Citrus Sinensis ID: 009298

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-------530-------54
MRFELLSARRFGVRAAMPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSVTEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAELPVSLRLIGLRVTQFNEDKVRAPSDPTQKTLTNFMTSGHASKKIVGDQNSLGSDINDDCLIDDKETSVSLDVSETNNYEFGDPVCDNSLPDLNDENCSFSNKISEVEKIHENEVSQLLEGNSLVLRQEEGSCCDGVEEVDKDITPDNKVGTSSNQKDQFIWLDDYKCSLCGTEMPPSFIEERQEHSDFHLAERLQKEESGSDLRILTHRERCVRTQRDHIASHRKRKKQKLFEKEGTHIPIDMFFAKRNRNF
cccccHHHHHHccccccHHHHHHHHccccEEEccccHHHHHHHHHHHHHHHHHccccccccHHHHHcccccccccccccHHHHHHHHHHHHHHHHcccEEEEccHHHHHHHHHccccccccEEEEcccHHHHHHHHHcccccccccccHHHHHHHHHccccccHHHHHHccHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHccccccEEEEEEEccccEEEEEEEEcccccccHHHHHHHHHHHHHHHccccEEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHccccHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHccHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccHHHHHccccc
ccccHHHHHHHcccccHHHHHHHHHcccEEEEcccHHHHHHHHHHHHHHHHHccccccccccccHEEEcccccccccccHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHcccccccEEEEccccccHHHHHccccccccccccHHHHHHHHHHcccccHHHHHHccHHHHHHHHcHHHHHHHHHHcccccccccccccEccccccccccccccHHHHHHHHHHHHHHHHHHHHHcccccEEEEEEEEccccEEEEcccccccccccHHHHHHHHHHHHHHcccccEEEEEEEEccccccHcccccccHHHHHHHHHHcHHHHccHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEccccccccccccccccccccccEEEEcccccccEEEEccEEEEEEccccccccHHHHHHHHHHHHHHHHHHHHccccccccccHHHHccccccccccccccccccccccccccccEEEEEEEccccc
MRFELLSARrfgvraampgfiarklcpelifvptdftkytyysdltrkvfckydpnfmaasLDEAYLDITEVCRERGISGIEIAEELRTSVyeeagltcsagvapNRLLAKVCsdinkpngqfvlpndRMAVMTFISslpirkiggigkvTEHILRDVFGINTCEEMLQKGSLLCAVFSHSTADFFLSvglglgstntpqarfrksissertfsvteDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAELPVSLRLIGLRVtqfnedkvrapsdptqktltnfmtsghaskkivgdqnslgsdinddcliddketsvsldvsetnnyefgdpvcdnslpdlndencsfsnKISEVEKIHENEVSQLLEGNSLVLRqeegsccdgveevdkditpdnkvgtssnqkdqfiwlddykcslcgtemppsfieerqeHSDFHLAERlqkeesgsdlrilTHRERCVRTQRDHIASHRKRKKQKLFekegthipidmffaKRNRNF
mrfellsarrfgvraampgfiarklcpelIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPngqfvlpndRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSLLCAVFSHSTADFFLSVGLGlgstntpqarfrksissertfsvtedkALLYRKLAEIAEMLSADmqkeglrgrtltlklktasfevrtrAVTLQKYISSSEDILKHASVLLKAELPVSLRLIGLrvtqfnedkvrapsdptqkTLTNfmtsghaskkivgdqnslgsDINDDCLIDDKETSVSLDVSETNNYEFGDPVCDNSLPDLNDENCSFSNKISEVEKIHENEVSQLLEGNSLVLRQEEGSCCdgveevdkditpdnkvgtssnqkdqfiWLDDYKCSLCGTEMPPSFIEERQEHSDFHLAERlqkeesgsdlrilthrercvrtqrdhiashrkrkkqklfekegthipidmffakrnrnf
MRFELLSARRFGVRAAMPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSVTEDKALLYRKLAEIAEMLSADMQKEglrgrtltlklktASFEVRTRAVTLQKYISSSEDILKHASVLLKAELPVSLRLIGLRVTQFNEDKVRAPSDPTQKTLTNFMTSGHASKKIVGDQNSLGSDINDDCLIDDKETSVSLDVSETNNYEFGDPVCDNSLPDLNDENCSFSNKISEVEKIHENEVSQLLEGNSLVLRQEEGSCCDGVEEVDKDITPDNKVGTSSNQKDQFIWLDDYKCSLCGTEMPPSFIEERQEHSDFHLAERLQKEESGSDLRILTHRERCVRTQRDHIASHRKRKKQKLFEKEGTHIPIDMFFAKRNRNF
*****LSARRFGVRAAMPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSLLCAVFSHSTADFFLSVGLGLGST****************FSVTEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAELPVSLRLIGLRVTQFN*****************************************DCLI****************YEFGDPVC*************************************LVL******CCD***********************QFIWLDDYKCSLCGTE*****************************************************************IPIDMFF*******
*RFELLSARRFGVRAAMPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSLLCAVFSHSTADFFLSVGLGLGSTNTPQA***KSISSERTFSVTEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAELPVSLRLIGLRVTQ****************LTNF******************************************************************************************************************************WLDDYKCSLCGTEMPPSFIEERQEHSDFHLA****************************************************FFAKRNR**
MRFELLSARRFGVRAAMPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSVTEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAELPVSLRLIGLRVTQFNEDKVRAPSDPTQKTLTNFMTSGHASKKIVGDQNSLGSDINDDCLIDDKETSVSLDVSETNNYEFGDPVCDNSLPDLNDENCSFSNKISEVEKIHENEVSQLLEGNSLVLRQEEGSCCDGVEEVDKDITPDNKVGTSSNQKDQFIWLDDYKCSLCGTEMPPSFIEERQEHSDFHLAERLQKEESGSDLRILTHRERCVRTQ*************KLFEKEGTHIPIDMFFAKRNRNF
****LLSARRFGVRAAMPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSVTEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAELPVSLRLIGLRVTQFNEDKVRAPSDPTQKTLTNFMTSGHASKKIVGDQNSLGSDINDDCLI***********SETNNYEFGDPVCDNSLPDLNDENCSFSNKISEVEK*******QLLEGNSLVLRQE*****************DNKVGTSSNQKDQFIWLDDYKCSLCGTEMPPSFIEERQEHSDFHLAERLQKE***************************************THIPIDMFFAKRN***
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MRFELLSARRFGVRAAMPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSVTEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAELPVSLRLIGLRVTQFNEDKVRAPSDPTQKTLTNFMTSGHASKKIVGDQNSLGSDINDDCLIDDKETSVSLDVSETNNYEFGDPVCDNSLPDLNDENCSFSNKISEVEKIHENEVSQLLEGNSLVLRQEEGSCCDGVEEVDKDITPDNKVGTSSNQKDQFIWLDDYKCSLCGTEMPPSFIEERQEHSDFHLAERLQKEESGSDLRILTHRERCVRTQRDHIASHRKRKKQKLFEKEGTHIPIDMFFAKRNRNF
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 ?
Query538 2.2.26 [Sep-21-2011]
Q9UBT6 870 DNA polymerase kappa OS=H yes no 0.457 0.282 0.449 2e-54
Q9QUG2 852 DNA polymerase kappa OS=M yes no 0.470 0.296 0.441 3e-54
O74944547 DNA polymerase kappa OS=S yes no 0.544 0.535 0.360 4e-51
P34409596 DNA polymerase kappa OS=C yes no 0.598 0.540 0.378 2e-50
P58965384 DNA polymerase IV OS=Ther yes no 0.533 0.747 0.362 4e-41
Q5FSM8356 DNA polymerase IV OS=Gluc yes no 0.539 0.814 0.364 8e-41
Q8UJK7357 DNA polymerase IV 2 OS=Ag yes no 0.544 0.820 0.357 9e-41
B4SIF5356 DNA polymerase IV OS=Sten yes no 0.529 0.800 0.379 7e-40
B2FLR2364 DNA polymerase IV OS=Sten yes no 0.529 0.782 0.379 1e-39
Q8PCW8359 DNA polymerase IV OS=Xant yes no 0.544 0.816 0.373 1e-38
>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: 77  GISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQF-VLPNDRMAVMTF 135
           G S  E+ +E+R  + ++  LT SAG+APN +LAKVCSD NKPNGQ+ +LPN R AVM F
Sbjct: 287 GTSAQEVVKEIRFRIEQKTTLTASAGIAPNTMLAKVCSDKNKPNGQYQILPN-RQAVMDF 345

Query: 136 ISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSLLCAVFSHSTADFFLSVGLGLGS 195
           I  LPIRK+ GIGKVTE +L+   GI TC E+ Q+ +LL  +FS ++  +FL + LGLGS
Sbjct: 346 IKDLPIRKVSGIGKVTEKMLK-ALGIITCTELYQQRALLSLLFSETSWHYFLHISLGLGS 404

Query: 196 TNTPQARFRKSISSERTFSVTEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTAS 255
           T+  +   RKS+S ERTFS        Y    E+   L+ D+QKE L+GRT+T+KLK  +
Sbjct: 405 THLTRDGERKSMSVERTFSEINKAEEQYSLCQELCSELAQDLQKERLKGRTVTIKLKNVN 464

Query: 256 FEVRTRAVTLQKYISSSEDILKHASVLLKAEL------PVSLRLIGLRVTQFNEDKVRAP 309
           FEV+TRA T+   +S++E+I   A  LLK E+      P+ LRL+G+R++ F  ++ R  
Sbjct: 465 FEVKTRASTVSSVVSTAEEIFAIAKELLKTEIDADFPHPLRLRLMGVRISSFPNEEDRKH 524

Query: 310 SDPTQKTLTNFMTSGHAS 327
               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|Q5FSM8|DPO4_GLUOX DNA polymerase IV OS=Gluconobacter oxydans (strain 621H) 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|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|Q8PCW8|DPO4_XANCP DNA polymerase IV OS=Xanthomonas campestris pv. campestris (strain ATCC 33913 / NCPPB 528 / LMG 568) 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 ?
Query538
296083048 704 unnamed protein product [Vitis vinifera] 0.973 0.744 0.637 0.0
225428993 661 PREDICTED: DNA polymerase kappa-like [Vi 0.942 0.767 0.658 0.0
356539372 663 PREDICTED: DNA polymerase kappa-like [Gl 0.953 0.773 0.639 0.0
449438619 693 PREDICTED: DNA polymerase kappa-like [Cu 0.979 0.760 0.596 0.0
357480655 706 DNA polymerase IV [Medicago truncatula] 0.866 0.660 0.614 1e-171
79362498 671 DNA polymerase kappa subunit [Arabidopsi 0.962 0.771 0.593 1e-169
297847332636 predicted protein [Arabidopsis lyrata su 0.899 0.761 0.580 1e-157
242038847 668 hypothetical protein SORBIDRAFT_01g01463 0.949 0.764 0.543 1e-152
293334565535 uncharacterized protein LOC100381652 [Ze 0.938 0.943 0.526 1e-150
413933667 670 hypothetical protein ZEAMMB73_188779 [Ze 0.946 0.759 0.530 1e-150
>gi|296083048|emb|CBI22452.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
 Score =  681 bits (1756), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 360/565 (63%), Positives = 419/565 (74%), Gaps = 41/565 (7%)

Query: 8   ARRFGVRAAMPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYL 67
           AR+FGVRAAMPGFIARKLCPELIFVPTDF KYTYYSDLTRKVF KYDPNFMAASLDEAYL
Sbjct: 147 ARKFGVRAAMPGFIARKLCPELIFVPTDFKKYTYYSDLTRKVFQKYDPNFMAASLDEAYL 206

Query: 68  DITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPN 127
           DITEVC ER ++  EIAEELRTSV+E  GLTCSAGVAPNRLLAKVCSDINKPNGQFVLP+
Sbjct: 207 DITEVCNERDLTSGEIAEELRTSVHEVTGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPS 266

Query: 128 DRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSLLCAVFSHSTADFFL 187
           +RMAVMTFISSLPIRKIGGIGKVTEHIL  VFGINTCEEMLQKG  LCA+FS S+ADFFL
Sbjct: 267 NRMAVMTFISSLPIRKIGGIGKVTEHILSGVFGINTCEEMLQKGGFLCALFSRSSADFFL 326

Query: 188 SVGLGLGSTNTPQARFRKSISSERTFSVTEDKALLYRKLAEIAEMLSADMQKEGLRGRTL 247
           SVGLGLG T+TPQ RFRKSIS+ERTFS T+D ALLY+KLAE++EMLS DMQKEGL GRTL
Sbjct: 327 SVGLGLGKTDTPQVRFRKSISNERTFSATDDTALLYQKLAELSEMLSIDMQKEGLSGRTL 386

Query: 248 TLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAELPVSLRLIGLRVTQFNEDKVR 307
           TLKLKTASFEVR+RAVT+QKYI S EDIL HA  LL AELP+SLRLIGLR++ FNEDK  
Sbjct: 387 TLKLKTASFEVRSRAVTMQKYICSREDILNHALKLLNAELPLSLRLIGLRISHFNEDKDG 446

Query: 308 APSDPTQKTLTNFMTSGHASKKIVGDQNSLGSDINDDCLIDDKETSVSLDVSETNNY--- 364
             SDPTQKTL NF+ SG AS K V + + LGSD +D   + D E  +S+D  ET +Y   
Sbjct: 447 HLSDPTQKTLANFIISGDASGKNVCEHSLLGSDTSDSHFMVDPENDLSIDNHETCHYVSE 506

Query: 365 --------------------EFGDPVCDNSLPDLNDE--NCSFSNKISEVEKIHENEVSQ 402
                                 G    +N LP LN      +  N +    K H+ +VS 
Sbjct: 507 DLLDSNLLSDLDHCNFNLSNNSGKIDNNNELP-LNGSVAKVNAPNVVGCAPKSHQIKVSH 565

Query: 403 LLEGNSLVLRQE-EGSCCDGVEEVDKDITPDNKVGTSSNQKDQFIWLDDYKCSLCGTEMP 461
           L+E +S    ++ E +  D     + D+  D+ V  SSNQK+QF+W++DYKCSLCG E+P
Sbjct: 566 LVEADSFSFSEQCESNRPDRARRTNNDL--DDGV-PSSNQKEQFLWVNDYKCSLCGIELP 622

Query: 462 PSFIEERQEHSDFHLAERLQKEESGSDLRILTHRERCVRTQRDHIASHRKRKKQ------ 515
           P+F+EERQEH DFHLAE+LQKEES +   ++ ++     +QRDH AS R+ K+       
Sbjct: 623 PNFVEERQEHFDFHLAEKLQKEESDNSRNLMLNQR---FSQRDHTASQRRHKRHKSSKKE 679

Query: 516 --KLFEKEGTHIPIDMFFAKRNRNF 538
             K  +KE  H+PIDMFF K N+NF
Sbjct: 680 GSKSSQKESKHLPIDMFFVKSNQNF 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 ?
Query538
TAIR|locus:2031050671 AT1G49980 [Arabidopsis thalian 0.959 0.769 0.584 2.9e-151
ZFIN|ZDB-GENE-060526-137 875 polk "polymerase (DNA directed 0.449 0.276 0.410 9.4e-69
UNIPROTKB|J9P5L3 861 POLK "Uncharacterized protein" 0.464 0.290 0.424 6.4e-68
UNIPROTKB|E2RAS5 871 POLK "Uncharacterized protein" 0.464 0.287 0.424 1.2e-67
UNIPROTKB|Q5Q9G8 780 POLK "Polymerase kappa isoform 0.453 0.312 0.421 2.6e-66
UNIPROTKB|G3V8W7 851 Polk "Protein Polk" [Rattus no 0.596 0.377 0.366 6.3e-66
UNIPROTKB|Q9UBT6 870 POLK "DNA polymerase kappa" [H 0.453 0.280 0.421 7.2e-66
MGI|MGI:1349767 852 Polk "polymerase (DNA directed 0.468 0.295 0.412 3.8e-65
UNIPROTKB|F1S2I2 878 POLK "Uncharacterized protein" 0.631 0.387 0.345 4.5e-65
UNIPROTKB|Q8AWW1 867 DINB1 "Uncharacterized protein 0.453 0.281 0.401 2.2e-64
TAIR|locus:2031050 AT1G49980 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 1476 (524.6 bits), Expect = 2.9e-151, P = 2.9e-151
 Identities = 312/534 (58%), Positives = 382/534 (71%)

Query:     8 ARRFGVRAAMPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYL 67
             AR+FGVRAAMPGFIARKLCP+LIFVP DFTKYT+YSDLTRKVF  YDP+F+A SLDEAYL
Sbjct:   145 ARKFGVRAAMPGFIARKLCPDLIFVPVDFTKYTHYSDLTRKVFRNYDPHFIAGSLDEAYL 204

Query:    68 DITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPN 127
             DITEVCRERG+SG EIAEELR+SVY E GLTCSAGVA NRLLAKVCSDINKPNGQFVL N
Sbjct:   205 DITEVCRERGLSGGEIAEELRSSVYSETGLTCSAGVAANRLLAKVCSDINKPNGQFVLQN 264

Query:   128 DRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSLLCAVFSHSTADFFL 187
             DR  VMTF+S LP+RKIGGIGKVTEHIL+D  GI TCEEM+QKGSLL A+FS S+ADFFL
Sbjct:   265 DRSTVMTFVSFLPVRKIGGIGKVTEHILKDALGIKTCEEMVQKGSLLYALFSQSSADFFL 324

Query:   188 SVGLGLGSTNTPQARFRKSISSERTFSVTEDKALLYRKLAEIAEMLSADMQKEXXXXXXX 247
             SVGLGLG TNTPQ R RKSISSERTF+ T D+ LLY KL E+AEMLS DM+KE       
Sbjct:   325 SVGLGLGGTNTPQVRSRKSISSERTFAATGDERLLYSKLDELAEMLSHDMKKEGLTARTL 384

Query:   248 XXXXXXASFEVRTRAVTLQKYISSSEDILKHASVLLKAELPVSLRLIGLRVTQFNEDKVR 307
                   ASFE+R+RAV+LQ+Y  SS+DILKHA+ LLKAELPVS+RLIGLR++QF E+ +R
Sbjct:   385 TLKLKTASFEIRSRAVSLQRYTCSSDDILKHATKLLKAELPVSVRLIGLRMSQFVEE-IR 443

Query:   308 APSDPTQKTLTNFMTSGHASKKI--VGDQNSLGSDINDDCLIDDKETSVSLDVSETNNYE 365
               SDP+Q T+T F+    +S++   + D +S   D N +CL +D+  +VS    ET++  
Sbjct:   444 N-SDPSQGTITKFIVQKDSSRQAQDLDDNDSFDLDANKNCLSNDESGNVSFGSHETSSAH 502

Query:   366 FGDPVCDNSLPDLNDENCSFSNK-ISEVEKIHENEVSQLLEGNSLVLRQEEGSCCDGVEE 424
               D V      +  + +   S K I   E + + E  Q+LEG+SL+ + +E  C      
Sbjct:   503 LKDVV------EYEERSQIDSGKVIPNQECMKKEERLQILEGDSLLKKYKE--CKPDTSH 554

Query:   425 VDKDITPDNKVGTSSNQKDQFIWLDDYKCSLCGTEMPPSFIEERQEHSDFHLAERLQKEE 484
                D +   +  +   Q +   W+D YKC LCG E+PPSF+EERQEHSDFHLA+RLQ EE
Sbjct:   555 SMNDNSNATEAVSVFPQTEPLYWIDGYKCVLCGIELPPSFVEERQEHSDFHLAQRLQNEE 614

Query:   485 SGSDLRILTHRERCVRTQRDHIASHRKRKKQKLFEKEGT-HIPIDMFFAKRNRN 537
             +GS       + R +  ++     + K KKQK  +K+ + HIPI  FF K N+N
Sbjct:   615 TGSSSSTTPSKRRILGKEK----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
MGI|MGI:1349767 Polk "polymerase (DNA directed), kappa" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|F1S2I2 POLK "Uncharacterized protein" [Sus scrofa (taxid:9823)] 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 ?
Query538
cd03586334 cd03586, PolY_Pol_IV_kappa, DNA Polymerase IV/Kapp 1e-108
PRK02406343 PRK02406, PRK02406, DNA polymerase IV; Validated 9e-75
COG0389354 COG0389, DinP, Nucleotidyltransferase/DNA polymera 2e-61
PRK14133347 PRK14133, PRK14133, DNA polymerase IV; Provisional 5e-61
PTZ00205571 PTZ00205, PTZ00205, DNA polymerase kappa; Provisio 4e-45
PRK03858396 PRK03858, PRK03858, DNA polymerase IV; Validated 9e-43
PRK02794419 PRK02794, PRK02794, DNA polymerase IV; Provisional 1e-42
PRK03348454 PRK03348, PRK03348, DNA polymerase IV; Provisional 4e-38
PRK01810407 PRK01810, PRK01810, DNA polymerase IV; Validated 1e-36
cd00424343 cd00424, PolY, Y-family of DNA polymerases 2e-35
pfam00817148 pfam00817, IMS, impB/mucB/samB family 8e-34
cd01701404 cd01701, PolY_Rev1, DNA polymerase Rev1 1e-32
PRK03352346 PRK03352, PRK03352, DNA polymerase IV; Validated 1e-30
cd01702359 cd01702, PolY_Pol_eta, DNA Polymerase eta 4e-30
PRK03103409 PRK03103, PRK03103, DNA polymerase IV; Reviewed 5e-28
PRK01216351 PRK01216, PRK01216, DNA polymerase IV; Validated 1e-27
cd01703379 cd01703, PolY_Pol_iota, DNA Polymerase iota 3e-24
cd01700344 cd01700, PolY_Pol_V_umuC, umuC subunit of DNA Poly 1e-21
pfam11799136 pfam11799, IMS_C, impB/mucB/samB family C-terminal 7e-12
PRK03609422 PRK03609, umuC, DNA polymerase V subunit UmuC; Rev 4e-06
cd03468335 cd03468, PolY_like, DNA Polymerase Y-family 7e-06
pfam1179832 pfam11798, IMS_HHH, IMS family HHH motif 1e-04
>gnl|CDD|176459 cd03586, PolY_Pol_IV_kappa, DNA Polymerase IV/Kappa Back     alignment and domain information 
 Score =  327 bits (841), Expect = e-108
 Identities = 126/296 (42%), Positives = 175/296 (59%), Gaps = 6/296 (2%)

Query: 8   ARRFGVRAAMPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYL 67
           AR+FGVR+AMP F A+KLCP LIFVP  F KY   S    ++  +Y P     S+DEAYL
Sbjct: 43  ARKFGVRSAMPIFQAKKLCPNLIFVPPRFDKYREVSRQIMEILREYTPLVEPLSIDEAYL 102

Query: 68  DITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPN 127
           D+T+       S  EIA+E+R  + EE GLT SAG+APN+ LAK+ SD+NKPNG  V+P 
Sbjct: 103 DVTD-YVRLFGSATEIAKEIRARIREETGLTASAGIAPNKFLAKIASDLNKPNGLTVIPP 161

Query: 128 DRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSLLCAVFSHSTADFFL 187
           +   V  F++ LP+RKI G+GKVT   L++  GI T  ++ +    L       +     
Sbjct: 162 E--DVEEFLAPLPVRKIPGVGKVTAEKLKE-LGIKTIGDLAKLDVELLKKLFGKSGRRLY 218

Query: 188 SVGLGLGSTNTPQARFRKSISSERTFSV-TEDKALLYRKLAEIAEMLSADMQKEGLRGRT 246
            +  G+ +      R RKSI  ERTFS    D   L  +L E+AE L+  ++K GL+GRT
Sbjct: 219 ELARGIDNRPVEPDRERKSIGVERTFSEDLTDPEELLEELLELAEELAERLRKRGLKGRT 278

Query: 247 LTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAELPV-SLRLIGLRVTQF 301
           +T+KLK A F  RTR+ TL +    +EDI + A  LL+  L    +RL+G+R++  
Sbjct: 279 VTVKLKYADFSTRTRSRTLPEPTDDAEDIYELALELLEELLDGRPIRLLGVRLSGL 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|235118 PRK03348, PRK03348, 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|176453 cd00424, PolY, Y-family of DNA polymerases Back     alignment and domain information
>gnl|CDD|216135 pfam00817, IMS, impB/mucB/samB family Back     alignment and domain information
>gnl|CDD|176455 cd01701, PolY_Rev1, DNA polymerase Rev1 Back     alignment and domain information
>gnl|CDD|179564 PRK03352, PRK03352, DNA polymerase IV; Validated Back     alignment and domain information
>gnl|CDD|176456 cd01702, PolY_Pol_eta, DNA Polymerase eta 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|176458 cd03468, PolY_like, DNA Polymerase Y-family Back     alignment and domain information
>gnl|CDD|204747 pfam11798, IMS_HHH, IMS family HHH motif Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 538
PTZ00205571 DNA polymerase kappa; Provisional 100.0
PRK01216351 DNA polymerase IV; Validated 100.0
PRK03858396 DNA polymerase IV; Validated 100.0
cd00424343 PolY Y-family of DNA polymerases. Y-family DNA pol 100.0
PRK14133347 DNA polymerase IV; Provisional 100.0
PRK02406343 DNA polymerase IV; Validated 100.0
cd01701404 PolY_Rev1 DNA polymerase Rev1. Rev1 is a translesi 100.0
KOG2094490 consensus Predicted DNA damage inducible protein [ 100.0
PRK02794419 DNA polymerase IV; Provisional 100.0
PRK03352346 DNA polymerase IV; Validated 100.0
cd03586334 PolY_Pol_IV_kappa DNA Polymerase IV/Kappa. Pol IV, 100.0
PRK03348454 DNA polymerase IV; Provisional 100.0
PRK01810407 DNA polymerase IV; Validated 100.0
PRK03103409 DNA polymerase IV; Reviewed 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 99.94
PF11799127 IMS_C: impB/mucB/samB family C-terminal domain; In 99.5
PF1179832 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 98.38
PRK04301317 radA DNA repair and recombination protein RadA; Va 97.41
TIGR02236310 recomb_radA DNA repair and recombination protein R 96.52
PF1452060 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU 96.12
PF1173193 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd 95.32
PF1039152 DNA_pol_lambd_f: Fingers domain of DNA polymerase 93.78
PF0499481 TfoX_C: TfoX C-terminal domain; InterPro: IPR00707 93.42
PF0882759 DUF1805: Domain of unknown function (DUF1805); Int 92.84
PF0311866 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha cha 91.89
COG3743133 Uncharacterized conserved protein [Function unknow 91.57
PRK12766232 50S ribosomal protein L32e; Provisional 91.26
PRK02362737 ski2-like helicase; Provisional 86.89
>PTZ00205 DNA polymerase kappa; Provisional Back     alignment and domain information 
Probab=100.00  E-value=5.5e-62  Score=526.09  Aligned_cols=328  Identities=30%  Similarity=0.473  Sum_probs=298.1

Q ss_pred             ccCHHHHHcCCCCCCcHHHHHhhCCCeEEEcCChHHHHHHHHHHHHHHHhcCCCeEeeCccEEEEEcCccchhcC--CCH
Q 009298            3 FELLSARRFGVRAAMPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERG--ISG   80 (538)
Q Consensus         3 ~~syeAR~~GVr~GM~l~~A~~LCP~Lvvvp~d~~~Y~~~s~~l~~il~~~sp~Ve~~SiDEafLDlT~~~~l~g--~~~   80 (538)
                      -|||+||+|||++|||+++|++|||+|+++|+|++.|+++|+++++++.+|+|.||++|+||+|||+|++...|+  .++
T Consensus       170 TaSYeARk~GVrsgMp~~~AkkLCP~Liivp~d~~~Y~~~S~~I~~il~~ysp~ve~~SIDEafLDlT~~~~~~~~~~~~  249 (571)
T PTZ00205        170 TANYVARGRGIRQGMPGFLALKICPNLLILPPDFDAYNEESNTVRRIVAEYDPNYISFGLDELTLEVSAYIERFEGTKTA  249 (571)
T ss_pred             EcCHHHHhhCCCcCCcHHHHHHhCCCCcEecCCHHHHHHHHHHHHHHHHhcCCcEEEeechhceeccCCchhhccCCCCH
Confidence            589999999999999999999999999999999999999999999999999999999999999999999876652  268


Q ss_pred             HHHHHHHHHHHHHHhCCceEEEecCChhHHHHHhcccCCCCeEEec-CChHHHHHhhcCCCcccccCCCHHHHHHHHhhc
Q 009298           81 IEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLP-NDRMAVMTFISSLPIRKIGGIGKVTEHILRDVF  159 (538)
Q Consensus        81 ~~la~~IR~~I~~~~Glt~S~GIA~nk~lAKLAS~~aKP~G~~vl~-~~~~~~~~fL~~lPl~~L~GIG~kt~~kL~~~l  159 (538)
                      .++|++||.+|++++|+|||||||+||++|||||+++||||+++++ ...+++..||+++||++|||||+++.++|.. +
T Consensus       250 ~~iA~~IR~~I~~~tgLt~SiGIA~NklLAKiASd~~KPnG~~vl~l~~~~~v~~fL~~LpV~ki~GIG~~t~~~L~~-~  328 (571)
T PTZ00205        250 EDVASELRVRVFGETKLTASAGIGPTAALAKIASNINKPNGQHDLNLHTRGDVMTYVRDLGLRSVPGVGKVTEALLKG-L  328 (571)
T ss_pred             HHHHHHHHHHHHHHHCCcEEEEEcCCHHHHHHhhhccCCCCCeEEecCCHHHHHHHHhCCCcceeCCcCHHHHHHHHH-c
Confidence            9999999999999999999999999999999999999999999874 2345899999999999999999999999997 9


Q ss_pred             CCCchHHHHhchH---------HHHHHcChhHHHHHHHhccCCCCCC-CC--CCCCCccceeeeccCccCCHHHHHHHHH
Q 009298          160 GINTCEEMLQKGS---------LLCAVFSHSTADFFLSVGLGLGSTN-TP--QARFRKSISSERTFSVTEDKALLYRKLA  227 (538)
Q Consensus       160 GI~TlgDL~~lp~---------~L~krFG~~~~~~L~~~a~Gid~~~-v~--~~~~pKSIs~e~tF~~~~d~e~L~~~L~  227 (538)
                      ||+||+||++.+.         .+...||...+.++|..++|+|..+ +.  ....+|||++++||+...+.+++...|.
T Consensus       329 GI~TigDLa~~~~~l~~~f~~k~l~~llG~~~G~~l~~~a~G~d~~~~v~~~~~~~rKSIg~ErTF~~~~d~~el~~~L~  408 (571)
T PTZ00205        329 GITTLSDIYNRRVELCYILHNNLFRFLLGASIGIMQWPDAATAANTENCEGATGGQRKAISSERSFTTPRTKEGLQEMVD  408 (571)
T ss_pred             CCCcHHHHhcCCHHHHHHhHHHHHHHHhCchhhHHHHHHhcCCCCCCccCCCCCCCCceeEEeEeCCCCCCHHHHHHHHH
Confidence            9999999999873         3567788766778888999999874 32  2456899999999998889999999999


Q ss_pred             HHHHHHHHHHHHhCCCccEEEEEEEEcCCceeEEEEecCCCCCCHHHHHHHHHHHHHhh-C-CCCEEEEEEEecCCCcCc
Q 009298          228 EIAEMLSADMQKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAE-L-PVSLRLIGLRVTQFNEDK  305 (538)
Q Consensus       228 ~Lae~L~~RLr~~gl~~rtLtL~Lr~~d~~~~srs~~L~~~t~~~~~L~~~a~~LL~~~-l-p~~VR~IGV~ls~L~~~~  305 (538)
                      .|+++|+.+|+++++.+++|+|++++++|++.+++.+++.||++...|++++..||+.. + +.+||+|||++++|....
T Consensus       409 ~L~~~v~~rLrk~~l~artVtlKlK~~dF~~~trs~tL~~pT~d~~~I~~aa~~Ll~~~~~~~~~vRLlGV~ls~L~~~~  488 (571)
T PTZ00205        409 TVFNGAYEEMRKSELMCRQISLTIRWASYRYQQYTKSLIQYSDDSATLRRAVDGLLLPHAAKYSEMCLLGVRFLDLISAK  488 (571)
T ss_pred             HHHHHHHHHHHhcCCCccEEEEEEEECCCCceEEEEECCCCcCCHHHHHHHHHHHHHhccccCCCEEEEEEEEcccCcHH
Confidence            99999999999999999999999999999999999999999999999999999999876 3 368999999999999976


Q ss_pred             cc--CCCCcccccHHHHhccCccccccc
Q 009298          306 VR--APSDPTQKTLTNFMTSGHASKKIV  331 (538)
Q Consensus       306 ~~--~~~~~~Q~tI~~ff~~~~~~~~~~  331 (538)
                      ..  -..++.|.+|..|..++.+...+.
T Consensus       489 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~  516 (571)
T PTZ00205        489 DFHMKRKGGNQLSISQFIRPKKPGEVTA  516 (571)
T ss_pred             HHHHHhcCCceeeHHHHcCCCCCCceee
Confidence            42  355799999999999888766443

>PRK01216 DNA polymerase IV; Validated Back     alignment and domain information
>PRK03858 DNA polymerase IV; Validated Back     alignment and domain information
>cd00424 PolY Y-family of DNA polymerases 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
>cd01701 PolY_Rev1 DNA polymerase Rev1 Back     alignment and domain information
>KOG2094 consensus Predicted DNA damage inducible protein [Replication, recombination and repair] 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
>cd03586 PolY_Pol_IV_kappa DNA Polymerase IV/Kappa Back     alignment and domain information
>PRK03348 DNA polymerase IV; Provisional Back     alignment and domain information
>PRK01810 DNA polymerase IV; Validated Back     alignment and domain information
>PRK03103 DNA polymerase IV; Reviewed 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
>PF08827 DUF1805: Domain of unknown function (DUF1805); InterPro: IPR014931 This protein is found in bacteria and archaea and has an N-terminal tetramerisation region that is composed of beta sheets 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
>COG3743 Uncharacterized conserved protein [Function unknown] Back     alignment and domain information
>PRK12766 50S ribosomal protein L32e; Provisional Back     alignment and domain information
>PRK02362 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 ?
Query538
2oh2_A508 Ternary Complex Of Human Dna Polymerase Length = 50 1e-47
3pzp_A517 Human Dna Polymerase Kappa Extending Opposite A Cis 1e-47
1t94_A459 Crystal Structure Of The Catalytic Core Of Human Dn 1e-47
4f4w_A361 Y-family Dna Polymerase Chimera Dbh-dpo4-dpo4 #1 Le 5e-23
4f4y_A362 Y-family Dna Polymerase Chimera Dbh-dpo4-dbh Length 1e-22
1k1q_A354 Crystal Structure Of A Dinb Family Error Prone Dna 7e-22
4f50_A361 Y-family Dna Polymerase Chimera Dbh-dbh-dpo4 Length 8e-22
3bq0_A354 Pre-insertion Binary Complex Of Dbh Dna Polymerase 9e-22
1im4_A221 Crystal Structure Of A Dinb Homolog (Dbh) Lesion By 1e-21
3v6k_A347 Replication Of N2,3-Ethenoguanine By Dna Polymerase 3e-19
2imw_P348 Mechanism Of Template-Independent Nucleotide Incorp 4e-19
3v6h_A348 Replication Of N2,3-Ethenoguanine By Dna Polymerase 4e-19
3pr4_A341 Dpo4 Y12a Mutant Incorporating Dadp Opposite Templa 5e-19
2ago_A341 Fidelity Of Dpo4: Effect Of Metal Ions, Nucleotide 5e-19
3pvx_A347 Binary Complex Of Aflatoxin B1 Adduct Modified Dna 5e-19
3gii_A341 Dpo4 Extension Ternary Complex With Disordered A Op 5e-19
2rdi_A342 Snapshots Of A Y-family Dna Polymerase In Replicati 5e-19
2uvv_A358 Crystal Structures Of Mutant Dpo4 Dna Polymerases W 5e-19
2bq3_A358 Dna Adduct Bypass Polymerization By Sulfolobus Solf 5e-19
1jxl_A352 Crystal Structure Of A Y-Family Dna Polymerase In A 5e-19
4gc7_A359 Crystal Structure Of Dpo4 In Complex With S-mc-dadp 5e-19
4dez_A356 Structure Of Msdpo4 Length = 356 6e-19
2asd_A360 Oxog-Modified Insertion Ternary Complex Length = 36 6e-19
2uvr_A358 Crystal Structures Of Mutant Dpo4 Dna Polymerases W 6e-19
3qz7_A360 T-3 Ternary Complex Of Dpo4 Length = 360 7e-19
2w9b_A358 Binary Complex Of Dpo4 Bound To N2,N2-Dimethyl- Deo 8e-19
4f4z_B361 Y-family Dna Polymerase Chimera Dpo4-dpo4-dbh Lengt 1e-18
1jx4_A352 Crystal Structure Of A Y-Family Dna Polymerase In A 3e-18
3gqc_A504 Structure Of Human Rev1-Dna-Dntp Ternary Complex Le 4e-17
2dpi_A420 Ternary Complex Of Hpoli With Dna And Dctp Length = 1e-13
3h40_A389 Binary Complex Of Human Dna Polymerase Iota With Te 1e-13
2alz_A390 Ternary Complex Of Hpoli With Dna And Dctp Length = 1e-13
1t3n_A388 Structure Of The Catalytic Core Of Dna Polymerase I 1e-13
3gv5_B420 Human Dna Polymerase Iota In Complex With T Templat 4e-12
3mr6_A435 Human Dna Polymerase Eta - Dna Ternary Complex With 4e-10
3mr2_A435 Human Dna Polymerase Eta In Complex With Normal Dna 4e-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 = 1e-47,   Method: Compositional matrix adjust.
 Identities = 105/238 (44%), Positives = 147/238 (61%), Gaps = 9/238 (3%)
Query: 77  GISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQF-VLPNDRMAVMTF 135
           G S  E+ +E+R  + ++  LT SAG+APN +LAKVCSD NKPNGQ+ +LPN R AVM F
Sbjct: 269 GTSAQEVVKEIRFRIEQKTTLTASAGIAPNTMLAKVCSDKNKPNGQYQILPN-RQAVMDF 327
Query: 136 ISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSLLCAVFSHSTADFFLSVGLGLGS 195
           I  LPIRK+ GIGKVTE +L+   GI TC E+ Q+ +LL  +FS ++  +FL + LGLGS
Sbjct: 328 IKDLPIRKVSGIGKVTEKMLK-ALGIITCTELYQQRALLSLLFSETSWHYFLHISLGLGS 386
Query: 196 TNTPQARFRKSISSERTFSVTEDKALLYRKLAEIAEMLSADMQKEXXXXXXXXXXXXXAS 255
           T+  +   RKS+S ERTFS        Y    E+   L+ D+QKE              +
Sbjct: 387 THLTRDGERKSMSVERTFSEINKAEEQYSLCQELCSELAQDLQKERLKGRTVTIKLKNVN 446
Query: 256 FEVRTRAVTLQKYISSSEDILKHASVLLKAEL------PVSLRLIGLRVTQFNEDKVR 307
           FEV+TRA T+   +S++E+I   A  LLK E+      P+ LRL+G+R++ F  ++ R
Sbjct: 447 FEVKTRASTVSSVVSTAEEIFAIAKELLKTEIDADFPHPLRLRLMGVRISSFPNEEDR 504
>pdb|3PZP|A Chain A, Human Dna Polymerase Kappa Extending Opposite A Cis-Syn Thymine Dimer Length = 517 Back     alignment and structure
>pdb|1T94|A Chain A, Crystal Structure Of The Catalytic Core Of Human Dna Polymerase Kappa Length = 459 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|4F50|A Chain A, Y-family Dna Polymerase Chimera Dbh-dbh-dpo4 Length = 361 Back     alignment and structure
>pdb|3BQ0|A Chain A, Pre-insertion Binary Complex Of Dbh Dna Polymerase Length = 354 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|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|3PR4|A Chain A, Dpo4 Y12a Mutant Incorporating Dadp Opposite Template Dt Length = 341 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|3GII|A Chain A, Dpo4 Extension Ternary Complex With Disordered A Opposite An Oxog In Anti Conformation Length = 341 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|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|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|4DEZ|A Chain A, Structure Of Msdpo4 Length = 356 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|3GQC|A Chain A, Structure Of Human Rev1-Dna-Dntp Ternary Complex Length = 504 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 ?
Query538
3osn_A420 DNA polymerase IOTA; hoogsteen base PAIR, protein- 5e-98
1t94_A459 Polymerase (DNA directed) kappa; replication, DNA 1e-94
3bq0_A354 POL IV, DBH, DNA polymerase IV; Y-family, lesion b 5e-94
3gqc_A504 DNA repair protein REV1; protein-DNA complex, DNA 4e-93
1jx4_A352 DNA polymerase IV (family Y); protein-DNA complex, 8e-93
3pzp_A517 DNA polymerase kappa; DNA nucleotidyltransferase, 1e-88
2aq4_A434 DNA repair protein REV1; polymerase, PAD, N-digit, 4e-83
1im4_A221 DBH; DNA polymerase PALM, thumb, fingers, helix-ha 2e-68
4ecq_A435 DNA polymerase ETA; transferase-DNA complex; HET: 5e-65
3mfi_A520 DNA polymerase ETA; DNA damage, DNA repair, DNA re 6e-37
3mfi_A520 DNA polymerase ETA; DNA damage, DNA repair, DNA re 4e-16
1unn_C115 POL IV, DNA polymerase IV; beta-clamp, translesion 8e-17
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 8e-12
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 3e-06
>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
 Score =  302 bits (775), Expect = 5e-98
 Identities = 82/352 (23%), Positives = 141/352 (40%), Gaps = 56/352 (15%)

Query: 8   ARRFGVRAAMPGFIARKLCPELIFVP-TDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAY 66
           AR+ GV+  M    A++ CP+L+ V   D T+Y   S    ++  ++ P       DE +
Sbjct: 70  ARKLGVKKLMNVRDAKEKCPQLVLVNGEDLTRYREMSYKVTELLEEFSPVVERLGFDENF 129

Query: 67  LDITEVCRERG---------------------------------ISGIEIAEELRTSVYE 93
           +D+TE+  +R                                  + G +IA E+R ++Y 
Sbjct: 130 VDLTEMVEKRLQQLQSDELSAVTVSGHVYNNQSINLLDVLHIRLLVGSQIAAEMREAMYN 189

Query: 94  EAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLP-IRKIGGIGKVTE 152
           + GLT  AGVA N+LLAK+ S + KPN Q VL  +  +    I SL  I++I GIG  T 
Sbjct: 190 QLGLTGCAGVASNKLLAKLVSGVFKPNQQTVLLPE--SCQHLIHSLNHIKEIPGIGYKTA 247

Query: 153 HILRDVFGINTCEEMLQKG-SLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSER 211
             L    GIN+  ++      +L      S A     +  G  ++    +   +S S E 
Sbjct: 248 KCLEA-LGINSVRDLQTFSPKILEKELGISVAQRIQKLSFGEDNSPVILSGPPQSFSEED 306

Query: 212 TFSVTEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISS 271
           +F     +     K+ E+   L   + ++G +  T+ L ++  S E      + Q  I S
Sbjct: 307 SFKKCSSEVEAKNKIEELLASLLNRVCQDGRKPHTVRLIIRRYSSEKHYGRESRQCPIPS 366

Query: 272 S-----------------EDILKHASVLLKAELPVSLRLIGLRVTQFNEDKV 306
                             + ++K    ++  ++P  L L+ +          
Sbjct: 367 HVIQKLGTGNYDVMTPMVDILMKLFRNMVNVKMPFHLTLLSVCFCNLKALNT 418
>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
>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
>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
>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 ?
Query538
3pzp_A517 DNA polymerase kappa; DNA nucleotidyltransferase, 100.0
1jx4_A352 DNA polymerase IV (family Y); protein-DNA complex, 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
3gqc_A504 DNA repair protein REV1; protein-DNA complex, DNA 100.0
1t94_A459 Polymerase (DNA directed) kappa; replication, DNA 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 99.42
2i5o_A39 DNA polymerase ETA; zinc finger, DNA polymerase,PO 98.84
1wcn_A70 Transcription elongation protein NUSA; RNA-binding 95.2
3mab_A93 Uncharacterized protein; NYSGXRC, PSI-2, structura 94.41
3bqs_A93 Uncharacterized protein; 10114F, NYSGXRC, PSI-2, s 93.91
2a1j_A63 DNA repair endonuclease XPF; XPF, xeroderma pigmen 93.36
1z3e_B73 DNA-directed RNA polymerase alpha chain; bacterial 92.32
1z00_B84 DNA repair endonuclease XPF; helix-hairpin-helix, 92.13
3gfk_B79 DNA-directed RNA polymerase subunit alpha; protein 88.68
3k4g_A86 DNA-directed RNA polymerase subunit alpha; bacteri 87.19
1b22_A114 DNA repair protein RAD51; DNA binding, riken struc 86.54
1ci4_A89 Protein (barrier-TO-autointegration factor (BAF) ) 86.31
1coo_A98 RNA polymerase alpha subunit; transcription regula 85.55
1kft_A78 UVRC, excinuclease ABC subunit C; helix-hairpin-he 83.0
2a1j_B91 DNA excision repair protein ERCC-1; XPF, xeroderma 81.63
1z00_A89 DNA excision repair protein ERCC-1; helix-hairpin- 81.37
>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=2.8e-63  Score=542.01  Aligned_cols=303  Identities=50%  Similarity=0.808  Sum_probs=287.1

Q ss_pred             CccCHHHHHcCCCCCCcHHHHHhhCCCeEEEcCChHHHHHHHHHHHHHHHhcCCCeEeeCccEEEEEcCccc--------
Q 009298            2 RFELLSARRFGVRAAMPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVC--------   73 (538)
Q Consensus         2 ~~~syeAR~~GVr~GM~l~~A~~LCP~Lvvvp~d~~~Y~~~s~~l~~il~~~sp~Ve~~SiDEafLDlT~~~--------   73 (538)
                      .-|||+||++||++|||+++|+++||+|+++|+|++.|+++|++++.||.+|+|.||++|+||+|||||++.        
T Consensus       126 ~t~nYeAR~~GVr~gMp~~~Ak~lCP~Lvvv~~d~~~Y~~~S~~v~~il~~ytp~ve~~SiDEafLDvT~~~~~~~~~~~  205 (517)
T 3pzp_A          126 STSNYHARRFGVRAAMPGFIAKRLCPQLIIVPPNFDKYRAVSKEVKEILADYDPNFMAMSLDEAYLNITKHLEERQNWPE  205 (517)
T ss_dssp             EEECHHHHTTTCCTTSCHHHHHHHCTTCEEECCCHHHHHHHHHHHHHHHHTTCTTCBCCSSSEEEEETHHHHHHHTSCCS
T ss_pred             EecCHHHHHcCCCCCCcHHHHHHhCCceEEECCCHHHHHHHHHHHHHHHHHcCCcEEEECCceEEEEccccccccccccc
Confidence            358999999999999999999999999999999999999999999999999999999999999999999874        


Q ss_pred             -------------------------------------------------------------------hhcCCCHHHHHHH
Q 009298           74 -------------------------------------------------------------------RERGISGIEIAEE   86 (538)
Q Consensus        74 -------------------------------------------------------------------~l~g~~~~~la~~   86 (538)
                                                                                         ++||.++.++|++
T Consensus       206 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfg~~~~~ia~~  285 (517)
T 3pzp_A          206 DKRRYFIKMGSSVENDNPGKEVNKLSEHERSISPLLFEESPSDVQPPGDPFQVNFEEQNNPQILQNSVVFGTSAQEVVKE  285 (517)
T ss_dssp             TTTEEECC--------------------------------------------------------CCEEECCSSHHHHHHH
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccchhhhhcCChHHHHHHH
Confidence                                                                               3466568999999


Q ss_pred             HHHHHHHHhCCceEEEecCChhHHHHHhcccCCCCeEEecCChHHHHHhhcCCCcccccCCCHHHHHHHHhhcCCCchHH
Q 009298           87 LRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEE  166 (538)
Q Consensus        87 IR~~I~~~~Glt~S~GIA~nk~lAKLAS~~aKP~G~~vl~~~~~~~~~fL~~lPl~~L~GIG~kt~~kL~~~lGI~TlgD  166 (538)
                      ||++|++++|||||+|||+||++||||++.+||||+++++++++++.+||+++||++|||||+++.++|++ +||+||+|
T Consensus       286 IR~~I~~~tGlt~S~GIA~Nk~LAKlAs~~~KP~G~~vl~~~~~~v~~fL~~LPV~kl~GIG~~t~~~L~~-lGI~TigD  364 (517)
T 3pzp_A          286 IRFRIEQKTTLTASAGIAPNTMLAKVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKVTEKMLKA-LGIITCTE  364 (517)
T ss_dssp             HHHHHHHHHSCCEEEEEESSHHHHHHHHHTTCSSCEEECCSSHHHHHHHHTTCBGGGSTTCCHHHHHHHHH-TTCCBHHH
T ss_pred             HHHHHHHHhCCeEEEEEcCCHHHHHHHhCcCCCCCEEEecCChHHHHHHHhcCChhhhccccHHHHHHHHH-hCCCcHHH
Confidence            99999999999999999999999999999999999999998755789999999999999999999999997 99999999


Q ss_pred             HHhchHHHHHHcChhHHHHHHHhccCCCCCCCCCCCCCccceeeeccCccCCHHHHHHHHHHHHHHHHHHHHHhCCCccE
Q 009298          167 MLQKGSLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSVTEDKALLYRKLAEIAEMLSADMQKEGLRGRT  246 (538)
Q Consensus       167 L~~lp~~L~krFG~~~~~~L~~~a~Gid~~~v~~~~~pKSIs~e~tF~~~~d~e~L~~~L~~Lae~L~~RLr~~gl~~rt  246 (538)
                      |++++..|.++||...+.++++.|+|++..++.+..++|||+.+++|+.+.+.+++..+|.+|+++|+.||+++++.+++
T Consensus       365 L~~~~~~L~~~fG~~~~~~l~~~a~Gid~~~v~~~~~~KSi~~e~tf~~~~~~e~l~~~l~~La~~l~~rLr~~~~~~~~  444 (517)
T 3pzp_A          365 LYQQRALLSLLFSETSWHYFLHISLGLGSTHLTRDGERKSMSVERTFSEINKAEEQYSLCQELCSELAQDLQKERLKGRT  444 (517)
T ss_dssp             HHHHHHHHHHHSCHHHHHHHHHHHTTCCCCSCCCCCCCCCEEEEEEEEEECCHHHHHHHHHHHHHHHHHHHHTTTCCBSC
T ss_pred             HHhhHHHHHHHhChHHHHHHHHHHcCCCcccccCCCCCccceeEEEcccccCHHHHHHHHHHHHHHHHHHHHHcCCceeE
Confidence            99998889999999888888899999999999888899999999999888889999999999999999999999999999


Q ss_pred             EEEEEEEcCCceeEEEEecCCCCCCHHHHHHHHHHHHHhhC------CCCEEEEEEEecCCCcCc
Q 009298          247 LTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAEL------PVSLRLIGLRVTQFNEDK  305 (538)
Q Consensus       247 LtL~Lr~~d~~~~srs~~L~~~t~~~~~L~~~a~~LL~~~l------p~~VR~IGV~ls~L~~~~  305 (538)
                      |+|++++++|.+.+++++++.||++..+|++++..||++.+      +..||+|||++++|.+..
T Consensus       445 vtlklk~~~f~~~tr~~tl~~~t~~~~~i~~~a~~Ll~~~~~~~~~~~~~iRllGV~~s~l~~~~  509 (517)
T 3pzp_A          445 VTIKLKNVNFEVKTRASTVSSVVSTAEEIFAIAKELLKTEIDADFPHPLRLRLMGVRISSFPNEE  509 (517)
T ss_dssp             EEEEEEETTSCEEEECCCCSSCBCSHHHHHHHHHHHHHHHHHHHTTSCCCEEEEEEEECCCCCCC
T ss_pred             EEEEEEecCCceeeEEEeCCCCCCCHHHHHHHHHHHHHHHhhhccCCCCcEEEEEEEecCCcChh
Confidence            99999999999999999999999999999999999999864      346999999999999874
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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

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 538
d1t94a2333 e.8.1.7 (A:75-407) DNA polymerase kappa {Human (Ho 1e-27
d1t94a2333 e.8.1.7 (A:75-407) DNA polymerase kappa {Human (Ho 8e-17
d1zeta2273 e.8.1.7 (A:27-299) DNA polymerase iota {Human (Hom 3e-26
d1im4a_209 e.8.1.7 (A:) DinB homolog (DBH) {Archaeon Sulfolob 2e-24
d1t94a1105 d.240.1.1 (A:411-515) DNA polymerase kappa {Human 1e-21
d1jiha2389 e.8.1.7 (A:1-389) DNA polymerase eta {Baker's yeas 2e-19
d1jiha2389 e.8.1.7 (A:1-389) DNA polymerase eta {Baker's yeas 3e-14
d1zeta1115 d.240.1.1 (A:300-414) DNA polymerase iota {Human ( 4e-18
d1jx4a2240 e.8.1.7 (A:1-240) DinB homolog (DBH) {Archaeon Sul 1e-13
d1jx4a1101 d.240.1.1 (A:241-341) DinB homolog (DBH) {Archaeon 3e-13
d1unnc_111 d.240.1.1 (C:) DNA polymerase IV {Escherichia coli 4e-13
d1k1sa1105 d.240.1.1 (A:240-344) DinB homolog (DBH) {Archaeon 7e-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 (277), Expect = 1e-27
 Identities = 65/141 (46%), Positives = 91/141 (64%), Gaps = 1/141 (0%)

Query: 57  FMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDI 116
           F     ++    I +     G S  E+ +E+R  + ++  LT SAG+APN +LAKVCSD 
Sbjct: 193 FQVNFEEQNNPQILQNSVVFGTSAQEVVKEIRFRIEQKTTLTASAGIAPNTMLAKVCSDK 252

Query: 117 NKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSLLCA 176
           NKPNGQ+ +  +R AVM FI  LPIRK+ GIGKVTE +L+   GI TC E+ Q+ +LL  
Sbjct: 253 NKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKVTEKMLKA-LGIITCTELYQQRALLSL 311

Query: 177 VFSHSTADFFLSVGLGLGSTN 197
           +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
>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
>d1t94a1 d.240.1.1 (A:411-515) DNA polymerase kappa {Human (Homo sapiens) [TaxId: 9606]} Length = 105 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
>d1jx4a2 e.8.1.7 (A:1-240) DinB homolog (DBH) {Archaeon Sulfolobus solfataricus, DNA polymerase IV [TaxId: 2287]} Length = 240 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 ?
Query538
d1t94a2333 DNA polymerase kappa {Human (Homo sapiens) [TaxId: 100.0
d1jx4a2240 DinB homolog (DBH) {Archaeon Sulfolobus solfataric 100.0
d1zeta2273 DNA polymerase iota {Human (Homo sapiens) [TaxId: 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: 99.58
d1jx4a1101 DinB homolog (DBH) {Archaeon Sulfolobus solfataric 99.51
d1unnc_111 DNA polymerase IV {Escherichia coli [TaxId: 562]} 99.45
d1k1sa1105 DinB homolog (DBH) {Archaeon Sulfolobus solfataric 99.43
d1zeta1115 DNA polymerase iota {Human (Homo sapiens) [TaxId: 99.31
d1jiha1120 DNA polymerase eta {Baker's yeast (Saccharomyces c 99.25
d2i1qa160 DNA repair protein Rad51, N-terminal domain {Archa 96.93
d1pzna161 DNA repair protein Rad51, N-terminal domain {Archa 95.87
d1szpa164 DNA repair protein Rad51, N-terminal domain {Baker 95.72
d2fmpa257 DNA polymerase beta {Human (Homo sapiens) [TaxId: 94.93
d2bcqa257 DNA polymerase lambda {Human (Homo sapiens) [TaxId 94.72
d1kfta_56 Excinuclease UvrC C-terminal domain {Escherichia c 94.38
d2a1ja162 DNA repair endonuclease XPF {Human (Homo sapiens) 94.05
d1jmsa360 Terminal deoxynucleotidyl transferase {Mouse (Mus 94.03
d2p6ra2198 Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22 91.59
d1gm5a2180 RecG "wedge" domain {Thermotoga maritima [TaxId: 2 91.32
d1doqa_69 C-terminal domain of RNA polymerase alpha subunit 90.82
d1b22a_70 DNA repair protein Rad51, N-terminal domain {Human 90.57
d2bgwa170 DNA repair endonuclease XPF {Aeropyrum pernix [Tax 90.02
d1x2ia168 ATP-dependent RNA helicase PF2015 {Pyrococcus furi 89.19
d1z3eb167 C-terminal domain of RNA polymerase alpha subunit 87.58
d1lb2b_72 C-terminal domain of RNA polymerase alpha subunit 87.23
d2a1jb178 DNA excision repair protein ERCC-1 {Human (Homo sa 83.92
>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=3.3e-47  Score=391.87  Aligned_cols=195  Identities=54%  Similarity=0.906  Sum_probs=182.4

Q ss_pred             ccCHHHHHcCCCCCCcHHHHHhhCCCeEEEcCChHHHHHHHHHHHHHHHhcCCCeEeeCccEEEEEcCccchh-------
Q 009298            3 FELLSARRFGVRAAMPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRE-------   75 (538)
Q Consensus         3 ~~syeAR~~GVr~GM~l~~A~~LCP~Lvvvp~d~~~Y~~~s~~l~~il~~~sp~Ve~~SiDEafLDlT~~~~l-------   75 (538)
                      -|||+||++||++||++++|+++||+++++++|++.|+++|+++++++.+|+|.||++|+||+|||+|+....       
T Consensus        64 a~nY~AR~~GVk~gm~i~eA~~lCP~lii~~~d~~~Yr~~S~~i~~il~~~~~~vE~~SIDE~flDlT~~~~~~~~~~~~  143 (333)
T d1t94a2          64 TSNYHARRFGVRAAMPGFIAKRLCPQLIIVPPNFDKYRAVSKEVKEILADYDPNFMAMSLDEAYLNITKHLEERQNWPED  143 (333)
T ss_dssp             EECHHHHHTTCCTTCCHHHHHHHCTTCEEECCCHHHHHHHHHHHHHHHHHHCTTCEECSSSEEEEECHHHHHHHTTCCGG
T ss_pred             ECCHHHHHhCCCCCCcHHHHHHhCCCcEEEcCcHHHHHHHHHHHHHHHHHcCCCEEEEeccEEEEecchhhhhhcccccc
Confidence            5899999999999999999999999999999999999999999999999999999999999999999975431       


Q ss_pred             --------------------------------------------------------------------cCCCHHHHHHHH
Q 009298           76 --------------------------------------------------------------------RGISGIEIAEEL   87 (538)
Q Consensus        76 --------------------------------------------------------------------~g~~~~~la~~I   87 (538)
                                                                                          ++..+.++|.+|
T Consensus       144 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~la~~I  223 (333)
T d1t94a2         144 KRRYFIKMGSSVENDNPGKEVNKLSEHERSISPLLFEESPSDVQPPGDPFQVNFEEQNNPQILQNSVVFGTSAQEVVKEI  223 (333)
T ss_dssp             GSEEECCC---CCCCCCCGGGGGGSTTTTTTGGGCC----------------------CCCCCCCEEECCSSHHHHHHHH
T ss_pred             hhhhhccccccccccccccccccccccccccccccccccccccccccccccccccccccchhhhhhhhccccHHHHHHHH
Confidence                                                                                122467899999


Q ss_pred             HHHHHHHhCCceEEEecCChhHHHHHhcccCCCCeEEecCChHHHHHhhcCCCcccccCCCHHHHHHHHhhcCCCchHHH
Q 009298           88 RTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEM  167 (538)
Q Consensus        88 R~~I~~~~Glt~S~GIA~nk~lAKLAS~~aKP~G~~vl~~~~~~~~~fL~~lPl~~L~GIG~kt~~kL~~~lGI~TlgDL  167 (538)
                      |++|++++|||||+|||+||++||||+..+|||||+++.++.+++..||+++||++|||||+++.++|+. +||+|++||
T Consensus       224 R~~I~~etG~t~SaGIa~NK~LAKLAs~~~KPngq~~i~~~~~~~~~~l~~lpi~~i~GiG~~~~~~L~~-~gi~ti~dl  302 (333)
T d1t94a2         224 RFRIEQKTTLTASAGIAPNTMLAKVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKVTEKMLKA-LGIITCTEL  302 (333)
T ss_dssp             HHHHHHHHSCCEEEEEESSHHHHHHHHHHTTTTCEEECCSSHHHHHHHHTTCBGGGCTTSCHHHHHHHHH-TTCCBHHHH
T ss_pred             HHHHHHHhCCCeEEeECccHHHHHHHHHhcCcCccceecCCHHHHHHHHhCCCccccCCcCHHHHHHHHH-cCCcCHHHH
Confidence            9999999999999999999999999999999999999988766789999999999999999999999997 999999999


Q ss_pred             HhchHHHHHHcChhHHHHHHHhccCCCCCCC
Q 009298          168 LQKGSLLCAVFSHSTADFFLSVGLGLGSTNT  198 (538)
Q Consensus       168 ~~lp~~L~krFG~~~~~~L~~~a~Gid~~~v  198 (538)
                      ++.+..|.+.||...+.|||+.++|+|++.|
T Consensus       303 ~~~~~~l~~~fG~~~g~~l~~~a~GID~~~v  333 (333)
T d1t94a2         303 YQQRALLSLLFSETSWHYFLHISLGLGSTHL  333 (333)
T ss_dssp             HHTHHHHHHHSCHHHHHHHHHHHTTCCCSCC
T ss_pred             hcCHHHHHHHhCHHHHHHHHHHhcCCCCCCC
Confidence            9987889999999989999999999998754
>d1jx4a2 e.8.1.7 (A:1-240) DinB homolog (DBH) {Archaeon Sulfolobus solfataricus, DNA polymerase IV [TaxId: 2287]} Back     information, alignment and structure
>d1zeta2 e.8.1.7 (A:27-299) DNA polymerase iota {Human (Homo sapiens) [TaxId: 9606]} 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
>d2a1ja1 a.60.2.5 (A:837-898) DNA repair endonuclease XPF {Human (Homo sapiens) [TaxId: 9606]} 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
>d2p6ra2 a.289.1.2 (A:489-686) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]} 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
>d1doqa_ a.60.3.1 (A:) C-terminal domain of RNA polymerase alpha subunit {Thermus thermophilus [TaxId: 274]} 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
>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
>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
>d1lb2b_ a.60.3.1 (B:) C-terminal domain of RNA polymerase alpha subunit {Escherichia coli [TaxId: 562]} 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