Citrus Sinensis ID: 012811

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------
MLFLLTNSFLLRFETAISNPKSKNFFTSLRTRGSSMSSWACKKCTFLNSPSRKSTCQICLTPSSSFSPPSKSSVSVPTWSCKACTFLNPYNNTSCELCNTRAPVSGLSSFEDLTDPALDSELDSSVGSVFLPLQLKACTGKRKIRDQDCDGDFDGFRVTNSVSIKDDTTSGPSADNSESGAVSGSLKILSYNVWFREDLEMHPRMKTIGDLIQLHSPDIICFQEITPNIYDILCKSSWWKGYRCSVPNEMADSRGYFCMQLSKLQAKSFTCEPFRNSIMGRELCVAEVEVQGKKPLVVATSHLESPCPGPPTWDQMFSKERVEQAKEAINLLKKNPNVIFCGDMNWDDKLDGKFPLPDGWVDAWTELRPGENGWTYDTKSNKMLSGNRTLQKRLDRFICSLRDFKIIRIDMIGVEAIPGLLYVKEKKVRKEMQKLELPVLPSDHYGLLLTISNNIG
cEEEccccccEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEcccccccccHHHHHHHHHHHHHccccEEEEEEccccHHHHHHHcccccccEEEcccccccccccEEEEEEEEccEEEEEEEccccccccEEEEEEEEEcccEEEEEEEEcccccccccccHHHHHHHHHHHHHHHHHHHHHccccEEEEEcccccccccccccccccHHHHHHHccccccccccccccccccccccccccccEEEEEEccccEEEEEEEEEEcccccccHHHHHHHHHHHHcccccccccccccEEEEEEcccc
cEEEEEHHHHHHHHHHcccccccccccccEccccccccccccccEEEcccccccccHHcccccccccccccccccccccccHHcccccccccccEEcccccccccccccccccccccccHHHHHHHHHHccccccccHccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEEcccccHHHHHHHHHHHHHHHHccccEEEEEEccHHHHHHHHHcccHccEEEEccccccccccEEEEEEEEEEccccEEEcccccccccEEEEEEEEEccccEEEEEEccccccccccccccHHHHHHHHHHHHHHHHHHHccccEEEEEcccccccccccccccccHHHHHHHHccccccccccccccccccccccccccccEEEEEccccccEEEEEEcccccccccccccccEcccccccccccccccccEEEEEEccccc
MLFLLTNSFLLRFETAisnpksknfftslrtrgssmsswackkctflnspsrkstcqicltpsssfsppskssvsvptwsckactflnpynntscelcntrapvsglssfedltdpaldseldssvgsvflplqlkactgkrkirdqdcdgdfdgfrvtnsvsikddttsgpsadnsesgavsgSLKILSYNVWfredlemhprmkTIGDLIqlhspdiicfqeitpnIYDILcksswwkgyrcsvpnemadsrgYFCMQLSKlqaksftcepfrnsimGRELCVAEVEVQGKKPLVVAtshlespcpgpptwdqmFSKERVEQAKEAINLlkknpnvifcgdmnwddkldgkfplpdgwvdawtelrpgengwtydtksnkmlsgnRTLQKRLDRFICSLRDFKIIRIDMIGVEAIPGLLYVKEKKVRKEMQklelpvlpsdhygLLLTISNNIG
mlflltnsFLLRFetaisnpksknffTSLRTrgssmsswACKKCTFLNSPSRKSTCQICLTpsssfsppskssVSVPTWSCKACTFLNPYNNTSCELCNTRAPVSGLSSFEDLTDPALDSELDSSVGSVFLPlqlkactgkrkirdqdcdgdfdgfrvtnsvsikddttsgpsadnsesgavsgslKILSYNVWFREDLEMHPRMKTIGDLIQLHSPDIICFQEITPNIYDILCKSSWWKGYRCSVPNEMADSRGYFCMQLSKLQAKSFTCEPFRNSIMGRELCVAEVEVQGKKPLVVATSHLESPCPGPPTWDQMFSKERVEQAKEAInllkknpnvIFCGDMNWDDKLDGKFPLPDGWVDAWTELRpgengwtydtksnkmlsgnrtLQKRLDRFICSLRDFKIIRIDMIGVEAIPGLLYVKEKKVRKEMQKlelpvlpsdhygllltisnnig
MLFLLTNSFLLRFETAISNPKSKNFFTSLRTRGSSMSSWACKKCTFLNSPSRKSTCQICLTpsssfsppskssvsvpTWSCKACTFLNPYNNTSCELCNTRAPVSGLSSFEDLTDPALDSELDSSVGSVFLPLQLKACTGKRKIRDQDCDGDFDGFRVTNSVSIKDDTTSGPSADNSESGAVSGSLKILSYNVWFREDLEMHPRMKTIGDLIQLHSPDIICFQEITPNIYDILCKSSWWKGYRCSVPNEMADSRGYFCMQLSKLQAKSFTCEPFRNSIMGRELCVAEVEVQGKKPLVVATSHLESPCPGPPTWDQMFSKERVEQAKEAINLLKKNPNVIFCGDMNWDDKLDGKFPLPDGWVDAWTELRPGENGWTYDTKSNKMLSGNRTLQKRLDRFICSLRDFKIIRIDMIGVEAIPGLLYVKEKKVRKEMQKLELPVLPSDHYGLLLTISNNIG
*LFLLTNSFLLRFETAISN****NFFTSL******MSSWACKKCTFLNS*****TCQICL***************VPTWSCKACTFLNPYNNTSCELCNTRAPVSGL*****************SVGSVFLPLQLKACTGKRKIRDQDCDGDFDGFRVT*************************SLKILSYNVWFREDLEMHPRMKTIGDLIQLHSPDIICFQEITPNIYDILCKSSWWKGYRCSVPNEMADSRGYFCMQLSKLQAKSFTCEPFRNSIMGRELCVAEVEVQGKKPLVVATSH************************EAINLLKKNPNVIFCGDMNWDDKLDGKFPLPDGWVDAWTELRPGENGWTYDTKSNKMLSGNRTLQKRLDRFICSLRDFKIIRIDMIGVEAIPGLLYVKEKKVRKEMQKLELPVLPSDHYGLLLTI*****
MLFL***SFL********************************KCTFLNSPSRKSTC***************************CTFLNPYNNTSCELCNTRAPV********LTDPALDSELDSSVGSVFLPLQLKACTGKRKIRDQDCDGDFDGFRVTNSVSIKDDTTSGPSADNSESGAVSGSLKILSYNVWFREDLEMHPRMKTIGDLIQLHSPDIICFQEITPNIYDILCKSSWWKGYRCSVPNEMADSRGYFCMQLSKLQAKSFTCEPFRNSIMGRELCVAEVEVQGKKPLVVATSHLESPCPGPPTWDQMFSKERVEQAKEAINLLKKNPNVIFCGDMNWDDKLDGKFPLPDGWVDAWTELRPGENGWTYDTKSNKMLSGNRTLQKRLDRFICSLRDFKIIRIDMIGVEAIPGLLYVKEKKVRKEMQKLELPVLPSDHYGLLLTISNN**
MLFLLTNSFLLRFETAISNPKSKNFFTSL********SWACKKCTFLNSPSRKSTCQICLT****************TWSCKACTFLNPYNNTSCELCNTRAPVSGLSSFEDLTDPALDSELDSSVGSVFLPLQLKACTGKRKIRDQDCDGDFDGFRVTNSVSIK******************GSLKILSYNVWFREDLEMHPRMKTIGDLIQLHSPDIICFQEITPNIYDILCKSSWWKGYRCSVPNEMADSRGYFCMQLSKLQAKSFTCEPFRNSIMGRELCVAEVEVQGKKPLVVATSHLESPCPGPPTWDQMFSKERVEQAKEAINLLKKNPNVIFCGDMNWDDKLDGKFPLPDGWVDAWTELRPGENGWTYDTKSNKMLSGNRTLQKRLDRFICSLRDFKIIRIDMIGVEAIPGLLYVKEKKVRKEMQKLELPVLPSDHYGLLLTISNNIG
MLFLLTNSFLLRFETAISN**SKNFFTSLRTRGSSMSSWACKKCTFLNSPSRKSTCQ*CL*****************TWSCKACTFLNPYNNTSCELCNTRAPVSGLSSFEDLTDPALDSELDSSVGSVFLPL*************************************************SGSLKILSYNVWFREDLEMHPRMKTIGDLIQLHSPDIICFQEITPNIYDILCKSSWWKGYRCSVPNEMADSRGYFCMQLSKLQAKSFTCEPFRNSIMGRELCVAEVEVQGKKPLVVATSHLESPCPGPPTWDQMFSKERVEQAKEAINLLKKNPNVIFCGDMNWDDKLDGKFPLPDGWVDAWTELRPGENGWTYDTKSNKMLSGNRTLQKRLDRFICSLRDFKIIRIDMIGVEAIPGLLYVKEKKVRKEMQKLELPVLPSDHYGLLLTISN***
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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SSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
SSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MLFLLTNSFLLRFETAISNPKSKNFFTSLRTRGSSMSSWACKKCTFLNSPSRKSTCQICLTPSSSFSPPSKSSVSVPTWSCKACTFLNPYNNTSCELCNTRAPVSGLSSFEDLTDPALDSELDSSVGSVFLPLQLKACTGKRKIRDQDCDGDFDGFRVTNSVSIKDDTTSGPSADNSESGAVSGSLKILSYNVWFREDLEMHPRMKTIGDLIQLHSPDIICFQEITPNIYDILCKSSWWKGYRCSVPNEMADSRGYFCMQLSKLQAKSFTCEPFRNSIMGRELCVAEVEVQGKKPLVVATSHLESPCPGPPTWDQMFSKERVEQAKEAINLLKKNPNVIFCGDMNWDDKLDGKFPLPDGWVDAWTELRPGENGWTYDTKSNKMLSGNRTLQKRLDRFICSLRDFKIIRIDMIGVEAIPGLLYVKEKKVRKEMQKLELPVLPSDHYGLLLTISNNIG
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 ?
Query456 2.2.26 [Sep-21-2011]
Q28FQ5373 Tyrosyl-DNA phosphodieste yes no 0.649 0.793 0.282 4e-18
A7YWI9364 Tyrosyl-DNA phosphodieste yes no 0.642 0.804 0.282 2e-17
Q9JJX7370 Tyrosyl-DNA phosphodieste yes no 0.519 0.640 0.285 6e-17
O95551362 Tyrosyl-DNA phosphodieste yes no 0.543 0.685 0.296 3e-16
A5D8M0371 Tyrosyl-DNA phosphodieste N/A no 0.508 0.625 0.299 4e-16
Q3T1H5366 Tyrosyl-DNA phosphodieste yes no 0.519 0.647 0.282 8e-16
F1NW29369 Tyrosyl-DNA phosphodieste yes no 0.548 0.677 0.303 1e-14
Q5XJA0369 Tyrosyl-DNA phosphodieste yes no 0.714 0.883 0.275 5e-13
A8XU68337 5'-tyrosyl-DNA phosphodie N/A no 0.478 0.646 0.256 3e-07
Q9XWG3362 5'-tyrosyl-DNA phosphodie yes no 0.440 0.555 0.261 1e-05
>sp|Q28FQ5|TYDP2_XENTR Tyrosyl-DNA phosphodiesterase 2 OS=Xenopus tropicalis GN=tdp2 PE=2 SV=2 Back     alignment and function desciption
 Score = 93.2 bits (230), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 97/343 (28%), Positives = 153/343 (44%), Gaps = 47/343 (13%)

Query: 115 DPALDSEL-DSSVGSVFLPLQLKACTGKRKIRDQDCDGDFDGFRVTNSVSIKDDTTSGPS 173
           +P ++S L + +   +  PL+ +  +G       D  GD     VT S +   ++++   
Sbjct: 62  EPGVESALQNKAAADIADPLKQETMSGTASDSCIDLTGD--DLVVTKSEATTSNSSTVKQ 119

Query: 174 ADNSESGAVSGSLKILSYNVWFREDLEMHPRMKTIGDLIQLHSPDIICFQEITPNIYDIL 233
            D S           L++N+   ++  +  R + +   + L+SPD++  QE+ P  Y+ L
Sbjct: 120 EDESH-------FSFLTWNIDGLDESNVAERARGVCSYLALYSPDVVFLQEVIPPYYEYL 172

Query: 234 CKSSWWKGYRCSVPNEMADSRGYFCMQLSKLQAKSFTCE--PFRNSIMGRELCVAEVEVQ 291
            K +    Y     NE      +  M L K + K  + E  P+ +++M R L VA V + 
Sbjct: 173 KKRA--VSYTIITGNE---DEYFTAMMLKKSRVKLISQEIVPYPSTVMMRNLLVANVNIS 227

Query: 292 GKKPLVVATSHLESPCPGPPTWDQMFSKERVEQAKEAINLLKKNP---NVIFCGDMNWDD 348
           G   + + TSHLES      T D   SKER++Q    +  +   P    VIF GD N  D
Sbjct: 228 GNS-ICLMTSHLES------TKDH--SKERLKQLDIVLKKMMDAPPLATVIFGGDTNLRD 278

Query: 349 KLDGKF-PLPDGWVDAWTEL-RPGENGWTYDTKSNKMLSGNRTLQKRLDRFICSLR-DFK 405
           +   K   +P+  +D W  L +P    +T+DTK NK L            +IC LR D  
Sbjct: 279 QEVAKIGGMPNNILDVWDFLGKPEHCRYTWDTKVNKNLRA---------PYICRLRFDRI 329

Query: 406 IIRIDMIGVEAIPGLLYVKEKKVRKEMQKLELPVLPSDHYGLL 448
             R    G + IP  LY+         +KL+    PSDH+GLL
Sbjct: 330 FFRASQEGSQVIPQSLYLAGT------EKLDCGRFPSDHWGLL 366
DNA repair enzyme that can remove a variety of covalent adducts from DNA through hydrolysis of a 5'-phosphodiester bond, giving rise to DNA with a free 5' phosphate. Catalyzes the hydrolysis of dead-end complexes between DNA and the topoisomerase 2 (top2) active site tyrosine residue. Hydrolyzes 5'-phosphoglycolates on protruding 5' ends on DNA double-strand breaks (DSBs) due to DNA damage by radiation and free radicals.
Xenopus tropicalis (taxid: 8364)
EC: 3EC: .EC: 1EC: .EC: 4EC: .EC: -
>sp|A7YWI9|TYDP2_BOVIN Tyrosyl-DNA phosphodiesterase 2 OS=Bos taurus GN=TDP2 PE=2 SV=1 Back     alignment and function description
>sp|Q9JJX7|TYDP2_MOUSE Tyrosyl-DNA phosphodiesterase 2 OS=Mus musculus GN=Tdp2 PE=1 SV=1 Back     alignment and function description
>sp|O95551|TYDP2_HUMAN Tyrosyl-DNA phosphodiesterase 2 OS=Homo sapiens GN=TDP2 PE=1 SV=1 Back     alignment and function description
>sp|A5D8M0|TYDP2_XENLA Tyrosyl-DNA phosphodiesterase 2 OS=Xenopus laevis GN=tdp2 PE=2 SV=1 Back     alignment and function description
>sp|Q3T1H5|TYDP2_RAT Tyrosyl-DNA phosphodiesterase 2 OS=Rattus norvegicus GN=Tdp2 PE=2 SV=1 Back     alignment and function description
>sp|F1NW29|TYDP2_CHICK Tyrosyl-DNA phosphodiesterase 2 OS=Gallus gallus GN=TDP2 PE=3 SV=2 Back     alignment and function description
>sp|Q5XJA0|TYDP2_DANRE Tyrosyl-DNA phosphodiesterase 2 OS=Danio rerio GN=tdp2 PE=1 SV=3 Back     alignment and function description
>sp|A8XU68|TYDP2_CAEBR 5'-tyrosyl-DNA phosphodiesterase OS=Caenorhabditis briggsae GN=CBG18823 PE=3 SV=2 Back     alignment and function description
>sp|Q9XWG3|TYDP2_CAEEL 5'-tyrosyl-DNA phosphodiesterase OS=Caenorhabditis elegans GN=Y63D3A.4 PE=1 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 ?
Query456
302144127 961 unnamed protein product [Vitis vinifera] 0.899 0.426 0.693 1e-160
224113265422 predicted protein [Populus trichocarpa] 0.896 0.969 0.702 1e-159
359483428447 PREDICTED: tyrosyl-DNA phosphodiesterase 0.901 0.919 0.689 1e-157
356563045401 PREDICTED: tyrosyl-DNA phosphodiesterase 0.877 0.997 0.650 1e-152
356563043402 PREDICTED: tyrosyl-DNA phosphodiesterase 0.879 0.997 0.650 1e-152
307136223481 endonuclease/exonuclease/phosphatase fam 0.892 0.846 0.641 1e-146
363808316393 uncharacterized protein LOC100776602 [Gl 0.859 0.997 0.646 1e-145
449471161485 PREDICTED: tyrosyl-DNA phosphodiesterase 0.942 0.886 0.596 1e-144
449488332463 PREDICTED: LOW QUALITY PROTEIN: tyrosyl- 0.936 0.922 0.597 1e-144
449454875482 PREDICTED: tyrosyl-DNA phosphodiesterase 0.942 0.892 0.596 1e-144
>gi|302144127|emb|CBI23232.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
 Score =  570 bits (1469), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 292/421 (69%), Positives = 330/421 (78%), Gaps = 11/421 (2%)

Query: 38  SWACKKCTFLNSPSRKSTCQICLTPSSSFSPPSKSSVSVPT---WSCKACTFLNPYNNTS 94
           SW C KCTF+N  S+ STC IC + SS    PS SS   P+   WSCKACTFLNPY N  
Sbjct: 546 SWTCSKCTFINPSSQTSTCLICSSSSSIPQSPSSSSAPSPSTPKWSCKACTFLNPYRNPI 605

Query: 95  CELCNTRAPVSGLSSFEDL--TDPALDSELDSSVGSVFLPLQLKACTGKRKIRDQDCDGD 152
           CE+C TRA VS LS FEDL  TDP  D ELDSSVGSVFLPLQ   C+ KRK RD   + D
Sbjct: 606 CEVCGTRASVSSLSCFEDLNCTDP--DGELDSSVGSVFLPLQ--RCS-KRKNRDP-VEID 659

Query: 153 FDGFRVTNSVSIKDDTTSGPSADNSESGAVSGSLKILSYNVWFREDLEMHPRMKTIGDLI 212
                      +K    +  + ++++S +V  SLKILSYNVWFREDLEM  RM+ +GDLI
Sbjct: 660 AAAGGSGGFGGVKSANKAVVALEDTDSDSVLSSLKILSYNVWFREDLEMDKRMQALGDLI 719

Query: 213 QLHSPDIICFQEITPNIYDILCKSSWWKGYRCSVPNEMADSRGYFCMQLSKLQAKSFTCE 272
           QLHSPD+ICFQE+TPNIYD+  +S WWK YRCSVPNEMA  R YFCM LSKL  KSF+C+
Sbjct: 720 QLHSPDLICFQEVTPNIYDVFQQSCWWKVYRCSVPNEMAHLRPYFCMLLSKLPVKSFSCK 779

Query: 273 PFRNSIMGRELCVAEVEVQGKKPLVVATSHLESPCPGPPTWDQMFSKERVEQAKEAINLL 332
            F NSIMGRELC+AE+EVQ  KPLV+ATSHLESPCP PP WDQM+SKERV+QAKEA+NLL
Sbjct: 780 RFSNSIMGRELCIAELEVQAGKPLVLATSHLESPCPAPPKWDQMYSKERVDQAKEALNLL 839

Query: 333 KKNPNVIFCGDMNWDDKLDGKFPLPDGWVDAWTELRPGENGWTYDTKSNKMLSGNRTLQK 392
            KNPNVIF GDMNWD+K DG+FPLPDGWVDAW +LRPGENGWTYDTKSN+MLSGNRTLQK
Sbjct: 840 TKNPNVIFGGDMNWDEKSDGQFPLPDGWVDAWADLRPGENGWTYDTKSNQMLSGNRTLQK 899

Query: 393 RLDRFICSLRDFKIIRIDMIGVEAIPGLLYVKEKKVRKEMQKLELPVLPSDHYGLLLTIS 452
           RLDRF+C L DFKI +IDMIG+E IPGL Y KEKKVRKEMQ+L LPVLPSDHYGLLLTIS
Sbjct: 900 RLDRFMCRLHDFKISKIDMIGMEPIPGLSYCKEKKVRKEMQQLVLPVLPSDHYGLLLTIS 959

Query: 453 N 453
           +
Sbjct: 960 S 960

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|224113265|ref|XP_002332611.1| predicted protein [Populus trichocarpa] gi|222832812|gb|EEE71289.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|359483428|ref|XP_002268030.2| PREDICTED: tyrosyl-DNA phosphodiesterase 2 [Vitis vinifera] Back     alignment and taxonomy information
>gi|356563045|ref|XP_003549776.1| PREDICTED: tyrosyl-DNA phosphodiesterase 2-like isoform 2 [Glycine max] Back     alignment and taxonomy information
>gi|356563043|ref|XP_003549775.1| PREDICTED: tyrosyl-DNA phosphodiesterase 2-like isoform 1 [Glycine max] Back     alignment and taxonomy information
>gi|307136223|gb|ADN34060.1| endonuclease/exonuclease/phosphatase family protein [Cucumis melo subsp. melo] Back     alignment and taxonomy information
>gi|363808316|ref|NP_001242502.1| uncharacterized protein LOC100776602 [Glycine max] gi|255637077|gb|ACU18870.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|449471161|ref|XP_004153226.1| PREDICTED: tyrosyl-DNA phosphodiesterase 2-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|449488332|ref|XP_004158004.1| PREDICTED: LOW QUALITY PROTEIN: tyrosyl-DNA phosphodiesterase 2-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|449454875|ref|XP_004145179.1| PREDICTED: tyrosyl-DNA phosphodiesterase 2-like [Cucumis sativus] 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 ?
Query456
TAIR|locus:2027417441 AT1G11800 [Arabidopsis thalian 0.927 0.959 0.601 1.8e-135
UNIPROTKB|Q28FQ5373 tdp2 "Tyrosyl-DNA phosphodiest 0.605 0.739 0.294 3.8e-16
UNIPROTKB|A7YWI9364 TDP2 "Tyrosyl-DNA phosphodiest 0.607 0.760 0.281 1.7e-15
UNIPROTKB|F1RUE1362 TDP2 "Uncharacterized protein" 0.517 0.651 0.302 4.9e-15
UNIPROTKB|O95551362 TDP2 "Tyrosyl-DNA phosphodiest 0.607 0.765 0.280 6.5e-15
MGI|MGI:1860486370 Tdp2 "tyrosyl-DNA phosphodiest 0.513 0.632 0.290 1.1e-13
UNIPROTKB|A5D8M0371 tdp2 "Tyrosyl-DNA phosphodiest 0.469 0.576 0.298 1.1e-13
UNIPROTKB|F1NW29369 TDP2 "Tyrosyl-DNA phosphodiest 0.519 0.642 0.308 1.8e-13
ZFIN|ZDB-GENE-050816-1383 tdp2b "tyrosyl-DNA phosphodies 0.644 0.767 0.270 4.5e-13
RGD|1560342366 Tdp2 "tyrosyl-DNA phosphodiest 0.513 0.639 0.286 5e-13
TAIR|locus:2027417 AT1G11800 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 1327 (472.2 bits), Expect = 1.8e-135, P = 1.8e-135
 Identities = 263/437 (60%), Positives = 311/437 (71%)

Query:    26 FTSLRTRGSSMSSWACKKCTFLNSPSRKSTCQICLTXXXXXXXX------XXXXXXXXTW 79
             F  + T  +  SSW+C KCTFLNS S+K  C ICL                        W
Sbjct:     7 FLRIVTSRAMSSSWSCNKCTFLNSASQKLNCMICLAPVSLPSLSPPPPSLSISANDEAKW 66

Query:    80 SCKACTFLNPYNNTSCELCNTRAPVSGLSSFEDLTDPALDS-ELDSSVGSVFLPLQLKAC 138
             +CKACTFLN Y N+ C++C TR+P S L  F+DLTD  L+S + DSSVGSVF PL  + C
Sbjct:    67 ACKACTFLNTYKNSICDVCGTRSPTSSLLGFQDLTDSGLESNDADSSVGSVFFPL--RRC 124

Query:   139 TGKRKIRDQDCDGDFDGFRVTNSVS---IKDDTTSGPSADNSESGAVSGSLKILSYNVWF 195
               KRK  D D   + DG  V  S S   +K +         S+SG     LKILSYNVWF
Sbjct:   125 I-KRKAMDDDVV-EVDGASVVCSESQGVMKKNKEIETKGVASDSGTPLTCLKILSYNVWF 182

Query:   196 REDLEMHPRMKTIGDLIQLHSPDIICFQEITPNIYDILCKSSWWKGYRCSVPNEMADSRG 255
             REDLE++ RM+ IG LIQLHSP +ICFQE+TP IYDI  KS+WWK Y CSV  ++A SRG
Sbjct:   183 REDLELNLRMRAIGHLIQLHSPHLICFQEVTPEIYDIFRKSNWWKAYSCSVSVDVAVSRG 242

Query:   256 YFCMQLSKLQAKSFTCEPFRNSIMGRELCVAEVEVQGKKPLVVATSHLESPCPGPPTWDQ 315
             Y+CM LSKL  KSF+ + F NSIMGREL +AEVEV G+KPLV ATSHLESPCPGPP WDQ
Sbjct:   243 YYCMLLSKLGVKSFSSKSFGNSIMGRELSIAEVEVPGRKPLVFATSHLESPCPGPPKWDQ 302

Query:   316 MFSKERVEQAKEAINLLKKNPNVIFCGDMNWDDKLDGKFPLPDGWVDAWTELRPGENGWT 375
             MFS+ERVEQAKEAI +L+ N NVIF GDMNW DKLDGKFPLPD WVD W  L+PG+ G+T
Sbjct:   303 MFSRERVEQAKEAIEILRPNANVIFGGDMNWCDKLDGKFPLPDKWVDVWEVLKPGDLGFT 362

Query:   376 YDTKSNKMLSGNRTLQKRLDRFICSLRDFKIIRIDMIGVEAIPGLLYVKEKKVRKEMQKL 435
             YDTK+N MLSGNR LQKRLDR +C L D+K+  I+M+G EAIPGL YVKEKKVR +++KL
Sbjct:   363 YDTKANPMLSGNRALQKRLDRILCRLDDYKLGGIEMVGKEAIPGLSYVKEKKVRGDIKKL 422

Query:   436 ELPVLPSDHYGLLLTIS 452
             ELPVLPSDH+GLL+T+S
Sbjct:   423 ELPVLPSDHFGLLVTLS 439
GO:0005622 "intracellular" evidence=IEA
GO:0005634 "nucleus" evidence=ISM
GO:0008270 "zinc ion binding" evidence=IEA
GO:0016787 "hydrolase activity" evidence=ISS
UNIPROTKB|Q28FQ5 tdp2 "Tyrosyl-DNA phosphodiesterase 2" [Xenopus (Silurana) tropicalis (taxid:8364)] Back     alignment and assigned GO terms
UNIPROTKB|A7YWI9 TDP2 "Tyrosyl-DNA phosphodiesterase 2" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|F1RUE1 TDP2 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|O95551 TDP2 "Tyrosyl-DNA phosphodiesterase 2" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
MGI|MGI:1860486 Tdp2 "tyrosyl-DNA phosphodiesterase 2" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|A5D8M0 tdp2 "Tyrosyl-DNA phosphodiesterase 2" [Xenopus laevis (taxid:8355)] Back     alignment and assigned GO terms
UNIPROTKB|F1NW29 TDP2 "Tyrosyl-DNA phosphodiesterase 2" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-050816-1 tdp2b "tyrosyl-DNA phosphodiesterase 2b" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
RGD|1560342 Tdp2 "tyrosyl-DNA phosphodiesterase 2" [Rattus norvegicus (taxid:10116)] 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 Layer3.1.40.691

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
fgenesh4_pg.C_scaffold_252000007
hypothetical protein (422 aa)
(Populus trichocarpa)
Predicted Functional Partners:
 
Sorry, there are no predicted associations at the current settings.
 

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query456
cd09080248 cd09080, TDP2, Phosphodiesterase domain of human T 7e-82
cd08372241 cd08372, EEP, Exonuclease-Endonuclease-Phosphatase 2e-13
cd09078280 cd09078, nSMase, Neutral sphingomyelinases (nSMase 2e-06
COG3568259 COG3568, ElsH, Metal-dependent hydrolase [General 3e-06
pfam03372143 pfam03372, Exo_endo_phos, Endonuclease/Exonuclease 2e-05
cd10281253 cd10281, Nape_like_AP-endo, Neisseria meningitides 8e-05
cd09073251 cd09073, ExoIII_AP-endo, Escherichia coli exonucle 3e-04
smart0054725 smart00547, ZnF_RBZ, Zinc finger domain 5e-04
cd09084246 cd09084, EEP-2, Exonuclease-Endonuclease-Phosphata 7e-04
cd10283266 cd10283, MnuA_DNase1-like, Mycoplasma pulmonis Mnu 0.002
>gnl|CDD|197314 cd09080, TDP2, Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains Back     alignment and domain information 
 Score =  252 bits (646), Expect = 7e-82
 Identities = 103/274 (37%), Positives = 135/274 (49%), Gaps = 34/274 (12%)

Query: 186 LKILSYNVWFREDLEMHPRMKTIGDLIQLHSPDIICFQEITPNIYDILCKSSWW-KGYRC 244
           LK+L++NV F +D+ +  RM+ I  L++   PD+I  QE+TP     L    W  K Y  
Sbjct: 1   LKVLTWNVDFLDDVNLAERMRAILKLLEELDPDVIFLQEVTPPFLAYLLSQPWVRKNYYF 60

Query: 245 SVPNEMADSRGYFCMQLSKLQAKSFTCE--PFRNSIMGRELCVAEVEVQGKKPLVVATSH 302
           S          Y  + LSK   KS      PF ++ MGR L  AE+ +   +PL +AT+H
Sbjct: 61  SEGPPSPAVDPYGVLILSK---KSLVVRRVPFTSTRMGRNLLAAEINLGSGEPLRLATTH 117

Query: 303 LESPCPGPPTWDQMFSKERVEQAKEAINLLKKNP---NVIFCGDMNWDDKLDGKFPLPDG 359
           LES              ER  Q +E    LKK P   NVI  GD N  DK D    LP+G
Sbjct: 118 LESLKSHSS--------ERTAQLEEIAKKLKKPPGAANVILGGDFNLRDKEDDTGGLPNG 169

Query: 360 WVDAWTELRP-GENGWTYDTKSNKML-SGNRTLQKRLDRFICSLRDFKIIRIDMIGVEAI 417
           +VDAW EL P GE G+T+DT+ N ML  G    +KR DR +    D K   I++IG E I
Sbjct: 170 FVDAWEELGPPGEPGYTWDTQKNPMLRKGEAGPRKRFDRVLLRGSDLKPKSIELIGTEPI 229

Query: 418 PGLLYVKEKKVRKEMQKLELPVLPSDHYGLLLTI 451
           PG                E  + PSDH+GLL  +
Sbjct: 230 PG---------------DEEGLFPSDHFGLLAEL 248

Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. Length = 248
>gnl|CDD|197306 cd08372, EEP, Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily Back     alignment and domain information
>gnl|CDD|197312 cd09078, nSMase, Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine Back     alignment and domain information
>gnl|CDD|226098 COG3568, ElsH, Metal-dependent hydrolase [General function prediction only] Back     alignment and domain information
>gnl|CDD|217520 pfam03372, Exo_endo_phos, Endonuclease/Exonuclease/phosphatase family Back     alignment and domain information
>gnl|CDD|197336 cd10281, Nape_like_AP-endo, Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases Back     alignment and domain information
>gnl|CDD|197307 cd09073, ExoIII_AP-endo, Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases Back     alignment and domain information
>gnl|CDD|197784 smart00547, ZnF_RBZ, Zinc finger domain Back     alignment and domain information
>gnl|CDD|197318 cd09084, EEP-2, Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2 Back     alignment and domain information
>gnl|CDD|197338 cd10283, MnuA_DNase1-like, Mycoplasma pulmonis MnuA nuclease-like Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 456
KOG2756349 consensus Predicted Mg2+-dependent phosphodiestera 100.0
TIGR03395283 sphingomy sphingomyelin phosphodiesterase. Members 99.97
PRK11756268 exonuclease III; Provisional 99.97
COG3568259 ElsH Metal-dependent hydrolase [General function p 99.96
PRK05421263 hypothetical protein; Provisional 99.95
COG0708261 XthA Exonuclease III [DNA replication, recombinati 99.95
PLN03144606 Carbon catabolite repressor protein 4 homolog; Pro 99.94
TIGR00195254 exoDNase_III exodeoxyribonuclease III. The model b 99.93
KOG3873 422 consensus Sphingomyelinase family protein [Signal 99.93
PRK13911250 exodeoxyribonuclease III; Provisional 99.93
PTZ00297 1452 pantothenate kinase; Provisional 99.92
TIGR00633255 xth exodeoxyribonuclease III (xth). This family is 99.92
PRK15251271 cytolethal distending toxin subunit CdtB; Provisio 99.81
smart00476276 DNaseIc deoxyribonuclease I. Deoxyribonuclease I c 99.81
KOG2338495 consensus Transcriptional effector CCR4-related pr 99.79
PF03372249 Exo_endo_phos: Endonuclease/Exonuclease/phosphatas 99.73
COG3021309 Uncharacterized protein conserved in bacteria [Fun 99.72
COG5239378 CCR4 mRNA deadenylase, exonuclease subunit and rel 99.62
COG2374798 Predicted extracellular nuclease [General function 99.57
KOG0620361 consensus Glucose-repressible alcohol dehydrogenas 99.5
smart00128310 IPPc Inositol polyphosphate phosphatase, catalytic 99.36
KOG0566 1080 consensus Inositol-1,4,5-triphosphate 5-phosphatas 99.03
PF0064130 zf-RanBP: Zn-finger in Ran binding protein and oth 98.56
COG5411 460 Phosphatidylinositol 5-phosphate phosphatase [Sign 98.53
KOG4198280 consensus RNA-binding Ran Zn-finger protein and re 98.45
KOG1294335 consensus Apurinic/apyrimidinic endonuclease and r 98.39
PF0064130 zf-RanBP: Zn-finger in Ran binding protein and oth 98.37
PF14529119 Exo_endo_phos_2: Endonuclease-reverse transcriptas 98.37
PLN03191621 Type I inositol-1,4,5-trisphosphate 5-phosphatase 98.25
smart0054726 ZnF_RBZ Zinc finger domain. Zinc finger domain in 98.1
smart0054726 ZnF_RBZ Zinc finger domain. Zinc finger domain in 97.82
KOG4198280 consensus RNA-binding Ran Zn-finger protein and re 97.05
KOG4345 774 consensus NF-kappa B regulator AP20/Cezanne [Signa 97.02
KOG4477228 consensus RING1 interactor RYBP and related Zn-fin 97.01
PF1277350 DZR: Double zinc ribbon 96.64
KOG4477228 consensus RING1 interactor RYBP and related Zn-fin 96.52
KOG4345 774 consensus NF-kappa B regulator AP20/Cezanne [Signa 96.14
PTZ00312 356 inositol-1,4,5-triphosphate 5-phosphatase; Provisi 96.0
PRK14559 645 putative protein serine/threonine phosphatase; Pro 95.42
KOG1976391 consensus Inositol polyphosphate 5-phosphatase, ty 94.87
PF1324826 zf-ribbon_3: zinc-ribbon domain 92.41
PF1324023 zinc_ribbon_2: zinc-ribbon domain 91.19
PF1324826 zf-ribbon_3: zinc-ribbon domain 88.67
KOG2760432 consensus Vacuolar sorting protein VPS36 [Intracel 87.52
cd0035033 rubredoxin_like Rubredoxin_like; nonheme iron bind 86.97
COG5100571 NPL4 Nuclear pore protein [Nuclear structure] 86.1
cd0035033 rubredoxin_like Rubredoxin_like; nonheme iron bind 83.68
COG5100571 NPL4 Nuclear pore protein [Nuclear structure] 83.03
KOG1995351 consensus Conserved Zn-finger protein [General fun 81.38
PF1324023 zinc_ribbon_2: zinc-ribbon domain 81.26
>KOG2756 consensus Predicted Mg2+-dependent phosphodiesterase TTRAP [Signal transduction mechanisms] Back     alignment and domain information 
Probab=100.00  E-value=5.2e-42  Score=307.21  Aligned_cols=312  Identities=25%  Similarity=0.303  Sum_probs=245.0

Q ss_pred             CCCCCCCC-CCccccccccccccCccccccCCCCCCCCCCCCCCCCcceecccccCCCCC-CCCCCCCCC--CCCCCCce
Q 012811          111 EDLTDPAL-DSELDSSVGSVFLPLQLKACTGKRKIRDQDCDGDFDGFRVTNSVSIKDDTT-SGPSADNSE--SGAVSGSL  186 (456)
Q Consensus       111 ~~~~d~~~-~~d~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~--~~~~~~~l  186 (456)
                      -++.+..| ..+.+.++|+.|.|++  +|-+..+   ++...      ++++....+.|. .......+-  .......+
T Consensus        32 fa~~~s~dea~aq~~l~~~dw~~~r--al~~~~~---se~~s------E~~~~~~~~~e~~t~s~~s~~~T~ed~~g~~~  100 (349)
T KOG2756|consen   32 FASVASCDAAVAQCFLAENDWEMER--ALNSYFE---PETIS------EPKTYVDLTNEETTDSTTSKISTSEDTQGSMF  100 (349)
T ss_pred             HHHhhhhHHHhHHHHhhcchhHHHH--HHHhhcC---ceeec------cchhhhhccccccccccccccCChhhhcccEE
Confidence            34444444 6788899999999998  4444322   11111      113333333321 111111111  11222468


Q ss_pred             EEEEEeccCCCCCChhhHHHHHHHHHhhCCCcEEEEeccCHhHHHHHHhCCCccceEEecCCCCCCCCCeEEEEEEeeec
Q 012811          187 KILSYNVWFREDLEMHPRMKTIGDLIQLHSPDIICFQEITPNIYDILCKSSWWKGYRCSVPNEMADSRGYFCMQLSKLQA  266 (456)
Q Consensus       187 rV~T~Nv~~~~~~~~~~r~~~i~~~I~~~~pDII~LQEv~~~~~~~L~~~~~~~~y~~~~~~~~~~~~~~g~ailSr~pi  266 (456)
                      .+++||+.++...+...|+.+++.+|+.++|||||||||.+.++.+|.+.  ...|.++.+ ..+...++.+++.||+.+
T Consensus       101 S~~~WnidgLdln~l~~RMrAv~H~i~l~sPdiiflQEV~p~~y~~~~K~--~s~y~i~~~-~~~~~~~~~~l~~s~~~V  177 (349)
T KOG2756|consen  101 SLITWNIDGLDLNNLSERMRAVCHYLALYSPDVIFLQEVIPPYYSYLKKR--SSNYEIITG-HEEGYFTAIMLKKSRVKV  177 (349)
T ss_pred             EEEEeeccccccchHHHHHHHHHHHHHhcCCCEEEEeecCchhhHHHHHh--hhheeEEEe-ccceeeeeeeeehhhcCc
Confidence            89999998887666789999999999999999999999999999999982  234444333 323334445666789999


Q ss_pred             ceeeEeeCCCCCCCCceEEEEEEeCCcceEEEEEeccCCCCCCCCccccccHHHHHHHHHHHHHHhhcCCCEEEEccCCC
Q 012811          267 KSFTCEPFRNSIMGRELCVAEVEVQGKKPLVVATSHLESPCPGPPTWDQMFSKERVEQAKEAINLLKKNPNVIFCGDMNW  346 (456)
Q Consensus       267 ~~~~~~~~~~~~~~R~~~~~~i~~~~g~~l~v~n~Hl~~~~~~~~~~~~~~~~~R~~Q~~~l~~~l~~~~pvIl~GDFN~  346 (456)
                      .+.+.++|+++.|+|.+.++++.++ |.++.+.++||.+.+++++.|++++. .|+.|++++++.+ .+..||++||+|.
T Consensus       178 ks~~~i~F~NS~M~R~L~I~Ev~v~-G~Kl~l~tsHLEStr~h~P~r~~qF~-~~~~k~~EaIe~l-PnA~ViFGGD~Nl  254 (349)
T KOG2756|consen  178 KSQEIIPFPNSKMMRNLLIVEVNVS-GNKLCLMTSHLESTRGHAPERMNQFK-MVLKKMQEAIESL-PNATVIFGGDTNL  254 (349)
T ss_pred             cccceeccCcchhhheeEEEEEeec-CceEEEEeccccCCCCCChHHHHHHH-HHHHHHHHHHHhC-CCceEEEcCcccc
Confidence            9999999999999999999999999 77899999999999999999988876 8999999999887 6788999999999


Q ss_pred             CCCCCCCcCCCCCccccccccc-CCCCCccccCCCCccccCCCccCCCccEEEEecCCCccceEEEeeccccCCchhhhh
Q 012811          347 DDKLDGKFPLPDGWVDAWTELR-PGENGWTYDTKSNKMLSGNRTLQKRLDRFICSLRDFKIIRIDMIGVEAIPGLLYVKE  425 (456)
Q Consensus       347 ~~~~~~~~~l~~gl~D~~~~~~-~~~~~~T~~~~~~~~~~~~~~~~~rID~I~~s~~~~~~~~~~~~g~d~~p~~~~~~~  425 (456)
                      .+.+...++++.+++|+|..++ |+..++||++..|+++.|++....|+|+||++..       ++.|....|.+.++++
T Consensus       255 rD~ev~r~~lPD~~vDvWE~lg~p~~~~FTwDT~~N~nl~G~~a~k~RfDRi~~r~~-------~~~G~~~~~~l~l~g~  327 (349)
T KOG2756|consen  255 RDREVTRCGLPDNIVDVWEFLGKPKHCQFTWDTQMNSNLGGTAACKLRFDRIFFRAA-------AEEGHIIPRSLDLLGL  327 (349)
T ss_pred             hhhhcccCCCCchHHHHHHHhCCCCcCceeeecccCcccchhHHHHHHHHHHhhhhh-------hhcCCcCccccchhhh
Confidence            9999999999999999999998 8899999999999999999899999999999842       5566667788888888


Q ss_pred             hhhhhhhhccCCCCCccCCcceeEEEE
Q 012811          426 KKVRKEMQKLELPVLPSDHYGLLLTIS  452 (456)
Q Consensus       426 ~~~~~~~~~~~~~~~~SDH~pV~~~~~  452 (456)
                      +++|.      ++++||||++|.++|.
T Consensus       328 ~kiRg------c~~fPSDHwgll~Tl~  348 (349)
T KOG2756|consen  328 EKLRG------CGRFPSDHWGLLCTLD  348 (349)
T ss_pred             hhhcc------CCCCCcccceeeeecc
Confidence            88775      6889999999999986

>TIGR03395 sphingomy sphingomyelin phosphodiesterase Back     alignment and domain information
>PRK11756 exonuclease III; Provisional Back     alignment and domain information
>COG3568 ElsH Metal-dependent hydrolase [General function prediction only] Back     alignment and domain information
>PRK05421 hypothetical protein; Provisional Back     alignment and domain information
>COG0708 XthA Exonuclease III [DNA replication, recombination, and repair] Back     alignment and domain information
>PLN03144 Carbon catabolite repressor protein 4 homolog; Provisional Back     alignment and domain information
>TIGR00195 exoDNase_III exodeoxyribonuclease III Back     alignment and domain information
>KOG3873 consensus Sphingomyelinase family protein [Signal transduction mechanisms] Back     alignment and domain information
>PRK13911 exodeoxyribonuclease III; Provisional Back     alignment and domain information
>PTZ00297 pantothenate kinase; Provisional Back     alignment and domain information
>TIGR00633 xth exodeoxyribonuclease III (xth) Back     alignment and domain information
>PRK15251 cytolethal distending toxin subunit CdtB; Provisional Back     alignment and domain information
>smart00476 DNaseIc deoxyribonuclease I Back     alignment and domain information
>KOG2338 consensus Transcriptional effector CCR4-related protein [Transcription] Back     alignment and domain information
>PF03372 Exo_endo_phos: Endonuclease/Exonuclease/phosphatase family Subset of Pfam family Subset of Pfam family; InterPro: IPR005135 This domain is found in a large number of proteins including magnesium dependent endonucleases and phosphatases involved in intracellular signalling [] Back     alignment and domain information
>COG3021 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>COG5239 CCR4 mRNA deadenylase, exonuclease subunit and related nucleases [RNA processing and modification] Back     alignment and domain information
>COG2374 Predicted extracellular nuclease [General function prediction only] Back     alignment and domain information
>KOG0620 consensus Glucose-repressible alcohol dehydrogenase transcriptional effector CCR4 and related proteins [Transcription] Back     alignment and domain information
>smart00128 IPPc Inositol polyphosphate phosphatase, catalytic domain homologues Back     alignment and domain information
>KOG0566 consensus Inositol-1,4,5-triphosphate 5-phosphatase (synaptojanin), INP51/INP52/INP53 family [Intracellular trafficking, secretion, and vesicular transport] Back     alignment and domain information
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule Back     alignment and domain information
>COG5411 Phosphatidylinositol 5-phosphate phosphatase [Signal transduction mechanisms] Back     alignment and domain information
>KOG4198 consensus RNA-binding Ran Zn-finger protein and related proteins [General function prediction only] Back     alignment and domain information
>KOG1294 consensus Apurinic/apyrimidinic endonuclease and related enzymes [Replication, recombination and repair] Back     alignment and domain information
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule Back     alignment and domain information
>PF14529 Exo_endo_phos_2: Endonuclease-reverse transcriptase ; PDB: 2EI9_A 1WDU_B Back     alignment and domain information
>PLN03191 Type I inositol-1,4,5-trisphosphate 5-phosphatase 2; Provisional Back     alignment and domain information
>smart00547 ZnF_RBZ Zinc finger domain Back     alignment and domain information
>smart00547 ZnF_RBZ Zinc finger domain Back     alignment and domain information
>KOG4198 consensus RNA-binding Ran Zn-finger protein and related proteins [General function prediction only] Back     alignment and domain information
>KOG4345 consensus NF-kappa B regulator AP20/Cezanne [Signal transduction mechanisms] Back     alignment and domain information
>KOG4477 consensus RING1 interactor RYBP and related Zn-finger-containing proteins [Transcription] Back     alignment and domain information
>PF12773 DZR: Double zinc ribbon Back     alignment and domain information
>KOG4477 consensus RING1 interactor RYBP and related Zn-finger-containing proteins [Transcription] Back     alignment and domain information
>KOG4345 consensus NF-kappa B regulator AP20/Cezanne [Signal transduction mechanisms] Back     alignment and domain information
>PTZ00312 inositol-1,4,5-triphosphate 5-phosphatase; Provisional Back     alignment and domain information
>PRK14559 putative protein serine/threonine phosphatase; Provisional Back     alignment and domain information
>KOG1976 consensus Inositol polyphosphate 5-phosphatase, type I [Lipid transport and metabolism] Back     alignment and domain information
>PF13248 zf-ribbon_3: zinc-ribbon domain Back     alignment and domain information
>PF13240 zinc_ribbon_2: zinc-ribbon domain Back     alignment and domain information
>PF13248 zf-ribbon_3: zinc-ribbon domain Back     alignment and domain information
>KOG2760 consensus Vacuolar sorting protein VPS36 [Intracellular trafficking, secretion, and vesicular transport] Back     alignment and domain information
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center Back     alignment and domain information
>COG5100 NPL4 Nuclear pore protein [Nuclear structure] Back     alignment and domain information
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center Back     alignment and domain information
>COG5100 NPL4 Nuclear pore protein [Nuclear structure] Back     alignment and domain information
>KOG1995 consensus Conserved Zn-finger protein [General function prediction only] Back     alignment and domain information
>PF13240 zinc_ribbon_2: zinc-ribbon domain 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 ?
Query456
4gz2_A255 Mus Musculus Tdp2 Excluded Ssdna Complex Length = 2 9e-18
4gyz_A256 Mus Musculus Tdp2 Bound To Damp And Mg2+ Length = 2 1e-17
4fpv_A257 Crystal Structure Of D. Rerio Tdp2 Complexed With S 2e-13
4f1h_A250 Crystal Structure Of Tdp2 From Danio Rerio Complexe 2e-13
4f1h_B251 Crystal Structure Of Tdp2 From Danio Rerio Complexe 2e-13
4fva_A256 Crystal Structure Of Truncated Caenorhabditis Elega 8e-07
4gew_A362 Crystal Structure Of Tdp2 From C. Elegans Length = 9e-07
4f1i_A362 Crystal Structure Of Semet Tdp2 From Caenorhabditis 8e-05
>pdb|4GZ2|A Chain A, Mus Musculus Tdp2 Excluded Ssdna Complex Length = 255 Back     alignment and structure 
Iteration: 1

 Score = 88.2 bits (217), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 80/280 (28%), Positives = 126/280 (45%), Gaps = 43/280 (15%)
Query: 183 SGSLKILSYNVWFREDLEMHPRMKTIGDLIQLHSPDIICFQEITPNIYDILCKSSWWKGY 242
           S ++  +++N+   +   +  R + +   + L+SPD++  QE+ P     L K +    Y
Sbjct: 7   SSTISFITWNIDGLDGCNLPERARGVCSCLALYSPDVVFLQEVIPPYCAYLKKRA--ASY 64
Query: 243 RCSVPNEMADSRGYFCMQL---SKLQAKSFTCEPFRNSIMGRELCVAEVEVQGKKPLVVA 299
                NE     GYF   L    +++ KS    PF N+ M R L    V + G +   + 
Sbjct: 65  TIITGNE----EGYFTAILLKKGRVKFKSQEIIPFPNTKMMRNLLCVNVSLGGNE-FCLM 119
Query: 300 TSHLESPCPGPPTWDQMFSKERVEQAKEAINLLKKNPN---VIFCGDMNWDDKLDGK-FP 355
           TSHLES         +  S ER+ Q K  +  +++ P+   VIF GD N  D+   K   
Sbjct: 120 TSHLES--------TREHSAERIRQLKTVLGKMQEAPDSTTVIFAGDTNLRDQEVIKCGG 171
Query: 356 LPDGWVDAWTEL-RPGENGWTYDTKSNKMLSGNRTLQKRLDRFICSLRDFKII--RIDMI 412
           LPD   DAW  L +P    +T+DTK+N  L      + R DR      +  +I   +D++
Sbjct: 172 LPDNVFDAWEFLGKPKHCQYTWDTKANNNLRIPAAYKHRFDRIFFRAEEGHLIPQSLDLV 231
Query: 413 GVEAIPGLLYVKEKKVRKEMQKLELPVLPSDHYGLLLTIS 452
           G+E                  KL+    PSDH+GLL T++
Sbjct: 232 GLE------------------KLDCGRFPSDHWGLLCTLN 253
>pdb|4GYZ|A Chain A, Mus Musculus Tdp2 Bound To Damp And Mg2+ Length = 256 Back     alignment and structure
>pdb|4FPV|A Chain A, Crystal Structure Of D. Rerio Tdp2 Complexed With Single Strand Dna Product Length = 257 Back     alignment and structure
>pdb|4F1H|A Chain A, Crystal Structure Of Tdp2 From Danio Rerio Complexed With A Single Strand Dna Length = 250 Back     alignment and structure
>pdb|4F1H|B Chain B, Crystal Structure Of Tdp2 From Danio Rerio Complexed With A Single Strand Dna Length = 251 Back     alignment and structure
>pdb|4FVA|A Chain A, Crystal Structure Of Truncated Caenorhabditis Elegans Tdp2 Length = 256 Back     alignment and structure
>pdb|4GEW|A Chain A, Crystal Structure Of Tdp2 From C. Elegans Length = 362 Back     alignment and structure
>pdb|4F1I|A Chain A, Crystal Structure Of Semet Tdp2 From Caenorhabditis Elegans Length = 362 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 ?
Query456
1zwx_A301 SMCL, sphingomyelinase-C; dnase1-like fold, beta-h 4e-28
2ddr_A306 Sphingomyelin phosphodiesterase; DNAse I like fold 4e-28
3i41_A317 Beta-hemolysin; beta toxin, sphingomyelinase, toxi 3e-23
3teb_A266 Endonuclease/exonuclease/phosphatase; PSI-biology, 3e-23
3mpr_A298 Putative endonuclease/exonuclease/phosphatase FAM 1e-17
3l1w_A257 Uncharacterized protein; APC29019.2, conserved pro 4e-17
3g6s_A267 Putative endonuclease/exonuclease/phosphatase fami 5e-16
3gj7_B98 Nuclear pore complex protein NUP153; G protein, GD 1e-09
1w7p_D566 VPS36P, YLR417W; ESCRT-II complex, endosomal prote 3e-09
1w7p_D566 VPS36P, YLR417W; ESCRT-II complex, endosomal prote 5e-04
3gj8_B92 Nuclear pore complex protein NUP153; G protein, GD 5e-09
2crc_A52 Ubiquitin conjugating enzyme 7 interacting protein 1e-05
2crc_A52 Ubiquitin conjugating enzyme 7 interacting protein 3e-04
1hd7_A318 DNA-(apurinic or apyrimidinic site) lyase; DNA rep 2e-05
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 6e-05
2o3h_A285 DNA-(apurinic or apyrimidinic site) lyase; APE, en 6e-05
2jc5_A259 Exodeoxyribonuclease; hydrolase, repair phosphodie 9e-05
1nj3_A31 NPL4; NZF domain, rubredoxin knuckle, beta-ribbon, 1e-04
1nj3_A31 NPL4; NZF domain, rubredoxin knuckle, beta-ribbon, 2e-04
3b08_B64 Ranbp-type and C3HC4-type zinc finger-containing; 2e-04
3b08_B64 Ranbp-type and C3HC4-type zinc finger-containing; 5e-04
3g91_A265 MTH0212, exodeoxyribonuclease; double-strand speci 5e-04
1jb7_A 495 Telomere-binding protein alpha subunit; DNA-protei 7e-04
>1zwx_A SMCL, sphingomyelinase-C; dnase1-like fold, beta-hairpin, hydrolase; 1.90A {Listeria ivanovii} SCOP: d.151.1.3 Length = 301 Back     alignment and structure
 Score =  112 bits (281), Expect = 4e-28
 Identities = 46/307 (14%), Positives = 85/307 (27%), Gaps = 48/307 (15%)

Query: 183 SGSLKILSYNVWFR-----EDLEMHPRMKTIGDLIQLHSPDIICFQEI-TPNIYDIL--- 233
            G+ KI S+NV+        +     R   I     + + D++   E    +    L   
Sbjct: 8   PGNFKITSHNVYLFSRNIYPNWGQMHRADLIAQADYMKNNDVVILNEAFDTSASHRLLNN 67

Query: 234 --------------CKSSWWKGYRCSVPNEMADSRGYFCMQLSKLQAKSFTCEPFRNS-- 277
                          K  W K         + D        +S+      +   F+    
Sbjct: 68  LREMYPHQTPVIGRSKHGWDKTEGNYSNFALEDGG---VAVVSQWPIVEKSQHIFQRGGG 124

Query: 278 ---IMGRELCVAEVEVQGKKPLVVATSHLESPCPGPPTWDQMFSKERVEQAKEAINLLK- 333
              +  +     ++   G KP  +  +H ++               R EQ +E    +  
Sbjct: 125 ADRLSNKGFAYVKIMKNG-KPYHIIGTHTQA--DDSLISKDTSRAIRAEQMQEIQTFIAK 181

Query: 334 ----KNPNVIFCGDMNWDDKLDGKFPLPDGWVDAWTELRPGENGWTYDTKSNKMLSGNRT 389
               K+  +   GD+N +   D    +     +  +         T+D  +N ML  +  
Sbjct: 182 KNIPKDEIIFIGGDLNVNYGTDEYHDMLKLL-NVSSPANFNGQMATWDPTTNSMLKESYP 240

Query: 390 LQ--KRLDRFICSLRDFKIIRIDMIGVEAIPGLLYVKEKKVRKEMQKLELPVLPSDHYGL 447
               + LD         +        +        VK        Q        SDHY +
Sbjct: 241 KAAPEYLDYIFVENGHARPHSWHNKVLHTKSPQWSVKSWFKTYTYQDF------SDHYPV 294

Query: 448 LLTISNN 454
           +    NN
Sbjct: 295 VGFTDNN 301
>2ddr_A Sphingomyelin phosphodiesterase; DNAse I like folding, riken structural genomics/proteomics initiative, RSGI, structural genomics, hydrolase; 1.40A {Bacillus cereus} SCOP: d.151.1.3 PDB: 2dds_A 2ddt_A* 2uyr_X Length = 306 Back     alignment and structure
>3i41_A Beta-hemolysin; beta toxin, sphingomyelinase, toxin; 1.75A {Staphylococcus aureus} PDB: 3i46_A 3i48_A 3i5v_A* 3k55_A Length = 317 Back     alignment and structure
>3teb_A Endonuclease/exonuclease/phosphatase; PSI-biology, MCSG, midwest center for structural genomics; 2.99A {Leptotrichia buccalis c-1013-b} Length = 266 Back     alignment and structure
>3mpr_A Putative endonuclease/exonuclease/phosphatase FAM protein; structural genomics, PSI-2, protein structure initiative; HET: MSE PEG; 1.90A {Bacteroides thetaiotaomicron} Length = 298 Back     alignment and structure
>3l1w_A Uncharacterized protein; APC29019.2, conserved protein, enterococcus faecalis V583, PSI-2, MCSG, structural genomics; 1.60A {Enterococcus faecalis} Length = 257 Back     alignment and structure
>3g6s_A Putative endonuclease/exonuclease/phosphatase family protein; alpha-beta protein, structural genomics, PSI-2; 2.50A {Bacteroides vulgatus atcc 8482} Length = 267 Back     alignment and structure
>3gj7_B Nuclear pore complex protein NUP153; G protein, GDP, RAN, zinc finger, acetylation, cytoplasm, GTP-binding, HOST-virus interaction; HET: GDP; 1.93A {Rattus norvegicus} PDB: 2k0c_A 3ch5_B* 3gj6_B* Length = 98 Back     alignment and structure
>1w7p_D VPS36P, YLR417W; ESCRT-II complex, endosomal protein sorting, protein transpo; 3.60A {Saccharomyces cerevisiae} SCOP: a.4.5.54 a.4.5.54 Length = 566 Back     alignment and structure
>1w7p_D VPS36P, YLR417W; ESCRT-II complex, endosomal protein sorting, protein transpo; 3.60A {Saccharomyces cerevisiae} SCOP: a.4.5.54 a.4.5.54 Length = 566 Back     alignment and structure
>3gj8_B Nuclear pore complex protein NUP153; G protein, GDP, RAN, zinc finger, acetylation, cytoplasm, GTP-binding, HOST-virus interaction; HET: GDP; 1.82A {Rattus norvegicus} PDB: 3gj4_B* Length = 92 Back     alignment and structure
>2crc_A Ubiquitin conjugating enzyme 7 interacting protein 3; ZF-ranbp domain, hepatitis B virus X-associated protein 4, HBV associated factor 4; NMR {Homo sapiens} Length = 52 Back     alignment and structure
>2crc_A Ubiquitin conjugating enzyme 7 interacting protein 3; ZF-ranbp domain, hepatitis B virus X-associated protein 4, HBV associated factor 4; NMR {Homo sapiens} Length = 52 Back     alignment and structure
>1hd7_A DNA-(apurinic or apyrimidinic site) lyase; DNA repair, endonuclease, APE1, HAP1, REF-1; 1.95A {Homo sapiens} SCOP: d.151.1.1 PDB: 1e9n_A 3u8u_A 2isi_A Length = 318 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
>2o3h_A DNA-(apurinic or apyrimidinic site) lyase; APE, endonuclease; 1.90A {Homo sapiens} PDB: 1bix_A 1dew_A* 1de8_B* 1de9_A* 2o3c_A Length = 285 Back     alignment and structure
>2jc5_A Exodeoxyribonuclease; hydrolase, repair phosphodiesterase, DNA repair, exonuclease, endonuclease; HET: BCN DIO GOL; 1.50A {Neisseria meningitidis} Length = 259 Back     alignment and structure
>1nj3_A NPL4; NZF domain, rubredoxin knuckle, beta-ribbon, zinc- finger, ubiquitin, protein binding; NMR {Rattus norvegicus} SCOP: g.41.11.1 PDB: 1q5w_A Length = 31 Back     alignment and structure
>1nj3_A NPL4; NZF domain, rubredoxin knuckle, beta-ribbon, zinc- finger, ubiquitin, protein binding; NMR {Rattus norvegicus} SCOP: g.41.11.1 PDB: 1q5w_A Length = 31 Back     alignment and structure
>3b08_B Ranbp-type and C3HC4-type zinc finger-containing; protein complex, signaling protein-metal binding protein COM; HET: TRE; 1.70A {Mus musculus} PDB: 3b0a_B* Length = 64 Back     alignment and structure
>3b08_B Ranbp-type and C3HC4-type zinc finger-containing; protein complex, signaling protein-metal binding protein COM; HET: TRE; 1.70A {Mus musculus} PDB: 3b0a_B* Length = 64 Back     alignment and structure
>3g91_A MTH0212, exodeoxyribonuclease; double-strand specific 3'-5' exonuclease, AP endonuclease; HET: PG4; 1.23A {Methanothermobacter thermautotrophicusorganism_taxid} PDB: 3fzi_A 3g0a_A 3g1k_A 3g2c_A 3g3c_A* 3g3y_A* 3g4t_A* 3g00_A 3g0r_A* 3g2d_A* 3g38_A 3g8v_A* 3ga6_A Length = 265 Back     alignment and structure
>1jb7_A Telomere-binding protein alpha subunit; DNA-protein interactions, DNA HYDR sodium ION, quadruplex DNA, DNA-binding protein-DNA complex; 1.86A {Sterkiella nova} SCOP: b.40.4.3 b.40.4.3 b.40.4.3 PDB: 1kix_A 1otc_A* 2i0q_A 1ph6_A 1ph1_A 1phj_A* 1ph3_A 1pa6_A 1ph4_A 1ph7_A 1ph8_A 1ph9_A 1ph5_A* 1ph2_A* 1k8g_A Length = 495 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query456
4gew_A362 5'-tyrosyl-DNA phosphodiesterase; 5'-phosphotyrosy 100.0
4fva_A256 5'-tyrosyl-DNA phosphodiesterase; 5'-phosphotyrosy 100.0
4gz1_A256 Tyrosyl-DNA phosphodiesterase 2; protein-DNA compl 100.0
4f1h_A250 Tyrosyl-DNA phosphodiesterase 2; hydrolase-DNA com 100.0
3l1w_A257 Uncharacterized protein; APC29019.2, conserved pro 100.0
3teb_A266 Endonuclease/exonuclease/phosphatase; PSI-biology, 99.98
3g6s_A267 Putative endonuclease/exonuclease/phosphatase fami 99.97
3mpr_A298 Putative endonuclease/exonuclease/phosphatase FAM 99.97
1zwx_A301 SMCL, sphingomyelinase-C; dnase1-like fold, beta-h 99.96
3i41_A317 Beta-hemolysin; beta toxin, sphingomyelinase, toxi 99.96
1ako_A268 Exonuclease III; AP-endonuclease, DNA repair; 1.70 99.95
2jc4_A256 Exodeoxyribonuclease III; hydrolase, repair phosph 99.95
2ddr_A306 Sphingomyelin phosphodiesterase; DNAse I like fold 99.95
1hd7_A318 DNA-(apurinic or apyrimidinic site) lyase; DNA rep 99.95
2j63_A467 AP-endonuclease; base excision repair, lyase; 2.48 99.94
2jc5_A259 Exodeoxyribonuclease; hydrolase, repair phosphodie 99.94
2o3h_A285 DNA-(apurinic or apyrimidinic site) lyase; APE, en 99.94
1vyb_A238 ORF2 contains A reverse transcriptase domain; endo 99.94
2voa_A257 AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP 99.94
3ngq_A398 CCR4-NOT transcription complex subunit 6-like; alp 99.94
3g91_A265 MTH0212, exodeoxyribonuclease; double-strand speci 99.93
1wdu_A245 TRAS1 ORF2P; four-layered alpha/beta sandwich, RNA 99.91
4b8c_D727 Glucose-repressible alcohol dehydrogenase transcr 99.9
2ei9_A240 Non-LTR retrotransposon R1BMKS ORF2 protein; four 99.87
2a40_B260 Deoxyribonuclease-1; WAVE, WH2, WAsp, actin, DNAse 99.86
2f1n_A262 CDT B, cytolethal distending toxin subunit B; E.co 99.86
1sr4_B261 CDT B, cytolethal distending toxin protein B; bact 99.85
2imq_X282 Salivary nitrophorin; ferrous heme, beta-sandwich, 99.78
1i9z_A347 Synaptojanin, phosphatidylinositol phosphate phosp 99.73
2xsw_A357 72 kDa inositol polyphosphate 5-phosphatase; inosi 99.58
3mtc_A313 Type II inositol-1,4,5-trisphosphate 5-phosphatas; 99.45
3gj7_B98 Nuclear pore complex protein NUP153; G protein, GD 99.44
4a9c_A316 Phosphatidylinositol-3,4,5-trisphosphate 5-phosph; 99.3
3gj8_B92 Nuclear pore complex protein NUP153; G protein, GD 99.25
1w7p_D566 VPS36P, YLR417W; ESCRT-II complex, endosomal prote 99.01
3a9j_C34 Mitogen-activated protein kinase kinase kinase 7- 98.8
2crc_A52 Ubiquitin conjugating enzyme 7 interacting protein 98.79
1nj3_A31 NPL4; NZF domain, rubredoxin knuckle, beta-ribbon, 98.78
2d9g_A53 YY1-associated factor 2; ZF-ranbp domain, structur 98.73
3gj3_B33 Nuclear pore complex protein NUP153; G protein, GD 98.71
3gj3_B33 Nuclear pore complex protein NUP153; G protein, GD 98.55
3b08_B64 Ranbp-type and C3HC4-type zinc finger-containing; 98.5
1nj3_A31 NPL4; NZF domain, rubredoxin knuckle, beta-ribbon, 98.47
3a9j_C34 Mitogen-activated protein kinase kinase kinase 7- 98.44
2d9g_A53 YY1-associated factor 2; ZF-ranbp domain, structur 98.41
2crc_A52 Ubiquitin conjugating enzyme 7 interacting protein 98.32
3gj5_B34 Nuclear pore complex protein NUP153; G protein, GD 98.24
2ebq_A47 Nuclear pore complex protein NUP153; ZF-ranbp doma 98.11
3gj5_B34 Nuclear pore complex protein NUP153; G protein, GD 98.07
2ebq_A47 Nuclear pore complex protein NUP153; ZF-ranbp doma 97.99
3b08_B64 Ranbp-type and C3HC4-type zinc finger-containing; 97.97
2ebr_A47 Nuclear pore complex protein NUP153; ZF-ranbp doma 97.96
2ebr_A47 Nuclear pore complex protein NUP153; ZF-ranbp doma 97.92
2ebv_A57 Nuclear pore complex protein NUP153; ZF-ranbp doma 97.66
2lk0_A32 RNA-binding protein 5; zinc finger; NMR {Homo sapi 97.65
2k1p_A33 Zinc finger RAN-binding domain-containing protein 97.61
2ebv_A57 Nuclear pore complex protein NUP153; ZF-ranbp doma 97.58
2k1p_A33 Zinc finger RAN-binding domain-containing protein 97.48
3gj7_B98 Nuclear pore complex protein NUP153; G protein, GD 97.41
2lk0_A32 RNA-binding protein 5; zinc finger; NMR {Homo sapi 97.33
1n0z_A45 ZNF265; zinc finger, RNA splicing, transcription; 97.18
3gj8_B92 Nuclear pore complex protein NUP153; G protein, GD 96.92
1n0z_A45 ZNF265; zinc finger, RNA splicing, transcription; 96.85
2j9u_B76 VPS36, vacuolar protein sorting-associated protein 95.93
1w7p_D566 VPS36P, YLR417W; ESCRT-II complex, endosomal prote 94.7
2cr8_A53 MDM4 protein; ZF-ranbp domain, P53-binding protein 93.25
2j9u_B76 VPS36, vacuolar protein sorting-associated protein 92.37
2c6a_A46 Ubiquitin-protein ligase E3 MDM2; zinc finger, hum 88.81
2cr8_A53 MDM4 protein; ZF-ranbp domain, P53-binding protein 82.99
1weo_A93 Cellulose synthase, catalytic subunit (IRX3); stru 82.38
>4gew_A 5'-tyrosyl-DNA phosphodiesterase; 5'-phosphotyrosyl-DNA diesterase, hydrolase; 2.35A {Caenorhabditis elegans} PDB: 4f1i_A Back     alignment and structure
Probab=100.00  E-value=2.7e-36  Score=300.19  Aligned_cols=240  Identities=23%  Similarity=0.318  Sum_probs=187.5

Q ss_pred             CCCCCCceEEEEEeccCCCCCChhhHHHHHHHHHhhCCCcEEEEeccCHhHHHHHHhCCCccceEEecCCCCCCCCCeEE
Q 012811          179 SGAVSGSLKILSYNVWFREDLEMHPRMKTIGDLIQLHSPDIICFQEITPNIYDILCKSSWWKGYRCSVPNEMADSRGYFC  258 (456)
Q Consensus       179 ~~~~~~~lrV~T~Nv~~~~~~~~~~r~~~i~~~I~~~~pDII~LQEv~~~~~~~L~~~~~~~~y~~~~~~~~~~~~~~g~  258 (456)
                      ...+...||||||||+++....+..|+.+|+++|+.++|||||||||.......|.+.+  .+|.+....   ...++|+
T Consensus       113 ~~~~~~~lkVlSWNI~Gl~~~~~~~R~~~I~~~I~~~~PDIV~LQEv~~~~~~~l~~~~--~~y~~~~~~---~~~~~G~  187 (362)
T 4gew_A          113 EDLKGFEVSVMSWNIDGLDGRSLLTRMKAVAHIVKNVNPDILFLQEVVDRDLAPIDKLQ--SLYKIYYSN---KGCQYYT  187 (362)
T ss_dssp             CTTTTCEEEEEEEECCTTCCTTHHHHHHHHHHHHHHHCCSEEEEEEECSTTCHHHHGGG--GTEEEEESS---TTSSSEE
T ss_pred             CCCCCCeEEEEEEEeCCCCCcCHHHHHHHHHHHHHHcCCCEEEEEcCChhHhHHHHHhc--CCceEEeCC---CCCCceE
Confidence            34445689999999999877778899999999999999999999999877777777653  345544432   2456899


Q ss_pred             EEEEeeecc--eeeEeeCCCCCCCCceEEEEEEeCCcceEEEEEeccCCCCCCCCccccccHHHHHHHHHHHHHHhhc--
Q 012811          259 MQLSKLQAK--SFTCEPFRNSIMGRELCVAEVEVQGKKPLVVATSHLESPCPGPPTWDQMFSKERVEQAKEAINLLKK--  334 (456)
Q Consensus       259 ailSr~pi~--~~~~~~~~~~~~~R~~~~~~i~~~~g~~l~v~n~Hl~~~~~~~~~~~~~~~~~R~~Q~~~l~~~l~~--  334 (456)
                      +||+|.|+.  ....+.++....+|.++.+.+.++ |..|.|+|+||++...        ....|..|+..+...+..  
T Consensus       188 aIlsk~~i~~~~~~~~~~~~~~~~r~~l~~~i~~~-g~~l~v~ntHL~s~~~--------~~~~R~~Q~~~l~~~~~~~~  258 (362)
T 4gew_A          188 AILVSKMFDVEKHDVIHFQNSGMYRTLQILEGSIG-GLKVFLLNTHLESTRE--------HRPQRCAQFGFCMDKVREII  258 (362)
T ss_dssp             EEEEETTEEEEEEEEEECTTCSSCCEEEEEEEEET-TEEEEEEEEECCCSGG--------GHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEeccCccccccccCCCCCcccceEEEEEEEEC-CEEEEEEEecCCcccc--------chhHHHHHHHHHHHHhHhhh
Confidence            999996654  444556666667788999999998 7899999999998732        356788888887776542  


Q ss_pred             ----CCCEEEEccCCCCCCCCCCcCCCCCccccccccc-CCCCCccccCCCCccccCCCccCCCccEEEEecCCCccceE
Q 012811          335 ----NPNVIFCGDMNWDDKLDGKFPLPDGWVDAWTELR-PGENGWTYDTKSNKMLSGNRTLQKRLDRFICSLRDFKIIRI  409 (456)
Q Consensus       335 ----~~pvIl~GDFN~~~~~~~~~~l~~gl~D~~~~~~-~~~~~~T~~~~~~~~~~~~~~~~~rID~I~~s~~~~~~~~~  409 (456)
                          +.|+|||||||..+.+..  ....+|.|+|+.++ +.+.+|||+...+........+..||||||+++ .+++..+
T Consensus       259 ~~~~~~pvIl~GDFN~~p~~~~--~~~~gl~Da~~~~~~~~~~~~Tw~~~~n~~~~~~~~~~~RIDyIf~s~-~l~~~~~  335 (362)
T 4gew_A          259 AQNPGALVFFGGDLNLRDEEVS--RVPDGVKDAWEAAGSDNKTKFTWDTFKNDNKQGFHGAKMRFDRLYWSG-PLDKVKF  335 (362)
T ss_dssp             HHCTTCEEEEEEECCCCGGGCC--CCCTTCEEHHHHTTCCGGGCCSEETTTCTTSCCSSCCEECCEEEEEES-SCCEEEE
T ss_pred             hcCCCCCeEEeecCCCCCcccc--hhcchHHHHHHHhCCCCCCCcCcccccCcccccCCCCCcceEEEEEcC-CcceeEE
Confidence                578999999998876543  34578999999886 456789998887766555556678999999995 6888888


Q ss_pred             EEeeccccCCchhhhhhhhhhhhhccCCCCCccCCcceeEEEE
Q 012811          410 DMIGVEAIPGLLYVKEKKVRKEMQKLELPVLPSDHYGLLLTIS  452 (456)
Q Consensus       410 ~~~g~d~~p~~~~~~~~~~~~~~~~~~~~~~~SDH~pV~~~~~  452 (456)
                      .+++.+.++.                 .+.++|||+||+++|+
T Consensus       336 ~vi~~~ri~~-----------------~~~~pSDH~pV~A~FS  361 (362)
T 4gew_A          336 TLEGRQRIRS-----------------CLCFPSDHWAINATFF  361 (362)
T ss_dssp             EEECCSCCTT-----------------TSSCSCSSCEEEEEEE
T ss_pred             EEEeeeecCC-----------------CCCCCCcccCEEEEEc
Confidence            8887766542                 2457999999999997
>4fva_A 5'-tyrosyl-DNA phosphodiesterase; 5'-phosphotyrosyl-DNA diesterase, hydrolase; HET: EDO; 2.07A {Caenorhabditis elegans} Back     alignment and structure
>4gz1_A Tyrosyl-DNA phosphodiesterase 2; protein-DNA complex, DNA repair, 5'-DNA END processing, endonuclease/exonuclease/phosphatase domain; HET: DNA EPE; 1.50A {Mus musculus} PDB: 4gyz_A* 4gz0_A* 4gz2_A* Back     alignment and structure
>4f1h_A Tyrosyl-DNA phosphodiesterase 2; hydrolase-DNA complex; HET: DNA; 1.66A {Danio rerio} PDB: 4fpv_A* 4f1h_B* Back     alignment and structure
>3l1w_A Uncharacterized protein; APC29019.2, conserved protein, enterococcus faecalis V583, PSI-2, MCSG, structural genomics; 1.60A {Enterococcus faecalis} Back     alignment and structure
>3teb_A Endonuclease/exonuclease/phosphatase; PSI-biology, MCSG, midwest center for structural genomics; 2.99A {Leptotrichia buccalis c-1013-b} Back     alignment and structure
>3g6s_A Putative endonuclease/exonuclease/phosphatase family protein; alpha-beta protein, structural genomics, PSI-2; 2.50A {Bacteroides vulgatus atcc 8482} Back     alignment and structure
>3mpr_A Putative endonuclease/exonuclease/phosphatase FAM protein; structural genomics, PSI-2, protein structure initiative; HET: MSE PEG; 1.90A {Bacteroides thetaiotaomicron} Back     alignment and structure
>1zwx_A SMCL, sphingomyelinase-C; dnase1-like fold, beta-hairpin, hydrolase; 1.90A {Listeria ivanovii} SCOP: d.151.1.3 Back     alignment and structure
>3i41_A Beta-hemolysin; beta toxin, sphingomyelinase, toxin; 1.75A {Staphylococcus aureus} PDB: 3i46_A 3i48_A 3i5v_A* 3k55_A Back     alignment and structure
>1ako_A Exonuclease III; AP-endonuclease, DNA repair; 1.70A {Escherichia coli} SCOP: d.151.1.1 Back     alignment and structure
>2jc4_A Exodeoxyribonuclease III; hydrolase, repair phosphodiesterase, DNA repair, exonuclease, endonuclease; HET: 1PE; 1.90A {Neisseria meningitidis} Back     alignment and structure
>2ddr_A Sphingomyelin phosphodiesterase; DNAse I like folding, riken structural genomics/proteomics initiative, RSGI, structural genomics, hydrolase; 1.40A {Bacillus cereus} SCOP: d.151.1.3 PDB: 2dds_A 2ddt_A* 2uyr_X Back     alignment and structure
>1hd7_A DNA-(apurinic or apyrimidinic site) lyase; DNA repair, endonuclease, APE1, HAP1, REF-1; 1.95A {Homo sapiens} SCOP: d.151.1.1 PDB: 1e9n_A 3u8u_A 2isi_A Back     alignment and structure
>2j63_A AP-endonuclease; base excision repair, lyase; 2.48A {Leishmania major} Back     alignment and structure
>2jc5_A Exodeoxyribonuclease; hydrolase, repair phosphodiesterase, DNA repair, exonuclease, endonuclease; HET: BCN DIO GOL; 1.50A {Neisseria meningitidis} Back     alignment and structure
>2o3h_A DNA-(apurinic or apyrimidinic site) lyase; APE, endonuclease; 1.90A {Homo sapiens} PDB: 1bix_A 1dew_A* 1de8_B* 1de9_A* 2o3c_A Back     alignment and structure
>1vyb_A ORF2 contains A reverse transcriptase domain; endonuclease, APE-1 type, retrotransposition, retrotransposon, transferase; 1.8A {Homo sapiens} SCOP: d.151.1.1 PDB: 2v0s_A 2v0r_A Back     alignment and structure
>2voa_A AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP endonuclease, lyase; 1.7A {Archaeoglobus fulgidus} Back     alignment and structure
>3ngq_A CCR4-NOT transcription complex subunit 6-like; alpha/beta sandwich fold, hydrolase; HET: 1PS; 1.80A {Homo sapiens} PDB: 3ngo_A 3ngn_A Back     alignment and structure
>3g91_A MTH0212, exodeoxyribonuclease; double-strand specific 3'-5' exonuclease, AP endonuclease; HET: PG4; 1.23A {Methanothermobacter thermautotrophicusorganism_taxid} PDB: 3fzi_A 3g0a_A 3g1k_A 3g2c_A 3g3c_A* 3g3y_A* 3g4t_A* 3g00_A 3g0r_A* 3g2d_A* 3g38_A 3g8v_A* 3ga6_A Back     alignment and structure
>1wdu_A TRAS1 ORF2P; four-layered alpha/beta sandwich, RNA binding protein; 2.40A {Bombyx mori} SCOP: d.151.1.1 Back     alignment and structure
>4b8c_D Glucose-repressible alcohol dehydrogenase transcr effector; hydrolase-cell cycle complex; 3.41A {Saccharomyces cerevisiae S288C} Back     alignment and structure
>2ei9_A Non-LTR retrotransposon R1BMKS ORF2 protein; four layered alpha beta sandwich, gene regulation; 2.00A {Bombyx mori} Back     alignment and structure
>2a40_B Deoxyribonuclease-1; WAVE, WH2, WAsp, actin, DNAse I, ARP2/3, structural protein; HET: HIC NAG ATP; 1.80A {Bos taurus} SCOP: d.151.1.1 PDB: 1dnk_A* 2a3z_B* 2a41_B* 2a42_B* 2d1k_B* 2dnj_A* 3cjc_D* 3dni_A* 1atn_D* Back     alignment and structure
>2f1n_A CDT B, cytolethal distending toxin subunit B; E.coli, DNAse I, microbatch; 1.73A {Escherichia coli} SCOP: d.151.1.1 Back     alignment and structure
>1sr4_B CDT B, cytolethal distending toxin protein B; bacterial, virulence, DNA damage, genotoxin, cytotoxins, cell cycle, apoptosis, lectin; 2.00A {Haemophilus ducreyi} SCOP: d.151.1.1 PDB: 2f2f_B Back     alignment and structure
>2imq_X Salivary nitrophorin; ferrous heme, beta-sandwich, transport protein; HET: HEM; 1.30A {Cimex lectularius} SCOP: d.151.1.2 PDB: 1ntf_A* 1y21_A* 1yjh_A* 1si6_X* Back     alignment and structure
>1i9z_A Synaptojanin, phosphatidylinositol phosphate phosphatase; spsynaptojanin, IPP5C, IP3, IP2,, hydrolase; HET: 2IP; 1.80A {Schizosaccharomyces pombe} SCOP: d.151.1.2 PDB: 1i9y_A* Back     alignment and structure
>2xsw_A 72 kDa inositol polyphosphate 5-phosphatase; inositol signalling, SGC stockholm, structural genomics CONS hydrolase; 1.90A {Homo sapiens} Back     alignment and structure
>3mtc_A Type II inositol-1,4,5-trisphosphate 5-phosphatas; INPP5BA,phosphoinositide 5-phosphatase, inositol signalling, phosphatase, magnesium; HET: PIF; 2.40A {Homo sapiens} PDB: 3n9v_A Back     alignment and structure
>3gj7_B Nuclear pore complex protein NUP153; G protein, GDP, RAN, zinc finger, acetylation, cytoplasm, GTP-binding, HOST-virus interaction; HET: GDP; 1.93A {Rattus norvegicus} PDB: 2k0c_A 3ch5_B* 3gj6_B* Back     alignment and structure
>4a9c_A Phosphatidylinositol-3,4,5-trisphosphate 5-phosph; SGC, signalling, structural genomics consortium stockholm, magnesium binding, hydrolase; HET: B5F; 2.10A {Homo sapiens} PDB: 3nr8_B* Back     alignment and structure
>3gj8_B Nuclear pore complex protein NUP153; G protein, GDP, RAN, zinc finger, acetylation, cytoplasm, GTP-binding, HOST-virus interaction; HET: GDP; 1.82A {Rattus norvegicus} PDB: 3gj4_B* Back     alignment and structure
>1w7p_D VPS36P, YLR417W; ESCRT-II complex, endosomal protein sorting, protein transpo; 3.60A {Saccharomyces cerevisiae} SCOP: a.4.5.54 a.4.5.54 Back     alignment and structure
>3a9j_C Mitogen-activated protein kinase kinase kinase 7- interacting protein 2; protein complex, cytoplasm, isopeptide bond, metal-binding, zinc; 1.18A {Mus musculus} PDB: 2wwz_C 2wx0_C 2wx1_C 3a9k_C Back     alignment and structure
>2crc_A Ubiquitin conjugating enzyme 7 interacting protein 3; ZF-ranbp domain, hepatitis B virus X-associated protein 4, HBV associated factor 4; NMR {Homo sapiens} Back     alignment and structure
>1nj3_A NPL4; NZF domain, rubredoxin knuckle, beta-ribbon, zinc- finger, ubiquitin, protein binding; NMR {Rattus norvegicus} SCOP: g.41.11.1 PDB: 1q5w_A Back     alignment and structure
>2d9g_A YY1-associated factor 2; ZF-ranbp domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>3gj3_B Nuclear pore complex protein NUP153; G protein, GDP, RAN, zinc finger, acetylation, cytoplasm, GTP-binding, HOST-virus interaction; HET: GDP; 1.79A {Rattus norvegicus} SCOP: g.41.11.1 PDB: 2gqe_A Back     alignment and structure
>3gj3_B Nuclear pore complex protein NUP153; G protein, GDP, RAN, zinc finger, acetylation, cytoplasm, GTP-binding, HOST-virus interaction; HET: GDP; 1.79A {Rattus norvegicus} SCOP: g.41.11.1 PDB: 2gqe_A Back     alignment and structure
>3b08_B Ranbp-type and C3HC4-type zinc finger-containing; protein complex, signaling protein-metal binding protein COM; HET: TRE; 1.70A {Mus musculus} PDB: 3b0a_B* Back     alignment and structure
>1nj3_A NPL4; NZF domain, rubredoxin knuckle, beta-ribbon, zinc- finger, ubiquitin, protein binding; NMR {Rattus norvegicus} SCOP: g.41.11.1 PDB: 1q5w_A Back     alignment and structure
>3a9j_C Mitogen-activated protein kinase kinase kinase 7- interacting protein 2; protein complex, cytoplasm, isopeptide bond, metal-binding, zinc; 1.18A {Mus musculus} PDB: 2wwz_C 2wx0_C 2wx1_C 3a9k_C Back     alignment and structure
>2d9g_A YY1-associated factor 2; ZF-ranbp domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2crc_A Ubiquitin conjugating enzyme 7 interacting protein 3; ZF-ranbp domain, hepatitis B virus X-associated protein 4, HBV associated factor 4; NMR {Homo sapiens} Back     alignment and structure
>3gj5_B Nuclear pore complex protein NUP153; G protein, GDP, RAN, zinc finger, acetylation, cytoplasm, GTP-binding, HOST-virus interaction; HET: GDP; 1.79A {Rattus norvegicus} SCOP: g.41.11.1 Back     alignment and structure
>2ebq_A Nuclear pore complex protein NUP153; ZF-ranbp domain, nucleoporin NUP153, 153 kDa nucleoporin, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>3gj5_B Nuclear pore complex protein NUP153; G protein, GDP, RAN, zinc finger, acetylation, cytoplasm, GTP-binding, HOST-virus interaction; HET: GDP; 1.79A {Rattus norvegicus} SCOP: g.41.11.1 Back     alignment and structure
>2ebq_A Nuclear pore complex protein NUP153; ZF-ranbp domain, nucleoporin NUP153, 153 kDa nucleoporin, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>3b08_B Ranbp-type and C3HC4-type zinc finger-containing; protein complex, signaling protein-metal binding protein COM; HET: TRE; 1.70A {Mus musculus} PDB: 3b0a_B* Back     alignment and structure
>2ebr_A Nuclear pore complex protein NUP153; ZF-ranbp domain, nucleoporin NUP153, 153 kDa nucleoporin, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2ebr_A Nuclear pore complex protein NUP153; ZF-ranbp domain, nucleoporin NUP153, 153 kDa nucleoporin, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2ebv_A Nuclear pore complex protein NUP153; ZF-ranbp domain, nucleoporin NUP153, 153 kDa nucleoporin, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2lk0_A RNA-binding protein 5; zinc finger; NMR {Homo sapiens} PDB: 2lk1_A* Back     alignment and structure
>2k1p_A Zinc finger RAN-binding domain-containing protein 2; ZNF265, RNA binding, ranbp2, RBZ, ZIS, alternative splicing, metal-binding, mRNA processing; NMR {Homo sapiens} PDB: 3g9y_A Back     alignment and structure
>2ebv_A Nuclear pore complex protein NUP153; ZF-ranbp domain, nucleoporin NUP153, 153 kDa nucleoporin, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2k1p_A Zinc finger RAN-binding domain-containing protein 2; ZNF265, RNA binding, ranbp2, RBZ, ZIS, alternative splicing, metal-binding, mRNA processing; NMR {Homo sapiens} PDB: 3g9y_A Back     alignment and structure
>3gj7_B Nuclear pore complex protein NUP153; G protein, GDP, RAN, zinc finger, acetylation, cytoplasm, GTP-binding, HOST-virus interaction; HET: GDP; 1.93A {Rattus norvegicus} PDB: 2k0c_A 3ch5_B* 3gj6_B* Back     alignment and structure
>2lk0_A RNA-binding protein 5; zinc finger; NMR {Homo sapiens} PDB: 2lk1_A* Back     alignment and structure
>1n0z_A ZNF265; zinc finger, RNA splicing, transcription; NMR {Homo sapiens} SCOP: g.41.11.1 Back     alignment and structure
>3gj8_B Nuclear pore complex protein NUP153; G protein, GDP, RAN, zinc finger, acetylation, cytoplasm, GTP-binding, HOST-virus interaction; HET: GDP; 1.82A {Rattus norvegicus} PDB: 3gj4_B* Back     alignment and structure
>1n0z_A ZNF265; zinc finger, RNA splicing, transcription; NMR {Homo sapiens} SCOP: g.41.11.1 Back     alignment and structure
>2j9u_B VPS36, vacuolar protein sorting-associated protein 36; zinc-finger, metal-binding, protein transport; 2.00A {Saccharomyces cerevisiae} SCOP: g.41.11.1 Back     alignment and structure
>1w7p_D VPS36P, YLR417W; ESCRT-II complex, endosomal protein sorting, protein transpo; 3.60A {Saccharomyces cerevisiae} SCOP: a.4.5.54 a.4.5.54 Back     alignment and structure
>2cr8_A MDM4 protein; ZF-ranbp domain, P53-binding protein MDM4, MDM2-like P53-binding DE protein, MDMX protein, double minute 4 protein; NMR {Homo sapiens} SCOP: g.41.11.1 Back     alignment and structure
>2j9u_B VPS36, vacuolar protein sorting-associated protein 36; zinc-finger, metal-binding, protein transport; 2.00A {Saccharomyces cerevisiae} SCOP: g.41.11.1 Back     alignment and structure
>2c6a_A Ubiquitin-protein ligase E3 MDM2; zinc finger, human MDM2, phosphorylation, alternative splicing, metal-binding, nuclear protein, proto- oncogene; NMR {Homo sapiens} SCOP: g.41.11.1 PDB: 2c6b_A Back     alignment and structure
>2cr8_A MDM4 protein; ZF-ranbp domain, P53-binding protein MDM4, MDM2-like P53-binding DE protein, MDMX protein, double minute 4 protein; NMR {Homo sapiens} SCOP: g.41.11.1 Back     alignment and structure
>1weo_A Cellulose synthase, catalytic subunit (IRX3); structure genomics, ring-finger, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: g.44.1.1 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 456
d2ddra1299 d.151.1.3 (A:7-305) Sphingomyelin phosphodiesteras 1e-19
d1zwxa1293 d.151.1.3 (A:41-333) Sphingomyelin phosphodiestera 5e-16
d1wdua_228 d.151.1.1 (A:) Endonuclease domain of TRAS1 retrot 7e-10
d2f1na1250 d.151.1.1 (A:1-250) Cytolethal distending toxin su 1e-09
d2a40b1260 d.151.1.1 (B:1-260) Deoxyribonuclease I {Cow (Bos 5e-09
d1sr4b_261 d.151.1.1 (B:) Cytolethal distending toxin subunit 1e-08
d1akoa_268 d.151.1.1 (A:) DNA-repair enzyme exonuclease III { 7e-07
d1hd7a_275 d.151.1.1 (A:) DNA repair endonuclease Hap1 {Human 4e-06
d1vyba_236 d.151.1.1 (A:) Endonuclease domain of LINE-1 rever 7e-06
d1q5wa_31 g.41.11.1 (A:) Npl4 {Rat (Rattus norvegicus) [TaxI 0.002
>d2ddra1 d.151.1.3 (A:7-305) Sphingomyelin phosphodiesterase C {Bacillus cereus [TaxId: 1396]} Length = 299 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: DNase I-like
superfamily: DNase I-like
family: Sphingomyelin phosphodiesterase-like
domain: Sphingomyelin phosphodiesterase C
species: Bacillus cereus [TaxId: 1396]

 Score = 87.0 bits (213), Expect = 1e-19
 Identities = 46/302 (15%), Positives = 83/302 (27%), Gaps = 40/302 (13%)

Query: 185 SLKILSYNVW-----FREDLEMHPRMKTIGDLIQLHSPDIICFQEIT------------- 226
           +LK++++NV+        +     R   IG    + + D++   E+              
Sbjct: 3   TLKVMTHNVYMLSTNLYPNWGQTERADLIGAADYIKNQDVVILNEVFDNSASDRLLGNLK 62

Query: 227 ---PNIYDILCKSSWWKGYRCSVPNEMADSRGYFCMQLSKLQAKSFTCEPFRNSIMGREL 283
              PN   +L +SS  +  +       +         +SK          F        L
Sbjct: 63  KEYPNQTAVLGRSSGSEWDKTLGNYSSSTPEDGGVAIVSKWPIAEKIQYVFAKGCGPDNL 122

Query: 284 CVAEVEV----QGKKPLVVATSHLESPCPGPPTWDQMFSKERV---EQAKEAINLLKKNP 336
                      +  + + V  +HL++             +       Q       +  N 
Sbjct: 123 SNKGFVYTKIKKNDRFVHVIGTHLQAEDSMCGKTSPASVRTNQLKEIQDFIKNKNIPNNE 182

Query: 337 NVIFCGDMNWDDKLDGKFPLPD--GWVDAWTELRPGENGWTY----DTKSNKMLSGNRTL 390
            V+  GDMN +          +            P   G T      T S    +   + 
Sbjct: 183 YVLIGGDMNVNKINAENNNDSEYASMFKTLNASVPSYTGHTATWDATTNSIAKYNFPDSP 242

Query: 391 QKRLDRFICSLRDFKIIRIDMIGVEAIPGLLYVKEKKVRKEMQKLELPVLPSDHYGLLLT 450
            + LD  I S        I+   ++       V     +            SDHY +  T
Sbjct: 243 AEYLDYIIASKDHANPSYIENKVLQPKSPQWTVTSWFQKYTYND------YSDHYPVEAT 296

Query: 451 IS 452
           IS
Sbjct: 297 IS 298
>d1zwxa1 d.151.1.3 (A:41-333) Sphingomyelin phosphodiesterase C {Listeria ivanovii [TaxId: 1638]} Length = 293 Back     information, alignment and structure
>d1wdua_ d.151.1.1 (A:) Endonuclease domain of TRAS1 retrotransposon (ORF2) {Silkworm (Bombyx mori) [TaxId: 7091]} Length = 228 Back     information, alignment and structure
>d2f1na1 d.151.1.1 (A:1-250) Cytolethal distending toxin subunit B {Escherichia coli [TaxId: 562]} Length = 250 Back     information, alignment and structure
>d2a40b1 d.151.1.1 (B:1-260) Deoxyribonuclease I {Cow (Bos taurus) [TaxId: 9913]} Length = 260 Back     information, alignment and structure
>d1sr4b_ d.151.1.1 (B:) Cytolethal distending toxin subunit B {Haemophilus ducreyi [TaxId: 730]} Length = 261 Back     information, alignment and structure
>d1akoa_ d.151.1.1 (A:) DNA-repair enzyme exonuclease III {Escherichia coli [TaxId: 562]} Length = 268 Back     information, alignment and structure
>d1hd7a_ d.151.1.1 (A:) DNA repair endonuclease Hap1 {Human (Homo sapiens) [TaxId: 9606]} Length = 275 Back     information, alignment and structure
>d1vyba_ d.151.1.1 (A:) Endonuclease domain of LINE-1 reverse transcriptase homolog {Human (Homo sapiens) [TaxId: 9606]} Length = 236 Back     information, alignment and structure
>d1q5wa_ g.41.11.1 (A:) Npl4 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 31 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 ?
Query456
d1zwxa1293 Sphingomyelin phosphodiesterase C {Listeria ivanov 99.95
d2ddra1299 Sphingomyelin phosphodiesterase C {Bacillus cereus 99.95
d1vyba_236 Endonuclease domain of LINE-1 reverse transcriptas 99.93
d2f1na1250 Cytolethal distending toxin subunit B {Escherichia 99.87
d2a40b1260 Deoxyribonuclease I {Cow (Bos taurus) [TaxId: 9913 99.87
d1wdua_228 Endonuclease domain of TRAS1 retrotransposon (ORF2 99.86
d1hd7a_275 DNA repair endonuclease Hap1 {Human (Homo sapiens) 99.84
d2imqx1280 Salivary nitrophorin {Bedbug (Cimex lectularius) [ 99.82
d1sr4b_261 Cytolethal distending toxin subunit B {Haemophilus 99.82
d1akoa_268 DNA-repair enzyme exonuclease III {Escherichia col 99.77
d1i9za_345 Synaptojanin, IPP5C domain {Fission yeast (Schizos 99.62
d1q5wa_31 Npl4 {Rat (Rattus norvegicus) [TaxId: 10116]} 98.88
d1q5wa_31 Npl4 {Rat (Rattus norvegicus) [TaxId: 10116]} 98.44
d2gqea129 Nuclear pore complex protein nup153 {Human (Homo s 98.04
d2gqea129 Nuclear pore complex protein nup153 {Human (Homo s 97.99
d1n0za_45 Znf265, first zinc-finger domain {Human (Homo sapi 96.99
d1n0za_45 Znf265, first zinc-finger domain {Human (Homo sapi 96.72
d2j9ub147 Vacuolar protein-sorting-associated protein 36, VP 95.31
d2cr8a141 MDM4 {Human (Homo sapiens) [TaxId: 9606]} 88.32
d2c6aa146 MDM2 {Human (Homo sapiens) [TaxId: 9606]} 86.84
d6rxna_45 Rubredoxin {Desulfovibrio desulfuricans, strain 27 86.3
d1yuza236 Nigerythrin, C-terminal domain {Desulfovibrio vulg 85.51
d1nnqa237 Rubrerythrin, C-terminal domain {Archaeon Pyrococc 84.97
d1yuza236 Nigerythrin, C-terminal domain {Desulfovibrio vulg 84.68
d1nnqa237 Rubrerythrin, C-terminal domain {Archaeon Pyrococc 84.53
d2j9ub147 Vacuolar protein-sorting-associated protein 36, VP 80.05
d1brfa_53 Rubredoxin {Archaeon Pyrococcus furiosus [TaxId: 2 80.03
>d1zwxa1 d.151.1.3 (A:41-333) Sphingomyelin phosphodiesterase C {Listeria ivanovii [TaxId: 1638]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: DNase I-like
superfamily: DNase I-like
family: Sphingomyelin phosphodiesterase-like
domain: Sphingomyelin phosphodiesterase C
species: Listeria ivanovii [TaxId: 1638]

Probab=99.95  E-value=1.8e-27  Score=225.52  Aligned_cols=258  Identities=16%  Similarity=0.079  Sum_probs=149.0

Q ss_pred             CCceEEEEEeccCCC-----CCChhhHHHHHHHHHhhCCCcEEEEeccCHh-HHHHHHhCCC-ccceEEecCCC------
Q 012811          183 SGSLKILSYNVWFRE-----DLEMHPRMKTIGDLIQLHSPDIICFQEITPN-IYDILCKSSW-WKGYRCSVPNE------  249 (456)
Q Consensus       183 ~~~lrV~T~Nv~~~~-----~~~~~~r~~~i~~~I~~~~pDII~LQEv~~~-~~~~L~~~~~-~~~y~~~~~~~------  249 (456)
                      .+.||||||||+++.     ......|...|++.|...+|||||||||... ..+.|.+... .+.+.......      
T Consensus         2 ~~~lki~s~Nv~~~~~~~~~~~~~~~r~~~i~~~i~~~~~DVi~LQEv~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~   81 (293)
T d1zwxa1           2 PGNFKITSHNVYLFSRNIYPNWGQMHRADLIAQADYMKNNDVVILNEAFDTSASHRLLNNLREMYPHQTPVIGRSKHGWD   81 (293)
T ss_dssp             CCSCEEEEEEEEECCTTTSTTSCHHHHHHHHHTSGGGSSCSEEEEEEECSHHHHHHHHHHTTTTCCEECCCTTSCSTTCS
T ss_pred             CCCCEEEEEecCcCccccCCCcCHHHHHHHHHHHHHhcCCCEEEEEccCCcchHHHHHHHHhhhccceehhccccccccc
Confidence            367999999998764     2245788999999999999999999999743 3333333221 11111111000      


Q ss_pred             -------CCCCCCeEEEEEEeeecceeeEeeCCCCC-----CCCceEEEEEEeCCcceEEEEEeccCCCCCCCCcccccc
Q 012811          250 -------MADSRGYFCMQLSKLQAKSFTCEPFRNSI-----MGRELCVAEVEVQGKKPLVVATSHLESPCPGPPTWDQMF  317 (456)
Q Consensus       250 -------~~~~~~~g~ailSr~pi~~~~~~~~~~~~-----~~R~~~~~~i~~~~g~~l~v~n~Hl~~~~~~~~~~~~~~  317 (456)
                             .......|++|+||+|+.....+.+....     ..|.++.+.+.+. |..+.|+++|+.+......  ....
T Consensus        82 ~~~~~~~~~~~~~~g~~ilsr~pi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~v~~~Hl~~~~~~~~--~~~~  158 (293)
T d1zwxa1          82 KTEGNYSNFALEDGGVAVVSQWPIVEKSQHIFQRGGGADRLSNKGFAYVKIMKN-GKPYHIIGTHTQADDSLIS--KDTS  158 (293)
T ss_dssp             EEEC-----CCBCCCCEEEESSCEEEEEEEECSCCCGGGGGBCCEEEEEEEEET-TEEEEEEEEECCCCCTTSC--HHHH
T ss_pred             ccccccccccccccceEEEeccCcccceeeeeeccccccccccceEEEEEEecC-CceEEEEEeeeeccCCccc--hhHH
Confidence                   01122357999999999887776654432     2466777788887 7899999999998755332  1223


Q ss_pred             HHHHHHHHHHHHHHhhc-----CCCEEEEccCCCCCCCCCCcCCCC--CcccccccccCCCCCccccCCCCccc--cCCC
Q 012811          318 SKERVEQAKEAINLLKK-----NPNVIFCGDMNWDDKLDGKFPLPD--GWVDAWTELRPGENGWTYDTKSNKML--SGNR  388 (456)
Q Consensus       318 ~~~R~~Q~~~l~~~l~~-----~~pvIl~GDFN~~~~~~~~~~l~~--gl~D~~~~~~~~~~~~T~~~~~~~~~--~~~~  388 (456)
                      ...|..|++.+..++.+     ..++||+||||..+.+..+..+..  ++.+.+..   .....+++...+...  ....
T Consensus       159 ~~~r~~~~~~~~~~~~~~~~~~~~~vil~GDfN~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~  235 (293)
T d1zwxa1         159 RAIRAEQMQEIQTFIAKKNIPKDEIIFIGGDLNVNYGTDEYHDMLKLLNVSSPANF---NGQMATWDPTTNSMLKESYPK  235 (293)
T ss_dssp             HHHHHHHHHHHHHHHHHHTCCTTSEEEEEEECCCCTTSHHHHHHHHHHTBCCCTTC---CTTSCSBCTTTCHHHHHHCTT
T ss_pred             HHHHHHHHHHhhhhhhhhccCCCCcEEEEeecCCCCCchHHHHHHhhccccchhhc---ccCCcccccccccccccccCC
Confidence            45688888888887753     568999999998876544332211  11111111   122222322222111  0112


Q ss_pred             ccCCCccEEEEecCCCccceEEEeeccccCCchhhhhhhhhhhhhccCCCCCccCCcceeEEEE
Q 012811          389 TLQKRLDRFICSLRDFKIIRIDMIGVEAIPGLLYVKEKKVRKEMQKLELPVLPSDHYGLLLTIS  452 (456)
Q Consensus       389 ~~~~rID~I~~s~~~~~~~~~~~~g~d~~p~~~~~~~~~~~~~~~~~~~~~~~SDH~pV~~~~~  452 (456)
                      ....||||||+++..+..........+.........      ..........+|||+||+|.+.
T Consensus       236 ~~~~~iD~I~~s~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~SDH~PV~A~~~  293 (293)
T d1zwxa1         236 AAPEYLDYIFVENGHARPHSWHNKVLHTKSPQWSVK------SWFKTYTYQDFSDHYPVVGFTD  293 (293)
T ss_dssp             SCCBCCEEEEEBTTSCCCSCEEEEECCCCCCCEEEE------ETTEEEEECCSSSSCCEEEEEC
T ss_pred             CCCceEEEEEEecccccccccceeEEeecccccccc------cccccCCCCCcCCcCCeEEEeC
Confidence            456899999999655544332221111110000000      0000011235799999999873
>d2ddra1 d.151.1.3 (A:7-305) Sphingomyelin phosphodiesterase C {Bacillus cereus [TaxId: 1396]} Back     information, alignment and structure
>d1vyba_ d.151.1.1 (A:) Endonuclease domain of LINE-1 reverse transcriptase homolog {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2f1na1 d.151.1.1 (A:1-250) Cytolethal distending toxin subunit B {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2a40b1 d.151.1.1 (B:1-260) Deoxyribonuclease I {Cow (Bos taurus) [TaxId: 9913]} Back     information, alignment and structure
>d1wdua_ d.151.1.1 (A:) Endonuclease domain of TRAS1 retrotransposon (ORF2) {Silkworm (Bombyx mori) [TaxId: 7091]} Back     information, alignment and structure
>d1hd7a_ d.151.1.1 (A:) DNA repair endonuclease Hap1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2imqx1 d.151.1.2 (X:3-282) Salivary nitrophorin {Bedbug (Cimex lectularius) [TaxId: 79782]} Back     information, alignment and structure
>d1sr4b_ d.151.1.1 (B:) Cytolethal distending toxin subunit B {Haemophilus ducreyi [TaxId: 730]} Back     information, alignment and structure
>d1akoa_ d.151.1.1 (A:) DNA-repair enzyme exonuclease III {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1i9za_ d.151.1.2 (A:) Synaptojanin, IPP5C domain {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]} Back     information, alignment and structure
>d1q5wa_ g.41.11.1 (A:) Npl4 {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d1q5wa_ g.41.11.1 (A:) Npl4 {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d2gqea1 g.41.11.1 (A:3-31) Nuclear pore complex protein nup153 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2gqea1 g.41.11.1 (A:3-31) Nuclear pore complex protein nup153 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1n0za_ g.41.11.1 (A:) Znf265, first zinc-finger domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1n0za_ g.41.11.1 (A:) Znf265, first zinc-finger domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2j9ub1 g.41.11.1 (B:115-161) Vacuolar protein-sorting-associated protein 36, VPS36 {Saccharomyces cerevisiae [TaxId: 4932]} Back     information, alignment and structure
>d2cr8a1 g.41.11.1 (A:8-48) MDM4 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2c6aa1 g.41.11.1 (A:290-335) MDM2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d6rxna_ g.41.5.1 (A:) Rubredoxin {Desulfovibrio desulfuricans, strain 27774 [TaxId: 876]} Back     information, alignment and structure
>d1yuza2 g.41.5.1 (A:167-202) Nigerythrin, C-terminal domain {Desulfovibrio vulgaris [TaxId: 881]} Back     information, alignment and structure
>d1nnqa2 g.41.5.1 (A:135-171) Rubrerythrin, C-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1yuza2 g.41.5.1 (A:167-202) Nigerythrin, C-terminal domain {Desulfovibrio vulgaris [TaxId: 881]} Back     information, alignment and structure
>d1nnqa2 g.41.5.1 (A:135-171) Rubrerythrin, C-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d2j9ub1 g.41.11.1 (B:115-161) Vacuolar protein-sorting-associated protein 36, VPS36 {Saccharomyces cerevisiae [TaxId: 4932]} Back     information, alignment and structure
>d1brfa_ g.41.5.1 (A:) Rubredoxin {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure