Citrus Sinensis ID: 019538

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-------280-------290-------300-------310-------320-------330-------34

MRTVPMCFSILEVPKGRINSLANFCRESFHSFSRRYGHSPSFKLLCSKTYGLEDQDSYTERWSRRRITTGTEGSKKTIQSHKLKNIKFEATSTTINVNKTEISKIQRIQHYDIEQIIAENKDLAKLVTAIVFDIETTGFSRENERIIEIAFQDLLGGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPLVGSAHRAMADVNCLSLILQRLTFDLKLSLCDLIERGFTPSDLINPKKKKKSKLVSNQE

cccccEEEEEEccccEEEccccHHHHHHHccccccccccccEEEEEEEcccccccccccccccccEEEEcccccccccccHHHHcccccccccccccccccccEEEcccccccHHHHHccccccccccEEEEEEcccccccccccEEEEEEEEEEcccccEEEEcccccccccccccccccHHHccccccccHHHHHHHHHHHHHcccccccccEEEEEccccccHHHHHHHHHHcccccccccccEEHHHHHHHHHccccccccccccHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccc

cccEEEEEEHccccccccccHHHHHHHHHccEEEEEccccHHHHHHcccccHHHHHHHHHHccccEEEEEccccccccHHHHHHHHHHcccEEEEEEEEEEEcccEEEEEcccccEcccccccccccEEEEEEEEccccccccccEEEEEEEEEccccEcccHEEcccccccccEEEccccHHHHcccccccHHHHHHHHHHHHHccccccccEEEEEEccccccHHHHHHHHHHccccccccccEEcHHHHHHHHcHHHcccccccccHHHHHHHccccEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHccccccEEEEEEccc

mrtvpmcfsilevpkgrINSLANFCRESFHsfsrryghspsfkllcsktygledqdsyterwsrrrittgtegskkTIQSHKLKNIKFEATSTTINVNKTEISKIQRIQHYDIEQIIAENKDLAKLVTAIVFDIettgfsreNERIIEIAFQdllggenstfqtlvnpkrqvpnahvhgittdmvckpdvprmedLIPILLHYVKsrqkpggyILFVAhnarsfdvpflINEFsrcsyevpnnwlfMDTLTLARELMksggsnlpskVSLQALREyygiplvgsahraMADVNCLSLILQRLTFDLKLSLCDLiergftpsdlinpkkkkksKLVSNQE

MRTVPMCFSILEVPKGRINSLANFCRESFHSfsrryghspSFKLLCSktygledqdsyterwsrrrittgtegskktiqshklknikfeatsttinvnkteiskiqriQHYDIEQIIAENKDLAKLVTAIVFDIettgfsreneRIIEIAFQDLLGGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPLVGSAHRAMADVNCLSLILQRLTFDLKLSLCDLIErgftpsdlinpkkkkksklvsnqe

****PMCFSILEVPKGRINSLANFCRESFHSFSRRYGHSPSFKLLCSKTYGLEDQDSYTERW********************LKNIKFEATSTTINVNKTEISKIQRIQHYDIEQIIAENKDLAKLVTAIVFDIETTGFSRENERIIEIAFQDLLGGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMK*****LPSKVSLQALREYYGIPLVGSAHRAMADVNCLSLILQRLTFDLKLSLCDLIERGFT********************

****PMCFSILEVPKGRINSLANFCRESFHS**********FKLLCSKTYG*****S*T*RWSRRRITTGTEGSKKTIQSHKLKNIKFEAT*****VNKTEISKIQRIQHYDIEQIIAENKDLAKLVTAIVFDIETTGFSRENERIIEIAFQDLLGGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPLVGSAHRAMADVNCLSLILQRLTFDLKLSLCDLIERGF*********************

MRTVPMCFSILEVPKGRINSLANFCRESFHSFSRRYGHSPSFKLLCSKTYGLEDQDSYTERWSRRRIT***********SHKLKNIKFEATSTTINVNKTEISKIQRIQHYDIEQIIAENKDLAKLVTAIVFDIETTGFSRENERIIEIAFQDLLGGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPLVGSAHRAMADVNCLSLILQRLTFDLKLSLCDLIERGFTPSDLINP*************

*RTVPMCFSILEVPKGRINSLANFCRESFHSFSRRYGHSPSFKLLCSKTYGLEDQDSYTERWSRRRITTGTEGSKKTIQSHKLKNIKFEATSTTINVNKTEISKIQRIQHYDIEQIIAENKDLAKLVTAIVFDIETTGFSRENERIIEIAFQDLLGGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPLVGSAHRAMADVNCLSLILQRLTFDLKLSLCDLIERGFTPSDLINPKKKKKSKLVSNQ*

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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
Query		339	2.2.26 [Sep-21-2011]
Q895K2		1427	DNA polymerase III PolC-t	yes	no	0.516	0.122	0.316	6e-13
Q8XJR3		1449	DNA polymerase III PolC-t	yes	no	0.451	0.105	0.350	9e-13
Q4L5W6		1438	DNA polymerase III PolC-t	yes	no	0.539	0.127	0.312	4e-12
P0C1P9		1435	DNA polymerase III PolC-t	yes	no	0.489	0.115	0.311	5e-12
Q5HPS7		1438	DNA polymerase III PolC-t	yes	no	0.489	0.115	0.311	6e-12
Q6GHH1		1438	DNA polymerase III PolC-t	yes	no	0.489	0.115	0.311	6e-12
P68852		1436	DNA polymerase III PolC-t	yes	no	0.489	0.115	0.311	6e-12
Q2G1Z8		1436	DNA polymerase III PolC-t	yes	no	0.489	0.115	0.311	6e-12
Q2FHH4		1436	DNA polymerase III PolC-t	N/A	no	0.489	0.115	0.311	6e-12
Q6G9U9		1438	DNA polymerase III PolC-t	yes	no	0.489	0.115	0.311	6e-12

>sp\|Q895K2\|DPO3_CLOTE DNA polymerase III PolC-type OS=Clostridium tetani (strain Massachusetts / E88) GN=polC PE=3 SV=1	Back alignment and function desciption

 Score = 75.1 bits (183), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 64/202 (31%), Positives = 102/202 (50%), Gaps = 27/202 (13%)

Query: 130 IVFDIETTGFSRENERIIEIAFQDLLGGE-NSTFQTLVNPKRQVPNAHVH--GITTDMVC 186
           +VFDIETTGFS +N++IIEI    +  G+    + T VNP+R +P   +   GI   MV 
Sbjct: 414 VVFDIETTGFSNKNDKIIEIGAVKIKEGKVVDKYSTFVNPERIIPEKIIELTGIHDYMV- 472

Query: 187 KPDVPRMEDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRC-SYEVPNNWL 245
             D P++E+++P  + +++         + VAHNA +FDV F+      C  + +  N  
Sbjct: 473 -KDAPKIEEVLPKFIDFIEDS-------ILVAHNA-NFDVSFIK---KNCKDFGIHFNNP 520

Query: 246 FMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPLVGSAHRAMADVNCLSLILQRLTFD 305
            +DT+ L + L          +  L  + ++ GIPL+ + HRA+ D      IL +   D
Sbjct: 521 ILDTIPLCKFLYPE-----LKRYKLNVVAKHLGIPLL-NHHRAVEDAKTTGDILLKAFED 574

Query: 306 LK----LSLCDLIERGFTPSDL 323
           LK    ++L  L E  F   D+
Sbjct: 575 LKDKEIMNLNMLNEEYFKNQDI 596

Required for replicative DNA synthesis. This DNA polymerase also exhibits 3' to 5' exonuclease activity.
Clostridium tetani (strain Massachusetts / E88) (taxid: 212717)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 7

>sp\|Q8XJR3\|DPO3_CLOPE DNA polymerase III PolC-type OS=Clostridium perfringens (strain 13 / Type A) GN=polC PE=3 SV=1	Back alignment and function description

>sp\|Q4L5W6\|DPO3_STAHJ DNA polymerase III PolC-type OS=Staphylococcus haemolyticus (strain JCSC1435) GN=polC PE=3 SV=1	Back alignment and function description

>sp\|P0C1P9\|DPO3_STAAU DNA polymerase III PolC-type OS=Staphylococcus aureus GN=polC PE=3 SV=1	Back alignment and function description

>sp\|Q5HPS7\|DPO3_STAEQ DNA polymerase III PolC-type OS=Staphylococcus epidermidis (strain ATCC 35984 / RP62A) GN=polC PE=3 SV=2	Back alignment and function description

>sp\|Q6GHH1\|DPO3_STAAR DNA polymerase III PolC-type OS=Staphylococcus aureus (strain MRSA252) GN=polC PE=3 SV=1	Back alignment and function description

>sp\|P68852\|DPO3_STAAW DNA polymerase III PolC-type OS=Staphylococcus aureus (strain MW2) GN=polC PE=3 SV=1	Back alignment and function description

>sp\|Q2G1Z8\|DPO3_STAA8 DNA polymerase III PolC-type OS=Staphylococcus aureus (strain NCTC 8325) GN=polC PE=3 SV=1	Back alignment and function description

>sp\|Q2FHH4\|DPO3_STAA3 DNA polymerase III PolC-type OS=Staphylococcus aureus (strain USA300) GN=polC PE=3 SV=1	Back alignment and function description

>sp\|Q6G9U9\|DPO3_STAAS DNA polymerase III PolC-type OS=Staphylococcus aureus (strain MSSA476) GN=polC 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
Query		339
225450649		337	PREDICTED: DNA polymerase III polC-type-	0.973	0.979	0.662	1e-121
296089746		332	unnamed protein product [Vitis vinifera]	0.958	0.978	0.657	1e-118
255542840		334	exonuclease, putative [Ricinus communis]	0.961	0.976	0.626	1e-114
357511765		332	DNA polymerase III polC-type [Medicago t	0.970	0.990	0.610	1e-110
356572944		329	PREDICTED: DNA polymerase III polC-type-	0.952	0.981	0.630	1e-109
356505791		329	PREDICTED: DNA polymerase III polC-type-	0.932	0.960	0.622	1e-101
449435615		327	PREDICTED: DNA polymerase III PolC-type-	0.946	0.981	0.566	1e-100
449517739		334	PREDICTED: DNA polymerase III PolC-type-	0.943	0.958	0.562	5e-99
147814790		340	hypothetical protein VITISV_042394 [Viti	0.740	0.738	0.688	2e-95
356533554		332	PREDICTED: DNA polymerase III polC-type-	0.967	0.987	0.559	6e-95

>gi\|225450649\|ref\|XP_002282861.1\| PREDICTED: DNA polymerase III polC-type-like isoform 2 [Vitis vinifera] gi\|225450651\|ref\|XP_002282855.1\| PREDICTED: DNA polymerase III polC-type-like isoform 1 [Vitis vinifera]	Back alignment and taxonomy information

 Score =  442 bits (1136), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 224/338 (66%), Positives = 263/338 (77%), Gaps = 8/338 (2%)

Query: 1   MRTVPMCFSILEVPKGRINSLANFCRESFHSFSRRYGHSPSFKLLCSKTYGLEDQDSYTE 60
           MRTVPMCFSIL+VP+ RI++LA+F RESFHS       S SFKLL S T GLE  +S   
Sbjct: 1   MRTVPMCFSILQVPRCRIHTLASFWRESFHSLGSTCRSSSSFKLLGSHTNGLEGGNS--R 58

Query: 61  RWSRRRITTGTEGSKKTIQSHKLKNIKFE------ATSTTINVNKTEISKIQRIQHYDIE 114
           RW+RR ITT +EG  K  QS K  NI+ E      +TST + V+K EIS+ QRIQ+ +++
Sbjct: 59  RWTRRPITTKSEGRNKYTQSSKRSNIRHEIVDGTVSTSTKLIVDKLEISESQRIQYCEVQ 118

Query: 115 QIIAENKDLAKLVTAIVFDIETTGFSRENERIIEIAFQDLLGGENSTFQTLVNPKRQVPN 174
           + + ENKDLAKLVT IVFD ETTG SR N+RIIEI  QDL GGENSTFQTLVNP+R VPN
Sbjct: 119 EKVTENKDLAKLVTVIVFDTETTGLSRANDRIIEIGLQDLGGGENSTFQTLVNPERIVPN 178

Query: 175 AHVHGITTDMVCKPDVPRMEDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFS 234
            HVHGITT MV +PDVPR +DLIPILL YV+SRQKPGG IL+VAHN RSFDVPFLINEFS
Sbjct: 179 PHVHGITTYMVNRPDVPRWKDLIPILLQYVESRQKPGGLILWVAHNGRSFDVPFLINEFS 238

Query: 235 RCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPLVGSAHRAMADVNC 294
           RC+ EVP NW F+DTL LAREL+KS GS+LP   SLQALREYY IPLVG AHR ++DV  
Sbjct: 239 RCNTEVPPNWRFLDTLPLARELIKSAGSDLPPGASLQALREYYRIPLVGPAHRVLSDVYT 298

Query: 295 LSLILQRLTFDLKLSLCDLIERGFTPSDLINPKKKKKS 332
           LS +LQ LTF+LK+S+ +L++R FT SD+INPKKKK S
Sbjct: 299 LSQVLQMLTFNLKVSVANLLDRSFTASDIINPKKKKNS 336

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|296089746\|emb\|CBI39565.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|255542840\|ref\|XP_002512483.1\| exonuclease, putative [Ricinus communis] gi\|223548444\|gb\|EEF49935.1\| exonuclease, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|357511765\|ref\|XP_003626171.1\| DNA polymerase III polC-type [Medicago truncatula] gi\|355501186\|gb\|AES82389.1\| DNA polymerase III polC-type [Medicago truncatula]	Back alignment and taxonomy information

>gi\|356572944\|ref\|XP_003554625.1\| PREDICTED: DNA polymerase III polC-type-like [Glycine max]	Back alignment and taxonomy information

>gi\|356505791\|ref\|XP_003521673.1\| PREDICTED: DNA polymerase III polC-type-like [Glycine max]	Back alignment and taxonomy information

>gi\|449435615\|ref\|XP_004135590.1\| PREDICTED: DNA polymerase III PolC-type-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449517739\|ref\|XP_004165902.1\| PREDICTED: DNA polymerase III PolC-type-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|147814790\|emb\|CAN74413.1\| hypothetical protein VITISV_042394 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|356533554\|ref\|XP_003535328.1\| PREDICTED: DNA polymerase III polC-type-like [Glycine max]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		339
TAIR\|locus:2148453		316	DPD1 "defective in pollen orga	0.899	0.965	0.495	4e-74
TIGR_CMR\|BA_3672		315	BA_3672 "DNA polymerase III, e	0.442	0.476	0.331	1.2e-11
UNIPROTKB\|Q74DD3		181	GSU1383 "3'-to-5' exonuclease,	0.424	0.795	0.331	1.3e-09
TIGR_CMR\|GSU_1383		181	GSU_1383 "exonuclease" [Geobac	0.424	0.795	0.331	1.3e-09
TIGR_CMR\|NSE_0470		228	NSE_0470 "DNA polymerase III,	0.486	0.723	0.297	3e-08
TIGR_CMR\|BA_3955		1433	BA_3955 "DNA polymerase III, a	0.510	0.120	0.312	4.4e-08
ZFIN\|ZDB-GENE-110411-9		235	si:ch1073-296i8.2 "si:ch1073-2	0.539	0.778	0.307	6.5e-08
TIGR_CMR\|CPS_0780		203	CPS_0780 "exonuclease" [Colwel	0.427	0.714	0.337	1.1e-06
TIGR_CMR\|CHY_1772		1407	CHY_1772 "DNA polymerase III,	0.651	0.157	0.283	1.2e-06
UNIPROTKB\|Q10384		645	MT2247 "Uncharacterized protei	0.471	0.248	0.315	1.2e-06

TAIR\|locus:2148453 DPD1 "defective in pollen organelle DNA degradation1" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 748 (268.4 bits), Expect = 4.0e-74, P = 4.0e-74
 Identities = 158/319 (49%), Positives = 214/319 (67%)

Query:     6 MCFSILEVPKGRINSLANFCRESFHSFSRRYGHSPSFKLLCSKTYGLEDQDSYTERWSRR 65
             MC SI +V + RI+S  + C E  H + +   +S S KLL  +   ++ +     RW RR
Sbjct:     1 MCISISQVSRLRIHSFGSSCCERVHGWIK---NSSSLKLLDVRASSVDGK----ARWIRR 53

Query:    66 RITTGTEGSKKTIQSHKLKNIKFEATSTTINVNKTEISKIQRIQHYDIEQIIAENKDLAK 125
              ++T T+GS+   +S  L          T  +++   +K+Q   +  ++Q +A++KDL+K
Sbjct:    54 NVSTTTQGSRSNTKSSVLGG----TVPVTRIIDEESRTKVQPFGN--LQQRLAQDKDLSK 107

Query:   126 LVTAIVFDIETTGFSRENERIIEIAFQDLLGGENSTFQTLVNPKR-QVPNAHVHGITTDM 184
             L+T IV D+ETTG  R+NERIIEIA QD+ GG  STFQTLVNP    + NAH+HGI  DM
Sbjct:   108 LLTVIVSDLETTGLHRKNERIIEIAAQDIAGGGYSTFQTLVNPGVVPITNAHIHGIRNDM 167

Query:   185 VCKPDVPRMEDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNW 244
             VC+P+VPRME+LIPI L YV+SRQKPGGY++ VAHN +SFD  FLINEF+RCSYE+P+NW
Sbjct:   168 VCRPEVPRMEELIPIFLRYVESRQKPGGYVMLVAHNGKSFDFQFLINEFNRCSYEIPHNW 227

Query:   245 LFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPLVGSAHRAMADVNCLSLILQRLTF 304
             L +D+L LARE MKS    +    SL+AL +YY +   G AHRA++DV  LS + Q+LT 
Sbjct:   228 LLLDSLPLARENMKSVEPTVKLSSSLEALADYYSLTREGDAHRALSDVLLLSKVFQKLTI 287

Query:   305 DLKLSLCDLIERGFTPSDL 323
             DLKLSL DL+ R  T SD+
Sbjct:   288 DLKLSLSDLVLRCHTASDI 306

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004527 "exonuclease activity" evidence=IEA;ISS;IDA

GO:0005622 "intracellular" evidence=IEA;ISS

GO:0000738 "DNA catabolic process, exonucleolytic" evidence=IMP

GO:0005739 "mitochondrion" evidence=IDA

GO:0009536 "plastid" evidence=IDA

TIGR_CMR\|BA_3672 BA_3672 "DNA polymerase III, epsilon subunit, putative" [Bacillus anthracis str. Ames (taxid:198094)]	Back alignment and assigned GO terms

UNIPROTKB\|Q74DD3 GSU1383 "3'-to-5' exonuclease, putative" [Geobacter sulfurreducens PCA (taxid:243231)]	Back alignment and assigned GO terms

TIGR_CMR\|GSU_1383 GSU_1383 "exonuclease" [Geobacter sulfurreducens PCA (taxid:243231)]	Back alignment and assigned GO terms

TIGR_CMR\|NSE_0470 NSE_0470 "DNA polymerase III, epsilon subunit" [Neorickettsia sennetsu str. Miyayama (taxid:222891)]	Back alignment and assigned GO terms

TIGR_CMR\|BA_3955 BA_3955 "DNA polymerase III, alpha subunit, Gram-positive type" [Bacillus anthracis str. Ames (taxid:198094)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-110411-9 si:ch1073-296i8.2 "si:ch1073-296i8.2" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

TIGR_CMR\|CPS_0780 CPS_0780 "exonuclease" [Colwellia psychrerythraea 34H (taxid:167879)]	Back alignment and assigned GO terms

TIGR_CMR\|CHY_1772 CHY_1772 "DNA polymerase III, alpha subunit, Gram-positive type" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]	Back alignment and assigned GO terms

UNIPROTKB\|Q10384 MT2247 "Uncharacterized protein Rv2191/MT2247" [Mycobacterium tuberculosis (taxid:1773)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	2.7.7	LOW CONFIDENCE prediction!
4th Layer	2.7.7.7	LOW CONFIDENCE prediction!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	AT5G26940	exonuclease family protein; exonuclease family protein; FUNCTIONS IN- exonuclease activity, nucleic acid binding; LOCATED IN- intracellular, chloroplast; EXPRESSED IN- 23 plant structures; EXPRESSED DURING- 13 growth stages; CONTAINS InterPro DOMAIN/s- Exonuclease (InterPro-IPR006055), Polynucleotidyl transferase, Ribonuclease H fold (InterPro-IPR012337), Exonuclease, RNase T and DNA polymerase III (InterPro-IPR013520); Has 2014 Blast hits to 2014 proteins in 626 species- Archae - 2; Bacteria - 1416; Metazoa - 38; Fungi - 0; Plants - 27; Viruses - 4; Other Eukaryotes - 527 (source- NCB [...] (316 aa)
		(Arabidopsis thaliana)
Predicted Functional Partners:
	AT2G13440	glucose-inhibited division family A protein; glucose-inhibited division family A protein; FUNCT [...] (723 aa)	•	0.446

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
Query		339
smart00479		169	smart00479, EXOIII, exonuclease domain in DNA-poly	2e-38
cd06127		159	cd06127, DEDDh, DEDDh 3'-5' exonuclease domain fam	2e-38
COG0847		243	COG0847, DnaQ, DNA polymerase III, epsilon subunit	9e-30
PRK06309		232	PRK06309, PRK06309, DNA polymerase III subunit eps	1e-28
PRK07883		557	PRK07883, PRK07883, hypothetical protein; Validate	2e-27
pfam00929		161	pfam00929, RNase_T, Exonuclease	1e-25
PRK00448		1437	PRK00448, polC, DNA polymerase III PolC; Validated	3e-20
PRK06807		313	PRK06807, PRK06807, DNA polymerase III subunit eps	3e-20
cd06131		167	cd06131, DNA_pol_III_epsilon_Ecoli_like, DEDDh 3'-	8e-20
PRK06063		313	PRK06063, PRK06063, DNA polymerase III subunit eps	2e-18
TIGR01405		1213	TIGR01405, polC_Gram_pos, DNA polymerase III, alph	8e-18
COG2176		1444	COG2176, PolC, DNA polymerase III, alpha subunit (	3e-17
PRK07740		244	PRK07740, PRK07740, hypothetical protein; Provisio	9e-17
PRK05711		240	PRK05711, PRK05711, DNA polymerase III subunit eps	1e-16
PRK06310		250	PRK06310, PRK06310, DNA polymerase III subunit eps	1e-15
TIGR01406		225	TIGR01406, dnaQ_proteo, DNA polymerase III, epsilo	1e-15
PRK08074		928	PRK08074, PRK08074, bifunctional ATP-dependent DNA	1e-14
TIGR01407		850	TIGR01407, dinG_rel, DnaQ family exonuclease/DinG	2e-14
TIGR00573		217	TIGR00573, dnaq, exonuclease, DNA polymerase III,	5e-12
cd06130		156	cd06130, DNA_pol_III_epsilon_like, an uncharacteri	6e-11
PRK08517		257	PRK08517, PRK08517, DNA polymerase III subunit eps	1e-09
PRK07942		232	PRK07942, PRK07942, DNA polymerase III subunit eps	2e-09
cd06133		176	cd06133, ERI-1_3'hExo_like, DEDDh 3'-5' exonucleas	2e-07
cd06136		177	cd06136, TREX1_2, DEDDh 3'-5' exonuclease domain o	2e-06
PRK09182		294	PRK09182, PRK09182, DNA polymerase III subunit eps	3e-05
pfam13482		163	pfam13482, RNase_H_2, RNase_H superfamily	6e-05

>gnl\|CDD\|214685 smart00479, EXOIII, exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases	Back alignment and domain information

 Score =  133 bits (338), Expect = 2e-38
 Identities = 56/177 (31%), Positives = 83/177 (46%), Gaps = 17/177 (9%)

Query: 130 IVFDIETTGFSRENERIIEIAFQDLLGGE-NSTFQTLVNPKRQVP--NAHVHGITTDMVC 186
           +V D ETTG     + IIEIA  D+ GGE    F T V P R +      +HGIT +M+ 
Sbjct: 3   VVIDCETTGLDPGKDEIIEIAAVDVDGGEIIEVFDTYVKPDRPITDYATEIHGITPEMLD 62

Query: 187 KPDVPRMEDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLF 246
               P  E+++  LL +++ R         VA N+  FD+ FL  E  R   + P     
Sbjct: 63  DA--PTFEEVLEELLEFLRGRI-------LVAGNSAHFDLRFLKLEHPRLGIKQPPKLPV 113

Query: 247 MDTLTLARELMKSGGSNLPSKVSLQALREYYGIPLVGSAHRAMADVNCLSLILQRLT 303
           +DTL LAR            K SL+ L +   + ++  AHRA+ D    + + ++L 
Sbjct: 114 IDTLKLARATNPG-----LPKYSLKKLAKRLLLEVIQRAHRALDDARATAKLFKKLL 165

Length = 169

>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\|180524 PRK06309, PRK06309, DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>gnl\|CDD\|236123 PRK07883, PRK07883, hypothetical protein; Validated	Back alignment and domain information

>gnl\|CDD\|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\|235864 PRK06807, PRK06807, DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>gnl\|CDD\|99835 cd06131, DNA_pol_III_epsilon_Ecoli_like, DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins	Back alignment and domain information

>gnl\|CDD\|180377 PRK06063, PRK06063, DNA polymerase III subunit epsilon; Provisional	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\|236085 PRK07740, PRK07740, hypothetical protein; Provisional	Back alignment and domain information

>gnl\|CDD\|235574 PRK05711, PRK05711, DNA polymerase III subunit epsilon; Provisional	Back alignment and domain information

>gnl\|CDD\|180525 PRK06310, PRK06310, DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>gnl\|CDD\|130473 TIGR01406, dnaQ_proteo, DNA polymerase III, epsilon subunit, Proteobacterial	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\|129663 TIGR00573, dnaq, exonuclease, DNA polymerase III, epsilon subunit family	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\|236281 PRK08517, PRK08517, DNA polymerase III subunit epsilon; Provisional	Back alignment and domain information

>gnl\|CDD\|181176 PRK07942, PRK07942, DNA polymerase III subunit epsilon; Provisional	Back alignment and domain information

>gnl\|CDD\|99836 cd06133, ERI-1_3'hExo_like, DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins	Back alignment and domain information

>gnl\|CDD\|99839 cd06136, TREX1_2, DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins	Back alignment and domain information

>gnl\|CDD\|236397 PRK09182, PRK09182, DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>gnl\|CDD\|222166 pfam13482, RNase_H_2, RNase_H superfamily	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		339
PRK08517		257	DNA polymerase III subunit epsilon; Provisional	100.0
PRK09146		239	DNA polymerase III subunit epsilon; Validated	99.98
PRK05711		240	DNA polymerase III subunit epsilon; Provisional	99.98
TIGR01406		225	dnaQ_proteo DNA polymerase III, epsilon subunit, P	99.98
PRK06310		250	DNA polymerase III subunit epsilon; Validated	99.98
PRK07740		244	hypothetical protein; Provisional	99.97
PRK07748		207	sporulation inhibitor KapD; Provisional	99.97
PRK07942		232	DNA polymerase III subunit epsilon; Provisional	99.97
PRK06309		232	DNA polymerase III subunit epsilon; Validated	99.97
cd06131		167	DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonucl	99.97
PRK06807		313	DNA polymerase III subunit epsilon; Validated	99.97
PRK06063		313	DNA polymerase III subunit epsilon; Provisional	99.97
TIGR00573		217	dnaq exonuclease, DNA polymerase III, epsilon subu	99.97
smart00479		169	EXOIII exonuclease domain in DNA-polymerase alpha	99.97
PRK07883		557	hypothetical protein; Validated	99.97
PRK06195		309	DNA polymerase III subunit epsilon; Validated	99.97
cd06130		156	DNA_pol_III_epsilon_like an uncharacterized bacter	99.97
cd06136		177	TREX1_2 DEDDh 3'-5' exonuclease domain of three pr	99.97
PRK09145		202	DNA polymerase III subunit epsilon; Validated	99.96
PRK05601		377	DNA polymerase III subunit epsilon; Validated	99.96
PRK05168		211	ribonuclease T; Provisional	99.96
COG2176		1444	PolC DNA polymerase III, alpha subunit (gram-posit	99.96
cd06134		189	RNaseT DEDDh 3'-5' exonuclease domain of RNase T.	99.96
PRK07247		195	DNA polymerase III subunit epsilon; Validated	99.96
PRK06722		281	exonuclease; Provisional	99.96
TIGR01298		200	RNaseT ribonuclease T. in gamma-subdivision Proteo	99.96
PRK07246		820	bifunctional ATP-dependent DNA helicase/DNA polyme	99.96
PRK07983		219	exodeoxyribonuclease X; Provisional	99.96
PRK08074		928	bifunctional ATP-dependent DNA helicase/DNA polyme	99.96
TIGR01407		850	dinG_rel DnaQ family exonuclease/DinG family helic	99.95
TIGR01405		1213	polC_Gram_pos DNA polymerase III, alpha chain, Gra	99.95
cd06133		176	ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain o	99.95
cd06138		183	ExoI_N N-terminal DEDDh 3'-5' exonuclease domain o	99.95
cd06137		161	DEDDh_RNase DEDDh 3'-5' exonuclease domain of the	99.94
cd06127		159	DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh	99.94
cd06149		157	ISG20 DEDDh 3'-5' exonuclease domain of Interferon	99.93
PRK09182		294	DNA polymerase III subunit epsilon; Validated	99.93
cd06145		150	REX1_like DEDDh 3'-5' exonuclease domain of RNA ex	99.93
COG0847		243	DnaQ DNA polymerase III, epsilon subunit and relat	99.93
PTZ00315		582	2'-phosphotransferase; Provisional	99.93
cd06144		152	REX4_like DEDDh 3'-5' exonuclease domain of RNA ex	99.93
PRK05359		181	oligoribonuclease; Provisional	99.92
cd06135		173	Orn DEDDh 3'-5' exonuclease domain of oligoribonuc	99.92
PRK00448		1437	polC DNA polymerase III PolC; Validated	99.92
PRK11779		476	sbcB exonuclease I; Provisional	99.91
PF00929		164	RNase_T: Exonuclease; InterPro: IPR013520 This ent	99.91
KOG0542		280	consensus Predicted exonuclease [Replication, reco	99.82
KOG4793		318	consensus Three prime repair exonuclease [Replicat	99.75
COG5018		210	KapD Inhibitor of the KinA pathway to sporulation,	99.73
KOG2249		280	consensus 3'-5' exonuclease [Replication, recombin	99.68
COG2925		475	SbcB Exonuclease I [DNA replication, recombination	99.58
cd06143		174	PAN2_exo DEDDh 3'-5' exonuclease domain of the euk	99.56
cd05160		199	DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain	99.54
COG1949		184	Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA	99.47
KOG3242		208	consensus Oligoribonuclease (3'->5' exoribonucleas	99.45
PF13482		164	RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A	99.2
cd05780		195	DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease dom	99.16
cd05781		188	DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of	99.11
cd06139		193	DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease	99.07
cd06125		96	DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonucleas	99.06
KOG2248		380	consensus 3'-5' exonuclease [Replication, recombin	98.99
COG3359		278	Predicted exonuclease [DNA replication, recombinat	98.9
cd05785		207	DNA_polB_like2_exo Uncharacterized bacterial subgr	98.86
PRK05755		880	DNA polymerase I; Provisional	98.86
cd05782		208	DNA_polB_like1_exo Uncharacterized bacterial subgr	98.85
cd05779		204	DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domai	98.81
PF10108		209	DNA_pol_B_exo2: Predicted 3'-5' exonuclease relate	98.78
cd05777		230	DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain	98.65
KOG4793		318	consensus Three prime repair exonuclease [Replicat	98.64
cd05784		193	DNA_polB_II_exo DEDDy 3'-5' exonuclease domain of	98.43
PF01612		176	DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR00	98.35
PHA02570		220	dexA exonuclease; Provisional	98.28
cd05783		204	DNA_polB_B1_exo DEDDy 3'-5' exonuclease domain of	98.26
PF04857		262	CAF1: CAF1 family ribonuclease; InterPro: IPR00694	98.23
cd05778		231	DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease	98.14
KOG0304		239	consensus mRNA deadenylase subunit [RNA processing	98.09
PTZ00166		1054	DNA polymerase delta catalytic subunit; Provisiona	98.08
cd06140		178	DNA_polA_I_Bacillus_like_exo inactive DEDDy 3'-5'	97.95
PF03104		325	DNA_pol_B_exo1: DNA polymerase family B, exonuclea	97.93
PRK05762		786	DNA polymerase II; Reviewed	97.93
cd00007		155	35EXOc 3'-5' exonuclease. The 35EXOc domain is res	97.91
smart00486		471	POLBc DNA polymerase type-B family. DNA polymerase	97.81
PHA02528		881	43 DNA polymerase; Provisional	97.76
cd06146		193	mut-7_like_exo DEDDy 3'-5' exonuclease domain of C	97.73
COG0749		593	PolA DNA polymerase I - 3'-5' exonuclease and poly	97.62
cd06141		170	WRN_exo DEDDy 3'-5' exonuclease domain of WRN and	97.59
KOG1275		1118	consensus PAB-dependent poly(A) ribonuclease, subu	97.57
COG0349		361	Rnd Ribonuclease D [Translation, ribosomal structu	97.57
cd05776		234	DNA_polB_alpha_exo inactive DEDDy 3'-5' exonucleas	97.52
cd06142		178	RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribon	97.51
PRK10829		373	ribonuclease D; Provisional	97.47
TIGR03491		457	RecB family nuclease, putative, TM0106 family. Mem	97.42
smart00474		172	35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proo	97.39
TIGR01388		367	rnd ribonuclease D. This model describes ribonucle	97.36
cd06129		161	RNaseD_like DEDDy 3'-5' exonuclease domain of RNas	97.33
KOG1798		2173	consensus DNA polymerase epsilon, catalytic subuni	97.07
cd06148		197	Egl_like_exo DEDDy 3'-5' exonuclease domain of Dro	97.0
TIGR00593		887	pola DNA polymerase I. This family is based on the	96.79
PHA02524		498	43A DNA polymerase subunit A; Provisional	96.71
TIGR00592		1172	pol2 DNA polymerase (pol2). This family is based o	96.57
COG0417		792	PolB DNA polymerase elongation subunit (family B)	96.4
PHA03036		1004	DNA polymerase; Provisional	95.98
KOG0969		1066	consensus DNA polymerase delta, catalytic subunit	95.82
cd06147		192	Rrp6p_like_exo DEDDy 3'-5' exonuclease domain of y	95.76
COG5228		299	POP2 mRNA deadenylase subunit [RNA processing and	94.4
PRK05761		787	DNA polymerase I; Reviewed	93.72
PHA02563		630	DNA polymerase; Provisional	93.28
cd09018		150	DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease	93.22
PF13017		213	Maelstrom: piRNA pathway germ-plasm component	89.58
cd06128		151	DNA_polA_exo DEDDy 3'-5' exonuclease domain of fam	88.72
PF11074		130	DUF2779: Domain of unknown function(DUF2779); Inte	82.84

>PRK08517 DNA polymerase III subunit epsilon; Provisional	Back alignment and domain information

Probab=100.00  E-value=2e-33  Score=261.48  Aligned_cols=208  Identities=25%  Similarity=0.349  Sum_probs=179.1

Q ss_pred             chhhhhhhhccchhh-hhhhh---hhccCccCCCcEEEEEEecCCCCCCCCcEEEEEEEEEcCCee-eeEEEEEcCCCCC
Q 019538           98 NKTEISKIQRIQHYD-IEQII---AENKDLAKLVTAIVFDIETTGFSRENERIIEIAFQDLLGGEN-STFQTLVNPKRQV  172 (339)
Q Consensus        98 ~~~~l~~~~~~~~~~-~~~~~---~~~~~l~~~~~~vviDiETTGl~p~~~~IIEIgav~v~~g~i-~~f~~lV~P~~~i  172 (339)
                      ...|+.+.+|++.+. .+..+   +..+++.+ ..||+||+||||+++..++|||||||.+++|.+ ++|+.+|+|. ++
T Consensus        36 ~~~~~~~~~g~~~~~~~~~~~~l~~~~~~~~~-~~~vv~DiETTG~~~~~~~IIEIGAv~v~~g~i~~~f~~~v~p~-~i  113 (257)
T PRK08517         36 IDLELLKALGLPLVENKENLITLKTRFTPIKD-QVFCFVDIETNGSKPKKHQIIEIGAVKVKNGEIIDRFESFVKAK-EV  113 (257)
T ss_pred             HHHHHHHHCCCceEEcCCCeEEeccCCCCCCC-CCEEEEEEeCCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECCC-CC
Confidence            447889999999944 33333   33456666 699999999999999889999999999998876 8999999996 67


Q ss_pred             CC--ccccCCcHHhhcCCCCCCHHHHHHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHH
Q 019538          173 PN--AHVHGITTDMVCKPDVPRMEDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTL  250 (339)
Q Consensus       173 ~~--~~itGIt~e~l~~~~ap~~~evl~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl  250 (339)
                      ++  +++|||+++++.  ++|++.+|+.+|.+|+++       .++||||+ .||+.||.+++.++|+.... ..++||+
T Consensus       114 p~~~~~itGIt~e~l~--~ap~~~evl~~f~~fl~~-------~v~VaHNa-~FD~~fL~~~l~r~g~~~~~-~~~ldtl  182 (257)
T PRK08517        114 PEYITELTGITYEDLE--NAPSLKEVLEEFRLFLGD-------SVFVAHNV-NFDYNFISRSLEEIGLGPLL-NRKLCTI  182 (257)
T ss_pred             ChhhhhhcCcCHHHHc--CCCCHHHHHHHHHHHHCC-------CeEEEECH-HHHHHHHHHHHHHcCCCCCC-CCcEehH
Confidence            66  899999999999  899999999999999974       48999999 99999999999999987553 3689999


Q ss_pred             HHHHHHHhcCCCCCCCCCCHHHHHHHhCCCCCCCCCChHHHHHHHHHHHHHHHHhhc---cCHHHHHHhcCCCCCCCC
Q 019538          251 TLARELMKSGGSNLPSKVSLQALREYYGIPLVGSAHRAMADVNCLSLILQRLTFDLK---LSLCDLIERGFTPSDLIN  325 (339)
Q Consensus       251 ~lar~l~~~~~~~l~~~~~L~~L~~~~gI~~~~~aH~Al~DA~~ta~L~~~l~~~l~---~tl~~L~~~s~~~~~~~~  325 (339)
                      .+++.+++..      +++|++|++++|++.+ .+|+|++||.+|++||..+..+++   .++.+|+.++..+..+..
T Consensus       183 ~la~~~~~~~------~~~L~~L~~~lgi~~~-~~HrAl~DA~ata~ll~~ll~~~~~~~~t~~~L~~~~k~~~~~~~  253 (257)
T PRK08517        183 DLAKRTIESP------RYGLSFLKELLGIEIE-VHHRAYADALAAYEIFKICLLNLPSYIKTTEDLIDFSKTAKTLKK  253 (257)
T ss_pred             HHHHHHccCC------CCCHHHHHHHcCcCCC-CCCChHHHHHHHHHHHHHHHHHhHHhhcCHHHHHHHhhhcccccC
Confidence            9999887653      8899999999999987 799999999999999999998775   588999999987666543

>PRK09146 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>PRK05711 DNA polymerase III subunit epsilon; Provisional	Back alignment and domain information

>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial	Back alignment and domain information

>PRK06310 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>PRK07740 hypothetical protein; Provisional	Back alignment and domain information

>PRK07748 sporulation inhibitor KapD; Provisional	Back alignment and domain information

>PRK07942 DNA polymerase III subunit epsilon; Provisional	Back alignment and domain information

>PRK06309 DNA polymerase III subunit epsilon; Validated	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

>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

>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases	Back alignment and domain information

>PRK07883 hypothetical protein; 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

>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins	Back alignment and domain information

>PRK09145 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>PRK05601 DNA polymerase III subunit epsilon; Validated	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

>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T	Back alignment and domain information

>PRK07247 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>PRK06722 exonuclease; Provisional	Back alignment and domain information

>TIGR01298 RNaseT ribonuclease T	Back alignment and domain information

>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>PRK07983 exodeoxyribonuclease X; Provisional	Back alignment and domain information

>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative	Back alignment and domain information

>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type	Back alignment and domain information

>cd06133 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins	Back alignment and domain information

>cd06138 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins	Back alignment and domain information

>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

>cd06127 DEDDh DEDDh 3'-5' exonuclease domain family	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

>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic 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

>PTZ00315 2'-phosphotransferase; Provisional	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

>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

>PRK00448 polC DNA polymerase III PolC; Validated	Back alignment and domain information

>PRK11779 sbcB exonuclease I; Provisional	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

>KOG0542 consensus Predicted exonuclease [Replication, recombination and repair]	Back alignment and domain information

>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]	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

>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]	Back alignment and domain information

>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]	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

>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

>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

>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

>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

>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

>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

>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]	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

>PRK05755 DNA polymerase I; Provisional	Back alignment and domain information

>cd05782 DNA_polB_like1_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases	Back alignment and domain information

>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

>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

>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

>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

>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

>PHA02570 dexA exonuclease; Provisional	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

>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation	Back alignment and domain information

>cd05778 DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase	Back alignment and domain information

>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]	Back alignment and domain information

>PTZ00166 DNA polymerase delta catalytic subunit; Provisional	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

>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

>PRK05762 DNA polymerase II; Reviewed	Back alignment and domain information

>cd00007 35EXOc 3'-5' exonuclease	Back alignment and domain information

>smart00486 POLBc DNA polymerase type-B family	Back alignment and domain information

>PHA02528 43 DNA polymerase; Provisional	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

>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]	Back alignment and domain information

>cd06141 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and similar proteins	Back alignment and domain information

>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]	Back alignment and domain information

>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]	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

>cd06142 RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins	Back alignment and domain information

>PRK10829 ribonuclease D; Provisional	Back alignment and domain information

>TIGR03491 RecB family nuclease, putative, TM0106 family	Back alignment and domain information

>smart00474 35EXOc 3'-5' exonuclease	Back alignment and domain information

>TIGR01388 rnd ribonuclease D	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

>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]	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

>TIGR00593 pola DNA polymerase I	Back alignment and domain information

>PHA02524 43A DNA polymerase subunit A; Provisional	Back alignment and domain information

>TIGR00592 pol2 DNA polymerase (pol2)	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

>KOG0969 consensus DNA polymerase delta, catalytic subunit [Replication, recombination and repair]	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

>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]	Back alignment and domain information

>PRK05761 DNA polymerase I; Reviewed	Back alignment and domain information

>PHA02563 DNA polymerase; Provisional	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

>PF13017 Maelstrom: piRNA pathway germ-plasm component	Back alignment and domain information

>cd06128 DNA_polA_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases	Back alignment and domain information

>PF11074 DUF2779: Domain of unknown function(DUF2779); InterPro: IPR021301 This domain is conserved in bacteria	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
Query		339
2p1j_A		186	Crystal Structure Of A Polc-Type Dna Polymerase Iii		8e-06
1y97_A		238	The Human Trex2 3' Exonuclease Structure Suggests A		2e-04

>pdb|2P1J|A Chain A, Crystal Structure Of A Polc-Type Dna Polymerase Iii Exonuclease Domain From Thermotoga Maritima Length = 186

Back alignment and structure

Iteration: 1

Score = 47.8 bits (112), Expect = 8e-06, Method: Compositional matrix adjust. Identities = 52/182 (28%), Positives = 87/182 (47%), Gaps = 27/182 (14%) Query: 128 TAIVFDIETTGFSRENERIIEIAFQDLLGGE-NSTFQTLVNPKRQVP--NAHVHGITTDM 184 T +V D ETTG + + IIEI + GG+ + TL+ P R++ ++ + GIT +M Sbjct: 13 TFVVLDFETTGLDPQVDEIIEIGAVKIQGGQIVDEYHTLIKPSREISRKSSEITGITQEM 72 Query: 185 VCKPDVPRMEDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFL---INEFSRCSYEVP 241 + + +E+++P L +++ + VAHNA +FD FL I + +E P Sbjct: 73 L--ENKRSIEEVLPEFLGFLEDS-------IIVAHNA-NFDYRFLRLWIKKVMGLDWERP 122 Query: 242 NNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPLVGSAHRAMADVNCLSLILQR 301 ++DTL LA+ L+K +L S V L + HRA+ D + + R Sbjct: 123 ----YIDTLALAKSLLKLRSYSLDSVVEKLGLGPF-------RHHRALDDARVTAQVFLR 171 Query: 302 LT 303 Sbjct: 172 FV 173

PyMOL of 2p1j

>pdb|1Y97|A Chain A, The Human Trex2 3' Exonuclease Structure Suggests A Mechanism For Efficient Non-Processive Dna Catalysis Length = 238

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
Query		339
1y97_A		238	Three prime repair exonuclease 2; TREX2, hydrolase	4e-55
3mxm_B		242	Three prime repair exonuclease 1; RNAse H-like fol	2e-44
3u3y_B		314	Three prime repair exonuclease 1; RNAse H fold, 3'	5e-43
2p1j_A		186	POLIII, DNA polymerase III POLC-type; structural g	3e-41
2f96_A		224	Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolas	2e-28
3v9w_A		235	Ribonuclease T; DEDD nucleases family, EXO-nucleas	4e-26
2gui_A		194	DNA polymerase III epsilon subunit; DNA polymerase	5e-24
3cg7_A		308	CRN-4, cell death-related nuclease 4; hydrolase, a	6e-22
1w0h_A		204	3'-5' exonuclease ERI1; nuclease domain, hydrolase	2e-21
2xri_A		224	ERI1 exoribonuclease 3; hydrolase, metal binding;	2e-21
1zbh_A		299	3'-5' exonuclease ERI1; histone mRNA 3'-END-specif	8e-20
1zbu_A		349	ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase;	7e-19
2gbz_A		194	Oligoribonuclease; ORN, deddh, structural genomics	2e-06
3tr8_A		186	Oligoribonuclease; transcription, hydrolase; 2.50A	5e-05
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-05
3f2b_A		1041	DNA-directed DNA polymerase III alpha chain; DNA p	9e-05

>1y97_A Three prime repair exonuclease 2; TREX2, hydrolase; 2.50A {Homo sapiens} SCOP: c.55.3.5 Length = 238	Back alignment and structure

 Score =  178 bits (454), Expect = 4e-55
 Identities = 47/239 (19%), Positives = 78/239 (32%), Gaps = 29/239 (12%)

Query: 118 AENKDLAKLVTAIVFDIETTGFSRENERIIEIAFQDLLGGENS----------------- 160
           A   +  +  T +  D+E TG       I E++   +                       
Sbjct: 1   AGMSEAPRAETFVFLDLEATGLPSVEPEIAELSLFAVHRSSLENPEHDESGALVLPRVLD 60

Query: 161 TFQTLVNPKRQVP--NAHVHGITTDMVCKPDVPRMEDLIPILLHYVKSRQKPGGYILFVA 218
                + P+R      + + G++++ + +      +  +   L    SRQ   G I  VA
Sbjct: 61  KLTLCMCPERPFTAKASEITGLSSEGLARCRKAGFDGAVVRTLQAFLSRQ--AGPICLVA 118

Query: 219 HNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNL----PSKVSLQALR 274
           HN   +D P L  E  R    +P + + +DTL   R L ++             SL +L 
Sbjct: 119 HNGFDYDFPLLCAELRRLGARLPRDTVCLDTLPALRGLDRAHSHGTRARGRQGYSLGSLF 178

Query: 275 EYYGIPLVGSAHRAMADVNCLSLILQRLTFDLKLSLCDLIERGFTPSDLINPKKKKKSK 333
             Y      +AH A  DV+ L LI      +L        +        I P       
Sbjct: 179 HRYFRAEPSAAHSAEGDVHTLLLIFLHRAAELL----AWADEQARGWAHIEPMYLPPDD 233

PyMOL of 1y97

>3mxm_B Three prime repair exonuclease 1; RNAse H-like fold, polyproline type II helix, hydrolase-DNA; HET: DNA; 1.75A {Mus musculus} PDB: 3mxj_B 2ioc_B 3mxi_B* 3b6o_A* 2o4g_A* 3b6p_A* 2o4i_A 2oa8_A Length = 242	Back alignment and structure

>3u3y_B Three prime repair exonuclease 1; RNAse H fold, 3' exonuclease, homodimer, hydrolase-DNA compl; HET: BU1; 2.28A {Mus musculus} PDB: 3u6f_B* Length = 314	Back alignment and structure

>2p1j_A POLIII, DNA polymerase III POLC-type; structural genomics, exonuclease, PSI-2, protein structure initiative; HET: DNA; 2.50A {Thermotoga maritima MSB8} Length = 186	Back alignment and structure

>2f96_A Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolase, SAD, PS protein structure initiative, midwest center for structural genomics; 2.09A {Pseudomonas aeruginosa} SCOP: c.55.3.5 Length = 224	Back alignment and structure

>3v9w_A Ribonuclease T; DEDD nucleases family, EXO-nucleases, hydrolase-DNA complex; HET: DNA; 1.70A {Escherichia coli} PDB: 3ngy_A 3v9u_A* 3ngz_A* 3va3_A* 3v9z_A* 3nh0_A 3nh2_A 3nh1_A* 3v9s_A* 3v9x_A* 3va0_A* 2is3_A Length = 235	Back alignment and structure

>2gui_A DNA polymerase III epsilon subunit; DNA polymerase proofreading domain, transferase; HET: DNA U5P; 1.60A {Escherichia coli} SCOP: c.55.3.5 PDB: 1j54_A* 1j53_A* 2ido_A* 2xy8_A* Length = 194	Back alignment and structure

>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

>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

>2xri_A ERI1 exoribonuclease 3; hydrolase, metal binding; 2.15A {Homo sapiens} Length = 224	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

>2gbz_A Oligoribonuclease; ORN, deddh, structural genomics, hydrolase; 2.30A {Xanthomonas campestris PV} Length = 194	Back alignment and structure

>3tr8_A Oligoribonuclease; transcription, hydrolase; 2.50A {Coxiella burnetii} Length = 186	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>3f2b_A DNA-directed DNA polymerase III alpha chain; DNA polymerase C, DNA polymerase III; HET: DGT; 2.39A {Geobacillus kaustophilus} PDB: 3f2c_A* 3f2d_A* Length = 1041	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		339
2p1j_A		186	POLIII, DNA polymerase III POLC-type; structural g	99.98
2gui_A		194	DNA polymerase III epsilon subunit; DNA polymerase	99.98
1w0h_A		204	3'-5' exonuclease ERI1; nuclease domain, hydrolase	99.97
3mxm_B		242	Three prime repair exonuclease 1; RNAse H-like fol	99.97
1y97_A		238	Three prime repair exonuclease 2; TREX2, hydrolase	99.97
3u3y_B		314	Three prime repair exonuclease 1; RNAse H fold, 3'	99.97
1zbh_A		299	3'-5' exonuclease ERI1; histone mRNA 3'-END-specif	99.96
2f96_A		224	Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolas	99.96
3v9w_A		235	Ribonuclease T; DEDD nucleases family, EXO-nucleas	99.96
2xri_A		224	ERI1 exoribonuclease 3; hydrolase, metal binding;	99.96
1zbu_A		349	ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase;	99.96
3cg7_A		308	CRN-4, cell death-related nuclease 4; hydrolase, a	99.95
1wlj_A		189	Interferon stimulated gene 20KDA; exoribonuclease,	99.94
2igi_A		180	Oligoribonuclease; RNAse, exoribonuclease, exonucl	99.94
3tr8_A		186	Oligoribonuclease; transcription, hydrolase; 2.50A	99.94
2qxf_A		482	Exodeoxyribonuclease I; alpha-beta domain, DNAQ su	99.94
2gbz_A		194	Oligoribonuclease; ORN, deddh, structural genomics	99.92
2kfn_A		605	Klenow fragment of DNA polymerase I; complex (poly	99.22
1x9m_A		698	DNA polymerase; DNA ploymerase, N-2-acetylaminoflu	98.95
4hec_A		190	Putative uncharacterized protein; ssgcid, structur	98.86
1qht_A		775	Protein (DNA polymerase); archaea, hyperthermostab	98.8
4gmj_B		285	CCR4-NOT transcription complex subunit 7; mRNA dec	98.73
1noy_A		388	Protein (DNA polymerase (E.C.2.7.7.7)); exonucleas	98.53
2d5r_A		252	CCR4-NOT transcription complex subunit 7; poly(A)	98.4
3iay_A		919	DNA polymerase delta catalytic subunit; protein-DN	98.39
4dfk_A		540	DNA polymerase I, thermostable; DNA polymerase, tr	98.34
2p51_A		333	SPCC18.06C protein; DEDD nuclease fold, hydrolase,	98.34
1uoc_A		289	POP2; hydrolase, DEDD nuclease, mRNA degradation,	98.33
2gv9_A		1193	DNA polymerase; polymerase alpha fold, transferase	98.2
3pv8_A		592	DNA polymerase I; DNA polymerase I, protein-DNA co	98.17
1s5j_A		847	DNA polymerase I; replication, disulfide bonds, tr	98.02
3qex_A		903	DNA polymerase, GP43; difluorotoluene nucleoside;	97.89
1yt3_A		375	Ribonuclease D, RNAse D; exoribonuclease, exonucle	97.82
3saf_A		428	Exosome component 10; exoribonuclease, RNA exosome	97.79
3k59_A		786	POL II, DNA polymerase II; protein-DNA complex, DN	97.74
2hbj_A		410	Exosome complex exonuclease RRP6; RNA metabolism,	97.61
2e6m_A		208	Werner syndrome ATP-dependent helicase homolog; AP	97.34
2py5_A		575	DNA polymerase; protein-DNA complex, replication,	96.99
3d45_A		507	Poly(A)-specific ribonuclease PARN; CAP analogue,	96.69
3cym_A		440	Uncharacterized protein BAD_0989; structural genom	96.62
2a1r_A		430	Poly(A)-specific ribonuclease PARN; DEDD, nuclease	95.98
1vk0_A		206	Hypothetical protein; homohexamer, AT5G06450, stru	95.3
1bgx_T		832	TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhi	94.73

>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

Probab=99.98  E-value=4.6e-32  Score=239.52  Aligned_cols=171  Identities=29%  Similarity=0.498  Sum_probs=146.7

Q ss_pred             hhccCccCCCcEEEEEEecCCCCCCCCcEEEEEEEEEcCCee-eeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCCCHH
Q 019538          118 AENKDLAKLVTAIVFDIETTGFSRENERIIEIAFQDLLGGEN-STFQTLVNPKRQVPN--AHVHGITTDMVCKPDVPRME  194 (339)
Q Consensus       118 ~~~~~l~~~~~~vviDiETTGl~p~~~~IIEIgav~v~~g~i-~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap~~~  194 (339)
                      +.+.++.+ .++|+||+||||++|..++|||||+|.+++|.+ +.|+++|+|..++++  +++|||++++++  ++|++.
T Consensus         4 ~~~~~l~~-~~~v~iD~ETTGl~~~~~~IieIg~v~~~~g~i~~~f~~lv~P~~~i~~~~~~i~GIt~~~l~--~~~~~~   80 (186)
T 2p1j_A            4 SDDSTFGD-ATFVVLDFETTGLDPQVDEIIEIGAVKIQGGQIVDEYHTLIKPSREISRKSSEITGITQEMLE--NKRSIE   80 (186)
T ss_dssp             ----------CEEEEEEEESCSCTTTCCEEEEEEEEEETTEEEEEEEEECBCSSCCCHHHHHHHCCCHHHHT--TCCBHH
T ss_pred             CcCCcCcC-CCEEEEEEECCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECcCCCCCHHHhhhcCCCHHHHh--cCCCHH
Confidence            34455665 589999999999999889999999999988876 899999999998887  899999999999  789999


Q ss_pred             HHHHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHH
Q 019538          195 DLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALR  274 (339)
Q Consensus       195 evl~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~  274 (339)
                      +|+.+|.+|+.+       .++||||+ .||+.||.+++.++|+.++. +.++||+.+++.++ .    .+ +++|++|+
T Consensus        81 ~v~~~~~~~l~~-------~~lv~hn~-~fD~~~L~~~~~~~g~~~~~-~~~iDt~~l~~~~~-~----~~-~~~L~~l~  145 (186)
T 2p1j_A           81 EVLPEFLGFLED-------SIIVAHNA-NFDYRFLRLWIKKVMGLDWE-RPYIDTLALAKSLL-K----LR-SYSLDSVV  145 (186)
T ss_dssp             HHHHHHHHHSSS-------CEEEETTH-HHHHHHHHHHHHHHHCCCCC-CCEEEHHHHHHHHT-C----CS-CCSHHHHH
T ss_pred             HHHHHHHHHHCC-------CEEEEECc-HHHHHHHHHHHHHcCCCCCC-CCEEeHHHHHHHHh-h----cC-CCCHHHHH
Confidence            999999999974       48999999 99999999999999988653 47899999999887 2    23 89999999


Q ss_pred             HHhCCCCCCCCCChHHHHHHHHHHHHHHHHhhc
Q 019538          275 EYYGIPLVGSAHRAMADVNCLSLILQRLTFDLK  307 (339)
Q Consensus       275 ~~~gI~~~~~aH~Al~DA~~ta~L~~~l~~~l~  307 (339)
                      ++||++.. .+|+|++||.+|++||.++..+.+
T Consensus       146 ~~~gi~~~-~~H~Al~Da~~t~~l~~~l~~~~~  177 (186)
T 2p1j_A          146 EKLGLGPF-RHHRALDDARVTAQVFLRFVEMMK  177 (186)
T ss_dssp             HHTTCCST-TCCHHHHHHHHHHHHHHHHTTCC-
T ss_pred             HHcCCCCC-CCcCHHHHHHHHHHHHHHHHHHHH
Confidence            99999987 589999999999999999987654

PyMOL of 2p1j

>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

>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

>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

>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

>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

>3v9w_A Ribonuclease T; DEDD nucleases family, EXO-nucleases, hydrolase-DNA complex; HET: DNA; 1.70A {Escherichia coli} PDB: 3ngy_A 3v9u_A* 3ngz_A* 3va3_A* 3v9z_A* 3nh0_A 3nh2_A 3nh1_A* 3v9s_A* 3v9x_A* 3va0_A* 2is3_A	Back alignment and structure

>2xri_A ERI1 exoribonuclease 3; hydrolase, metal binding; 2.15A {Homo sapiens}	Back alignment and structure

>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

>1wlj_A Interferon stimulated gene 20KDA; exoribonuclease, hydrolase; HET: U5P; 1.90A {Homo sapiens} SCOP: c.55.3.5	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

>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

>2gbz_A Oligoribonuclease; ORN, deddh, structural genomics, hydrolase; 2.30A {Xanthomonas campestris PV}	Back alignment and structure

>2kfn_A Klenow fragment of DNA polymerase I; complex (polymerase/DNA), exonuclease, transferase, transferase/DNA complex; HET: US1; 2.03A {Escherichia coli} SCOP: c.55.3.5 e.8.1.1 PDB: 1d9f_A* 1d9d_A* 1krp_A* 1ksp_A* 1qsl_A* 1kfs_A* 2kfz_A* 2kzm_A* 2kzz_A* 1dpi_A* 1kfd_A* 1kln_A* 1d8y_A*	Back alignment and structure

>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

>4hec_A Putative uncharacterized protein; ssgcid, structural genomics, SEA structural genomics center for infectious disease, unknown; 1.80A {Mycobacterium tuberculosis}	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

>4gmj_B CCR4-NOT transcription complex subunit 7; mRNA decay, deadenylase, RNA bindin; HET: GOL; 2.70A {Homo sapiens}	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

>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

>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

>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

>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

>2gv9_A DNA polymerase; polymerase alpha fold, transferase; HET: DNA; 2.68A {Human herpesvirus 1} PDB: 1dml_B*	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

>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

>1yt3_A Ribonuclease D, RNAse D; exoribonuclease, exonuclease, hydrolase, tRNA processing, hydrolase,translation; 1.60A {Escherichia coli} SCOP: a.60.8.3 a.60.8.3 c.55.3.5	Back alignment and structure

>3saf_A Exosome component 10; exoribonuclease, RNA exosome, hydrolase; 2.50A {Homo sapiens} PDB: 3sag_A 3sah_A 2cpr_A	Back alignment and structure

>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

>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

>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

>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

>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

>3cym_A Uncharacterized protein BAD_0989; structural genomics, unknown function; 2.10A {Bifidobacterium adolescentis atcc 1570ORGANISM_TAXID}	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

>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

>1bgx_T TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhibition, helix-coil dynamics, inhibitor design, complex (polymerase/inhibitor); 2.30A {Thermus aquaticus} SCOP: a.60.7.1 c.120.1.2 c.55.3.5 e.8.1.1 PDB: 1cmw_A 1tau_A* 1taq_A*	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Alignment Graph	Length	Definition	E-value
Query		339
d1y97a1		228	c.55.3.5 (A:1-228) Three prime repair exonuclease	5e-28
d3b6oa1		226	c.55.3.5 (A:9-234) Three prime repair exonuclease	3e-24
d1w0ha_		200	c.55.3.5 (A:) Exonuclease ERI1 {Human (Homo sapien	2e-21
d2f96a1		202	c.55.3.5 (A:19-220) Ribonuclease T {Pseudomonas ae	2e-19
d2guia1		174	c.55.3.5 (A:7-180) N-terminal exonuclease domain o	4e-17
d1x9ma1		204	c.55.3.5 (A:1-210) Exonuclease domain of T7 DNA po	5e-12
d2qxfa1		467	c.55.3.5 (A:8-474) Exonuclease I {Escherichia coli	1e-10
d2igia1		180	c.55.3.5 (A:1-180) Oligoribonuclease {Escherichia	4e-10
d1wlja_		173	c.55.3.5 (A:) Interferon-stimulated gene 20 kDa pr	3e-07

>d1y97a1 c.55.3.5 (A:1-228) Three prime repair exonuclease 2, TREX2 {Human (Homo sapiens) [TaxId: 9606]} Length = 228	Back information, alignment and structure


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

 Score =  106 bits (266), Expect = 5e-28
 Identities = 42/208 (20%), Positives = 74/208 (35%), Gaps = 25/208 (12%)

Query: 122 DLAKLVTAIVFDIETTGFSRENERIIEIAFQDLLGGEN-----------------STFQT 164
           +  +  T +  D+E TG       I E++   +                           
Sbjct: 3   EAPRAETFVFLDLEATGLPSVEPEIAELSLFAVHRSSLENPEHDESGALVLPRVLDKLTL 62

Query: 165 LVNPKRQVP--NAHVHGITTDMVCKPDVPRMEDLIPILLHYVKSRQKPGGYILFVAHNAR 222
            + P+R      + + G++++ + +      +  +   L    SRQ        VAHN  
Sbjct: 63  CMCPERPFTAKASEITGLSSEGLARCRKAGFDGAVVRTLQAFLSRQAGPIC--LVAHNGF 120

Query: 223 SFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSK----VSLQALREYYG 278
            +D P L  E  R    +P + + +DTL   R L ++      ++     SL +L   Y 
Sbjct: 121 DYDFPLLCAELRRLGARLPRDTVCLDTLPALRGLDRAHSHGTRARGRQGYSLGSLFHRYF 180

Query: 279 IPLVGSAHRAMADVNCLSLILQRLTFDL 306
                +AH A  DV+ L LI      +L
Sbjct: 181 RAEPSAAHSAEGDVHTLLLIFLHRAAEL 208

PyMOL of d1y97a1

>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

>d1w0ha_ c.55.3.5 (A:) Exonuclease ERI1 {Human (Homo sapiens) [TaxId: 9606]} Length = 200	Back information, alignment and structure

>d2f96a1 c.55.3.5 (A:19-220) Ribonuclease T {Pseudomonas aeruginosa [TaxId: 287]} Length = 202	Back information, alignment and structure

>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

>d1x9ma1 c.55.3.5 (A:1-210) Exonuclease domain of T7 DNA polymerase {Bacteriophage T7 [TaxId: 10760]} Length = 204	Back information, alignment and structure

>d2qxfa1 c.55.3.5 (A:8-474) Exonuclease I {Escherichia coli K12 (Escherichia coli K-12) [TaxId: 83333]} Length = 467	Back information, alignment and structure

>d2igia1 c.55.3.5 (A:1-180) Oligoribonuclease {Escherichia coli [TaxId: 562]} Length = 180	Back information, alignment and structure

>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

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		339
d2guia1		174	N-terminal exonuclease domain of the epsilon subun	99.96
d3b6oa1		226	Three prime repair exonuclease 1, TREX1 {Mouse (Mu	99.95
d1y97a1		228	Three prime repair exonuclease 2, TREX2 {Human (Ho	99.94
d1w0ha_		200	Exonuclease ERI1 {Human (Homo sapiens) [TaxId: 960	99.94
d1wlja_		173	Interferon-stimulated gene 20 kDa protein, ISG20 {	99.94
d2qxfa1		467	Exonuclease I {Escherichia coli K12 (Escherichia c	99.87
d2f96a1		202	Ribonuclease T {Pseudomonas aeruginosa [TaxId: 287	99.84
d2igia1		180	Oligoribonuclease {Escherichia coli [TaxId: 562]}	99.75
d1x9ma1		204	Exonuclease domain of T7 DNA polymerase {Bacteriop	98.99
d1kfsa1		195	Exonuclease domain of prokaryotic DNA polymerase {	98.93
d2d5ra1		252	CCR4-NOT transcription complex subunit 7, CAF1 {Hu	98.9
d2hhva1		171	Exonuclease domain of prokaryotic DNA polymerase {	98.74
d1tgoa1		347	Exonuclease domain of family B DNA polymerases {Ar	98.68
d1uoca_		286	Pop2 RNase D domain {Baker's yeast (Saccharomyces	98.48
d1yt3a3		193	Ribonuclease D, catalytic domain {Escherichia coli	98.32
d2hbka2		292	Exosome complex exonuclease RRP6 {Baker's yeast (S	98.12
d1q8ia1		388	Exonuclease domain of family B DNA polymerases {Es	97.87
d1s5ja1		410	Exonuclease domain of family B DNA polymerases {Su	97.84
d1ih7a1		375	Exonuclease domain of family B DNA polymerases {Ba	97.44
d1noya_		372	Exonuclease domain of family B DNA polymerases {Ba	97.35
d1vk0a_		206	Hypothetical protein AT5G06450 {Thale-cress (Arabi	97.22
d2py5a1		183	Exonuclease domain of phi29 DNA polymerase {Bacter	95.54

>d2guia1 c.55.3.5 (A:7-180) N-terminal exonuclease domain of the epsilon subunit of DNA polymerase III {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: DnaQ-like 3'-5' exonuclease
domain: N-terminal exonuclease domain of the epsilon subunit of DNA polymerase III
species: Escherichia coli [TaxId: 562]

Probab=99.96  E-value=1.7e-28  Score=209.20  Aligned_cols=160  Identities=30%  Similarity=0.498  Sum_probs=140.7

Q ss_pred             cEEEEEEecCCCCCC-----CCcEEEEEEEEEcCCee--eeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCCCHHHHHH
Q 019538          128 TAIVFDIETTGFSRE-----NERIIEIAFQDLLGGEN--STFQTLVNPKRQVPN--AHVHGITTDMVCKPDVPRMEDLIP  198 (339)
Q Consensus       128 ~~vviDiETTGl~p~-----~~~IIEIgav~v~~g~i--~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap~~~evl~  198 (339)
                      ++||||+||||++|.     .++|||||+|.++++.+  +.|+.+|+|..+++.  +++|||+++++.  ++|++.+++.
T Consensus         1 r~vv~D~ETTGl~~~~~~~~~d~IIeIg~v~~~~~~~~~~~~~~~v~P~~~i~~~~~~i~gIt~e~~~--~~~~~~~~~~   78 (174)
T d2guia1           1 RQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLL--DKPTFAEVAD   78 (174)
T ss_dssp             EEEEEEEEESCCCSSSSTTTTCCEEEEEEEEEETTEECSCCEEEECCCSSCCCHHHHHHHCCCHHHHT--TSCCHHHHHH
T ss_pred             CEEEEEeeCCCCCcccccCCCCEEEEEEEEEEECCEEeeeEEEEEeccCccchhhhhhccccchhhhh--cchhHHHHHH
Confidence            579999999999873     47899999999998865  789999999988877  899999999999  8899999999


Q ss_pred             HHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCC---CceeeHHHHHHHHHhcCCCCCCCCCCHHHHHH
Q 019538          199 ILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNN---WLFMDTLTLARELMKSGGSNLPSKVSLQALRE  275 (339)
Q Consensus       199 ~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~---~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~  275 (339)
                      +|.+|+.+       ..+|+||. .||..++...+.+.+...+..   ..++|++.+++.+++..      .++|..+++
T Consensus        79 ~~~~~~~~-------~~~v~~~~-~~d~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~------~~~L~~l~~  144 (174)
T d2guia1          79 EFMDYIRG-------AELVIHNA-AFDIGFMDYEFSLLKRDIPKTNTFCKVTDSLAVARKMFPGK------RNSLDALCA  144 (174)
T ss_dssp             HHHHHHTT-------SEEEETTH-HHHHHHHHHHHHHTCSCCCCGGGTSEEEEHHHHHHHHSTTS------CCSHHHHHH
T ss_pred             HHHHhcCC-------CeEEEeec-chhhHHHHHHHHHhCCCCCCcccccchhhHHHHHHHHcCCC------CCCHHHHHH
Confidence            99999974       47999999 999999999999988765532   34689999999988764      789999999


Q ss_pred             HhCCCCCC-CCCChHHHHHHHHHHHHHHH
Q 019538          276 YYGIPLVG-SAHRAMADVNCLSLILQRLT  303 (339)
Q Consensus       276 ~~gI~~~~-~aH~Al~DA~~ta~L~~~l~  303 (339)
                      +||++..+ .+|+|++||.+|++||.+|+
T Consensus       145 ~~~~~~~~~~~H~Al~Da~~ta~v~~~l~  173 (174)
T d2guia1         145 RYEIDNSKRTLHGALLDAQILAEVYLAMT  173 (174)
T ss_dssp             HTTCCCTTCSSCCHHHHHHHHHHHHHHHT
T ss_pred             HcCCCCCCCCCcCHHHHHHHHHHHHHHHc
Confidence            99998764 48999999999999999985

PyMOL of d2guia1

>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

>d1wlja_ c.55.3.5 (A:) Interferon-stimulated gene 20 kDa protein, ISG20 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2qxfa1 c.55.3.5 (A:8-474) Exonuclease I {Escherichia coli K12 (Escherichia coli K-12) [TaxId: 83333]}	Back information, alignment and structure

>d2f96a1 c.55.3.5 (A:19-220) Ribonuclease T {Pseudomonas aeruginosa [TaxId: 287]}	Back information, alignment and structure

>d2igia1 c.55.3.5 (A:1-180) Oligoribonuclease {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>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

>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

>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

>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

>d1uoca_ c.55.3.9 (A:) Pop2 RNase D domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	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

>d2hbka2 c.55.3.5 (A:129-420) Exosome complex exonuclease RRP6 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	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

>d1ih7a1 c.55.3.5 (A:1-375) Exonuclease domain of family B DNA polymerases {Bacteriophage RB69 [TaxId: 12353]}	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

>d1vk0a_ c.55.3.5 (A:) Hypothetical protein AT5G06450 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]}	Back information, alignment and structure

>d2py5a1 c.55.3.5 (A:5-187) Exonuclease domain of phi29 DNA polymerase {Bacteriophage phi-29 [TaxId: 10756]}	Back information, alignment and structure