Citrus Sinensis ID: 010297

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-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510---

MGPTQDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLGQQTHRSLDDVRMNLEVLKYCATVLFLESSLPDIFTVNSWVSPNATTRSRSNAKSSPEGTSQNLSTPSSKFKFENASNASPPDQGKEEIHPIFSLVTQGTAEVDSVLAVTTADQPNPFDMSQLSNQMETQSLQPDDTMEDKSAPESREMCSTASVSEGSSGYAGFMEPDEVSLSSISDGVVPLFPGSQIQKIKLLHNDVILQLCCSRLKIRFGISTKFVDQAGRPRLSFVVDISQSLCTVLDACEVIVRKLVEDSGSSSEWRHVVTRKGGFFNHPTARLHIPTVVFGNVARYATEMYQKEASGTIQKLVFVKFDAAELDSLLKPGTFVDAFLSLDPYDYQQSAGIRLVAKKLIIHSE

cccccccccEEEEEEcccccccccccccEEEEEEEEEEcccEEEEEEEEccccccccccccccccccccccHHHHcccccHHHHHHHHHHHHcccEEEEEccccccHHHHHHHHHHcccccccccccEEcHHHHHHHHccccccccHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHcccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHcccccccccccccHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHcccccEEEEEccccEEEEcccHHHcccccccEEEEEEEccHHHHHHHHHHHHHHHHHHccccccccccccEEEccccccccEEEEEccccccccccEEEEEEEEcccccccEEEEEccccHHHHHHHcccccEEEEEEEccccHHHcccccHHHHHHHHcccc

ccccccccEEEEEEEEcccccccccccEEEEEEEEEEEccccEEEEEEEEEEcccccccccHHHEEEccccHHHHcccccHHHHHHHHHHHHcccEEEEEccccccHHHHHHHHHHccccccccccHHcHHHHHHHHHccccccccHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEccccHHHHHHccccccccccccHHHcccccccccccccccHcccccccHccccccccccccccccccccccccccHHEEEEEEccccccccccEEEEEEccccEEEEccccEEEEEEcccccccccccEEEEEEcccHHHHHHHHHHHHHHHHccccccccccccEEEEEccccccccEEEEEEEEEEcccccEEEEEEEEEcccccEEEEEEccccHHHHHHHcccccEEEEEEEEcccHHHHHccHHEEEEEEEEEcc

mgptqdrseiaffdvettvptrpgqrfailEFGAILvcpkkleelhnystlvrpadpeliSSLSVrcngitpdavvssptfadIADTVFDILHGRIWAGHNILRFDCARIREAFAeigrpapepkgtiDSLALLTQRFGRRAGDMKMASLATYFglgqqthrsLDDVRMNLEVLKYCATVLFlesslpdiftvnswvspnattrsrsnaksspegtsqnlstpsskfkfenasnasppdqgkeeihpifslvtqgtaevDSVLAVttadqpnpfdmsqlsnqmetqslqpddtmedksapesremcstasvsegssgyagfmepdevslssisdgvvplfpgsqiqkiKLLHNDVILQLCCSRLKirfgistkfvdqagrprlsFVVDISQSLCTVLDACEVIVRKLVedsgsssewrhvvtrkggffnhptarlhiptvVFGNVARYATEMYQKEASGTIQKLVFVKFDAAeldsllkpgtfvdaflsldpydyqqsaGIRLVAKKLIIHSE

mgptqdrseiaffdvettvptrpgqRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITpdavvssptfADIADTVFDILHGRIWAGHNILRFDCARIREAFAEigrpapepkgtidsLALLTQRFGRRAGDMKMASLATYFGLGQQTHRSLDDVRMNLEVLKYCATVLFLESSLPDIFTVNSWVSPNAttrsrsnaksspegtsqnlstpsskfkfENASNASPPDQGKEEIHPIFSLVTQGTAEVDSVLAVTTADQPNPFDMSQLSNQMETQSLQPDDTMEDKSAPESREMCSTASVSEGSSGYAGFMEPDEVSLSSISDGVVPLFPGSQIQKIKLLHNDVILQLCCSRLKIRFGISTkfvdqagrPRLSFVVDISQSLCTVLDACEVIVRKlvedsgsssewrHVVTRKGgffnhptarlhiptVVFGNVARYATEMYQKEASGTIQKLVFVKFDAAELDSLLKPGTFVDAFLSLDPYDYQQSAGIRLVAKKLIIHSE

*********IAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTVFDILHGRIWAGHNILRFDCARIREAFAEIGR*******TIDSLALLTQRFGRRAGDMKMASLATYFGLGQQTHRSLDDVRMNLEVLKYCATVLFLESSLPDIFTVNSWV*************************************************PIFSLVTQGTAEVDSVLAV******************************************************************ISDGVVPLFPGSQIQKIKLLHNDVILQLCCSRLKIRFGISTKFVDQAGRPRLSFVVDISQSLCTVLDACEVIVRKLVEDSGSSSEWRHVVTRKGGFFNHPTARLHIPTVVFGNVARYATEMYQKEASGTIQKLVFVKFDAAELDSLLKPGTFVDAFLSLDPYDYQQSAGIRLVAKKLII***

****QDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLGQQTHRSLDDVRMNLEVLKYCATVLFLESSLPDIFT***************************LSTPS*KFKFENA**********************************TADQPNPFDMSQLSN*************************STASVSEGSSGYAGFMEPDEVSLSSISDGVVP*F*GSQIQKIKLLHNDVILQLCCSRLKIRFGISTKFVDQAGRPRLSFVVDISQSLCTVLDACEV******************VTRKGGFFNHPTARLHIPTVVFGNVARYATEMYQKEAS**I**LVFVKFDAAELDSLLKPGTFVDAFLSLDPYDYQQSAGIRLVAKKLIIHS*

MGPTQDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLGQQTHRSLDDVRMNLEVLKYCATVLFLESSLPDIFTVNSWVSPN************************SKFKF************KEEIHPIFSLVTQGTAEVDSVLAVTTADQPNPFDMSQLSNQ*********************************SGYAGFMEPDEVSLSSISDGVVPLFPGSQIQKIKLLHNDVILQLCCSRLKIRFGISTKFVDQAGRPRLSFVVDISQSLCTVLDACEVIVRKLVE********RHVVTRKGGFFNHPTARLHIPTVVFGNVARYATEMYQKEASGTIQKLVFVKFDAAELDSLLKPGTFVDAFLSLDPYDYQQSAGIRLVAKKLIIHSE

*****DRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLGQQTHRSLDDVRMNLEVLKYCATVLFLESSLPDIFT*****************************************************HPIFSLVTQGTAEVDSVLAVTTADQPNPFDMSQLSNQMET*********************************AGFMEPDEVSLSSISDGVVPLFPGSQIQKIKLLHNDVILQLCCSRLKIRFGISTKFVDQAGRPRLSFVVDISQSLCTVLDACEVIVRKLVEDSGSSSEWRHVVTRKGGFFNHPTARLHIPTVVFGNVARYATEMYQKEASGTIQKLVFVKFDAAELDSLLKPGTFVDAFLSLDPYDYQQSAGIRLVAKKLIIHS*

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

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		513	2.2.26 [Sep-21-2011]
Q10384		645	Uncharacterized protein R	yes	no	0.265	0.210	0.318	1e-06
Q8XJR3		1449	DNA polymerase III PolC-t	yes	no	0.360	0.127	0.24	1e-05
Q8RA32		1401	DNA polymerase III PolC-t	yes	no	0.304	0.111	0.245	7e-05
O83649		215	DNA polymerase III subuni	yes	no	0.307	0.734	0.281	0.0001
P03007		243	DNA polymerase III subuni	N/A	no	0.239	0.506	0.297	0.0002
P0A1G9		243	DNA polymerase III subuni	yes	no	0.239	0.506	0.297	0.0003
P0A1H0		243	DNA polymerase III subuni	N/A	no	0.239	0.506	0.297	0.0003

>sp\|Q10384\|Y2191_MYCTU Uncharacterized protein Rv2191/MT2247 OS=Mycobacterium tuberculosis GN=Rv2191 PE=4 SV=1	Back alignment and function desciption

 Score = 55.1 bits (131), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 49/154 (31%), Positives = 69/154 (44%), Gaps = 18/154 (11%)

Query: 28  AILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADT 87
           AI E GA+ VC   +  L  ++TLV P     I    VR  GIT   V ++PT   +   
Sbjct: 65  AITEIGAVKVCGGAV--LGEFATLVNPQ--HSIPPQIVRLTGITTAMVGNAPTIDAVLPM 120

Query: 88  VFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRR------ 141
            F+     +   HN   FD   +R A        P+P+       L T R  RR      
Sbjct: 121 FFEFAGDSVLVAHNA-GFDIGFLRAAARRCDITWPQPQ------VLCTMRLARRVLSRDE 173

Query: 142 AGDMKMASLATYFGLGQQ-THRSLDDVRMNLEVL 174
           A  +++A+LA  F +    THR+LDD R  ++VL
Sbjct: 174 APSVRLAALARLFAVASNPTHRALDDARATVDVL 207

Mycobacterium tuberculosis (taxid: 1773)

>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\|Q8RA32\|DPO3_THETN DNA polymerase III PolC-type OS=Thermoanaerobacter tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4) GN=polC PE=3 SV=1	Back alignment and function description

>sp\|O83649\|DPO3E_TREPA DNA polymerase III subunit epsilon OS=Treponema pallidum (strain Nichols) GN=dnaQ PE=3 SV=1	Back alignment and function description

>sp\|P03007\|DPO3E_ECOLI DNA polymerase III subunit epsilon OS=Escherichia coli (strain K12) GN=dnaQ PE=1 SV=1	Back alignment and function description

>sp\|P0A1G9\|DPO3E_SALTY DNA polymerase III subunit epsilon OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=dnaQ PE=3 SV=1	Back alignment and function description

>sp\|P0A1H0\|DPO3E_SALTI DNA polymerase III subunit epsilon OS=Salmonella typhi GN=dnaQ 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		513
225457353		497	PREDICTED: uncharacterized protein LOC10	0.968	1.0	0.682	0.0
147817752		535	hypothetical protein VITISV_031720 [Viti	0.968	0.928	0.633	0.0
255547339		501	exonuclease, putative [Ricinus communis]	0.970	0.994	0.673	0.0
449440810		471	PREDICTED: uncharacterized protein LOC10	0.912	0.993	0.646	1e-180
224124082		470	predicted protein [Populus trichocarpa]	0.914	0.997	0.646	1e-180
356512002		501	PREDICTED: uncharacterized protein LOC10	0.972	0.996	0.624	1e-179
297733948		447	unnamed protein product [Vitis vinifera]	0.871	1.0	0.639	1e-179
356562862		501	PREDICTED: uncharacterized protein LOC10	0.972	0.996	0.626	1e-179
297806807		468	exonuclease family protein [Arabidopsis	0.904	0.991	0.597	1e-159
15240840		468	exonuclease family protein [Arabidopsis	0.910	0.997	0.592	1e-159

>gi\|225457353\|ref\|XP_002281793.1\| PREDICTED: uncharacterized protein LOC100265514 [Vitis vinifera]	Back alignment and taxonomy information

 Score =  707 bits (1824), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 350/513 (68%), Positives = 410/513 (79%), Gaps = 16/513 (3%)

Query: 1   MGPTQDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELI 60
           MGP ++RSEIAFFDVETTVPTR GQ FAILEFGAILVCP+KL EL +YSTLVRP D  L+
Sbjct: 1   MGPGEERSEIAFFDVETTVPTRVGQGFAILEFGAILVCPRKLVELESYSTLVRPHDLSLV 60

Query: 61  SSLSVRCNGITPDAVVSSPTFADIADTVFDILHGRIWAGHNILRFDCARIREAFAEIGRP 120
           SSLSVRCNGIT DAVVS+P F DIAD V+DILHGRIWAGHNILRFDCARIREAFAEIGRP
Sbjct: 61  SSLSVRCNGITRDAVVSAPNFRDIADRVYDILHGRIWAGHNILRFDCARIREAFAEIGRP 120

Query: 121 APEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLGQQTHRSLDDVRMNLEVLKYCATV 180
           APEPKG+IDSLALLTQRFGRRAGDMKMA+LATYFGLGQQTHRSLDDVRMNLEVLKYCATV
Sbjct: 121 APEPKGSIDSLALLTQRFGRRAGDMKMATLATYFGLGQQTHRSLDDVRMNLEVLKYCATV 180

Query: 181 LFLESSLPDIFTVNSWVSPNATTRSRSNAKSSPEGTSQNLSTPSSKFKFENASNASPPDQ 240
           LFLESSLPDIFT NSWVSPNA TRSRSN K+SP G + N+STPSS  KFEN  ++     
Sbjct: 181 LFLESSLPDIFTTNSWVSPNAVTRSRSNGKASPVGMNLNMSTPSSSIKFEN--HSISSPS 238

Query: 241 GKEEIHPIFSLVTQGTAEVDSVLAVTTADQPNPFDMSQLSNQMETQSLQPDDTMEDKSAP 300
               +  I +LV   T            +QP+PF++  LS+++E +SL+PD  +E+K   
Sbjct: 239 THSSMEGILNLVEPNT------------NQPDPFNLGALSSEIERESLKPDYALEEKPVT 286

Query: 301 ESREMCSTASVSEGSSGYAGFMEPDEVSLSSISDGVVPLFPGSQIQKIKLLHNDVILQLC 360
           ES EM ST + S+    YAGF++P EVS++SIS   VPL+ G+  +++++LHNDV L L 
Sbjct: 287 ESLEMLSTTTASQDCCDYAGFLDPAEVSVASISASFVPLYRGT--RRMQILHNDVKLLLH 344

Query: 361 CSRLKIRFGISTKFVDQAGRPRLSFVVDISQSLCTVLDACEVIVRKLVEDSGSSSEWRHV 420
           C++L++RFGIST+FVD AGRPRLSFVVD S SLC VLDAC+ +  KL  DSGSSSEWR V
Sbjct: 345 CTQLRVRFGISTRFVDPAGRPRLSFVVDGSPSLCQVLDACDQLAYKLSVDSGSSSEWRPV 404

Query: 421 VTRKGGFFNHPTARLHIPTVVFGNVARYATEMYQKEASGTIQKLVFVKFDAAELDSLLKP 480
           V RK GF N PT RL IPTV  G++A YATE+YQK+ SGT Q+L+F +FDAAELD+L  P
Sbjct: 405 VIRKTGFLNTPTIRLSIPTVTNGDIAIYATEIYQKDPSGTTQRLIFSRFDAAELDTLFVP 464

Query: 481 GTFVDAFLSLDPYDYQQSAGIRLVAKKLIIHSE 513
           GT VD + +LDPYDYQQ+AGI+LVAKKLIIH +
Sbjct: 465 GTLVDTYFALDPYDYQQNAGIKLVAKKLIIHGK 497

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|147817752\|emb\|CAN66660.1\| hypothetical protein VITISV_031720 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|255547339\|ref\|XP_002514727.1\| exonuclease, putative [Ricinus communis] gi\|223546331\|gb\|EEF47833.1\| exonuclease, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|449440810\|ref\|XP_004138177.1\| PREDICTED: uncharacterized protein LOC101203629 [Cucumis sativus]	Back alignment and taxonomy information

>gi\|224124082\|ref\|XP_002330100.1\| predicted protein [Populus trichocarpa] gi\|222871234\|gb\|EEF08365.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|356512002\|ref\|XP_003524710.1\| PREDICTED: uncharacterized protein LOC100788659 [Glycine max]	Back alignment and taxonomy information

>gi\|297733948\|emb\|CBI15195.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|356562862\|ref\|XP_003549687.1\| PREDICTED: uncharacterized protein LOC100818863 [Glycine max]	Back alignment and taxonomy information

>gi\|297806807\|ref\|XP_002871287.1\| exonuclease family protein [Arabidopsis lyrata subsp. lyrata] gi\|297317124\|gb\|EFH47546.1\| exonuclease family protein [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi\|15240840\|ref\|NP_196388.1\| exonuclease family protein [Arabidopsis thaliana] gi\|9759593\|dbj\|BAB11450.1\| exonuclease-like protein [Arabidopsis thaliana] gi\|332003813\|gb\|AED91196.1\| exonuclease family protein [Arabidopsis thaliana]	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		513
TAIR\|locus:2160359		468	AT5G07710 [Arabidopsis thalian	0.452	0.495	0.740	7.5e-148
TAIR\|locus:2019100		506	AT1G74390 [Arabidopsis thalian	0.961	0.974	0.549	3.8e-133
TAIR\|locus:2163208		487	AT5G61390 [Arabidopsis thalian	0.575	0.605	0.574	1.7e-82
TAIR\|locus:2135302		255	AT4G39810 [Arabidopsis thalian	0.467	0.941	0.549	2.5e-65
UNIPROTKB\|Q10384		645	MT2247 "Uncharacterized protei	0.302	0.240	0.305	1.7e-06
TIGR_CMR\|CJE_0502		233	CJE_0502 "exonuclease, DNA pol	0.307	0.678	0.279	2.4e-06
UNIPROTKB\|Q74DD3		181	GSU1383 "3'-to-5' exonuclease,	0.296	0.839	0.278	3.6e-05
TIGR_CMR\|GSU_1383		181	GSU_1383 "exonuclease" [Geobac	0.296	0.839	0.278	3.6e-05
UNIPROTKB\|Q9KPX9		247	VC_2233 "DNA polymerase III, e	0.372	0.773	0.268	4.3e-05
TIGR_CMR\|VC_2233		247	VC_2233 "DNA polymerase III, e	0.372	0.773	0.268	4.3e-05

TAIR\|locus:2160359 AT5G07710 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 836 (299.3 bits), Expect = 7.5e-148, Sum P(2) = 7.5e-148
 Identities = 177/239 (74%), Positives = 192/239 (80%)

Query:     1 MGPTQDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELI 60
             M P +DRSEIAFFDVETTVP R GQRFAILEFG+ILVCPKKL EL +Y+TLV+PAD  LI
Sbjct:     1 MDP-EDRSEIAFFDVETTVPKR-GQRFAILEFGSILVCPKKLTELRSYTTLVQPADLSLI 58

Query:    61 SSLSVRCNGITPDAVVSSPTFADIADTVFDILHGRIWAGHNILRFDCARIREAFAEIGRP 120
             SSLSVRCNGI  D VV +P FADIADTV+DILHGRIWAGHNILRFDCARIREAFAEIGR 
Sbjct:    59 SSLSVRCNGIKRDDVVLAPLFADIADTVYDILHGRIWAGHNILRFDCARIREAFAEIGRQ 118

Query:   121 APEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLGQQTHRSLDDVRMNLEVLKYCATV 180
              PEPKG IDSL LLTQ+FGRRAGDMKMA+LA YFGLG QTHRSLDDVRMNLEVLKYCATV
Sbjct:   119 PPEPKGAIDSLGLLTQKFGRRAGDMKMATLARYFGLGNQTHRSLDDVRMNLEVLKYCATV 178

Query:   181 LFLESSLPDIFTVNSWVSPNATTRSRSNAKSSPEGTSQNLSTPSSKFKFENASNASPPD 239
             LFLESSLP     NS VSP  T  SR    +S EG   N  T S +    + ++A+ PD
Sbjct:   179 LFLESSLPYAHVDNS-VSPE-TISSRRRIDASREG---NTVTTSVRLPSISENSAAQPD 232

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005622 "intracellular" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

TAIR\|locus:2019100 AT1G74390 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2163208 AT5G61390 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2135302 AT4G39810 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

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

TIGR_CMR\|CJE_0502 CJE_0502 "exonuclease, DNA polymerase III, epsilon subunit family" [Campylobacter jejuni RM1221 (taxid:195099)]	Back alignment and assigned GO terms

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

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

UNIPROTKB\|Q9KPX9 VC_2233 "DNA polymerase III, epsilon subunit" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)]	Back alignment and assigned GO terms

TIGR_CMR\|VC_2233 VC_2233 "DNA polymerase III, epsilon subunit" [Vibrio cholerae O1 biovar El Tor (taxid:686)]	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!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	gw1.129.103.1	hypothetical protein (455 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
		Sorry, there are no predicted associations at the current settings.

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		513
smart00479		169	smart00479, EXOIII, exonuclease domain in DNA-poly	9e-30
cd06127		159	cd06127, DEDDh, DEDDh 3'-5' exonuclease domain fam	7e-27
pfam00929		161	pfam00929, RNase_T, Exonuclease	2e-20
COG0847		243	COG0847, DnaQ, DNA polymerase III, epsilon subunit	2e-19
PRK07883		557	PRK07883, PRK07883, hypothetical protein; Validate	4e-16
PRK06063		313	PRK06063, PRK06063, DNA polymerase III subunit eps	2e-13
cd06130		156	cd06130, DNA_pol_III_epsilon_like, an uncharacteri	2e-12
TIGR00573		217	TIGR00573, dnaq, exonuclease, DNA polymerase III,	5e-12
cd06133		176	cd06133, ERI-1_3'hExo_like, DEDDh 3'-5' exonucleas	3e-10
cd06131		167	cd06131, DNA_pol_III_epsilon_Ecoli_like, DEDDh 3'-	4e-09
PRK08074		928	PRK08074, PRK08074, bifunctional ATP-dependent DNA	2e-08
TIGR01407		850	TIGR01407, dinG_rel, DnaQ family exonuclease/DinG	3e-08
PRK08517		257	PRK08517, PRK08517, DNA polymerase III subunit eps	1e-07
TIGR01405		1213	TIGR01405, polC_Gram_pos, DNA polymerase III, alph	2e-07
PRK06807		313	PRK06807, PRK06807, DNA polymerase III subunit eps	5e-07
PRK05711		240	PRK05711, PRK05711, DNA polymerase III subunit eps	1e-06
PRK00448		1437	PRK00448, polC, DNA polymerase III PolC; Validated	9e-06
PRK07740		244	PRK07740, PRK07740, hypothetical protein; Provisio	2e-05
COG2176		1444	COG2176, PolC, DNA polymerase III, alpha subunit (	5e-05
PRK06310		250	PRK06310, PRK06310, DNA polymerase III subunit eps	6e-05
cd06138		183	cd06138, ExoI_N, N-terminal DEDDh 3'-5' exonucleas	8e-05
PRK06309		232	PRK06309, PRK06309, DNA polymerase III subunit eps	4e-04
TIGR01406		225	TIGR01406, dnaQ_proteo, DNA polymerase III, epsilo	6e-04

>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 =  114 bits (287), Expect = 9e-30
 Identities = 47/176 (26%), Positives = 75/176 (42%), Gaps = 9/176 (5%)

Query: 9   EIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCN 68
            +   D ETT    PG+   I+E  A+ V   ++ E+  + T V+P  P  I+  +   +
Sbjct: 1   TLVVIDCETT-GLDPGK-DEIIEIAAVDVDGGEIIEV--FDTYVKPDRP--ITDYATEIH 54

Query: 69  GITPDAVVSSPTFADIADTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTI 128
           GITP+ +  +PTF ++ + + + L GRI    N   FD   ++     +G   P     I
Sbjct: 55  GITPEMLDDAPTFEEVLEELLEFLRGRILVAGNSAHFDLRFLKLEHPRLGIKQPPKLPVI 114

Query: 129 DSLALLTQRFGRRAGDMKMASLATYFGLGQQ--THRSLDDVRMNLEVLKYCATVLF 182
           D+L L             +  LA    L      HR+LDD R   ++ K     L 
Sbjct: 115 DTLKLARATNPGL-PKYSLKKLAKRLLLEVIQRAHRALDDARATAKLFKKLLERLE 169

Length = 169

>gnl\|CDD\|176648 cd06127, DEDDh, DEDDh 3'-5' exonuclease domain family	Back alignment and domain information

>gnl\|CDD\|216200 pfam00929, RNase_T, Exonuclease	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\|236123 PRK07883, PRK07883, hypothetical protein; Validated	Back alignment and domain information

>gnl\|CDD\|180377 PRK06063, PRK06063, DNA polymerase III subunit epsilon; Provisional	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\|129663 TIGR00573, dnaq, exonuclease, DNA polymerase III, epsilon subunit family	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\|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\|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\|236281 PRK08517, PRK08517, 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\|235864 PRK06807, PRK06807, DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

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

>gnl\|CDD\|234767 PRK00448, polC, DNA polymerase III PolC; Validated	Back alignment and domain information

>gnl\|CDD\|236085 PRK07740, PRK07740, hypothetical protein; Provisional	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\|180525 PRK06310, PRK06310, DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>gnl\|CDD\|99841 cd06138, ExoI_N, N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins	Back alignment and domain information

>gnl\|CDD\|180524 PRK06309, PRK06309, 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		513
COG2176		1444	PolC DNA polymerase III, alpha subunit (gram-posit	100.0
PRK09146		239	DNA polymerase III subunit epsilon; Validated	100.0
TIGR00573		217	dnaq exonuclease, DNA polymerase III, epsilon subu	100.0
PRK05711		240	DNA polymerase III subunit epsilon; Provisional	100.0
PRK07942		232	DNA polymerase III subunit epsilon; Provisional	100.0
TIGR01406		225	dnaQ_proteo DNA polymerase III, epsilon subunit, P	100.0
PRK06807		313	DNA polymerase III subunit epsilon; Validated	100.0
PRK07748		207	sporulation inhibitor KapD; Provisional	100.0
smart00479		169	EXOIII exonuclease domain in DNA-polymerase alpha	100.0
cd06131		167	DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonucl	100.0
PRK08517		257	DNA polymerase III subunit epsilon; Provisional	99.98
cd06130		156	DNA_pol_III_epsilon_like an uncharacterized bacter	99.98
PRK06195		309	DNA polymerase III subunit epsilon; Validated	99.98
PRK07740		244	hypothetical protein; Provisional	99.98
PRK06310		250	DNA polymerase III subunit epsilon; Validated	99.98
PRK06063		313	DNA polymerase III subunit epsilon; Provisional	99.98
TIGR01405		1213	polC_Gram_pos DNA polymerase III, alpha chain, Gra	99.97
PRK09145		202	DNA polymerase III subunit epsilon; Validated	99.97
TIGR01298		200	RNaseT ribonuclease T. in gamma-subdivision Proteo	99.97
PRK06309		232	DNA polymerase III subunit epsilon; Validated	99.97
cd06136		177	TREX1_2 DEDDh 3'-5' exonuclease domain of three pr	99.97
PRK07247		195	DNA polymerase III subunit epsilon; Validated	99.97
PRK07883		557	hypothetical protein; Validated	99.97
PRK05168		211	ribonuclease T; Provisional	99.97
PRK06722		281	exonuclease; Provisional	99.97
cd06134		189	RNaseT DEDDh 3'-5' exonuclease domain of RNase T.	99.97
cd06133		176	ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain o	99.97
PRK07246		820	bifunctional ATP-dependent DNA helicase/DNA polyme	99.96
cd06138		183	ExoI_N N-terminal DEDDh 3'-5' exonuclease domain o	99.96
PRK08074		928	bifunctional ATP-dependent DNA helicase/DNA polyme	99.96
cd06127		159	DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh	99.96
TIGR01407		850	dinG_rel DnaQ family exonuclease/DinG family helic	99.96
PRK05601		377	DNA polymerase III subunit epsilon; Validated	99.96
PRK07983		219	exodeoxyribonuclease X; Provisional	99.95
PRK00448		1437	polC DNA polymerase III PolC; Validated	99.95
cd06137		161	DEDDh_RNase DEDDh 3'-5' exonuclease domain of the	99.95
COG0847		243	DnaQ DNA polymerase III, epsilon subunit and relat	99.95
cd06149		157	ISG20 DEDDh 3'-5' exonuclease domain of Interferon	99.94
PRK05359		181	oligoribonuclease; Provisional	99.94
cd06135		173	Orn DEDDh 3'-5' exonuclease domain of oligoribonuc	99.94
cd06144		152	REX4_like DEDDh 3'-5' exonuclease domain of RNA ex	99.94
PRK09182		294	DNA polymerase III subunit epsilon; Validated	99.94
PTZ00315		582	2'-phosphotransferase; Provisional	99.94
cd06145		150	REX1_like DEDDh 3'-5' exonuclease domain of RNA ex	99.94
PF00929		164	RNase_T: Exonuclease; InterPro: IPR013520 This ent	99.94
PRK11779		476	sbcB exonuclease I; Provisional	99.93
KOG0542		280	consensus Predicted exonuclease [Replication, reco	99.73
COG5018		210	KapD Inhibitor of the KinA pathway to sporulation,	99.69
COG1949		184	Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA	99.68
KOG3242		208	consensus Oligoribonuclease (3'->5' exoribonucleas	99.6
KOG2249		280	consensus 3'-5' exonuclease [Replication, recombin	99.53
cd05160		199	DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain	99.46
COG2925		475	SbcB Exonuclease I [DNA replication, recombination	99.45
cd06143		174	PAN2_exo DEDDh 3'-5' exonuclease domain of the euk	99.36
cd06125		96	DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonucleas	99.13
cd05780		195	DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease dom	98.9
PF13482		164	RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A	98.89
KOG2248		380	consensus 3'-5' exonuclease [Replication, recombin	98.79
cd05781		188	DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of	98.76
COG3359		278	Predicted exonuclease [DNA replication, recombinat	98.73
cd05779		204	DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domai	98.68
cd06139		193	DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease	98.64
cd05785		207	DNA_polB_like2_exo Uncharacterized bacterial subgr	98.62
KOG4793		318	consensus Three prime repair exonuclease [Replicat	98.56
PHA02570		220	dexA exonuclease; Provisional	98.49
cd05777		230	DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain	98.36
PRK05755		880	DNA polymerase I; Provisional	98.33
cd05782		208	DNA_polB_like1_exo Uncharacterized bacterial subgr	98.23
cd05783		204	DNA_polB_B1_exo DEDDy 3'-5' exonuclease domain of	98.19
PF10108		209	DNA_pol_B_exo2: Predicted 3'-5' exonuclease relate	98.11
cd05784		193	DNA_polB_II_exo DEDDy 3'-5' exonuclease domain of	98.05
PF04857		262	CAF1: CAF1 family ribonuclease; InterPro: IPR00694	98.04
cd05778		231	DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease	98.01
PF01612		176	DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR00	97.9
PF03104		325	DNA_pol_B_exo1: DNA polymerase family B, exonuclea	97.81
PTZ00166		1054	DNA polymerase delta catalytic subunit; Provisiona	97.8
smart00486		471	POLBc DNA polymerase type-B family. DNA polymerase	97.56
PRK05762		786	DNA polymerase II; Reviewed	97.51
PHA02528		881	43 DNA polymerase; Provisional	97.31
cd05776		234	DNA_polB_alpha_exo inactive DEDDy 3'-5' exonucleas	97.23
TIGR03491		457	RecB family nuclease, putative, TM0106 family. Mem	97.17
PHA02524		498	43A DNA polymerase subunit A; Provisional	96.64
cd06146		193	mut-7_like_exo DEDDy 3'-5' exonuclease domain of C	96.58
KOG1275		1118	consensus PAB-dependent poly(A) ribonuclease, subu	96.23
cd06141		170	WRN_exo DEDDy 3'-5' exonuclease domain of WRN and	96.21
KOG0304		239	consensus mRNA deadenylase subunit [RNA processing	96.02
cd00007		155	35EXOc 3'-5' exonuclease. The 35EXOc domain is res	95.85
cd06129		161	RNaseD_like DEDDy 3'-5' exonuclease domain of RNas	95.81
COG0349		361	Rnd Ribonuclease D [Translation, ribosomal structu	95.61
COG0417		792	PolB DNA polymerase elongation subunit (family B)	95.3
PRK10829		373	ribonuclease D; Provisional	95.24
TIGR00592		1172	pol2 DNA polymerase (pol2). This family is based o	95.14
TIGR01388		367	rnd ribonuclease D. This model describes ribonucle	94.64
KOG1798		2173	consensus DNA polymerase epsilon, catalytic subuni	94.56
PHA03036		1004	DNA polymerase; Provisional	93.56
cd06140		178	DNA_polA_I_Bacillus_like_exo inactive DEDDy 3'-5'	93.32
PRK05761		787	DNA polymerase I; Reviewed	92.91
KOG4793		318	consensus Three prime repair exonuclease [Replicat	92.87
cd06148		197	Egl_like_exo DEDDy 3'-5' exonuclease domain of Dro	92.83
smart00474		172	35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proo	92.04
KOG0969		1066	consensus DNA polymerase delta, catalytic subunit	89.98
COG0749		593	PolA DNA polymerase I - 3'-5' exonuclease and poly	87.57
cd06142		178	RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribon	86.39
PHA02563		630	DNA polymerase; Provisional	82.29
TIGR00593		887	pola DNA polymerase I. This family is based on the	82.25

>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]	Back alignment and domain information

Probab=100.00  E-value=1.4e-37  Score=349.39  Aligned_cols=218  Identities=18%  Similarity=0.263  Sum_probs=205.8

Q ss_pred             CCCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHH
Q 010297            4 TQDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFAD   83 (513)
Q Consensus         4 t~~~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~E   83 (513)
                      ...+.+|||||+|||||++  ..+.|||||||++.+|  +++++|+.||+|..  +++..++++||||++||+++++..+
T Consensus       417 ~l~datyVVfDiETTGLs~--~~d~iIE~aAvKikng--~iId~f~~Fi~P~~--pl~~~~telTgITdeml~~a~~i~~  490 (1444)
T COG2176         417 KLDDATYVVFDIETTGLSP--VYDEIIEIAAVKIKNG--RIIDKFQFFIKPGR--PLSATITELTGITDEMLENAPEIEE  490 (1444)
T ss_pred             ccccccEEEEEeecCCcCc--ccchhhhheeeeeeCC--cchHHHHHhcCCCC--cCchhhhhccccCHHHHcCCccHHH
Confidence            4567889999999999998  8899999999999998  67899999999999  9999999999999999999999999


Q ss_pred             HHHHHHHHHcCCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCCC
Q 010297           84 IADTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG-QQTHR  162 (513)
Q Consensus        84 Vl~ef~efL~g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI~-~~aHR  162 (513)
                      |+.+|.+|++++++||||+ .||++||+..+.++|+++..+ ++||||.++| .+.|..++|+|..||+.||+. ++|||
T Consensus       491 vL~kf~~~~~d~IlVAHNa-sFD~gFl~~~~~k~~~~~~~~-pvIDTL~lar-~L~P~~ksh~Lg~l~kk~~v~le~hHR  567 (1444)
T COG2176         491 VLEKFREFIGDSILVAHNA-SFDMGFLNTNYEKYGLEPLTN-PVIDTLELAR-ALNPEFKSHRLGTLCKKLGVELERHHR  567 (1444)
T ss_pred             HHHHHHHHhcCcEEEeccC-ccchhHHHHHHHHhCCccccC-chhhHHHHHH-HhChhhhhcchHHHHHHhCccHHHhhh
Confidence            9999999999999999999 999999999999999986654 7999999997 688999999999999999999 89999


Q ss_pred             hHHHHHHHHHHHHHHHHHhhcccCCCCcccccccc-CCCccccccCCccccC---CCCCCC---CCCCCCcccccc
Q 010297          163 SLDDVRMNLEVLKYCATVLFLESSLPDIFTVNSWV-SPNATTRSRSNAKSSP---EGTSQN---LSTPSSKFKFEN  231 (513)
Q Consensus       163 ALdDA~aTA~Ll~~ll~~L~~~~~~P~v~~~~~l~-~~~~~~r~r~~h~~~~---~~~~~~---~~s~~~~~~~~~  231 (513)
                      |.+||.+|+++|..+++.+.+. ++.++.++|..+ +...++|.|++|++.+   |.|+||   ++|-|...||.+
T Consensus       568 A~yDaeat~~vf~~f~~~~ke~-Gi~~l~eln~~l~~~~~ykr~r~~h~~i~vknq~GlKnLykLvS~s~~kyf~~  642 (1444)
T COG2176         568 ADYDAEATAKVFFVFLKDLKEK-GITNLSELNDKLSSEDLYKRLRPKHATIYVKNQVGLKNLYKLVSISHTKYFYG  642 (1444)
T ss_pred             hhhhHHHHHHHHHHHHHHHHHh-chhhHHHHhHhhhhhHHHhhccccceEEEEechHhHHHHHHHHHHHHHHhhcc
Confidence            9999999999999999999998 899999999855 7778999999999888   899999   999999999999

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

>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family	Back alignment and domain information

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

>PRK07942 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

>PRK06807 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>PRK07748 sporulation inhibitor KapD; 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

>PRK08517 DNA polymerase III subunit epsilon; Provisional	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

>PRK06195 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>PRK07740 hypothetical protein; Provisional	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

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

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

>TIGR01298 RNaseT ribonuclease T	Back alignment and domain information

>PRK06309 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

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

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

>PRK07883 hypothetical protein; Validated	Back alignment and domain information

>PRK05168 ribonuclease T; Provisional	Back alignment and domain information

>PRK06722 exonuclease; Provisional	Back alignment and domain information

>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T	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

>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated	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

>cd06127 DEDDh DEDDh 3'-5' exonuclease domain family	Back alignment and domain information

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

>PRK05601 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>PRK07983 exodeoxyribonuclease X; Provisional	Back alignment and domain information

>PRK00448 polC DNA polymerase III PolC; Validated	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

>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]	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

>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

>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

>PRK09182 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>PTZ00315 2'-phosphotransferase; Provisional	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

>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

>PRK11779 sbcB exonuclease I; Provisional	Back alignment and domain information

>KOG0542 consensus Predicted 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

>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

>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]	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

>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

>cd06125 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily	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

>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

>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

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

>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

>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

>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]	Back alignment and domain information

>PHA02570 dexA exonuclease; Provisional	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

>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

>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

>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

>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

>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

>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

>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

>PTZ00166 DNA polymerase delta catalytic subunit; Provisional	Back alignment and domain information

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

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

>PHA02528 43 DNA polymerase; Provisional	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

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

>PHA02524 43A DNA polymerase subunit A; 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

>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [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

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

>cd00007 35EXOc 3'-5' exonuclease	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

>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]	Back alignment and domain information

>PRK10829 ribonuclease D; Provisional	Back alignment and domain information

>TIGR00592 pol2 DNA polymerase (pol2)	Back alignment and domain information

>TIGR01388 rnd ribonuclease D	Back alignment and domain information

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

>PHA03036 DNA polymerase; 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

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

>KOG4793 consensus Three prime repair exonuclease [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

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

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

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

>PHA02563 DNA polymerase; Provisional	Back alignment and domain information

>TIGR00593 pola DNA polymerase I	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		513
1j53_A		186	Structure Of The N-Terminal Exonuclease Domain Of T		1e-05
2gui_A		194	Structure And Function Of Cyclized Versions Of The		2e-05

>pdb|1J53|A Chain A, Structure Of The N-Terminal Exonuclease Domain Of The Epsilon Subunit Of E.Coli Dna Polymerase Iii At Ph 8.5 Length = 186

Back alignment and structure

Iteration: 1

Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust. Identities = 41/138 (29%), Positives = 62/138 (44%), Gaps = 15/138 (10%) Query: 13 FDVETTVPTRPGQRF---AILEFGAILVCPKKL--EELHNYSTLVRPADPELISSLSVRC 67 D ETT + G + I+E GA+ V ++L H Y R DPE + Sbjct: 11 LDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPE-----AFGV 65 Query: 68 NGITPDAVVSSPTFADIADTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPK-- 125 +GI + ++ PTFA++AD D + G HN FD + F+ + R P+ Sbjct: 66 HGIADEFLLDKPTFAEVADEFMDYIRGAELVIHNA-AFDIGFMDYEFSLLKRDIPKTNTF 124 Query: 126 -GTIDSLALLTQRF-GRR 141 DSLA+ + F G+R Sbjct: 125 CKVTDSLAVARKMFPGKR 142

PyMOL of 1j53

>pdb|2GUI|A Chain A, Structure And Function Of Cyclized Versions Of The Proofread Exonuclease Subunit Of E. Coli Dna Polymerase Iii Length = 194

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		513
2p1j_A		186	POLIII, DNA polymerase III POLC-type; structural g	7e-22
1w0h_A		204	3'-5' exonuclease ERI1; nuclease domain, hydrolase	1e-20
1zbu_A		349	ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase;	1e-19
2xri_A		224	ERI1 exoribonuclease 3; hydrolase, metal binding;	2e-19
1zbh_A		299	3'-5' exonuclease ERI1; histone mRNA 3'-END-specif	3e-18
3mxm_B		242	Three prime repair exonuclease 1; RNAse H-like fol	2e-17
3u3y_B		314	Three prime repair exonuclease 1; RNAse H fold, 3'	5e-17
1y97_A		238	Three prime repair exonuclease 2; TREX2, hydrolase	8e-16
3cg7_A		308	CRN-4, cell death-related nuclease 4; hydrolase, a	1e-15
2f96_A		224	Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolas	7e-14
3v9w_A		235	Ribonuclease T; DEDD nucleases family, EXO-nucleas	8e-14
2igi_A		180	Oligoribonuclease; RNAse, exoribonuclease, exonucl	4e-06
2gui_A		194	DNA polymerase III epsilon subunit; DNA polymerase	7e-06
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-05
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-04
3tr8_A		186	Oligoribonuclease; transcription, hydrolase; 2.50A	2e-04

>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

 Score = 92.2 bits (230), Expect = 7e-22
 Identities = 43/174 (24%), Positives = 70/174 (40%), Gaps = 23/174 (13%)

Query: 11  AFFDVETTVPTRPGQRFA---ILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRC 67
              D ETT     G       I+E GA+ +  +  + +  Y TL++P+    IS  S   
Sbjct: 15  VVLDFETT-----GLDPQVDEIIEIGAVKI--QGGQIVDEYHTLIKPSRE--ISRKSSEI 65

Query: 68  NGITPDAVVSSPTFADIADTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGT 127
            GIT + + +  +  ++       L   I   HN   FD   +R    ++     E    
Sbjct: 66  TGITQEMLENKRSIEEVLPEFLGFLEDSIIVAHNA-NFDYRFLRLWIKKVMGLDWERP-Y 123

Query: 128 IDSLALLTQRFGRRAGDM---KMASLATYFGLG-QQTHRSLDDVRMNLEVLKYC 177
           ID+LAL      +    +    + S+    GLG  + HR+LDD R+  +V    
Sbjct: 124 IDTLAL-----AKSLLKLRSYSLDSVVEKLGLGPFRHHRALDDARVTAQVFLRF 172

PyMOL of 2p1j

>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

>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

>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

>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

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

>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

>2igi_A Oligoribonuclease; RNAse, exoribonuclease, exonuclease, hydrolase, mRNA decay; 1.70A {Escherichia coli} SCOP: c.55.3.5 PDB: 1yta_A 1j9a_A Length = 180	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

>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

>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

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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		513
2p1j_A		186	POLIII, DNA polymerase III POLC-type; structural g	100.0
1w0h_A		204	3'-5' exonuclease ERI1; nuclease domain, hydrolase	100.0
3mxm_B		242	Three prime repair exonuclease 1; RNAse H-like fol	100.0
2gui_A		194	DNA polymerase III epsilon subunit; DNA polymerase	100.0
1y97_A		238	Three prime repair exonuclease 2; TREX2, hydrolase	100.0
2f96_A		224	Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolas	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	99.97
2xri_A		224	ERI1 exoribonuclease 3; hydrolase, metal binding;	99.97
3v9w_A		235	Ribonuclease T; DEDD nucleases family, EXO-nucleas	99.97
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	99.96
3tr8_A		186	Oligoribonuclease; transcription, hydrolase; 2.50A	99.96
2igi_A		180	Oligoribonuclease; RNAse, exoribonuclease, exonucl	99.96
2gbz_A		194	Oligoribonuclease; ORN, deddh, structural genomics	99.95
1wlj_A		189	Interferon stimulated gene 20KDA; exoribonuclease,	99.95
2qxf_A		482	Exodeoxyribonuclease I; alpha-beta domain, DNAQ su	99.95
2kfn_A		605	Klenow fragment of DNA polymerase I; complex (poly	99.04
4hec_A		190	Putative uncharacterized protein; ssgcid, structur	98.82
1x9m_A		698	DNA polymerase; DNA ploymerase, N-2-acetylaminoflu	98.6
4gmj_B		285	CCR4-NOT transcription complex subunit 7; mRNA dec	98.46
1qht_A		775	Protein (DNA polymerase); archaea, hyperthermostab	98.44
1noy_A		388	Protein (DNA polymerase (E.C.2.7.7.7)); exonucleas	98.28
3iay_A		919	DNA polymerase delta catalytic subunit; protein-DN	98.14
1s5j_A		847	DNA polymerase I; replication, disulfide bonds, tr	97.99
2d5r_A		252	CCR4-NOT transcription complex subunit 7; poly(A)	97.9
4dfk_A		540	DNA polymerase I, thermostable; DNA polymerase, tr	97.76
1uoc_A		289	POP2; hydrolase, DEDD nuclease, mRNA degradation,	97.75
2p51_A		333	SPCC18.06C protein; DEDD nuclease fold, hydrolase,	97.73
2gv9_A		1193	DNA polymerase; polymerase alpha fold, transferase	97.69
3qex_A		903	DNA polymerase, GP43; difluorotoluene nucleoside;	97.41
3k59_A		786	POL II, DNA polymerase II; protein-DNA complex, DN	97.28
3saf_A		428	Exosome component 10; exoribonuclease, RNA exosome	96.35
2a1r_A		430	Poly(A)-specific ribonuclease PARN; DEDD, nuclease	96.0
2e6m_A		208	Werner syndrome ATP-dependent helicase homolog; AP	95.85
3d45_A		507	Poly(A)-specific ribonuclease PARN; CAP analogue,	95.79
3pv8_A		592	DNA polymerase I; DNA polymerase I, protein-DNA co	95.72
2hbj_A		410	Exosome complex exonuclease RRP6; RNA metabolism,	95.21
2py5_A		575	DNA polymerase; protein-DNA complex, replication,	93.63
1yt3_A		375	Ribonuclease D, RNAse D; exoribonuclease, exonucle	92.69
1vk0_A		206	Hypothetical protein; homohexamer, AT5G06450, stru	90.43
3cym_A		440	Uncharacterized protein BAD_0989; structural genom	89.14

>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=100.00  E-value=1.2e-33  Score=264.44  Aligned_cols=170  Identities=26%  Similarity=0.345  Sum_probs=150.4

Q ss_pred             CCCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHH
Q 010297            4 TQDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFAD   83 (513)
Q Consensus         4 t~~~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~E   83 (513)
                      ...+.+||+||+||||+++  ..++|||||||.++++  +++++|+.+|+|..  +++++++++||||+++|++++++.+
T Consensus         8 ~l~~~~~v~iD~ETTGl~~--~~~~IieIg~v~~~~g--~i~~~f~~lv~P~~--~i~~~~~~i~GIt~~~l~~~~~~~~   81 (186)
T 2p1j_A            8 TFGDATFVVLDFETTGLDP--QVDEIIEIGAVKIQGG--QIVDEYHTLIKPSR--EISRKSSEITGITQEMLENKRSIEE   81 (186)
T ss_dssp             -----CEEEEEEEESCSCT--TTCCEEEEEEEEEETT--EEEEEEEEECBCSS--CCCHHHHHHHCCCHHHHTTCCBHHH
T ss_pred             cCcCCCEEEEEEECCCCCC--CCCeEEEEEEEEEECC--EEEEEEEEEECcCC--CCCHHHhhhcCCCHHHHhcCCCHHH
Confidence            3456799999999999987  6789999999999876  56789999999998  8999999999999999999999999


Q ss_pred             HHHHHHHHHcCCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCCC
Q 010297           84 IADTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG-QQTHR  162 (513)
Q Consensus        84 Vl~ef~efL~g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI~-~~aHR  162 (513)
                      |+.+|.+|+++.++||||+ .||++||++.++++|++++.+ .++||+.+++..+  ..++++|.+++++||++ ..+||
T Consensus        82 v~~~~~~~l~~~~lv~hn~-~fD~~~L~~~~~~~g~~~~~~-~~iDt~~l~~~~~--~~~~~~L~~l~~~~gi~~~~~H~  157 (186)
T 2p1j_A           82 VLPEFLGFLEDSIIVAHNA-NFDYRFLRLWIKKVMGLDWER-PYIDTLALAKSLL--KLRSYSLDSVVEKLGLGPFRHHR  157 (186)
T ss_dssp             HHHHHHHHSSSCEEEETTH-HHHHHHHHHHHHHHHCCCCCC-CEEEHHHHHHHHT--CCSCCSHHHHHHHTTCCSTTCCH
T ss_pred             HHHHHHHHHCCCEEEEECc-HHHHHHHHHHHHHcCCCCCCC-CEEeHHHHHHHHh--hcCCCCHHHHHHHcCCCCCCCcC
Confidence            9999999999999999999 999999999999999987544 6999999988654  56789999999999998 67999


Q ss_pred             hHHHHHHHHHHHHHHHHHhhc
Q 010297          163 SLDDVRMNLEVLKYCATVLFL  183 (513)
Q Consensus       163 ALdDA~aTA~Ll~~ll~~L~~  183 (513)
                      |++||++|+++|.++++...+
T Consensus       158 Al~Da~~t~~l~~~l~~~~~~  178 (186)
T 2p1j_A          158 ALDDARVTAQVFLRFVEMMKK  178 (186)
T ss_dssp             HHHHHHHHHHHHHHHTTCC--
T ss_pred             HHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999998776444

PyMOL of 2p1j

>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

>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

>1y97_A Three prime repair exonuclease 2; TREX2, hydrolase; 2.50A {Homo sapiens} SCOP: c.55.3.5	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

>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

>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

>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

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

>2igi_A Oligoribonuclease; RNAse, exoribonuclease, exonuclease, hydrolase, mRNA decay; 1.70A {Escherichia coli} SCOP: c.55.3.5 PDB: 1yta_A 1j9a_A	Back alignment and structure

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

>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

>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

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

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

>1qht_A Protein (DNA polymerase); archaea, hyperthermostable, family B polymer alpha family polymerase, transferase; 2.10A {Thermococcus SP} SCOP: c.55.3.5 e.8.1.1 PDB: 1tgo_A 2xhb_A* 2vwj_A* 2vwk_A* 1wns_A* 1wn7_A 1qqc_A* 4ahc_A* 4ail_C* 3a2f_A* 2jgu_A* 1d5a_A	Back alignment and structure

>1noy_A Protein (DNA polymerase (E.C.2.7.7.7)); exonuclease, DNA-binding, complex (nucleotidyltransferase/DNA); HET: DNA; 2.20A {Enterobacteria phage T4} SCOP: c.55.3.5 PDB: 1noz_A*	Back alignment and structure

>3iay_A DNA polymerase delta catalytic subunit; protein-DNA complex, DNA replication, DNA-BI DNA-directed DNA polymerase, exonuclease, hydrolase; HET: DNA DOC DCP; 2.00A {Saccharomyces cerevisiae}	Back alignment and structure

>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

>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

>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

>1uoc_A POP2; hydrolase, DEDD nuclease, mRNA degradation, poly(A) tail, transcription regulation, repressor, phosphorylation.; 2.3A {Saccharomyces cerevisiae} SCOP: c.55.3.9	Back alignment and structure

>2p51_A SPCC18.06C protein; DEDD nuclease fold, hydrolase, gene regulation; 1.40A {Schizosaccharomyces pombe} PDB: 3g0z_A 3g10_A	Back alignment and structure

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

>3saf_A Exosome component 10; exoribonuclease, RNA exosome, hydrolase; 2.50A {Homo sapiens} PDB: 3sag_A 3sah_A 2cpr_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

>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

>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

>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

>2hbj_A Exosome complex exonuclease RRP6; RNA metabolism, RNA surveillance, RNA processing, hydrolase, gene regulation; 2.10A {Saccharomyces cerevisiae} SCOP: a.60.8.4 c.55.3.5 PDB: 2hbk_A 2hbl_A* 2hbm_A*	Back alignment and structure

>2py5_A DNA polymerase; protein-DNA complex, replication, transferase/DNA complex; HET: DNA; 1.60A {Bacillus phage PHI29} SCOP: c.55.3.5 e.8.1.1 PDB: 1xhz_A* 1xhx_A* 2ex3_A* 1xi1_A* 2pyj_A* 2pyl_A* 2pzs_A*	Back alignment and structure

>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

>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

>3cym_A Uncharacterized protein BAD_0989; structural genomics, unknown function; 2.10A {Bifidobacterium adolescentis atcc 1570ORGANISM_TAXID}	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		513
d1y97a1		228	c.55.3.5 (A:1-228) Three prime repair exonuclease	4e-18
d1w0ha_		200	c.55.3.5 (A:) Exonuclease ERI1 {Human (Homo sapien	9e-18
d3b6oa1		226	c.55.3.5 (A:9-234) Three prime repair exonuclease	6e-13
d2guia1		174	c.55.3.5 (A:7-180) N-terminal exonuclease domain o	8e-11
d2f96a1		202	c.55.3.5 (A:19-220) Ribonuclease T {Pseudomonas ae	1e-08
d2qxfa1		467	c.55.3.5 (A:8-474) Exonuclease I {Escherichia coli	1e-08
d2igia1		180	c.55.3.5 (A:1-180) Oligoribonuclease {Escherichia	3e-07
d1wlja_		173	c.55.3.5 (A:) Interferon-stimulated gene 20 kDa pr	2e-04

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


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

 Score = 81.2 bits (199), Expect = 4e-18
 Identities = 37/232 (15%), Positives = 59/232 (25%), Gaps = 37/232 (15%)

Query: 1   MGPTQDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEE--------------LH 46
           M          F D+E T    P     I E     V    LE               L 
Sbjct: 1   MSEAPRAETFVFLDLEAT--GLPSVEPEIAELSLFAVHRSSLENPEHDESGALVLPRVLD 58

Query: 47  NYSTLVRPADPELISSLSVRCNGITPDAVVS--SPTFADIADTVFDILHGR-----IWAG 99
             +  + P  P   ++ +    G++ + +       F             R         
Sbjct: 59  KLTLCMCPERP--FTAKASEITGLSSEGLARCRKAGFDGAVVRTLQAFLSRQAGPICLVA 116

Query: 100 HNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQ--------RFGRRAGDMKMASLA 151
           HN   +D   +      +G   P     +D+L  L             R      + SL 
Sbjct: 117 HNGFDYDFPLLCAELRRLGARLPRDTVCLDTLPALRGLDRAHSHGTRARGRQGYSLGSLF 176

Query: 152 T-YFGL-GQQTHRSLDDVRMNLEVLKYCATVL--FLESSLPDIFTVNSWVSP 199
             YF       H +  DV   L +  + A  L  + +        +     P
Sbjct: 177 HRYFRAEPSAAHSAEGDVHTLLLIFLHRAAELLAWADEQARGWAHIEPMYLP 228

PyMOL of d1y97a1

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

>d3b6oa1 c.55.3.5 (A:9-234) Three prime repair exonuclease 1, TREX1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 226	Back information, alignment and structure

>d2guia1 c.55.3.5 (A:7-180) N-terminal exonuclease domain of the epsilon subunit of DNA polymerase III {Escherichia coli [TaxId: 562]} Length = 174	Back information, alignment and structure

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

>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		513
d2guia1		174	N-terminal exonuclease domain of the epsilon subun	99.97
d3b6oa1		226	Three prime repair exonuclease 1, TREX1 {Mouse (Mu	99.96
d1y97a1		228	Three prime repair exonuclease 2, TREX2 {Human (Ho	99.96
d1w0ha_		200	Exonuclease ERI1 {Human (Homo sapiens) [TaxId: 960	99.96
d1wlja_		173	Interferon-stimulated gene 20 kDa protein, ISG20 {	99.95
d2qxfa1		467	Exonuclease I {Escherichia coli K12 (Escherichia c	99.89
d2f96a1		202	Ribonuclease T {Pseudomonas aeruginosa [TaxId: 287	99.89
d2igia1		180	Oligoribonuclease {Escherichia coli [TaxId: 562]}	99.83
d2d5ra1		252	CCR4-NOT transcription complex subunit 7, CAF1 {Hu	98.53
d1x9ma1		204	Exonuclease domain of T7 DNA polymerase {Bacteriop	98.52
d1tgoa1		347	Exonuclease domain of family B DNA polymerases {Ar	98.3
d1kfsa1		195	Exonuclease domain of prokaryotic DNA polymerase {	98.2
d1uoca_		286	Pop2 RNase D domain {Baker's yeast (Saccharomyces	97.84
d1yt3a3		193	Ribonuclease D, catalytic domain {Escherichia coli	97.55
d2hhva1		171	Exonuclease domain of prokaryotic DNA polymerase {	97.55
d1s5ja1		410	Exonuclease domain of family B DNA polymerases {Su	97.32
d1q8ia1		388	Exonuclease domain of family B DNA polymerases {Es	97.31
d2hbka2		292	Exosome complex exonuclease RRP6 {Baker's yeast (S	96.61
d1noya_		372	Exonuclease domain of family B DNA polymerases {Ba	96.47
d1ih7a1		375	Exonuclease domain of family B DNA polymerases {Ba	96.46
d1vk0a_		206	Hypothetical protein AT5G06450 {Thale-cress (Arabi	96.0

>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=99.97  E-value=7.5e-30  Score=227.29  Aligned_cols=164  Identities=24%  Similarity=0.370  Sum_probs=143.3

Q ss_pred             cEEEEEEecCCCCCCC---CCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHH
Q 010297            9 EIAFFDVETTVPTRPG---QRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIA   85 (513)
Q Consensus         9 ~~VVfDlETTGLd~~g---~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl   85 (513)
                      ++||||+||||+++.+   ..|+|||||||+++++. .+.++|+.+|+|..  ++++.+.++||||++++.+++++.+++
T Consensus         1 r~vv~D~ETTGl~~~~~~~~~d~IIeIg~v~~~~~~-~~~~~~~~~v~P~~--~i~~~~~~i~gIt~e~~~~~~~~~~~~   77 (174)
T d2guia1           1 RQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRR-LTGNNFHVYLKPDR--LVDPEAFGVHGIADEFLLDKPTFAEVA   77 (174)
T ss_dssp             EEEEEEEEESCCCSSSSTTTTCCEEEEEEEEEETTE-ECSCCEEEECCCSS--CCCHHHHHHHCCCHHHHTTSCCHHHHH
T ss_pred             CEEEEEeeCCCCCcccccCCCCEEEEEEEEEEECCE-EeeeEEEEEeccCc--cchhhhhhccccchhhhhcchhHHHHH
Confidence            5899999999998732   35789999999998763 34678999999987  899999999999999999999999999


Q ss_pred             HHHHHHHcCCeEEEeCcchHHHHHHHHHHHHcCCCCCCC---CcceeHHHHHHHHhcCCCCCCCHHHHHHHhCCC---CC
Q 010297           86 DTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEP---KGTIDSLALLTQRFGRRAGDMKMASLATYFGLG---QQ  159 (513)
Q Consensus        86 ~ef~efL~g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~---~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI~---~~  159 (513)
                      .+|.+|+++..+|+||. .||..++...+++++...+..   ..++|++.+++. +.+. ..++|..++++||++   .+
T Consensus        78 ~~~~~~~~~~~~v~~~~-~~d~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~-~~~~-~~~~L~~l~~~~~~~~~~~~  154 (174)
T d2guia1          78 DEFMDYIRGAELVIHNA-AFDIGFMDYEFSLLKRDIPKTNTFCKVTDSLAVARK-MFPG-KRNSLDALCARYEIDNSKRT  154 (174)
T ss_dssp             HHHHHHHTTSEEEETTH-HHHHHHHHHHHHHTCSCCCCGGGTSEEEEHHHHHHH-HSTT-SCCSHHHHHHHTTCCCTTCS
T ss_pred             HHHHHhcCCCeEEEeec-chhhHHHHHHHHHhCCCCCCcccccchhhHHHHHHH-HcCC-CCCCHHHHHHHcCCCCCCCC
Confidence            99999999999999999 999999999999998765532   256899999875 4443 467999999999997   35


Q ss_pred             CCChHHHHHHHHHHHHHHH
Q 010297          160 THRSLDDVRMNLEVLKYCA  178 (513)
Q Consensus       160 aHRALdDA~aTA~Ll~~ll  178 (513)
                      +|||++||++|+++|.+|+
T Consensus       155 ~H~Al~Da~~ta~v~~~l~  173 (174)
T d2guia1         155 LHGALLDAQILAEVYLAMT  173 (174)
T ss_dssp             SCCHHHHHHHHHHHHHHHT
T ss_pred             CcCHHHHHHHHHHHHHHHc
Confidence            8999999999999999875

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

>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

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

>d1tgoa1 c.55.3.5 (A:1-347) Exonuclease domain of family B DNA polymerases {Archaeon Thermococcus gorgonarius [TaxId: 71997]}	Back information, alignment and structure

>d1kfsa1 c.55.3.5 (A:324-518) Exonuclease domain of prokaryotic DNA polymerase {Escherichia coli [TaxId: 562]}	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

>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

>d1s5ja1 c.55.3.5 (A:40-449) Exonuclease domain of family B DNA polymerases {Sulfolobus solfataricus [TaxId: 2287]}	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

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

>d1noya_ c.55.3.5 (A:) Exonuclease domain of family B DNA polymerases {Bacteriophage T4 [TaxId: 10665]}	Back information, alignment and structure

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

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