Citrus Sinensis ID: 009922

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-------520--
MPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSVTEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAELPVSLRLIGLRVTQFNEDKVRAPSDPTQKTLTNFMTSGHASKKIVGDQNSLGSDINDDCLIDDKETSVSLDVSETNNYEFGDPVCDNSLPDLNDENCSFSNKISEVEKIHENEVSQLLEGNSLVLRQEEGSCCDGVEEVDKDITPDNKVGTSSNQKDQFIWLDDYKCSLCGTEMPPSFIEERQEHSDFHLAERLQKEESGSDLRILTHRERCVRTQRDHIASHRKRKKQKLFEKEGTHIPIDMFFAKRNRNF
ccHHHHHHHccccEEEccccHHHHHHHHHHHHHHHHcccccccccccHHccccccccccccccHHHHHHHHHHHHHHHHcccEEEEccHHHHHHHHHccccccccEEEEcccHHHHHHHHHcccccccccccHHHHHHHHHccccccHHHHHHccHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHccccccEEEEEEEccccEEEEEEEEcccccccHHHHHHHHHHHHHHHccccEEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHcccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHcHHHHHHHHHcccccccccHHHcccccccccccHHHccccccccccccccccHHHHHccccc
ccHHHHHHHcccEEEEcccHHHHHHHHHHHHHHHHHHccccccccccHHEEEcccccccccccHHHHHHHHHHHHHHHHcccEEccccHHHHHHHHHHcccccccEEEEcccccHHHHHHccccccccccccHHHHHHHHHHHccccHHHHHHccHHHHHHHHccHHHHHHHHHccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHcccccEEEEEEEEEcccEEEEcccccccccccHHHHHHHHHHHHHHHccccEEEEEEEEcccccccccccccHHHHHHHHHHHcHHHHHHHHHHHHHHHHHcccccEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEcccccccccccccccccccEEEEccEEEEEEccEcccccHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHcccccccccccccccccccccccccccEEEEEEEccccc
mpgfiarklcpelifvptdftkytyysdltrkvfckydpnfmaasLDEAYLDITEVCRERGISGIEIAEELRTSVyeeagltcsagvapNRLLAKVCsdinkpngqfvlpndRMAVMTFISslpirkiggigkvTEHILRDVFGINTCEEMLQKGSLLCAVFSHSTADFFLSvglglgstntpqarfrksissertfsvteDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAELPVSLRLIGLRVtqfnedkvrapsdptqktltnfmtsghaskkivgdqnslgsdinddcliddketsvsldvsetnnyefgdpvcdnslpdlndencsfsnKISEVEKIHENEVSQLLEGNSLVLRqeegsccdgveevdkditpdnkvgtssnqkdqfiwlddykcslcgtemppsfieerqeHSDFHLAERlqkeesgsdlrilTHRERCVRTQRDHIASHRKRKKQKLFekegthipidmffaKRNRNF
mpgfiarklcpelifvptdfTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPngqfvlpndRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSLLCAVFSHSTADFFLSVGLGlgstntpqarfrksissertfsvtedkALLYRKLAEIAEMLSADmqkeglrgrtltlklktasfevrtrAVTLQKYISSSEDILKHASVLLKAELPVSLRLIGLrvtqfnedkvrapsdptqkTLTNfmtsghaskkivgdqnslgsDINDDCLIDDKETSVSLDVSETNNYEFGDPVCDNSLPDLNDENCSFSNKISEVEKIHENEVSQLLEGNSLVLRQEEGSCCdgveevdkditpdnkvgtssnqkdqfiWLDDYKCSLCGTEMPPSFIEERQEHSDFHLAERlqkeesgsdlrilthrercvrtqrdhiashrkrkkqklfekegthipidmffakrnrnf
MPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSVTEDKALLYRKLAEIAEMLSADMQKEglrgrtltlklktASFEVRTRAVTLQKYISSSEDILKHASVLLKAELPVSLRLIGLRVTQFNEDKVRAPSDPTQKTLTNFMTSGHASKKIVGDQNSLGSDINDDCLIDDKETSVSLDVSETNNYEFGDPVCDNSLPDLNDENCSFSNKISEVEKIHENEVSQLLEGNSLVLRQEEGSCCDGVEEVDKDITPDNKVGTSSNQKDQFIWLDDYKCSLCGTEMPPSFIEERQEHSDFHLAERLQKEESGSDLRILTHRERCVRTQRDHIASHRKRKKQKLFEKEGTHIPIDMFFAKRNRNF
***FIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSLLCAVFSHSTADFFLSVGLGLGST****************FSVTEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAELPVSLRLIGLRVTQFN*****************************************DCLI****************YEFGDPVC*************************************LVL******CCD***********************QFIWLDDYKCSLCGTE*****************************************************************IPIDMFF*******
*PGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSLLCAVFSHSTADFFLSVGLGLGSTNTPQ****KSISSERTFSVTEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAELPVSLRLIGLRVTQ*****************TN*******************************************************************************************************************************WLDDYKCSLCGTEMPPSFIEERQEHSDFHLAE***************************************************FFAKRNR**
MPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSVTEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAELPVSLRLIGLRVTQFNEDKVRAPSDPTQKTLTNFMTSGHASKKIVGDQNSLGSDINDDCLIDDKETSVSLDVSETNNYEFGDPVCDNSLPDLNDENCSFSNKISEVEKIHENEVSQLLEGNSLVLRQEEGSCCDGVEEVDKDITPDNKVGTSSNQKDQFIWLDDYKCSLCGTEMPPSFIEERQEHSDFHLAERLQKEESGSDLRILTHRERCVRTQ*************KLFEKEGTHIPIDMFFAKRNRNF
*PGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSVTEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAELPVSLRLIGLRVTQFNEDKVRAPSDPTQKTLTNFMTSGHASKKIVGDQNSLGSDINDDCLIDDKE********ETNNYEFGDPVCDN*L******************************************************************KDQFIWLDDYKCSLCGTEMPPSFIEERQEHSDFHLAERLQKEES*************************************THIPIDMFFAKRN***
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MPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSVTEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAELPVSLRLIGLRVTQFNEDKVRAPSDPTQKTLTNFMTSGHASKKIVGDQNSLGSDINDDCLIDDKETSVSLDVSETNNYEFGDPVCDNSLPDLNDENCSFSNKISEVEKIHENEVSQLLEGNSLVLRQEEGSCCDGVEEVDKDITPDNKVGTSSNQKDQFIWLDDYKCSLCGTEMPPSFIEERQEHSDFHLAERLQKEESGSDLRILTHRERCVRTQRDHIASHRKRKKQKLFEKEGTHIPIDMFFAKRNRNF
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 ?
Query522 2.2.26 [Sep-21-2011]
Q9UBT6 870 DNA polymerase kappa OS=H yes no 0.471 0.282 0.449 2e-54
Q9QUG2 852 DNA polymerase kappa OS=M yes no 0.484 0.296 0.441 2e-54
O74944547 DNA polymerase kappa OS=S yes no 0.544 0.519 0.348 3e-46
P34409596 DNA polymerase kappa OS=C yes no 0.599 0.525 0.366 2e-45
P58965384 DNA polymerase IV OS=Ther yes no 0.532 0.723 0.359 2e-37
Q8UJK7357 DNA polymerase IV 2 OS=Ag yes no 0.544 0.795 0.344 2e-36
Q5FSM8356 DNA polymerase IV OS=Gluc yes no 0.538 0.789 0.348 5e-36
B4SIF5356 DNA polymerase IV OS=Sten yes no 0.528 0.775 0.367 5e-36
B2FLR2364 DNA polymerase IV OS=Sten yes no 0.528 0.758 0.367 9e-36
Q9JRG1352 DNA polymerase IV OS=Neis yes no 0.513 0.761 0.343 8e-35
>sp|Q9UBT6|POLK_HUMAN DNA polymerase kappa OS=Homo sapiens GN=POLK PE=1 SV=1 Back     alignment and function desciption
 Score =  214 bits (544), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 116/258 (44%), Positives = 168/258 (65%), Gaps = 12/258 (4%)

Query: 61  GISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQF-VLPNDRMAVMTF 119
           G S  E+ +E+R  + ++  LT SAG+APN +LAKVCSD NKPNGQ+ +LPN R AVM F
Sbjct: 287 GTSAQEVVKEIRFRIEQKTTLTASAGIAPNTMLAKVCSDKNKPNGQYQILPN-RQAVMDF 345

Query: 120 ISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSLLCAVFSHSTADFFLSVGLGLGS 179
           I  LPIRK+ GIGKVTE +L+   GI TC E+ Q+ +LL  +FS ++  +FL + LGLGS
Sbjct: 346 IKDLPIRKVSGIGKVTEKMLK-ALGIITCTELYQQRALLSLLFSETSWHYFLHISLGLGS 404

Query: 180 TNTPQARFRKSISSERTFSVTEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTAS 239
           T+  +   RKS+S ERTFS        Y    E+   L+ D+QKE L+GRT+T+KLK  +
Sbjct: 405 THLTRDGERKSMSVERTFSEINKAEEQYSLCQELCSELAQDLQKERLKGRTVTIKLKNVN 464

Query: 240 FEVRTRAVTLQKYISSSEDILKHASVLLKAEL------PVSLRLIGLRVTQFNEDKVRAP 293
           FEV+TRA T+   +S++E+I   A  LLK E+      P+ LRL+G+R++ F  ++ R  
Sbjct: 465 FEVKTRASTVSSVVSTAEEIFAIAKELLKTEIDADFPHPLRLRLMGVRISSFPNEEDRKH 524

Query: 294 SDPTQKTLTNFMTSGHAS 311
               Q+++  F+ +G+ +
Sbjct: 525 Q---QRSIIGFLQAGNQA 539
DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high-fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Depending on the context, it inserts the correct base, but causes frequent base transitions, transversions and frameshifts. Lacks 3'-5' proofreading exonuclease activity. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but does not have lyase activity.
Homo sapiens (taxid: 9606)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 7
>sp|Q9QUG2|POLK_MOUSE DNA polymerase kappa OS=Mus musculus GN=Polk PE=1 SV=1 Back     alignment and function description
>sp|O74944|POLK_SCHPO DNA polymerase kappa OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=mug40 PE=1 SV=3 Back     alignment and function description
>sp|P34409|POLK_CAEEL DNA polymerase kappa OS=Caenorhabditis elegans GN=polk-1 PE=3 SV=3 Back     alignment and function description
>sp|P58965|DPO4_THETN DNA polymerase IV OS=Thermoanaerobacter tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4) GN=dinB PE=3 SV=1 Back     alignment and function description
>sp|Q8UJK7|DPO42_AGRT5 DNA polymerase IV 2 OS=Agrobacterium tumefaciens (strain C58 / ATCC 33970) GN=dinB2 PE=3 SV=2 Back     alignment and function description
>sp|Q5FSM8|DPO4_GLUOX DNA polymerase IV OS=Gluconobacter oxydans (strain 621H) GN=dinB PE=3 SV=1 Back     alignment and function description
>sp|B4SIF5|DPO4_STRM5 DNA polymerase IV OS=Stenotrophomonas maltophilia (strain R551-3) GN=dinB PE=3 SV=1 Back     alignment and function description
>sp|B2FLR2|DPO4_STRMK DNA polymerase IV OS=Stenotrophomonas maltophilia (strain K279a) GN=dinB PE=3 SV=1 Back     alignment and function description
>sp|Q9JRG1|DPO4_NEIMA DNA polymerase IV OS=Neisseria meningitidis serogroup A / serotype 4A (strain Z2491) GN=dinB 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 ?
Query522
296083048 704 unnamed protein product [Vitis vinifera] 0.986 0.731 0.633 0.0
225428993 661 PREDICTED: DNA polymerase kappa-like [Vi 0.954 0.753 0.654 0.0
356539372 663 PREDICTED: DNA polymerase kappa-like [Gl 0.965 0.760 0.635 0.0
449438619 693 PREDICTED: DNA polymerase kappa-like [Cu 0.992 0.747 0.593 1e-180
357480655 706 DNA polymerase IV [Medicago truncatula] 0.875 0.647 0.611 1e-166
79362498 671 DNA polymerase kappa subunit [Arabidopsi 0.975 0.758 0.588 1e-163
297847332 636 predicted protein [Arabidopsis lyrata su 0.909 0.746 0.574 1e-152
242038847 668 hypothetical protein SORBIDRAFT_01g01463 0.961 0.751 0.537 1e-146
293334565535 uncharacterized protein LOC100381652 [Ze 0.957 0.934 0.526 1e-145
413933667 670 hypothetical protein ZEAMMB73_188779 [Ze 0.957 0.746 0.524 1e-145
>gi|296083048|emb|CBI22452.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
 Score =  662 bits (1709), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 352/556 (63%), Positives = 410/556 (73%), Gaps = 41/556 (7%)

Query: 1   MPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRER 60
           MPGFIARKLCPELIFVPTDF KYTYYSDLTRKVF KYDPNFMAASLDEAYLDITEVC ER
Sbjct: 156 MPGFIARKLCPELIFVPTDFKKYTYYSDLTRKVFQKYDPNFMAASLDEAYLDITEVCNER 215

Query: 61  GISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFI 120
            ++  EIAEELRTSV+E  GLTCSAGVAPNRLLAKVCSDINKPNGQFVLP++RMAVMTFI
Sbjct: 216 DLTSGEIAEELRTSVHEVTGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPSNRMAVMTFI 275

Query: 121 SSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSLLCAVFSHSTADFFLSVGLGLGST 180
           SSLPIRKIGGIGKVTEHIL  VFGINTCEEMLQKG  LCA+FS S+ADFFLSVGLGLG T
Sbjct: 276 SSLPIRKIGGIGKVTEHILSGVFGINTCEEMLQKGGFLCALFSRSSADFFLSVGLGLGKT 335

Query: 181 NTPQARFRKSISSERTFSVTEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASF 240
           +TPQ RFRKSIS+ERTFS T+D ALLY+KLAE++EMLS DMQKEGL GRTLTLKLKTASF
Sbjct: 336 DTPQVRFRKSISNERTFSATDDTALLYQKLAELSEMLSIDMQKEGLSGRTLTLKLKTASF 395

Query: 241 EVRTRAVTLQKYISSSEDILKHASVLLKAELPVSLRLIGLRVTQFNEDKVRAPSDPTQKT 300
           EVR+RAVT+QKYI S EDIL HA  LL AELP+SLRLIGLR++ FNEDK    SDPTQKT
Sbjct: 396 EVRSRAVTMQKYICSREDILNHALKLLNAELPLSLRLIGLRISHFNEDKDGHLSDPTQKT 455

Query: 301 LTNFMTSGHASKKIVGDQNSLGSDINDDCLIDDKETSVSLDVSETNNY------------ 348
           L NF+ SG AS K V + + LGSD +D   + D E  +S+D  ET +Y            
Sbjct: 456 LANFIISGDASGKNVCEHSLLGSDTSDSHFMVDPENDLSIDNHETCHYVSEDLLDSNLLS 515

Query: 349 -----------EFGDPVCDNSLPDLNDE--NCSFSNKISEVEKIHENEVSQLLEGNSLVL 395
                        G    +N LP LN      +  N +    K H+ +VS L+E +S   
Sbjct: 516 DLDHCNFNLSNNSGKIDNNNELP-LNGSVAKVNAPNVVGCAPKSHQIKVSHLVEADSFSF 574

Query: 396 RQE-EGSCCDGVEEVDKDITPDNKVGTSSNQKDQFIWLDDYKCSLCGTEMPPSFIEERQE 454
            ++ E +  D     + D+  D+ V  SSNQK+QF+W++DYKCSLCG E+PP+F+EERQE
Sbjct: 575 SEQCESNRPDRARRTNNDL--DDGV-PSSNQKEQFLWVNDYKCSLCGIELPPNFVEERQE 631

Query: 455 HSDFHLAERLQKEESGSDLRILTHRERCVRTQRDHIASHRKRKKQ--------KLFEKEG 506
           H DFHLAE+LQKEES +   ++ ++     +QRDH AS R+ K+         K  +KE 
Sbjct: 632 HFDFHLAEKLQKEESDNSRNLMLNQR---FSQRDHTASQRRHKRHKSSKKEGSKSSQKES 688

Query: 507 THIPIDMFFAKRNRNF 522
            H+PIDMFF K N+NF
Sbjct: 689 KHLPIDMFFVKSNQNF 704

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|225428993|ref|XP_002264518.1| PREDICTED: DNA polymerase kappa-like [Vitis vinifera] Back     alignment and taxonomy information
>gi|356539372|ref|XP_003538172.1| PREDICTED: DNA polymerase kappa-like [Glycine max] Back     alignment and taxonomy information
>gi|449438619|ref|XP_004137085.1| PREDICTED: DNA polymerase kappa-like [Cucumis sativus] gi|449495765|ref|XP_004159938.1| PREDICTED: DNA polymerase kappa-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|357480655|ref|XP_003610613.1| DNA polymerase IV [Medicago truncatula] gi|355511948|gb|AES93571.1| DNA polymerase IV [Medicago truncatula] Back     alignment and taxonomy information
>gi|79362498|ref|NP_175420.3| DNA polymerase kappa subunit [Arabidopsis thaliana] gi|46394839|gb|AAS91582.1| DNA-directed polymerase kappa [Arabidopsis thaliana] gi|332194382|gb|AEE32503.1| DNA polymerase kappa subunit [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|297847332|ref|XP_002891547.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297337389|gb|EFH67806.1| predicted protein [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|242038847|ref|XP_002466818.1| hypothetical protein SORBIDRAFT_01g014630 [Sorghum bicolor] gi|241920672|gb|EER93816.1| hypothetical protein SORBIDRAFT_01g014630 [Sorghum bicolor] Back     alignment and taxonomy information
>gi|293334565|ref|NP_001167938.1| uncharacterized protein LOC100381652 [Zea mays] gi|223944997|gb|ACN26582.1| unknown [Zea mays] Back     alignment and taxonomy information
>gi|413933667|gb|AFW68218.1| hypothetical protein ZEAMMB73_188779 [Zea mays] 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 ?
Query522
TAIR|locus:2031050671 AT1G49980 [Arabidopsis thalian 0.971 0.755 0.579 5e-147
ZFIN|ZDB-GENE-060526-137 875 polk "polymerase (DNA directed 0.463 0.276 0.410 3e-64
UNIPROTKB|J9P5L3 861 POLK "Uncharacterized protein" 0.478 0.290 0.424 2e-63
UNIPROTKB|E2RAS5 871 POLK "Uncharacterized protein" 0.478 0.287 0.424 3.9e-63
UNIPROTKB|Q5Q9G8 780 POLK "Polymerase kappa isoform 0.467 0.312 0.421 8.8e-62
UNIPROTKB|G3V8W7 851 Polk "Protein Polk" [Rattus no 0.614 0.377 0.366 2.1e-61
UNIPROTKB|Q9UBT6 870 POLK "DNA polymerase kappa" [H 0.467 0.280 0.421 2.4e-61
UNIPROTKB|F1S2I2 878 POLK "Uncharacterized protein" 0.651 0.387 0.345 2.8e-61
MGI|MGI:1349767 852 Polk "polymerase (DNA directed 0.482 0.295 0.412 1.3e-60
UNIPROTKB|Q8AWW1 867 DINB1 "Uncharacterized protein 0.467 0.281 0.401 7e-60
TAIR|locus:2031050 AT1G49980 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 1436 (510.6 bits), Expect = 5.0e-147, P = 5.0e-147
 Identities = 304/525 (57%), Positives = 373/525 (71%)

Query:     1 MPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRER 60
             MPGFIARKLCP+LIFVP DFTKYT+YSDLTRKVF  YDP+F+A SLDEAYLDITEVCRER
Sbjct:   154 MPGFIARKLCPDLIFVPVDFTKYTHYSDLTRKVFRNYDPHFIAGSLDEAYLDITEVCRER 213

Query:    61 GISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFI 120
             G+SG EIAEELR+SVY E GLTCSAGVA NRLLAKVCSDINKPNGQFVL NDR  VMTF+
Sbjct:   214 GLSGGEIAEELRSSVYSETGLTCSAGVAANRLLAKVCSDINKPNGQFVLQNDRSTVMTFV 273

Query:   121 SSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSLLCAVFSHSTADFFLSVGLGLGST 180
             S LP+RKIGGIGKVTEHIL+D  GI TCEEM+QKGSLL A+FS S+ADFFLSVGLGLG T
Sbjct:   274 SFLPVRKIGGIGKVTEHILKDALGIKTCEEMVQKGSLLYALFSQSSADFFLSVGLGLGGT 333

Query:   181 NTPQARFRKSISSERTFSVTEDKALLYRKLAEIAEMLSADMQKEXXXXXXXXXXXXXASF 240
             NTPQ R RKSISSERTF+ T D+ LLY KL E+AEMLS DM+KE             ASF
Sbjct:   334 NTPQVRSRKSISSERTFAATGDERLLYSKLDELAEMLSHDMKKEGLTARTLTLKLKTASF 393

Query:   241 EVRTRAVTLQKYISSSEDILKHASVLLKAELPVSLRLIGLRVTQFNEDKVRAPSDPTQKT 300
             E+R+RAV+LQ+Y  SS+DILKHA+ LLKAELPVS+RLIGLR++QF E+ +R  SDP+Q T
Sbjct:   394 EIRSRAVSLQRYTCSSDDILKHATKLLKAELPVSVRLIGLRMSQFVEE-IRN-SDPSQGT 451

Query:   301 LTNFMTSGHASKKI--VGDQNSLGSDINDDCLIDDKETSVSLDVSETNNYEFGDPVCDNS 358
             +T F+    +S++   + D +S   D N +CL +D+  +VS    ET++    D V    
Sbjct:   452 ITKFIVQKDSSRQAQDLDDNDSFDLDANKNCLSNDESGNVSFGSHETSSAHLKDVV---- 507

Query:   359 LPDLNDENCSFSNK-ISEVEKIHENEVSQLLEGNSLVLRQEEGSCCDGVEEVDKDITPDN 417
               +  + +   S K I   E + + E  Q+LEG+SL+ + +E  C         D +   
Sbjct:   508 --EYEERSQIDSGKVIPNQECMKKEERLQILEGDSLLKKYKE--CKPDTSHSMNDNSNAT 563

Query:   418 KVGTSSNQKDQFIWLDDYKCSLCGTEMPPSFIEERQEHSDFHLAERLQKEESGSDLRILT 477
             +  +   Q +   W+D YKC LCG E+PPSF+EERQEHSDFHLA+RLQ EE+GS      
Sbjct:   564 EAVSVFPQTEPLYWIDGYKCVLCGIELPPSFVEERQEHSDFHLAQRLQNEETGSSSSTTP 623

Query:   478 HRERCVRTQRDHIASHRKRKKQKLFEKEGT-HIPIDMFFAKRNRN 521
              + R +  ++     + K KKQK  +K+ + HIPI  FF K N+N
Sbjct:   624 SKRRILGKEK----VNSKPKKQKPDQKDSSKHIPIHAFFTKSNQN 664
GO:0003684 "damaged DNA binding" evidence=IEA
GO:0003887 "DNA-directed DNA polymerase activity" evidence=IEA
GO:0005737 "cytoplasm" evidence=ISM
GO:0006281 "DNA repair" evidence=IEA;ISS
GO:0016020 "membrane" evidence=IDA
ZFIN|ZDB-GENE-060526-137 polk "polymerase (DNA directed) kappa" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
UNIPROTKB|J9P5L3 POLK "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|E2RAS5 POLK "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|Q5Q9G8 POLK "Polymerase kappa isoform 1" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|G3V8W7 Polk "Protein Polk" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|Q9UBT6 POLK "DNA polymerase kappa" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|F1S2I2 POLK "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
MGI|MGI:1349767 Polk "polymerase (DNA directed), kappa" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|Q8AWW1 DINB1 "Uncharacterized protein" [Gallus gallus (taxid:9031)] 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 LevelEC numberConfidence of Prediction
3rd Layer2.7.7LOW CONFIDENCE prediction!
4th Layer2.7.7.7LOW CONFIDENCE prediction!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query522
cd03586334 cd03586, PolY_Pol_IV_kappa, DNA Polymerase IV/Kapp 1e-101
PRK02406343 PRK02406, PRK02406, DNA polymerase IV; Validated 2e-67
COG0389354 COG0389, DinP, Nucleotidyltransferase/DNA polymera 8e-57
PRK14133347 PRK14133, PRK14133, DNA polymerase IV; Provisional 4e-56
PTZ00205571 PTZ00205, PTZ00205, DNA polymerase kappa; Provisio 3e-42
PRK03858396 PRK03858, PRK03858, DNA polymerase IV; Validated 7e-38
PRK02794419 PRK02794, PRK02794, DNA polymerase IV; Provisional 4e-37
PRK01810407 PRK01810, PRK01810, DNA polymerase IV; Validated 7e-33
PRK03348454 PRK03348, PRK03348, DNA polymerase IV; Provisional 3e-32
cd00424343 cd00424, PolY, Y-family of DNA polymerases 2e-31
cd01701404 cd01701, PolY_Rev1, DNA polymerase Rev1 2e-29
pfam00817148 pfam00817, IMS, impB/mucB/samB family 2e-28
cd01702359 cd01702, PolY_Pol_eta, DNA Polymerase eta 1e-27
PRK03352346 PRK03352, PRK03352, DNA polymerase IV; Validated 3e-25
PRK03103409 PRK03103, PRK03103, DNA polymerase IV; Reviewed 8e-25
PRK01216351 PRK01216, PRK01216, DNA polymerase IV; Validated 4e-23
cd01703379 cd01703, PolY_Pol_iota, DNA Polymerase iota 5e-22
cd01700344 cd01700, PolY_Pol_V_umuC, umuC subunit of DNA Poly 4e-20
pfam11799136 pfam11799, IMS_C, impB/mucB/samB family C-terminal 4e-12
PRK03609422 PRK03609, umuC, DNA polymerase V subunit UmuC; Rev 1e-05
pfam1179832 pfam11798, IMS_HHH, IMS family HHH motif 1e-04
cd03468335 cd03468, PolY_like, DNA Polymerase Y-family 0.001
>gnl|CDD|176459 cd03586, PolY_Pol_IV_kappa, DNA Polymerase IV/Kappa Back     alignment and domain information 
 Score =  307 bits (790), Expect = e-101
 Identities = 119/287 (41%), Positives = 166/287 (57%), Gaps = 6/287 (2%)

Query: 1   MPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRER 60
           MP F A+KLCP LIFVP  F KY   S    ++  +Y P     S+DEAYLD+T+     
Sbjct: 52  MPIFQAKKLCPNLIFVPPRFDKYREVSRQIMEILREYTPLVEPLSIDEAYLDVTD-YVRL 110

Query: 61  GISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFI 120
             S  EIA+E+R  + EE GLT SAG+APN+ LAK+ SD+NKPNG  V+P +   V  F+
Sbjct: 111 FGSATEIAKEIRARIREETGLTASAGIAPNKFLAKIASDLNKPNGLTVIPPE--DVEEFL 168

Query: 121 SSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSLLCAVFSHSTADFFLSVGLGLGST 180
           + LP+RKI G+GKVT   L++  GI T  ++ +    L       +      +  G+ + 
Sbjct: 169 APLPVRKIPGVGKVTAEKLKE-LGIKTIGDLAKLDVELLKKLFGKSGRRLYELARGIDNR 227

Query: 181 NTPQARFRKSISSERTFSV-TEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTAS 239
                R RKSI  ERTFS    D   L  +L E+AE L+  ++K GL+GRT+T+KLK A 
Sbjct: 228 PVEPDRERKSIGVERTFSEDLTDPEELLEELLELAEELAERLRKRGLKGRTVTVKLKYAD 287

Query: 240 FEVRTRAVTLQKYISSSEDILKHASVLLKAELPV-SLRLIGLRVTQF 285
           F  RTR+ TL +    +EDI + A  LL+  L    +RL+G+R++  
Sbjct: 288 FSTRTRSRTLPEPTDDAEDIYELALELLEELLDGRPIRLLGVRLSGL 334

Pol IV, also known as Pol kappa, DinB, and Dpo4, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Known primarily as Pol IV in prokaryotes and Pol kappa in eukaryotes, this polymerase has a propensity for generating frameshift mutations. The eukaryotic Pol kappa differs from Pol IV and Dpo4 by an N-terminal extension of ~75 residues known as the "N-clasp" region. The structure of Pol kappa shows DNA that is almost totally encircled by Pol kappa, with the N-clasp region augmenting the interactions between DNA and the polymerase. Pol kappa is more resistant than Pol eta and Pol iota to bulky guanine adducts and is efficient at catalyzing the incorporation of dCTP. Bacterial pol IV has a higher error rate than other Y-family polymerases. Length = 334
>gnl|CDD|235035 PRK02406, PRK02406, DNA polymerase IV; Validated Back     alignment and domain information
>gnl|CDD|223466 COG0389, DinP, Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|184529 PRK14133, PRK14133, DNA polymerase IV; Provisional Back     alignment and domain information
>gnl|CDD|140232 PTZ00205, PTZ00205, DNA polymerase kappa; Provisional Back     alignment and domain information
>gnl|CDD|179663 PRK03858, PRK03858, DNA polymerase IV; Validated Back     alignment and domain information
>gnl|CDD|179473 PRK02794, PRK02794, DNA polymerase IV; Provisional Back     alignment and domain information
>gnl|CDD|179337 PRK01810, PRK01810, DNA polymerase IV; Validated Back     alignment and domain information
>gnl|CDD|235118 PRK03348, PRK03348, DNA polymerase IV; Provisional Back     alignment and domain information
>gnl|CDD|176453 cd00424, PolY, Y-family of DNA polymerases Back     alignment and domain information
>gnl|CDD|176455 cd01701, PolY_Rev1, DNA polymerase Rev1 Back     alignment and domain information
>gnl|CDD|216135 pfam00817, IMS, impB/mucB/samB family Back     alignment and domain information
>gnl|CDD|176456 cd01702, PolY_Pol_eta, DNA Polymerase eta Back     alignment and domain information
>gnl|CDD|179564 PRK03352, PRK03352, DNA polymerase IV; Validated Back     alignment and domain information
>gnl|CDD|235104 PRK03103, PRK03103, DNA polymerase IV; Reviewed Back     alignment and domain information
>gnl|CDD|179251 PRK01216, PRK01216, DNA polymerase IV; Validated Back     alignment and domain information
>gnl|CDD|176457 cd01703, PolY_Pol_iota, DNA Polymerase iota Back     alignment and domain information
>gnl|CDD|176454 cd01700, PolY_Pol_V_umuC, umuC subunit of DNA Polymerase V Back     alignment and domain information
>gnl|CDD|221229 pfam11799, IMS_C, impB/mucB/samB family C-terminal Back     alignment and domain information
>gnl|CDD|179607 PRK03609, umuC, DNA polymerase V subunit UmuC; Reviewed Back     alignment and domain information
>gnl|CDD|204747 pfam11798, IMS_HHH, IMS family HHH motif Back     alignment and domain information
>gnl|CDD|176458 cd03468, PolY_like, DNA Polymerase Y-family Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 522
PTZ00205571 DNA polymerase kappa; Provisional 100.0
PRK01216351 DNA polymerase IV; Validated 100.0
KOG2094490 consensus Predicted DNA damage inducible protein [ 100.0
cd00424343 PolY Y-family of DNA polymerases. Y-family DNA pol 100.0
PRK03858396 DNA polymerase IV; Validated 100.0
cd01701404 PolY_Rev1 DNA polymerase Rev1. Rev1 is a translesi 100.0
PRK14133347 DNA polymerase IV; Provisional 100.0
PRK02406343 DNA polymerase IV; Validated 100.0
PRK02794419 DNA polymerase IV; Provisional 100.0
PRK03352346 DNA polymerase IV; Validated 100.0
PRK03348454 DNA polymerase IV; Provisional 100.0
PRK03103409 DNA polymerase IV; Reviewed 100.0
cd03586334 PolY_Pol_IV_kappa DNA Polymerase IV/Kappa. Pol IV, 100.0
PRK01810407 DNA polymerase IV; Validated 100.0
cd01703379 PolY_Pol_iota DNA Polymerase iota. Pol iota, also 100.0
cd01702359 PolY_Pol_eta DNA Polymerase eta. Pol eta, also cal 100.0
cd01700344 PolY_Pol_V_umuC umuC subunit of DNA Polymerase V. 100.0
PRK03609422 umuC DNA polymerase V subunit UmuC; Reviewed 100.0
COG0389354 DinP Nucleotidyltransferase/DNA polymerase involve 100.0
cd03468335 PolY_like DNA Polymerase Y-family. Y-family DNA po 100.0
KOG20931016 consensus Translesion DNA polymerase - REV1 deoxyc 100.0
KOG2095656 consensus DNA polymerase iota/DNA damage inducible 100.0
PF00817149 IMS: impB/mucB/samB family; InterPro: IPR001126 In 99.86
PF11799127 IMS_C: impB/mucB/samB family C-terminal domain; In 99.5
PF1179832 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 98.48
PRK04301317 radA DNA repair and recombination protein RadA; Va 97.61
TIGR02236310 recomb_radA DNA repair and recombination protein R 96.67
PF1452060 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU 96.34
PF1173193 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd 95.63
PF1039152 DNA_pol_lambd_f: Fingers domain of DNA polymerase 94.39
PF0499481 TfoX_C: TfoX C-terminal domain; InterPro: IPR00707 93.99
PF0311866 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha cha 92.06
PRK12766232 50S ribosomal protein L32e; Provisional 91.98
COG3743133 Uncharacterized conserved protein [Function unknow 91.43
PRK02362737 ski2-like helicase; Provisional 89.03
PF1282664 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS 83.1
PRK14672691 uvrC excinuclease ABC subunit C; Provisional 82.01
PF14229122 DUF4332: Domain of unknown function (DUF4332) 81.99
COG2251474 Predicted nuclease (RecB family) [General function 81.83
smart00483334 POLXc DNA polymerase X family. includes vertebrate 81.39
PRK08609570 hypothetical protein; Provisional 80.72
PRK01172674 ski2-like helicase; Provisional 80.7
>PTZ00205 DNA polymerase kappa; Provisional Back     alignment and domain information 
Probab=100.00  E-value=3.2e-58  Score=496.09  Aligned_cols=311  Identities=30%  Similarity=0.482  Sum_probs=281.3

Q ss_pred             CcHHHHHHhCCCcEEECCChHHHHHHHHHHHHHHHhhCCCEEeecccEEEEEcCcchhhcC--CCHHHHHHHHHHHHHHH
Q 009922            1 MPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERG--ISGIEIAEELRTSVYEE   78 (522)
Q Consensus         1 Mpl~~A~kLCPdLvvvp~d~~~Y~~~s~~i~~il~~~tp~VE~~SiDEafLDvT~~~~l~g--~~~~~lA~~IR~~I~~e   78 (522)
                      ||+++|+++||+|++||+||+.|..+|+++++++.+|+|.||++||||+|||||+....++  .++.++|++||++|+++
T Consensus       184 Mp~~~AkkLCP~Liivp~d~~~Y~~~S~~I~~il~~ysp~ve~~SIDEafLDlT~~~~~~~~~~~~~~iA~~IR~~I~~~  263 (571)
T PTZ00205        184 MPGFLALKICPNLLILPPDFDAYNEESNTVRRIVAEYDPNYISFGLDELTLEVSAYIERFEGTKTAEDVASELRVRVFGE  263 (571)
T ss_pred             CcHHHHHHhCCCCcEecCCHHHHHHHHHHHHHHHHhcCCcEEEeechhceeccCCchhhccCCCCHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999876652  26899999999999999


Q ss_pred             hCCceEEeccCChhHHHHHhhcCCCCcEEEEc-CChHHHHHhhcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhchHH
Q 009922           79 AGLTCSAGVAPNRLLAKVCSDINKPNGQFVLP-NDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSL  157 (522)
Q Consensus        79 tGlt~S~GIA~NKllAKLAS~~~KP~G~~vI~-~~~~~~~~fL~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~~~  157 (522)
                      ||||||||||+||++|||||+++||||+++++ ...+++.+||+++||++|||||++++++|+. +||+||+||++.+..
T Consensus       264 tgLt~SiGIA~NklLAKiASd~~KPnG~~vl~l~~~~~v~~fL~~LpV~ki~GIG~~t~~~L~~-~GI~TigDLa~~~~~  342 (571)
T PTZ00205        264 TKLTASAGIGPTAALAKIASNINKPNGQHDLNLHTRGDVMTYVRDLGLRSVPGVGKVTEALLKG-LGITTLSDIYNRRVE  342 (571)
T ss_pred             HCCcEEEEEcCCHHHHHHhhhccCCCCCeEEecCCHHHHHHHHhCCCcceeCCcCHHHHHHHHH-cCCCcHHHHhcCCHH
Confidence            99999999999999999999999999999874 2345899999999999999999999999997 999999999987733


Q ss_pred             ---------HHHHcChhHHHHHHHhccCCCCCC-CC--CCCCCCcceeecccCCcCCHHHHHHHHHHHHHHHHHHHHHhC
Q 009922          158 ---------LCAVFSHSTADFFLSVGLGLGSTN-TP--QARFRKSISSERTFSVTEDKALLYRKLAEIAEMLSADMQKEG  225 (522)
Q Consensus       158 ---------L~~~FG~~~~~~l~~~a~G~d~~~-v~--~~~~~KSIs~e~tF~~~~~~e~L~~~L~~La~~L~~RLr~~g  225 (522)
                               +...||...|.++|..++|+|..+ +.  ....+|||++++||+...+.+++...|..|+++|+.||++++
T Consensus       343 l~~~f~~k~l~~llG~~~G~~l~~~a~G~d~~~~v~~~~~~~rKSIg~ErTF~~~~d~~el~~~L~~L~~~v~~rLrk~~  422 (571)
T PTZ00205        343 LCYILHNNLFRFLLGASIGIMQWPDAATAANTENCEGATGGQRKAISSERSFTTPRTKEGLQEMVDTVFNGAYEEMRKSE  422 (571)
T ss_pred             HHHHhHHHHHHHHhCchhhHHHHHHhcCCCCCCccCCCCCCCCceeEEeEeCCCCCCHHHHHHHHHHHHHHHHHHHHhcC
Confidence                     567788767888889999999874 32  245689999999999888999999999999999999999999


Q ss_pred             CCccEEEEEEEecCCeeeEEEEEcCCCCCCHHHHHHHHHHHHHhh-C-CCCEEEEEEEeecCCcCCcc--CCCCcccchH
Q 009922          226 LRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAE-L-PVSLRLIGLRVTQFNEDKVR--APSDPTQKTL  301 (522)
Q Consensus       226 ~~artltLkL~~~d~~~~srs~~L~~pt~d~~~L~~~a~~LL~~~-l-~~~IR~lGV~vs~L~~~~~~--~~~~~~q~si  301 (522)
                      +.+++|+|++++.+|.+.+++.+++.||++...|++++..||+.. + ..+||+|||++++|.....-  -.+++.|.+|
T Consensus       423 l~artVtlKlK~~dF~~~trs~tL~~pT~d~~~I~~aa~~Ll~~~~~~~~~vRLlGV~ls~L~~~~~~~~~~~~~~~~~~  502 (571)
T PTZ00205        423 LMCRQISLTIRWASYRYQQYTKSLIQYSDDSATLRRAVDGLLLPHAAKYSEMCLLGVRFLDLISAKDFHMKRKGGNQLSI  502 (571)
T ss_pred             CCccEEEEEEEECCCCceEEEEECCCCcCCHHHHHHHHHHHHHhccccCCCEEEEEEEEcccCcHHHHHHHhcCCceeeH
Confidence            999999999999999999999999999999999999999999876 3 36899999999999987521  2457899999


Q ss_pred             HHhhccCcccc
Q 009922          302 TNFMTSGHASK  312 (522)
Q Consensus       302 ~~ff~~~~~~~  312 (522)
                      ..|..++.+..
T Consensus       503 ~~~~~~~~~~~  513 (571)
T PTZ00205        503 SQFIRPKKPGE  513 (571)
T ss_pred             HHHcCCCCCCc
Confidence            99999877553

>PRK01216 DNA polymerase IV; Validated Back     alignment and domain information
>KOG2094 consensus Predicted DNA damage inducible protein [Replication, recombination and repair] Back     alignment and domain information
>cd00424 PolY Y-family of DNA polymerases Back     alignment and domain information
>PRK03858 DNA polymerase IV; Validated Back     alignment and domain information
>cd01701 PolY_Rev1 DNA polymerase Rev1 Back     alignment and domain information
>PRK14133 DNA polymerase IV; Provisional Back     alignment and domain information
>PRK02406 DNA polymerase IV; Validated Back     alignment and domain information
>PRK02794 DNA polymerase IV; Provisional Back     alignment and domain information
>PRK03352 DNA polymerase IV; Validated Back     alignment and domain information
>PRK03348 DNA polymerase IV; Provisional Back     alignment and domain information
>PRK03103 DNA polymerase IV; Reviewed Back     alignment and domain information
>cd03586 PolY_Pol_IV_kappa DNA Polymerase IV/Kappa Back     alignment and domain information
>PRK01810 DNA polymerase IV; Validated Back     alignment and domain information
>cd01703 PolY_Pol_iota DNA Polymerase iota Back     alignment and domain information
>cd01702 PolY_Pol_eta DNA Polymerase eta Back     alignment and domain information
>cd01700 PolY_Pol_V_umuC umuC subunit of DNA Polymerase V Back     alignment and domain information
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed Back     alignment and domain information
>COG0389 DinP Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair] Back     alignment and domain information
>cd03468 PolY_like DNA Polymerase Y-family Back     alignment and domain information
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair] Back     alignment and domain information
>KOG2095 consensus DNA polymerase iota/DNA damage inducible protein [Replication, recombination and repair] Back     alignment and domain information
>PF00817 IMS: impB/mucB/samB family; InterPro: IPR001126 In Escherichia coli, UV and many chemicals appear to cause mutagenesis by a process of translesion synthesis that requires DNA polymerase III and the SOS-regulated proteins UmuD, UmuC and RecA Back     alignment and domain information
>PF11799 IMS_C: impB/mucB/samB family C-terminal domain; InterPro: IPR017961 This entry represents the little finger domain found in Y-family (lesion bypass) DNA polymerases Back     alignment and domain information
>PF11798 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 This helix-hairpin-helix motif is found in proteins belonging to the type-Y family of DNA polymerases [] Back     alignment and domain information
>PRK04301 radA DNA repair and recombination protein RadA; Validated Back     alignment and domain information
>TIGR02236 recomb_radA DNA repair and recombination protein RadA Back     alignment and domain information
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A Back     alignment and domain information
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria [] Back     alignment and domain information
>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains Back     alignment and domain information
>PF04994 TfoX_C: TfoX C-terminal domain; InterPro: IPR007077 This domain is found in a number of bacterial proteins including the TfoX gene product of Haemophilus influenzae Back     alignment and domain information
>PF03118 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha chain C terminal domain; InterPro: IPR011260 The core of the bacterial RNA polymerase (RNAP) consists of four subunits, two alpha, a beta and a beta', which are conserved from bacteria to mammals Back     alignment and domain information
>PRK12766 50S ribosomal protein L32e; Provisional Back     alignment and domain information
>COG3743 Uncharacterized conserved protein [Function unknown] Back     alignment and domain information
>PRK02362 ski2-like helicase; Provisional Back     alignment and domain information
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B Back     alignment and domain information
>PRK14672 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>PF14229 DUF4332: Domain of unknown function (DUF4332) Back     alignment and domain information
>COG2251 Predicted nuclease (RecB family) [General function prediction only] Back     alignment and domain information
>smart00483 POLXc DNA polymerase X family Back     alignment and domain information
>PRK08609 hypothetical protein; Provisional Back     alignment and domain information
>PRK01172 ski2-like helicase; Provisional Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query522
2oh2_A508 Ternary Complex Of Human Dna Polymerase Length = 50 9e-48
1t94_A459 Crystal Structure Of The Catalytic Core Of Human Dn 1e-47
3pzp_A517 Human Dna Polymerase Kappa Extending Opposite A Cis 1e-47
4f4w_A361 Y-family Dna Polymerase Chimera Dbh-dpo4-dpo4 #1 Le 2e-19
4f4y_A362 Y-family Dna Polymerase Chimera Dbh-dpo4-dbh Length 5e-19
1k1q_A354 Crystal Structure Of A Dinb Family Error Prone Dna 3e-18
3bq0_A354 Pre-insertion Binary Complex Of Dbh Dna Polymerase 3e-18
4f50_A361 Y-family Dna Polymerase Chimera Dbh-dbh-dpo4 Length 4e-18
1im4_A221 Crystal Structure Of A Dinb Homolog (Dbh) Lesion By 6e-18
4dez_A356 Structure Of Msdpo4 Length = 356 2e-15
3gqc_A504 Structure Of Human Rev1-Dna-Dntp Ternary Complex Le 2e-15
3v6k_A347 Replication Of N2,3-Ethenoguanine By Dna Polymerase 6e-15
2imw_P348 Mechanism Of Template-Independent Nucleotide Incorp 8e-15
3v6h_A348 Replication Of N2,3-Ethenoguanine By Dna Polymerase 8e-15
2rdi_A342 Snapshots Of A Y-family Dna Polymerase In Replicati 9e-15
3gii_A341 Dpo4 Extension Ternary Complex With Disordered A Op 9e-15
3pr4_A341 Dpo4 Y12a Mutant Incorporating Dadp Opposite Templa 9e-15
2bq3_A358 Dna Adduct Bypass Polymerization By Sulfolobus Solf 1e-14
1jxl_A352 Crystal Structure Of A Y-Family Dna Polymerase In A 1e-14
4gc7_A359 Crystal Structure Of Dpo4 In Complex With S-mc-dadp 1e-14
2uvv_A358 Crystal Structures Of Mutant Dpo4 Dna Polymerases W 1e-14
2ago_A341 Fidelity Of Dpo4: Effect Of Metal Ions, Nucleotide 1e-14
3pvx_A347 Binary Complex Of Aflatoxin B1 Adduct Modified Dna 1e-14
2asd_A360 Oxog-Modified Insertion Ternary Complex Length = 36 1e-14
2uvr_A358 Crystal Structures Of Mutant Dpo4 Dna Polymerases W 1e-14
3qz7_A360 T-3 Ternary Complex Of Dpo4 Length = 360 1e-14
2w9b_A358 Binary Complex Of Dpo4 Bound To N2,N2-Dimethyl- Deo 1e-14
4f4z_B361 Y-family Dna Polymerase Chimera Dpo4-dpo4-dbh Lengt 3e-14
1jx4_A352 Crystal Structure Of A Y-Family Dna Polymerase In A 4e-14
2dpi_A420 Ternary Complex Of Hpoli With Dna And Dctp Length = 1e-11
3h40_A389 Binary Complex Of Human Dna Polymerase Iota With Te 1e-11
2alz_A390 Ternary Complex Of Hpoli With Dna And Dctp Length = 1e-11
1t3n_A388 Structure Of The Catalytic Core Of Dna Polymerase I 1e-11
3gv5_B420 Human Dna Polymerase Iota In Complex With T Templat 7e-11
3mr6_A435 Human Dna Polymerase Eta - Dna Ternary Complex With 4e-10
3mr2_A435 Human Dna Polymerase Eta In Complex With Normal Dna 5e-10
>pdb|2OH2|A Chain A, Ternary Complex Of Human Dna Polymerase Length = 508 Back     alignment and structure 
Iteration: 1

 Score =  187 bits (476), Expect = 9e-48,   Method: Compositional matrix adjust.
 Identities = 105/238 (44%), Positives = 147/238 (61%), Gaps = 9/238 (3%)
Query: 61  GISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQF-VLPNDRMAVMTF 119
           G S  E+ +E+R  + ++  LT SAG+APN +LAKVCSD NKPNGQ+ +LPN R AVM F
Sbjct: 269 GTSAQEVVKEIRFRIEQKTTLTASAGIAPNTMLAKVCSDKNKPNGQYQILPN-RQAVMDF 327
Query: 120 ISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSLLCAVFSHSTADFFLSVGLGLGS 179
           I  LPIRK+ GIGKVTE +L+   GI TC E+ Q+ +LL  +FS ++  +FL + LGLGS
Sbjct: 328 IKDLPIRKVSGIGKVTEKMLK-ALGIITCTELYQQRALLSLLFSETSWHYFLHISLGLGS 386
Query: 180 TNTPQARFRKSISSERTFSVTEDKALLYRKLAEIAEMLSADMQKEXXXXXXXXXXXXXAS 239
           T+  +   RKS+S ERTFS        Y    E+   L+ D+QKE              +
Sbjct: 387 THLTRDGERKSMSVERTFSEINKAEEQYSLCQELCSELAQDLQKERLKGRTVTIKLKNVN 446
Query: 240 FEVRTRAVTLQKYISSSEDILKHASVLLKAEL------PVSLRLIGLRVTQFNEDKVR 291
           FEV+TRA T+   +S++E+I   A  LLK E+      P+ LRL+G+R++ F  ++ R
Sbjct: 447 FEVKTRASTVSSVVSTAEEIFAIAKELLKTEIDADFPHPLRLRLMGVRISSFPNEEDR 504
>pdb|1T94|A Chain A, Crystal Structure Of The Catalytic Core Of Human Dna Polymerase Kappa Length = 459 Back     alignment and structure
>pdb|3PZP|A Chain A, Human Dna Polymerase Kappa Extending Opposite A Cis-Syn Thymine Dimer Length = 517 Back     alignment and structure
>pdb|4F4W|A Chain A, Y-family Dna Polymerase Chimera Dbh-dpo4-dpo4 #1 Length = 361 Back     alignment and structure
>pdb|4F4Y|A Chain A, Y-family Dna Polymerase Chimera Dbh-dpo4-dbh Length = 362 Back     alignment and structure
>pdb|1K1Q|A Chain A, Crystal Structure Of A Dinb Family Error Prone Dna Polymerase From Sulfolobus Solfataricus Length = 354 Back     alignment and structure
>pdb|3BQ0|A Chain A, Pre-insertion Binary Complex Of Dbh Dna Polymerase Length = 354 Back     alignment and structure
>pdb|4F50|A Chain A, Y-family Dna Polymerase Chimera Dbh-dbh-dpo4 Length = 361 Back     alignment and structure
>pdb|1IM4|A Chain A, Crystal Structure Of A Dinb Homolog (Dbh) Lesion Bypass Dna Polymerase Catalytic Fragment From Sulfolobus Solfataricus Length = 221 Back     alignment and structure
>pdb|4DEZ|A Chain A, Structure Of Msdpo4 Length = 356 Back     alignment and structure
>pdb|3GQC|A Chain A, Structure Of Human Rev1-Dna-Dntp Ternary Complex Length = 504 Back     alignment and structure
>pdb|3V6K|A Chain A, Replication Of N2,3-Ethenoguanine By Dna Polymerases Length = 347 Back     alignment and structure
>pdb|2IMW|P Chain P, Mechanism Of Template-Independent Nucleotide Incorporation Catalyzed By A Template-Dependent Dna Polymerase Length = 348 Back     alignment and structure
>pdb|3V6H|A Chain A, Replication Of N2,3-Ethenoguanine By Dna Polymerases Length = 348 Back     alignment and structure
>pdb|2RDI|A Chain A, Snapshots Of A Y-family Dna Polymerase In Replication: Dpo4 In Apo And Binary/ternary Complex Forms Length = 342 Back     alignment and structure
>pdb|3GII|A Chain A, Dpo4 Extension Ternary Complex With Disordered A Opposite An Oxog In Anti Conformation Length = 341 Back     alignment and structure
>pdb|3PR4|A Chain A, Dpo4 Y12a Mutant Incorporating Dadp Opposite Template Dt Length = 341 Back     alignment and structure
>pdb|2BQ3|A Chain A, Dna Adduct Bypass Polymerization By Sulfolobus Solfataricus Dpo4. Analysis And Crystal Structures Of Multiple Base- Pair Substitution And Frameshift Products With The Adduct 1,N2-Ethenoguanine Length = 358 Back     alignment and structure
>pdb|1JXL|A Chain A, Crystal Structure Of A Y-Family Dna Polymerase In A Ternary Complex With Dna Substrates And An Incoming Nucleotide Length = 352 Back     alignment and structure
>pdb|4GC7|A Chain A, Crystal Structure Of Dpo4 In Complex With S-mc-dadp Opposite Dt Length = 359 Back     alignment and structure
>pdb|2UVV|A Chain A, Crystal Structures Of Mutant Dpo4 Dna Polymerases With 8- Oxog Containing Dna Template-Primer Constructs Length = 358 Back     alignment and structure
>pdb|2AGO|A Chain A, Fidelity Of Dpo4: Effect Of Metal Ions, Nucleotide Selection And Pyrophosphorolysis Length = 341 Back     alignment and structure
>pdb|3PVX|A Chain A, Binary Complex Of Aflatoxin B1 Adduct Modified Dna (Afb1-Fapy) With Dna Polymerase Iv Length = 347 Back     alignment and structure
>pdb|2ASD|A Chain A, Oxog-Modified Insertion Ternary Complex Length = 360 Back     alignment and structure
>pdb|2UVR|A Chain A, Crystal Structures Of Mutant Dpo4 Dna Polymerases With 8- Oxog Containing Dna Template-Primer Constructs Length = 358 Back     alignment and structure
>pdb|3QZ7|A Chain A, T-3 Ternary Complex Of Dpo4 Length = 360 Back     alignment and structure
>pdb|2W9B|A Chain A, Binary Complex Of Dpo4 Bound To N2,N2-Dimethyl- Deoxyguanosine Modified Dna Length = 358 Back     alignment and structure
>pdb|4F4Z|B Chain B, Y-family Dna Polymerase Chimera Dpo4-dpo4-dbh Length = 361 Back     alignment and structure
>pdb|1JX4|A Chain A, Crystal Structure Of A Y-Family Dna Polymerase In A Ternary Complex With Dna Substrates And An Incoming Nucleotide Length = 352 Back     alignment and structure
>pdb|2DPI|A Chain A, Ternary Complex Of Hpoli With Dna And Dctp Length = 420 Back     alignment and structure
>pdb|3H40|A Chain A, Binary Complex Of Human Dna Polymerase Iota With Template UT Length = 389 Back     alignment and structure
>pdb|2ALZ|A Chain A, Ternary Complex Of Hpoli With Dna And Dctp Length = 390 Back     alignment and structure
>pdb|1T3N|A Chain A, Structure Of The Catalytic Core Of Dna Polymerase Iota In Complex With Dna And Dttp Length = 388 Back     alignment and structure
>pdb|3GV5|B Chain B, Human Dna Polymerase Iota In Complex With T Template Dna And Incoming Ddadp Length = 420 Back     alignment and structure
>pdb|3MR6|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex With A Cpd 2bp Upstream Of The Active Site (Tt4) Length = 435 Back     alignment and structure
>pdb|3MR2|A Chain A, Human Dna Polymerase Eta In Complex With Normal Dna And Incoming Nucleotide (Nrm) Length = 435 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 ?
Query522
1t94_A459 Polymerase (DNA directed) kappa; replication, DNA 2e-93
1t94_A459 Polymerase (DNA directed) kappa; replication, DNA 7e-14
3osn_A420 DNA polymerase IOTA; hoogsteen base PAIR, protein- 5e-91
3pzp_A517 DNA polymerase kappa; DNA nucleotidyltransferase, 7e-88
3bq0_A354 POL IV, DBH, DNA polymerase IV; Y-family, lesion b 1e-86
3gqc_A504 DNA repair protein REV1; protein-DNA complex, DNA 5e-86
1jx4_A352 DNA polymerase IV (family Y); protein-DNA complex, 1e-85
2aq4_A434 DNA repair protein REV1; polymerase, PAD, N-digit, 4e-76
1im4_A221 DBH; DNA polymerase PALM, thumb, fingers, helix-ha 6e-61
4ecq_A435 DNA polymerase ETA; transferase-DNA complex; HET: 4e-59
3mfi_A520 DNA polymerase ETA; DNA damage, DNA repair, DNA re 3e-37
3mfi_A520 DNA polymerase ETA; DNA damage, DNA repair, DNA re 6e-11
1unn_C115 POL IV, DNA polymerase IV; beta-clamp, translesion 5e-17
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 1e-11
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 4e-06
>1t94_A Polymerase (DNA directed) kappa; replication, DNA repair, Y-family DNA polymerase, translesion DNA synthesis, lesion bypass; 2.40A {Homo sapiens} SCOP: d.240.1.1 e.8.1.7 PDB: 2oh2_A* 2w7o_A* 2w7p_A* 3hed_A* 3in5_A* Length = 459 Back     alignment and structure
 Score =  291 bits (745), Expect = 2e-93
 Identities = 119/336 (35%), Positives = 178/336 (52%), Gaps = 45/336 (13%)

Query: 2   PGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCK-------------------YDPNFM 42
           P F+A  L    + +     +   + +  R+ F K                   ++ +  
Sbjct: 123 PNFMAMSLDEAYLNITKHLEERQNWPEDKRRYFIKMGSSVENDNPGKEVNKLSEHERSIS 182

Query: 43  AASLDEAYLDITEVCRE-------------------RGISGIEIAEELRTSVYEEAGLTC 83
               +E+  D+                          G S  E+ +E+R  + ++  LT 
Sbjct: 183 PLLFEESPSDVQPPGDPFQVNFEEQNNPQILQNSVVFGTSAQEVVKEIRFRIEQKTTLTA 242

Query: 84  SAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVF 143
           SAG+APN +LAKVCSD NKPNGQ+ +  +R AVM FI  LPIRK+ GIGKVTE +L+   
Sbjct: 243 SAGIAPNTMLAKVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKVTEKMLKA-L 301

Query: 144 GINTCEEMLQKGSLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSVTEDK 203
           GI TC E+ Q+ +LL  +FS ++  +FL + LGLGST+  +   RKS+S ERTFS     
Sbjct: 302 GIITCTELYQQRALLSLLFSETSWHYFLHISLGLGSTHLTRDGERKSMSVERTFSEINKA 361

Query: 204 ALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHA 263
              Y    E+   L+ D+QKE L+GRT+T+KLK  +FEV+TRA T+   +S++E+I   A
Sbjct: 362 EEQYSLCQELCSELAQDLQKERLKGRTVTIKLKNVNFEVKTRASTVSSVVSTAEEIFAIA 421

Query: 264 SVLLKAEL------PVSLRLIGLRVTQFNEDKVRAP 293
             LLK E+      P+ LRL+G+R++ F  ++ R  
Sbjct: 422 KELLKTEIDADFPHPLRLRLMGVRISSFPNEEDRKH 457
>1t94_A Polymerase (DNA directed) kappa; replication, DNA repair, Y-family DNA polymerase, translesion DNA synthesis, lesion bypass; 2.40A {Homo sapiens} SCOP: d.240.1.1 e.8.1.7 PDB: 2oh2_A* 2w7o_A* 2w7p_A* 3hed_A* 3in5_A* Length = 459 Back     alignment and structure
>3osn_A DNA polymerase IOTA; hoogsteen base PAIR, protein-DNA complex, Y-family DNA polym translesion synthesis, nucleoside triphosphate; HET: DNA DOC 6OG TTP; 1.90A {Homo sapiens} PDB: 2dpj_A* 2fll_A* 2fln_A* 2flp_A* 3epg_A* 3epi_A* 2dpi_A* 3g6v_A* 3g6y_A* 3g6x_A* 3gv7_B* 3gv8_B* 3ngd_A* 3gv5_B* 3q8p_B* 3q8q_B* 3q8r_B* 3q8s_B* 3h4d_A* 3h4b_A* ... Length = 420 Back     alignment and structure
>3pzp_A DNA polymerase kappa; DNA nucleotidyltransferase, DNA binding nucleotide binding M binding, nucleus; HET: DNA TTD DTP; 3.34A {Homo sapiens} Length = 517 Back     alignment and structure
>3bq0_A POL IV, DBH, DNA polymerase IV; Y-family, lesion bypass; HET: DNA; 2.60A {Sulfolobus acidocaldarius} SCOP: d.240.1.1 e.8.1.7 PDB: 3bq1_A* 3bq2_A* 1k1q_A 1k1s_A Length = 354 Back     alignment and structure
>3gqc_A DNA repair protein REV1; protein-DNA complex, DNA damage, DNA repair, DNA synthesis, binding, magnesium, metal-binding; HET: DNA DOC DCP; 2.50A {Homo sapiens} Length = 504 Back     alignment and structure
>1jx4_A DNA polymerase IV (family Y); protein-DNA complex, Y-family, transferase-D complex; HET: DNA MSE ADI; 1.70A {Sulfolobus solfataricus} SCOP: d.240.1.1 e.8.1.7 PDB: 1jxl_A* 1n48_A* 1n56_A* 1ryr_A* 1rys_A* 1s0m_A* 1s0n_A* 1s0o_A* 1s10_A* 1s97_A* 1s9f_A* 2ia6_A* 2ibk_A* 2r8g_A* 2r8h_A* 2r8i_A* 2rdj_A* 3fds_A* 3m9m_B* 3m9n_B* ... Length = 352 Back     alignment and structure
>2aq4_A DNA repair protein REV1; polymerase, PAD, N-digit, G-loop, transferase; HET: DNA DOC DCP; 2.32A {Saccharomyces cerevisiae} PDB: 3bjy_A* 3osp_A* Length = 434 Back     alignment and structure
>1im4_A DBH; DNA polymerase PALM, thumb, fingers, helix-hairpin-helix, fidelity, processivity, transferase; 2.30A {Sulfolobus solfataricus} SCOP: e.8.1.7 Length = 221 Back     alignment and structure
>4ecq_A DNA polymerase ETA; transferase-DNA complex; HET: DNA DTP; 1.50A {Homo sapiens} PDB: 3mr2_A* 3mr4_A* 3mr5_A* 3si8_A* 4dl2_A* 4dl3_A* 4dl4_A* 4dl5_A* 4dl6_A* 4dl7_A* 3mr3_A* 4ecr_A* 4ecs_A* 4ect_A* 4ecu_A* 4ecv_A* 4ecw_A* 4ecx_A* 4ecy_A* 4ecz_A* ... Length = 435 Back     alignment and structure
>3mfi_A DNA polymerase ETA; DNA damage, DNA repair, DNA replication, DNA synthesis, NUCL binding, magnesium; HET: DNA DOC TTD DTP; 1.76A {Saccharomyces cerevisiae} PDB: 3mfh_A* 3oha_A* 3ohb_A* 2r8j_A* 2r8k_A* 2wtf_A* 2xgp_A* 2xgq_A* 1jih_A* Length = 520 Back     alignment and structure
>3mfi_A DNA polymerase ETA; DNA damage, DNA repair, DNA replication, DNA synthesis, NUCL binding, magnesium; HET: DNA DOC TTD DTP; 1.76A {Saccharomyces cerevisiae} PDB: 3mfh_A* 3oha_A* 3ohb_A* 2r8j_A* 2r8k_A* 2wtf_A* 2xgp_A* 2xgq_A* 1jih_A* Length = 520 Back     alignment and structure
>1unn_C POL IV, DNA polymerase IV; beta-clamp, translesion, transferase, DNA-directed D polymerase, DNA replication; HET: DNA; 1.9A {Escherichia coli} SCOP: d.240.1.1 Length = 115 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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query522
3pzp_A517 DNA polymerase kappa; DNA nucleotidyltransferase, 100.0
3gqc_A504 DNA repair protein REV1; protein-DNA complex, DNA 100.0
1jx4_A352 DNA polymerase IV (family Y); protein-DNA complex, 100.0
1t94_A459 Polymerase (DNA directed) kappa; replication, DNA 100.0
3bq0_A354 POL IV, DBH, DNA polymerase IV; Y-family, lesion b 100.0
4f4y_A362 POL IV, DNA polymerase IV; Y-family polymerase, tr 100.0
4dez_A356 POL IV 1, DNA polymerase IV 1; Y-family, transfera 100.0
3osn_A420 DNA polymerase IOTA; hoogsteen base PAIR, protein- 100.0
2aq4_A434 DNA repair protein REV1; polymerase, PAD, N-digit, 100.0
4ecq_A435 DNA polymerase ETA; transferase-DNA complex; HET: 100.0
3mfi_A520 DNA polymerase ETA; DNA damage, DNA repair, DNA re 100.0
1im4_A221 DBH; DNA polymerase PALM, thumb, fingers, helix-ha 100.0
1unn_C115 POL IV, DNA polymerase IV; beta-clamp, translesion 99.46
2i5o_A39 DNA polymerase ETA; zinc finger, DNA polymerase,PO 98.83
1wcn_A70 Transcription elongation protein NUSA; RNA-binding 95.64
3mab_A93 Uncharacterized protein; NYSGXRC, PSI-2, structura 94.79
3bqs_A93 Uncharacterized protein; 10114F, NYSGXRC, PSI-2, s 94.45
2a1j_A63 DNA repair endonuclease XPF; XPF, xeroderma pigmen 93.74
1z00_B84 DNA repair endonuclease XPF; helix-hairpin-helix, 92.83
1z3e_B73 DNA-directed RNA polymerase alpha chain; bacterial 91.67
1b22_A114 DNA repair protein RAD51; DNA binding, riken struc 90.0
3k4g_A86 DNA-directed RNA polymerase subunit alpha; bacteri 88.85
1ci4_A89 Protein (barrier-TO-autointegration factor (BAF) ) 88.23
3gfk_B79 DNA-directed RNA polymerase subunit alpha; protein 87.47
1kft_A78 UVRC, excinuclease ABC subunit C; helix-hairpin-he 85.04
1coo_A98 RNA polymerase alpha subunit; transcription regula 84.91
2a1j_B91 DNA excision repair protein ERCC-1; XPF, xeroderma 82.79
1z00_A89 DNA excision repair protein ERCC-1; helix-hairpin- 82.66
2nrt_A220 Uvrabc system protein C; UVRC, endonuclease, RNAse 80.97
1pzn_A349 RAD51, DNA repair and recombination protein RAD51, 80.6
>3pzp_A DNA polymerase kappa; DNA nucleotidyltransferase, DNA binding nucleotide binding M binding, nucleus; HET: DNA TTD DTP; 3.34A {Homo sapiens} Back     alignment and structure
Probab=100.00  E-value=1e-59  Score=512.04  Aligned_cols=288  Identities=49%  Similarity=0.812  Sum_probs=272.8

Q ss_pred             CcHHHHHHhCCCcEEECCChHHHHHHHHHHHHHHHhhCCCEEeecccEEEEEcCcch-----------------------
Q 009922            1 MPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVC-----------------------   57 (522)
Q Consensus         1 Mpl~~A~kLCPdLvvvp~d~~~Y~~~s~~i~~il~~~tp~VE~~SiDEafLDvT~~~-----------------------   57 (522)
                      ||+++|+++||+|++||+||+.|+.+|++++.|+.+|+|.||++||||+|||||++.                       
T Consensus       141 Mp~~~Ak~lCP~Lvvv~~d~~~Y~~~S~~v~~il~~ytp~ve~~SiDEafLDvT~~~~~~~~~~~~~~~~~~~~~~~~~~  220 (517)
T 3pzp_A          141 MPGFIAKRLCPQLIIVPPNFDKYRAVSKEVKEILADYDPNFMAMSLDEAYLNITKHLEERQNWPEDKRRYFIKMGSSVEN  220 (517)
T ss_dssp             SCHHHHHHHCTTCEEECCCHHHHHHHHHHHHHHHHTTCTTCBCCSSSEEEEETHHHHHHHTSCCSTTTEEECC-------
T ss_pred             CcHHHHHHhCCceEEECCCHHHHHHHHHHHHHHHHHcCCcEEEECCceEEEEcccccccccccccccccccccccccccc
Confidence            999999999999999999999999999999999999999999999999999999874                       


Q ss_pred             ----------------------------------------------------hhcCCCHHHHHHHHHHHHHHHhCCceEE
Q 009922           58 ----------------------------------------------------RERGISGIEIAEELRTSVYEEAGLTCSA   85 (522)
Q Consensus        58 ----------------------------------------------------~l~g~~~~~lA~~IR~~I~~etGlt~S~   85 (522)
                                                                          ++||.++.++|++||++|+++|||||||
T Consensus       221 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfg~~~~~ia~~IR~~I~~~tGlt~S~  300 (517)
T 3pzp_A          221 DNPGKEVNKLSEHERSISPLLFEESPSDVQPPGDPFQVNFEEQNNPQILQNSVVFGTSAQEVVKEIRFRIEQKTTLTASA  300 (517)
T ss_dssp             -------------------------------------------------CCEEECCSSHHHHHHHHHHHHHHHHSCCEEE
T ss_pred             ccccccccccccccccccccccccccccccccccccccccccccccccchhhhhcCChHHHHHHHHHHHHHHHhCCeEEE
Confidence                                                                3456468999999999999999999999


Q ss_pred             eccCChhHHHHHhhcCCCCcEEEEcCChHHHHHhhcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhchHHHHHHcChh
Q 009922           86 GVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSLLCAVFSHS  165 (522)
Q Consensus        86 GIA~NKllAKLAS~~~KP~G~~vI~~~~~~~~~fL~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~~~L~~~FG~~  165 (522)
                      |||+||++|||||+.+||||+++|+++.+++.+||+++||++|||||++++++|++ +||+||+||++.+..|.++||..
T Consensus       301 GIA~Nk~LAKlAs~~~KP~G~~vl~~~~~~v~~fL~~LPV~kl~GIG~~t~~~L~~-lGI~TigDL~~~~~~L~~~fG~~  379 (517)
T 3pzp_A          301 GIAPNTMLAKVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKVTEKMLKA-LGIITCTELYQQRALLSLLFSET  379 (517)
T ss_dssp             EEESSHHHHHHHHHTTCSSCEEECCSSHHHHHHHHTTCBGGGSTTCCHHHHHHHHH-TTCCBHHHHHHHHHHHHHHSCHH
T ss_pred             EEcCCHHHHHHHhCcCCCCCEEEecCChHHHHHHHhcCChhhhccccHHHHHHHHH-hCCCcHHHHHhhHHHHHHHhChH
Confidence            99999999999999999999999998755789999999999999999999999997 99999999999888899999998


Q ss_pred             HHHHHHHhccCCCCCCCCCCCCCCcceeecccCCcCCHHHHHHHHHHHHHHHHHHHHHhCCCccEEEEEEEecCCeeeEE
Q 009922          166 TADFFLSVGLGLGSTNTPQARFRKSISSERTFSVTEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFEVRTR  245 (522)
Q Consensus       166 ~~~~l~~~a~G~d~~~v~~~~~~KSIs~e~tF~~~~~~e~L~~~L~~La~~L~~RLr~~g~~artltLkL~~~d~~~~sr  245 (522)
                      .+.++++.|+|++.+++.+..++|||+.++||+.+.+.+++..+|..|+++|+.||+++++.+++|+|++++.+|.+.++
T Consensus       380 ~~~~l~~~a~Gid~~~v~~~~~~KSi~~e~tf~~~~~~e~l~~~l~~La~~l~~rLr~~~~~~~~vtlklk~~~f~~~tr  459 (517)
T 3pzp_A          380 SWHYFLHISLGLGSTHLTRDGERKSMSVERTFSEINKAEEQYSLCQELCSELAQDLQKERLKGRTVTIKLKNVNFEVKTR  459 (517)
T ss_dssp             HHHHHHHHHTTCCCCSCCCCCCCCCEEEEEEEEEECCHHHHHHHHHHHHHHHHHHHHTTTCCBSCEEEEEEETTSCEEEE
T ss_pred             HHHHHHHHHcCCCcccccCCCCCccceeEEEcccccCHHHHHHHHHHHHHHHHHHHHHcCCceeEEEEEEEecCCceeeE
Confidence            88889899999999999888889999999999988889999999999999999999999999999999999999999999


Q ss_pred             EEEcCCCCCCHHHHHHHHHHHHHhhC------CCCEEEEEEEeecCCcCC
Q 009922          246 AVTLQKYISSSEDILKHASVLLKAEL------PVSLRLIGLRVTQFNEDK  289 (522)
Q Consensus       246 s~~L~~pt~d~~~L~~~a~~LL~~~l------~~~IR~lGV~vs~L~~~~  289 (522)
                      +++++.||+++..|+++|..||++.+      +.+||+|||++++|.+..
T Consensus       460 ~~tl~~~t~~~~~i~~~a~~Ll~~~~~~~~~~~~~iRllGV~~s~l~~~~  509 (517)
T 3pzp_A          460 ASTVSSVVSTAEEIFAIAKELLKTEIDADFPHPLRLRLMGVRISSFPNEE  509 (517)
T ss_dssp             CCCCSSCBCSHHHHHHHHHHHHHHHHHHHTTSCCCEEEEEEEECCCCCCC
T ss_pred             EEeCCCCCCCHHHHHHHHHHHHHHHhhhccCCCCcEEEEEEEecCCcChh
Confidence            99999999999999999999998864      346999999999999874
>3gqc_A DNA repair protein REV1; protein-DNA complex, DNA damage, DNA repair, DNA synthesis, binding, magnesium, metal-binding; HET: DNA DOC DCP; 2.50A {Homo sapiens} Back     alignment and structure
>1jx4_A DNA polymerase IV (family Y); protein-DNA complex, Y-family, transferase-D complex; HET: DNA MSE ADI; 1.70A {Sulfolobus solfataricus} SCOP: d.240.1.1 e.8.1.7 PDB: 1jxl_A* 1n48_A* 1n56_A* 1ryr_A* 1rys_A* 1s0m_A* 1s0n_A* 1s0o_A* 1s10_A* 1s97_A* 1s9f_A* 2ia6_A* 2ibk_A* 2r8g_A* 2r8h_A* 2r8i_A* 2rdj_A* 3fds_A* 3m9m_B* 3m9n_B* ... Back     alignment and structure
>1t94_A Polymerase (DNA directed) kappa; replication, DNA repair, Y-family DNA polymerase, translesion DNA synthesis, lesion bypass; 2.40A {Homo sapiens} SCOP: d.240.1.1 e.8.1.7 PDB: 2oh2_A* 2w7o_A* 2w7p_A* 3hed_A* 3in5_A* Back     alignment and structure
>3bq0_A POL IV, DBH, DNA polymerase IV; Y-family, lesion bypass; HET: DNA; 2.60A {Sulfolobus acidocaldarius} SCOP: d.240.1.1 e.8.1.7 PDB: 3bq1_A* 3bq2_A* 1k1q_A 1k1s_A Back     alignment and structure
>4f4y_A POL IV, DNA polymerase IV; Y-family polymerase, transferase-DNA complex; HET: DNA DCP; 2.34A {Sulfolobus acidocaldarius} PDB: 3bq0_A* 3bq1_A* 3bq2_A* 4hyk_A* 1k1q_A 1k1s_A Back     alignment and structure
>4dez_A POL IV 1, DNA polymerase IV 1; Y-family, transferase; HET: DNA; 2.60A {Mycobacterium smegmatis} Back     alignment and structure
>3osn_A DNA polymerase IOTA; hoogsteen base PAIR, protein-DNA complex, Y-family DNA polym translesion synthesis, nucleoside triphosphate; HET: DNA DOC 6OG TTP; 1.90A {Homo sapiens} PDB: 2dpj_A* 2fll_A* 2fln_A* 2flp_A* 3epg_A* 3epi_A* 2dpi_A* 3g6v_A* 3g6y_A* 3g6x_A* 3gv7_B* 3gv8_B* 3ngd_A* 3gv5_B* 3q8p_B* 3q8q_B* 3q8r_B* 3q8s_B* 4ebc_A* 4ebd_A* ... Back     alignment and structure
>2aq4_A DNA repair protein REV1; polymerase, PAD, N-digit, G-loop, transferase; HET: DNA DOC DCP; 2.32A {Saccharomyces cerevisiae} PDB: 3bjy_A* 3osp_A* Back     alignment and structure
>4ecq_A DNA polymerase ETA; transferase-DNA complex; HET: DNA DTP; 1.50A {Homo sapiens} PDB: 3mr2_A* 3mr4_A* 3mr5_A* 3si8_A* 4dl2_A* 4dl3_A* 4dl4_A* 4dl5_A* 4dl6_A* 4dl7_A* 3mr3_A* 4ecr_A* 4ecs_A* 4ect_A* 4ecu_A* 4ecv_A* 4ecw_A* 4ecx_A* 4ecy_A* 4ecz_A* ... Back     alignment and structure
>3mfi_A DNA polymerase ETA; DNA damage, DNA repair, DNA replication, DNA synthesis, NUCL binding, magnesium; HET: DNA DOC TTD DTP; 1.76A {Saccharomyces cerevisiae} PDB: 3mfh_A* 3oha_A* 3ohb_A* 2r8j_A* 2r8k_A* 2wtf_A* 2xgp_A* 2xgq_A* 1jih_A* Back     alignment and structure
>1im4_A DBH; DNA polymerase PALM, thumb, fingers, helix-hairpin-helix, fidelity, processivity, transferase; 2.30A {Sulfolobus solfataricus} SCOP: e.8.1.7 Back     alignment and structure
>1unn_C POL IV, DNA polymerase IV; beta-clamp, translesion, transferase, DNA-directed D polymerase, DNA replication; HET: DNA; 1.9A {Escherichia coli} SCOP: d.240.1.1 Back     alignment and structure
>2i5o_A DNA polymerase ETA; zinc finger, DNA polymerase,POL ETA, UBZ, ubiquitin-binding zinc finger, translesion synthesis, ubiquitin-binding domain; HET: DNA; NMR {Homo sapiens} Back     alignment and structure
>1wcn_A Transcription elongation protein NUSA; RNA-binding protein, escherichia coli NUSA, transcription regulation, regulation of RNA binding; NMR {Escherichia coli} PDB: 2jzb_B Back     alignment and structure
>3mab_A Uncharacterized protein; NYSGXRC, PSI-2, structural genomics; 1.42A {Listeria monocytogenes} PDB: 3bqt_A Back     alignment and structure
>2a1j_A DNA repair endonuclease XPF; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 PDB: 2kn7_A* Back     alignment and structure
>1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 PDB: 2aq0_A* Back     alignment and structure
>1z3e_B DNA-directed RNA polymerase alpha chain; bacterial transcription regulation, disulfide stress; 1.50A {Bacillus subtilis} SCOP: a.60.3.1 PDB: 3ihq_B Back     alignment and structure
>1b22_A DNA repair protein RAD51; DNA binding, riken structural genomics/proteomics initiative, RSGI, structural genomics, DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: a.60.4.1 Back     alignment and structure
>3k4g_A DNA-directed RNA polymerase subunit alpha; bacterial transcription regulation, DNA-directed RNA polymer nucleotidyltransferase; HET: MLY; 2.05A {Escherichia coli k-12} SCOP: a.60.3.1 PDB: 3n4m_B* 1lb2_B* 3n97_B* 1xs9_D Back     alignment and structure
>1ci4_A Protein (barrier-TO-autointegration factor (BAF) ); DNA binding protein, retroviral integration, preintegration complex; 1.90A {Homo sapiens} SCOP: a.60.5.1 PDB: 1qck_A 2bzf_A 2ezx_A 2ezy_A 2ezz_A 2odg_A Back     alignment and structure
>3gfk_B DNA-directed RNA polymerase subunit alpha; protein-protein complex, cytoplasm, redox-active center, stress response, transcription; 2.30A {Bacillus subtilis} SCOP: a.60.3.1 Back     alignment and structure
>1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain, DNA-binding domain, DNA binding protein; NMR {Escherichia coli} SCOP: a.60.2.3 Back     alignment and structure
>1coo_A RNA polymerase alpha subunit; transcription regulation, nucleotidyl transferase; NMR {Escherichia coli} SCOP: a.60.3.1 PDB: 2jzb_A Back     alignment and structure
>2a1j_B DNA excision repair protein ERCC-1; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 Back     alignment and structure
>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 Back     alignment and structure
>2nrt_A Uvrabc system protein C; UVRC, endonuclease, RNAse H, helix hairpin helix, NER, hydrolase; 1.50A {Thermotoga maritima} PDB: 2nrv_A 2nrw_A 2nrx_A 2nrz_A Back     alignment and structure
>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerizat motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1 c.37.1.11 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 522
d1t94a2333 e.8.1.7 (A:75-407) DNA polymerase kappa {Human (Ho 9e-28
d1t94a2333 e.8.1.7 (A:75-407) DNA polymerase kappa {Human (Ho 3e-12
d1t94a1105 d.240.1.1 (A:411-515) DNA polymerase kappa {Human 9e-22
d1zeta2273 e.8.1.7 (A:27-299) DNA polymerase iota {Human (Hom 2e-21
d1im4a_209 e.8.1.7 (A:) DinB homolog (DBH) {Archaeon Sulfolob 2e-21
d1jiha2389 e.8.1.7 (A:1-389) DNA polymerase eta {Baker's yeas 1e-19
d1jiha2389 e.8.1.7 (A:1-389) DNA polymerase eta {Baker's yeas 8e-10
d1zeta1115 d.240.1.1 (A:300-414) DNA polymerase iota {Human ( 3e-18
d1jx4a1101 d.240.1.1 (A:241-341) DinB homolog (DBH) {Archaeon 2e-13
d1unnc_111 d.240.1.1 (C:) DNA polymerase IV {Escherichia coli 3e-13
d1k1sa1105 d.240.1.1 (A:240-344) DinB homolog (DBH) {Archaeon 6e-13
d1jiha1120 d.240.1.1 (A:390-509) DNA polymerase eta {Baker's 8e-10
>d1t94a2 e.8.1.7 (A:75-407) DNA polymerase kappa {Human (Homo sapiens) [TaxId: 9606]} Length = 333 Back     information, alignment and structure

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: Lesion bypass DNA polymerase (Y-family), catalytic domain
domain: DNA polymerase kappa
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  111 bits (278), Expect = 9e-28
 Identities = 65/141 (46%), Positives = 91/141 (64%), Gaps = 1/141 (0%)

Query: 41  FMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDI 100
           F     ++    I +     G S  E+ +E+R  + ++  LT SAG+APN +LAKVCSD 
Sbjct: 193 FQVNFEEQNNPQILQNSVVFGTSAQEVVKEIRFRIEQKTTLTASAGIAPNTMLAKVCSDK 252

Query: 101 NKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSLLCA 160
           NKPNGQ+ +  +R AVM FI  LPIRK+ GIGKVTE +L+   GI TC E+ Q+ +LL  
Sbjct: 253 NKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKVTEKMLKA-LGIITCTELYQQRALLSL 311

Query: 161 VFSHSTADFFLSVGLGLGSTN 181
           +FS ++  +FL + LGLGST+
Sbjct: 312 LFSETSWHYFLHISLGLGSTH 332
>d1t94a2 e.8.1.7 (A:75-407) DNA polymerase kappa {Human (Homo sapiens) [TaxId: 9606]} Length = 333 Back     information, alignment and structure
>d1t94a1 d.240.1.1 (A:411-515) DNA polymerase kappa {Human (Homo sapiens) [TaxId: 9606]} Length = 105 Back     information, alignment and structure
>d1zeta2 e.8.1.7 (A:27-299) DNA polymerase iota {Human (Homo sapiens) [TaxId: 9606]} Length = 273 Back     information, alignment and structure
>d1im4a_ e.8.1.7 (A:) DinB homolog (DBH) {Archaeon Sulfolobus solfataricus [TaxId: 2287]} Length = 209 Back     information, alignment and structure
>d1jiha2 e.8.1.7 (A:1-389) DNA polymerase eta {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 389 Back     information, alignment and structure
>d1jiha2 e.8.1.7 (A:1-389) DNA polymerase eta {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 389 Back     information, alignment and structure
>d1zeta1 d.240.1.1 (A:300-414) DNA polymerase iota {Human (Homo sapiens) [TaxId: 9606]} Length = 115 Back     information, alignment and structure
>d1jx4a1 d.240.1.1 (A:241-341) DinB homolog (DBH) {Archaeon Sulfolobus solfataricus, DNA polymerase IV [TaxId: 2287]} Length = 101 Back     information, alignment and structure
>d1unnc_ d.240.1.1 (C:) DNA polymerase IV {Escherichia coli [TaxId: 562]} Length = 111 Back     information, alignment and structure
>d1k1sa1 d.240.1.1 (A:240-344) DinB homolog (DBH) {Archaeon Sulfolobus solfataricus [TaxId: 2287]} Length = 105 Back     information, alignment and structure
>d1jiha1 d.240.1.1 (A:390-509) DNA polymerase eta {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 120 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 ?
Query522
d1t94a2333 DNA polymerase kappa {Human (Homo sapiens) [TaxId: 100.0
d1zeta2273 DNA polymerase iota {Human (Homo sapiens) [TaxId: 100.0
d1jx4a2240 DinB homolog (DBH) {Archaeon Sulfolobus solfataric 100.0
d1im4a_209 DinB homolog (DBH) {Archaeon Sulfolobus solfataric 100.0
d1jiha2389 DNA polymerase eta {Baker's yeast (Saccharomyces c 100.0
d1t94a1105 DNA polymerase kappa {Human (Homo sapiens) [TaxId: 99.63
d1jx4a1101 DinB homolog (DBH) {Archaeon Sulfolobus solfataric 99.57
d1unnc_111 DNA polymerase IV {Escherichia coli [TaxId: 562]} 99.5
d1k1sa1105 DinB homolog (DBH) {Archaeon Sulfolobus solfataric 99.5
d1zeta1115 DNA polymerase iota {Human (Homo sapiens) [TaxId: 99.35
d1jiha1120 DNA polymerase eta {Baker's yeast (Saccharomyces c 99.28
d2i1qa160 DNA repair protein Rad51, N-terminal domain {Archa 97.04
d1pzna161 DNA repair protein Rad51, N-terminal domain {Archa 96.61
d1szpa164 DNA repair protein Rad51, N-terminal domain {Baker 96.42
d2fmpa257 DNA polymerase beta {Human (Homo sapiens) [TaxId: 95.34
d2bcqa257 DNA polymerase lambda {Human (Homo sapiens) [TaxId 95.13
d1kfta_56 Excinuclease UvrC C-terminal domain {Escherichia c 94.99
d1jmsa360 Terminal deoxynucleotidyl transferase {Mouse (Mus 94.64
d2a1ja162 DNA repair endonuclease XPF {Human (Homo sapiens) 94.52
d1b22a_70 DNA repair protein Rad51, N-terminal domain {Human 93.98
d2p6ra2198 Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22 92.74
d1doqa_69 C-terminal domain of RNA polymerase alpha subunit 92.43
d1gm5a2180 RecG "wedge" domain {Thermotoga maritima [TaxId: 2 92.19
d2bgwa170 DNA repair endonuclease XPF {Aeropyrum pernix [Tax 91.84
d1x2ia168 ATP-dependent RNA helicase PF2015 {Pyrococcus furi 91.11
d1lb2b_72 C-terminal domain of RNA polymerase alpha subunit 89.89
d1z3eb167 C-terminal domain of RNA polymerase alpha subunit 89.87
d2a1jb178 DNA excision repair protein ERCC-1 {Human (Homo sa 87.74
d1ci4a_89 Barrier-to-autointegration factor, BAF {Human (Hom 84.29
>d1t94a2 e.8.1.7 (A:75-407) DNA polymerase kappa {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: Lesion bypass DNA polymerase (Y-family), catalytic domain
domain: DNA polymerase kappa
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=3.1e-43  Score=360.93  Aligned_cols=181  Identities=54%  Similarity=0.916  Sum_probs=169.0

Q ss_pred             CcHHHHHHhCCCcEEECCChHHHHHHHHHHHHHHHhhCCCEEeecccEEEEEcCcchhh---------------------
Q 009922            1 MPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRE---------------------   59 (522)
Q Consensus         1 Mpl~~A~kLCPdLvvvp~d~~~Y~~~s~~i~~il~~~tp~VE~~SiDEafLDvT~~~~l---------------------   59 (522)
                      ||+++|+++||+++++++|++.|+.+|.++++++.+|+|.||++||||+|||||+....                     
T Consensus        78 m~i~eA~~lCP~lii~~~d~~~Yr~~S~~i~~il~~~~~~vE~~SIDE~flDlT~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (333)
T d1t94a2          78 MPGFIAKRLCPQLIIVPPNFDKYRAVSKEVKEILADYDPNFMAMSLDEAYLNITKHLEERQNWPEDKRRYFIKMGSSVEN  157 (333)
T ss_dssp             CCHHHHHHHCTTCEEECCCHHHHHHHHHHHHHHHHHHCTTCEECSSSEEEEECHHHHHHHTTCCGGGSEEECCC---CCC
T ss_pred             CcHHHHHHhCCCcEEEcCcHHHHHHHHHHHHHHHHHcCCCEEEEeccEEEEecchhhhhhcccccchhhhhccccccccc
Confidence            99999999999999999999999999999999999999999999999999999975432                     


Q ss_pred             ------------------------------------------------------cCCCHHHHHHHHHHHHHHHhCCceEE
Q 009922           60 ------------------------------------------------------RGISGIEIAEELRTSVYEEAGLTCSA   85 (522)
Q Consensus        60 ------------------------------------------------------~g~~~~~lA~~IR~~I~~etGlt~S~   85 (522)
                                                                            ++..+.++|.+||++|+++||||||+
T Consensus       158 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~la~~IR~~I~~etG~t~Sa  237 (333)
T d1t94a2         158 DNPGKEVNKLSEHERSISPLLFEESPSDVQPPGDPFQVNFEEQNNPQILQNSVVFGTSAQEVVKEIRFRIEQKTTLTASA  237 (333)
T ss_dssp             CCCCGGGGGGSTTTTTTGGGCC----------------------CCCCCCCEEECCSSHHHHHHHHHHHHHHHHSCCEEE
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccchhhhhhhhccccHHHHHHHHHHHHHHHhCCCeEE
Confidence                                                                  11246789999999999999999999


Q ss_pred             eccCChhHHHHHhhcCCCCcEEEEcCChHHHHHhhcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhchHHHHHHcChh
Q 009922           86 GVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSLLCAVFSHS  165 (522)
Q Consensus        86 GIA~NKllAKLAS~~~KP~G~~vI~~~~~~~~~fL~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~~~L~~~FG~~  165 (522)
                      |||+||++|||||+++||||+++|.|+.+++.+||+++||++|||||++++++|+. +||+||+||++.+..|.+.||..
T Consensus       238 GIa~NK~LAKLAs~~~KPngq~~i~~~~~~~~~~l~~lpi~~i~GiG~~~~~~L~~-~gi~ti~dl~~~~~~l~~~fG~~  316 (333)
T d1t94a2         238 GIAPNTMLAKVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKVTEKMLKA-LGIITCTELYQQRALLSLLFSET  316 (333)
T ss_dssp             EEESSHHHHHHHHHHTTTTCEEECCSSHHHHHHHHTTCBGGGCTTSCHHHHHHHHH-TTCCBHHHHHHTHHHHHHHSCHH
T ss_pred             eECccHHHHHHHHHhcCcCccceecCCHHHHHHHHhCCCccccCCcCHHHHHHHHH-cCCcCHHHHhcCHHHHHHHhCHH
Confidence            99999999999999999999999988766789999999999999999999999997 99999999999878899999999


Q ss_pred             HHHHHHHhccCCCCCCC
Q 009922          166 TADFFLSVGLGLGSTNT  182 (522)
Q Consensus       166 ~~~~l~~~a~G~d~~~v  182 (522)
                      .+.|+|..++|+|++.+
T Consensus       317 ~g~~l~~~a~GID~~~v  333 (333)
T d1t94a2         317 SWHYFLHISLGLGSTHL  333 (333)
T ss_dssp             HHHHHHHHHTTCCCSCC
T ss_pred             HHHHHHHHhcCCCCCCC
Confidence            99999999999998754
>d1zeta2 e.8.1.7 (A:27-299) DNA polymerase iota {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1jx4a2 e.8.1.7 (A:1-240) DinB homolog (DBH) {Archaeon Sulfolobus solfataricus, DNA polymerase IV [TaxId: 2287]} Back     information, alignment and structure
>d1im4a_ e.8.1.7 (A:) DinB homolog (DBH) {Archaeon Sulfolobus solfataricus [TaxId: 2287]} Back     information, alignment and structure
>d1jiha2 e.8.1.7 (A:1-389) DNA polymerase eta {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1t94a1 d.240.1.1 (A:411-515) DNA polymerase kappa {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1jx4a1 d.240.1.1 (A:241-341) DinB homolog (DBH) {Archaeon Sulfolobus solfataricus, DNA polymerase IV [TaxId: 2287]} Back     information, alignment and structure
>d1unnc_ d.240.1.1 (C:) DNA polymerase IV {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1k1sa1 d.240.1.1 (A:240-344) DinB homolog (DBH) {Archaeon Sulfolobus solfataricus [TaxId: 2287]} Back     information, alignment and structure
>d1zeta1 d.240.1.1 (A:300-414) DNA polymerase iota {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1jiha1 d.240.1.1 (A:390-509) DNA polymerase eta {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d2i1qa1 a.60.4.1 (A:5-64) DNA repair protein Rad51, N-terminal domain {Archaeon Methanococcus voltae [TaxId: 2188]} Back     information, alignment and structure
>d1pzna1 a.60.4.1 (A:35-95) DNA repair protein Rad51, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1szpa1 a.60.4.1 (A:81-144) DNA repair protein Rad51, N-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d2fmpa2 a.60.12.1 (A:92-148) DNA polymerase beta {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2bcqa2 a.60.12.1 (A:329-385) DNA polymerase lambda {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1kfta_ a.60.2.3 (A:) Excinuclease UvrC C-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1jmsa3 a.60.12.1 (A:243-302) Terminal deoxynucleotidyl transferase {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2a1ja1 a.60.2.5 (A:837-898) DNA repair endonuclease XPF {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1b22a_ a.60.4.1 (A:) DNA repair protein Rad51, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2p6ra2 a.289.1.2 (A:489-686) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d1doqa_ a.60.3.1 (A:) C-terminal domain of RNA polymerase alpha subunit {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1gm5a2 b.40.4.9 (A:106-285) RecG "wedge" domain {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 56636]} Back     information, alignment and structure
>d1x2ia1 a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1lb2b_ a.60.3.1 (B:) C-terminal domain of RNA polymerase alpha subunit {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1z3eb1 a.60.3.1 (B:245-311) C-terminal domain of RNA polymerase alpha subunit {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure
>d2a1jb1 a.60.2.5 (B:219-296) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1ci4a_ a.60.5.1 (A:) Barrier-to-autointegration factor, BAF {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure