Citrus Sinensis ID: 036883

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-------
FEYYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYFHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGDVRCNLKEAVELAGLIWQGRVHCGLDDAINIARLLSVIMRRGFKFSITKSLTPQANPNCLTWNRHHFLEPQAMYTPPHTSLIHEFEDCRYCYCGAKSIKKVIQRPGPKRGSFFFGCGNWTPNRGACCNYFQWATTS
ccEEEEEEEEEccccccccccccEEEEcEEEEEccccEEEEEEcccccccccccccHHHHHHHcccHHHHHccccHHHHHHHHHHHHHHcccccccEEEEEcccccHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHccccccHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHcccEEEEccccccccccccccccccccccccccccccccccccccccccEEEccccccccccccccccccccEEEcccccccccccccccEEcccc
ccEEEEEEEEEcccccccccccEEEEEcEEEEEcccccHHHHHHHHccccccccHHHHHHHHccccHHHHcccccHHHHHHHHHHHHHHHccccccEEEEEcccccHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHccccccHHHHHHHccccEcccccccHHHHHHHHHHHHHHHHcccEEEEEcccccccccccccccccccccccccccccccccccccccccEEEcccccccEEEEccccccccEEEccccccccccccccEEEEEccc
FEYYVVIDFEatcdkernlhpqeiiefpsvvvsgVSGEIIACFqtyvrptfeplLTDFCKELTGIQQHQVDNGITLGEALYFHDKWLLQmglnntnfsvvtwsdwdCQVMLESECRIkkiqkpayfnqwinlrvpfskvfgDVRCNLKEAVELAGLIWQGRVHCGLDDAINIARLLSVIMRRGFKFsitksltpqanpncltwnrhhflepqamytpphtslihefedcrycycgaksikkviqrpgpkrgsfffgcgnwtpnrgaccnyfqwatts
FEYYVVIdfeatcdkernlhpqeiIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYFHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGDVRCNLKEAVELAGLIWQGRVHCGLDDAINIARLLSVIMRRGFKFSITKSLTPQANPNCLTWNRHHFLEPQAMYTPPHTSLIHEFEDCRYCYCGAKSIKkviqrpgpkRGSFFFgcgnwtpnrgACCNYFQWATTS
FEYYVVIDFEATCDKERNLHPQEIIEFPsvvvsgvsgEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYFHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGDVRCNLKEAVELAGLIWQGRVHCGLDDAINIARLLSVIMRRGFKFSITKSLTPQANPNCLTWNRHHFLEPQAMYTPPHTSLIHEFEDCRYCYCGAKSIKKVIQRPGPKRGSFFFGCGNWTPNRGACCNYFQWATTS
**YYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYFHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGDVRCNLKEAVELAGLIWQGRVHCGLDDAINIARLLSVIMRRGFKFSITKSLTPQANPNCLTWNRHHFLEPQAMYTPPHTSLIHEFEDCRYCYCGAKSIKKVIQRPGPKRGSFFFGCGNWTPNRGACCNYFQWA***
FEYYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYFHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGDVRCNLKEAVELAGLIWQGRVHCGLDDAINIARLLSVIMRRGFKFSITKSL*******************************HEFEDCRYCYCGAKSIKKV**RPGPKRGSFFFGCGNWTPNRGACCNYFQWAT**
FEYYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYFHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGDVRCNLKEAVELAGLIWQGRVHCGLDDAINIARLLSVIMRRGFKFSITKSLTPQANPNCLTWNRHHFLEPQAMYTPPHTSLIHEFEDCRYCYCGAKSIKKVIQRPGPKRGSFFFGCGNWTPNRGACCNYFQWATTS
FEYYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYFHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGDVRCNLKEAVELAGLIWQGRVHCGLDDAINIARLLSVIMRRGFKFSITKSLT*********************YTPPHTSLIHEFEDCRYCYCGAKSIKKVIQRPGPKRGSFFFGCGNWTPNRGACCNYFQWAT**
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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FEYYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEALYFHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGDVRCNLKEAVELAGLIWQGRVHCGLDDAINIARLLSVIMRRGFKFSITKSLTPQANPNCLTWNRHHFLEPQAMYTPPHTSLIHEFEDCRYCYCGAKSIKKVIQRPGPKRGSFFFGCGNWTPNRGACCNYFQWATTS
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 ?
Query277 2.2.26 [Sep-21-2011]
Q5HZL1 687 ERI1 exoribonuclease 2 OS N/A no 0.693 0.279 0.403 2e-36
A8K979 691 ERI1 exoribonuclease 2 OS yes no 0.693 0.277 0.401 5e-36
Q5BKS4 688 ERI1 exoribonuclease 2 OS yes no 0.732 0.295 0.386 1e-34
A6QLH5337 ERI1 exoribonuclease 3 OS yes no 0.671 0.551 0.403 1e-33
O43414337 ERI1 exoribonuclease 3 OS no no 0.671 0.551 0.403 1e-33
Q8C460337 ERI1 exoribonuclease 3 OS no no 0.671 0.551 0.403 2e-33
Q502M8 555 ERI1 exoribonuclease 2 OS yes no 0.682 0.340 0.372 2e-30
Q8IV48349 3'-5' exoribonuclease 1 O no no 0.685 0.544 0.353 3e-27
Q7TMF2345 3'-5' exoribonuclease 1 O no no 0.682 0.547 0.351 3e-26
Q5FVR4345 3'-5' exoribonuclease 1 O no no 0.682 0.547 0.351 1e-25
>sp|Q5HZL1|ERI2_XENLA ERI1 exoribonuclease 2 OS=Xenopus laevis GN=eri2 PE=2 SV=1 Back     alignment and function desciption
 Score =  153 bits (386), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 84/208 (40%), Positives = 119/208 (57%), Gaps = 16/208 (7%)

Query: 1   FEYYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCK 60
           FEY ++IDFE+TC K+     QEIIEFP+V+++  +GEI + F TYV+P   P+L+DFC 
Sbjct: 35  FEYLIIIDFESTCWKDGKHSTQEIIEFPAVLLNVSNGEIESEFHTYVQPQEHPILSDFCT 94

Query: 61  ELTGIQQHQVDNGITLGEALYFHDKWLLQM----------------GLNNTNFSVVTWSD 104
           ELTGI Q QVD+G+ L   L   + W+ ++                   +   + VTWSD
Sbjct: 95  ELTGINQQQVDDGVPLKICLSQFNSWIQKLQKEKGIAFVTAVPTHSTAEHKMCAFVTWSD 154

Query: 105 WDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGDVRCNLKEAVELAGLIWQGRVHC 164
           WD  V L  ECR K+++KP   N WI+LR  +   +      L  A++  G+ + GR H 
Sbjct: 155 WDLGVCLLYECRRKQMKKPDILNSWIDLRATYKLFYNRRPKGLNGALQDLGIEFSGREHS 214

Query: 165 GLDDAINIARLLSVIMRRGFKFSITKSL 192
           GLDD+ N A+L S ++  G    ITKSL
Sbjct: 215 GLDDSRNTAKLASRMICDGCVMKITKSL 242

Xenopus laevis (taxid: 8355)
EC: 3EC: .EC: 1EC: .EC: -EC: .EC: -
>sp|A8K979|ERI2_HUMAN ERI1 exoribonuclease 2 OS=Homo sapiens GN=ERI2 PE=2 SV=2 Back     alignment and function description
>sp|Q5BKS4|ERI2_MOUSE ERI1 exoribonuclease 2 OS=Mus musculus GN=Eri2 PE=2 SV=1 Back     alignment and function description
>sp|A6QLH5|ERI3_BOVIN ERI1 exoribonuclease 3 OS=Bos taurus GN=ERI3 PE=2 SV=1 Back     alignment and function description
>sp|O43414|ERI3_HUMAN ERI1 exoribonuclease 3 OS=Homo sapiens GN=ERI3 PE=1 SV=2 Back     alignment and function description
>sp|Q8C460|ERI3_MOUSE ERI1 exoribonuclease 3 OS=Mus musculus GN=Eri3 PE=1 SV=1 Back     alignment and function description
>sp|Q502M8|ERI2_DANRE ERI1 exoribonuclease 2 OS=Danio rerio GN=eri2 PE=2 SV=1 Back     alignment and function description
>sp|Q8IV48|ERI1_HUMAN 3'-5' exoribonuclease 1 OS=Homo sapiens GN=ERI1 PE=1 SV=3 Back     alignment and function description
>sp|Q7TMF2|ERI1_MOUSE 3'-5' exoribonuclease 1 OS=Mus musculus GN=Eri1 PE=1 SV=2 Back     alignment and function description
>sp|Q5FVR4|ERI1_RAT 3'-5' exoribonuclease 1 OS=Rattus norvegicus GN=Eri1 PE=2 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 ?
Query277
296087843 520 unnamed protein product [Vitis vinifera] 0.981 0.523 0.65 1e-102
359487133 415 PREDICTED: uncharacterized protein LOC10 0.981 0.655 0.65 1e-102
255578253 409 conserved hypothetical protein [Ricinus 0.992 0.672 0.647 1e-100
357515343 415 ERI1 exoribonuclease [Medicago truncatul 0.974 0.650 0.628 1e-100
356556782 414 PREDICTED: uncharacterized protein LOC10 0.981 0.657 0.620 1e-100
356548831 414 PREDICTED: uncharacterized protein LOC10 0.974 0.652 0.612 2e-99
449458085 414 PREDICTED: 3'-5' exoribonuclease 1-like 0.967 0.647 0.612 1e-97
118489625 409 unknown [Populus trichocarpa x Populus d 0.989 0.669 0.631 2e-97
224057242 409 predicted protein [Populus trichocarpa] 0.989 0.669 0.631 5e-97
225435848 425 PREDICTED: uncharacterized protein LOC10 0.992 0.647 0.593 1e-95
>gi|296087843|emb|CBI35099.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
 Score =  376 bits (965), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 182/280 (65%), Positives = 216/280 (77%), Gaps = 8/280 (2%)

Query: 1   FEYYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCK 60
           F+Y+VVIDFEATCDK +N HPQEIIEFPSV+VS V+G++ ACFQTYVRPT   +L+DFCK
Sbjct: 243 FQYFVVIDFEATCDKGKNPHPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQILSDFCK 302

Query: 61  ELTGIQQHQVDNGITLGEALYFHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKI 120
           +LTGIQQ QVD G+TL EAL  HDKWL + G+ NTNF+VVTWS+WDC+VMLESECR KKI
Sbjct: 303 DLTGIQQIQVDRGVTLSEALLRHDKWLEKKGIKNTNFAVVTWSNWDCRVMLESECRFKKI 362

Query: 121 QKPAYFNQWINLRVPFSKVFGDVRCNLKEAVELAGLIWQGRVHCGLDDAINIARLLSVIM 180
           +KP YFN+WINL+VPF +VFG V CNLKEAVE+AGL WQGR HCGLDDA N ARLL+ +M
Sbjct: 363 RKPPYFNRWINLKVPFREVFGGVWCNLKEAVEMAGLAWQGRAHCGLDDAKNTARLLAFLM 422

Query: 181 RRGFKFSITKSLTPQANPNCLTWNRHHFLEPQAMYTP-----PHTSLIHEFEDCRYCYCG 235
            RGFKFSIT SL  QA  +  +W +   L     Y P     P   L H      YCYCG
Sbjct: 423 HRGFKFSITNSLMWQATDHPESWKQSPELSSFPEYHPQKLREPTIPLFHYHP---YCYCG 479

Query: 236 AKSIKKVIQRPGPKRGSFFFGCGNWTPNRGACCNYFQWAT 275
            KS K ++++PGPK+GSFFFGCGNWT  RGA C+YF+WA+
Sbjct: 480 VKSSKGMVRKPGPKQGSFFFGCGNWTAARGARCHYFEWAS 519

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|359487133|ref|XP_003633521.1| PREDICTED: uncharacterized protein LOC100853630 [Vitis vinifera] Back     alignment and taxonomy information
>gi|255578253|ref|XP_002529994.1| conserved hypothetical protein [Ricinus communis] gi|223530517|gb|EEF32399.1| conserved hypothetical protein [Ricinus communis] Back     alignment and taxonomy information
>gi|357515343|ref|XP_003627960.1| ERI1 exoribonuclease [Medicago truncatula] gi|355521982|gb|AET02436.1| ERI1 exoribonuclease [Medicago truncatula] gi|388515457|gb|AFK45790.1| unknown [Medicago truncatula] Back     alignment and taxonomy information
>gi|356556782|ref|XP_003546701.1| PREDICTED: uncharacterized protein LOC100780340 [Glycine max] Back     alignment and taxonomy information
>gi|356548831|ref|XP_003542802.1| PREDICTED: uncharacterized protein LOC100811151 [Glycine max] Back     alignment and taxonomy information
>gi|449458085|ref|XP_004146778.1| PREDICTED: 3'-5' exoribonuclease 1-like [Cucumis sativus] gi|449511572|ref|XP_004163993.1| PREDICTED: 3'-5' exoribonuclease 1-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|118489625|gb|ABK96614.1| unknown [Populus trichocarpa x Populus deltoides] Back     alignment and taxonomy information
>gi|224057242|ref|XP_002299190.1| predicted protein [Populus trichocarpa] gi|222846448|gb|EEE83995.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|225435848|ref|XP_002262814.1| PREDICTED: uncharacterized protein LOC100263388 [Vitis vinifera] 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 ?
Query277
UNIPROTKB|A8K979 691 ERI2 "ERI1 exoribonuclease 2" 0.624 0.250 0.391 3.2e-35
UNIPROTKB|F1P8R6 658 ERI2 "Uncharacterized protein" 0.617 0.259 0.385 6.4e-34
MGI|MGI:1918401 688 Eri2 "exoribonuclease 2" [Mus 0.685 0.276 0.371 1.3e-33
UNIPROTKB|E1BJE4 689 ERI2 "Uncharacterized protein" 0.685 0.275 0.366 9.2e-33
UNIPROTKB|A6QLH5337 ERI3 "ERI1 exoribonuclease 3" 0.667 0.548 0.425 1.4e-32
UNIPROTKB|O43414337 ERI3 "ERI1 exoribonuclease 3" 0.667 0.548 0.425 1.4e-32
MGI|MGI:2153887337 Eri3 "exoribonuclease 3" [Mus 0.667 0.548 0.425 1.8e-32
UNIPROTKB|E2RAN5337 ERI3 "Uncharacterized protein" 0.667 0.548 0.420 3.7e-32
RGD|1583889 687 Eri2 "ERI1 exoribonuclease fam 0.685 0.276 0.361 8e-32
WB|WBGene00019724266 M02B7.2 [Caenorhabditis elegan 0.689 0.718 0.4 1.6e-31
UNIPROTKB|A8K979 ERI2 "ERI1 exoribonuclease 2" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
 Score = 310 (114.2 bits), Expect = 3.2e-35, Sum P(2) = 3.2e-35
 Identities = 74/189 (39%), Positives = 102/189 (53%)

Query:    20 HPQEIIEFPXXXXXXXXXEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEA 79
             H QEIIEFP         +I + FQ YV+P   P+L++FC ELTGI+Q QVD G+ L   
Sbjct:    54 HSQEIIEFPAVLLNTSTGQIDSEFQAYVQPQEHPILSEFCMELTGIKQAQVDEGVPLKIC 113

Query:    80 LYFHDKWL--LQM--------GLNNTNFS------VVTWSDWDCQVMLESECRIKKIQKP 123
             L    KW+  +Q         G++  + S       VTWSDWD  V LE EC+ K++ KP
Sbjct:   114 LSQFCKWIHKIQQQKNIIFATGISEPSASEVKLCAFVTWSDWDLGVCLEYECKRKQLLKP 173

Query:   124 AYFNQWINLRVPFSKVFGDVRCNLKEAVELAGLIWQGRVHCGLDDAINIARLLSVIMRRG 183
              + N WI+LR  +   +      L  A++  G+ + GR H GLDD+ N A L   ++R G
Sbjct:   174 VFLNSWIDLRATYKLFYRRKPKGLSGALQEVGIEFSGREHSGLDDSRNTALLAWKMIRDG 233

Query:   184 FKFSITKSL 192
                 IT+SL
Sbjct:   234 CVMKITRSL 242
GO:0003676 "nucleic acid binding" evidence=IEA
GO:0005622 "intracellular" evidence=IEA
GO:0008270 "zinc ion binding" evidence=IEA
GO:0004527 "exonuclease activity" evidence=IEA
UNIPROTKB|F1P8R6 ERI2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
MGI|MGI:1918401 Eri2 "exoribonuclease 2" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|E1BJE4 ERI2 "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|A6QLH5 ERI3 "ERI1 exoribonuclease 3" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|O43414 ERI3 "ERI1 exoribonuclease 3" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
MGI|MGI:2153887 Eri3 "exoribonuclease 3" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|E2RAN5 ERI3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
RGD|1583889 Eri2 "ERI1 exoribonuclease family member 2" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
WB|WBGene00019724 M02B7.2 [Caenorhabditis elegans (taxid:6239)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

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

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
GSVIVG00002005001
SubName- Full=Chromosome undetermined scaffold_125, whole genome shotgun sequence; (282 aa)
(Vitis vinifera)
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 ?
Query277
cd06133176 cd06133, ERI-1_3'hExo_like, DEDDh 3'-5' exonucleas 7e-63
PTZ00315 582 PTZ00315, PTZ00315, 2'-phosphotransferase; Provisi 4e-41
COG5018210 COG5018, KapD, Inhibitor of the KinA pathway to sp 4e-32
PRK07748207 PRK07748, PRK07748, sporulation inhibitor KapD; Pr 3e-27
smart00479169 smart00479, EXOIII, exonuclease domain in DNA-poly 2e-25
pfam00929161 pfam00929, RNase_T, Exonuclease 3e-19
PRK00448 1437 PRK00448, polC, DNA polymerase III PolC; Validated 5e-10
cd06127159 cd06127, DEDDh, DEDDh 3'-5' exonuclease domain fam 2e-09
TIGR01405 1213 TIGR01405, polC_Gram_pos, DNA polymerase III, alph 2e-09
COG2176 1444 COG2176, PolC, DNA polymerase III, alpha subunit ( 1e-08
PRK08074 928 PRK08074, PRK08074, bifunctional ATP-dependent DNA 9e-07
TIGR01407 850 TIGR01407, dinG_rel, DnaQ family exonuclease/DinG 3e-06
PRK06722281 PRK06722, PRK06722, exonuclease; Provisional 2e-05
PRK07246 820 PRK07246, PRK07246, bifunctional ATP-dependent DNA 2e-04
pfam0683945 pfam06839, zf-GRF, GRF zinc finger 3e-04
PRK06807313 PRK06807, PRK06807, DNA polymerase III subunit eps 0.002
>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 
 Score =  195 bits (497), Expect = 7e-63
 Identities = 80/176 (45%), Positives = 110/176 (62%), Gaps = 7/176 (3%)

Query: 4   YVVIDFEATC--DKERNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKE 61
           Y+VIDFEATC     +  +P EIIE  +V+V   + EII  F +YV+P   P L+DFC E
Sbjct: 1   YLVIDFEATCWEGNSKPDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTE 60

Query: 62  LTGIQQHQVDNGITLGEALYFHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQ 121
           LTGI Q  VDN  +  E L    +WL +    N  ++ VTW DWD + +L+++C+ K I 
Sbjct: 61  LTGITQEDVDNAPSFPEVLKEFLEWLGK----NGKYAFVTWGDWDLKDLLQNQCKYKIIN 116

Query: 122 KPAYFNQWINLRVPFSKVFGDV-RCNLKEAVELAGLIWQGRVHCGLDDAINIARLL 176
            P +F QWI+L+  F+K +G   R  L +A+E  GL ++GR H GLDDA NIAR+L
Sbjct: 117 LPPFFRQWIDLKKEFAKFYGLKKRTGLSKALEYLGLEFEGRHHRGLDDARNIARIL 172

This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These 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. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional homolog of either ERI-1 or 3'hExo. Length = 176
>gnl|CDD|240356 PTZ00315, PTZ00315, 2'-phosphotransferase; Provisional Back     alignment and domain information
>gnl|CDD|227351 COG5018, KapD, Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only] Back     alignment and domain information
>gnl|CDD|236087 PRK07748, PRK07748, sporulation inhibitor KapD; Provisional 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|216200 pfam00929, RNase_T, Exonuclease Back     alignment and domain information
>gnl|CDD|234767 PRK00448, polC, DNA polymerase III PolC; Validated Back     alignment and domain information
>gnl|CDD|176648 cd06127, DEDDh, DEDDh 3'-5' exonuclease domain family 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|225087 COG2176, PolC, DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair] 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|233398 TIGR01407, dinG_rel, DnaQ family exonuclease/DinG family helicase, putative Back     alignment and domain information
>gnl|CDD|180670 PRK06722, PRK06722, exonuclease; Provisional 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|219199 pfam06839, zf-GRF, GRF zinc finger Back     alignment and domain information
>gnl|CDD|235864 PRK06807, PRK06807, DNA polymerase III subunit epsilon; 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 277
KOG0542280 consensus Predicted exonuclease [Replication, reco 100.0
PTZ00315 582 2'-phosphotransferase; Provisional 100.0
PRK07748207 sporulation inhibitor KapD; Provisional 100.0
PRK06722281 exonuclease; Provisional 100.0
cd06133176 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain o 100.0
TIGR01406225 dnaQ_proteo DNA polymerase III, epsilon subunit, P 100.0
PRK05711240 DNA polymerase III subunit epsilon; Provisional 100.0
smart00479169 EXOIII exonuclease domain in DNA-polymerase alpha 100.0
cd06131167 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonucl 100.0
PRK06807313 DNA polymerase III subunit epsilon; Validated 100.0
PRK06195309 DNA polymerase III subunit epsilon; Validated 99.98
cd06130156 DNA_pol_III_epsilon_like an uncharacterized bacter 99.98
PRK08517257 DNA polymerase III subunit epsilon; Provisional 99.98
COG5018210 KapD Inhibitor of the KinA pathway to sporulation, 99.97
PRK07740244 hypothetical protein; Provisional 99.97
PRK09145202 DNA polymerase III subunit epsilon; Validated 99.97
PRK06310250 DNA polymerase III subunit epsilon; Validated 99.97
PRK06063313 DNA polymerase III subunit epsilon; Provisional 99.97
TIGR00573217 dnaq exonuclease, DNA polymerase III, epsilon subu 99.97
PRK09146239 DNA polymerase III subunit epsilon; Validated 99.97
PRK07247195 DNA polymerase III subunit epsilon; Validated 99.97
PRK07942232 DNA polymerase III subunit epsilon; Provisional 99.97
PRK05168211 ribonuclease T; Provisional 99.97
cd06134189 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. 99.97
cd06136177 TREX1_2 DEDDh 3'-5' exonuclease domain of three pr 99.97
PRK06309232 DNA polymerase III subunit epsilon; Validated 99.97
TIGR01298200 RNaseT ribonuclease T. in gamma-subdivision Proteo 99.96
PRK07883 557 hypothetical protein; Validated 99.96
PRK07246 820 bifunctional ATP-dependent DNA helicase/DNA polyme 99.96
PRK05601377 DNA polymerase III subunit epsilon; Validated 99.96
COG2176 1444 PolC DNA polymerase III, alpha subunit (gram-posit 99.96
cd06138183 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain o 99.95
PRK08074 928 bifunctional ATP-dependent DNA helicase/DNA polyme 99.95
TIGR01405 1213 polC_Gram_pos DNA polymerase III, alpha chain, Gra 99.95
TIGR01407 850 dinG_rel DnaQ family exonuclease/DinG family helic 99.95
cd06127159 DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh 99.95
PRK07983219 exodeoxyribonuclease X; Provisional 99.95
cd06137161 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the 99.94
cd06135173 Orn DEDDh 3'-5' exonuclease domain of oligoribonuc 99.93
cd06144152 REX4_like DEDDh 3'-5' exonuclease domain of RNA ex 99.93
COG0847243 DnaQ DNA polymerase III, epsilon subunit and relat 99.93
PF00929164 RNase_T: Exonuclease; InterPro: IPR013520 This ent 99.93
cd06145150 REX1_like DEDDh 3'-5' exonuclease domain of RNA ex 99.93
cd06149157 ISG20 DEDDh 3'-5' exonuclease domain of Interferon 99.92
PRK09182294 DNA polymerase III subunit epsilon; Validated 99.92
PRK00448 1437 polC DNA polymerase III PolC; Validated 99.92
PRK05359181 oligoribonuclease; Provisional 99.91
PRK11779 476 sbcB exonuclease I; Provisional 99.9
KOG2249280 consensus 3'-5' exonuclease [Replication, recombin 99.55
PF0683945 zf-GRF: GRF zinc finger; InterPro: IPR010666 Zinc 99.47
cd06143174 PAN2_exo DEDDh 3'-5' exonuclease domain of the euk 99.33
cd05160199 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain 99.17
PHA02570220 dexA exonuclease; Provisional 99.14
COG2925 475 SbcB Exonuclease I [DNA replication, recombination 99.05
COG1949184 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA 99.03
KOG3242208 consensus Oligoribonuclease (3'->5' exoribonucleas 98.97
cd0612596 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonucleas 98.91
KOG2248380 consensus 3'-5' exonuclease [Replication, recombin 98.82
cd05781188 DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of 98.63
cd05780195 DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease dom 98.59
cd05782208 DNA_polB_like1_exo Uncharacterized bacterial subgr 98.51
PF13482164 RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A 98.42
KOG1956758 consensus DNA topoisomerase III alpha [Replication 98.42
PF04857262 CAF1: CAF1 family ribonuclease; InterPro: IPR00694 98.35
KOG0304239 consensus mRNA deadenylase subunit [RNA processing 98.29
PF10108209 DNA_pol_B_exo2: Predicted 3'-5' exonuclease relate 98.28
cd06139193 DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease 98.11
cd05779204 DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domai 98.11
PRK05755 880 DNA polymerase I; Provisional 97.9
cd05785207 DNA_polB_like2_exo Uncharacterized bacterial subgr 97.87
TIGR03491457 RecB family nuclease, putative, TM0106 family. Mem 97.57
cd05783204 DNA_polB_B1_exo DEDDy 3'-5' exonuclease domain of 97.56
cd05777230 DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain 97.49
KOG4793318 consensus Three prime repair exonuclease [Replicat 97.37
COG3359278 Predicted exonuclease [DNA replication, recombinat 97.2
cd05784193 DNA_polB_II_exo DEDDy 3'-5' exonuclease domain of 96.95
smart00486 471 POLBc DNA polymerase type-B family. DNA polymerase 96.85
cd05778231 DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease 96.68
PTZ00166 1054 DNA polymerase delta catalytic subunit; Provisiona 96.53
PRK05762 786 DNA polymerase II; Reviewed 95.98
PF03104325 DNA_pol_B_exo1: DNA polymerase family B, exonuclea 95.85
PF01612176 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR00 95.71
PF13017213 Maelstrom: piRNA pathway germ-plasm component 95.49
cd05776234 DNA_polB_alpha_exo inactive DEDDy 3'-5' exonucleas 94.9
COG5228299 POP2 mRNA deadenylase subunit [RNA processing and 94.89
COG0349 361 Rnd Ribonuclease D [Translation, ribosomal structu 94.57
KOG1798 2173 consensus DNA polymerase epsilon, catalytic subuni 94.43
TIGR00592 1172 pol2 DNA polymerase (pol2). This family is based o 93.88
KOG4793318 consensus Three prime repair exonuclease [Replicat 93.83
cd00007155 35EXOc 3'-5' exonuclease. The 35EXOc domain is res 93.21
cd06146193 mut-7_like_exo DEDDy 3'-5' exonuclease domain of C 93.2
PHA02528 881 43 DNA polymerase; Provisional 92.94
KOG12751118 consensus PAB-dependent poly(A) ribonuclease, subu 92.47
TIGR01388 367 rnd ribonuclease D. This model describes ribonucle 90.97
cd06141170 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and 90.47
COG0417 792 PolB DNA polymerase elongation subunit (family B) 90.15
PHA03036 1004 DNA polymerase; Provisional 88.8
PRK05761 787 DNA polymerase I; Reviewed 87.99
smart00474172 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proo 87.32
PHA02524498 43A DNA polymerase subunit A; Provisional 87.1
>KOG0542 consensus Predicted exonuclease [Replication, recombination and repair] Back     alignment and domain information 
Probab=100.00  E-value=5e-43  Score=303.64  Aligned_cols=192  Identities=42%  Similarity=0.764  Sum_probs=177.9

Q ss_pred             CCeEEEEEEccCCCCCCC-CCCCcEEEEceEEEECC-CCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHH
Q 036883            1 FEYYVVIDFEATCDKERN-LHPQEIIEFPSVVVSGV-SGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGE   78 (277)
Q Consensus         1 f~~~vviDlETTg~~~~~-~~~~eIIEIgAV~vd~~-~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~e   78 (277)
                      |+++++||||+||.++.. .+.+||||+.||.+|.. ++.|.++|+.||||..+|.++++|+++|||.|++|+.||+|.+
T Consensus        55 fdYLliiDFEaTC~e~~~~~~~~EIIEfP~V~l~~~~~~~Ie~eF~qYVrP~~np~LS~fC~~lTgI~Q~tVD~a~~f~~  134 (280)
T KOG0542|consen   55 FDYLLILDFEATCEEGNKPHYVQEIIEFPAVLLDNTETSIIEDEFHQYVRPVENPRLSDFCTSLTGIQQETVDEAPTFPQ  134 (280)
T ss_pred             cceEEEEeeeeeccccCCCCcchheeecceeEeeccchhhHHHHHHhhcCcccCchHHHHHHHhhCchHhhhccCCCHHH
Confidence            799999999999998766 46899999999966544 4555569999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhhcCCC--CCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCC-CCCCHHHHHHHhC
Q 036883           79 ALYFHDKWLLQMGLN--NTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGD-VRCNLKEAVELAG  155 (277)
Q Consensus        79 vl~~f~~fl~~~~l~--~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~-~~~~L~~l~~~~g  155 (277)
                      |+.+|..||....+.  ++++++|+||+|||+.||..+|.+.+|..|.|+++|||+++.|+..+.. .+.++..|++++|
T Consensus       135 vl~~f~~Wlr~~~~~~k~~~~Afvtdg~wDl~~~l~~qck~~~i~~P~~f~qwInirk~yk~~y~~~~~t~it~mLe~~g  214 (280)
T KOG0542|consen  135 VLSEFDSWLRKDSLGDKNGKFAFVTDGDWDLWVFLQYQCKLKNIRIPAFFNQWINIRKIYKNFYNRPAPTNITGMLEHYG  214 (280)
T ss_pred             HHHHHHHHHHHhhcccccCceEEEeCchhhHHHHHHHHHHHhcCCCcHHHHHHhHHHHHHHHHhcCccccCHHHHHHHhC
Confidence            999999999887664  3789999999999999999999999999999999999999999999987 5789999999999


Q ss_pred             CCCCCCCCchHHHHHHHHHHHHHHHHhcCccCcCccc
Q 036883          156 LIWQGRVHCGLDDAINIARLLSVIMRRGFKFSITKSL  192 (277)
Q Consensus       156 i~~~~~~H~Al~DA~~ta~l~~~l~~~g~~~~i~~~l  192 (277)
                      |+++|++|+++|||+++|.|..+|++.|..+.||+.-
T Consensus       215 L~f~Gr~HsGiDDa~Nia~I~~kM~~dg~~~~In~~~  251 (280)
T KOG0542|consen  215 LQFEGRAHSGIDDARNIARIAQKMIRDGAEFRINELC  251 (280)
T ss_pred             CcccCCcccCchhHHHHHHHHHHHHhCCcEEEechhh
Confidence            9999999999999999999999999999999999663

>PTZ00315 2'-phosphotransferase; Provisional Back     alignment and domain information
>PRK07748 sporulation inhibitor KapD; Provisional Back     alignment and domain information
>PRK06722 exonuclease; 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
>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
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases 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
>PRK06807 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK06195 DNA polymerase III subunit epsilon; Validated 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
>PRK08517 DNA polymerase III subunit epsilon; Provisional 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
>PRK07740 hypothetical protein; Provisional Back     alignment and domain information
>PRK09145 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK06310 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK06063 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family Back     alignment and domain information
>PRK09146 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK07247 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK07942 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>PRK05168 ribonuclease T; Provisional Back     alignment and domain information
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T 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
>PRK06309 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>TIGR01298 RNaseT ribonuclease T 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
>PRK05601 DNA polymerase III subunit epsilon; Validated 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
>cd06138 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins Back     alignment and domain information
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated 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
>cd06127 DEDDh DEDDh 3'-5' exonuclease domain family Back     alignment and domain information
>PRK07983 exodeoxyribonuclease X; Provisional 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
>cd06135 Orn DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar 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
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair] 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
>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic 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
>PRK09182 DNA polymerase III subunit epsilon; Validated 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
>PRK11779 sbcB exonuclease I; Provisional Back     alignment and domain information
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair] Back     alignment and domain information
>PF06839 zf-GRF: GRF zinc finger; InterPro: IPR010666 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule Back     alignment and domain information
>cd06143 PAN2_exo DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2 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
>PHA02570 dexA exonuclease; Provisional Back     alignment and domain information
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair] Back     alignment and domain information
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification] Back     alignment and domain information
>KOG3242 consensus Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification] Back     alignment and domain information
>cd06125 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily Back     alignment and domain information
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair] 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
>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
>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
>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
>KOG1956 consensus DNA topoisomerase III alpha [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
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification] 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
>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
>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
>PRK05755 DNA polymerase I; Provisional 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
>TIGR03491 RecB family nuclease, putative, TM0106 family 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
>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
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair] Back     alignment and domain information
>COG3359 Predicted exonuclease [DNA 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
>smart00486 POLBc DNA polymerase type-B family 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
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional Back     alignment and domain information
>PRK05762 DNA polymerase II; 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
>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
>PF13017 Maelstrom: piRNA pathway germ-plasm component 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
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification] Back     alignment and domain information
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis] 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
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair] Back     alignment and domain information
>cd00007 35EXOc 3'-5' exonuclease 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
>PHA02528 43 DNA polymerase; Provisional Back     alignment and domain information
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair] Back     alignment and domain information
>TIGR01388 rnd ribonuclease D Back     alignment and domain information
>cd06141 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and similar proteins Back     alignment and domain information
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair] Back     alignment and domain information
>PHA03036 DNA polymerase; Provisional Back     alignment and domain information
>PRK05761 DNA polymerase I; Reviewed Back     alignment and domain information
>smart00474 35EXOc 3'-5' exonuclease Back     alignment and domain information
>PHA02524 43A DNA polymerase subunit A; Provisional Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query277
2xri_A224 Crystal Structure Of Human Eri1 Exoribonuclease 3 L 4e-33
4hxh_B303 Structure Of Mrna Stem-loop, Human Stem-loop Bindin 2e-26
1w0h_A204 Crystallographic Structure Of The Nuclease Domain O 4e-26
1zbh_A299 3'-End Specific Recognition Of Histone Mrna Stem-Lo 9e-26
1zbu_A349 Crystal Structure Of Full-Length 3'-Exonuclease Len 1e-25
3cg7_A308 Crystal Structure Of Cell-Death Related Nuclease 4 9e-20
>pdb|2XRI|A Chain A, Crystal Structure Of Human Eri1 Exoribonuclease 3 Length = 224 Back     alignment and structure 
Iteration: 1

 Score =  138 bits (347), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 78/195 (40%), Positives = 108/195 (55%), Gaps = 10/195 (5%)
Query: 1   FEYYVVIDFEATCDKERNLHPQEIIEFPXXXXXXXXXEIIACFQTYVRPTFEPLLTDFCK 60
           + Y++V+DFEATCDK + +HPQEIIEFP         EI + F  YV+P   P LT FC 
Sbjct: 30  YHYFLVLDFEATCDKPQ-IHPQEIIEFPILKLNGRTMEIESTFHMYVQPVVHPQLTPFCT 88
Query: 61  ELTGIQQHQVDNGITLGEALYFHDKWLLQMGLNNTNFS--VVTWSDWDCQVMLESECRIK 118
           ELTGI Q  VD   +L + L   D+W+ + GL + N     VT  DWD +VML  +C+  
Sbjct: 89  ELTGIIQAMVDGQPSLQQVLERVDEWMAKEGLLDPNVKSIFVTCGDWDLKVMLPGQCQYL 148
Query: 119 KIQKPAYFNQWINLRVPFSKVFG----DVRCNLKEAVELAGLIWQGRVHCGLDDAINIAR 174
            +    YF QWINL+  +S   G    +   ++ + + L  +   GR H G+DD  NIA 
Sbjct: 149 GLPVADYFKQWINLKKAYSFAMGCWPKNGLLDMNKGLSLQHI---GRPHSGIDDCKNIAN 205
Query: 175 LLSVIMRRGFKFSIT 189
           ++  +  RGF F  T
Sbjct: 206 IMKTLAYRGFIFKQT 220
>pdb|4HXH|B Chain B, Structure Of Mrna Stem-loop, Human Stem-loop Binding Protein And 3'hexo Ternary Complex Length = 303 Back     alignment and structure
>pdb|1W0H|A Chain A, Crystallographic Structure Of The Nuclease Domain Of 3'hexo, A Deddh Family Member, Bound To Ramp Length = 204 Back     alignment and structure
>pdb|1ZBH|A Chain A, 3'-End Specific Recognition Of Histone Mrna Stem-Loop By 3'- Exonuclease Length = 299 Back     alignment and structure
>pdb|1ZBU|A Chain A, Crystal Structure Of Full-Length 3'-Exonuclease Length = 349 Back     alignment and structure
>pdb|3CG7|A Chain A, Crystal Structure Of Cell-Death Related Nuclease 4 (Crn-4) Length = 308 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query277
1zbh_A299 3'-5' exonuclease ERI1; histone mRNA 3'-END-specif 2e-70
1zbu_A349 ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; 7e-70
2xri_A224 ERI1 exoribonuclease 3; hydrolase, metal binding; 3e-69
1w0h_A204 3'-5' exonuclease ERI1; nuclease domain, hydrolase 1e-68
3cg7_A308 CRN-4, cell death-related nuclease 4; hydrolase, a 2e-68
2p1j_A186 POLIII, DNA polymerase III POLC-type; structural g 2e-06
>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
 Score =  218 bits (556), Expect = 2e-70
 Identities = 66/204 (32%), Positives = 105/204 (51%), Gaps = 4/204 (1%)

Query: 1   FEYYVVIDFEATCDKERN-LHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFC 59
           ++Y  +IDFEATC++        EIIEFP V+++  + EI   FQ YVRP     L+DFC
Sbjct: 77  YDYICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFC 136

Query: 60  KELTGIQQHQVDNGITLGEALYFHDKWLLQMGL-NNTNFSVVTWSDWDCQVMLESECRIK 118
             LTGI Q QVD   T  + L      +    L     +S++T   WD    L  +C++ 
Sbjct: 137 ISLTGITQDQVDRADTFPQVLKKVIDLMKLKELGTKYKYSLLTDGSWDMSKFLNIQCQLS 196

Query: 119 KIQKPAYFNQWINLRVPFSKVFGDVR--CNLKEAVELAGLIWQGRVHCGLDDAINIARLL 176
           +++ P +  +WIN+R  +   +   R    L   +E  G+ + GR +CGLDD+ NIAR+ 
Sbjct: 197 RLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTIMLEKLGMDYDGRPNCGLDDSKNIARIA 256

Query: 177 SVIMRRGFKFSITKSLTPQANPNC 200
             +++ G +  I + +      + 
Sbjct: 257 VRMLQDGCELRINEKMHAGQLMSV 280
>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
>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
>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 ?
Query277
3cg7_A308 CRN-4, cell death-related nuclease 4; hydrolase, a 100.0
1w0h_A204 3'-5' exonuclease ERI1; nuclease domain, hydrolase 100.0
1zbh_A299 3'-5' exonuclease ERI1; histone mRNA 3'-END-specif 100.0
2xri_A224 ERI1 exoribonuclease 3; hydrolase, metal binding; 100.0
1zbu_A349 ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; 100.0
2gui_A194 DNA polymerase III epsilon subunit; DNA polymerase 100.0
2p1j_A186 POLIII, DNA polymerase III POLC-type; structural g 100.0
3mxm_B242 Three prime repair exonuclease 1; RNAse H-like fol 99.98
2f96_A224 Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolas 99.97
3u3y_B314 Three prime repair exonuclease 1; RNAse H fold, 3' 99.97
1y97_A238 Three prime repair exonuclease 2; TREX2, hydrolase 99.97
3v9w_A235 Ribonuclease T; DEDD nucleases family, EXO-nucleas 99.97
2igi_A180 Oligoribonuclease; RNAse, exoribonuclease, exonucl 99.95
1wlj_A189 Interferon stimulated gene 20KDA; exoribonuclease, 99.94
2qxf_A 482 Exodeoxyribonuclease I; alpha-beta domain, DNAQ su 99.94
2gbz_A194 Oligoribonuclease; ORN, deddh, structural genomics 99.94
3tr8_A186 Oligoribonuclease; transcription, hydrolase; 2.50A 99.93
4hec_A190 Putative uncharacterized protein; ssgcid, structur 99.04
4gmj_B285 CCR4-NOT transcription complex subunit 7; mRNA dec 98.84
2kfn_A 605 Klenow fragment of DNA polymerase I; complex (poly 98.58
2d5r_A252 CCR4-NOT transcription complex subunit 7; poly(A) 98.57
2p51_A333 SPCC18.06C protein; DEDD nuclease fold, hydrolase, 98.51
1uoc_A289 POP2; hydrolase, DEDD nuclease, mRNA degradation, 98.46
1qht_A 775 Protein (DNA polymerase); archaea, hyperthermostab 98.09
1x9m_A 698 DNA polymerase; DNA ploymerase, N-2-acetylaminoflu 98.07
3iay_A 919 DNA polymerase delta catalytic subunit; protein-DN 97.62
1s5j_A 847 DNA polymerase I; replication, disulfide bonds, tr 97.58
3d45_A507 Poly(A)-specific ribonuclease PARN; CAP analogue, 97.5
2gv9_A 1193 DNA polymerase; polymerase alpha fold, transferase 97.48
1noy_A388 Protein (DNA polymerase (E.C.2.7.7.7)); exonucleas 97.37
4dfk_A 540 DNA polymerase I, thermostable; DNA polymerase, tr 96.04
3qex_A 903 DNA polymerase, GP43; difluorotoluene nucleoside; 96.03
3k59_A 786 POL II, DNA polymerase II; protein-DNA complex, DN 95.16
2a1r_A430 Poly(A)-specific ribonuclease PARN; DEDD, nuclease 92.72
3saf_A428 Exosome component 10; exoribonuclease, RNA exosome 91.67
1vk0_A206 Hypothetical protein; homohexamer, AT5G06450, stru 87.35
1yt3_A 375 Ribonuclease D, RNAse D; exoribonuclease, exonucle 84.19
3pv8_A 592 DNA polymerase I; DNA polymerase I, protein-DNA co 82.05
>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
Probab=100.00  E-value=4.5e-42  Score=314.53  Aligned_cols=246  Identities=26%  Similarity=0.359  Sum_probs=196.9

Q ss_pred             CCeEEEEEEccCCCCCCCCCCCcEEEEceEEEECCCCEEEe--EEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHH
Q 036883            1 FEYYVVIDFEATCDKERNLHPQEIIEFPSVVVSGVSGEIIA--CFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGE   78 (277)
Q Consensus         1 f~~~vviDlETTg~~~~~~~~~eIIEIgAV~vd~~~g~i~~--~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~e   78 (277)
                      |++|||||+||||++.....+.||||||||++|.++|++++  +|++||||...+.|+++++++||||++||++||+|++
T Consensus        18 ~~~~vviD~ETTGl~~~~d~~~eIIEIgaV~vd~~~g~i~~~~~f~~lV~P~~~p~i~~~~~~ltGIt~e~v~~ap~~~e   97 (308)
T 3cg7_A           18 FDTLLILDFETTSDAANQDYPCEVIQFAIVAYDVPNDKIREDISFNKYVKPVLNRTLTKNCVDFTGIPQRSIDTADTFDV   97 (308)
T ss_dssp             CSEEEEEEEEECCBTTBCSCCCCEEEEEEEEEETTTTEEEEEEEEEEECBCSSBCSCCHHHHHHHCCCHHHHHTSCBHHH
T ss_pred             CCeEEEEEeecCCCCCCCCCCCCeEEEEEEEEEcCCCEEeeccceeeEECCCCCCCCCHHHHHHcCCCHHHHhcCCCHHH
Confidence            57899999999997532112359999999999977899988  9999999986445999999999999999999999999


Q ss_pred             HHHHHHHHHhhcCCCCCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCCC-------CCCHHHHH
Q 036883           79 ALYFHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGDV-------RCNLKEAV  151 (277)
Q Consensus        79 vl~~f~~fl~~~~l~~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~~-------~~~L~~l~  151 (277)
                      |+.+|.+||++..+++++.++|+||.||++.||+++|+++|++.|.++.+|+|++.+++.+++..       +++|++|+
T Consensus        98 vl~~f~~~l~~~~lvahn~~lv~~g~fD~~~fL~~~~~~~g~~~p~~~~~~iDt~~l~~~~~~~~~~~~~~~~~~L~~l~  177 (308)
T 3cg7_A           98 VYEQFQQWLITLGLEEGKFAFVCDSRQDLWRIAQYQMKLSNIQMPAFFRQYINLYKIFTNEMDRMGPKELSATTNIGKMN  177 (308)
T ss_dssp             HHHHHHHHHHHHCCCTTSEEEEESSSHHHHTHHHHHHHHTTCCCCGGGSEEEEHHHHHHHHHHHHCCCCCCCCSHHHHHH
T ss_pred             HHHHHHHHHHhCCcCCcceEEeccCcccHHHHHHHHHHHcCCCCchhhcceeeHHHHHHHHhccccccccccCcCHHHHH
Confidence            99999999999999999999999999997469999999999998876678999999988776531       47899999


Q ss_pred             HHhCCCCCCCCCchHHHHHHHHHHHHHHHHhcCccCcCcccccccCCCcccccccCC-CCCCC------CCCCCCCccc-
Q 036883          152 ELAGLIWQGRVHCGLDDAINIARLLSVIMRRGFKFSITKSLTPQANPNCLTWNRHHF-LEPQA------MYTPPHTSLI-  223 (277)
Q Consensus       152 ~~~gi~~~~~~H~Al~DA~~ta~l~~~l~~~g~~~~i~~~l~~~~~~~~~~~~~~~~-~~~~~------~~~~~~~~~~-  223 (277)
                      +++|++..+++|+|++||++||+||.+|++++..+++++.+.....++..+....+. .++.+      .+--+.++.. 
T Consensus       178 ~~~gi~~~~~~HrAl~DA~ata~l~~~l~~~~~~~~i~~~~~~s~~~~~~~~~~~~~w~~~~~~~~~~~~~~~p~~~~~~  257 (308)
T 3cg7_A          178 EYYDLPTIGRAHDAMDDCLNIATILQRMINMGAKVTVNELLTCCASWRRQPLVYNKEWRSSFMDAGKIFERVLPLVVTTI  257 (308)
T ss_dssp             HHTTCCCCSCTTCHHHHHHHHHHHHHHHHHTTCCCCCCEEEESCCGGGSSCCCCCTTGGGCHHHHHHHHHHHSSCEEEEC
T ss_pred             HHcCCCCCCCCcCHHHHHHHHHHHHHHHHHcCCCCChHHHHhhcCCccccccccCcccccchHHHHHHHHHhcccceeee
Confidence            999999987789999999999999999999999999999987665554444332110 01100      0001222222 


Q ss_pred             -----ccCCceeeeecCCccccceeccCCCCCC
Q 036883          224 -----HEFEDCRYCYCGAKSIKKVIQRPGPKRG  251 (277)
Q Consensus       224 -----~~~~~~~~c~c~~~~~~~~~~~~g~~~g  251 (277)
                           ..+++..+|+|+.....+     |+-|+
T Consensus       258 ~~~~~~~~~~~~~~~c~~~~~~~-----~~~~~  285 (308)
T 3cg7_A          258 RAGDFRLEMYGVCRYCRKGMDVC-----GTSHQ  285 (308)
T ss_dssp             CGGGCCGGGTTBCTTTCCBTTTT-----TSSCS
T ss_pred             eccccchhhcccCCcCCCccccc-----ccccC
Confidence                 125668899999998665     55555
>1w0h_A 3'-5' exonuclease ERI1; nuclease domain, hydrolase; HET: AMP; 1.59A {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
>1zbu_A ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; HET: AMP; 3.00A {Homo sapiens} 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* 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
>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
>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
>1y97_A Three prime repair exonuclease 2; TREX2, hydrolase; 2.50A {Homo sapiens} SCOP: c.55.3.5 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
>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
>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
>4hec_A Putative uncharacterized protein; ssgcid, structural genomics, SEA structural genomics center for infectious disease, unknown; 1.80A {Mycobacterium tuberculosis} 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
>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
>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
>2p51_A SPCC18.06C protein; DEDD nuclease fold, hydrolase, gene regulation; 1.40A {Schizosaccharomyces pombe} PDB: 3g0z_A 3g10_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
>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
>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
>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
>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
>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
>2gv9_A DNA polymerase; polymerase alpha fold, transferase; HET: DNA; 2.68A {Human herpesvirus 1} PDB: 1dml_B* 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
>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
>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
>2a1r_A Poly(A)-specific ribonuclease PARN; DEDD, nuclease domain, hydrolase-RNA complex; 2.60A {Homo sapiens} PDB: 2a1s_A 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
>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
>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
>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

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 277
d1w0ha_200 c.55.3.5 (A:) Exonuclease ERI1 {Human (Homo sapien 1e-33
d2f96a1202 c.55.3.5 (A:19-220) Ribonuclease T {Pseudomonas ae 4e-06
d2guia1174 c.55.3.5 (A:7-180) N-terminal exonuclease domain o 1e-05
d1y97a1228 c.55.3.5 (A:1-228) Three prime repair exonuclease 2e-05
d3b6oa1226 c.55.3.5 (A:9-234) Three prime repair exonuclease 2e-05
>d1w0ha_ c.55.3.5 (A:) Exonuclease ERI1 {Human (Homo sapiens) [TaxId: 9606]} Length = 200 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: Exonuclease ERI1
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  119 bits (298), Expect = 1e-33
 Identities = 68/196 (34%), Positives = 105/196 (53%), Gaps = 4/196 (2%)

Query: 1   FEYYVVIDFEATCDKE-RNLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFC 59
           ++Y  +IDFEATC++        EIIEFP V+++  + EI   FQ YVRP     L+DFC
Sbjct: 5   YDYICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFC 64

Query: 60  KELTGIQQHQVDNGITLGEALYFHDKWLLQMGLN-NTNFSVVTWSDWDCQVMLESECRIK 118
             LTGI Q QVD   T  + L     W+    L     +S++T   WD    L  +C++ 
Sbjct: 65  ISLTGITQDQVDRADTFPQVLKKVIDWMKLKELGTKYKYSLLTDGSWDMSKFLNIQCQLS 124

Query: 119 KIQKPAYFNQWINLRVPFSKVFGDVRCN--LKEAVELAGLIWQGRVHCGLDDAINIARLL 176
           +++ P +  +WIN+R  +   +   R    L   +E  G+ + GR HCGLDD+ NIAR+ 
Sbjct: 125 RLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTIMLEKLGMDYDGRPHCGLDDSKNIARIA 184

Query: 177 SVIMRRGFKFSITKSL 192
             +++ G +  I + +
Sbjct: 185 VRMLQDGCELRINEKM 200
>d2f96a1 c.55.3.5 (A:19-220) Ribonuclease T {Pseudomonas aeruginosa [TaxId: 287]} Length = 202 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
>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
>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 ?
Query277
d1w0ha_200 Exonuclease ERI1 {Human (Homo sapiens) [TaxId: 960 100.0
d2guia1174 N-terminal exonuclease domain of the epsilon subun 99.97
d3b6oa1226 Three prime repair exonuclease 1, TREX1 {Mouse (Mu 99.95
d1wlja_173 Interferon-stimulated gene 20 kDa protein, ISG20 { 99.94
d1y97a1228 Three prime repair exonuclease 2, TREX2 {Human (Ho 99.94
d2f96a1202 Ribonuclease T {Pseudomonas aeruginosa [TaxId: 287 99.89
d2qxfa1 467 Exonuclease I {Escherichia coli K12 (Escherichia c 99.87
d2igia1180 Oligoribonuclease {Escherichia coli [TaxId: 562]} 99.76
d2d5ra1252 CCR4-NOT transcription complex subunit 7, CAF1 {Hu 98.89
d1uoca_286 Pop2 RNase D domain {Baker's yeast (Saccharomyces 98.57
d1tgoa1347 Exonuclease domain of family B DNA polymerases {Ar 97.72
d1x9ma1204 Exonuclease domain of T7 DNA polymerase {Bacteriop 97.51
d1kfsa1195 Exonuclease domain of prokaryotic DNA polymerase { 96.82
d2hhva1171 Exonuclease domain of prokaryotic DNA polymerase { 96.09
d1yt3a3193 Ribonuclease D, catalytic domain {Escherichia coli 95.47
d1q8ia1388 Exonuclease domain of family B DNA polymerases {Es 94.22
d1s5ja1410 Exonuclease domain of family B DNA polymerases {Su 93.89
d2hbka2292 Exosome complex exonuclease RRP6 {Baker's yeast (S 91.09
d1vk0a_206 Hypothetical protein AT5G06450 {Thale-cress (Arabi 81.38
>d1w0ha_ c.55.3.5 (A:) Exonuclease ERI1 {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: Exonuclease ERI1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=5.8e-39  Score=271.69  Aligned_cols=192  Identities=35%  Similarity=0.673  Sum_probs=172.8

Q ss_pred             CCeEEEEEEccCCCCCC-CCCCCcEEEEceEEEECCCCEEEeEEEEeecCCCCCCCChhhHhHhCCChHHHhCCCCHHHH
Q 036883            1 FEYYVVIDFEATCDKER-NLHPQEIIEFPSVVVSGVSGEIIACFQTYVRPTFEPLLTDFCKELTGIQQHQVDNGITLGEA   79 (277)
Q Consensus         1 f~~~vviDlETTg~~~~-~~~~~eIIEIgAV~vd~~~g~i~~~f~~lVrP~~~~~i~~~~~~ltGIt~~~l~~ap~f~ev   79 (277)
                      |++|||||+||||.+|+ .+..++|||||||++|.+++++.++|+.+|+|.....+++.++++||||+++|.+++++.+|
T Consensus         5 ~~~~iv~D~EtT~~~~~~~~~~~~Iieigav~~d~~~~~~~~~f~~~v~P~~~~~i~~~~~~itgit~e~l~~~~~~~~~   84 (200)
T d1w0ha_           5 YDYICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFCISLTGITQDQVDRADTFPQV   84 (200)
T ss_dssp             SSEEEECCCEECCCTTCCTTSCCCEEEEEEEEEETTTCSEEEEEEEEBCCSSSCSCCHHHHHHHCCCHHHHHTSBCHHHH
T ss_pred             CCEEEEEEEecCCCCCCCCCCCCcEEEEEEEEEECCCCeEEEEEEEEEecCccccCCHHHHHHHCCCHHHhhhhhhhHhH
Confidence            78999999999988754 45678999999999998899999999999999876679999999999999999999999999


Q ss_pred             HHHHHHHHhhcCCC-CCcEEEEEeccchHHHHHHHHHHHhCCCCCCCCcchhhhHHHHhHhcCCC--CCCHHHHHHHhCC
Q 036883           80 LYFHDKWLLQMGLN-NTNFSVVTWSDWDCQVMLESECRIKKIQKPAYFNQWINLRVPFSKVFGDV--RCNLKEAVELAGL  156 (277)
Q Consensus        80 l~~f~~fl~~~~l~-~~~~~vv~~~~fDl~~~L~~~~~~~gi~~p~~~~~~iDl~~~~~~~~~~~--~~~L~~l~~~~gi  156 (277)
                      +.+|.+|+....+. ++++.+++|+.+|+..||+.+|++.+++.|.+...++|++.++...++..  +.+|++|++++|+
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~L~~~~~~~~~~~p~~~~~~~d~~~~~~~~~~~~~~~~~L~~l~~~~gi  164 (200)
T d1w0ha_          85 LKKVIDWMKLKELGTKYKYSLLTDGSWDMSKFLNIQCQLSRLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTIMLEKLGM  164 (200)
T ss_dssp             HHHHHHHHHHTTBTTTBCEEEEESSTTTTHHHHHHHHHHHTCCCCGGGSEEEEHHHHHHHHHTCCGGGCSHHHHHHHTTC
T ss_pred             HHHHHHHhcCCcEEeeeeeeeccchhhhHHHHHHHHHHhccCCCcccccceeeHHhHhhhhccccccchHHHHHHHHcCC
Confidence            99999999998664 45677888998876689999999999998877888999999888877643  5799999999999


Q ss_pred             CCCCCCCchHHHHHHHHHHHHHHHHhcCccCcCccc
Q 036883          157 IWQGRVHCGLDDAINIARLLSVIMRRGFKFSITKSL  192 (277)
Q Consensus       157 ~~~~~~H~Al~DA~~ta~l~~~l~~~g~~~~i~~~l  192 (277)
                      +..+++|+|++||++||+|+.+|+++|.++.|++++
T Consensus       165 ~~~~~aH~Al~Da~~~a~v~~~ll~~g~~~~i~~~~  200 (200)
T d1w0ha_         165 DYDGRPHCGLDDSKNIARIAVRMLQDGCELRINEKM  200 (200)
T ss_dssp             CCCSCTTCHHHHHHHHHHHHHHHHHTTCCCCCCEEC
T ss_pred             CCCCCCcChHHHHHHHHHHHHHHHHcCCCCCCCCCC
Confidence            998788999999999999999999999999999875
>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
>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
>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
>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
>d1uoca_ c.55.3.9 (A:) Pop2 RNase D domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} 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
>d1x9ma1 c.55.3.5 (A:1-210) Exonuclease domain of T7 DNA polymerase {Bacteriophage T7 [TaxId: 10760]} 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
>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
>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
>d2hbka2 c.55.3.5 (A:129-420) Exosome complex exonuclease RRP6 {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