Psyllid ID: psy14503

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

MHRHIVLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGLTTKFLKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLGYSNFTKYIYRITDTLLMARKIHTGKRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYLAMTRGQSNLNFKPKINNSNNIETKIKIPNNIPIKLANSNELVQHNMILSKIDKHSNGRCIWKK

ccEEEEEEEcccccccccccEEEEEEEEEEEccEEccccccccccccccccHHHHHHHcccHHHHcccccHHHHHHHHHHHHcccEEEEEcccccHHHHHHHHHHcccccccccccccccHHHHHHHHcccccccHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccEEEccHHHHHHHHHHHHHHHHcccccccccc

cccEEEEEEEEccccccccccEEEEEEEEEEccEEccccEEEEccccccccHHHHHHHcccHHHHcccccHHHHHHHHHHHHcccEEEEccHHHHHHHHHHHHHHccccccHHHccEEEEHHHHHHHHcccccccHHHHHHHccccccccccccHHHHHHHHHHHHHHHcccccEEEEccccccccccEEccccccccEEEEccHHHHHHHHHHHHHHHHHccccEEEcc

MHRHIVLDIettglniidghRIIEIGCVEiknrqitgnnlhyyinpgrdsekSALAIHGLTTKFLKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLGYSNFTKYIYRITDTLLMARKIHTGKRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYLAMTrgqsnlnfkpkinnsnnietkikipnnipiklansneLVQHNMILSkidkhsngrciwkk

mhrhivldiettglniidghRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGLTTKFLKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLGYSNFTKYIYRITDTLLMARKIHTGKRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYLAMTRgqsnlnfkpkinnsnnIETKIKIPNNIPIKLANSNELVQHNMIlskidkhsngrciwkk

MHRHIVLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGlttkflknklkfSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLGYSNFTKYIYRITDTLLMARKIHTGKRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYLAMTRGQSNLNFKPKINNSnnietkikipnnipikLANSNELVQHNMILSKIDKHSNGRCIWKK

***HIVLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGLTTKFLKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLGYSNFTKYIYRITDTLLMARKIHTGKRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYLAMTRGQSNLNFKPKINNSNNIETKIKIPNNIPIKLANSNELVQHNMILSKIDKHSNGRCIW**

MHRHIVLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGLTTKFLKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLGYSNFTKYIYRITDTLLMARKIHTGKRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYLAMTRGQS***********************IPIKLANSNELVQHNMILSKIDKHSNGRCIWKK

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oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

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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		230	2.2.26 [Sep-21-2011]
P03007		243	DNA polymerase III subuni	N/A	N/A	0.982	0.930	0.447	1e-55
P0A1G9		243	DNA polymerase III subuni	yes	N/A	0.982	0.930	0.447	2e-55
P0A1H0		243	DNA polymerase III subuni	N/A	N/A	0.982	0.930	0.447	2e-55
Q9CPE0		253	DNA polymerase III subuni	yes	N/A	0.991	0.901	0.459	8e-54
P43745		256	DNA polymerase III subuni	yes	N/A	0.991	0.890	0.440	4e-52
Q89AN3		245	DNA polymerase III subuni	yes	N/A	0.978	0.918	0.455	4e-49
P57337		237	DNA polymerase III subuni	yes	N/A	0.852	0.827	0.492	8e-46
Q1RJM1		229	DNA polymerase III subuni	yes	N/A	0.956	0.960	0.431	2e-45
Q68W16		229	DNA polymerase III subuni	yes	N/A	0.930	0.934	0.461	2e-44
Q9ZCJ9		229	DNA polymerase III subuni	yes	N/A	0.930	0.934	0.448	4e-44

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

 Score =  216 bits (550), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 106/237 (44%), Positives = 149/237 (62%), Gaps = 11/237 (4%)

Query: 3   RHIVLDIETTGLNII----DGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIH 58
           R IVLD ETTG+N I    +GH+IIEIG VE+ NR++TGNN H Y+ P R  +  A  +H
Sbjct: 7   RQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVH 66

Query: 59  GLTTKFLKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLGYS-NFTKYIYR 117
           G+  +FL +K  F+E+ D F++Y+  +E++IHNAAFD+GF+D E SLL      T    +
Sbjct: 67  GIADEFLLDKPTFAEVADEFMDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCK 126

Query: 118 ITDTLLMARKIHTGKRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYLAMTRGQSNLN 177
           +TD+L +ARK+  GKRNSLDALC RY I    RTLHG LLDA++LAEVYLAMT GQ+++ 
Sbjct: 127 VTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLHGALLDAQILAEVYLAMTGGQTSMA 186

Query: 178 FK-----PKINNSNNIETKIKIPNNIPIKLANSNELVQHNMILSKIDKHSNGRCIWK 229
           F       +      I+  ++  + + +  A   E+  H   L  + K   G C+W+
Sbjct: 187 FAMEGETQQQQGEATIQRIVRQASKLRVVFATDEEIAAHEARLDLVQK-KGGSCLWR 242

DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. The epsilon subunit contain the editing function and is a proofreading 3'-5' exonuclease.
Escherichia coli (strain K12) (taxid: 83333)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 7

>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

>sp\|Q9CPE0\|DPO3E_PASMU DNA polymerase III subunit epsilon OS=Pasteurella multocida (strain Pm70) GN=dnaQ PE=3 SV=1	Back alignment and function description

>sp\|P43745\|DPO3E_HAEIN DNA polymerase III subunit epsilon OS=Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) GN=dnaQ PE=3 SV=1	Back alignment and function description

>sp\|Q89AN3\|DPO3E_BUCBP DNA polymerase III subunit epsilon OS=Buchnera aphidicola subsp. Baizongia pistaciae (strain Bp) GN=dnaQ PE=3 SV=1	Back alignment and function description

>sp\|P57337\|DPO3E_BUCAI DNA polymerase III subunit epsilon OS=Buchnera aphidicola subsp. Acyrthosiphon pisum (strain APS) GN=dnaQ PE=3 SV=1	Back alignment and function description

>sp\|Q1RJM1\|DPO3E_RICBR DNA polymerase III subunit epsilon OS=Rickettsia bellii (strain RML369-C) GN=dnaQ PE=3 SV=1	Back alignment and function description

>sp\|Q68W16\|DPO3E_RICTY DNA polymerase III subunit epsilon OS=Rickettsia typhi (strain ATCC VR-144 / Wilmington) GN=dnaQ PE=3 SV=1	Back alignment and function description

>sp\|Q9ZCJ9\|DPO3E_RICPR DNA polymerase III subunit epsilon OS=Rickettsia prowazekii (strain Madrid E) 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		230
134095496		234	DNA polymerase III subunit epsilon [Herm	0.986	0.970	0.554	9e-71
167562346		240	DNA polymerase III subunit epsilon [Burk	0.986	0.945	0.538	5e-70
399019667		241	DNA polymerase III, epsilon subunit [Her	0.986	0.941	0.560	6e-70
83720697		241	DNA polymerase III subunit epsilon [Burk	0.986	0.941	0.525	7e-69
167836205		241	DNA polymerase III subunit epsilon [Burk	0.991	0.946	0.532	1e-68
167582322		241	DNA polymerase III subunit epsilon [Burk	0.986	0.941	0.525	1e-68
398832629		246	DNA polymerase III, epsilon subunit [Her	0.986	0.922	0.543	1e-68
415940406		244	DNA polymerase III epsilon subunit [Herb	0.986	0.930	0.530	2e-68
76810101		253	DNA polymerase III subunit epsilon [Burk	0.986	0.897	0.529	2e-68
53718980		240	DNA polymerase III subunit epsilon [Burk	0.986	0.945	0.529	2e-68

>gi\|134095496\|ref\|YP_001100571.1\| DNA polymerase III subunit epsilon [Herminiimonas arsenicoxydans] gi\|133739399\|emb\|CAL62449.1\| DNA polymerase III subunit epsilon [Herminiimonas arsenicoxydans]	Back alignment and taxonomy information

 Score =  272 bits (695), Expect = 9e-71,   Method: Compositional matrix adjust.
 Identities = 127/229 (55%), Positives = 169/229 (73%), Gaps = 2/229 (0%)

Query: 3   RHIVLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGLTT 62
           R IVLD ETTGLN   G RIIEIGCVE+ +R++TGNN H+YINP RDSE+ ALA+HGLTT
Sbjct: 2   RQIVLDTETTGLNPRSGDRIIEIGCVELIDRRLTGNNFHHYINPERDSEEGALAVHGLTT 61

Query: 63  KFLKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLGYSNFTKYIYRITDTL 122
           +FL +K KF+EIVD F +Y+S +E++IHNA FDVGFLD EL  +    F  ++  I DTL
Sbjct: 62  EFLSDKPKFAEIVDEFRDYISGAEVVIHNAPFDVGFLDAELKRVEMPLFKDHVGGILDTL 121

Query: 123 LMARKIHTGKRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYLAMTRGQSNL--NFKP 180
             A+++H GKRNSLDALCDRY +S  HRTLHG LLDAELLAEVYLAMTRGQ++L  +   
Sbjct: 122 QQAKELHPGKRNSLDALCDRYGVSNAHRTLHGALLDAELLAEVYLAMTRGQNSLSMDLGG 181

Query: 181 KINNSNNIETKIKIPNNIPIKLANSNELVQHNMILSKIDKHSNGRCIWK 229
           +  +S+ I  ++    +I ++ A + EL +H +++  +DK   G+C+W+
Sbjct: 182 QDADSDGIALEVVAIADILLQPATAEELAEHELLMQSLDKEVKGQCLWR 230

Source: Herminiimonas arsenicoxydans

Species: Herminiimonas arsenicoxydans

Genus: Herminiimonas

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi\|167562346\|ref\|ZP_02355262.1\| DNA polymerase III subunit epsilon [Burkholderia oklahomensis EO147] gi\|167574356\|ref\|ZP_02367230.1\| DNA polymerase III subunit epsilon [Burkholderia oklahomensis C6786]	Back alignment and taxonomy information

>gi\|399019667\|ref\|ZP_10721813.1\| DNA polymerase III, epsilon subunit [Herbaspirillum sp. CF444] gi\|398097558\|gb\|EJL87862.1\| DNA polymerase III, epsilon subunit [Herbaspirillum sp. CF444]	Back alignment and taxonomy information

>gi\|83720697\|ref\|YP_443303.1\| DNA polymerase III subunit epsilon [Burkholderia thailandensis E264] gi\|257139540\|ref\|ZP_05587802.1\| DNA polymerase III subunit epsilon [Burkholderia thailandensis E264] gi\|83654522\|gb\|ABC38585.1\| DNA polymerase III, epsilon subunit [Burkholderia thailandensis E264]	Back alignment and taxonomy information

>gi\|167836205\|ref\|ZP_02463088.1\| DNA polymerase III subunit epsilon [Burkholderia thailandensis MSMB43] gi\|424903985\|ref\|ZP_18327495.1\| DNA polymerase III subunit epsilon [Burkholderia thailandensis MSMB43] gi\|390929963\|gb\|EIP87365.1\| DNA polymerase III subunit epsilon [Burkholderia thailandensis MSMB43]	Back alignment and taxonomy information

>gi\|167582322\|ref\|ZP_02375196.1\| DNA polymerase III subunit epsilon [Burkholderia thailandensis TXDOH] gi\|167620419\|ref\|ZP_02389050.1\| DNA polymerase III subunit epsilon [Burkholderia thailandensis Bt4]	Back alignment and taxonomy information

>gi\|398832629\|ref\|ZP_10590786.1\| DNA polymerase III, epsilon subunit [Herbaspirillum sp. YR522] gi\|398222966\|gb\|EJN09322.1\| DNA polymerase III, epsilon subunit [Herbaspirillum sp. YR522]	Back alignment and taxonomy information

>gi\|415940406\|ref\|ZP_11555640.1\| DNA polymerase III epsilon subunit [Herbaspirillum frisingense GSF30] gi\|407759177\|gb\|EKF68908.1\| DNA polymerase III epsilon subunit [Herbaspirillum frisingense GSF30]	Back alignment and taxonomy information

>gi|76810101|ref|YP_333003.1| DNA polymerase III subunit epsilon [Burkholderia pseudomallei 1710b] gi|121601053|ref|YP_992607.1| DNA polymerase III subunit epsilon [Burkholderia mallei SAVP1] gi|124385495|ref|YP_001026592.1| DNA polymerase III subunit epsilon [Burkholderia mallei NCTC 10229] gi|126441990|ref|YP_001058508.1| DNA polymerase III subunit epsilon [Burkholderia pseudomallei 668] gi|126455280|ref|YP_001065768.1| DNA polymerase III subunit epsilon [Burkholderia pseudomallei 1106a] gi|134282747|ref|ZP_01769450.1| DNA polymerase III, epsilon subunit [Burkholderia pseudomallei 305] gi|217423557|ref|ZP_03455058.1| DNA polymerase III, epsilon subunit [Burkholderia pseudomallei 576] gi|226196200|ref|ZP_03791785.1| DNA polymerase III, epsilon subunit [Burkholderia pseudomallei Pakistan 9] gi|237811761|ref|YP_002896212.1| DNA polymerase III subunit epsilon [Burkholderia pseudomallei MSHR346] gi|238563612|ref|ZP_00438559.2| DNA polymerase III, epsilon subunit [Burkholderia mallei GB8 horse 4] gi|242318034|ref|ZP_04817050.1| DNA polymerase III, epsilon subunit [Burkholderia pseudomallei 1106b] gi|251767848|ref|ZP_02268597.2| DNA polymerase III, epsilon subunit [Burkholderia mallei PRL-20] gi|254177751|ref|ZP_04884406.1| DNA polymerase III, epsilon subunit [Burkholderia mallei ATCC 10399] gi|254180217|ref|ZP_04886816.1| DNA polymerase III, epsilon subunit [Burkholderia pseudomallei 1655] gi|254197669|ref|ZP_04904091.1| DNA polymerase III, epsilon subunit [Burkholderia pseudomallei S13] gi|254199436|ref|ZP_04905802.1| DNA polymerase III, epsilon subunit [Burkholderia mallei FMH] gi|254258454|ref|ZP_04949508.1| DNA polymerase III, epsilon subunit [Burkholderia pseudomallei 1710a] gi|254298053|ref|ZP_04965506.1| DNA polymerase III, epsilon subunit [Burkholderia pseudomallei 406e] gi|254358851|ref|ZP_04975124.1| DNA polymerase III, epsilon subunit [Burkholderia mallei 2002721280] gi|76579554|gb|ABA49029.1| DNA polymerase III, epsilon subunit [Burkholderia pseudomallei 1710b] gi|121229863|gb|ABM52381.1| DNA polymerase III, epsilon subunit [Burkholderia mallei SAVP1] gi|124293515|gb|ABN02784.1| DNA polymerase III, epsilon subunit [Burkholderia mallei NCTC 10229] gi|126221483|gb|ABN84989.1| DNA polymerase III, epsilon subunit [Burkholderia pseudomallei 668] gi|126228922|gb|ABN92462.1| DNA polymerase III, epsilon subunit [Burkholderia pseudomallei 1106a] gi|134245833|gb|EBA45924.1| DNA polymerase III, epsilon subunit [Burkholderia pseudomallei 305] gi|147749032|gb|EDK56106.1| DNA polymerase III, epsilon subunit [Burkholderia mallei FMH] gi|148027978|gb|EDK85999.1| DNA polymerase III, epsilon subunit [Burkholderia mallei 2002721280] gi|157807726|gb|EDO84896.1| DNA polymerase III, epsilon subunit [Burkholderia pseudomallei 406e] gi|160698790|gb|EDP88760.1| DNA polymerase III, epsilon subunit [Burkholderia mallei ATCC 10399] gi|169654410|gb|EDS87103.1| DNA polymerase III, epsilon subunit [Burkholderia pseudomallei S13] gi|184210757|gb|EDU07800.1| DNA polymerase III, epsilon subunit [Burkholderia pseudomallei 1655] gi|217393415|gb|EEC33436.1| DNA polymerase III, epsilon subunit [Burkholderia pseudomallei 576] gi|225931786|gb|EEH27788.1| DNA polymerase III, epsilon subunit [Burkholderia pseudomallei Pakistan 9] gi|237504517|gb|ACQ96835.1| DNA polymerase III, epsilon subunit [Burkholderia pseudomallei MSHR346] gi|238520320|gb|EEP83781.1| DNA polymerase III, epsilon subunit [Burkholderia mallei GB8 horse 4] gi|242141273|gb|EES27675.1| DNA polymerase III, epsilon subunit [Burkholderia pseudomallei 1106b] gi|243061566|gb|EES43752.1| DNA polymerase III, epsilon subunit [Burkholderia mallei PRL-20] gi|254217143|gb|EET06527.1| DNA polymerase III, epsilon subunit [Burkholderia pseudomallei 1710a]

Back alignment and taxonomy information

>gi|53718980|ref|YP_107966.1| DNA polymerase III subunit epsilon [Burkholderia pseudomallei K96243] gi|53725133|ref|YP_102525.1| DNA polymerase III subunit epsilon [Burkholderia mallei ATCC 23344] gi|126449393|ref|YP_001080124.1| DNA polymerase III subunit epsilon [Burkholderia mallei NCTC 10247] gi|167719045|ref|ZP_02402281.1| DNA polymerase III subunit epsilon [Burkholderia pseudomallei DM98] gi|167738046|ref|ZP_02410820.1| DNA polymerase III subunit epsilon [Burkholderia pseudomallei 14] gi|167815230|ref|ZP_02446910.1| DNA polymerase III subunit epsilon [Burkholderia pseudomallei 91] gi|167823638|ref|ZP_02455109.1| DNA polymerase III subunit epsilon [Burkholderia pseudomallei 9] gi|167845182|ref|ZP_02470690.1| DNA polymerase III subunit epsilon [Burkholderia pseudomallei B7210] gi|167893733|ref|ZP_02481135.1| DNA polymerase III subunit epsilon [Burkholderia pseudomallei 7894] gi|167902185|ref|ZP_02489390.1| DNA polymerase III subunit epsilon [Burkholderia pseudomallei NCTC 13177] gi|167910426|ref|ZP_02497517.1| DNA polymerase III subunit epsilon [Burkholderia pseudomallei 112] gi|167918451|ref|ZP_02505542.1| DNA polymerase III subunit epsilon [Burkholderia pseudomallei BCC215] gi|254188362|ref|ZP_04894873.1| DNA polymerase III, epsilon subunit [Burkholderia pseudomallei Pasteur 52237] gi|386862256|ref|YP_006275205.1| DNA polymerase III subunit epsilon [Burkholderia pseudomallei 1026b] gi|403518197|ref|YP_006652330.1| DNA polymerase III subunit epsilon [Burkholderia pseudomallei BPC006] gi|418387758|ref|ZP_12967594.1| DNA polymerase III subunit epsilon [Burkholderia pseudomallei 354a] gi|418538822|ref|ZP_13104424.1| DNA polymerase III subunit epsilon [Burkholderia pseudomallei 1026a] gi|418541386|ref|ZP_13106870.1| DNA polymerase III subunit epsilon [Burkholderia pseudomallei 1258a] gi|418547630|ref|ZP_13112774.1| DNA polymerase III subunit epsilon [Burkholderia pseudomallei 1258b] gi|418553789|ref|ZP_13118597.1| DNA polymerase III subunit epsilon [Burkholderia pseudomallei 354e] gi|52209394|emb|CAH35339.1| DNA polymerase III, epsilon chain [Burkholderia pseudomallei K96243] gi|52428556|gb|AAU49149.1| DNA polymerase III, epsilon subunit [Burkholderia mallei ATCC 23344] gi|126242263|gb|ABO05356.1| DNA polymerase III, epsilon subunit [Burkholderia mallei NCTC 10247] gi|157936041|gb|EDO91711.1| DNA polymerase III, epsilon subunit [Burkholderia pseudomallei Pasteur 52237] gi|385347107|gb|EIF53777.1| DNA polymerase III subunit epsilon [Burkholderia pseudomallei 1026a] gi|385358228|gb|EIF64248.1| DNA polymerase III subunit epsilon [Burkholderia pseudomallei 1258a] gi|385360443|gb|EIF66375.1| DNA polymerase III subunit epsilon [Burkholderia pseudomallei 1258b] gi|385371189|gb|EIF76392.1| DNA polymerase III subunit epsilon [Burkholderia pseudomallei 354e] gi|385376063|gb|EIF80781.1| DNA polymerase III subunit epsilon [Burkholderia pseudomallei 354a] gi|385659384|gb|AFI66807.1| DNA polymerase III subunit epsilon [Burkholderia pseudomallei 1026b] gi|403073840|gb|AFR15420.1| DNA polymerase III subunit epsilon [Burkholderia pseudomallei BPC006]

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		230
UNIPROTKB\|P03007		243	dnaQ "DNA polymerase III, epsi	0.982	0.930	0.426	1.3e-45
UNIPROTKB\|Q9KPX9		247	VC_2233 "DNA polymerase III, e	0.978	0.910	0.411	1e-43
TIGR_CMR\|VC_2233		247	VC_2233 "DNA polymerase III, e	0.978	0.910	0.411	1e-43
TIGR_CMR\|CBU_0317		236	CBU_0317 "DNA polymerase III,	0.969	0.944	0.437	5.7e-43
TIGR_CMR\|SO_2559		242	SO_2559 "DNA polymerase III, e	0.978	0.929	0.404	3.2e-42
TIGR_CMR\|NSE_0470		228	NSE_0470 "DNA polymerase III,	0.760	0.767	0.451	2.1e-36
TIGR_CMR\|APH_0730		244	APH_0730 "DNA polymerase III,	0.786	0.741	0.440	4.7e-32
TIGR_CMR\|SPO_3889		241	SPO_3889 "DNA polymerase III,	0.734	0.701	0.407	1.7e-27
TIGR_CMR\|CPS_0780		203	CPS_0780 "exonuclease" [Colwel	0.691	0.783	0.295	2.6e-15
TIGR_CMR\|SO_2245		212	SO_2245 "DNA polymerase III, e	0.695	0.754	0.309	4.9e-14

UNIPROTKB\|P03007 dnaQ "DNA polymerase III, epsilon subunit" [Escherichia coli K-12 (taxid:83333)]	Back alignment and assigned GO terms

 Score = 479 (173.7 bits), Expect = 1.3e-45, P = 1.3e-45
 Identities = 101/237 (42%), Positives = 135/237 (56%)

Query:     3 RHIVLDIETTGLNII----DGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIH 58
             R IVLD ETTG+N I    +GH+IIEIG VE+ NR++TGNN H Y+ P R  +  A  +H
Sbjct:     7 RQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVH 66

Query:    59 GXXXXXXXXXXXXSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLGYS-NFTKYIYR 117
             G            +E+ D F++Y+  +E++IHNAAFD+GF+D E SLL      T    +
Sbjct:    67 GIADEFLLDKPTFAEVADEFMDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCK 126

Query:   118 ITDTLLMARKIHTGKRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYLAMTRGQSNLN 177
             +TD+L +ARK+  GKRNSLDALC RY I    RTLHG LLDA++LAEVYLAMT GQ+++ 
Sbjct:   127 VTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLHGALLDAQILAEVYLAMTGGQTSMA 186

Query:   178 FK-----PKINNSXXXXXXXXXXXXXXXXLANSNELVQHNMILSKIDKHSNGRCIWK 229
             F       +                     A   E+  H   L  + K   G C+W+
Sbjct:   187 FAMEGETQQQQGEATIQRIVRQASKLRVVFATDEEIAAHEARLDLVQK-KGGSCLWR 242

GO:0005622 "intracellular" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0090305 "nucleic acid phosphodiester bond hydrolysis" evidence=IEA

GO:0045004 "DNA replication proofreading" evidence=IMP

GO:0046872 "metal ion binding" evidence=IEA

GO:0016779 "nucleotidyltransferase activity" evidence=IEA

GO:0016740 "transferase activity" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

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

GO:0003887 "DNA-directed DNA polymerase activity" evidence=IEA

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

TIGR_CMR\|CBU_0317 CBU_0317 "DNA polymerase III, epsilon subunit" [Coxiella burnetii RSA 493 (taxid:227377)]	Back alignment and assigned GO terms

TIGR_CMR\|SO_2559 SO_2559 "DNA polymerase III, epsilon subunit" [Shewanella oneidensis MR-1 (taxid:211586)]	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\|APH_0730 APH_0730 "DNA polymerase III, epsilon subunit" [Anaplasma phagocytophilum HZ (taxid:212042)]	Back alignment and assigned GO terms

TIGR_CMR\|SPO_3889 SPO_3889 "DNA polymerase III, epsilon subunit" [Ruegeria pomeroyi DSS-3 (taxid:246200)]	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\|SO_2245 SO_2245 "DNA polymerase III, epsilon subunit" [Shewanella oneidensis MR-1 (taxid:211586)]	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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9CPE0	DPO3E_PASMU	2, ., 7, ., 7, ., 7	0.4599	0.9913	0.9011	yes	N/A
Q89AN3	DPO3E_BUCBP	2, ., 7, ., 7, ., 7	0.4553	0.9782	0.9183	yes	N/A
Q08880	DPO3E_BUCAP	2, ., 7, ., 7, ., 7	0.4757	0.9130	0.9012	yes	N/A
Q92GL1	DPO3E_RICCN	2, ., 7, ., 7, ., 7	0.4577	0.9391	0.9391	yes	N/A
Q1RJM1	DPO3E_RICBR	2, ., 7, ., 7, ., 7	0.4311	0.9565	0.9606	yes	N/A
Q9ZCJ9	DPO3E_RICPR	2, ., 7, ., 7, ., 7	0.4484	0.9304	0.9344	yes	N/A
Q68W16	DPO3E_RICTY	2, ., 7, ., 7, ., 7	0.4618	0.9304	0.9344	yes	N/A
P0A1G9	DPO3E_SALTY	2, ., 7, ., 7, ., 7	0.4472	0.9826	0.9300	yes	N/A
P43745	DPO3E_HAEIN	2, ., 7, ., 7, ., 7	0.4403	0.9913	0.8906	yes	N/A
P57337	DPO3E_BUCAI	2, ., 7, ., 7, ., 7	0.4926	0.8521	0.8270	yes	N/A
Q4UN31	DPO3E_RICFE	2, ., 7, ., 7, ., 7	0.4439	0.9478	0.9519	yes	N/A

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	2.7.7	0.921
4th Layer	2.7.7.7	0.914

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Alignment Graph	Length	Definition	E-value
Query		230
PRK05711		240	PRK05711, PRK05711, DNA polymerase III subunit eps	1e-107
cd06131		167	cd06131, DNA_pol_III_epsilon_Ecoli_like, DEDDh 3'-	1e-94
TIGR01406		225	TIGR01406, dnaQ_proteo, DNA polymerase III, epsilo	8e-86
TIGR00573		217	TIGR00573, dnaq, exonuclease, DNA polymerase III,	2e-54
COG0847		243	COG0847, DnaQ, DNA polymerase III, epsilon subunit	3e-48
cd06127		159	cd06127, DEDDh, DEDDh 3'-5' exonuclease domain fam	4e-38
smart00479		169	smart00479, EXOIII, exonuclease domain in DNA-poly	3e-34
pfam00929		161	pfam00929, RNase_T, Exonuclease	1e-30
PRK00448		1437	PRK00448, polC, DNA polymerase III PolC; Validated	1e-20
TIGR01405		1213	TIGR01405, polC_Gram_pos, DNA polymerase III, alph	9e-19
COG2176		1444	COG2176, PolC, DNA polymerase III, alpha subunit (	1e-18
PRK06310		250	PRK06310, PRK06310, DNA polymerase III subunit eps	1e-17
PRK07740		244	PRK07740, PRK07740, hypothetical protein; Provisio	2e-17
PRK08074		928	PRK08074, PRK08074, bifunctional ATP-dependent DNA	8e-16
PRK07883		557	PRK07883, PRK07883, hypothetical protein; Validate	4e-15
TIGR01407		850	TIGR01407, dinG_rel, DnaQ family exonuclease/DinG	1e-14
PRK09145		202	PRK09145, PRK09145, DNA polymerase III subunit eps	2e-13
PRK06807		313	PRK06807, PRK06807, DNA polymerase III subunit eps	3e-13
PRK06309		232	PRK06309, PRK06309, DNA polymerase III subunit eps	2e-12
PRK06063		313	PRK06063, PRK06063, DNA polymerase III subunit eps	4e-12
cd06130		156	cd06130, DNA_pol_III_epsilon_like, an uncharacteri	5e-11
PRK07942		232	PRK07942, PRK07942, DNA polymerase III subunit eps	2e-08
PRK08517		257	PRK08517, PRK08517, DNA polymerase III subunit eps	6e-07
PRK07983		219	PRK07983, PRK07983, exodeoxyribonuclease X; Provis	1e-06
PRK09146		239	PRK09146, PRK09146, DNA polymerase III subunit eps	2e-06
PRK09182		294	PRK09182, PRK09182, DNA polymerase III subunit eps	1e-05
TIGR01298		200	TIGR01298, RNaseT, ribonuclease T	1e-05
PRK06195		309	PRK06195, PRK06195, DNA polymerase III subunit eps	4e-04
PRK07246		820	PRK07246, PRK07246, bifunctional ATP-dependent DNA	7e-04

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

 Score =  309 bits (793), Expect = e-107
 Identities = 119/235 (50%), Positives = 155/235 (65%), Gaps = 9/235 (3%)

Query: 3   RHIVLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGLTT 62
           R IVLD ETTGLN  +GHRIIEIG VE+ NR++TG N H YI P R  +  ALA+HG+T 
Sbjct: 5   RQIVLDTETTGLNQREGHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITD 64

Query: 63  KFLKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLG--YSNFTKYIYRITD 120
           +FL +K  F+E+ D FL+++  +E+IIHNA FD+GF+D E +LLG        +  ++TD
Sbjct: 65  EFLADKPTFAEVADEFLDFIRGAELIIHNAPFDIGFMDYEFALLGRDIPKTNTFC-KVTD 123

Query: 121 TLLMARKIHTGKRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYLAMTRGQSNLNF-- 178
           TL MAR++  GKRNSLDALC RY I   HRTLHG LLDAE+LAEVYLAMT GQ++L F  
Sbjct: 124 TLAMARRMFPGKRNSLDALCKRYGIDNSHRTLHGALLDAEILAEVYLAMTGGQTSLGFAM 183

Query: 179 KPKINNSNNIETKIKIP---NNIPIKLANSNELVQHNMILSKIDKHSNGRCIWKK 230
           + +       ET  +I    + +P+  A   EL  H   L  +DK   G C+W+K
Sbjct: 184 EGETQQQQGEETIQRIVRQRSRLPVVRATDEELAAHEARLDLLDK-KGGSCLWRK 237

Length = 240

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

>gnl\|CDD\|130473 TIGR01406, dnaQ_proteo, DNA polymerase III, epsilon subunit, Proteobacterial	Back alignment and domain information

>gnl\|CDD\|129663 TIGR00573, dnaq, exonuclease, DNA polymerase III, epsilon subunit 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\|176648 cd06127, DEDDh, DEDDh 3'-5' exonuclease domain family	Back alignment and domain information

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

>gnl\|CDD\|216200 pfam00929, RNase_T, Exonuclease	Back alignment and domain information

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

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

>gnl\|CDD\|236085 PRK07740, PRK07740, hypothetical protein; Provisional	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\|236123 PRK07883, PRK07883, hypothetical protein; 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\|236391 PRK09145, PRK09145, DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

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

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

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

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

>gnl\|CDD\|236281 PRK08517, PRK08517, DNA polymerase III subunit epsilon; Provisional	Back alignment and domain information

>gnl\|CDD\|181186 PRK07983, PRK07983, exodeoxyribonuclease X; Provisional	Back alignment and domain information

>gnl\|CDD\|236392 PRK09146, PRK09146, DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

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

>gnl\|CDD\|188129 TIGR01298, RNaseT, ribonuclease T	Back alignment and domain information

>gnl\|CDD\|235735 PRK06195, PRK06195, DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>gnl\|CDD\|180905 PRK07246, PRK07246, bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		230
PRK05711		240	DNA polymerase III subunit epsilon; Provisional	100.0
TIGR01406		225	dnaQ_proteo DNA polymerase III, epsilon subunit, P	100.0
cd06131		167	DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonucl	100.0
TIGR00573		217	dnaq exonuclease, DNA polymerase III, epsilon subu	100.0
COG0847		243	DnaQ DNA polymerase III, epsilon subunit and relat	100.0
PRK09146		239	DNA polymerase III subunit epsilon; Validated	100.0
PRK07740		244	hypothetical protein; Provisional	100.0
PRK08517		257	DNA polymerase III subunit epsilon; Provisional	100.0
PRK07942		232	DNA polymerase III subunit epsilon; Provisional	100.0
PRK06310		250	DNA polymerase III subunit epsilon; Validated	100.0
PRK06807		313	DNA polymerase III subunit epsilon; Validated	100.0
PRK05168		211	ribonuclease T; Provisional	100.0
TIGR01298		200	RNaseT ribonuclease T. in gamma-subdivision Proteo	100.0
PRK09145		202	DNA polymerase III subunit epsilon; Validated	100.0
cd06134		189	RNaseT DEDDh 3'-5' exonuclease domain of RNase T.	100.0
PRK06309		232	DNA polymerase III subunit epsilon; Validated	100.0
PRK07748		207	sporulation inhibitor KapD; Provisional	100.0
cd06136		177	TREX1_2 DEDDh 3'-5' exonuclease domain of three pr	100.0
smart00479		169	EXOIII exonuclease domain in DNA-polymerase alpha	100.0
PRK06063		313	DNA polymerase III subunit epsilon; Provisional	100.0
PRK06195		309	DNA polymerase III subunit epsilon; Validated	100.0
cd06130		156	DNA_pol_III_epsilon_like an uncharacterized bacter	100.0
PRK06722		281	exonuclease; Provisional	100.0
PRK05601		377	DNA polymerase III subunit epsilon; Validated	100.0
PRK07883		557	hypothetical protein; Validated	100.0
PRK08074		928	bifunctional ATP-dependent DNA helicase/DNA polyme	100.0
PRK07247		195	DNA polymerase III subunit epsilon; Validated	100.0
COG2176		1444	PolC DNA polymerase III, alpha subunit (gram-posit	100.0
PRK07983		219	exodeoxyribonuclease X; Provisional	100.0
PRK07246		820	bifunctional ATP-dependent DNA helicase/DNA polyme	100.0
cd06133		176	ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain o	100.0
cd06138		183	ExoI_N N-terminal DEDDh 3'-5' exonuclease domain o	99.98
TIGR01407		850	dinG_rel DnaQ family exonuclease/DinG family helic	99.97
TIGR01405		1213	polC_Gram_pos DNA polymerase III, alpha chain, Gra	99.97
cd06137		161	DEDDh_RNase DEDDh 3'-5' exonuclease domain of the	99.97
cd06127		159	DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh	99.97
cd06145		150	REX1_like DEDDh 3'-5' exonuclease domain of RNA ex	99.96
cd06149		157	ISG20 DEDDh 3'-5' exonuclease domain of Interferon	99.96
cd06144		152	REX4_like DEDDh 3'-5' exonuclease domain of RNA ex	99.96
PRK09182		294	DNA polymerase III subunit epsilon; Validated	99.96
PRK11779		476	sbcB exonuclease I; Provisional	99.96
PTZ00315		582	2'-phosphotransferase; Provisional	99.96
cd06135		173	Orn DEDDh 3'-5' exonuclease domain of oligoribonuc	99.95
PRK05359		181	oligoribonuclease; Provisional	99.95
PRK00448		1437	polC DNA polymerase III PolC; Validated	99.95
PF00929		164	RNase_T: Exonuclease; InterPro: IPR013520 This ent	99.95
KOG0542\|consensus		280		99.8
COG5018		210	KapD Inhibitor of the KinA pathway to sporulation,	99.63
KOG2249\|consensus		280		99.6
COG2925		475	SbcB Exonuclease I [DNA replication, recombination	99.54
cd05160		199	DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain	99.49
cd06143		174	PAN2_exo DEDDh 3'-5' exonuclease domain of the euk	99.46
cd06125		96	DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonucleas	99.3
COG1949		184	Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA	99.23
cd06139		193	DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease	99.21
KOG3242\|consensus		208		99.08
PF13482		164	RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A	99.07
PRK05755		880	DNA polymerase I; Provisional	98.98
cd05781		188	DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of	98.96
KOG2248\|consensus		380		98.89
COG3359		278	Predicted exonuclease [DNA replication, recombinat	98.83
cd05780		195	DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease dom	98.82
PF10108		209	DNA_pol_B_exo2: Predicted 3'-5' exonuclease relate	98.77
cd05782		208	DNA_polB_like1_exo Uncharacterized bacterial subgr	98.76
PF01612		176	DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR00	98.6
cd05785		207	DNA_polB_like2_exo Uncharacterized bacterial subgr	98.58
cd05779		204	DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domai	98.58
KOG4793\|consensus		318		98.57
cd00007		155	35EXOc 3'-5' exonuclease. The 35EXOc domain is res	98.43
COG0349		361	Rnd Ribonuclease D [Translation, ribosomal structu	98.4
PHA02570		220	dexA exonuclease; Provisional	98.39
PF04857		262	CAF1: CAF1 family ribonuclease; InterPro: IPR00694	98.3
cd05784		193	DNA_polB_II_exo DEDDy 3'-5' exonuclease domain of	98.2
cd05777		230	DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain	98.18
cd06129		161	RNaseD_like DEDDy 3'-5' exonuclease domain of RNas	98.16
KOG0304\|consensus		239		98.11
cd06141		170	WRN_exo DEDDy 3'-5' exonuclease domain of WRN and	98.06
smart00474		172	35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proo	97.93
cd06146		193	mut-7_like_exo DEDDy 3'-5' exonuclease domain of C	97.85
PRK10829		373	ribonuclease D; Provisional	97.8
cd06148		197	Egl_like_exo DEDDy 3'-5' exonuclease domain of Dro	97.77
TIGR01388		367	rnd ribonuclease D. This model describes ribonucle	97.77
cd06140		178	DNA_polA_I_Bacillus_like_exo inactive DEDDy 3'-5'	97.76
cd06142		178	RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribon	97.76
cd05783		204	DNA_polB_B1_exo DEDDy 3'-5' exonuclease domain of	97.76
TIGR03491		457	RecB family nuclease, putative, TM0106 family. Mem	97.74
cd05778		231	DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease	97.68
PTZ00166		1054	DNA polymerase delta catalytic subunit; Provisiona	97.67
COG0749		593	PolA DNA polymerase I - 3'-5' exonuclease and poly	97.66
PF03104		325	DNA_pol_B_exo1: DNA polymerase family B, exonuclea	97.58
PRK05762		786	DNA polymerase II; Reviewed	97.54
smart00486		471	POLBc DNA polymerase type-B family. DNA polymerase	97.54
cd09018		150	DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease	97.35
cd05776		234	DNA_polB_alpha_exo inactive DEDDy 3'-5' exonucleas	97.34
TIGR00593		887	pola DNA polymerase I. This family is based on the	96.93
cd06147		192	Rrp6p_like_exo DEDDy 3'-5' exonuclease domain of y	96.45
PHA02528		881	43 DNA polymerase; Provisional	96.41
COG0417		792	PolB DNA polymerase elongation subunit (family B)	96.15
PHA02524		498	43A DNA polymerase subunit A; Provisional	95.93
cd06128		151	DNA_polA_exo DEDDy 3'-5' exonuclease domain of fam	95.87
KOG1798\|consensus		2173		95.56
TIGR00592		1172	pol2 DNA polymerase (pol2). This family is based o	95.21
KOG1275\|consensus		1118		94.64
PHA02563		630	DNA polymerase; Provisional	94.39
KOG4793\|consensus		318		93.12
PHA03036		1004	DNA polymerase; Provisional	92.43
COG5228		299	POP2 mRNA deadenylase subunit [RNA processing and	91.39
PF11074		130	DUF2779: Domain of unknown function(DUF2779); Inte	88.21
KOG0969\|consensus		1066		83.81
PF00843		533	Arena_nucleocap: Arenavirus nucleocapsid protein;	83.77
PF13017		213	Maelstrom: piRNA pathway germ-plasm component	80.72

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

Probab=100.00  E-value=3.1e-57  Score=379.73  Aligned_cols=227  Identities=52%  Similarity=0.876  Sum_probs=200.3

Q ss_pred             CceEEEEecCCCCCCCCCCceEEEEEEEEECCEEecceeEEEEcCCCCCChhhHhhcCCCHHHHhCCCCHHHHHHHHHHh
Q psy14503          2 HRHIVLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGLTTKFLKNKLKFSEIVDNFLNY   81 (230)
Q Consensus         2 ~~~ivlD~ETTGl~~~~~~~IieIg~v~~~~~~~~~~~f~~~i~P~~~i~~~a~~i~Git~e~l~~~~~~~ev~~~~~~f   81 (230)
                      |++|+|||||||++|..+++|||||||.+.++.++++.|+.||+|++++++++++|||||++++.++|+|.+++.+|.+|
T Consensus         4 ~r~vvlDtETTGldp~~~drIIEIGaV~v~~~~~~~~~f~~~i~P~~~i~~~a~~VHGIT~e~l~~~p~f~ev~~~f~~f   83 (240)
T PRK05711          4 MRQIVLDTETTGLNQREGHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEFLDF   83 (240)
T ss_pred             CeEEEEEeeCCCcCCCCCCeEEEEEEEEEECCEEeccEEEEEECcCCcCCHHHhhhcCCCHHHHcCCCCHHHHHHHHHHH
Confidence            79999999999999974599999999999999888889999999999999999999999999999999999999999999


Q ss_pred             cCCCeEEEEcccccHHHHHHHHHHcCCC--CcccccchHhHHHHHHHHHcCCCCCcHHHHHHHhCCCCCCCCCCCHHHHH
Q psy14503         82 VSNSEIIIHNAAFDVGFLDMELSLLGYS--NFTKYIYRITDTLLMARKIHTGKRNSLDALCDRYNISKIHRTLHGGLLDA  159 (230)
Q Consensus        82 l~~~~lV~hna~FD~~~L~~~l~~~g~~--~~~~~~~~~iDtl~lar~~~p~~~~~L~~L~~~~gi~~~~r~~H~Al~Da  159 (230)
                      ++++++|+||+.||++||++++.++|.+  +...+|. ++||+.++|.++|+.+++|++||++|||+.++|++|+|+.||
T Consensus        84 i~~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~-~iDTl~lar~~~p~~~~~L~aL~~~~gi~~~~r~~H~AL~DA  162 (240)
T PRK05711         84 IRGAELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCK-VTDTLAMARRMFPGKRNSLDALCKRYGIDNSHRTLHGALLDA  162 (240)
T ss_pred             hCCCEEEEEccHHhHHHHHHHHHHhCCCCCcccccCc-eeeHHHHHHHHcCCCCCCHHHHHHHCCCCCCCCCCCCHHHHH
Confidence            9999999999999999999999999843  2223455 999999999999999899999999999999988899999999


Q ss_pred             HHHHHHHHHHHcCCCccccccCCCC--C-C-ccccccc-CCCCCCcccCCHHHHHHHHHHHHHhhhcCCCCCccCC
Q psy14503        160 ELLAEVYLAMTRGQSNLNFKPKINN--S-N-NIETKIK-IPNNIPIKLANSNELVQHNMILSKIDKHSNGRCIWKK  230 (230)
Q Consensus       160 ~~~a~v~~~l~~~~~~l~~~~~~~~--~-~-~~~~~~~-~~~~~~~~~~~~~e~~~h~~~~~~~~~~~~~~~~w~~  230 (230)
                      ++|++||++|+++|.+|.++.....  . . ....... .+..++++++|++|+++|++||+.|.| +|++|+|++
T Consensus       163 ~~~A~v~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~h~~~~~~~~~-~~~~~~w~~  237 (240)
T PRK05711        163 EILAEVYLAMTGGQTSLGFAMEGETQQQQGEETIQRIVRQRSRLPVVRATDEELAAHEARLDLLDK-KGGSCLWRK  237 (240)
T ss_pred             HHHHHHHHHHHCccccccccCCccccccccccccccccccCCcccCCCCCHHHHHHHHHHHHHHHh-hCCCccCcc
Confidence            9999999999999999988644321  1 1 1111222 245677899999999999999999987 588999974

>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial	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

>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family	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

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

>PRK07740 hypothetical protein; Provisional	Back alignment and domain information

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

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

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

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

>PRK05168 ribonuclease T; Provisional	Back alignment and domain information

>TIGR01298 RNaseT ribonuclease T	Back alignment and domain information

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

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

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

>PRK07748 sporulation inhibitor KapD; Provisional	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

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

>PRK06063 DNA polymerase III subunit epsilon; Provisional	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

>PRK06722 exonuclease; Provisional	Back alignment and domain information

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

>PRK07883 hypothetical protein; Validated	Back alignment and domain information

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

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

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

>PRK07983 exodeoxyribonuclease X; Provisional	Back alignment and domain information

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

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

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

>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

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

>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins	Back alignment and domain information

>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

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

>PTZ00315 2'-phosphotransferase; Provisional	Back alignment and domain information

>cd06135 Orn DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins	Back alignment and domain information

>PRK05359 oligoribonuclease; Provisional	Back alignment and domain information

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

>PF00929 RNase_T: Exonuclease; InterPro: IPR013520 This entry includes a variety of exonuclease proteins, such as ribonuclease T [] and the epsilon subunit of DNA polymerase III	Back alignment and domain information

>KOG0542\|consensus	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	Back alignment and domain information

>COG2925 SbcB Exonuclease I [DNA 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

>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

>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]	Back alignment and domain information

>cd06139 DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases	Back alignment and domain information

>KOG3242\|consensus	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

>PRK05755 DNA polymerase I; Provisional	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

>KOG2248\|consensus	Back alignment and domain information

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

>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

>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

>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

>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

>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

>KOG4793\|consensus	Back alignment and domain information

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

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

>PHA02570 dexA exonuclease; Provisional	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

>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

>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

>cd06129 RNaseD_like DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins	Back alignment and domain information

>KOG0304\|consensus	Back alignment and domain information

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

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

>cd06146 mut-7_like_exo DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins	Back alignment and domain information

>PRK10829 ribonuclease D; Provisional	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

>TIGR01388 rnd ribonuclease D	Back alignment and domain information

>cd06140 DNA_polA_I_Bacillus_like_exo inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases	Back alignment and domain information

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

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

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

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

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

>PF03104 DNA_pol_B_exo1: DNA polymerase family B, exonuclease domain Several related DNA polymerases were too dissimilar to be included	Back alignment and domain information

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

>smart00486 POLBc DNA polymerase type-B family	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

>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

>TIGR00593 pola DNA polymerase I	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

>PHA02528 43 DNA polymerase; Provisional	Back alignment and domain information

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

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

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

>KOG1798\|consensus	Back alignment and domain information

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

>KOG1275\|consensus	Back alignment and domain information

>PHA02563 DNA polymerase; Provisional	Back alignment and domain information

>KOG4793\|consensus	Back alignment and domain information

>PHA03036 DNA polymerase; Provisional	Back alignment and domain information

>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]	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

>KOG0969\|consensus	Back alignment and domain information

>PF00843 Arena_nucleocap: Arenavirus nucleocapsid protein; InterPro: IPR000229 Arenaviruses are single stranded RNA viruses	Back alignment and domain information

>PF13017 Maelstrom: piRNA pathway germ-plasm component	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		230
1j53_A		186	Structure Of The N-Terminal Exonuclease Domain Of T		2e-48
2gui_A		194	Structure And Function Of Cyclized Versions Of The		2e-48
2p1j_A		186	Crystal Structure Of A Polc-Type Dna Polymerase Iii		8e-12

>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 = 188 bits (478), Expect = 2e-48, Method: Compositional matrix adjust. Identities = 92/179 (51%), Positives = 121/179 (67%), Gaps = 5/179 (2%) Query: 3 RHIVLDIETTGLNII----DGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIH 58 R IVLD ETTG+N I +GH+IIEIG VE+ NR++TGNN H Y+ P R + A +H Sbjct: 7 RQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVH 66 Query: 59 GXXXXXXXXXXXXSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLGYS-NFTKYIYR 117 G +E+ D F++Y+ +E++IHNAAFD+GF+D E SLL T + Sbjct: 67 GIADEFLLDKPTFAEVADEFMDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCK 126 Query: 118 ITDTLLMARKIHTGKRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYLAMTRGQSNL 176 +TD+L +ARK+ GKRNSLDALC RY I RTLHG LLDA++LAEVYLAMT GQ+++ Sbjct: 127 VTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLHGALLDAQILAEVYLAMTGGQTSM 185

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

>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

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		230
2gui_A		194	DNA polymerase III epsilon subunit; DNA polymerase	2e-95
3v9w_A		235	Ribonuclease T; DEDD nucleases family, EXO-nucleas	3e-43
2f96_A		224	Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolas	3e-42
2p1j_A		186	POLIII, DNA polymerase III POLC-type; structural g	2e-40
1y97_A		238	Three prime repair exonuclease 2; TREX2, hydrolase	1e-32
3mxm_B		242	Three prime repair exonuclease 1; RNAse H-like fol	7e-28
3u3y_B		314	Three prime repair exonuclease 1; RNAse H fold, 3'	1e-27
2xri_A		224	ERI1 exoribonuclease 3; hydrolase, metal binding;	3e-18
1zbu_A		349	ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase;	4e-18
1w0h_A		204	3'-5' exonuclease ERI1; nuclease domain, hydrolase	5e-18
3cg7_A		308	CRN-4, cell death-related nuclease 4; hydrolase, a	1e-16
1zbh_A		299	3'-5' exonuclease ERI1; histone mRNA 3'-END-specif	2e-15

>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

 Score =  275 bits (707), Expect = 2e-95
 Identities = 95/184 (51%), Positives = 130/184 (70%), Gaps = 5/184 (2%)

Query: 1   MHRHIVLDIETTGLNII----DGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALA 56
           + R IVLD ETTG+N I    +GH+IIEIG VE+ NR++TGNN H Y+ P R  +  A  
Sbjct: 8   ITRQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFG 67

Query: 57  IHGLTTKFLKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLGYSNFTKYIY 116
           +HG+  +FL +K  F+E+ D F++Y+  +E++IHNAAFD+GF+D E SLL         +
Sbjct: 68  VHGIADEFLLDKPTFAEVADEFMDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTF 127

Query: 117 -RITDTLLMARKIHTGKRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYLAMTRGQSN 175
            ++TD+L +ARK+  GKRNSLDALC RY I    RTLHG LLDA++LAEVYLAMT GQ++
Sbjct: 128 CKVTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLHGALLDAQILAEVYLAMTGGQTS 187

Query: 176 LNFK 179
           +  +
Sbjct: 188 MATR 191

PyMOL of 2gui

>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

>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

>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

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

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

>1w0h_A 3'-5' exonuclease ERI1; nuclease domain, hydrolase; HET: AMP; 1.59A {Homo sapiens} SCOP: c.55.3.5 Length = 204	Back alignment and structure

>3cg7_A CRN-4, cell death-related nuclease 4; hydrolase, apoptosis, 3'-5' exonuclease, deddh; 2.50A {Caenorhabditis elegans} PDB: 3cm5_A 3cm6_A Length = 308	Back alignment and structure

>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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		230
2gui_A		194	DNA polymerase III epsilon subunit; DNA polymerase	100.0
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
3u3y_B		314	Three prime repair exonuclease 1; RNAse H fold, 3'	100.0
2f96_A		224	Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolas	100.0
2xri_A		224	ERI1 exoribonuclease 3; hydrolase, metal binding;	100.0
1zbh_A		299	3'-5' exonuclease ERI1; histone mRNA 3'-END-specif	100.0
3v9w_A		235	Ribonuclease T; DEDD nucleases family, EXO-nucleas	100.0
1y97_A		238	Three prime repair exonuclease 2; TREX2, hydrolase	100.0
1zbu_A		349	ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase;	100.0
3cg7_A		308	CRN-4, cell death-related nuclease 4; hydrolase, a	99.98
2qxf_A		482	Exodeoxyribonuclease I; alpha-beta domain, DNAQ su	99.97
1wlj_A		189	Interferon stimulated gene 20KDA; exoribonuclease,	99.97
3tr8_A		186	Oligoribonuclease; transcription, hydrolase; 2.50A	99.97
2igi_A		180	Oligoribonuclease; RNAse, exoribonuclease, exonucl	99.97
2gbz_A		194	Oligoribonuclease; ORN, deddh, structural genomics	99.96
2kfn_A		605	Klenow fragment of DNA polymerase I; complex (poly	99.41
4hec_A		190	Putative uncharacterized protein; ssgcid, structur	99.31
1x9m_A		698	DNA polymerase; DNA ploymerase, N-2-acetylaminoflu	99.15
4dfk_A		540	DNA polymerase I, thermostable; DNA polymerase, tr	98.8
4gmj_B		285	CCR4-NOT transcription complex subunit 7; mRNA dec	98.77
2d5r_A		252	CCR4-NOT transcription complex subunit 7; poly(A)	98.43
1qht_A		775	Protein (DNA polymerase); archaea, hyperthermostab	98.42
2p51_A		333	SPCC18.06C protein; DEDD nuclease fold, hydrolase,	98.4
1uoc_A		289	POP2; hydrolase, DEDD nuclease, mRNA degradation,	98.25
3pv8_A		592	DNA polymerase I; DNA polymerase I, protein-DNA co	98.24
3saf_A		428	Exosome component 10; exoribonuclease, RNA exosome	98.21
1noy_A		388	Protein (DNA polymerase (E.C.2.7.7.7)); exonucleas	98.2
3iay_A		919	DNA polymerase delta catalytic subunit; protein-DN	98.18
2e6m_A		208	Werner syndrome ATP-dependent helicase homolog; AP	97.96
1yt3_A		375	Ribonuclease D, RNAse D; exoribonuclease, exonucle	97.94
2hbj_A		410	Exosome complex exonuclease RRP6; RNA metabolism,	97.79
2gv9_A		1193	DNA polymerase; polymerase alpha fold, transferase	97.77
1s5j_A		847	DNA polymerase I; replication, disulfide bonds, tr	97.72
3cym_A		440	Uncharacterized protein BAD_0989; structural genom	97.61
3qex_A		903	DNA polymerase, GP43; difluorotoluene nucleoside;	97.26
3k59_A		786	POL II, DNA polymerase II; protein-DNA complex, DN	97.17
3d45_A		507	Poly(A)-specific ribonuclease PARN; CAP analogue,	96.73
2py5_A		575	DNA polymerase; protein-DNA complex, replication,	96.69
1vk0_A		206	Hypothetical protein; homohexamer, AT5G06450, stru	96.52
1bgx_T		832	TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhi	96.42
2a1r_A		430	Poly(A)-specific ribonuclease PARN; DEDD, nuclease	96.19
3q7c_A		243	Nucleoprotein; deddh exonuclease, 3' exonuclease,	80.84

>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

Probab=100.00  E-value=1.9e-39  Score=263.41  Aligned_cols=174  Identities=54%  Similarity=0.945  Sum_probs=155.1

Q ss_pred             CceEEEEecCCCCCC----CCCCceEEEEEEEEECCEEecceeEEEEcCCCCCChhhHhhcCCCHHHHhCCCCHHHHHHH
Q psy14503          2 HRHIVLDIETTGLNI----IDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGLTTKFLKNKLKFSEIVDN   77 (230)
Q Consensus         2 ~~~ivlD~ETTGl~~----~~~~~IieIg~v~~~~~~~~~~~f~~~i~P~~~i~~~a~~i~Git~e~l~~~~~~~ev~~~   77 (230)
                      |++++||+||||+++    ..+++|||||+|.++++.++++.|+.+|+|..+++++++++||||++++.++|+|.+++.+
T Consensus         9 ~~~vviD~ETTGl~~~~~~~~~~~Iieig~v~~~~~~~~~~~f~~lv~P~~~i~~~~~~i~GIt~~~l~~~~~~~~v~~~   88 (194)
T 2gui_A            9 TRQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADE   88 (194)
T ss_dssp             CEEEEEEEEESCCCSSSSTTTTCCEEEEEEEEEETTEECSCCEEEECCCSSCCCHHHHHHHCCCHHHHTTSCCHHHHHHH
T ss_pred             CCEEEEEeeCCCCCCcccCCCCCEEEEEEEEEEECCeEeccEEEEEECcCCcCCHHHHHhhCcCHHHHhCCCCHHHHHHH
Confidence            799999999999998    2348999999999998888766799999999999999999999999999999999999999


Q ss_pred             HHHhcCCCeEEEEcccccHHHHHHHHHHcCCCC--cccccchHhHHHHHHHHHcCCCCCcHHHHHHHhCCCCCCCCCCCH
Q psy14503         78 FLNYVSNSEIIIHNAAFDVGFLDMELSLLGYSN--FTKYIYRITDTLLMARKIHTGKRNSLDALCDRYNISKIHRTLHGG  155 (230)
Q Consensus        78 ~~~fl~~~~lV~hna~FD~~~L~~~l~~~g~~~--~~~~~~~~iDtl~lar~~~p~~~~~L~~L~~~~gi~~~~r~~H~A  155 (230)
                      |.+|+++..+|+||+.||+.||++++.++|++.  +...+ .++||+.+++.++|+.+++|++||++||++..+|..|+|
T Consensus        89 ~~~~l~~~~lv~hn~~fD~~~L~~~~~~~g~~~p~~~~~~-~~iDt~~l~~~~~p~~~~~L~~l~~~~gi~~~~~~~H~A  167 (194)
T 2gui_A           89 FMDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFC-KVTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLHGA  167 (194)
T ss_dssp             HHHHHTTSEEEETTHHHHHHHHHHHHHHTCSCCCCGGGTS-EEEEHHHHHHHHSTTSCCSHHHHHHHTTCCCTTCSSCCH
T ss_pred             HHHHHCCCeEEEEchHHhHHHHHHHHHHcCCCCccccccC-ceeeHHHHHHHHcCCCCCCHHHHHHHcCcCCCCCCCCCh
Confidence            999999999999999999999999999999872  32123 389999999999998888999999999999987668999


Q ss_pred             HHHHHHHHHHHHHHHcCCCcc
Q psy14503        156 LLDAELLAEVYLAMTRGQSNL  176 (230)
Q Consensus       156 l~Da~~~a~v~~~l~~~~~~l  176 (230)
                      +.||.++++||.+|.++.+++
T Consensus       168 l~Da~~ta~l~~~l~~~~~~~  188 (194)
T 2gui_A          168 LLDAQILAEVYLAMTGGQTSM  188 (194)
T ss_dssp             HHHHHHHHHHHHHHTC-----
T ss_pred             HHHHHHHHHHHHHHHhccchh
Confidence            999999999999999886654

PyMOL of 2gui

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

>1w0h_A 3'-5' exonuclease ERI1; nuclease domain, hydrolase; HET: AMP; 1.59A {Homo sapiens} SCOP: c.55.3.5	Back alignment and structure

>3mxm_B Three prime repair exonuclease 1; RNAse H-like fold, polyproline type II helix, hydrolase-DNA; HET: DNA; 1.75A {Mus musculus} SCOP: c.55.3.5 PDB: 3mxj_B 2ioc_B 3mxi_B* 3b6o_A* 2o4g_A* 3b6p_A* 2o4i_A 2oa8_A	Back alignment and structure

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

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

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

>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

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

>1zbu_A ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; HET: AMP; 3.00A {Homo sapiens}	Back alignment and structure

>3cg7_A CRN-4, cell death-related nuclease 4; hydrolase, apoptosis, 3'-5' exonuclease, deddh; 2.50A {Caenorhabditis elegans} PDB: 3cm5_A 3cm6_A	Back alignment and structure

>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

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

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

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

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

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

>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

>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

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

>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

>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

>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

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

>2e6m_A Werner syndrome ATP-dependent helicase homolog; APO form, hydrolase; 2.00A {Mus musculus} PDB: 2e6l_A 2fby_A 2fbv_A 2fbx_A 2fbt_A 2fc0_A*	Back alignment and structure

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

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

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

>1s5j_A DNA polymerase I; replication, disulfide bonds, transferase; HET: DNA; 2.40A {Sulfolobus solfataricus} SCOP: c.55.3.5 e.8.1.1	Back alignment and structure

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

>3qex_A DNA polymerase, GP43; difluorotoluene nucleoside; HET: DNA DOC DGT; 1.73A {Enterobacteria phage RB69} PDB: 3qei_A* 3qer_A* 3qes_A* 3qet_A* 3qep_A* 3qew_A* 3qev_A* 3s9h_A* 3sq0_A* 4dtn_A* 4dto_A* 4dtp_A* 4dtr_A* 4dts_A* 4dtu_A* 4dtx_A* 4e3s_A* 4fjm_A* 4fjl_A* 3spz_A* ...	Back alignment and structure

>3k59_A POL II, DNA polymerase II; protein-DNA complex, DNA damage, DNA repair, DNA-binding; HET: DNA DOC DCP; 1.92A {Escherichia coli} PDB: 3k57_A* 3k58_A* 3k5l_A* 3k5m_A* 3k5n_A* 3k5o_A* 3maq_A* 1q8i_A*	Back alignment and structure

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}	Back alignment and structure

>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

>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

>2a1r_A Poly(A)-specific ribonuclease PARN; DEDD, nuclease domain, hydrolase-RNA complex; 2.60A {Homo sapiens} PDB: 2a1s_A	Back alignment and structure

>3q7c_A Nucleoprotein; deddh exonuclease, 3' exonuclease, hydrolase; 1.50A {Lassa virus} PDB: 3q7b_A 4fvu_A	Back alignment and structure

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		230
d2guia1		174	c.55.3.5 (A:7-180) N-terminal exonuclease domain o	4e-39
d1y97a1		228	c.55.3.5 (A:1-228) Three prime repair exonuclease	2e-21
d2f96a1		202	c.55.3.5 (A:19-220) Ribonuclease T {Pseudomonas ae	2e-20
d1w0ha_		200	c.55.3.5 (A:) Exonuclease ERI1 {Human (Homo sapien	8e-19
d3b6oa1		226	c.55.3.5 (A:9-234) Three prime repair exonuclease	7e-18
d1wlja_		173	c.55.3.5 (A:) Interferon-stimulated gene 20 kDa pr	5e-17
d2qxfa1		467	c.55.3.5 (A:8-474) Exonuclease I {Escherichia coli	3e-10
d2igia1		180	c.55.3.5 (A:1-180) Oligoribonuclease {Escherichia	8e-06

>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


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]

 Score =  131 bits (329), Expect = 4e-39
 Identities = 93/173 (53%), Positives = 122/173 (70%), Gaps = 5/173 (2%)

Query: 3   RHIVLDIETTGLN----IIDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIH 58
           R IVLD ETTG+N      +GH+IIEIG VE+ NR++TGNN H Y+ P R  +  A  +H
Sbjct: 1   RQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVH 60

Query: 59  GLTTKFLKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLGYS-NFTKYIYR 117
           G+  +FL +K  F+E+ D F++Y+  +E++IHNAAFD+GF+D E SLL      T    +
Sbjct: 61  GIADEFLLDKPTFAEVADEFMDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCK 120

Query: 118 ITDTLLMARKIHTGKRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYLAMT 170
           +TD+L +ARK+  GKRNSLDALC RY I    RTLHG LLDA++LAEVYLAMT
Sbjct: 121 VTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLHGALLDAQILAEVYLAMT 173

PyMOL of d2guia1

>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

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

>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

>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

>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

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		230
d2guia1		174	N-terminal exonuclease domain of the epsilon subun	100.0
d3b6oa1		226	Three prime repair exonuclease 1, TREX1 {Mouse (Mu	99.97
d1wlja_		173	Interferon-stimulated gene 20 kDa protein, ISG20 {	99.97
d1w0ha_		200	Exonuclease ERI1 {Human (Homo sapiens) [TaxId: 960	99.96
d1y97a1		228	Three prime repair exonuclease 2, TREX2 {Human (Ho	99.95
d2qxfa1		467	Exonuclease I {Escherichia coli K12 (Escherichia c	99.91
d2f96a1		202	Ribonuclease T {Pseudomonas aeruginosa [TaxId: 287	99.91
d2igia1		180	Oligoribonuclease {Escherichia coli [TaxId: 562]}	99.76
d1x9ma1		204	Exonuclease domain of T7 DNA polymerase {Bacteriop	98.99
d2d5ra1		252	CCR4-NOT transcription complex subunit 7, CAF1 {Hu	98.98
d1kfsa1		195	Exonuclease domain of prokaryotic DNA polymerase {	98.94
d2hhva1		171	Exonuclease domain of prokaryotic DNA polymerase {	98.79
d1yt3a3		193	Ribonuclease D, catalytic domain {Escherichia coli	98.56
d1uoca_		286	Pop2 RNase D domain {Baker's yeast (Saccharomyces	98.34
d2hbka2		292	Exosome complex exonuclease RRP6 {Baker's yeast (S	98.28
d1tgoa1		347	Exonuclease domain of family B DNA polymerases {Ar	97.97
d1vk0a_		206	Hypothetical protein AT5G06450 {Thale-cress (Arabi	97.42
d1s5ja1		410	Exonuclease domain of family B DNA polymerases {Su	97.19
d1q8ia1		388	Exonuclease domain of family B DNA polymerases {Es	96.89
d1ih7a1		375	Exonuclease domain of family B DNA polymerases {Ba	90.35
d1noya_		372	Exonuclease domain of family B DNA polymerases {Ba	90.24
d2py5a1		183	Exonuclease domain of phi29 DNA polymerase {Bacter	87.09

>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=100.00  E-value=9.2e-38  Score=245.25  Aligned_cols=168  Identities=55%  Similarity=0.947  Sum_probs=154.1

Q ss_pred             ceEEEEecCCCCCCC----CCCceEEEEEEEEECCEEecceeEEEEcCCCCCChhhHhhcCCCHHHHhCCCCHHHHHHHH
Q psy14503          3 RHIVLDIETTGLNII----DGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGLTTKFLKNKLKFSEIVDNF   78 (230)
Q Consensus         3 ~~ivlD~ETTGl~~~----~~~~IieIg~v~~~~~~~~~~~f~~~i~P~~~i~~~a~~i~Git~e~l~~~~~~~ev~~~~   78 (230)
                      |+|+||+||||++|.    .+++|||||+|.++++.++.+.|+.+|+|..++++.+.++||||++++.+++++.+++.+|
T Consensus         1 r~vv~D~ETTGl~~~~~~~~~d~IIeIg~v~~~~~~~~~~~~~~~v~P~~~i~~~~~~i~gIt~e~~~~~~~~~~~~~~~   80 (174)
T d2guia1           1 RQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEF   80 (174)
T ss_dssp             EEEEEEEEESCCCSSSSTTTTCCEEEEEEEEEETTEECSCCEEEECCCSSCCCHHHHHHHCCCHHHHTTSCCHHHHHHHH
T ss_pred             CEEEEEeeCCCCCcccccCCCCEEEEEEEEEEECCEEeeeEEEEEeccCccchhhhhhccccchhhhhcchhHHHHHHHH
Confidence            789999999999974    2379999999999999888778999999999999999999999999999999999999999


Q ss_pred             HHhcCCCeEEEEcccccHHHHHHHHHHcCCCCc--ccccchHhHHHHHHHHHcCCCCCcHHHHHHHhCCCCCCCCCCCHH
Q psy14503         79 LNYVSNSEIIIHNAAFDVGFLDMELSLLGYSNF--TKYIYRITDTLLMARKIHTGKRNSLDALCDRYNISKIHRTLHGGL  156 (230)
Q Consensus        79 ~~fl~~~~lV~hna~FD~~~L~~~l~~~g~~~~--~~~~~~~iDtl~lar~~~p~~~~~L~~L~~~~gi~~~~r~~H~Al  156 (230)
                      .+|++++.+|+||..||..++...+.+.+.+..  ...+. ++|++.+++.++|+.+.+|..+|++||++..++.+|+|+
T Consensus        81 ~~~~~~~~~v~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~-~~d~~~~~~~~~~~~~~~L~~l~~~~~~~~~~~~~H~Al  159 (174)
T d2guia1          81 MDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCK-VTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLHGAL  159 (174)
T ss_dssp             HHHHTTSEEEETTHHHHHHHHHHHHHHTCSCCCCGGGTSE-EEEHHHHHHHHSTTSCCSHHHHHHHTTCCCTTCSSCCHH
T ss_pred             HHhcCCCeEEEeecchhhHHHHHHHHHhCCCCCCcccccc-hhhHHHHHHHHcCCCCCCHHHHHHHcCCCCCCCCCcCHH
Confidence            999999999999999999999999999887532  22333 789999999999998899999999999998887799999


Q ss_pred             HHHHHHHHHHHHHHc
Q psy14503        157 LDAELLAEVYLAMTR  171 (230)
Q Consensus       157 ~Da~~~a~v~~~l~~  171 (230)
                      .||.+|++||++|+|
T Consensus       160 ~Da~~ta~v~~~l~~  174 (174)
T d2guia1         160 LDAQILAEVYLAMTG  174 (174)
T ss_dssp             HHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHcC
Confidence            999999999999975

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

>d1wlja_ c.55.3.5 (A:) Interferon-stimulated gene 20 kDa protein, ISG20 {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

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

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

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

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

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

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

>d2hhva1 c.55.3.5 (A:298-468) Exonuclease domain of prokaryotic DNA polymerase {Bacillus stearothermophilus, newly identified strain as yet unnamed [TaxId: 1422]}	Back information, alignment and structure

>d1yt3a3 c.55.3.5 (A:1-193) Ribonuclease D, catalytic domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

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

>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

>d1vk0a_ c.55.3.5 (A:) Hypothetical protein AT5G06450 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]}	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

>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

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