Citrus Sinensis ID: 002593

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-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760-------770-------780-------790-------800-------810-------820-------830-------840-------850-------860-------870-------880-------890-------900---

MNDSDSFFNKTNNNKRSGENYLPSSISSPRGKSIIVSKTAVVRLQILHLPLVSTATGSPVDSLTLEPDRPYSIGRASINCDFTFDNRLVSRQHCQILFDSSERKIYVLDGTFLLPAFSSVVNEFRKKRDKSLEDEEEDEGFSRVMVSLNGVFVNGIRLKSGIVRELNAGDEVLFVCRDESLCRLQTRIGFLILGIIFKEEVVLKRPRLVGTMASSGHSQGSVSSGTRSKRVFALRENDVSNPDSVFPKLKRRDIFGRASFLLSQCRNILNSNDPVSCIQQIANSDMGIMSTYGCFSTKFPGRSSIDGELKVKKIERISQQERKPCDESIYVGQPGSITFEDERVVDLEAEGDPVDPCVHNDHLHHKDSVGISNKNATPGVKSKLLNSVDRQNATHFGSMDKSKSLGSSCSPPGKKFYLNRLEFMDLTSLNYDVISLPELLYPVESISRMFIATFTSDILWFMSYCEIPSHLPVTIACHNTERCWSTSADKRTSVPYPNFPNLVLVFPPFPESVAFGENCKKQGIACHHPKLFVLQREDSIRVIVTSANLGAKQWNAVTNTVWWQDFPRRCAPDYLSLFVQTPVEEINQDSRSDFTAQLASFMASLVIDVPSQAHWIVELTKYDFASAAGHLVASVPGIHSYRNPNLSESTYSKPVDHGAIWSSDGKFLGSVETSVVGLSHLFRTAADSNGTQIKKLAAFLGKSFSAHGMLKILLRRNTNVPADANAVSVLVPNPDELSDGDCIQLGFMPRDIAKWVSPLWDIGFIRFSGFISRDEVLAAALEGISKKVQLILHVSQGPKFSDISKMMQIEHVVALSSLIASIQRCRGLWRLQEVLGQYRWPELQESDFSYGSSSIGSINAQFLAAFAAASGKKSLRFYDSEESDPEYFFTVSKSGAAGVLVKN

cccccccccccccccccccccccccccccccccEEEEcEEEEEEEEccccccccccccccccccccccccEEcccccccccEEEcccccccccEEEEEcccccEEEEEcccccccccHHHHHHHHHcccccccccccccccEEEEEEcccEEEccEEEccccEEEEccccEEEEEEcccccccccccEEEEEEEEEEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHcccccccHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEccccccccccccccccccccccccHHHHHHHHccccHHHHHHHccccccccEEEEEcccccccccccccccccccccccccEEEcccccccccccccccccccccccccEEEEEEcccEEEEEEcccccHHHHcccccEEEEEcccccccccccccccccccccccccccccHHHHHHHHHHHHccccccHHHHHHHHcccccccccEEEEEcccccccccccccccccccccccccccccccccccccHHHHHHHcccccccccccccHHHHHHHHHHcccccccccEEEEEEcccccccccccEEEEEccccccccccccccccccHHHHHHHcccccccEEEEEccccHHHHHHHHHccccccEEEEEEEcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccEEEEccccccccHHHHHHHHHHHccccccccccccccccccccccccccccccccc

cccccccccccccccccccccccccccccccccHHHHHEEEEEEccccccEEcccccccccEEEEccccccEcccccccccEEEccccEcccccEEEEcccccEEEEEccEEEEccHHHHHHHHHHHHHcHHcccccccccEEEEEcccEEEEccEEEccccEEEEEcccEEEEEEccccccccccEEEEEEEEEEEEEEEEcccccHHEEEccccccccEEEccccccEEEEEEccccccccccccccccccHHHHHHHHHHHHHHHHcccccHHHHHHHHccccccccccccccccccccccEEcccccccccccHHHHccccccccccccccccHHHHccccHHHHHccccccccccHHHccccccccccccccccHccccccccccccccccccccccccccccccccccEEEEEEEEcccccccccccEEHHHHHccccHHHHHHHHHHHccHHHHHHcccccccccEEEEEEcccccccccccccccccccccccEEEEccccccccccccccccccccccccEEEEEEccccEEEEEEcccccHHHHHccccEEEEccccccccccccHHccccccccccccccHHHHHHHHHHHHHHccccccHHHHHHHHHHccccccEEEEEEEccccccccccccccccccccHHHHHHHHHHHHHccEEEHHHHcccccccccccccHHHHHHHHHHHcccccccccEEEEEEcccccccccccEEEEEcccccccccccEEcccccHHHHHHHccHHHcccEEEEEEEcHHHHHHHHHcccccEEEEEEEEcccccHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccEEEEcccHccccHHHHHHHHHHHccccccccccccccHHHHHHHHccccccccccc

mndsdsffnktnnnkrsgenylpssissprgksiivSKTAVVRLQILHlplvstatgspvdsltlepdrpysigrasincdftfdnrlvsRQHCQILFDSSERKIYVLDGTFLLPAFSSVVNEFRKKRdksledeeedegFSRVMVSLNGVFVNGIRLKSGIVRELNAGDEVLFVCRDESLCRLQTRIGFLILGIIFKEevvlkrprlvgtmassghsqgsvssgtrsKRVFALrendvsnpdsvfpklkrrdifGRASFLLSQCRnilnsndpvscIQQIansdmgimstygcfstkfpgrssidgelKVKKIERISqqerkpcdesiyvgqpgsitfedervvdleaegdpvdpcvhndhlhhkdsvgisnknatpgvkskLLNSVdrqnathfgsmdkskslgsscsppgkkfylnrlefmdltslnydvislpellypveSISRMFIATFTSDILWFMSyceipshlpvtiachntercwstsadkrtsvpypnfpnlvlvfppfpesvafgenckkqgiachhpklfvlqREDSIRVIVTSANLGAKQWNAVTNTVwwqdfprrcapdylslfvqtpveeinqdsrSDFTAQLASFMASLVIDVPSQAHWIVELTKYdfasaaghlvasvpgihsyrnpnlsestyskpvdhgaiwssdgkflgSVETSVVGLSHLFRTAADSNGTQIKKLAAFLGKSFSAHGMLKILLRRntnvpadanavsvlvpnpdelsdgdciqlgfmprdiakwvsplwdigfirfsgfiSRDEVLAAALEGISKKVQLILHVsqgpkfsdisKMMQIEHVVALSSLIASIQRCRGLWRLQEVLgqyrwpelqesdfsygsssigsINAQFLAAFAAASGkkslrfydseesdpeyfftvsksgaagvlvkn

mndsdsffnktnnnkrsgenylpssissprgKSIIVSKTAVVRLQILHLPlvstatgspvdsltlEPDRPYSIGRASINCDFTFDNRLVSRQHCQILFDSSERKIYVLDGTFllpafssvvnEFRKKrdksledeeedegfsrvMVSLNGVFVNGIRLKSGIVRELNAGDEVLFVCRDESLCRLQTRIGFLILGIIFKEEVVLKRPRLVGtmassghsqgsvssgtrSKRVFAlrendvsnpdsvfpklkrrDIFGRASFLLSQCRNILNSNDPVSCIQQIANSDMGIMSTYGCFSTkfpgrssidgelKVKKIerisqqerkpcdesiyvgqpgsitFEDERVVDLEAEGDPVDPCVHNDHLHhkdsvgisnknatpgvKSKLLNSVDRQNAThfgsmdkskslgsscspPGKKFYLNRLEFMDLTSLNYDVISLPELLYPVESISRMFIATFTSDILWFMSYCEIPSHLPVTIACHNTERCWSTSADKRTSVPYPNFPNLVLVFPPFPESVAFGENCKKQGIACHHPKLFVLQREDSIRVIVTsanlgakqwnAVTNTVWWQDFPRRCAPDYLSLFVQTPVEEINQDSRSDFTAQLASFMASLVIDVPSQAHWIVELTKYDFASAAGHLVASVPGIHSYRNPNLSESTYSKPVDHGAIWSSDGKFLGSVETSVVGLSHLFRTAADSNGTQIKKLAAFLGKSFSAHGMLKILLRRNTNVPADANAVSVLVPNPDELSDGDCIQLGFMPRDIAKWVSPLWDIGFIRFSGFISRDEVLAAALEGISKKVQLILHVSQGPKFSDISKMMQIEHVVALSSLIASIQRCRGLWRLQEVLGQYRWPELQESDFSYGSSSIGSINAQFLAAFAAASGKKSLRFYDSEESDPEYfftvsksgaagvlvkn

MNDSDSFFNKTNNNKRSGENYLPSSISSPRGKSIIVSKTAVVRLQILHLPLVSTATGSPVDSLTLEPDRPYSIGRASINCDFTFDNRLVSRQHCQILFDSSERKIYVLDGTFLLPAFSSVVNEFRKKRDKSLEDEEEDEGFSRVMVSLNGVFVNGIRLKSGIVRELNAGDEVLFVCRDESLCRLQTRIGFLILGIIFKEEVVLKRPRLVGTMAssghsqgsvssgTRSKRVFALRENDVSNPDSVFPKLKRRDIFGRASFLLSQCRNILNSNDPVSCIQQIANSDMGIMSTYGCFSTKFPGRSSIDGELKVKKIERISQQERKPCDESIYVGQPGSITFEDERVVDLEAEGDPVDPCVHNDHLHHKDSVGISNKNATPGVKSKLLNSVDRQNATHFGSMDKSKSLGSSCSPPGKKFYLNRLEFMDLTSLNYDVISLPELLYPVESISRMFIATFTSDILWFMSYCEIPSHLPVTIACHNTERCWSTSADKRTSVPYpnfpnlvlvfppfpESVAFGENCKKQGIACHHPKLFVLQREDSIRVIVTSANLGAKQWNAVTNTVWWQDFPRRCAPDYLSLFVQTPVEEINQDSRSDFTAQLASFMASLVIDVPSQAHWIVELTKYDFASAAGHLVASVPGIHSYRNPNLSESTYSKPVDHGAIWSSDGKFLGSVETSVVGLSHLFRTAADSNGTQIKKLAAFLGKSFSAHGMLKILLRRNTNVPADANAVSVLVPNPDELSDGDCIQLGFMPRDIAKWVSPLWDIGFIRFSGFISRDEVLAAALEGISKKVQLILHVSQGPKFSDISKMMQIEHVVALSSLIASIQRCRGLWRLQEVLGQYRWPELQESDFsygsssigsiNaqflaafaaaSGKKSLRFYDSEESDPEYFFTVSKSGAAGVLVKN

*********************************IIVSKTAVVRLQILHLPLVSTATGSPVDSLTLEPDRPYSIGRASINCDFTFDNRLVSRQHCQILFDSSERKIYVLDGTFLLPAFSSVVNEF****************FSRVMVSLNGVFVNGIRLKSGIVRELNAGDEVLFVCRDESLCRLQTRIGFLILGIIFKEEVVLKRPRLV************************************FPKLKRRDIFGRASFLLSQCRNILNSNDPVSCIQQIANSDMGIMSTYGCFSTKFPG***************************IYVGQPGSITFEDERVVDL*********CV********************************************************KFYLNRLEFMDLTSLNYDVISLPELLYPVESISRMFIATFTSDILWFMSYCEIPSHLPVTIACHNTERCWSTSADKRTSVPYPNFPNLVLVFPPFPESVAFGENCKKQGIACHHPKLFVLQREDSIRVIVTSANLGAKQWNAVTNTVWWQDFPRRCAPDYLSLFVQTPVEEINQDSRSDFTAQLASFMASLVIDVPSQAHWIVELTKYDFASAAGHLVASVPGIHSYRNP******YSKPVDHGAIWSSDGKFLGSVETSVVGLSHLFRTAADSNGTQIKKLAAFLGKSFSAHGMLKILLRRNTNVPADANAVSVLVPNPDELSDGDCIQLGFMPRDIAKWVSPLWDIGFIRFSGFISRDEVLAAALEGISKKVQLILHVSQGPKFSDISKMMQIEHVVALSSLIASIQRCRGLWRLQEVLGQYRWPELQESDFSYGSSSIGSINAQFLAAFAAASGKKSLRFY********YFFTV************

**********************************IVSKTAVVRLQILHLPLVSTATGSPVDSLTLEPDRPYSIGRASINCDFTFDNRLVSRQHCQILFDSSERKIYVLDGTFLLPAFSSVVNEFRKKRDKSLEDEEEDEGFSRVMVSLNGVFVNGIRLKSGIVRELNAGDEVLFVCRDESLCRLQTRIGFLILGIIFKEEVVL*****************************************VFPKLKRRDIFG*************************************************************************************************************************************************************KKFYLNRLEFMDLTSLNYDVISLPELLYPVESISRMFIATFTSDILWFMSYCEIPSHLPVTIACHNTE**************YPNFPNLVLVFPPFPESVAFGENCKKQGIACHHPKLFVLQREDSIRVIVTSANLGAKQWNAVTNTVWWQDFPRRC***********************FTAQLASFMASLVIDVPSQAHWIVELTKYDFASAAGHLVASVPGIHSYRNPNLSESTYSKPV*****************TSVVGLS********************************ILLRRNTNVPADANAVSVLVPNPDELSDGDCIQLGFMPRDIAKWVSPLWDIGFIRFSGFISRDEVLAAALEGISKKVQLILHVSQGPKFSDISKMMQIEHVVALSSLIASIQRCRGLWRLQEVLGQYRWPELQESDFSYGSSSIGSINAQFLAAFAAAS************S**EYFFTVSKSG********

********NKTNNNKRSGENYLPSSISSPRGKSIIVSKTAVVRLQILHLPLVSTATGSPVDSLTLEPDRPYSIGRASINCDFTFDNRLVSRQHCQILFDSSERKIYVLDGTFLLPAFSSVVNE*****************FSRVMVSLNGVFVNGIRLKSGIVRELNAGDEVLFVCRDESLCRLQTRIGFLILGIIFKEEVVLKRPRLVGT****************SKRVFALRENDVSNPDSVFPKLKRRDIFGRASFLLSQCRNILNSNDPVSCIQQIANSDMGIMSTYGCFSTKFPGRSSIDGELKVKKIERISQQERKPCDESIYVGQPGSITFEDERVVDLEAEGDPVDPCVHNDHLHHKDSVGISNKNATPGVKSKLLNSVDRQNATHFGS***********SPPGKKFYLNRLEFMDLTSLNYDVISLPELLYPVESISRMFIATFTSDILWFMSYCEIPSHLPVTIACHNTERCWSTSADKRTSVPYPNFPNLVLVFPPFPESVAFGENCKKQGIACHHPKLFVLQREDSIRVIVTSANLGAKQWNAVTNTVWWQDFPRRCAPDYLSLFVQTPVEEINQDSRSDFTAQLASFMASLVIDVPSQAHWIVELTKYDFASAAGHLVASVPGIHSYRNPNLSESTYSKPVDHGAIWSSDGKFLGSVETSVVGLSHLFRTAADSNGTQIKKLAAFLGKSFSAHGMLKILLRRNTNVPADANAVSVLVPNPDELSDGDCIQLGFMPRDIAKWVSPLWDIGFIRFSGFISRDEVLAAALEGISKKVQLILHVSQGPKFSDISKMMQIEHVVALSSLIASIQRCRGLWRLQEVLGQYRWPELQESDFSYGSSSIGSINAQFLAAFAAASGKKSLRFYDSEESDPEYFFTVSKSGAAGVLVKN

********************YLPSSISSPRGKSIIVSKTAVVRLQILHLPLVSTATGSPVDSLTLEPDRPYSIGRASINCDFTFDNRLVSRQHCQILFDSSERKIYVLDGTFLLPAFSSVVNEFRKKRDKSLEDEEEDEGFSRVMVSLNGVFVNGIRLKSGIVRELNAGDEVLFVCRDESLCRLQTRIGFLILGIIFKEEVVLKRPRLVGTMASS*****SVSSGTRSKRVFALRENDVSNPDSVFPKLKRRDIFGRASFLLSQCRNILNSNDPVSCIQQIANSDMGIMSTYGCFSTKFPGRSSIDGELKVKKIERISQ*ERKPCDESIYVGQPGSITFEDERVVDLEAEG*****C**************************************************SCSPPGKKFYLNRLEFMDLTSLNYDVISLPELLYPVESISRMFIATFTSDILWFMSYCEIPSHLPVTIACHNTERCWSTSADKRTSVPYPNFPNLVLVFPPFPESVAFGENCKKQGIACHHPKLFVLQREDSIRVIVTSANLGAKQWNAVTNTVWWQDFPRRCAPDYL************QDSRSDFTAQLASFMASLVIDVPSQAHWIVELTKYDFASAAGHLVASVPGIHSYRNPNLSESTYSKPVDHGAIWSSDGKFLGSVETSVVGLSHLFRTAADSNGTQIKKLAAFLGKSFSAHGMLKILLRRNTNVPADANAVSVLVPNPDELSDGDCIQLGFMPRDIAKWVSPLWDIGFIRFSGFISRDEVLAAALEGISKKVQLILHVSQGPKFSDISKMMQIEHVVALSSLIASIQRCRGLWRLQEVLGQYRWPELQESDFSYGSSSIGSINAQFLAAFAAASG*********EESDPEYFFTVSKSG*A******

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		903	2.2.26 [Sep-21-2011]
Q9NUW8		608	Tyrosyl-DNA phosphodieste	yes	no	0.114	0.169	0.260	8e-05
Q4G056		609	Tyrosyl-DNA phosphodieste	yes	no	0.114	0.169	0.234	9e-05

>sp\|Q9NUW8\|TYDP1_HUMAN Tyrosyl-DNA phosphodiesterase 1 OS=Homo sapiens GN=TDP1 PE=1 SV=2	Back alignment and function desciption

 Score = 50.1 bits (118), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 30/115 (26%), Positives = 54/115 (46%), Gaps = 12/115 (10%)

Query: 523 GIACHHPKLFVLQREDSIRVIVTSANLGAKQWNAVTNTVWWQDFPRRCAPDYLSLFVQTP 582
               HH K+ +L  E+ +RV++ ++NL    W+  T  +W        +P Y  +   T 
Sbjct: 258 AFGTHHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIW-------LSPLYPRIADGT- 309

Query: 583 VEEINQDSRSDFTAQLASFMASLVIDVPSQAHWIVELTKYDFASAAGHLVASVPG 637
               + +S + F A L S++  +  + PS   WI  + K+D +    +L+ S PG
Sbjct: 310 --HKSGESPTHFKADLISYL--MAYNAPSLKEWIDVIHKHDLSETNVYLIGSTPG 360

DNA repair enzyme that can remove a variety of covalent adducts from DNA through hydrolysis of a 3'-phosphodiester bond, giving rise to DNA with a free 3' phosphate. Catalyzes the hydrolysis of dead-end complexes between DNA and the topoisomerase I active site tyrosine residue. Hydrolyzes 3'-phosphoglycolates on protruding 3' ends on DNA double-strand breaks due to DNA damage by radiation and free radicals. Acts on blunt-ended double-strand DNA breaks and on single-stranded DNA. Has low 3'exonuclease activity and can remove a single nucleoside from the 3'end of DNA and RNA molecules with 3'hydroxyl groups. Has no exonuclease activity towards DNA or RNA with a 3'phosphate.
Homo sapiens (taxid: 9606)
EC: 3EC: .EC: 1EC: .EC: 4EC: .EC: -

>sp\|Q4G056\|TYDP1_RAT Tyrosyl-DNA phosphodiesterase 1 OS=Rattus norvegicus GN=Tdp1 PE=2 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		903
255539987		1148	tyrosyl-DNA phosphodiesterase, putative	0.926	0.729	0.545	0.0
224119906		1131	predicted protein [Populus trichocarpa]	0.949	0.757	0.542	0.0
359493967		1091	PREDICTED: uncharacterized protein LOC10	0.883	0.731	0.535	0.0
297806769		1083	predicted protein [Arabidopsis lyrata su	0.900	0.750	0.514	0.0
42567721		1084	forkhead-associated domainand FHA domain	0.903	0.752	0.504	0.0
147770909		1423	hypothetical protein VITISV_012382 [Viti	0.902	0.572	0.489	0.0
302142785		1032	unnamed protein product [Vitis vinifera]	0.833	0.729	0.513	0.0
7576178		1075	hypothetical protein [Arabidopsis thalia	0.893	0.750	0.496	0.0
357520291		1064	Tyrosyl-DNA phosphodiesterase [Medicago	0.890	0.755	0.490	0.0
242072904		972	hypothetical protein SORBIDRAFT_06g01512	0.709	0.659	0.436	1e-153

>gi\|255539987\|ref\|XP_002511058.1\| tyrosyl-DNA phosphodiesterase, putative [Ricinus communis] gi\|223550173\|gb\|EEF51660.1\| tyrosyl-DNA phosphodiesterase, putative [Ricinus communis]	Back alignment and taxonomy information

 Score =  907 bits (2345), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 489/897 (54%), Positives = 620/897 (69%), Gaps = 60/897 (6%)

Query: 14  NKRSGENYLPSSISSPRGKSIIVSKTAVVRLQILHLPLVSTATGSPVDSLTLEPDRPYSI 73
           +K+     LP+S      K   ++K+A + LQ L +PL+S ATGSP+DS+ LEPDRPY+I
Sbjct: 23  DKKDNNPLLPTSTCK---KPKQINKSAFIHLQSLDVPLISPATGSPLDSICLEPDRPYTI 79

Query: 74  GRASIN--CDFTFDNRLVSRQHCQILFDSSERKIYVLDGTFLLPAFSS--VVNEFRKK-R 128
           GR+S +  CDF F +R VS+QHCQILFDS  RK+Y+LDG  LL + SS  VV+EFRK+ R
Sbjct: 80  GRSSTDPDCDFVFSDRRVSKQHCQILFDSVNRKVYILDGILLLHSISSIRVVSEFRKRLR 139

Query: 129 DKSLEDEEEDEGFS--RVMVSLNGVFVNGIRLKSGIVRELNAGDEVLFVCRDESLCRLQT 186
           +    + EE EGF   R+  S+NGVF+NGIR+K GIVREL  GDEVLFVC +E LC L  
Sbjct: 140 NYDQLEGEEKEGFECLRIRFSMNGVFINGIRVKRGIVRELCTGDEVLFVCGNEGLCNLGV 199

Query: 187 RIGFLILGIIFKEEVV-------LKRPRLVGTMASS-GHSQGSVSSGTRSKRVFALREND 238
           RIGFLI G++FKEEVV       L RP L+GT + S GHSQGSVSSG+R+KRVFA+R N+
Sbjct: 200 RIGFLIQGVVFKEEVVIGSNEIQLGRPCLLGTSSMSVGHSQGSVSSGSRTKRVFAVRANE 259

Query: 239 VSNPDSVFPKLKRRDIFGRASFLLSQCRNILNSNDPVSCIQQIANSDMGIMSTYGCFSTK 298
           V   +  F +LK   I  RA FL+SQCR IL+S DP+S  QQ + SD            +
Sbjct: 260 VMANEYDFLELKLGGIVKRARFLVSQCRQILHSGDPISYFQQCSLSDF-----------R 308

Query: 299 FPGRSSIDGELKVKKIERISQQERKPCDESIYVGQPGSITFEDERVVDLEAEGDPVDPCV 358
              R  ++ +L      R+    R P  +   V     +  +  +  +       ++   
Sbjct: 309 METRDVLNSKLDCGACGRVCDNSRIPVVDGSEVNNAALVFRQAAKCCENSHINLNIE--- 365

Query: 359 HNDHLHHKDSVGISNKNATPGVKSKLLNSVD-----RQNATHFGSMDKSKSLGSSCSPPG 413
           +N  +   + V     +      S++   +D     +++A H     + K+  + C  PG
Sbjct: 366 NNKEIGDMECVSFGGNSMCQKDISEVHFEIDFDYSHKKDAPHLAD-SQMKTQENYCQLPG 424

Query: 414 KKFYLNRLEFMDLTSLNY-DVISLPELLYPVESISRMFIATFTSDILWFMSYCEIPSHLP 472
           KKFYLNRL FM+  S ++ +V+SLPELL+P+E+I R+FIATFTSDILWF+SYCEIPSHLP
Sbjct: 425 KKFYLNRLHFMEHGSFSHQNVVSLPELLHPIENIMRIFIATFTSDILWFLSYCEIPSHLP 484

Query: 473 VTIACHNTERCWSTSADKRTSVPYPNFPNLVLVFPPFPESVAFGENCKKQGIACHHPKLF 532
           VTIACHNTERCWS++ DKR S+PY NFPNL +VFPPFPE++AFG + ++QGIACHHPKL 
Sbjct: 485 VTIACHNTERCWSSNPDKRISMPYSNFPNLSVVFPPFPEAIAFGNDRRRQGIACHHPKLL 544

Query: 533 VLQREDSIRVIVTSANLGAKQWNAVTNTVWWQDFPRRCAPDYLSLFVQTPVEEINQDSRS 592
           VLQRE+SIRVI+TSANL   QW+ VTNT+WWQDFPRR  PD  SLF +    EI+QDSRS
Sbjct: 545 VLQRENSIRVIITSANLVPNQWHNVTNTIWWQDFPRRSTPDLSSLFTRVSDGEISQDSRS 604

Query: 593 DFTAQLASFMASLVIDVPSQAHWIVELTKYDFASAAGHLVASVPGIHSYRNPNLSESTYS 652
           DF AQLA F+ASLVIDVPSQAHW+VELTKY+F  A G+LVAS+PGIHS   P   +    
Sbjct: 605 DFAAQLAGFIASLVIDVPSQAHWVVELTKYNFDGALGYLVASIPGIHSRGTPYACQY--- 661

Query: 653 KPVDHGAIWSSDGKFLGSVETSVVGLSHLFRTAADSNGTQIKKLAAFLGK-SFSAHGMLK 711
                 A+ S D KFLGSVE SVVGLSHLF T+ D+NG  +KKLAAFLG+   +A+GM +
Sbjct: 662 ------AMKSIDVKFLGSVEASVVGLSHLFHTSTDTNGALLKKLAAFLGRFPENAYGMSE 715

Query: 712 ILLRRNTNVPADANAVSVLVPNPDELSDGDCIQLGFMPRDIAKWVSPLWDIGFIRFSGFI 771
           I+LRRNTNVPAD NAVS+L+PNPD+ S GDC+QLGF+PR +AKWVSPLWD GF +FSG+I
Sbjct: 716 IILRRNTNVPADVNAVSILIPNPDKFS-GDCVQLGFLPRYVAKWVSPLWDSGFFKFSGYI 774

Query: 772 SRDEVLAAALEGISKKVQLILHVSQGPKFSDISKMMQIEHVVALSSLIASIQRCRGLWRL 831
              E L AA  G   +         GP F DI KMM  +HV+A+ SL+ASIQRC GLWRL
Sbjct: 775 HPKEALEAASGGNDMR---------GPCFPDIMKMMLPQHVIAVCSLVASIQRCTGLWRL 825

Query: 832 QEVLGQYRWPELQESDFSY-GSSSIGSINAQFLAAFAAASGKKSLRFYDSEESDPEY 887
           QEVL QY+WPE+++SDF Y  SS   SINAQFL+AF+AA+GK+SL+ +DSEESDPE+
Sbjct: 826 QEVLDQYKWPEVEQSDFIYGSSSIGSSINAQFLSAFSAAAGKRSLQLFDSEESDPEW 882

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|224119906\|ref\|XP_002318192.1\| predicted protein [Populus trichocarpa] gi\|222858865\|gb\|EEE96412.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|359493967\|ref\|XP_002283806.2\| PREDICTED: uncharacterized protein LOC100243589 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|297806769\|ref\|XP_002871268.1\| predicted protein [Arabidopsis lyrata subsp. lyrata] gi\|297317105\|gb\|EFH47527.1\| predicted protein [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi\|42567721\|ref\|NP_196357.2\| forkhead-associated domainand FHA domain-containing protein [Arabidopsis thaliana] gi\|30102672\|gb\|AAP21254.1\| At5g07400 [Arabidopsis thaliana] gi\|110743660\|dbj\|BAE99667.1\| hypothetical protein [Arabidopsis thaliana] gi\|332003770\|gb\|AED91153.1\| forkhead-associated domainand FHA domain-containing protein [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|147770909\|emb\|CAN67540.1\| hypothetical protein VITISV_012382 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|302142785\|emb\|CBI20080.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|7576178\|emb\|CAB87929.1\| hypothetical protein [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|357520291\|ref\|XP_003630434.1\| Tyrosyl-DNA phosphodiesterase [Medicago truncatula] gi\|355524456\|gb\|AET04910.1\| Tyrosyl-DNA phosphodiesterase [Medicago truncatula]	Back alignment and taxonomy information

>gi\|242072904\|ref\|XP_002446388.1\| hypothetical protein SORBIDRAFT_06g015125 [Sorghum bicolor] gi\|241937571\|gb\|EES10716.1\| hypothetical protein SORBIDRAFT_06g015125 [Sorghum bicolor]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		903
TAIR\|locus:2183319		1084	AT5G07400 [Arabidopsis thalian	0.706	0.588	0.506	1.2e-159
UNIPROTKB\|G4N013		555	MGG_06176 "Uncharacterized pro	0.133	0.218	0.301	2.7e-05
TAIR\|locus:2150931		605	TDP1 "tyrosyl-DNA phosphodiest	0.122	0.183	0.303	0.00033

TAIR\|locus:2183319 AT5G07400 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1555 (552.4 bits), Expect = 1.2e-159, P = 1.2e-159
 Identities = 338/667 (50%), Positives = 433/667 (64%)

Query:   227 RSKRVFALRENDVSNPDSVFPKLKRRDIFGRASFLLSQCRNILNSNDPVSCIQQIANSDM 286
             RSKRVFA  EN++++P S F   K   +  R + L+S CR+IL S+DP+SC++    S  
Sbjct:   189 RSKRVFAPMENEINSPVSGFYPPKAVGVVERVNSLVSYCRHILKSDDPLSCLRLSIISHS 248

Query:   287 GIMSTYGCFSTKFPGRSSIDGELK-VKKIERISQQERKPCDESIYVGQPGSITFEDER-- 343
             G      C S  F  +  I  + + VK  E             + + +P S    D R  
Sbjct:   249 GKECLSCCTSKMFRSKVGIVADDRGVKSAEINHDMGHGLSGLRLSIERPNSNLHVDRRLG 308

Query:   344 VVDLEAEGDPVDPCVHNDHLHHKDSVGISNKNATPGVKSKLLNSVDRQNATHFGSMDKSK 403
             V DL +E       + N+         IS+K  T      L    ++ N      ++K K
Sbjct:   309 VSDLISE-------IENEFAA---CTFISDKTRT-----MLPFDGEKVNTPDITCINKEK 353

Query:   404 SLGSSCSPPGKKFYLNRLEFMDLTSLNYD-VISLPELLYPVESISRMFIATFTSDILWFM 462
             S  SS   PGK FYLNRL++++ +S     V+SLPELL+PVESI ++F+ATFTSDILWF+
Sbjct:   354 SYQSSLQAPGKNFYLNRLQYIEQSSTGCQRVVSLPELLHPVESIQQIFLATFTSDILWFL 413

Query:   463 SYCEIPSHLPVTIACHNTERCWSTSADKRTSVPYXXXXXXXXXXXXXXESVAFGENCKKQ 522
             + C+ P HLPVTIACHN ERCWS++ D RT+VP               E +AFG++   +
Sbjct:   414 TCCDTPRHLPVTIACHNAERCWSSNPDARTAVPLPNYPNVTMVYPPFPEEIAFGKDRTNR 473

Query:   523 GIACHHPKLFVLQREDSIRVIVTSANLGAKQWNAVTNTVWWQDFPRRCAPDYLSLFVQTP 582
             GIACHHPKLF+LQR+DSIRVI+TSANL A+QWN VTNTVWWQDFPRR  PD LSLF    
Sbjct:   474 GIACHHPKLFILQRKDSIRVIITSANLVARQWNDVTNTVWWQDFPRRADPDLLSLFGHCQ 533

Query:   583 VEEINQDSRSDFTAQLASFMASLVIDVPSQAHWIVELTKYDFASAAGHLVASVPGIHSYR 642
               E N   + DF AQLA F ASL+ DVPSQAHWI+E TKY+F  +AGHLVASVPGIHSY+
Sbjct:   534 -RETNHGLKPDFCAQLAGFAASLLTDVPSQAHWILEFTKYNFEHSAGHLVASVPGIHSYK 592

Query:   643 NPNLSESTYSKPVDHGAIWSSDGKFLGSVETSVVGLSHLFRTAADSNGTQIKKLAAFLGK 702
                L+ES  S       I+S +  FLGSVE SVVGLS+LFR+A DS G Q+K+LA+++ +
Sbjct:   593 PSYLTESGCSN-----TIFSEE--FLGSVEASVVGLSYLFRSANDSTGAQLKRLASYIRR 645

Query:   703 SF-SAHGMLKILLRRNTNVPADANAVSVLVPNPDELSDGDCIQLGFMPRDIAKWVSPLWD 761
             +  ++ GML+++LRRNTNVPAD NAV VLVPNPD+ S  D +QLGF+PR IAKWVSPLWD
Sbjct:   646 TRENSLGMLELVLRRNTNVPADPNAVRVLVPNPDDDSRDDFVQLGFLPRSIAKWVSPLWD 705

Query:   762 IGFIRFSGFISRDEVLAAALEGISKKVQLILHVSQGPKFSDISKMMQIEHVVALSSLIAS 821
             IGF +F G++ RDEVL AA    ++KVQL+LHV QG   SD+SK++Q  HVVAL SLIAS
Sbjct:   706 IGFFKFVGYVYRDEVLGAASCRSNEKVQLVLHVLQGVSISDMSKLIQPYHVVALCSLIAS 765

Query:   822 IQRCRGLWRLQEVLGQYRWPELQESDFXXXXXXXX-XXNXXXXXXXXXXSGKKSLRFYDS 880
             +QRC G+WRLQEVLG+Y+WPE QESDF                      +GKK+L+ +DS
Sbjct:   766 LQRCTGIWRLQEVLGRYKWPESQESDFVYSASSIGGSATTGFQADFSSAAGKKALQHFDS 825

Query:   881 EESDPEY 887
             +ESDPE+
Sbjct:   826 QESDPEW 832

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0008081 "phosphoric diester hydrolase activity" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016818 "hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides" evidence=IEA

UNIPROTKB\|G4N013 MGG_06176 "Uncharacterized protein" [Magnaporthe oryzae 70-15 (taxid:242507)]	Back alignment and assigned GO terms

TAIR\|locus:2150931 TDP1 "tyrosyl-DNA phosphodiesterase 1" [Arabidopsis thaliana (taxid:3702)]	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

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	fgenesh4_pg.C_LG_XII001080	hypothetical protein (1131 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
		Sorry, there are no predicted associations at the current settings.

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		903
cd09122		145	cd09122, PLDc_Tdp1_1, Catalytic domain, repeat 1,	4e-32
pfam06087		433	pfam06087, Tyr-DNA_phospho, Tyrosyl-DNA phosphodie	2e-14
cd00060		102	cd00060, FHA, Forkhead associated domain (FHA); fo	5e-14
pfam08797		95	pfam08797, HIRAN, HIRAN domain	3e-11
cd09194		166	cd09194, PLDc_yTdp1_1, Catalytic domain, repeat 1,	3e-08
pfam00498		67	pfam00498, FHA, FHA domain	3e-08
smart00910		90	smart00910, HIRAN, The HIRAN protein (HIP116, Rad5	1e-07
cd09193		169	cd09193, PLDc_mTdp1_1, Catalytic domain, repeat 1,	8e-06
smart00240		52	smart00240, FHA, Forkhead associated domain	1e-05

>gnl\|CDD\|197221 cd09122, PLDc_Tdp1_1, Catalytic domain, repeat 1, of Tyrosyl-DNA phosphodiesterase	Back alignment and domain information

 Score =  121 bits (306), Expect = 4e-32
 Identities = 43/168 (25%), Positives = 67/168 (39%), Gaps = 24/168 (14%)

Query: 434 ISLPELLYPVESISRMFIATFTSDILWFMSYCEIPSHLPVTIACHNTERCWSTSADKRTS 493
           +SL +LL   + +    ++++  DI W +S   +   +PVTI     +            
Sbjct: 1   LSLKDLLGG-DDLESALLSSYMLDIDWLLSQLPLLKIVPVTIVHGEKKEATKR---ASMI 56

Query: 494 VPYPNFPNLVLVFPPFPESVAFGENCKKQGIACHHPKLFVLQREDSIRVIVTSANLGAKQ 553
                 PN  LV+PP P            G   HH KL +L+    +RV++ +ANL    
Sbjct: 57  AQLNGLPNWTLVYPPLP-----------GGYGTHHSKLILLKYPTGLRVVIPTANLTPYD 105

Query: 554 WNAVTNTVWWQDFPRRCAPDYLSLFVQTPVEEINQDSRSDFTAQLASF 601
           W   +  +W QDFP +      S          N ++ SDF   L  F
Sbjct: 106 WGEKSQGIWVQDFPLKNKRSASSG---------NNENPSDFKEDLIRF 144

Catalytic domain, repeat 1, of Tyrosyl-DNA phosphodiesterase (Tdp1, EC 3.1.4.-), which exists in eukaryotes but not in prokaryotes. Tdp1 acts as an important DNA repair enzyme that removes stalled topoisomerase I-DNA complexes by catalyzing the hydrolysis of a phosphodiester bond between a tyrosine side chain and a DNA 3'-phosphate. It is a monomeric protein that contains two copies of a variant HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue), which consists of the highly conserved histidine and lysine residues, but lacks the aspartate residue that is well conserved in other phospholipase D (PLD, EC 3.1.4.4) enzymes. Thus, this family represents a distinct class within the PLD superfamily. Like other PLD enzymes, Tdp1 may utilize a common two-step general acid/base catalytic mechanism, involving a DNA-enzyme intermediate to cleave phosphodiester bonds. A single active site involved in phosphatidyl group transfer would be formed by the two variant HKD motifs from the N- and C-terminal domains in a pseudodimeric way. Length = 145

>gnl\|CDD\|218888 pfam06087, Tyr-DNA_phospho, Tyrosyl-DNA phosphodiesterase	Back alignment and domain information

>gnl\|CDD\|238017 cd00060, FHA, Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins	Back alignment and domain information

>gnl\|CDD\|220020 pfam08797, HIRAN, HIRAN domain	Back alignment and domain information

>gnl\|CDD\|197290 cd09194, PLDc_yTdp1_1, Catalytic domain, repeat 1, of yeast tyrosyl-DNA phosphodiesterase	Back alignment and domain information

>gnl\|CDD\|215951 pfam00498, FHA, FHA domain	Back alignment and domain information

>gnl\|CDD\|214906 smart00910, HIRAN, The HIRAN protein (HIP116, Rad5p N-terminal) is found in the N-terminal regions of the SWI2/SNF2 proteins typified by HIP116 and Rad5p	Back alignment and domain information

>gnl\|CDD\|197289 cd09193, PLDc_mTdp1_1, Catalytic domain, repeat 1, of metazoan tyrosyl-DNA phosphodiesterase	Back alignment and domain information

>gnl\|CDD\|214578 smart00240, FHA, Forkhead associated domain	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		903
PF06087		443	Tyr-DNA_phospho: Tyrosyl-DNA phosphodiesterase; In	100.0
KOG2031		519	consensus Tyrosyl-DNA phosphodiesterase [Replicati	100.0
PF00498		68	FHA: FHA domain; InterPro: IPR000253 The forkhead-	99.47
cd00060		102	FHA Forkhead associated domain (FHA); found in euk	99.1
TIGR03354		396	VI_FHA type VI secretion system FHA domain protein	98.96
KOG1882		293	consensus Transcriptional regulator SNIP1, contain	98.93
COG1716		191	FOG: FHA domain [Signal transduction mechanisms]	98.93
smart00240		52	FHA Forkhead associated domain. Found in eukaryoti	98.7
PLN02927		668	antheraxanthin epoxidase/zeaxanthin epoxidase	98.67
COG3456		430	Predicted component of the type VI protein secreti	98.4
KOG1881		793	consensus Anion exchanger adaptor protein Kanadapt	97.87
KOG0615		475	consensus Serine/threonine protein kinase Chk2 and	97.8
KOG1880		337	consensus Nuclear inhibitor of phosphatase-1 [Gene	97.06
TIGR02500		410	type_III_yscD type III secretion apparatus protein	95.99
PF06087		443	Tyr-DNA_phospho: Tyrosyl-DNA phosphodiesterase; In	95.01
KOG0245		1221	consensus Kinesin-like protein [Cytoskeleton]	91.25
PF08797		107	HIRAN: HIRAN domain; InterPro: IPR014905 The HIRAN	91.17
TIGR01663		526	PNK-3'Pase polynucleotide 5'-kinase 3'-phosphatase	90.51

>PF06087 Tyr-DNA_phospho: Tyrosyl-DNA phosphodiesterase; InterPro: IPR010347 Covalent intermediates between topoisomerase I and DNA can become dead-end complexes that lead to cell death	Back alignment and domain information

Probab=100.00  E-value=1.7e-52  Score=471.62  Aligned_cols=301  Identities=26%  Similarity=0.435  Sum_probs=196.0

Q ss_pred             CcEEEEEeccCCCC-CCCCCccccccccCCchhHHHHHHhhcccchhhhhhhcCCC-C-CCcEEEEEccCccccccCCCC
Q 002593          414 KKFYLNRLEFMDLT-SLNYDVISLPELLYPVESISRMFIATFTSDILWFMSYCEIP-S-HLPVTIACHNTERCWSTSADK  490 (903)
Q Consensus       414 spFyLnrI~~lp~~-~~n~dtISL~DLLgP~~~L~~allfnF~~DidWLLs~f~~~-r-~lpVtIVvh~~~~~wk~e~~~  490 (903)
                      .+|++|++.+.+.. ..+.++|||+|||++ ++|+++|+||||+|++|||++|+.. + .+||+++.+.......    .
T Consensus         2 ~~~~~~~i~~~~~~~~~~~~~itl~dil~~-~~l~~~~~~nf~~D~~wll~~~~~~~~~~~~i~~v~g~~~~~~~----~   76 (443)
T PF06087_consen    2 FKLYLTTIYDLPPRSNNNPDTITLEDILGD-PDLEEALLFNFMIDLDWLLSQFPPSTRKNIPITIVHGTKDPPDK----R   76 (443)
T ss_dssp             CEEEEBTTTTS-GG--GTTTEE-HHHHCSG-TTEEEEEEE-SSEEHHHHHCCS-CCGTTCEEEEEECTSEEHHHH----H
T ss_pred             cceEEeeecCCCccccCCCCcEeHHHHcCC-ccHHHHHhhhheeeHHHHHHhCCHhhcccceEEEEeCCCcchhh----h
Confidence            46899999999987 347999999999997 6899999999999999999999842 2 4688886442222111    1


Q ss_pred             CcCCCCCCCCCeEEEcCCCCccccccccccCCCcccccceEEEEEeCCc-EEEEEeCCCCCHHhhccccCeEEeecC-CC
Q 002593          491 RTSVPYPNFPNLVLVFPPFPESVAFGENCKKQGIACHHPKLFVLQREDS-IRVIVTSANLGAKQWNAVTNTVWWQDF-PR  568 (903)
Q Consensus       491 rl~~~~~~~pNv~li~PpMPe~I~FG~d~~~~g~GtHHSKMmIL~Y~D~-LRVVI~TANLi~~DW~~~TQ~VWiQDF-P~  568 (903)
                      .+......++|+++|.||||  ++||         |||||||||+|+|+ ||||||||||++.||+.+||+||+||| |+
T Consensus        77 ~~~~~~~~~~nv~~~~~~mp--~~~g---------~hHsKm~ll~y~~~~lRVvI~TaNl~~~Dw~~~~q~vw~~d~lP~  145 (443)
T PF06087_consen   77 EIRQQAAIYPNVKLIFPPMP--IPFG---------THHSKMMLLFYEDGSLRVVIPTANLTPYDWNNKTQGVWIQDFLPR  145 (443)
T ss_dssp             HHHHHHCCHTTEEEEEE-----STT-----------B--EEEEEEETTCEEEEEEESS-BSHHHHCSSB-EEEE---E-B
T ss_pred             hhhhhcccCCCeEEEccCCC--cccc---------cccceeEEEEeCCccEEEEEECCCCCHHHHCCcceeEEEecccCc
Confidence            11112347899999999999  4687         99999999999987 999999999999999999999999999 99


Q ss_pred             CCCCCccccccCCCcccccCCCCCcHHHHHHHHHHHhccCCCchHHHHHhhcccccccccEEEEEecCCcccCCCCCCCC
Q 002593          569 RCAPDYLSLFVQTPVEEINQDSRSDFTAQLASFMASLVIDVPSQAHWIVELTKYDFASAAGHLVASVPGIHSYRNPNLSE  648 (903)
Q Consensus       569 l~~~~~~~~~~~~~~~e~~~~~~sdFk~dL~~YL~sy~~~~Ps~~~~i~~L~kyDFSsakv~LVaSVPG~H~g~~~~~~~  648 (903)
                      ++.....           ....+++|+.+|++||.+|+.  +....|++.|++||||+++|+||+||||+|. .+    .
T Consensus       146 ~~~~~~~-----------~~~~~~~F~~dL~~yL~~y~~--~~~~~~~~~l~~yDFS~~~v~lV~SvPG~h~-~~----~  207 (443)
T PF06087_consen  146 LPSSKSS-----------SEESGSRFKKDLVAYLNSYGK--SPLDKLIERLRKYDFSSARVHLVASVPGKHK-ED----K  207 (443)
T ss_dssp             -ECTS-S-------------SSTTHHHHHHHHHHHTT----HHHHHCHHHHHTEE-CCGTSEEEEE-SECCC-GG----G
T ss_pred             ccccccc-----------cCCCCCchHHHHHHHHHHhCC--cchhHHHHHHHhcCCccCceEEEeccCcccc-CC----C
Confidence            9752211           135789999999999999984  3366899999999999999999999999999 21    1


Q ss_pred             CcccCCCcCCcccccccccccceeccc----cCcceeEEeecccccchhhhhH-HHhhhhh-hcccchhh--hhc-----
Q 002593          649 STYSKPVDHGAIWSSDGKFLGSVETSV----VGLSHLFRTAADSNGTQIKKLA-AFLGKSF-SAHGMLKI--LLR-----  715 (903)
Q Consensus       649 ~~~G~~~l~n~~~~~~~s~LgSv~~s~----~g~s~l~~q~~DSs~asLg~~~-~wL~~~~-~~~~~~E~--v~~-----  715 (903)
                      ..||+++|        ++.|.......    ....+++.|+  ||+++++... .||...+ ..+.....  ...     
T Consensus       208 ~~~G~~~L--------~~~L~~~~~~~~~~~~~~~~~~~Q~--SSIGs~~~~~~~Wl~~~f~~sl~~~~~~~~~~~~~~~  277 (443)
T PF06087_consen  208 DKWGHMRL--------RKVLKRLGLPSNKDKDKESDIVCQF--SSIGSLGSSPKDWLTSEFLTSLYPASFSSPSTPSSKS  277 (443)
T ss_dssp             GGSHHHHH--------HHHHHHCCTT---TTCCCCEEEEE---SBB---SSSTTTTTTTHHHHHCCHHCCT------HHH
T ss_pred             cchhHHHH--------HHHHHhccccccCCcCCCCeEEEEc--ccccccCcchhhhHHHHHHHHHhhccccccccccccc
Confidence            26997655        44444433332    1246888898  8899997555 3765433 33322100  000     


Q ss_pred             cCCCCCCCCCCeEEEecCCCccc-------CCcee-----------ecCCcchhhhcccCC
Q 002593          716 RNTNVPADANAVSVLVPNPDELS-------DGDCI-----------QLGFMPRDIAKWVSP  758 (903)
Q Consensus       716 sn~n~p~~~~~~~IIfPT~deVr-------sg~Sk-----------QL~fL~~~l~kW~s~  758 (903)
                      .........++++|||||.++|+       +|+++           +..||+++||+|.++
T Consensus       278 ~~~~~~~~~~~~~IvfPT~e~Vr~S~~G~~~ggsi~~~~~~~~~~~~~~~l~~~~~~w~~~  338 (443)
T PF06087_consen  278 SSSQQENNRPPLKIVFPTVEEVRNSPEGYNGGGSIPFKYKWWEPNFPQEWLRPYFHKWYAS  338 (443)
T ss_dssp             HHHHCCHHTEEEEEE--BCHHHCTSTTGGGGGGGSB--HC--GHHCCHHHHHHCCE-EEEC
T ss_pred             cccccccCCCCceEECCCHHHHhhCccCCcCceeEEecchhccccchHHHHHHHHhhhccc
Confidence            00011123678999999999999       55552           235889999999887

Tyrosyl-DNA phosphodiesterase can hydrolyse the bond between topoisomerase I and DNA [].; GO: 0008081 phosphoric diester hydrolase activity, 0006281 DNA repair, 0005634 nucleus; PDB: 3SQ8_A 3SQ5_B 3SQ3_A 1Q32_D 3SQ7_A 1QZQ_A 1RGU_B 1RG2_B 1MU9_B 1RFI_B ....

>KOG2031 consensus Tyrosyl-DNA phosphodiesterase [Replication, recombination and repair]	Back alignment and domain information

>PF00498 FHA: FHA domain; InterPro: IPR000253 The forkhead-associated (FHA) domain [] is a phosphopeptide recognition domain found in many regulatory proteins	Back alignment and domain information

>cd00060 FHA Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins	Back alignment and domain information

>TIGR03354 VI_FHA type VI secretion system FHA domain protein	Back alignment and domain information

>KOG1882 consensus Transcriptional regulator SNIP1, contains FHA domain [Signal transduction mechanisms]	Back alignment and domain information

>COG1716 FOG: FHA domain [Signal transduction mechanisms]	Back alignment and domain information

>smart00240 FHA Forkhead associated domain	Back alignment and domain information

>PLN02927 antheraxanthin epoxidase/zeaxanthin epoxidase	Back alignment and domain information

>COG3456 Predicted component of the type VI protein secretion system, contains a FHA domain [Intracellular trafficking, secretion, and vesicular transport; Signal transduction mechanisms]	Back alignment and domain information

>KOG1881 consensus Anion exchanger adaptor protein Kanadaptin, contains FHA domain [General function prediction only]	Back alignment and domain information

>KOG0615 consensus Serine/threonine protein kinase Chk2 and related proteins [Cell cycle control, cell division, chromosome partitioning]	Back alignment and domain information

>KOG1880 consensus Nuclear inhibitor of phosphatase-1 [General function prediction only]	Back alignment and domain information

>TIGR02500 type_III_yscD type III secretion apparatus protein, YscD/HrpQ family	Back alignment and domain information

>PF06087 Tyr-DNA_phospho: Tyrosyl-DNA phosphodiesterase; InterPro: IPR010347 Covalent intermediates between topoisomerase I and DNA can become dead-end complexes that lead to cell death	Back alignment and domain information

>KOG0245 consensus Kinesin-like protein [Cytoskeleton]	Back alignment and domain information

>PF08797 HIRAN: HIRAN domain; InterPro: IPR014905 The HIRAN protein (HIP116, Rad5p N-terminal) is found in the N-terminal regions of the SWI2/SNF2 proteins typified by HIP116 and Rad5p	Back alignment and domain information

>TIGR01663 PNK-3'Pase polynucleotide 5'-kinase 3'-phosphatase	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		903
1qzq_A		483	Human Tyrosyl Dna Phosphodiesterase Length = 483		7e-06
1mu7_A		485	Crystal Structure Of A Human Tyrosyl-dna Phosphodie		9e-06
1jy1_A		464	Crystal Structure Of Human Tyrosyl-Dna Phosphodiest		2e-04

>pdb|1QZQ|A Chain A, Human Tyrosyl Dna Phosphodiesterase Length = 483

Back alignment and structure

Iteration: 1

Score = 49.7 bits (117), Expect = 7e-06, Method: Compositional matrix adjust. Identities = 30/115 (26%), Positives = 54/115 (46%), Gaps = 12/115 (10%) Query: 523 GIACHHPKLFVLQREDSIRVIVTSANLGAKQWNAVTNTVWWQDFPRRCAPDYLSLFVQTP 582 HH K+ +L E+ +RV++ ++NL W+ T +W +P Y + T Sbjct: 133 AFGTHHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIW-------LSPLYPRIADGT- 184 Query: 583 VEEINQDSRSDFTAQLASFMASLVIDVPSQAHWIVELTKYDFASAAGHLVASVPG 637 + +S + F A L S++ + + PS WI + K+D + +L+ S PG Sbjct: 185 --HKSGESPTHFKADLISYL--MAYNAPSLKEWIDVIHKHDLSETNVYLIGSTPG 235

PyMOL of 1qzq

>pdb|1MU7|A Chain A, Crystal Structure Of A Human Tyrosyl-dna Phosphodiesterase (tdp1)- Tungstate Complex Length = 485

Back alignment and structure

>pdb|1JY1|A Chain A, Crystal Structure Of Human Tyrosyl-Dna Phosphodiesterase (Tdp1) Length = 464

Back alignment and structure

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		903
1jy1_A		464	TDP1, tyrosyl-DNA phosphodiesterase; PLD superfami	1e-35
3sq7_A		470	Tyrosyl-DNA phosphodiesterase 1; DNA binding, nucl	1e-33
1q32_A		544	TDP1P;, tyrosyl-DNA phosphodiesterase; DNA repair,	9e-33
1lgp_A		116	Cell cycle checkpoint protein CHFR; FHA, tungstate	1e-12
2jpe_A		140	Nuclear inhibitor of protein phosphatase 1; FHA do	4e-12
1uht_A		118	Expressed protein; FHA domain, beta-sandwich, anti	1e-11
3gqs_A		106	Adenylate cyclase-like protein; FHA domain, struct	6e-11
2pie_A		138	E3 ubiquitin-protein ligase RNF8; FHA domain, comp	7e-11
1qu5_A		182	Protein kinase SPK1; FHA, RAD53, transferase; NMR	5e-10
3hx1_A		131	SLR1951 protein; P74513_SYNY3, adenylate cyclase-l	5e-10
2csw_A		145	Ubiquitin ligase protein RNF8; 11-stranded beta sa	7e-10
1dmz_A		158	Protein (protein kinase SPK1); beta-sandwich, anti	1e-09
1g3g_A		164	Protien kinase SPK1; FHA domain, RAD53, phosphopep	2e-09
1g6g_A		127	Protein kinase RAD53; beta-sandwich, phosphopeptid	2e-09
2jqj_A		151	DNA damage response protein kinase DUN1; protein/p	8e-09
3po8_A		100	RV0020C protein, putative uncharacterized protein	2e-08
3va4_A		132	Mediator of DNA damage checkpoint protein 1; cell	4e-08
1r21_A		128	Antigen KI-67; beta sandwich, cell cycle; NMR {Hom	4e-08
2xt9_B		115	Putative signal transduction protein GARA; lyase-s	5e-08
3els_A		158	PRE-mRNA leakage protein 1; intrinsically unstruct	9e-08
3oun_A		157	Putative uncharacterized protein TB39.8; peptidogl	9e-08
2kfu_A		162	RV1827 PThr 22; FHA domain, phosphorylation, intra	1e-07
1gxc_A		149	CHK2, CDS1, serine/threonine-protein kinase CHK2;	1e-07
2kb3_A		143	Oxoglutarate dehydrogenase inhibitor; forkhead-ass	2e-07
3elv_A		205	PRE-mRNA leakage protein 1; intrinsically unstruct	1e-06
1mzk_A		139	Kinase associated protein phosphatase; beta sandwi	1e-06
2l1i_A		122	HLTF protein; hiran domain, transcription factor,	8e-05
3i6u_A		419	CDS1, serine/threonine-protein kinase CHK2; Ser/Th	2e-04

>1jy1_A TDP1, tyrosyl-DNA phosphodiesterase; PLD superfamily, hydrolase; 1.69A {Homo sapiens} SCOP: d.136.1.3 d.136.1.3 PDB: 1rff_A* 1mu9_A 1nop_A 1mu7_A* 1rfi_A* 1rg1_A* 1rg2_A* 1rgt_A* 1rgu_A* 1rh0_A* 1qzq_A Length = 464	Back alignment and structure

 Score =  140 bits (353), Expect = 1e-35
 Identities = 59/370 (15%), Positives = 121/370 (32%), Gaps = 53/370 (14%)

Query: 400 DKSKSLGSSCSPPGKKFYLNRLEFMDLTSLNYDVISLPELLYPVE-SISRMFIATFTSDI 458
                +    +P   +FYL R+  +     N   + + ++L P+  ++       +  D+
Sbjct: 8   QDIWDMLDKGNPF--QFYLTRVSGVKPKY-NSGALHIKDILSPLFGTLVSSAQFNYCFDV 64

Query: 459 LWFMS-YCEIPSHLPVTIACHNTERCWSTSADKRTSVPYPNFPNLVLVFPPFPESVAFGE 517
            W +  Y       P+ +  H  +R        +       + N+ L         AFG 
Sbjct: 65  DWLVKQYPPEFRKKPILLV-HGDKREAKAHLHAQ----AKPYENISLCQAKLDI--AFG- 116

Query: 518 NCKKQGIACHHPKLFVLQREDSIRVIVTSANLGAKQWNAVTNTVWWQDFPRRCAPDYLSL 577
                    HH K+ +L  E+ +RV++ ++NL    W+  T  +W      R A      
Sbjct: 117 --------THHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADG---- 164

Query: 578 FVQTPVEEINQDSRSDFTAQLASFMASLVIDVPSQAHWIVELTKYDFASAAGHLVASVPG 637
                    + +S + F A L S++ +   + PS   WI  + K+D +    +L+ S PG
Sbjct: 165 ------THKSGESPTHFKANLISYLTAY--NAPSLKEWIDVIHKHDLSETNVYLIGSTPG 216

Query: 638 IHSYRNPNLSESTYSKPVDHGAIWSSDGKFLGSVETSVVGLSHLFRTAADSNGTQIKKLA 697
                  +       K +      S        V      +  L          + K L 
Sbjct: 217 RFQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSL-------GADESKWLC 269

Query: 698 AFLGKSFSAHGMLKILLRRNTNVPADANAVSVLVPNPDELSD-------GDCIQLGFMPR 750
           +   +S    G      + +      +  + ++ P+ + +         G  +       
Sbjct: 270 SEFKESMLTLG------KESKTPGKSSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTA 323

Query: 751 DIAKWVSPLW 760
           +   W+   +
Sbjct: 324 EKQNWLHSYF 333

PyMOL of 1jy1

>3sq7_A Tyrosyl-DNA phosphodiesterase 1; DNA binding, nuclear, hydrolase; 2.00A {Saccharomyces cerevisiae} PDB: 3sq5_A 3sq8_A* 3sq3_A Length = 470	Back alignment and structure

>1q32_A TDP1P;, tyrosyl-DNA phosphodiesterase; DNA repair, replication, transcription, hydrolase, replication,transcription, hydrolase; 2.03A {Saccharomyces cerevisiae} SCOP: d.136.1.3 d.136.1.3 Length = 544	Back alignment and structure

>1lgp_A Cell cycle checkpoint protein CHFR; FHA, tungstate, domain swapping; 2.00A {Homo sapiens} SCOP: b.26.1.2 PDB: 1lgq_A Length = 116	Back alignment and structure

>2jpe_A Nuclear inhibitor of protein phosphatase 1; FHA domain, NIPP1, mRNA splicing, transcription; NMR {Mus musculus} Length = 140	Back alignment and structure

>1uht_A Expressed protein; FHA domain, beta-sandwich, antiparallel beta-sheets, phosphopeptide binding motif, structural genomics; NMR {Arabidopsis thaliana} SCOP: b.26.1.2 Length = 118	Back alignment and structure

>3gqs_A Adenylate cyclase-like protein; FHA domain, structural genomics, PSI-2, protein structure in midwest center for structural genomics, MCSG; 2.20A {Chlamydia trachomatis} Length = 106	Back alignment and structure

>2pie_A E3 ubiquitin-protein ligase RNF8; FHA domain, complex, ligase, signaling protein; HET: TPO; 1.35A {Homo sapiens} SCOP: b.26.1.2 Length = 138	Back alignment and structure

>1qu5_A Protein kinase SPK1; FHA, RAD53, transferase; NMR {Saccharomyces cerevisiae} SCOP: b.26.1.2 Length = 182	Back alignment and structure

>3hx1_A SLR1951 protein; P74513_SYNY3, adenylate cyclase-like protein, NESG, structural genomics, PSI-2, protein structure initiative; 2.50A {Synechocystis SP} Length = 131	Back alignment and structure

>2csw_A Ubiquitin ligase protein RNF8; 11-stranded beta sandwich, ring finger protein 8, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: b.26.1.2 Length = 145	Back alignment and structure

>1dmz_A Protein (protein kinase SPK1); beta-sandwich, antiparallel beta-sheets, transferase; NMR {Saccharomyces cerevisiae} SCOP: b.26.1.2 PDB: 1fhq_A 1fhr_A* 1j4k_A* 1j4l_A* 1k2m_A* 1k2n_A* Length = 158	Back alignment and structure

>1g3g_A Protien kinase SPK1; FHA domain, RAD53, phosphopeptide, phosphoprotein, transferase; NMR {Saccharomyces cerevisiae} SCOP: b.26.1.2 PDB: 1j4o_A 1j4p_A* 1j4q_A* 1k3j_A 1k3n_A* 1k3q_A* 2a0t_A* 2jqi_A* Length = 164	Back alignment and structure

>1g6g_A Protein kinase RAD53; beta-sandwich, phosphopeptide complex, cell cycle; HET: TPO; 1.60A {Saccharomyces cerevisiae} SCOP: b.26.1.2 Length = 127	Back alignment and structure

>2jqj_A DNA damage response protein kinase DUN1; protein/phosphopeptide, cell cycle; HET: DNA; NMR {Saccharomyces cerevisiae} PDB: 2jql_A* Length = 151	Back alignment and structure

>3po8_A RV0020C protein, putative uncharacterized protein TB39.8; FHA domain, synthetic peptide, peptide binding protein; 1.50A {Mycobacterium tuberculosis} PDB: 3poa_A* 2lc1_A Length = 100	Back alignment and structure

>3va4_A Mediator of DNA damage checkpoint protein 1; cell cycle, FHA domain, DNA-damage, CHK2 and MDC1 dimerizati; HET: TPO; 1.54A {Mus musculus} PDB: 3va1_A* 3umz_A 3unm_A 3unn_A* 3uot_A* 3un0_B Length = 132	Back alignment and structure

>1r21_A Antigen KI-67; beta sandwich, cell cycle; NMR {Homo sapiens} SCOP: b.26.1.2 PDB: 2aff_A* Length = 128	Back alignment and structure

>2xt9_B Putative signal transduction protein GARA; lyase-signaling protein complex, KDH, KGD; HET: TPP; 2.20A {Mycobacterium smegmatis} Length = 115	Back alignment and structure

>3els_A PRE-mRNA leakage protein 1; intrinsically unstructured domain, forkhead-associated domai domain, PRE-mRNA retention and splicing; 1.80A {Saccharomyces cerevisiae} Length = 158	Back alignment and structure

>3oun_A Putative uncharacterized protein TB39.8; peptidoglycan, Ser/Thr kinase, pseudokinase, FHA domain, REG phosphorylation; HET: TPO; 2.71A {Mycobacterium tuberculosis} Length = 157	Back alignment and structure

>2kfu_A RV1827 PThr 22; FHA domain, phosphorylation, intramolecular interaction, glutamate metabolism, phosphoprotein, protein binding; HET: TPO; NMR {Mycobacterium tuberculosis} PDB: 2kkl_A Length = 162	Back alignment and structure

>1gxc_A CHK2, CDS1, serine/threonine-protein kinase CHK2; phosphoprotein-binding domain, checkpoint kinase, transferase; HET: TPO; 2.7A {Homo sapiens} SCOP: b.26.1.2 Length = 149	Back alignment and structure

>2kb3_A Oxoglutarate dehydrogenase inhibitor; forkhead-associated domain, kinase substrate, GARA, FHA, cytoplasm, phosphoprotein; HET: TPO; NMR {Corynebacterium glutamicum} PDB: 2kb4_A Length = 143	Back alignment and structure

>3elv_A PRE-mRNA leakage protein 1; intrinsically unstructured domain, forkhead-associated domai domain, PRE-mRNA retention and splicing; 2.40A {Saccharomyces cerevisiae} PDB: 2jkd_A Length = 205	Back alignment and structure

>2l1i_A HLTF protein; hiran domain, transcription factor, DNA repair, transc regulation, transcription, structural genomics, structural consortium, SGC; NMR {Homo sapiens} Length = 122	Back alignment and structure

>3i6u_A CDS1, serine/threonine-protein kinase CHK2; Ser/Thr protein kinase, FHA domain, ATP-binding, cell cycle, mutation, LI-fraumeni syndrome, magnesium; 3.00A {Homo sapiens} PDB: 3i6w_A Length = 419	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

No hit with probability above 80.00

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		903
d1q32a1		215	d.136.1.3 (A:79-293) Tyrosyl-DNA phosphodiesterase	2e-47
d1jy1a1		206	d.136.1.3 (A:145-350) Tyrosyl-DNA phosphodiesteras	6e-32
d1dmza_		158	b.26.1.2 (A:) Phosphotyrosine binding domain of Ra	4e-10
d1uhta_		118	b.26.1.2 (A:) FHA domain containing protein At4G14	7e-09
d1g6ga_		127	b.26.1.2 (A:) Phosphotyrosine binding domain of Ra	3e-05
d1jy1a2		258	d.136.1.3 (A:351-608) Tyrosyl-DNA phosphodiesteras	4e-04
d1mzka_		122	b.26.1.2 (A:) Kinase associated protein phosphatas	4e-04
d2piea1		127	b.26.1.2 (A:13-139) Ubiquitin ligase protein RNF8	5e-04
d1gxca_		116	b.26.1.2 (A:) Chk2 kinase {Human (Homo sapiens) [T	0.002

>d1q32a1 d.136.1.3 (A:79-293) Tyrosyl-DNA phosphodiesterase TDP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 215	Back information, alignment and structure


class: Alpha and beta proteins (a+b)
fold: Phospholipase D/nuclease
superfamily: Phospholipase D/nuclease
family: Tyrosyl-DNA phosphodiesterase TDP1
domain: Tyrosyl-DNA phosphodiesterase TDP1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  165 bits (420), Expect = 2e-47
 Identities = 31/237 (13%), Positives = 68/237 (28%), Gaps = 39/237 (16%)

Query: 413 GKKFYLNRLEFMDL---TSLNYDVISLPELLYPVESISRMFIATFTSDILWFMSYCEIPS 469
           G  F L + +F +         D+I+L ++    E++ R  + +F  ++ + +       
Sbjct: 1   GAVFKLMKSDFYEREDFMGEVEDMITLKDIFGT-ETLKRSILFSFQYELDFLLRQF--HQ 57

Query: 470 HLPVTIACHNTERCWSTSADKRTSVPYPNFPNLVLVFPPFPESVAFGENCKKQGIACHHP 529
           ++                A    +        + L+    P    F           HH 
Sbjct: 58  NVENITIVGQKGTIMPIEARAMDATLAVILKKVKLIEITMP---PFA---------SHHT 105

Query: 530 KLFVLQRED-SIRVIVTSANLGAKQWNAVTNTVWWQDFPRRCAPDYLSLFVQTPVEEINQ 588
           KL +   ++   ++ + S N  + + N      W     +         F          
Sbjct: 106 KLIINFYDNGECKIFLPSNNFTSMETNLPQQVCWCSPLLKIGKEGLPVPF---------- 155

Query: 589 DSRSDFTAQLASFMASLVIDVPSQAHWIVE-LTKYDFASAAG-HLVASVPGIHSYRN 643
             +      L S+       +      I + + + +FA  +    V S P       
Sbjct: 156 --KRSLIEYLNSY------HLKDIDELITKSVEEVNFAPLSELEFVYSTPSKFQSSG 204

PyMOL of d1q32a1

>d1jy1a1 d.136.1.3 (A:145-350) Tyrosyl-DNA phosphodiesterase TDP1 {Human (Homo sapiens) [TaxId: 9606]} Length = 206	Back information, alignment and structure

>d1dmza_ b.26.1.2 (A:) Phosphotyrosine binding domain of Rad53 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 158	Back information, alignment and structure

>d1uhta_ b.26.1.2 (A:) FHA domain containing protein At4G14490 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 118	Back information, alignment and structure

>d1g6ga_ b.26.1.2 (A:) Phosphotyrosine binding domain of Rad53 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 127	Back information, alignment and structure

>d1jy1a2 d.136.1.3 (A:351-608) Tyrosyl-DNA phosphodiesterase TDP1 {Human (Homo sapiens) [TaxId: 9606]} Length = 258	Back information, alignment and structure

>d1mzka_ b.26.1.2 (A:) Kinase associated protein phosphatase {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 122	Back information, alignment and structure

>d2piea1 b.26.1.2 (A:13-139) Ubiquitin ligase protein RNF8 {Human (Homo sapiens) [TaxId: 9606]} Length = 127	Back information, alignment and structure

>d1gxca_ b.26.1.2 (A:) Chk2 kinase {Human (Homo sapiens) [TaxId: 9606]} Length = 116	Back information, alignment and structure

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		903
d1q32a1		215	Tyrosyl-DNA phosphodiesterase TDP1 {Baker's yeast	100.0
d1jy1a1		206	Tyrosyl-DNA phosphodiesterase TDP1 {Human (Homo sa	100.0
d1dmza_		158	Phosphotyrosine binding domain of Rad53 {Baker's y	99.67
d1uhta_		118	FHA domain containing protein At4G14490 {Thale cre	99.64
d1mzka_		122	Kinase associated protein phosphatase {Thale cress	99.63
d1lgpa_		113	Cell cycle checkpoint protein Chfr {Human (Homo sa	99.62
d1g6ga_		127	Phosphotyrosine binding domain of Rad53 {Baker's y	99.61
d1gxca_		116	Chk2 kinase {Human (Homo sapiens) [TaxId: 9606]}	99.6
d2piea1		127	Ubiquitin ligase protein RNF8 {Human (Homo sapiens	99.57
d2brfa1		101	Polynucleotide kinase 3'-phosphatase {Human (Homo	99.55
d2ff4a3		99	Probable regulatory protein EmbR, C-terminal domai	99.55
d1jy1a2		258	Tyrosyl-DNA phosphodiesterase TDP1 {Human (Homo sa	99.51
d2affa1		98	Antigen ki-67 {Human (Homo sapiens) [TaxId: 9606]}	99.39
d2g1la1		102	Kinesin-like protein kif1c {Human (Homo sapiens) [	99.21
d1wlna1		107	Afadin {Mouse (Mus musculus) [TaxId: 10090]}	99.1
d1q32a2		237	Tyrosyl-DNA phosphodiesterase TDP1 {Baker's yeast	96.98
d1jy1a2		258	Tyrosyl-DNA phosphodiesterase TDP1 {Human (Homo sa	96.52
d1q32a2		237	Tyrosyl-DNA phosphodiesterase TDP1 {Baker's yeast	85.01
d1mv5a_		242	Multidrug resistance ABC transporter LmrA, C-termi	83.19

>d1q32a1 d.136.1.3 (A:79-293) Tyrosyl-DNA phosphodiesterase TDP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Phospholipase D/nuclease
superfamily: Phospholipase D/nuclease
family: Tyrosyl-DNA phosphodiesterase TDP1
domain: Tyrosyl-DNA phosphodiesterase TDP1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=0  Score=369.95  Aligned_cols=199  Identities=16%  Similarity=0.243  Sum_probs=160.2

Q ss_pred             CCCEEEEEECCCCCCC---CCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHCC-CCCCCCEEEEECCCCCCCCCCC
Q ss_conf             9867998815578879---99986233412588412779898630126666632059-9999759999805765444587
Q 002593          413 GKKFYLNRLEFMDLTS---LNYDVISLPELLYPVESISRMFIATFTSDILWFMSYCE-IPSHLPVTIACHNTERCWSTSA  488 (903)
Q Consensus       413 gspF~LnrI~~lp~~~---~n~dtISL~DLLgP~~~L~~ailsSF~iDidWLLs~f~-~~r~lpVtIVv~~~~g~wk~e~  488 (903)
                      |+.|+|++...|+...   .|+|+|+|+|||++ ++|++||+||||+|++|||++|+ ..+.+++++   ..++.|..+.
T Consensus         1 ~~~f~l~~~~~~d~~~~~~~~~d~I~l~evl~~-~~L~~a~l~nF~~Di~wLl~~~~~~~~~~~~v~---~~~~~~~~~~   76 (215)
T d1q32a1           1 GAVFKLMKSDFYEREDFMGEVEDMITLKDIFGT-ETLKRSILFSFQYELDFLLRQFHQNVENITIVG---QKGTIMPIEA   76 (215)
T ss_dssp             CCEEEEECCTTTTCCC-------EECHHHHHCC-TTEEEEEEECSCEEHHHHHTTSCTTCCEEEEEE---ETTCEECCCG
T ss_pred             CCCEEEECCCCCCCCCCCCCCCCEEEHHHHCCC-HHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEE---ECCCCCCCCC
T ss_conf             981598426433467655788980455895486-179999988877649899976784446517999---8177454320


Q ss_pred             CCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEEECC-CEEEEEECCCCCHHHHCCCCCEEEEECCC
Q ss_conf             77767788999992999589986412366555788542114099998579-27999928999977431345869964277
Q 002593          489 DKRTSVPYPNFPNLVLVFPPFPESVAFGENCKKQGIACHHPKLFVLQRED-SIRVIVTSANLGAKQWNAVTNTVWWQDFP  567 (903)
Q Consensus       489 ~~rl~~~~~~~pNv~lv~PpLPe~IaFG~d~~~~g~GTHHSKLmIL~y~D-~lRVVI~TANLi~~DW~~~TQ~VW~QDFP  567 (903)
                      ..........+||+++|.||||   +||         |||||||||+|+| ++|||||||||++.||++|||++|+||||
T Consensus        77 ~~~~~~~~~~~~nv~~~~~~mp---~fG---------tHHSKmmiL~y~dg~lRVVI~TANLi~~DW~~~tQ~vW~sp~l  144 (215)
T d1q32a1          77 RAMDATLAVILKKVKLIEITMP---PFA---------SHHTKLIINFYDNGECKIFLPSNNFTSMETNLPQQVCWCSPLL  144 (215)
T ss_dssp             GGCCHHHHHHHTTEEEEEECCC---TTC---------CBCCCEEEEEESTTEEEEEEESSCBSHHHHHSSBCEEEECCCE
T ss_pred             HHHHHHHHCCCCCEEEEECCCC---CCC---------CCCCEEEEEEECCCCEEEEEECCCCCHHHHCCEEEEEEECCCC
T ss_conf             0204656313786179943689---866---------5531368999359978999955877854646660049967876


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHH-HHHCCCCCCCC-CEEEEEECCCCCCCCCCC
Q ss_conf             8889996663457983223688978479999999998124988437999-75125346663-189997049955689999
Q 002593          568 RRCAPDYLSLFVQTPVEEINQDSRSDFTAQLASFMASLVIDVPSQAHWI-VELTKYDFASA-AGHLVASVPGIHSYRNPN  645 (903)
Q Consensus       568 ~l~~~~~~~~~~~~~~~e~~~~~~sdFk~dL~~YL~sy~~~~ps~~~li-~~L~kyDFS~a-kv~LVaSVPG~H~g~~~~  645 (903)
                      .+..                .+++++|+.||++||++|+.  +.+..|+ +.|++||||++ +|+||+||||+|.|.+..
T Consensus       145 ~~~s----------------~~~~~~F~~dL~~yL~~y~~--~~~~~~i~~~l~~~Dfs~~~~v~lV~SvPG~~~g~~~~  206 (215)
T d1q32a1         145 KIGK----------------EGLPVPFKRSLIEYLNSYHL--KDIDELITKSVEEVNFAPLSELEFVYSTPSKFQSSGLL  206 (215)
T ss_dssp             EECC----------------CSSCCHHHHHHHHHHHTTCC--HHHHHHTHHHHHTEECGGGTTCEEEEECCCTTSCCHHH
T ss_pred             CCCC----------------CCCCCCHHHHHHHHHHHCCC--CHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCCCCCHH
T ss_conf             6789----------------98888368999999998397--40158999999876966678889999479674077646

PyMOL of d1q32a1

>d1jy1a1 d.136.1.3 (A:145-350) Tyrosyl-DNA phosphodiesterase TDP1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1dmza_ b.26.1.2 (A:) Phosphotyrosine binding domain of Rad53 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1uhta_ b.26.1.2 (A:) FHA domain containing protein At4G14490 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}	Back information, alignment and structure

>d1mzka_ b.26.1.2 (A:) Kinase associated protein phosphatase {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}	Back information, alignment and structure

>d1lgpa_ b.26.1.2 (A:) Cell cycle checkpoint protein Chfr {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1g6ga_ b.26.1.2 (A:) Phosphotyrosine binding domain of Rad53 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1gxca_ b.26.1.2 (A:) Chk2 kinase {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2piea1 b.26.1.2 (A:13-139) Ubiquitin ligase protein RNF8 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2brfa1 b.26.1.2 (A:8-108) Polynucleotide kinase 3'-phosphatase {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2ff4a3 b.26.1.2 (A:284-382) Probable regulatory protein EmbR, C-terminal domain {Mycobacterium tuberculosis [TaxId: 1773]}	Back information, alignment and structure

>d1jy1a2 d.136.1.3 (A:351-608) Tyrosyl-DNA phosphodiesterase TDP1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2affa1 b.26.1.2 (A:3-100) Antigen ki-67 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2g1la1 b.26.1.2 (A:498-599) Kinesin-like protein kif1c {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wlna1 b.26.1.2 (A:8-114) Afadin {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1q32a2 d.136.1.3 (A:302-538) Tyrosyl-DNA phosphodiesterase TDP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1jy1a2 d.136.1.3 (A:351-608) Tyrosyl-DNA phosphodiesterase TDP1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1q32a2 d.136.1.3 (A:302-538) Tyrosyl-DNA phosphodiesterase TDP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1mv5a_ c.37.1.12 (A:) Multidrug resistance ABC transporter LmrA, C-terminal domain {Lactococcus lactis [TaxId: 1358]}	Back information, alignment and structure