reviewed 96.71
COG3359278 Predicted exonuclease [DNA replication, recombinat 96.64
smart00486 471 POLBc DNA polymerase type-B family. DNA polymerase 96.09
PHA02570220 dexA exonuclease; Provisional 95.89
PHA02524 498 43A DNA polymerase subunit A; Provisional 95.67
KOG1798 2173 consensus DNA polymerase epsilon, catalytic subuni 95.67
cd05776234 DNA_polB_alpha_exo inactive DEDDy 3'-5' exonucleas 95.47
cd06128151 DNA_polA_exo DEDDy 3'-5' exonuclease domain of fam 94.89
KOG0969 1066 consensus DNA polymerase delta, catalytic subunit 94.47
COG0417 792 PolB DNA polymerase elongation subunit (family B) 94.01
PF03104325 DNA_pol_B_exo1: DNA polymerase family B, exonuclea 93.81
TIGR03491457 RecB family nuclease, putative, TM0106 family. Mem 93.02
KOG3657 1075 consensus Mitochondrial DNA polymerase gamma, cata 92.62
PF00843533 Arena_nucleocap: Arenavirus nucleocapsid protein; 91.78
COG5228299 POP2 mRNA deadenylase subunit [RNA processing and 91.75
PRK05761 787 DNA polymerase I; Reviewed 90.4
TIGR00592 1172 pol2 DNA polymerase (pol2). This family is based o 86.99
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair] Back     alignment and domain information 
Probab=100.00  E-value=9.4e-41  Score=288.93  Aligned_cols=169  Identities=51%  Similarity=0.841  Sum_probs=160.1

Q ss_pred             CCCCCcEEEEEEeccCCCC-CCeeEEEEEEEEeCCCcEEEEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHH
Q 023843           76 DFSLTDVVAMDCEMVGISQ-GNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAE  154 (276)
Q Consensus        76 ~~~~~~~VaiD~EttG~~~-~~iiei~~v~v~~~~g~ii~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~  154 (276)
                      ..+.+++||+||||+|.++ |+...+|+|+|+|+.|.++||.||+|+++|+||+|.++||+++++.+|++|..|+.++.+
T Consensus       101 ~~~~~r~vAmDCEMVG~Gp~G~~s~lARvSIVN~~G~VvyDkyVkP~~~VtDyRT~vSGIrpehm~~A~pf~~aQ~ev~k  180 (280)
T KOG2249|consen  101 MGSLTRVVAMDCEMVGVGPDGRESLLARVSIVNYHGHVVYDKYVKPTEPVTDYRTRVSGIRPEHMRDAMPFKVAQKEVLK  180 (280)
T ss_pred             ccccceEEEEeeeEeccCCCccceeeeEEEEeeccCcEeeeeecCCCcccccceeeecccCHHHhccCccHHHHHHHHHH
Confidence            3445679999999999996 577899999999999999999999999999999999999999999999999999999999


Q ss_pred             HhcCCeEEEEchhhHHHHhcccCCCCceeehhhhchhhh--CCCCCccHHHHHHHHhCCcCCCCCCChHHHHHHHHHHHH
Q 023843          155 LIEGRILVGHALHNDLKALLLTHSKKDLRDTSEYQPFLN--RNGRSKALRHLAAEILAVEIQNGEHCPIDDARAAMLLYM  232 (276)
Q Consensus       155 ~l~~~~lVgHn~~~D~~~L~~~~~~~~~~Dt~~~~~~~~--~~~~~~sL~~La~~~lgi~~~~~~H~Al~DA~at~~L~~  232 (276)
                      ||.|+|||||.+++|+++|.+.||+..++||+.+.+++.  .....+||+.|+.++||++++.+.|++++||+|||+||.
T Consensus       181 lL~gRIlVGHaLhnDl~~L~l~hp~s~iRDTs~~~pl~k~~~~~~tpSLK~Lt~~~Lg~~IQ~GeHsSvEDA~AtM~LY~  260 (280)
T KOG2249|consen  181 LLKGRILVGHALHNDLQALKLEHPRSMIRDTSKYPPLMKLLSKKATPSLKKLTEALLGKDIQVGEHSSVEDARATMELYK  260 (280)
T ss_pred             HHhCCEEeccccccHHHHHhhhCchhhhcccccCchHHHHhhccCCccHHHHHHHHhchhhhccccCcHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999987  467889999999999999999999999999999999999


Q ss_pred             HhHHHHHHHHHH
Q 023843          233 KNRKQWEKSVKD  244 (276)
Q Consensus       233 ~l~~~~e~~~~~  244 (276)
                      +++.+||+....
T Consensus       261 ~vk~qwe~~~~r  272 (280)
T KOG2249|consen  261 RVKVQWEKIEAR  272 (280)
T ss_pred             HHHHHHHHHhhc
Confidence            999999988764

>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
>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins Back     alignment and domain information
>cd06143 PAN2_exo DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2 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
>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
>PRK07740 hypothetical protein; Provisional Back     alignment and domain information
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial Back     alignment and domain information
>PRK05711 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>PRK07247 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK08517 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>PRK06195 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK06807 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK09146 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK06063 DNA polymerase III subunit epsilon; 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
>PRK06310 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family Back     alignment and domain information
>PRK07748 sporulation inhibitor KapD; Provisional Back     alignment and domain information
>PRK06309 DNA polymerase III subunit epsilon; Validated 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
>PRK07983 exodeoxyribonuclease X; Provisional Back     alignment and domain information
>PRK09145 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK07942 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>PRK06722 exonuclease; Provisional Back     alignment and domain information
>PRK07883 hypothetical protein; Validated Back     alignment and domain information
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated 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
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR01298 RNaseT ribonuclease T Back     alignment and domain information
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated 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
>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins 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
>PRK05601 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>cd06127 DEDDh DEDDh 3'-5' exonuclease domain family Back     alignment and domain information
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair] 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
>PTZ00315 2'-phosphotransferase; Provisional 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
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK11779 sbcB exonuclease I; Provisional Back     alignment and domain information
>PRK00448 polC DNA polymerase III PolC; Validated Back     alignment and domain information
>PRK05359 oligoribonuclease; Provisional Back     alignment and domain information
>cd06135 Orn DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins Back     alignment and domain information
>KOG0542 consensus Predicted exonuclease [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
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair] Back     alignment and domain information
>KOG3242 consensus Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification] 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
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification] 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
>cd05160 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain of family-B DNA polymerases 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
>PRK05755 DNA polymerase I; Provisional Back     alignment and domain information
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis] 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
>cd06141 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and similar proteins 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
>cd00007 35EXOc 3'-5' exonuclease 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
>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
>cd06125 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily Back     alignment and domain information
>TIGR01388 rnd ribonuclease D 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
>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
>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
>smart00474 35EXOc 3'-5' exonuclease 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
>cd06142 RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribonuclease D 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
>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
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification] 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
>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
>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
>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
>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
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair] 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
>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
>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
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional Back     alignment and domain information
>TIGR00593 pola DNA polymerase I Back     alignment and domain information
>PHA02528 43 DNA polymerase; Provisional 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
>PRK05762 DNA polymerase II; Reviewed Back     alignment and domain information
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair] Back     alignment and domain information
>smart00486 POLBc DNA polymerase type-B family Back     alignment and domain information
>PHA02570 dexA exonuclease; Provisional Back     alignment and domain information
>PHA02524 43A DNA polymerase subunit A; Provisional Back     alignment and domain information
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [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
>cd06128 DNA_polA_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases Back     alignment and domain information
>KOG0969 consensus DNA polymerase delta, catalytic subunit [Replication, recombination and repair] Back     alignment and domain information
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair] 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
>TIGR03491 RecB family nuclease, putative, TM0106 family Back     alignment and domain information
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair] Back     alignment and domain information
>PF00843 Arena_nucleocap: Arenavirus nucleocapsid protein; InterPro: IPR000229 Arenaviruses are single stranded RNA viruses Back     alignment and domain information
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification] Back     alignment and domain information
>PRK05761 DNA polymerase I; Reviewed Back     alignment and domain information
>TIGR00592 pol2 DNA polymerase (pol2) 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 ?
Query276
1wlj_A189 Human Isg20 Length = 189 1e-24
>pdb|1WLJ|A Chain A, Human Isg20 Length = 189 Back     alignment and structure 
Iteration: 1

 Score =  110 bits (274), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 61/167 (36%), Positives = 98/167 (58%), Gaps = 16/167 (9%)
Query: 81  DVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLR 140
           +VVAMDCEMVG+    +S L R SLVN  G ++YD+F+RP   + D+RTR+SG+ P+ + 
Sbjct: 6   EVVAMDCEMVGLGPHRESGLARCSLVNVHGAVLYDKFIRPEGEITDYRTRVSGVTPQHMV 65
Query: 141 KAKDFPTVQKKVAELIEGRILVGHALHNDLKALLLTHSKKDLRDTSEYQPFLNR------ 194
            A  F   + ++ +L++G+++VGH L +D +AL     K+D+   + Y    +R      
Sbjct: 66  GATPFAVARLEILQLLKGKLVVGHDLKHDFQAL-----KEDMSGYTIYDTSTDRLLWREA 120
Query: 195 ---NGRSKALRHLAAEILAVEIQNG--EHCPIDDARAAMLLYMKNRK 236
              + R  +LR L+  +L   IQN    H  ++DARA M LY  +++
Sbjct: 121 KLDHCRRVSLRVLSERLLHKSIQNSLLGHSSVEDARATMELYQISQR 167

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query276
1wlj_A189 Interferon stimulated gene 20KDA; exoribonuclease, 1e-74
3cg7_A308 CRN-4, cell death-related nuclease 4; hydrolase, a 1e-08
2xri_A224 ERI1 exoribonuclease 3; hydrolase, metal binding; 1e-08
1w0h_A204 3'-5' exonuclease ERI1; nuclease domain, hydrolase 9e-07
1zbh_A299 3'-5' exonuclease ERI1; histone mRNA 3'-END-specif 1e-06
1zbu_A349 ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; 2e-06
2p1j_A186 POLIII, DNA polymerase III POLC-type; structural g 7e-06
>1wlj_A Interferon stimulated gene 20KDA; exoribonuclease, hydrolase; HET: U5P; 1.90A {Homo sapiens} SCOP: c.55.3.5 Length = 189 Back     alignment and structure
 Score =  225 bits (575), Expect = 1e-74
 Identities = 61/167 (36%), Positives = 97/167 (58%), Gaps = 6/167 (3%)

Query: 80  TDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDL 139
            +VVAMDCEMVG+    +S L R SLVN  G ++YD+F+RP   + D+RTR+SG+ P+ +
Sbjct: 5   REVVAMDCEMVGLGPHRESGLARCSLVNVHGAVLYDKFIRPEGEITDYRTRVSGVTPQHM 64

Query: 140 RKAKDFPTVQKKVAELIEGRILVGHALHNDLKALLLTHSKKDLRDTSEYQPFLNR----N 195
             A  F   + ++ +L++G+++VGH L +D +AL    S   + DTS  +         +
Sbjct: 65  VGATPFAVARLEILQLLKGKLVVGHDLKHDFQALKEDMSGYTIYDTSTDRLLWREAKLDH 124

Query: 196 GRSKALRHLAAEILAVEIQNG--EHCPIDDARAAMLLYMKNRKQWEK 240
            R  +LR L+  +L   IQN    H  ++DARA M LY  +++   +
Sbjct: 125 CRRVSLRVLSERLLHKSIQNSLLGHSSVEDARATMELYQISQRIRAR 171
>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
>2xri_A ERI1 exoribonuclease 3; hydrolase, metal binding; 2.15A {Homo sapiens} Length = 224 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
>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
>1zbu_A ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; HET: AMP; 3.00A {Homo sapiens} Length = 349 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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query276
1wlj_A189 Interferon stimulated gene 20KDA; exoribonuclease, 99.98
2gui_A194 DNA polymerase III epsilon subunit; DNA polymerase 99.97
2p1j_A186 POLIII, DNA polymerase III POLC-type; structural g 99.97
1w0h_A204 3'-5' exonuclease ERI1; nuclease domain, hydrolase 99.96
3mxm_B242 Three prime repair exonuclease 1; RNAse H-like fol 99.96
1y97_A238 Three prime repair exonuclease 2; TREX2, hydrolase 99.94
1zbh_A299 3'-5' exonuclease ERI1; histone mRNA 3'-END-specif 99.94
2xri_A224 ERI1 exoribonuclease 3; hydrolase, metal binding; 99.94
3u3y_B314 Three prime repair exonuclease 1; RNAse H fold, 3' 99.94
2f96_A224 Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolas 99.93
1zbu_A349 ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; 99.93
3cg7_A308 CRN-4, cell death-related nuclease 4; hydrolase, a 99.93
3v9w_A235 Ribonuclease T; DEDD nucleases family, EXO-nucleas 99.93
2igi_A180 Oligoribonuclease; RNAse, exoribonuclease, exonucl 99.92
2gbz_A194 Oligoribonuclease; ORN, deddh, structural genomics 99.91
3tr8_A186 Oligoribonuclease; transcription, hydrolase; 2.50A 99.91
2qxf_A 482 Exodeoxyribonuclease I; alpha-beta domain, DNAQ su 99.91
2kfn_A 605 Klenow fragment of DNA polymerase I; complex (poly 99.15
1x9m_A 698 DNA polymerase; DNA ploymerase, N-2-acetylaminoflu 99.03
4dfk_A 540 DNA polymerase I, thermostable; DNA polymerase, tr 98.79
4hec_A190 Putative uncharacterized protein; ssgcid, structur 98.78
3saf_A 428 Exosome component 10; exoribonuclease, RNA exosome 98.75
4gmj_B285 CCR4-NOT transcription complex subunit 7; mRNA dec 98.69
3pv8_A 592 DNA polymerase I; DNA polymerase I, protein-DNA co 98.51
2e6m_A208 Werner syndrome ATP-dependent helicase homolog; AP 98.38
1yt3_A 375 Ribonuclease D, RNAse D; exoribonuclease, exonucle 98.35
2hbj_A 410 Exosome complex exonuclease RRP6; RNA metabolism, 98.34
2d5r_A252 CCR4-NOT transcription complex subunit 7; poly(A) 98.25
1vk0_A206 Hypothetical protein; homohexamer, AT5G06450, stru 98.2
1uoc_A289 POP2; hydrolase, DEDD nuclease, mRNA degradation, 98.2
2p51_A333 SPCC18.06C protein; DEDD nuclease fold, hydrolase, 98.16
3cym_A 440 Uncharacterized protein BAD_0989; structural genom 98.13
1qht_A 775 Protein (DNA polymerase); archaea, hyperthermostab 97.84
1noy_A388 Protein (DNA polymerase (E.C.2.7.7.7)); exonucleas 97.64
3iay_A 919 DNA polymerase delta catalytic subunit; protein-DN 97.41
2gv9_A 1193 DNA polymerase; polymerase alpha fold, transferase 97.34
1s5j_A 847 DNA polymerase I; replication, disulfide bonds, tr 97.25
3qex_A 903 DNA polymerase, GP43; difluorotoluene nucleoside; 97.19
3k59_A 786 POL II, DNA polymerase II; protein-DNA complex, DN 97.1
3d45_A507 Poly(A)-specific ribonuclease PARN; CAP analogue, 96.93
2a1r_A430 Poly(A)-specific ribonuclease PARN; DEDD, nuclease 96.91
1bgx_T 832 TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhi 95.54
3q7c_A243 Nucleoprotein; deddh exonuclease, 3' exonuclease, 93.98
3ikm_A 1172 DNA polymerase subunit gamma-1; human mitochondria 93.91
3mwp_A577 Nucleoprotein; structural genomics, scottish struc 90.25
2py5_A 575 DNA polymerase; protein-DNA complex, replication, 85.76
>1wlj_A Interferon stimulated gene 20KDA; exoribonuclease, hydrolase; HET: U5P; 1.90A {Homo sapiens} SCOP: c.55.3.5 Back     alignment and structure
Probab=99.98  E-value=1.1e-31  Score=227.66  Aligned_cols=163  Identities=37%  Similarity=0.628  Sum_probs=136.9

Q ss_pred             CCcEEEEEEeccCCCCCCeeEEEEEEEEeCCCcEEEEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHHHhcC
Q 023843           79 LTDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEG  158 (276)
Q Consensus        79 ~~~~VaiD~EttG~~~~~iiei~~v~v~~~~g~ii~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~l~~  158 (276)
                      ..++|+|||||||+++....+|+.|.+++.+|+++|+.||+|..+|+++++.+||||++++.++++|.+|+.+|.+|+++
T Consensus         4 ~~~~vviD~ETTGl~~~~~~~iiei~~v~~~g~~i~~~lV~P~~~i~~~~~~i~GIt~~~l~~a~~~~~v~~~~~~~l~~   83 (189)
T 1wlj_A            4 SREVVAMDCEMVGLGPHRESGLARCSLVNVHGAVLYDKFIRPEGEITDYRTRVSGVTPQHMVGATPFAVARLEILQLLKG   83 (189)
T ss_dssp             --CEEEEEEEEEEETTTTEEEEEEEEEECTTCCEEEEEEEECSSCEEECCHHHHCCCHHHHTTCEEHHHHHHHHHHHHTT
T ss_pred             CCeEEEEEeECcCcCCCCCceEEEEEEEeCCCCEEEeeEecCCCCCCccccCCCCCCHHHHcCCCCHHHHHHHHHHHHCC
Confidence            35799999999999865433444455566779999999999999999999999999999999999999999999999999


Q ss_pred             CeEEEEchhhHHHHhcccCCCCceeehhhhchhh----hCCCCCccHHHHHHHHhCCcCCCC--CCChHHHHHHHHHHHH
Q 023843          159 RILVGHALHNDLKALLLTHSKKDLRDTSEYQPFL----NRNGRSKALRHLAAEILAVEIQNG--EHCPIDDARAAMLLYM  232 (276)
Q Consensus       159 ~~lVgHn~~~D~~~L~~~~~~~~~~Dt~~~~~~~----~~~~~~~sL~~La~~~lgi~~~~~--~H~Al~DA~at~~L~~  232 (276)
                      .++||||+.||+.||...++...++||+.+....    .+...+++|+.|+..+||++++++  +|+|++||++|++||.
T Consensus        84 ~~lV~hn~~fD~~~L~~~~~~~~~idt~~~~~~~~~~~~p~~~~~~L~~l~~~~lgi~~~~~~~~H~Al~Da~ata~l~~  163 (189)
T 1wlj_A           84 KLVVGHDLKHDFQALKEDMSGYTIYDTSTDRLLWREAKLDHCRRVSLRVLSERLLHKSIQNSLLGHSSVEDARATMELYQ  163 (189)
T ss_dssp             SEEEESSHHHHHHHTTCCCTTCEEEEGGGCHHHHHHHTC-----CCHHHHHHHHTCCCCSCCTTCCCHHHHHHHHHHHHH
T ss_pred             CEEEECCcHHHHHHHHHhCCCCceechHhhhhhhhcccCCCCCCccHHHHHHHHcCCCCCCCCCCcCcHHHHHHHHHHHH
Confidence            9999999999999999888877799999875432    223478999999955689999854  8999999999999999


Q ss_pred             HhHHHHHHH
Q 023843          233 KNRKQWEKS  241 (276)
Q Consensus       233 ~l~~~~e~~  241 (276)
                      ++...|+..
T Consensus       164 ~l~~~~~~~  172 (189)
T 1wlj_A          164 ISQRIRARR  172 (189)
T ss_dssp             HHHHHHHHT
T ss_pred             HHHHHHHHh
Confidence            999888754
>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
>1w0h_A 3'-5' exonuclease ERI1; nuclease domain, hydrolase; HET: AMP; 1.59A {Homo sapiens} SCOP: c.55.3.5 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
>1y97_A Three prime repair exonuclease 2; TREX2, hydrolase; 2.50A {Homo sapiens} SCOP: c.55.3.5 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
>2xri_A ERI1 exoribonuclease 3; hydrolase, metal binding; 2.15A {Homo sapiens} 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
>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
>1zbu_A ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; HET: AMP; 3.00A {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
>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
>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
>3tr8_A Oligoribonuclease; transcription, hydrolase; 2.50A {Coxiella burnetii} 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
>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
>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
>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
>4hec_A Putative uncharacterized protein; ssgcid, structural genomics, SEA structural genomics center for infectious disease, unknown; 1.80A {Mycobacterium tuberculosis} 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
>4gmj_B CCR4-NOT transcription complex subunit 7; mRNA decay, deadenylase, RNA bindin; HET: GOL; 2.70A {Homo sapiens} 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
>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
>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
>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
>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
>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
>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
>2p51_A SPCC18.06C protein; DEDD nuclease fold, hydrolase, gene regulation; 1.40A {Schizosaccharomyces pombe} PDB: 3g0z_A 3g10_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
>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
>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
>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
>2gv9_A DNA polymerase; polymerase alpha fold, transferase; HET: DNA; 2.68A {Human herpesvirus 1} PDB: 1dml_B* 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
>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
>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
>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
>2a1r_A Poly(A)-specific ribonuclease PARN; DEDD, nuclease domain, hydrolase-RNA complex; 2.60A {Homo sapiens} PDB: 2a1s_A 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
>3q7c_A Nucleoprotein; deddh exonuclease, 3' exonuclease, hydrolase; 1.50A {Lassa virus} PDB: 3q7b_A 4fvu_A 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
>3mwp_A Nucleoprotein; structural genomics, scottish structural PROT facility, SSPF, nuclear protein; 1.79A {Lassa virus josiah} PDB: 3mwt_A 3mx2_A* 3mx5_A* 3r3l_A 3t5q_A 3t5n_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

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 276
d1wlja_173 c.55.3.5 (A:) Interferon-stimulated gene 20 kDa pr 6e-26
d1w0ha_200 c.55.3.5 (A:) Exonuclease ERI1 {Human (Homo sapien 5e-06
d3b6oa1226 c.55.3.5 (A:9-234) Three prime repair exonuclease 0.004
>d1wlja_ c.55.3.5 (A:) Interferon-stimulated gene 20 kDa protein, ISG20 {Human (Homo sapiens) [TaxId: 9606]} Length = 173 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: Interferon-stimulated gene 20 kDa protein, ISG20
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 98.5 bits (244), Expect = 6e-26
 Identities = 61/166 (36%), Positives = 97/166 (58%), Gaps = 6/166 (3%)

Query: 81  DVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLR 140
           +VVAMDCEMVG+    +S L R SLVN  G ++YD+F+RP   + D+RTR+SG+ P+ + 
Sbjct: 1   EVVAMDCEMVGLGPHRESGLARCSLVNVHGAVLYDKFIRPEGEITDYRTRVSGVTPQHMV 60

Query: 141 KAKDFPTVQKKVAELIEGRILVGHALHNDLKALLLTHSKKDLRDTSEYQPFL----NRNG 196
            A  F   + ++ +L++G+++VGH L +D +AL    S   + DTS  +         + 
Sbjct: 61  GATPFAVARLEILQLLKGKLVVGHDLKHDFQALKEDMSGYTIYDTSTDRLLWREAKLDHC 120

Query: 197 RSKALRHLAAEILAVEIQNGE--HCPIDDARAAMLLYMKNRKQWEK 240
           R  +LR L+  +L   IQN    H  ++DARA M LY  +++   +
Sbjct: 121 RRVSLRVLSERLLHKSIQNSLLGHSSVEDARATMELYQISQRIRAR 166
>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

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query276
d1wlja_173 Interferon-stimulated gene 20 kDa protein, ISG20 { 99.97
d2guia1174 N-terminal exonuclease domain of the epsilon subun 99.94
d3b6oa1226 Three prime repair exonuclease 1, TREX1 {Mouse (Mu 99.91
d1y97a1228 Three prime repair exonuclease 2, TREX2 {Human (Ho 99.88
d1w0ha_200 Exonuclease ERI1 {Human (Homo sapiens) [TaxId: 960 99.88
d2f96a1202 Ribonuclease T {Pseudomonas aeruginosa [TaxId: 287 99.77
d2qxfa1 467 Exonuclease I {Escherichia coli K12 (Escherichia c 99.77
d2igia1180 Oligoribonuclease {Escherichia coli [TaxId: 562]} 99.59
d1kfsa1195 Exonuclease domain of prokaryotic DNA polymerase { 99.23
d1yt3a3193 Ribonuclease D, catalytic domain {Escherichia coli 99.1
d2hhva1171 Exonuclease domain of prokaryotic DNA polymerase { 99.01
d2hbka2292 Exosome complex exonuclease RRP6 {Baker's yeast (S 98.95
d2d5ra1252 CCR4-NOT transcription complex subunit 7, CAF1 {Hu 98.85
d1vk0a_206 Hypothetical protein AT5G06450 {Thale-cress (Arabi 98.32
d1uoca_286 Pop2 RNase D domain {Baker's yeast (Saccharomyces 98.22
d1x9ma1204 Exonuclease domain of T7 DNA polymerase {Bacteriop 98.15
d1tgoa1347 Exonuclease domain of family B DNA polymerases {Ar 97.84
d1q8ia1388 Exonuclease domain of family B DNA polymerases {Es 97.46
d1s5ja1410 Exonuclease domain of family B DNA polymerases {Su 97.34
d1noya_372 Exonuclease domain of family B DNA polymerases {Ba 96.06
d1ih7a1375 Exonuclease domain of family B DNA polymerases {Ba 95.44
d2py5a1183 Exonuclease domain of phi29 DNA polymerase {Bacter 80.61
>d1wlja_ c.55.3.5 (A:) Interferon-stimulated gene 20 kDa protein, ISG20 {Human (Homo sapiens) [TaxId: 9606]} 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: Interferon-stimulated gene 20 kDa protein, ISG20
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=1.5e-30  Score=213.99  Aligned_cols=156  Identities=37%  Similarity=0.627  Sum_probs=128.9

Q ss_pred             cEEEEEEeccCCCCCCeeEEEEEEEEeCCCcEEEEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHHHhcCCe
Q 023843           81 DVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEGRI  160 (276)
Q Consensus        81 ~~VaiD~EttG~~~~~iiei~~v~v~~~~g~ii~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~l~~~~  160 (276)
                      ++|+|||||||++++.-..|..+.|++.+|+++|+.||+|..+++++++.+||||++++.++++|.+++.+|.+|+++.+
T Consensus         1 ~~v~iD~EttGl~~~~~~ii~~~~iv~~~g~~i~~~~v~p~~~i~~~~~~i~GIt~e~~~~~~~~~~~~~~~~~~~~~~~   80 (173)
T d1wlja_           1 EVVAMDCEMVGLGPHRESGLARCSLVNVHGAVLYDKFIRPEGEITDYRTRVSGVTPQHMVGATPFAVARLEILQLLKGKL   80 (173)
T ss_dssp             CEEEEEEEEEEETTTTEEEEEEEEEECTTCCEEEEEEEECSSCEEECCHHHHCCCHHHHTTCEEHHHHHHHHHHHHTTSE
T ss_pred             CEEEEEEEcCCCCCCCCcEEEEEEEEEecCeEEEEEeeecccccCcceeEEecCcchhhhcCCcHHHHHHHHHhhcccce
Confidence            58999999999997643344456667888999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEchhhHHHHhcccCCCCce----eehhhhchhhhCCCCCccHHHHHHHHhCCcCC--CCCCChHHHHHHHHHHHHHh
Q 023843          161 LVGHALHNDLKALLLTHSKKDL----RDTSEYQPFLNRNGRSKALRHLAAEILAVEIQ--NGEHCPIDDARAAMLLYMKN  234 (276)
Q Consensus       161 lVgHn~~~D~~~L~~~~~~~~~----~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~--~~~H~Al~DA~at~~L~~~l  234 (276)
                      +||||+.||+.+|+...++..+    +|++.+.+...+....++|+.|+..+++..++  ..+|+|++||++|++||+.+
T Consensus        81 lv~hn~~fD~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~~~~~~~~i~~~~~~H~Al~Da~at~~l~~~~  160 (173)
T d1wlja_          81 VVGHDLKHDFQALKEDMSGYTIYDTSTDRLLWREAKLDHCRRVSLRVLSERLLHKSIQNSLLGHSSVEDARATMELYQIS  160 (173)
T ss_dssp             EEESSHHHHHHHTTCCCTTCEEEEGGGCHHHHHHHTC-----CCHHHHHHHHTCCCCSCCTTCCCHHHHHHHHHHHHHHH
T ss_pred             EEeechHhHHHHHHHhhccCcccchhHHHHHHHHHhhcccCCcCHHHHHHHHhCCcccCCCCCCChHHHHHHHHHHHHHH
Confidence            9999999999999966665433    45666666666566789999999888887764  35799999999999999765


Q ss_pred             HH
Q 023843          235 RK  236 (276)
Q Consensus       235 ~~  236 (276)
                      .+
T Consensus       161 ~~  162 (173)
T d1wlja_         161 QR  162 (173)
T ss_dssp             HH
T ss_pred             HH
Confidence            43
>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
>d3b6oa1 c.55.3.5 (A:9-234) Three prime repair exonuclease 1, TREX1 {Mouse (Mus musculus) [TaxId: 10090]} 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
>d1w0ha_ c.55.3.5 (A:) Exonuclease ERI1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2f96a1 c.55.3.5 (A:19-220) Ribonuclease T {Pseudomonas aeruginosa [TaxId: 287]} 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
>d2igia1 c.55.3.5 (A:1-180) Oligoribonuclease {Escherichia coli [TaxId: 562]} 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
>d1yt3a3 c.55.3.5 (A:1-193) Ribonuclease D, catalytic domain {Escherichia coli [TaxId: 562]} 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
>d2hbka2 c.55.3.5 (A:129-420) Exosome complex exonuclease RRP6 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} 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
>d1vk0a_ c.55.3.5 (A:) Hypothetical protein AT5G06450 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]} 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
>d1x9ma1 c.55.3.5 (A:1-210) Exonuclease domain of T7 DNA polymerase {Bacteriophage T7 [TaxId: 10760]} 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
>d1q8ia1 c.55.3.5 (A:2-389) Exonuclease domain of family B DNA polymerases {Escherichia coli [TaxId: 562]} 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
>d1noya_ c.55.3.5 (A:) Exonuclease domain of family B DNA polymerases {Bacteriophage T4 [TaxId: 10665]} 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
>d2py5a1 c.55.3.5 (A:5-187) Exonuclease domain of phi29 DNA polymerase {Bacteriophage phi-29 [TaxId: 10756]} Back     information, alignment and structure