Citrus Sinensis ID: 010545

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-------

MMELQMENLVQRKCDSNEEALCNFHVSRDKLPSTFRLLRVQGLPAWANTSCVSIRDVIQGDIIVAILSNYMVDIDWLLPACPVLAKIPHVLVIHGESDGTLEHMKRNKPANWILHKPPLPISFGTHHSKAMLLIYPRGVRIIVHTANLIHVDWNNKSQGLWMQDFPLKDQNNLSEECGFENDLIDYLSTLKWPEFSANLPAHGNFKINPSFFKKFNFSSAAVRLIASVPGYHTGSSLKKWGHMKLRTVLQECTFEKGFKKSPLVYQFSSLGSLDEKWMAELSSSMSSGFSEDKTPLGIGEPLIVWPTVEDVRCSLEGYAAGNAIPSPQKNVDKDFLKKYWAKWKASHTGRSRAMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCGFSCTSNIVPSEIKSGSTETSQIQKTKLVTLTWHGSSDAGASSEVVYLPVPYELPPQRYSSEDVPWSWDKRYTKKDVYGQVWPRHFQLYAFQDS

cccccccccccccccccHHHHcccccccccccccEEEEEEcccccccccccccHHHHcHHHHHHHHHHHHHccHHHHHHHccccccccEEEEEEccccHHHHHHHccccccEEEEcccccccccccEEEEEEEEEccccEEEEEcccccHHHHcccccEEEEEEcccccccccccccccHHHHHHHHHHccccccccccccccccccccccccccccccccEEEEEccccccccccccHHHHHHHHHHHHHcccccccccccEEEEEcccccccHHHHHHHHHHHccccccccccccccccEEEccccHHHHcccccccccccccccccHHHHHHHHHHHHHHccccccccccccccEEEEEcccccEEEEEEEcccccHHHHccccccccEEEEEEEEEEEEEcccccccccccccccccccccccccccccHHHHccccccccccccccccccccEEEccccccccccccccccccEEEcccccccccccccccccccccccccc

ccHHHHHHcccccccccHHccccccccHccccccEEEEEEccccccccccHHHHHHHHcccHHHHHHHHHHHcHHHHHHHccHHccccEEEEEEccccHHHHHHHHcccccEEEEEccccccccccccEEEEEEEccccEEEEEcccccHHHHcccccEEEEccccccccccccccccHHHHHHHHHHHcccccHHHHHccccccccHHHHHHHccccccEEEEEEcccccccccccccccHHHHHHHHHHcccccccccccEEEEEEcHccccHHHHHHHHHHHHcccccccccccccccEEEEccHHHHHHcccccccccccccHHHHHHHHHHHHHHHHccccccccccccccEEEEEcccccccEEEEEEcHHHHHHHHHHHcccccEEEEEEEEEEEEEccHHccccccccccccccccccccccccccccccccEEEccccccccccccccEEEEcccccccccccccccccEEEEccccccccccccccccEEEEEcccc

MMELQMENLVQRKCDSNEEALCNFHVSRDKLPSTFRLLRvqglpawantscvsiRDVIQGDIIVAILSNYMVDidwllpacpvlakiphvlvihgesdgtlehmkrnkpanwilhkpplpisfgthhsKAMLLIYPRGVRIIVHTANLIHvdwnnksqglwmqdfplkdqnnlseecgfeNDLIDYLstlkwpefsanlpahgnfkinpsffkkfnfSSAAVRLIAsvpgyhtgsslkkwgHMKLRTVLQEctfekgfkksplvyqfsslgslDEKWMAELSSsmssgfsedktplgigeplivwptvedvrcslegyaagnaipspqknvdKDFLKKYWAKWKAshtgrsramphiKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLilpsakrhgcgfsctsnivpseiksgstetSQIQKTKLVTltwhgssdagassevvylpvpyelppqryssedvpwswdkrytkkdvygqvwprhfqlyafqds

MMELQMENLVQRKCDSNEEALCNFHVSRDKLPSTFRLLRVQGLpawantscvsiRDVIQGDIIVAILSNYMVDIDWLLPACPVLAKIPHVLVIHGESDGTLEHMKRNKPANWILHKPPLPISFGTHHSKAMLLIYPRGVRIIVHTANLIHVDWNNKSQGLWMQDFPLKDQNNLSEECGFENDLIDYLSTLKWPEFSANLPAHGNFKINPSFFKKFNFSSAAVRLIASVPGYHTGSSLKKWGHMKLRTVLQECTFEKGFKKSPLVYQFSSLGSLDEKWMAELSSSMSSGFSEDKTPLGIGEPLIVWPTVEDVRCSLEGyaagnaipspqknvDKDFLKKYWAKWKashtgrsrampHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCGFSCTSNIVpseiksgstetSQIQKTKLVTLTWHGSSDAGASSEVVYLPVPYELppqryssedvpwswdkrytkkDVYGQVWPRHFQLYAFQDS

MMELQMENLVQRKCDSNEEALCNFHVSRDKLPSTFRLLRVQGLPAWANTSCVSIRDVIQGDIIVAILSNYMVDIDWLLPACPVLAKIPHVLVIHGESDGTLEHMKRNKPANWILHKPPLPISFGTHHSKAMLLIYPRGVRIIVHTANLIHVDWNNKSQGLWMQDFPLKDQNNLSEECGFENDLIDYLSTLKWPEFSANLPAHGnfkinpsffkkfnfssAAVRLIASVPGYHTGSSLKKWGHMKLRTVLQECTFEKGFKKSPLVYQFSSLGSLDEKWMAELsssmssgfsEDKTPLGIGEPLIVWPTVEDVRCSLEGYAAGNAIPSPQKNVDKDFLKKYWAKWKASHTGRSRAMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCGFSCTSNIVPSEIKSGSTETSQIQKTKLVTLTWHGSSDAGASSevvylpvpyelppQRYSSEDVPWSWDKRYTKKDVYGQVWPRHFQLYAFQDS

*******************ALCNFHVSRDKLPSTFRLLRVQGLPAWANTSCVSIRDVIQGDIIVAILSNYMVDIDWLLPACPVLAKIPHVLVIHGESDGTLEHMKRNKPANWILHKPPLPISFGTHHSKAMLLIYPRGVRIIVHTANLIHVDWNNKSQGLWMQDFPLKDQNNLSEECGFENDLIDYLSTLKWPEFSANLPAHGNFKINPSFFKKFNFSSAAVRLIASVPGYHTGSSLKKWGHMKLRTVLQECTFEKGFKKSPLVYQFSSLGSLDEKW******************LGIGEPLIVWPTVEDVRCSLEGYAAGNAIPSPQKNVDKDFLKKYWAKWKASHTGRSRAMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCGFSCTSNIVP***************TKLVTLTWHGSSDAGASSEVVYLPVPYELPPQRYSSEDVPWSWDKRYTKKDVYGQVWPRHFQLYAF***

********************************STFRLLRVQGLPAWANTSCVSIRDVIQGDIIVAILSNYMVDIDWLLPACPVLAKIPHVLVIHGESDGTLEHMKRNKPANWILHKPPLPISFGTHHSKAMLLIYPRGVRIIVHTANLIHVDWNNKSQGLWM********************LIDYLSTLKWPEFSANLPAHGNFKINPSFFKKFNFSSAAVRLIASVPGYHTGSSLKKWGHMKLRTVLQECT*****KKSPLVYQFSSLGSLDEKWMAELSS*****************PLIVWPTVEDVRCSLEGYAAGNAIPSPQKNVDKDFLKKYWAKWKASHTGRSRAMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCG******************************************EVVYLPVPYELPPQRYSSEDVPWSWDKRYTKKDVYGQVWPRHFQLY*****

MMELQMENLVQRKCDSNEEALCNFHVSRDKLPSTFRLLRVQGLPAWANTSCVSIRDVIQGDIIVAILSNYMVDIDWLLPACPVLAKIPHVLVIHGESDGTLEHMKRNKPANWILHKPPLPISFGTHHSKAMLLIYPRGVRIIVHTANLIHVDWNNKSQGLWMQDFPLKDQNNLSEECGFENDLIDYLSTLKWPEFSANLPAHGNFKINPSFFKKFNFSSAAVRLIASVPGYHTGSSLKKWGHMKLRTVLQECTFEKGFKKSPLVYQFSSLGSLDEKWMAEL**********DKTPLGIGEPLIVWPTVEDVRCSLEGYAAGNAIPSPQKNVDKDFLKKYWAKWKASHTGRSRAMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCGFSCTSNIVPSEI**********QKTKLVTLTWHGSSDAGASSEVVYLPVPYELPPQRYSSEDVPWSWDKRYTKKDVYGQVWPRHFQLYAFQDS

***********************FHVSRDKLPSTFRLLRVQGLPAWANTSCVSIRDVIQGDIIVAILSNYMVDIDWLLPACPVLAKIPHVLVIHGESDGTLEHMKRNKPANWILHKPPLPISFGTHHSKAMLLIYPRGVRIIVHTANLIHVDWNNKSQGLWMQDFPLKD*****EECGFENDLIDYLSTLKWPEFSANLPAHGNFKINPSFFKKFNFSSAAVRLIASVPGYHTGSSLKKWGHMKLRTVLQECTFEKGFKKSPLVYQFSSLGSLDEKWMAELSSSMSSGFSEDKTPLGIGEPLIVWPTVEDVRCSLEGYAAGNAIPSPQKNVDKDFLKKYWAKWKASHTGRSRAMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCGFSCTSNIVPS**************TKLVTLTWHGSSDAGASSEVVYLPVPYELPPQRYSSEDVPWSWDKRYTKKDVYGQVWPRHFQLYAF***

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		507	2.2.26 [Sep-21-2011]
Q9NUW8		608	Tyrosyl-DNA phosphodieste	yes	no	0.836	0.697	0.391	2e-78
Q8BJ37		609	Tyrosyl-DNA phosphodieste	yes	no	0.834	0.694	0.382	6e-76
Q4G056		609	Tyrosyl-DNA phosphodieste	yes	no	0.834	0.694	0.380	2e-75
Q9VQM4		580	Probable tyrosyl-DNA phos	yes	no	0.668	0.584	0.350	1e-42
Q9TXV7		451	Probable tyrosyl-DNA phos	yes	no	0.735	0.827	0.301	8e-41
Q9USG9		536	Probable tyrosyl-DNA phos	yes	no	0.875	0.828	0.261	6e-31

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

 Score =  293 bits (750), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 189/483 (39%), Positives = 265/483 (54%), Gaps = 59/483 (12%)

Query: 32  PSTFRLLRVQGLPAWANTSCVSIRDVIQ---GDIIVAILSNYMVDIDWLLPACPVLAKIP 88
           P  F L RV G+    N+  + I+D++    G ++ +   NY  D+DWL+   P   +  
Sbjct: 163 PFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKK 222

Query: 89  HVLVIHGESDGTLEHM-KRNKP-ANWILHKPPLPISFGTHHSKAMLLIYPRGVRIIVHTA 146
            +L++HG+      H+  + KP  N  L +  L I+FGTHH+K MLL+Y  G+R+++HT+
Sbjct: 223 PILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTS 282

Query: 147 NLIHVDWNNKSQGLWMQD-FP-LKDQNNLSEE--CGFENDLIDYLSTLKWPEFSANLPAH 202
           NLIH DW+ K+QG+W+   +P + D  + S E    F+ DLI YL     P     +   
Sbjct: 283 NLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKADLISYLMAYNAPSLKEWI--- 339

Query: 203 GNFKINPSFFKKFNFSSAAVRLIASVPGYHTGSSLKKWGHMKLRTVLQECTFEKGFKKS- 261
                      K + S   V LI S PG   GS    WGH +L+ +L++        +S 
Sbjct: 340 -------DVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESW 392

Query: 262 PLVYQFSSLGSL---DEKWM-AELSSSMSSGFSEDKTPLGIGEPL-IVWPTVEDVRCSLE 316
           P+V QFSS+GSL   + KW+ +E   SM +   E KTP     PL +++P+VE+VR SLE
Sbjct: 393 PVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSSVPLYLIYPSVENVRTSLE 452

Query: 317 GYAAGNAIP-SPQKNVDKDFLKKYWAKWKASHTGRSRAMPHIKTFARY--NGQKLAWFLL 373
           GY AG ++P S Q    +++L  Y+ KW A  +GRS AMPHIKT+ R   +  K+AWFL+
Sbjct: 453 GYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLV 512

Query: 374 TSANLSKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCGFSCTSNIVPSEIKSGSTET 433
           TSANLSKAAWGAL+KN +QLMIRSYELGVL LPSA      F   S  V  +  +GS E 
Sbjct: 513 TSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSA------FGLDSFKVKQKFFAGSQEP 566

Query: 434 SQIQKTKLVTLTWHGSSDAGASSEVVYLPVPYELPPQRYSSEDVPWSWDKRYTKK-DVYG 492
                                   +   PVPY+LPP+ Y S+D PW W+  Y K  D +G
Sbjct: 567 ------------------------MATFPVPYDLPPELYGSKDRPWIWNIPYVKAPDTHG 602

Query: 493 QVW 495
            +W
Sbjct: 603 NMW 605

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\|Q8BJ37\|TYDP1_MOUSE Tyrosyl-DNA phosphodiesterase 1 OS=Mus musculus GN=Tdp1 PE=2 SV=2	Back alignment and function description

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

>sp\|Q9VQM4\|TYDP1_DROME Probable tyrosyl-DNA phosphodiesterase OS=Drosophila melanogaster GN=gkt PE=2 SV=1	Back alignment and function description

>sp\|Q9TXV7\|TYDP1_CAEEL Probable tyrosyl-DNA phosphodiesterase OS=Caenorhabditis elegans GN=F52C12.1 PE=3 SV=1	Back alignment and function description

>sp\|Q9USG9\|TYDP1_SCHPO Probable tyrosyl-DNA phosphodiesterase OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPCP31B10.05 PE=3 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		507
302144065		678	unnamed protein product [Vitis vinifera]	0.968	0.724	0.786	0.0
359483320		621	PREDICTED: tyrosyl-DNA phosphodiesterase	0.996	0.813	0.766	0.0
255554997		665	tyrosyl-DNA phosphodiesterase, putative	0.966	0.736	0.770	0.0
224078752		599	predicted protein [Populus trichocarpa]	0.950	0.804	0.765	0.0
449479663		959	PREDICTED: tyrosyl-DNA phosphodiesterase	0.980	0.518	0.718	0.0
356507526		599	PREDICTED: tyrosyl-DNA phosphodiesterase	0.952	0.806	0.773	0.0
356507524		610	PREDICTED: tyrosyl-DNA phosphodiesterase	0.952	0.791	0.773	0.0
449434370		613	PREDICTED: tyrosyl-DNA phosphodiesterase	0.970	0.802	0.713	0.0
297811655		612	hypothetical protein ARALYDRAFT_488358 [	0.950	0.787	0.725	0.0
22326821		605	tyrosyl-DNA phosphodiesterase 1 [Arabido	0.950	0.796	0.713	0.0

>gi\|302144065\|emb\|CBI23170.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

 Score =  824 bits (2128), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 386/491 (78%), Positives = 434/491 (88%)

Query: 17  NEEALCNFHVSRDKLPSTFRLLRVQGLPAWANTSCVSIRDVIQGDIIVAILSNYMVDIDW 76
           N EA+ +F + +D LP T+RLLRV+ LPAWANTS VSIRDVIQGD+++A+LSNYMVDIDW
Sbjct: 188 NSEAIRHFSIPKDNLPLTYRLLRVKDLPAWANTSSVSIRDVIQGDVLIAVLSNYMVDIDW 247

Query: 77  LLPACPVLAKIPHVLVIHGESDGTLEHMKRNKPANWILHKPPLPISFGTHHSKAMLLIYP 136
           LL +CP LAKIPHVLVIHGE DGTL+HMK+NKP NWILHKPPLPISFGTHHSKAMLL+YP
Sbjct: 248 LLSSCPTLAKIPHVLVIHGEGDGTLDHMKKNKPPNWILHKPPLPISFGTHHSKAMLLVYP 307

Query: 137 RGVRIIVHTANLIHVDWNNKSQGLWMQDFPLKDQNNLSEECGFENDLIDYLSTLKWPEFS 196
           RGVR+IVHTANLI+VDWNNKSQGLWMQDFP K Q  LS+ C FENDLIDYLS LKWPEF+
Sbjct: 308 RGVRVIVHTANLIYVDWNNKSQGLWMQDFPWKVQKELSKGCAFENDLIDYLSVLKWPEFT 367

Query: 197 ANLPAHGNFKINPSFFKKFNFSSAAVRLIASVPGYHTGSSLKKWGHMKLRTVLQECTFEK 256
           ANLPA G+F IN SFFKKF++S+A VRLIASVPGYHTGS+LKKWGHMKL +VLQEC F+K
Sbjct: 368 ANLPALGSFNINSSFFKKFDYSNAVVRLIASVPGYHTGSNLKKWGHMKLCSVLQECIFDK 427

Query: 257 GFKKSPLVYQFSSLGSLDEKWMAELSSSMSSGFSEDKTPLGIGEPLIVWPTVEDVRCSLE 316
            F+KSPL YQFSSLGSLDEKWM EL+SSMSSG  +DKTPLG+G+PLI+WPTVEDVRCSLE
Sbjct: 428 EFQKSPLAYQFSSLGSLDEKWMTELASSMSSGSCDDKTPLGLGKPLIIWPTVEDVRCSLE 487

Query: 317 GYAAGNAIPSPQKNVDKDFLKKYWAKWKASHTGRSRAMPHIKTFARYNGQKLAWFLLTSA 376
           GYAAGNAIPSPQKNV+K+FLKKYWAKWKA+HTGR RAMPHIKT+ RYNGQ LAWFLLTSA
Sbjct: 488 GYAAGNAIPSPQKNVEKEFLKKYWAKWKATHTGRCRAMPHIKTYTRYNGQNLAWFLLTSA 547

Query: 377 NLSKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCGFSCTSNIVPSEIKSGSTETSQI 436
           NLSKAAWGALQKNNSQLMIRSYELGVL LPS    G GFSCT N  PS+ K G +E ++ 
Sbjct: 548 NLSKAAWGALQKNNSQLMIRSYELGVLFLPSPINRGQGFSCTDNGSPSKNKCGLSENTKS 607

Query: 437 QKTKLVTLTWHGSSDAGASSEVVYLPVPYELPPQRYSSEDVPWSWDKRYTKKDVYGQVWP 496
           Q+TKLVTLTW G+  + +SSEV+ LPVPYELPP++YSSEDVPWSWD+RY KKDV GQVWP
Sbjct: 608 QRTKLVTLTWEGNRSSDSSSEVIPLPVPYELPPKQYSSEDVPWSWDRRYYKKDVCGQVWP 667

Query: 497 RHFQLYAFQDS 507
           RH QLY+  DS
Sbjct: 668 RHVQLYSSPDS 678

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|359483320\|ref\|XP_002265078.2\| PREDICTED: tyrosyl-DNA phosphodiesterase 1-like [Vitis vinifera]	Back alignment and taxonomy information

>gi\|255554997\|ref\|XP_002518536.1\| tyrosyl-DNA phosphodiesterase, putative [Ricinus communis] gi\|223542381\|gb\|EEF43923.1\| tyrosyl-DNA phosphodiesterase, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|224078752\|ref\|XP_002305614.1\| predicted protein [Populus trichocarpa] gi\|222848578\|gb\|EEE86125.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|449479663\|ref\|XP_004155668.1\| PREDICTED: tyrosyl-DNA phosphodiesterase 1-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|356507526\|ref\|XP_003522515.1\| PREDICTED: tyrosyl-DNA phosphodiesterase 1-like isoform 2 [Glycine max]	Back alignment and taxonomy information

>gi\|356507524\|ref\|XP_003522514.1\| PREDICTED: tyrosyl-DNA phosphodiesterase 1-like isoform 1 [Glycine max]	Back alignment and taxonomy information

>gi\|449434370\|ref\|XP_004134969.1\| PREDICTED: tyrosyl-DNA phosphodiesterase 1-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|297811655\|ref\|XP_002873711.1\| hypothetical protein ARALYDRAFT_488358 [Arabidopsis lyrata subsp. lyrata] gi\|297319548\|gb\|EFH49970.1\| hypothetical protein ARALYDRAFT_488358 [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi\|22326821\|ref\|NP_197021.2\| tyrosyl-DNA phosphodiesterase 1 [Arabidopsis thaliana] gi\|23297734\|gb\|AAN13014.1\| unknown protein [Arabidopsis thaliana] gi\|226511716\|gb\|ACO60340.1\| tyrosyl-DNA phosphodiesterase I [Arabidopsis thaliana] gi\|332004741\|gb\|AED92124.1\| tyrosyl-DNA phosphodiesterase 1 [Arabidopsis thaliana]	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		507
TAIR\|locus:2150931		605	TDP1 "tyrosyl-DNA phosphodiest	0.948	0.795	0.669	1.1e-179
UNIPROTKB\|E2REL5		609	TDP1 "Uncharacterized protein"	0.757	0.630	0.402	5.3e-73
UNIPROTKB\|Q9NUW8		608	TDP1 "Tyrosyl-DNA phosphodiest	0.723	0.603	0.410	6.7e-73
MGI\|MGI:1920036		609	Tdp1 "tyrosyl-DNA phosphodiest	0.721	0.600	0.411	3.3e-71
RGD\|1309618		609	Tdp1 "tyrosyl-DNA phosphodiest	0.721	0.600	0.409	1.1e-70
UNIPROTKB\|F1MST1		612	TDP1 "Uncharacterized protein"	0.757	0.627	0.396	2.3e-70
UNIPROTKB\|F1NSQ5		602	TDP1 "Uncharacterized protein"	0.769	0.647	0.379	2.3e-70
UNIPROTKB\|F1SDA7		607	LOC100625067 "Uncharacterized	0.751	0.627	0.401	2.9e-70
ZFIN\|ZDB-GENE-090909-1		615	tdp1 "tyrosyl-DNA phosphodiest	0.747	0.616	0.388	1.6e-69
UNIPROTKB\|G3V2F4		578	TDP1 "Tyrosyl-DNA phosphodiest	0.735	0.645	0.410	2.7e-68

TAIR\|locus:2150931 TDP1 "tyrosyl-DNA phosphodiesterase 1" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1744 (619.0 bits), Expect = 1.1e-179, P = 1.1e-179
 Identities = 328/490 (66%), Positives = 374/490 (76%)

Query:    12 RKCDSNEEALCNFHVSRDKLPSTFRLLRVQGLPAWANTSCVSIRDVIQGDIIVAILSNYM 71
             RK + + EA+  F    +KLPSTFRLL V  LP WANTSCVSI DVI+GD++ AILSNYM
Sbjct:   121 RKAEDDVEAIRRFCPPNEKLPSTFRLLSVDALPDWANTSCVSINDVIEGDVVAAILSNYM 180

Query:    72 VDIDWLLPACPVLAKIPHVLVIHGESDGTLEHMKRNKPANWILHKPPLPISFGTHHSKAM 131
             VDIDWL+ ACP LA IP V+VIHGE DG  E+++R KPANWILHKP LPISFGTHHSKA+
Sbjct:   181 VDIDWLMSACPKLANIPQVMVIHGEGDGRQEYIQRKKPANWILHKPRLPISFGTHHSKAI 240

Query:   132 LLIYPRGVRIIVHTANLIHVDWNNKSQGLWMQDFPLKDQN-NLSEECGFENDLIDYLSTL 190
              L+YPRGVR++VHTANLIHVDWNNKSQGLWMQDFP KD + +  + CGFE DLIDYL+ L
Sbjct:   241 FLVYPRGVRVVVHTANLIHVDWNNKSQGLWMQDFPWKDDDKDPPKGCGFEGDLIDYLNVL 300

Query:   191 KWPEFSANLPAHGXXXXXXXXXXXXXXXXAAVRLIASVPGYHTGSSLKKWGHMKLRTVLQ 250
             KWPEF+ANLP  G                A VRLIASVPGYHTG +L KWGHMKLRT+LQ
Sbjct:   301 KWPEFTANLPGRGNVKINAAFFKKFDYSDATVRLIASVPGYHTGFNLNKWGHMKLRTILQ 360

Query:   251 ECTFEKGFKKSPLVYQFSSLGSLDEKWMAELXXXXXXXXXEDKTPLGIGEPLIVWPTVED 310
             EC F++ F++SPL+YQFSSLGSLDEKW+AE          EDKTPLG G+ LI+WPTVED
Sbjct:   361 ECIFDREFRRSPLIYQFSSLGSLDEKWLAEFGNSLSSGITEDKTPLGPGDSLIIWPTVED 420

Query:   311 VRCSLEGYAAGNAIPSPQKNVDKDFLKKYWAKWKASHTGRSRAMPHIKTFARYNGQKLAW 370
             VRCSLEGYAAGNAIPSP KNV+K FLKKYWA+WKA H+ R RAMPHIKTF RYN QK+AW
Sbjct:   421 VRCSLEGYAAGNAIPSPLKNVEKPFLKKYWARWKADHSARGRAMPHIKTFTRYNDQKIAW 480

Query:   371 FLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILPSA-KRHGCGFSCT-SNIVPSEIKS 428
             FLLTS+NLSKAAWGALQKNNSQLMIRSYELGVL LPS  K  GC FSCT SN  PS +K+
Sbjct:   481 FLLTSSNLSKAAWGALQKNNSQLMIRSYELGVLFLPSPIKTQGCVFSCTESN--PSVMKA 538

Query:   429 GSTETSQIQK-TKLVTLTWHGSSDAGASSXXXXXXXXXXXXXQRYSSEDVPWSWDKRYTK 487
                   +++K +KLVT+TW G  D                  + YS EDVPWSWD+ Y+K
Sbjct:   539 KQETKDEVEKRSKLVTMTWQGDRDL---PEIISLPVPYQLPPKPYSPEDVPWSWDRGYSK 595

Query:   488 KDVYGQVWPR 497
             KDVYGQVWPR
Sbjct:   596 KDVYGQVWPR 605

GO:0005634 "nucleus" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

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

GO:0017005 "3'-tyrosyl-DNA phosphodiesterase activity" evidence=IDA

GO:0009616 "virus induced gene silencing" evidence=RCA

GO:0010050 "vegetative phase change" evidence=RCA

UNIPROTKB\|E2REL5 TDP1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|Q9NUW8 TDP1 "Tyrosyl-DNA phosphodiesterase 1" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

MGI\|MGI:1920036 Tdp1 "tyrosyl-DNA phosphodiesterase 1" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

RGD\|1309618 Tdp1 "tyrosyl-DNA phosphodiesterase 1" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|F1MST1 TDP1 "Uncharacterized protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|F1NSQ5 TDP1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|F1SDA7 LOC100625067 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-090909-1 tdp1 "tyrosyl-DNA phosphodiesterase 1" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

UNIPROTKB\|G3V2F4 TDP1 "Tyrosyl-DNA phosphodiesterase 1" [Homo sapiens (taxid:9606)]	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:
	GSVIVG00006918001	SubName- Full=Chromosome chr10 scaffold_179, whole genome shotgun sequence; (584 aa)
		(Vitis vinifera)
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		507
pfam06087		433	pfam06087, Tyr-DNA_phospho, Tyrosyl-DNA phosphodie	1e-100
cd09195		191	cd09195, PLDc_mTdp1_2, Catalytic domain, repeat 2,	2e-74
cd09123		182	cd09123, PLDc_Tdp1_2, Catalytic domain, repeat 2,	2e-60
cd09122		145	cd09122, PLDc_Tdp1_1, Catalytic domain, repeat 1,	5e-53
cd09193		169	cd09193, PLDc_mTdp1_1, Catalytic domain, repeat 1,	4e-31
cd09194		166	cd09194, PLDc_yTdp1_1, Catalytic domain, repeat 1,	2e-26
cd09196		200	cd09196, PLDc_yTdp1_2, Catalytic domain, repeat 2,	1e-19

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

 Score =  308 bits (791), Expect = e-100
 Identities = 145/455 (31%), Positives = 224/455 (49%), Gaps = 69/455 (15%)

Query: 48  NTSCVSIRDVIQ-GDIIVAILSNYMVDIDWLLPACPVLAKIPHVLVIHGESDG--TLEHM 104
           N   +++ D++   D+  +   N+M D+D+LL       +   + ++ G  +     E +
Sbjct: 19  NPDTITLEDILGDPDLEESWQFNFMFDLDFLLDQFDPSGRENKITIVTGTDNLLEKREII 78

Query: 105 KRNKPANWILHKPPLPISFGTHHSKAMLLIYPRG-VRIIVHTANLIHVDWNNKSQGLWMQ 163
           +     N  + K  +P  FGTHH+K M+L Y  G  R+++ TANL   DW N +QGLW+ 
Sbjct: 79  EDCGYPNVTVIKAKMPGPFGTHHTKMMILFYEDGSCRVVIPTANLTPGDWGNMTQGLWIS 138

Query: 164 DFPLKDQNNLSEE-CGFENDLIDYLSTLKWPEFSANLPAHGNFKINPSFFKKFNFSSAAV 222
                 ++ L E    F+ DL++YLS          L             +K++FSS  V
Sbjct: 139 PLLKIGKSELEESSTRFKRDLLEYLSEYGAKTLLEPLID---------RLRKYDFSSVNV 189

Query: 223 RLIASVPGYHTGSSLKKWGHMKLRTVLQE---CTFEKGFKKSPLVYQFSSLGSLD--EKW 277
            L+ASVPG HTG+   KWG  +L +VL+     T ++  ++  +V Q SS+GSL    K 
Sbjct: 190 ELVASVPGKHTGNK-DKWGLPRLGSVLRANPLLTKDEKDEQVHVVCQSSSIGSLGVTPKD 248

Query: 278 ------MAELSSSMSSGFSEDKTPLGIGE----PLIVWPTVEDVRCSLEGYAAGNAIP-- 325
                 +  L  +  S   ++ +     E    P I++PTV++VR SL+GY +G ++   
Sbjct: 249 WLKSNFLGSLYPASFSSEGQESSINQQKERKPKPRIIYPTVDEVRTSLDGYDSGGSLHFK 308

Query: 326 --SPQKNVDKDFLKKYWAKWKASH--TGRSRAMPHIKTFARYNGQK---LAWFLLTSANL 378
             S      +++L+ Y  KWK+S+   GR+RA PHIKT+ R+N +    L W L+TSANL
Sbjct: 309 KQSYATKFPQEWLRPYLHKWKSSNADKGRTRAPPHIKTYIRFNDEDFKDLDWALVTSANL 368

Query: 379 SKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCGFSCTSNIVPSEIKSGSTETSQIQK 438
           SKAAWGAL KN +QL IRSYELGVL  P++                        T     
Sbjct: 369 SKAAWGALVKNETQLRIRSYELGVLYWPTSA-----------------------TPLDVF 405

Query: 439 TKLVTLTWHGSSDAGASSEVVYLPVPYELPPQRYS 473
           +               S + + +P+P++LPP  Y 
Sbjct: 406 SLKD-------VIYRQSKQTIGVPMPFDLPPTPYG 433

Covalent intermediates between topoisomerase I and DNA can become dead-end complexes that lead to cell death. Tyrosyl-DNA phosphodiesterase can hydrolyse the bond between topoisomerase I and DNA. Length = 433

>gnl\|CDD\|197291 cd09195, PLDc_mTdp1_2, Catalytic domain, repeat 2, of metazoan tyrosyl-DNA phosphodiesterase	Back alignment and domain information

>gnl\|CDD\|197222 cd09123, PLDc_Tdp1_2, Catalytic domain, repeat 2, of tyrosyl-DNA phosphodiesterase	Back alignment and domain information

>gnl\|CDD\|197221 cd09122, PLDc_Tdp1_1, Catalytic domain, repeat 1, of Tyrosyl-DNA phosphodiesterase	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\|197290 cd09194, PLDc_yTdp1_1, Catalytic domain, repeat 1, of yeast tyrosyl-DNA phosphodiesterase	Back alignment and domain information

>gnl\|CDD\|197292 cd09196, PLDc_yTdp1_2, Catalytic domain, repeat 2, of yeast tyrosyl-DNA phosphodiesterase	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		507
KOG2031		519	consensus Tyrosyl-DNA phosphodiesterase [Replicati	100.0
PF06087		443	Tyr-DNA_phospho: Tyrosyl-DNA phosphodiesterase; In	100.0
PF13091		126	PLDc_2: PLD-like domain; PDB: 2ZE4_A 2ZE9_A 1BYS_A	95.08
smart00155		28	PLDc Phospholipase D. Active site motifs. Phosphat	90.71
PRK13912		177	nuclease NucT; Provisional	89.74
PF00614		28	PLDc: Phospholipase D Active site motif; InterPro:	86.58
smart00155		28	PLDc Phospholipase D. Active site motifs. Phosphat	85.98
PF09565		296	RE_NgoFVII: NgoFVII restriction endonuclease; Inte	84.18
COG1502		438	Cls Phosphatidylserine/phosphatidylglycerophosphat	82.52
cd00138		176	PLDc Phospholipase D. Active site motifs; The PLD	81.89

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

Probab=100.00  E-value=4.5e-103  Score=804.24  Aligned_cols=427  Identities=43%  Similarity=0.726  Sum_probs=354.2

Q ss_pred             eEEEEecCCCCCCCCCceeecccc---cccHHhhhhhhcccChhhhcccCCCCCCCCeEEEEeCCCCChhhhhhhcCCCc
Q 010545           35 FRLLRVQGLPAWANTSCVSIRDVI---QGDIIVAILSNYMVDIDWLLPACPVLAKIPHVLVIHGESDGTLEHMKRNKPAN  111 (507)
Q Consensus        35 F~L~~~~~~~~~~n~~~itl~Dll---~~~l~~a~l~sF~~Dl~WLl~~~~~~~~~~~i~vv~g~~~~~~~~~~~~~~~n  111 (507)
                      |.+++.+..|+.+....+++.+|+   .|++..+++||||+|++||+.+||...+.+.|+++||+.++.........+.+
T Consensus        82 ft~v~~~s~~~~~s~~s~sl~~il~~i~g~~v~silfsfmvdid~Lv~~y~~~~~~~~i~l~~G~~d~~~~~~~~K~~~l  161 (519)
T KOG2031|consen   82 FTTVKGDSVPRYDSMGSVSLMEILADIFGTPVNSILFSFMVDIDWLVGQYPPSVRIKPITLVHGEPDEARLLAQTKAPIL  161 (519)
T ss_pred             ccccccccccccCcccchHHHHHHHHhhCCchhheEEEEEeEHHHHHhhCcchhccCceEEEecCCchHHHHhhhhccce
Confidence            333333345554444666666664   56899999999999999999999865556668889998774333333345678


Q ss_pred             eEEecCCCCCCCCCccceeeEeeeCCccEEEEeCCCCCccccccccceEEEeecCCCCCCCCCCCCCcHHHHHHHHHhcC
Q 010545          112 WILHKPPLPISFGTHHSKAMLLIYPRGVRIIVHTANLIHVDWNNKSQGLWMQDFPLKDQNNLSEECGFENDLIDYLSTLK  191 (507)
Q Consensus       112 ~~~~~p~mp~~fGthHSKmmlL~y~d~lRVVI~TANL~~~DW~~~tQ~vW~qdfP~~~~~~~~~~t~F~~dL~~yL~ay~  191 (507)
                      +.++.+.||++|||||+|||+|+|++|+||||+||||++.||++++|++|+++++++.......++.|+.||++||++|+
T Consensus       162 ~~~~~~~LpipF~thHtKm~~l~y~~G~rvvv~taNl~~~Dw~~ktQ~~w~sp~~~~~~~~g~~~~~Fk~DLi~YL~~Y~  241 (519)
T KOG2031|consen  162 VTVKLASLPIPFGTHHTKMIILFYEEGCRVVVHTANLIHDDWNNKTQGFWCSPLLKIGDKKGVSPTGFKQDLIEYLNSYR  241 (519)
T ss_pred             eeeecccccccccccccceEEEeccCccEEEEecCCcceecccccccceeecCCcccccCCCCCCCchHHHHHHHHHHhc
Confidence            99999999999999999999999999999999999999999999999999999888776677899999999999999999


Q ss_pred             CCccccCCCCCCCccccccccccccccccceEEEEccCCCCCCCccchhcHHHHHHHHhhccccCCCcccCeEEEecCCC
Q 010545          192 WPEFSANLPAHGNFKINPSFFKKFNFSSAAVRLIASVPGYHTGSSLKKWGHMKLRTVLQECTFEKGFKKSPLVYQFSSLG  271 (507)
Q Consensus       192 ~~~~~~~~~~l~~~~i~~~~l~~~DFS~~~v~LV~SvPG~h~g~~~~~~G~~~L~~~L~~~~~~~~~~~~~i~~Q~SSiG  271 (507)
                      ++.+.          .|+++|+++|||.++|+||+||||++.|.....|||.||+++|+++......++++++||+||+|
T Consensus       242 ~~~l~----------~~i~~lkk~DfS~i~v~fIgStPG~f~gs~~~~WGh~kL~kiL~~~~~~~~~~r~~~v~q~sS~g  311 (519)
T KOG2031|consen  242 LPQLK----------EWIASLKKVDFSAINVRFIGSTPGKFQGSGLLSWGHNKLKKILKEHAASPYLERTPVVGQSSSIG  311 (519)
T ss_pred             cchhH----------HHHHHHHhcchhhceEEEEeecCCcccCcccccccHHHHHHHHHhhccCcccccCceeeeeeccc
Confidence            87543          34689999999999999999999988887766799999999999987655567899999999999


Q ss_pred             cCchHHHHHHHHhccCCCCCCCCCCCC--CCcEEEccCchhhhcCcccCCCCccccCCCccch-hHHHHHHHhhhcCCCC
Q 010545          272 SLDEKWMAELSSSMSSGFSEDKTPLGI--GEPLIVWPTVEDVRCSLEGYAAGNAIPSPQKNVD-KDFLKKYWAKWKASHT  348 (507)
Q Consensus       272 sl~~~wl~~f~~sl~~~~~~~~~~~~~--~~~~IifPT~e~Vr~S~~G~~~gg~i~~~~~~~~-~~~l~~~~~kw~~~~~  348 (507)
                      +++..|...|...+..+..++..+.+.  ++++|||||+||||+|.+||.+||||||..++.+ +.|+++|||||.+.++
T Consensus       312 sl~~~~~~~~~~~f~~~l~kdt~~~gk~~~~~yiIfPTveeVrtS~~G~~~Ggsipy~~~~~~kq~~lk~y~~kW~A~~s  391 (519)
T KOG2031|consen  312 SLGSLWSAWFIGDFVESLAKDTTPPGKLRPPFYIIFPTVEEVRTSLLGYAGGGSLPYGKNTNEKQPWLKKYLCKWKAMDS  391 (519)
T ss_pred             cccchhhhhhhhhhccchhhccCCCCCCCCCeeEEcccHHHhhccccccccCceecccchhhhhhHHHHHHHHhhhhhhh
Confidence            999887766666655554444444433  4689999999999999999999999999876665 5899999999999999


Q ss_pred             CCCCCCCcceeeeeec--CCceeEEEEeccccchhhhhccccCCc---eeeeeeeeeeeEEcCCcccCCCccccccCCCC
Q 010545          349 GRSRAMPHIKTFARYN--GQKLAWFLLTSANLSKAAWGALQKNNS---QLMIRSYELGVLILPSAKRHGCGFSCTSNIVP  423 (507)
Q Consensus       349 ~R~~~~pH~K~y~r~~--~~~~~W~lltSaNLS~aAWG~~~k~~~---ql~i~nyElGVl~~P~~~~~~~~~~~~~~~~~  423 (507)
                      +|+|||||||||||++  ++.+.|+|||||||||||||+++++++   ||+|||||+||||+|..+.+..+++       
T Consensus       392 ~R~ramPHiKtYmr~~~d~q~l~W~LlTSANLSKaAWG~l~kn~sk~~~LmIRsYEaGVLf~p~~~~~~kt~k-------  464 (519)
T KOG2031|consen  392 RRSRAMPHIKTYMRFNLDDQKLAWFLLTSANLSKAAWGTLSKNKSKQPQLMIRSYEAGVLFLPRFFANLKTFK-------  464 (519)
T ss_pred             hccccCCcceeeeeecCCCCEEEEEEEeccccchhhhhhhccCCCCCchheeeecccceEecchhhhcccccc-------
Confidence            9999999999999999  689999999999999999999998875   8999999999999999765321111       


Q ss_pred             ccccCCCccchhcccceeeeeecCCCCCCCCCCcccccccccCCCCCCCCCCCCCceecCCCCCccCCCCCCccc
Q 010545          424 SEIKSGSTETSQIQKTKLVTLTWHGSSDAGASSEVVYLPVPYELPPQRYSSEDVPWSWDKRYTKKDVYGQVWPRH  498 (507)
Q Consensus       424 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vPy~lP~~~Y~~~D~Pw~~~~~y~~~D~~G~~w~~~  498 (507)
                                       ++.-++.++..   ......||||||+|++||++.|+||++++.+..+||+|++|.+.
T Consensus       465 -----------------~~~~tf~~~~~---~~~v~~vpvpydlPp~pY~~~d~~~~~~~~~~~~d~lG~vW~p~  519 (519)
T KOG2031|consen  465 -----------------VVEDTFPRDNN---GDGVIAVPVPYDLPPVPYSPKDEPFFTDIYRQGPDWLGCVWTPN  519 (519)
T ss_pred             -----------------ccceecccccC---CCCcceeccccCCCCcCCCccCCceeecccccCCcceeeccCCC
Confidence                             11111222221   12247899999999999999999999997777899999999873

>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

>PF13091 PLDc_2: PLD-like domain; PDB: 2ZE4_A 2ZE9_A 1BYS_A 1BYR_A 1V0T_A 1V0U_A 1V0V_A 1V0S_A 1V0R_A 1V0W_A	Back alignment and domain information

>smart00155 PLDc Phospholipase D	Back alignment and domain information

>PRK13912 nuclease NucT; Provisional	Back alignment and domain information

>PF00614 PLDc: Phospholipase D Active site motif; InterPro: IPR001736 Phosphatidylcholine-hydrolysing phospholipase D (PLD) isoforms are activated by ADP-ribosylation factors (ARFs)	Back alignment and domain information

>smart00155 PLDc Phospholipase D	Back alignment and domain information

>PF09565 RE_NgoFVII: NgoFVII restriction endonuclease; InterPro: IPR019065 There are four classes of restriction endonucleases: types I, II,III and IV	Back alignment and domain information

>COG1502 Cls Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthases and related enzymes [Lipid metabolism]	Back alignment and domain information

>cd00138 PLDc Phospholipase D	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		507
1qzq_A		483	Human Tyrosyl Dna Phosphodiesterase Length = 483		5e-70
1mu7_A		485	Crystal Structure Of A Human Tyrosyl-dna Phosphodie		5e-69
1jy1_A		464	Crystal Structure Of Human Tyrosyl-Dna Phosphodiest		8e-65

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

Back alignment and structure

Iteration: 1

Score = 261 bits (668), Expect = 5e-70, Method: Compositional matrix adjust. Identities = 179/483 (37%), Positives = 252/483 (52%), Gaps = 59/483 (12%) Query: 32 PSTFRLLRVQGLPAWANTSCVSIRDVIQ---GDIIVAILSNYMVDIDWLLPACPVLAKIP 88 P F L RV G+ N+ + I+D++ G ++ + NY D+DWL+ P + Sbjct: 38 PFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKK 97 Query: 89 HVLVIHGESDGTLEHM-KRNKP-ANWILHKPPLPISFGTHHSKAMLLIYPRGVRIIVHTA 146 +L++HG+ H+ + KP N L + L I+FGTHH+K MLL+Y G+R+++HT+ Sbjct: 98 PILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTS 157 Query: 147 NLIHVDWNNKSQGLWMQD-FP-LKDQNNLSEE--CGFENDLIDYLSTLKWPEFSANLPAH 202 NLIH DW+ K+QG+W+ +P + D + S E F+ DLI YL P + Sbjct: 158 NLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKADLISYLMAYNAPSLKEWIDV- 216 Query: 203 GXXXXXXXXXXXXXXXXAAVRLIASVPGYHTGSSLKKWGHMKLRTVLQECTFEKGFKKS- 261 V LI S PG GS WGH +L+ +L++ +S Sbjct: 217 ---------IHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESW 267 Query: 262 PLVYQFSSLGSL---DEKWM-AELXXXXXXXXXEDKTPLGIGEPL-IVWPTVEDVRCSLE 316 P+V QFSS+GSL + KW+ +E E KTP PL +++P+VE+VR SLE Sbjct: 268 PVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSSVPLYLIYPSVENVRTSLE 327 Query: 317 GYAAGNAIP-SPQKNVDKDFLKKYWAKWKASHTGRSRAMPHIKTFARY--NGQKLAWFLL 373 GY AG ++P S Q +++L Y+ KW A +GRS AMPHIKT+ R + K+AWFL+ Sbjct: 328 GYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLV 387 Query: 374 TSANLSKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCGFSCTSNIVPSEIKSGSTET 433 TSANLSKAAWGAL+KN +QLMIRSYELGVL LPSA F S V + +GS E Sbjct: 388 TSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSA------FGLDSFKVKQKFFAGSQEP 441 Query: 434 SQIQKTKLVTLTWHGSSDAGASSXXXXXXXXXXXXXQRYSSEDVPWSWDKRYTKK-DVYG 492 + T + Y S+D PW W+ Y K D +G Sbjct: 442 -------MATFP-----------------VPYDLPPELYGSKDRPWIWNIPYVKAPDTHG 477 Query: 493 QVW 495 +W Sbjct: 478 NMW 480

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		507
1jy1_A		464	TDP1, tyrosyl-DNA phosphodiesterase; PLD superfami	1e-139
3sq7_A		470	Tyrosyl-DNA phosphodiesterase 1; DNA binding, nucl	2e-96
1q32_A		544	TDP1P;, tyrosyl-DNA phosphodiesterase; DNA repair,	5e-93

>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 =  407 bits (1047), Expect = e-139
 Identities = 178/501 (35%), Positives = 259/501 (51%), Gaps = 59/501 (11%)

Query: 15  DSNEEALCNFHVSRDKLPSTFRLLRVQGLPAWANTSCVSIRDVIQ---GDIIVAILSNYM 71
           +   E    + +     P  F L RV G+    N+  + I+D++    G ++ +   NY 
Sbjct: 2   EDPGEGQDIWDMLDKGNPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYC 61

Query: 72  VDIDWLLPACPVLAKIPHVLVIHGESDGTLEHMKRNKPA--NWILHKPPLPISFGTHHSK 129
            D+DWL+   P   +   +L++HG+      H+        N  L +  L I+FGTHH+K
Sbjct: 62  FDVDWLVKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTK 121

Query: 130 AMLLIYPRGVRIIVHTANLIHVDWNNKSQGLWMQDFPLKDQNNLSEE----CGFENDLID 185
            MLL+Y  G+R+++HT+NLIH DW+ K+QG+W+     +  +   +       F+ +LI 
Sbjct: 122 MMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKANLIS 181

Query: 186 YLSTLKWPEFSANLPAHGNFKINPSFFKKFNFSSAAVRLIASVPGYHTGSSLKKWGHMKL 245
           YL+    P     +              K + S   V LI S PG   GS    WGH +L
Sbjct: 182 YLTAYNAPSLKEWI----------DVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRL 231

Query: 246 RTVLQECTFEKGF-KKSPLVYQFSSLGSL---DEKWM-AELSSSMSSGFSEDKTPLGIGE 300
           + +L++        +  P+V QFSS+GSL   + KW+ +E   SM +   E KTP     
Sbjct: 232 KKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSSV 291

Query: 301 PL-IVWPTVEDVRCSLEGYAAGNAIPSPQKNVDK-DFLKKYWAKWKASHTGRSRAMPHIK 358
           PL +++P+VE+VR SLEGY AG ++P   +  +K ++L  Y+ KW A  +GRS AMPHIK
Sbjct: 292 PLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIK 351

Query: 359 TFARYNG--QKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCGFS 416
           T+ R +    K+AWFL+TSANLSKAAWGAL+KN +QLMIRSYELGVL LPSA        
Sbjct: 352 TYMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSAL------- 404

Query: 417 CTSNIVPSEIKSGSTETSQIQKTKLVTLTWHGSSDAGASSEVVYLPVPYELPPQRYSSED 476
                                   L +        AG+   +   PVPY+LPP+ Y S+D
Sbjct: 405 -----------------------GLDSFKVKQKFFAGSQEPMATFPVPYDLPPELYGSKD 441

Query: 477 VPWSWDKRYTKK-DVYGQVWP 496
            PW W+  Y K  D +G +W 
Sbjct: 442 RPWIWNIPYVKAPDTHGNMWV 462

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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		507
1jy1_A		464	TDP1, tyrosyl-DNA phosphodiesterase; PLD superfami	100.0
3sq7_A		470	Tyrosyl-DNA phosphodiesterase 1; DNA binding, nucl	100.0
1q32_A		544	TDP1P;, tyrosyl-DNA phosphodiesterase; DNA repair,	100.0
1byr_A		155	Protein (endonuclease); phosphodiesterase,; 2.00A	87.84
4ggj_A		196	Mitochondrial cardiolipin hydrolase; piRNA pathway	84.88
3hsi_A		458	Phosphatidylserine synthase; CDP- diacylglycerol--	81.88

>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	Back alignment and structure

Probab=100.00  E-value=5.9e-113  Score=912.21  Aligned_cols=443  Identities=40%  Similarity=0.741  Sum_probs=369.2

Q ss_pred             cCchhhhcccCCCCCCCCCceEEEEecCCCCCCCCCceeecccccc---cHHhhhhhhcccChhhhcccCCC-CCCCCeE
Q 010545           15 DSNEEALCNFHVSRDKLPSTFRLLRVQGLPAWANTSCVSIRDVIQG---DIIVAILSNYMVDIDWLLPACPV-LAKIPHV   90 (507)
Q Consensus        15 ~~~~~~~~~~~~~~~~~~~~F~L~~~~~~~~~~n~~~itl~Dll~~---~l~~a~l~sF~~Dl~WLl~~~~~-~~~~~~i   90 (507)
                      +..+|+++.++.....-|++|+||+|++.+..+|.++|||+|||++   ++++|++||||+|++||+++|+. .+++| |
T Consensus         2 ~~~~~~~~~~~~~~~~~p~~~~l~~i~~~~~~~n~~~itl~diL~~~~g~l~~a~~~nf~~D~~WLl~~~~~~~~~~~-v   80 (464)
T 1jy1_A            2 EDPGEGQDIWDMLDKGNPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKKP-I   80 (464)
T ss_dssp             CCTTTTCCGGGTSCTTCSSCEEEBCCTTSCGGGGTTCBCHHHHTSGGGCCEEEEEEECSCBCHHHHHHHSCGGGTTSC-E
T ss_pred             CCcccccchhhhhcccCCceEEEEeecCCCcccCCCceeHHHHhCCccccHHHHHhHHhHHhHHHHHhhCcccccCCc-E
Confidence            3568899999988877888999999999998889999999999975   58899999999999999999974 45664 7


Q ss_pred             EEEeCCCCChhhhh--hhcCCCceEEecCCCCCCCCCccceeeEeeeCCccEEEEeCCCCCccccccccceEEEee-cCC
Q 010545           91 LVIHGESDGTLEHM--KRNKPANWILHKPPLPISFGTHHSKAMLLIYPRGVRIIVHTANLIHVDWNNKSQGLWMQD-FPL  167 (507)
Q Consensus        91 ~vv~g~~~~~~~~~--~~~~~~n~~~~~p~mp~~fGthHSKmmlL~y~d~lRVVI~TANL~~~DW~~~tQ~vW~qd-fP~  167 (507)
                      +||+|++++....+  .....+|+++|+|+||.+|||||||||||+|+||||||||||||+++||+++||+||+|| ||+
T Consensus        81 ~iv~g~~~~~~~~l~~~~~~~~nv~~~~p~mp~~fGthHsKmmiL~y~~glRVVI~TANL~~~DW~~~tQ~vW~sd~lP~  160 (464)
T 1jy1_A           81 LLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPR  160 (464)
T ss_dssp             EEEECCCHHHHHHHHHHHTTCTTEEEEECCCCSTTCCBCCCEEEEEESSCEEEEEECCCBSGGGGTSSBCEEEECCCBCB
T ss_pred             EEEeCCCcccchhhHHhhccCCCeEEEeCCCCCcccccchhhheeecCCceEEEEeCCCCChhHhccccceEEecccCcC
Confidence            88889754322222  223457999999999999999999999999999999999999999999999999999999 798


Q ss_pred             CCCCC---CCCCCCcHHHHHHHHHhcCCCccccCCCCCCCccccccccccccccccceEEEEccCCCCCCCccchhcHHH
Q 010545          168 KDQNN---LSEECGFENDLIDYLSTLKWPEFSANLPAHGNFKINPSFFKKFNFSSAAVRLIASVPGYHTGSSLKKWGHMK  244 (507)
Q Consensus       168 ~~~~~---~~~~t~F~~dL~~yL~ay~~~~~~~~~~~l~~~~i~~~~l~~~DFS~~~v~LV~SvPG~h~g~~~~~~G~~~  244 (507)
                      ++..+   .+++++|++||++||++|+.+....          +++.|++||||.++|+||+||||+|.|.+..+|||+|
T Consensus       161 ~~~~~~~~~~~~~~Fk~dL~~yL~ay~~~~~~~----------~i~~L~~~DFS~~~v~LVaSvPG~h~~~~~~~~G~~~  230 (464)
T 1jy1_A          161 IADGTHKSGESPTHFKANLISYLTAYNAPSLKE----------WIDVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFR  230 (464)
T ss_dssp             CCTTCCCCCCCTTCHHHHHHHHHHTTCCGGGHH----------HHHHHHTBCCTTCCSEEEEECSEEEEGGGGGGSHHHH
T ss_pred             CCccccccCCCCCchHHHHHHHHHHhCCchhHH----------HHHHHHhcCCcccCcEEEEeCCcCCcCCcchhhhHHH
Confidence            65433   3678999999999999998764322          2588999999999999999999999999999999999


Q ss_pred             HHHHHhhccccC-CCcccCeEEEecCCCcCc---hHHH-HHHHHhccCCCCCCCCC-CCCCCcEEEccCchhhhcCcccC
Q 010545          245 LRTVLQECTFEK-GFKKSPLVYQFSSLGSLD---EKWM-AELSSSMSSGFSEDKTP-LGIGEPLIVWPTVEDVRCSLEGY  318 (507)
Q Consensus       245 L~~~L~~~~~~~-~~~~~~i~~Q~SSiGsl~---~~wl-~~f~~sl~~~~~~~~~~-~~~~~~~IifPT~e~Vr~S~~G~  318 (507)
                      |+++|+++.... ..+.++|+||+||||+++   .+|| ++|+.+|.+...+.+.+ ...++++|||||+||||+|.+|+
T Consensus       231 L~~~L~~~~~~~~~~~~~~i~~Q~SSIGslg~~~~~Wl~~~f~~sl~~~~~~~~~~~~~~~~~~iifPT~e~Vr~S~~G~  310 (464)
T 1jy1_A          231 LKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSSVPLYLIYPSVENVRTSLEGY  310 (464)
T ss_dssp             HHHHHHHHC-----CCSCCEEEECSCBCCCCSSTTTTTTTTHHHHHTCCC---------CCCEEEECCBHHHHHTSSSCG
T ss_pred             HHHHHHHhccCCCccCCCcEEEEeecccccCcchhHHHHHHHHHHhhhhcccccccccCCCceEEEcCCHHHHHhccccc
Confidence            999999987532 225789999999999997   4899 68999997753222211 23467999999999999999999


Q ss_pred             CCCccccCCCccch-hHHHHHHHhhhcCCCCCCCCCCCcceeeeeecC--CceeEEEEeccccchhhhhccccCCceeee
Q 010545          319 AAGNAIPSPQKNVD-KDFLKKYWAKWKASHTGRSRAMPHIKTFARYNG--QKLAWFLLTSANLSKAAWGALQKNNSQLMI  395 (507)
Q Consensus       319 ~~gg~i~~~~~~~~-~~~l~~~~~kw~~~~~~R~~~~pH~K~y~r~~~--~~~~W~lltSaNLS~aAWG~~~k~~~ql~i  395 (507)
                      .+|||||++.+.++ +.|++++||+|+++.++|++++||||+|+|++.  ..++|+||||||||+||||+++++++||+|
T Consensus       311 ~~ggsi~~~~~~~~~~~~l~~~l~~w~~~~~~R~~a~pHiKty~r~~~~~~~~~W~lltSaNLSkaAWG~~~k~~~~l~I  390 (464)
T 1jy1_A          311 PAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQLMI  390 (464)
T ss_dssp             GGGGGSCCCHHHHTTCGGGGGGEECCCCGGGTCTTSCBCCEEEEEECTTSSEEEEEEEESCCBSHHHHCEEETTTTEEEE
T ss_pred             CCcceeeccchhhhhhhhhHHHHHHhccCccCCCCcCCceeeEEecCCCCCeecEEEEccccCCHHHhCccccCCCceeE
Confidence            99999999866554 469999999999999999999999999999985  479999999999999999999999999999


Q ss_pred             eeeeeeeEEcCCcccCCCccccccCCCCccccCCCccchhcccceeeeeecCCCCCCCCCCcccccccccCCCCCCCCCC
Q 010545          396 RSYELGVLILPSAKRHGCGFSCTSNIVPSEIKSGSTETSQIQKTKLVTLTWHGSSDAGASSEVVYLPVPYELPPQRYSSE  475 (507)
Q Consensus       396 ~nyElGVl~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vPy~lP~~~Y~~~  475 (507)
                      |||||||||+|..+.+. .+....                    +.    .  +.   .....+.|||||++|++||+++
T Consensus       391 ~nyElGVl~~P~~~~~~-~~~~~~--------------------~~----~--~~---~~~~~~~~~vPy~lP~~~Y~~~  440 (464)
T 1jy1_A          391 RSYELGVLFLPSALGLD-SFKVKQ--------------------KF----F--AG---SQEPMATFPVPYDLPPELYGSK  440 (464)
T ss_dssp             CSBEEEEEECGGGGTCS-CEEEC----------------------------------------CEECCSSCSSCCBCCTT
T ss_pred             eeeeeeEEEeccccccc-ccccCc--------------------cc----c--cc---ccCcccceeecCCCCCcCCCCC
Confidence            99999999999875432 121110                    00    0  00   0122468999999999999999


Q ss_pred             CCCceecCCCCCc-cCCCCCCccc
Q 010545          476 DVPWSWDKRYTKK-DVYGQVWPRH  498 (507)
Q Consensus       476 D~Pw~~~~~y~~~-D~~G~~w~~~  498 (507)
                      |+||+++++|.+| |++|++|++.
T Consensus       441 D~Pw~~~~~~~~~~D~~G~~w~p~  464 (464)
T 1jy1_A          441 DRPWIWNIPYVKAPDTHGNMWVPS  464 (464)
T ss_dssp             CCBCCTTSCBCSSCCTTSCCBCCC
T ss_pred             CCCeeCCCCCCCcccCCcCcCCCC
Confidence            9999999999997 9999999873

PyMOL of 1jy1

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

>1byr_A Protein (endonuclease); phosphodiesterase,; 2.00A {Salmonella typhimurium} SCOP: d.136.1.1 PDB: 1bys_A	Back alignment and structure

>4ggj_A Mitochondrial cardiolipin hydrolase; piRNA pathway, protein-RNA interactions, piRNA RNAI, HKD MOT zinc finger, nuclease, nucleic acid binding; 1.75A {Mus musculus} PDB: 4ggk_A	Back alignment and structure

>3hsi_A Phosphatidylserine synthase; CDP- diacylglycerol--serine O-phosphatidyltransferase, structura genomics, PSI-2; HET: MSE; 2.20A {Haemophilus influenzae}	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		507
d1jy1a2		258	d.136.1.3 (A:351-608) Tyrosyl-DNA phosphodiesteras	5e-88
d1q32a1		215	d.136.1.3 (A:79-293) Tyrosyl-DNA phosphodiesterase	6e-60
d1jy1a1		206	d.136.1.3 (A:145-350) Tyrosyl-DNA phosphodiesteras	7e-54
d1q32a2		237	d.136.1.3 (A:302-538) Tyrosyl-DNA phosphodiesteras	1e-41

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

 Score =  268 bits (687), Expect = 5e-88
 Identities = 120/285 (42%), Positives = 160/285 (56%), Gaps = 40/285 (14%)

Query: 222 VRLIASVPGYHTGSSLKKWGHMKLRTVLQECTFEKGF-KKSPLVYQFSSLGSL---DEKW 277
           V LI S PG   GS    WGH +L+ +L++        +  P+V QFSS+GSL   + KW
Sbjct: 2   VYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKW 61

Query: 278 M-AELSSSMSSGFSEDKTPLGIGEPL-IVWPTVEDVRCSLEGYAAGNAIPSPQKNVDK-D 334
           + +E   SM +   E KTP     PL +++P+VE+VR SLEGY AG ++P   +  +K +
Sbjct: 62  LCSEFKESMLTLGKESKTPGKSSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQN 121

Query: 335 FLKKYWAKWKASHTGRSRAMPHIKTFARYN--GQKLAWFLLTSANLSKAAWGALQKNNSQ 392
           +L  Y+ KW A  +GRS AMPHIKT+ R +    K+AWFL+TSANLSKAAWGAL+KN +Q
Sbjct: 122 WLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQ 181

Query: 393 LMIRSYELGVLILPSAKRHGCGFSCTSNIVPSEIKSGSTETSQIQKTKLVTLTWHGSSDA 452
           LMIRSYELGVL LPSA                                L +        A
Sbjct: 182 LMIRSYELGVLFLPSA------------------------------LGLDSFKVKQKFFA 211

Query: 453 GASSEVVYLPVPYELPPQRYSSEDVPWSWDKRYTK-KDVYGQVWP 496
           G+   +   PVPY+LPP+ Y S+D PW W+  Y K  D +G +W 
Sbjct: 212 GSQEPMATFPVPYDLPPELYGSKDRPWIWNIPYVKAPDTHGNMWV 256

PyMOL of d1jy1a2

>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

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

>d1q32a2 d.136.1.3 (A:302-538) Tyrosyl-DNA phosphodiesterase TDP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 237	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		507
d1jy1a2		258	Tyrosyl-DNA phosphodiesterase TDP1 {Human (Homo sa	100.0
d1q32a1		215	Tyrosyl-DNA phosphodiesterase TDP1 {Baker's yeast	100.0
d1jy1a1		206	Tyrosyl-DNA phosphodiesterase TDP1 {Human (Homo sa	100.0
d1q32a2		237	Tyrosyl-DNA phosphodiesterase TDP1 {Baker's yeast	100.0
d1byra_		152	Nuclease Nuc {Salmonella typhimurium [TaxId: 90371	92.47
d1v0wa2		246	Phospholipase D {Streptomyces sp. [TaxId: 1931]}	87.5

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

Probab=100.00  E-value=2.6e-70  Score=539.54  Aligned_cols=247  Identities=47%  Similarity=0.837  Sum_probs=201.1

Q ss_pred             ceEEEEccCCCCCCCccchhcHHHHHHHHhhcccc-CCCcccCeEEEecCCCcCc---hHHH-HHHHHhccCCCCCCCCC
Q 010545          221 AVRLIASVPGYHTGSSLKKWGHMKLRTVLQECTFE-KGFKKSPLVYQFSSLGSLD---EKWM-AELSSSMSSGFSEDKTP  295 (507)
Q Consensus       221 ~v~LV~SvPG~h~g~~~~~~G~~~L~~~L~~~~~~-~~~~~~~i~~Q~SSiGsl~---~~wl-~~f~~sl~~~~~~~~~~  295 (507)
                      +|+||+||||+|.|.++.+|||+||+++|++++.. ...++.+|+||+||||||+   .+|| ++|..+|.+...+.+++
T Consensus         1 nV~lV~SvPG~h~g~~~~~~G~~~L~~~l~~~~~~~~~~~~~~iv~Q~SSiGSlg~~~~~wl~~~~~~sl~~~~~~~~~~   80 (258)
T d1jy1a2           1 NVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTP   80 (258)
T ss_dssp             CSEEEEECSEEEEGGGGGGSHHHHHHHHHHHHC-----CCSCCEEEECSCBCCCCSSTTTTTTTTHHHHHTCCC------
T ss_pred             CeEEEEeCCccccCCccccccHHHHHHHHHHcCCCCCcCcCCCEEEEeCCcccCCcCHHHHHHHHHHHhhhcccccccCc
Confidence            68999999999999999999999999999987654 2345689999999999997   3799 68988887654433322


Q ss_pred             -CCCCCcEEEccCchhhhcCcccCCCCccccCCCccch-hHHHHHHHhhhcCCCCCCCCCCCcceeeeeecC--CceeEE
Q 010545          296 -LGIGEPLIVWPTVEDVRCSLEGYAAGNAIPSPQKNVD-KDFLKKYWAKWKASHTGRSRAMPHIKTFARYNG--QKLAWF  371 (507)
Q Consensus       296 -~~~~~~~IifPT~e~Vr~S~~G~~~gg~i~~~~~~~~-~~~l~~~~~kw~~~~~~R~~~~pH~K~y~r~~~--~~~~W~  371 (507)
                       ...++++|||||+||||+|.+|+.+|||||++.++++ +.|++++||+|.++.++|++++||||||+|+++  +.++|+
T Consensus        81 ~~~~~~~~iifPT~~~Vr~S~~G~~~ggsi~~~~~~~~~~~~l~~~l~~w~~~~~gR~~a~PHiKty~r~~~d~~~i~W~  160 (258)
T d1jy1a2          81 GKSSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWF  160 (258)
T ss_dssp             ---CCCEEEECCBHHHHHTSSSCGGGGGGSCCCHHHHTTCGGGGGGEECCCCGGGTCTTSCBCCEEEEEECTTSSEEEEE
T ss_pred             ccCCCCeEEEcCCHHHHhccccCcCCcceeecCchhhhhhhhHHHHHHhcCCCcCCCCCCCCeeEEEEEECCCCCeeeEE
Confidence             2345799999999999999999999999999977665 469999999999999999999999999999986  579999


Q ss_pred             EEeccccchhhhhccccCCceeeeeeeeeeeEEcCCcccCCCccccccCCCCccccCCCccchhcccceeeeeecCCCCC
Q 010545          372 LLTSANLSKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCGFSCTSNIVPSEIKSGSTETSQIQKTKLVTLTWHGSSD  451 (507)
Q Consensus       372 lltSaNLS~aAWG~~~k~~~ql~i~nyElGVl~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  451 (507)
                      ||||||||+||||+++++++||+||||||||||+|..+... .|....                             ...
T Consensus       161 lltSaNLSkaAWG~~~~~~~~l~I~nyElGVL~~p~~~~~~-~~~~~~-----------------------------~~~  210 (258)
T d1jy1a2         161 LVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSALGLD-SFKVKQ-----------------------------KFF  210 (258)
T ss_dssp             EEESCCBSHHHHCEEETTTTEEEECSBEEEEEECGGGGTCS-CEEEC---------------------------------
T ss_pred             EEccccCCHHHhCcccCCCCeEEeecceeEEEEcccccCCC-cccccc-----------------------------ccc
Confidence            99999999999999999999999999999999998864322 121110                             000


Q ss_pred             CCCCCcccccccccCCCCCCCCCCCCCceecCCCCC-ccCCCCCCcc
Q 010545          452 AGASSEVVYLPVPYELPPQRYSSEDVPWSWDKRYTK-KDVYGQVWPR  497 (507)
Q Consensus       452 ~~~~~~~~~~~vPy~lP~~~Y~~~D~Pw~~~~~y~~-~D~~G~~w~~  497 (507)
                      ....+..+.|||||+||++||+++|+|||+|++|.+ ||++|++|++
T Consensus       211 ~~~~~~~~~~~vPy~lP~~~Y~~~D~PW~~~~~~~e~pD~~G~~w~p  257 (258)
T d1jy1a2         211 AGSQEPMATFPVPYDLPPELYGSKDRPWIWNIPYVKAPDTHGNMWVP  257 (258)
T ss_dssp             -------CEECCSSCSSCCBCCTTCCBCCTTSCBCSSCCTTSCCBCC
T ss_pred             cCccCcCCcceecCCCCCcCCCCCCcCeeccCCcccCCCCCCCcCCC
Confidence            001123467999999999999999999999999975 9999999987

PyMOL of d1jy1a2

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

>d1jy1a1 d.136.1.3 (A:145-350) 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

>d1byra_ d.136.1.1 (A:) Nuclease Nuc {Salmonella typhimurium [TaxId: 90371]}	Back information, alignment and structure

>d1v0wa2 d.136.1.2 (A:264-514) Phospholipase D {Streptomyces sp. [TaxId: 1931]}	Back information, alignment and structure