Citrus Sinensis ID: 013748

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-------

MVDIDWLLPACPVLAKIPHVLVIHGESDGTLEHMKRNKPANWILHKPPLPISFGTHHSKAMLLIYPRGVRIIVHTANLIHVDWNNKSQGLWMQDFPLKDQNNLSEECGFENDLIDYLSTLKWPEFSANLPAHGNFKINPSFFKKFNFSSAAVRLIASVPGYHTGSSLKKWGHMKLRTVLQECTFEKGFKKSPLVYQFSSLGSLDEKWMAELSSSMSSGFSEDKTPLGIGEPLIVWPTVEDVRCSLEGYAAGNAIPSPQKNVDKDFLKKYWAKWKASHTGRSRAMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCGFSCTSNIVPSEIKSGSTETSQIQKTKLVTLTWHGSSDAGASSEVVYLPVPYELPPQRYSSEDVPWSWDKRYTKKDVYGQVWPRHFQLYAFQDS

cccHHcccccccccccccEEEEEEccccHHHHHHHHcccccEEEEcccccccccccccEEEEEEEcccEEEEEEcccccHHcccccccEEEEEccccccccccccccccHHHHHHHHHHcccccccccccccccccccccccccccccccccEEEEEcccccccccccHHHHHHHHHHHHHcccccccccccEEEEEcccccccHHHHHHHHHHHccccccccccccccccEEEccccHHHHcccccccccccccccccccHHHHHHHHHHHHccccccccccccccEEEEEcccccEEEEEEccccccHHHHccccccccEEEEEEEEEEEEEccccccccccccccccccccccccccccccHHccccEEEcccccccccccccccEEccccccccccccccccccEEEcccccccccccccccccccccccccc

cccHHHHHHHccHHccccEEEEEEccccHHHHHHHHcccccEEEEEccccccccccccEEEEEEcccccEEEEEcccccHHHHcccccEEEEccccccccccccccccHHHHHHHHHHHcccccHHHHHcccccccHHHHHHHHccccccEEEEEEcccccccccccccccHHHHHHHHHHcccccccccccEEEEEEcHccccHHHHHHHHHHHHcccccccccccccccEEEEccHHHHHHccccccccccccccHHHHHHHHHHHHHHHccccccccccccccEEEEEcccccccEEEEEEcHHHHHHHHHHHcccccEEEEEEEEEEEEEccHHccccccccccccccccccccccccccccccccEEEccccccccccccccEEEEcccccccccccccccccEEEEccccccccccccccccEEEEEcccc

mvdidwllpacpvlakiphvlvihgesdgtlehmkrnkpanwilhkpplpisfgthhsKAMLLIYPRGVRIIVHTANLIHvdwnnksqglwmqdfplkdqnnlseecgfeNDLIDYLstlkwpefsanlpahgnfkinpsffkkfnfSSAAVRLIAsvpgyhtgsslkkwgHMKLRTVLQEctfekgfkksplvyqfsslgslDEKWMAELSSsmssgfsedktplgigeplivwptvedvrcslegyaagnaipspqknvdKDFLKKYWAKWKAshtgrsramphiKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLilpsakrhgcgfsctsnivpseiksgstetSQIQKTKLVTltwhgssdagassevvylpvpyelppqryssedvpwswdkrytkkdvygqvwprhfqlyafqds

MVDIDWLLPACPVLAKIPHVLVIHGESDGTLEHMKRNKPANWILHKPPLPISFGTHHSKAMLLIYPRGVRIIVHTANLIHVDWNNKSQGLWMQDFPLKDQNNLSEECGFENDLIDYLSTLKWPEFSANLPAHGNFKINPSFFKKFNFSSAAVRLIASVPGYHTGSSLKKWGHMKLRTVLQECTFEKGFKKSPLVYQFSSLGSLDEKWMAELSSSMSSGFSEDKTPLGIGEPLIVWPTVEDVRCSLEGyaagnaipspqknvDKDFLKKYWAKWKashtgrsrampHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCGFSCTSNIVpseiksgstetSQIQKTKLVTLTWHGSSDAGASSEVVYLPVPYELppqryssedvpwswdkrytkkDVYGQVWPRHFQLYAFQDS

MVDIDWLLPACPVLAKIPHVLVIHGESDGTLEHMKRNKPANWILHKPPLPISFGTHHSKAMLLIYPRGVRIIVHTANLIHVDWNNKSQGLWMQDFPLKDQNNLSEECGFENDLIDYLSTLKWPEFSANLPAHGnfkinpsffkkfnfssAAVRLIASVPGYHTGSSLKKWGHMKLRTVLQECTFEKGFKKSPLVYQFSSLGSLDEKWMAELsssmssgfsEDKTPLGIGEPLIVWPTVEDVRCSLEGYAAGNAIPSPQKNVDKDFLKKYWAKWKASHTGRSRAMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCGFSCTSNIVPSEIKSGSTETSQIQKTKLVTLTWHGSSDAGASSevvylpvpyelppQRYSSEDVPWSWDKRYTKKDVYGQVWPRHFQLYAFQDS

**DIDWLLPACPVLAKIPHVLVIHGESDGTLEHMKRNKPANWILHKPPLPISFGTHHSKAMLLIYPRGVRIIVHTANLIHVDWNNKSQGLWMQDFPLKDQNNLSEECGFENDLIDYLSTLKWPEFSANLPAHGNFKINPSFFKKFNFSSAAVRLIASVPGYHTGSSLKKWGHMKLRTVLQECTFEKGFKKSPLVYQFSSLGSLDEKW******************LGIGEPLIVWPTVEDVRCSLEGYAAGNAIPSPQKNVDKDFLKKYWAKWKASHTGRSRAMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCGFSCTSNIVP***************TKLVTLTWHGSSDAGASSEVVYLPVPYELPPQRYSSEDVPWSWDKRYTKKDVYGQVWPRHFQLYAF***

MVDIDWLLPACPVLAKIPHVLVIHGES*********NKPANWILHKPPLPISFGTHHSKAMLLIYPRGVRIIVHTANLIHVDWNNKSQGLWM********************LIDYLSTLKWPEFSANLPAHGNFKINPSFFKKFNFSSAAVRLIASVPGYHTGSSLKKWGHMKLRTVLQECT***GFKKSPLVYQFSSLGSLDEKWMAELSS******************LIVWPTVEDVRCSLEGYAAGNAIPSPQKNVDKDFLKKYWAKWKASHTGRSRAMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCG******************************************EVVYLPVPYELPPQRYSSEDVPWSWDKRYTKKDVYGQVWPRHFQLY*****

MVDIDWLLPACPVLAKIPHVLVIHGESDGTLEHMKRNKPANWILHKPPLPISFGTHHSKAMLLIYPRGVRIIVHTANLIHVDWNNKSQGLWMQDFPLKDQNNLSEECGFENDLIDYLSTLKWPEFSANLPAHGNFKINPSFFKKFNFSSAAVRLIASVPGYHTGSSLKKWGHMKLRTVLQECTFEKGFKKSPLVYQFSSLGSLDEKWMAEL**********DKTPLGIGEPLIVWPTVEDVRCSLEGYAAGNAIPSPQKNVDKDFLKKYWAKWKASHTGRSRAMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCGFSCTSNIVPSEI**********QKTKLVTLTWHGSSDAGASSEVVYLPVPYELPPQRYSSEDVPWSWDKRYTKKDVYGQVWPRHFQLYAFQDS

MVDIDWLLPACPVLAKIPHVLVIHGESDGTLEHMKRNKPANWILHKPPLPISFGTHHSKAMLLIYPRGVRIIVHTANLIHVDWNNKSQGLWMQDFPLKD***LSEECGFENDLIDYLSTLKWPEFSANLPAHGNFKINPSFFKKFNFSSAAVRLIASVPGYHTGSSLKKWGHMKLRTVLQECTFEKGFKKSPLVYQFSSLGSLDEKWMAELSSSMSSGFSEDKTPLGIGEPLIVWPTVEDVRCSLEGYAAGNAIPSPQKNVDKDFLKKYWAKWKASHTGRSRAMPHIKTFARYNGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCGFSCTSNIVP***************TKLVTLTWHGSSDAGASSEVVYLPVPYELPPQRYSSEDVPWSWDKRYTKKDVYGQVWPRHFQLYAF***

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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		437	2.2.26 [Sep-21-2011]
Q9NUW8		608	Tyrosyl-DNA phosphodieste	yes	no	0.876	0.629	0.403	2e-72
Q8BJ37		609	Tyrosyl-DNA phosphodieste	yes	no	0.874	0.627	0.390	2e-69
Q4G056		609	Tyrosyl-DNA phosphodieste	yes	no	0.874	0.627	0.388	9e-69
Q9VQM4		580	Probable tyrosyl-DNA phos	yes	no	0.736	0.555	0.352	7e-41
Q9TXV7		451	Probable tyrosyl-DNA phos	yes	no	0.819	0.793	0.301	4e-40
Q9USG9		536	Probable tyrosyl-DNA phos	yes	no	0.913	0.744	0.267	1e-28

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

 Score =  273 bits (698), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 177/439 (40%), Positives = 244/439 (55%), Gaps = 56/439 (12%)

Query: 3   DIDWLLPACPVLAKIPHVLVIHGESDGTLEHM-KRNKP-ANWILHKPPLPISFGTHHSKA 60
           D+DWL+   P   +   +L++HG+      H+  + KP  N  L +  L I+FGTHH+K 
Sbjct: 207 DVDWLVKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKM 266

Query: 61  MLLIYPRGVRIIVHTANLIHVDWNNKSQGLWMQD-FP-LKDQNNLSEE--CGFENDLIDY 116
           MLL+Y  G+R+++HT+NLIH DW+ K+QG+W+   +P + D  + S E    F+ DLI Y
Sbjct: 267 MLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKADLISY 326

Query: 117 LSTLKWPEFSANLPAHGNFKINPSFFKKFNFSSAAVRLIASVPGYHTGSSLKKWGHMKLR 176
           L     P     +              K + S   V LI S PG   GS    WGH +L+
Sbjct: 327 LMAYNAPSLKEWI----------DVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLK 376

Query: 177 TVLQECTFEKGFKKS-PLVYQFSSLGSL---DEKWM-AELSSSMSSGFSEDKTPLGIGEP 231
            +L++        +S P+V QFSS+GSL   + KW+ +E   SM +   E KTP     P
Sbjct: 377 KLLKDHASSMPNAESWPVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSSVP 436

Query: 232 L-IVWPTVEDVRCSLEGYAAGNAIP-SPQKNVDKDFLKKYWAKWKASHTGRSRAMPHIKT 289
           L +++P+VE+VR SLEGY AG ++P S Q    +++L  Y+ KW A  +GRS AMPHIKT
Sbjct: 437 LYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKT 496

Query: 290 FARY--NGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCGFSC 347
           + R   +  K+AWFL+TSANLSKAAWGAL+KN +QLMIRSYELGVL LPSA      F  
Sbjct: 497 YMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSA------FGL 550

Query: 348 TSNIVPSEIKSGSTETSQIQKTKLVTLTWHGSSDAGASSEVVYLPVPYELPPQRYSSEDV 407
            S  V  +  +GS E                         +   PVPY+LPP+ Y S+D 
Sbjct: 551 DSFKVKQKFFAGSQEP------------------------MATFPVPYDLPPELYGSKDR 586

Query: 408 PWSWDKRYTKK-DVYGQVW 425
           PW W+  Y K  D +G +W
Sbjct: 587 PWIWNIPYVKAPDTHGNMW 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		437
302144065		678	unnamed protein product [Vitis vinifera]	1.0	0.644	0.800	0.0
359483320		621	PREDICTED: tyrosyl-DNA phosphodiesterase	1.0	0.703	0.800	0.0
255554997		665	tyrosyl-DNA phosphodiesterase, putative	0.995	0.654	0.778	0.0
224078752		599	predicted protein [Populus trichocarpa]	0.972	0.709	0.773	0.0
449479663		959	PREDICTED: tyrosyl-DNA phosphodiesterase	0.979	0.446	0.744	0.0
449434370		613	PREDICTED: tyrosyl-DNA phosphodiesterase	0.979	0.698	0.734	0.0
356507526		599	PREDICTED: tyrosyl-DNA phosphodiesterase	0.977	0.712	0.773	0.0
356507524		610	PREDICTED: tyrosyl-DNA phosphodiesterase	0.977	0.7	0.773	0.0
297811655		612	hypothetical protein ARALYDRAFT_488358 [	0.967	0.691	0.734	0.0
22326821		605	tyrosyl-DNA phosphodiesterase 1 [Arabido	0.967	0.699	0.725	0.0

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

 Score =  746 bits (1925), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 350/437 (80%), Positives = 388/437 (88%)

Query: 1   MVDIDWLLPACPVLAKIPHVLVIHGESDGTLEHMKRNKPANWILHKPPLPISFGTHHSKA 60
           MVDIDWLL +CP LAKIPHVLVIHGE DGTL+HMK+NKP NWILHKPPLPISFGTHHSKA
Sbjct: 242 MVDIDWLLSSCPTLAKIPHVLVIHGEGDGTLDHMKKNKPPNWILHKPPLPISFGTHHSKA 301

Query: 61  MLLIYPRGVRIIVHTANLIHVDWNNKSQGLWMQDFPLKDQNNLSEECGFENDLIDYLSTL 120
           MLL+YPRGVR+IVHTANLI+VDWNNKSQGLWMQDFP K Q  LS+ C FENDLIDYLS L
Sbjct: 302 MLLVYPRGVRVIVHTANLIYVDWNNKSQGLWMQDFPWKVQKELSKGCAFENDLIDYLSVL 361

Query: 121 KWPEFSANLPAHGNFKINPSFFKKFNFSSAAVRLIASVPGYHTGSSLKKWGHMKLRTVLQ 180
           KWPEF+ANLPA G+F IN SFFKKF++S+A VRLIASVPGYHTGS+LKKWGHMKL +VLQ
Sbjct: 362 KWPEFTANLPALGSFNINSSFFKKFDYSNAVVRLIASVPGYHTGSNLKKWGHMKLCSVLQ 421

Query: 181 ECTFEKGFKKSPLVYQFSSLGSLDEKWMAELSSSMSSGFSEDKTPLGIGEPLIVWPTVED 240
           EC F+K F+KSPL YQFSSLGSLDEKWM EL+SSMSSG  +DKTPLG+G+PLI+WPTVED
Sbjct: 422 ECIFDKEFQKSPLAYQFSSLGSLDEKWMTELASSMSSGSCDDKTPLGLGKPLIIWPTVED 481

Query: 241 VRCSLEGYAAGNAIPSPQKNVDKDFLKKYWAKWKASHTGRSRAMPHIKTFARYNGQKLAW 300
           VRCSLEGYAAGNAIPSPQKNV+K+FLKKYWAKWKA+HTGR RAMPHIKT+ RYNGQ LAW
Sbjct: 482 VRCSLEGYAAGNAIPSPQKNVEKEFLKKYWAKWKATHTGRCRAMPHIKTYTRYNGQNLAW 541

Query: 301 FLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCGFSCTSNIVPSEIKSGS 360
           FLLTSANLSKAAWGALQKNNSQLMIRSYELGVL LPS    G GFSCT N  PS+ K G 
Sbjct: 542 FLLTSANLSKAAWGALQKNNSQLMIRSYELGVLFLPSPINRGQGFSCTDNGSPSKNKCGL 601

Query: 361 TETSQIQKTKLVTLTWHGSSDAGASSEVVYLPVPYELPPQRYSSEDVPWSWDKRYTKKDV 420
           +E ++ Q+TKLVTLTW G+  + +SSEV+ LPVPYELPP++YSSEDVPWSWD+RY KKDV
Sbjct: 602 SENTKSQRTKLVTLTWEGNRSSDSSSEVIPLPVPYELPPKQYSSEDVPWSWDRRYYKKDV 661

Query: 421 YGQVWPRHFQLYAFQDS 437
            GQVWPRH QLY+  DS
Sbjct: 662 CGQVWPRHVQLYSSPDS 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\|449434370\|ref\|XP_004134969.1\| 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\|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		437
TAIR\|locus:2150931		605	TDP1 "tyrosyl-DNA phosphodiest	0.965	0.697	0.675	2e-159
UNIPROTKB\|Q9NUW8		608	TDP1 "Tyrosyl-DNA phosphodiest	0.745	0.536	0.427	4.7e-68
UNIPROTKB\|E2REL5		609	TDP1 "Uncharacterized protein"	0.784	0.563	0.417	4.7e-68
MGI\|MGI:1920036		609	Tdp1 "tyrosyl-DNA phosphodiest	0.743	0.533	0.426	9.8e-66
UNIPROTKB\|F1NSQ5		602	TDP1 "Uncharacterized protein"	0.800	0.581	0.393	9.8e-66
RGD\|1309618		609	Tdp1 "tyrosyl-DNA phosphodiest	0.743	0.533	0.423	3.3e-65
UNIPROTKB\|F1MST1		612	TDP1 "Uncharacterized protein"	0.784	0.560	0.408	5.4e-65
UNIPROTKB\|F1SDA7		607	LOC100625067 "Uncharacterized	0.778	0.560	0.414	5.4e-65
ZFIN\|ZDB-GENE-090909-1		615	tdp1 "tyrosyl-DNA phosphodiest	0.780	0.554	0.402	5.4e-65
UNIPROTKB\|G3V2F4		578	TDP1 "Tyrosyl-DNA phosphodiest	0.759	0.574	0.427	2e-63

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

 Score = 1553 (551.7 bits), Expect = 2.0e-159, P = 2.0e-159
 Identities = 291/431 (67%), Positives = 330/431 (76%)

Query:     1 MVDIDWLLPACPVLAKIPHVLVIHGESDGTLEHMKRNKPANWILHKPPLPISFGTHHSKA 60
             MVDIDWL+ ACP LA IP V+VIHGE DG  E+++R KPANWILHKP LPISFGTHHSKA
Sbjct:   180 MVDIDWLMSACPKLANIPQVMVIHGEGDGRQEYIQRKKPANWILHKPRLPISFGTHHSKA 239

Query:    61 MLLIYPRGVRIIVHTANLIHVDWNNKSQGLWMQDFPLKDQN-NLSEECGFENDLIDYLST 119
             + L+YPRGVR++VHTANLIHVDWNNKSQGLWMQDFP KD + +  + CGFE DLIDYL+ 
Sbjct:   240 IFLVYPRGVRVVVHTANLIHVDWNNKSQGLWMQDFPWKDDDKDPPKGCGFEGDLIDYLNV 299

Query:   120 LKWPEFSANLPAHGXXXXXXXXXXXXXXXXAAVRLIASVPGYHTGSSLKKWGHMKLRTVL 179
             LKWPEF+ANLP  G                A VRLIASVPGYHTG +L KWGHMKLRT+L
Sbjct:   300 LKWPEFTANLPGRGNVKINAAFFKKFDYSDATVRLIASVPGYHTGFNLNKWGHMKLRTIL 359

Query:   180 QECTFEKGFKKSPLVYQFSSLGSLDEKWMAELXXXXXXXXXEDKTPLGIGEPLIVWPTVE 239
             QEC F++ F++SPL+YQFSSLGSLDEKW+AE          EDKTPLG G+ LI+WPTVE
Sbjct:   360 QECIFDREFRRSPLIYQFSSLGSLDEKWLAEFGNSLSSGITEDKTPLGPGDSLIIWPTVE 419

Query:   240 DVRCSLEGYAAGNAIPSPQKNVDKDFLKKYWAKWKASHTGRSRAMPHIKTFARYNGQKLA 299
             DVRCSLEGYAAGNAIPSP KNV+K FLKKYWA+WKA H+ R RAMPHIKTF RYN QK+A
Sbjct:   420 DVRCSLEGYAAGNAIPSPLKNVEKPFLKKYWARWKADHSARGRAMPHIKTFTRYNDQKIA 479

Query:   300 WFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILPSA-KRHGCGFSCT-SNIVPSEIK 357
             WFLLTS+NLSKAAWGALQKNNSQLMIRSYELGVL LPS  K  GC FSCT SN  PS +K
Sbjct:   480 WFLLTSSNLSKAAWGALQKNNSQLMIRSYELGVLFLPSPIKTQGCVFSCTESN--PSVMK 537

Query:   358 SGSTETSQIQK-TKLVTLTWHGSSDAGASSXXXXXXXXXXXXXQRYSSEDVPWSWDKRYT 416
             +      +++K +KLVT+TW G  D                  + YS EDVPWSWD+ Y+
Sbjct:   538 AKQETKDEVEKRSKLVTMTWQGDRDL---PEIISLPVPYQLPPKPYSPEDVPWSWDRGYS 594

Query:   417 KKDVYGQVWPR 427
             KKDVYGQVWPR
Sbjct:   595 KKDVYGQVWPR 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\|Q9NUW8 TDP1 "Tyrosyl-DNA phosphodiesterase 1" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

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

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

UNIPROTKB\|F1NSQ5 TDP1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	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\|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		437
pfam06087		433	pfam06087, Tyr-DNA_phospho, Tyrosyl-DNA phosphodie	6e-95
cd09195		191	cd09195, PLDc_mTdp1_2, Catalytic domain, repeat 2,	4e-74
cd09123		182	cd09123, PLDc_Tdp1_2, Catalytic domain, repeat 2,	3e-60
cd09122		145	cd09122, PLDc_Tdp1_1, Catalytic domain, repeat 1,	1e-44
cd09193		169	cd09193, PLDc_mTdp1_1, Catalytic domain, repeat 1,	5e-27
cd09194		166	cd09194, PLDc_yTdp1_1, Catalytic domain, repeat 1,	3e-21
cd09196		200	cd09196, PLDc_yTdp1_2, Catalytic domain, repeat 2,	3e-19

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

 Score =  291 bits (748), Expect = 6e-95
 Identities = 141/431 (32%), Positives = 212/431 (49%), Gaps = 68/431 (15%)

Query: 1   MVDIDWLLPACPVLAKIPHVLVIHGESDG--TLEHMKRNKPANWILHKPPLPISFGTHHS 58
           M D+D+LL       +   + ++ G  +     E ++     N  + K  +P  FGTHH+
Sbjct: 43  MFDLDFLLDQFDPSGRENKITIVTGTDNLLEKREIIEDCGYPNVTVIKAKMPGPFGTHHT 102

Query: 59  KAMLLIYPRG-VRIIVHTANLIHVDWNNKSQGLWMQDFPLKDQNNLSEE-CGFENDLIDY 116
           K M+L Y  G  R+++ TANL   DW N +QGLW+       ++ L E    F+ DL++Y
Sbjct: 103 KMMILFYEDGSCRVVIPTANLTPGDWGNMTQGLWISPLLKIGKSELEESSTRFKRDLLEY 162

Query: 117 LSTLKWPEFSANLPAHGNFKINPSFFKKFNFSSAAVRLIASVPGYHTGSSLKKWGHMKLR 176
           LS          L             +K++FSS  V L+ASVPG HTG+   KWG  +L 
Sbjct: 163 LSEYGAKTLLEPLID---------RLRKYDFSSVNVELVASVPGKHTGNK-DKWGLPRLG 212

Query: 177 TVLQE---CTFEKGFKKSPLVYQFSSLGSLD--EKW------MAELSSSMSSGFSEDKTP 225
           +VL+     T ++  ++  +V Q SS+GSL    K       +  L  +  S   ++ + 
Sbjct: 213 SVLRANPLLTKDEKDEQVHVVCQSSSIGSLGVTPKDWLKSNFLGSLYPASFSSEGQESSI 272

Query: 226 LGIGE----PLIVWPTVEDVRCSLEGYAAGNAIP----SPQKNVDKDFLKKYWAKWKASH 277
               E    P I++PTV++VR SL+GY +G ++     S      +++L+ Y  KWK+S+
Sbjct: 273 NQQKERKPKPRIIYPTVDEVRTSLDGYDSGGSLHFKKQSYATKFPQEWLRPYLHKWKSSN 332

Query: 278 --TGRSRAMPHIKTFARYNGQK---LAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGV 332
              GR+RA PHIKT+ R+N +    L W L+TSANLSKAAWGAL KN +QL IRSYELGV
Sbjct: 333 ADKGRTRAPPHIKTYIRFNDEDFKDLDWALVTSANLSKAAWGALVKNETQLRIRSYELGV 392

Query: 333 LILPSAKRHGCGFSCTSNIVPSEIKSGSTETSQIQKTKLVTLTWHGSSDAGASSEVVYLP 392
           L  P++                        T     +               S + + +P
Sbjct: 393 LYWPTSA-----------------------TPLDVFSLKD-------VIYRQSKQTIGVP 422

Query: 393 VPYELPPQRYS 403
           +P++LPP  Y 
Sbjct: 423 MPFDLPPTPYG 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		437
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	95.21
PF00614		28	PLDc: Phospholipase D Active site motif; InterPro:	90.27
smart00155		28	PLDc Phospholipase D. Active site motifs. Phosphat	89.04
PRK13912		177	nuclease NucT; Provisional	88.96
smart00155		28	PLDc Phospholipase D. Active site motifs. Phosphat	88.75
PF09565		296	RE_NgoFVII: NgoFVII restriction endonuclease; Inte	84.87
cd00138		176	PLDc Phospholipase D. Active site motifs; The PLD	84.46
COG1502		438	Cls Phosphatidylserine/phosphatidylglycerophosphat	81.88

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

Probab=100.00  E-value=4.2e-102  Score=781.57  Aligned_cols=391  Identities=45%  Similarity=0.748  Sum_probs=333.8

Q ss_pred             CcchhhhcccCCCCCCCCeEEEEeCCCCchhhhhhhcCCCceEEEcCCCCCCCCccccceeeeeeCCceEEEEeCCCCCc
Q 013748            1 MVDIDWLLPACPVLAKIPHVLVIHGESDGTLEHMKRNKPANWILHKPPLPISFGTHHSKAMLLIYPRGVRIIVHTANLIH   80 (437)
Q Consensus         1 m~Dl~WLl~~~~~~~~~~~i~iv~g~~~~~~~~~~~~~~~n~~~~~p~mp~~~G~hHsKm~il~y~d~lRVVI~SANL~~   80 (437)
                      |+|++||+.+||...+.+.|+++||+.++.........+.+++++.+.||++|||||+|||+|+|++|+||||+||||++
T Consensus       121 mvdid~Lv~~y~~~~~~~~i~l~~G~~d~~~~~~~~K~~~l~~~~~~~LpipF~thHtKm~~l~y~~G~rvvv~taNl~~  200 (519)
T KOG2031|consen  121 MVDIDWLVGQYPPSVRIKPITLVHGEPDEARLLAQTKAPILVTVKLASLPIPFGTHHTKMIILFYEEGCRVVVHTANLIH  200 (519)
T ss_pred             EeEHHHHHhhCcchhccCceEEEecCCchHHHHhhhhccceeeeecccccccccccccceEEEeccCccEEEEecCCcce
Confidence            89999999999865566778999998764433334456789999999999999999999999999999999999999999


Q ss_pred             cccccccceEEeecccCCCCCCCCCCCCcHHHHHHHHHhcCCCcccccCCCCCCccccccccccccccccceEEEEccCC
Q 013748           81 VDWNNKSQGLWMQDFPLKDQNNLSEECGFENDLIDYLSTLKWPEFSANLPAHGNFKINPSFFKKFNFSSAAVRLIASVPG  160 (437)
Q Consensus        81 ~DW~~~tQ~vW~~dfP~~~~~~~~~~~~F~~dL~~yL~ay~~~~~~~~~~~l~~~~i~~~~L~~yDFS~~~v~LV~SvPG  160 (437)
                      .||++++|++|++|++++.......++.|+.||++||++|++|...          .|+++|+++|||.++|+||+||||
T Consensus       201 ~Dw~~ktQ~~w~sp~~~~~~~~g~~~~~Fk~DLi~YL~~Y~~~~l~----------~~i~~lkk~DfS~i~v~fIgStPG  270 (519)
T KOG2031|consen  201 DDWNNKTQGFWCSPLLKIGDKKGVSPTGFKQDLIEYLNSYRLPQLK----------EWIASLKKVDFSAINVRFIGSTPG  270 (519)
T ss_pred             ecccccccceeecCCcccccCCCCCCCchHHHHHHHHHHhccchhH----------HHHHHHHhcchhhceEEEEeecCC
Confidence            9999999999999988776667789999999999999999987543          346899999999999999999999


Q ss_pred             CCCCCcchhhcHHHHHHHHHhccccCCCcccCeEEEecCCCCCchHHHHHHHHhccCCCCCCCCCCCC--CCcEEEccCc
Q 013748          161 YHTGSSLKKWGHMKLRTVLQECTFEKGFKKSPLVYQFSSLGSLDEKWMAELSSSMSSGFSEDKTPLGI--GEPLIVWPTV  238 (437)
Q Consensus       161 ~h~g~~~~~~G~~~L~~~l~~~~~~~~~~~~~i~~Q~SSiGsl~~~wl~~f~~sl~~~~~~~~~~~~~--~~~~iifPT~  238 (437)
                      ++.|.....|||.||+++|+.+......++++++||+||+|+++..|...|...+..+..++..+.+.  ++++||||||
T Consensus       271 ~f~gs~~~~WGh~kL~kiL~~~~~~~~~~r~~~v~q~sS~gsl~~~~~~~~~~~f~~~l~kdt~~~gk~~~~~yiIfPTv  350 (519)
T KOG2031|consen  271 KFQGSGLLSWGHNKLKKILKEHAASPYLERTPVVGQSSSIGSLGSLWSAWFIGDFVESLAKDTTPPGKLRPPFYIIFPTV  350 (519)
T ss_pred             cccCcccccccHHHHHHHHHhhccCcccccCceeeeeeccccccchhhhhhhhhhccchhhccCCCCCCCCCeeEEcccH
Confidence            88887776799999999999987656668999999999999999887766666665554444444432  4689999999


Q ss_pred             hhhhcCcccccCCccccCCCccch-hHHHHHHHhhhcCCCCCCCCCCCcceeeEeec--CCceeEEEEeccccchhhhhc
Q 013748          239 EDVRCSLEGYAAGNAIPSPQKNVD-KDFLKKYWAKWKASHTGRSRAMPHIKTFARYN--GQKLAWFLLTSANLSKAAWGA  315 (437)
Q Consensus       239 ~~V~~S~~G~~~gg~i~~~~~~~~-~~~l~~~~~~w~~~~~~R~~~~PH~K~y~r~~--~~~~~W~lltSaNLS~aAWG~  315 (437)
                      ||||+|++||.+||||||..++.+ +.|+++|||||.+.+++|+|||||||||||++  ++.+.|||||||||||||||.
T Consensus       351 eeVrtS~~G~~~Ggsipy~~~~~~kq~~lk~y~~kW~A~~s~R~ramPHiKtYmr~~~d~q~l~W~LlTSANLSKaAWG~  430 (519)
T KOG2031|consen  351 EEVRTSLLGYAGGGSLPYGKNTNEKQPWLKKYLCKWKAMDSRRSRAMPHIKTYMRFNLDDQKLAWFLLTSANLSKAAWGT  430 (519)
T ss_pred             HHhhccccccccCceecccchhhhhhHHHHHHHHhhhhhhhhccccCCcceeeeeecCCCCEEEEEEEeccccchhhhhh
Confidence            999999999999999999877666 58999999999999999999999999999998  789999999999999999999


Q ss_pred             cccCCc---eeeeeeeeeeeEEcCCcccCCCccccccCCCCcccccCCccchhhccceeeeeecCCCCCCCCCCcccccc
Q 013748          316 LQKNNS---QLMIRSYELGVLILPSAKRHGCGFSCTSNIVPSEIKSGSTETSQIQKTKLVTLTWHGSSDAGASSEVVYLP  392 (437)
Q Consensus       316 ~~k~~~---ql~i~nyElGVl~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  392 (437)
                      ++++++   ||+|||||+||||+|..+.+..+++.                        +.-++..+..   ....+.||
T Consensus       431 l~kn~sk~~~LmIRsYEaGVLf~p~~~~~~kt~k~------------------------~~~tf~~~~~---~~~v~~vp  483 (519)
T KOG2031|consen  431 LSKNKSKQPQLMIRSYEAGVLFLPRFFANLKTFKV------------------------VEDTFPRDNN---GDGVIAVP  483 (519)
T ss_pred             hccCCCCCchheeeecccceEecchhhhccccccc------------------------cceecccccC---CCCcceec
Confidence            999875   99999999999999998764222211                        1111222211   12247899


Q ss_pred             cccCCCCCCCCCCCCCceecCCCCCccCCCCCCccc
Q 013748          393 VPYELPPQRYSSEDVPWSWDKRYTKKDVYGQVWPRH  428 (437)
Q Consensus       393 vPy~lP~~~Y~~~D~Pw~~~~~y~~~D~~G~~w~~~  428 (437)
                      ||||||++||++.|+||++++.+..+|++|++|++.
T Consensus       484 vpydlPp~pY~~~d~~~~~~~~~~~~d~lG~vW~p~  519 (519)
T KOG2031|consen  484 VPYDLPPVPYSPKDEPFFTDIYRQGPDWLGCVWTPN  519 (519)
T ss_pred             cccCCCCcCCCccCCceeecccccCCcceeeccCCC
Confidence            999999999999999999997778899999999873

>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

>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

>PRK13912 nuclease NucT; Provisional	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

>cd00138 PLDc Phospholipase D	Back alignment and domain information

>COG1502 Cls Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthases and related enzymes [Lipid metabolism]	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		437
1qzq_A		483	Human Tyrosyl Dna Phosphodiesterase Length = 483		8e-64
1mu7_A		485	Crystal Structure Of A Human Tyrosyl-dna Phosphodie		7e-63
1jy1_A		464	Crystal Structure Of Human Tyrosyl-Dna Phosphodiest		1e-58

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

Back alignment and structure

Iteration: 1

Score = 241 bits (614), Expect = 8e-64, Method: Compositional matrix adjust. Identities = 167/439 (38%), Positives = 231/439 (52%), Gaps = 56/439 (12%) Query: 3 DIDWLLPACPVLAKIPHVLVIHGESDGTLEHM-KRNKP-ANWILHKPPLPISFGTHHSKA 60 D+DWL+ P + +L++HG+ H+ + KP N L + L I+FGTHH+K Sbjct: 82 DVDWLVKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKM 141 Query: 61 MLLIYPRGVRIIVHTANLIHVDWNNKSQGLWMQD-FP-LKDQNNLSEE--CGFENDLIDY 116 MLL+Y G+R+++HT+NLIH DW+ K+QG+W+ +P + D + S E F+ DLI Y Sbjct: 142 MLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKADLISY 201 Query: 117 LSTLKWPEFSANLPAHGXXXXXXXXXXXXXXXXAAVRLIASVPGYHTGSSLKKWGHMKLR 176 L P + V LI S PG GS WGH +L+ Sbjct: 202 LMAYNAPSLKEWIDV----------IHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLK 251 Query: 177 TVLQECTFEKGFKKS-PLVYQFSSLGSL---DEKWM-AELXXXXXXXXXEDKTPLGIGEP 231 +L++ +S P+V QFSS+GSL + KW+ +E E KTP P Sbjct: 252 KLLKDHASSMPNAESWPVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSSVP 311 Query: 232 L-IVWPTVEDVRCSLEGYAAGNAIP-SPQKNVDKDFLKKYWAKWKASHTGRSRAMPHIKT 289 L +++P+VE+VR SLEGY AG ++P S Q +++L Y+ KW A +GRS AMPHIKT Sbjct: 312 LYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKT 371 Query: 290 FARY--NGQKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCGFSC 347 + R + K+AWFL+TSANLSKAAWGAL+KN +QLMIRSYELGVL LPSA F Sbjct: 372 YMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSA------FGL 425 Query: 348 TSNIVPSEIKSGSTETSQIQKTKLVTLTWHGSSDAGASSXXXXXXXXXXXXXQRYSSEDV 407 S V + +GS E + T + Y S+D Sbjct: 426 DSFKVKQKFFAGSQEP-------MATFP-----------------VPYDLPPELYGSKDR 461 Query: 408 PWSWDKRYTKK-DVYGQVW 425 PW W+ Y K D +G +W Sbjct: 462 PWIWNIPYVKAPDTHGNMW 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		437
1jy1_A		464	TDP1, tyrosyl-DNA phosphodiesterase; PLD superfami	1e-121
3sq7_A		470	Tyrosyl-DNA phosphodiesterase 1; DNA binding, nucl	3e-83
1q32_A		544	TDP1P;, tyrosyl-DNA phosphodiesterase; DNA repair,	2e-81

>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 =  359 bits (921), Expect = e-121
 Identities = 165/442 (37%), Positives = 234/442 (52%), Gaps = 56/442 (12%)

Query: 1   MVDIDWLLPACPVLAKIPHVLVIHGESDGTLEHMKRNKPA--NWILHKPPLPISFGTHHS 58
             D+DWL+   P   +   +L++HG+      H+        N  L +  L I+FGTHH+
Sbjct: 61  CFDVDWLVKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHT 120

Query: 59  KAMLLIYPRGVRIIVHTANLIHVDWNNKSQGLWMQDFPLKDQNNLSEE----CGFENDLI 114
           K MLL+Y  G+R+++HT+NLIH DW+ K+QG+W+     +  +   +       F+ +LI
Sbjct: 121 KMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKANLI 180

Query: 115 DYLSTLKWPEFSANLPAHGNFKINPSFFKKFNFSSAAVRLIASVPGYHTGSSLKKWGHMK 174
            YL+    P     +              K + S   V LI S PG   GS    WGH +
Sbjct: 181 SYLTAYNAPSLKEWI----------DVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFR 230

Query: 175 LRTVLQECTFEKGF-KKSPLVYQFSSLGSL---DEKWM-AELSSSMSSGFSEDKTPLGIG 229
           L+ +L++        +  P+V QFSS+GSL   + KW+ +E   SM +   E KTP    
Sbjct: 231 LKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSS 290

Query: 230 EPL-IVWPTVEDVRCSLEGYAAGNAIPSPQKNVDK-DFLKKYWAKWKASHTGRSRAMPHI 287
            PL +++P+VE+VR SLEGY AG ++P   +  +K ++L  Y+ KW A  +GRS AMPHI
Sbjct: 291 VPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHI 350

Query: 288 KTFARYNG--QKLAWFLLTSANLSKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCGF 345
           KT+ R +    K+AWFL+TSANLSKAAWGAL+KN +QLMIRSYELGVL LPSA       
Sbjct: 351 KTYMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSAL------ 404

Query: 346 SCTSNIVPSEIKSGSTETSQIQKTKLVTLTWHGSSDAGASSEVVYLPVPYELPPQRYSSE 405
                                    L +        AG+   +   PVPY+LPP+ Y S+
Sbjct: 405 ------------------------GLDSFKVKQKFFAGSQEPMATFPVPYDLPPELYGSK 440

Query: 406 DVPWSWDKRYTKK-DVYGQVWP 426
           D PW W+  Y K  D +G +W 
Sbjct: 441 DRPWIWNIPYVKAPDTHGNMWV 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		437
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	86.07
3hsi_A		458	Phosphatidylserine synthase; CDP- diacylglycerol--	82.58
4ggj_A		196	Mitochondrial cardiolipin hydrolase; piRNA pathway	82.28
1byr_A		155	Protein (endonuclease); phosphodiesterase,; 2.00A	80.96

>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=1.2e-105  Score=837.59  Aligned_cols=387  Identities=42%  Similarity=0.795  Sum_probs=319.8

Q ss_pred             CcchhhhcccCCC-CCCCCeEEEEeCCCCchhhhh--hhcCCCceEEEcCCCCCCCCccccceeeeeeCCceEEEEeCCC
Q 013748            1 MVDIDWLLPACPV-LAKIPHVLVIHGESDGTLEHM--KRNKPANWILHKPPLPISFGTHHSKAMLLIYPRGVRIIVHTAN   77 (437)
Q Consensus         1 m~Dl~WLl~~~~~-~~~~~~i~iv~g~~~~~~~~~--~~~~~~n~~~~~p~mp~~~G~hHsKm~il~y~d~lRVVI~SAN   77 (437)
                      |+|++|||++|+. .+++| |+||||++++....+  .....+|+++|+|+||.+|||||||||||+|+|||||||||||
T Consensus        61 ~~D~~WLl~~~~~~~~~~~-v~iv~g~~~~~~~~l~~~~~~~~nv~~~~p~mp~~fGthHsKmmiL~y~~glRVVI~TAN  139 (464)
T 1jy1_A           61 CFDVDWLVKQYPPEFRKKP-ILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTSN  139 (464)
T ss_dssp             CBCHHHHHHHSCGGGTTSC-EEEEECCCHHHHHHHHHHHTTCTTEEEEECCCCSTTCCBCCCEEEEEESSCEEEEEECCC
T ss_pred             HHhHHHHHhhCcccccCCc-EEEEeCCCcccchhhHHhhccCCCeEEEeCCCCCcccccchhhheeecCCceEEEEeCCC
Confidence            8999999999984 45664 888999764322222  2245679999999999999999999999999999999999999


Q ss_pred             CCccccccccceEEeec-ccCCCCCC---CCCCCCcHHHHHHHHHhcCCCcccccCCCCCCccccccccccccccccceE
Q 013748           78 LIHVDWNNKSQGLWMQD-FPLKDQNN---LSEECGFENDLIDYLSTLKWPEFSANLPAHGNFKINPSFFKKFNFSSAAVR  153 (437)
Q Consensus        78 L~~~DW~~~tQ~vW~~d-fP~~~~~~---~~~~~~F~~dL~~yL~ay~~~~~~~~~~~l~~~~i~~~~L~~yDFS~~~v~  153 (437)
                      |+++||+++||+||+|| ||+++..+   .+++++|++||++||++|+.+....          +++.|++||||+++|+
T Consensus       140 L~~~DW~~~tQ~vW~sd~lP~~~~~~~~~~~~~~~Fk~dL~~yL~ay~~~~~~~----------~i~~L~~~DFS~~~v~  209 (464)
T 1jy1_A          140 LIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKANLISYLTAYNAPSLKE----------WIDVIHKHDLSETNVY  209 (464)
T ss_dssp             BSGGGGTSSBCEEEECCCBCBCCTTCCCCCCCTTCHHHHHHHHHHTTCCGGGHH----------HHHHHHTBCCTTCCSE
T ss_pred             CChhHhccccceEEecccCcCCCccccccCCCCCchHHHHHHHHHHhCCchhHH----------HHHHHHhcCCcccCcE
Confidence            99999999999999999 79865432   3688999999999999999764322          2588999999999999


Q ss_pred             EEEccCCCCCCCcchhhcHHHHHHHHHhccccC-CCcccCeEEEecCCCCCc---hHHH-HHHHHhccCCCCCCCCC-CC
Q 013748          154 LIASVPGYHTGSSLKKWGHMKLRTVLQECTFEK-GFKKSPLVYQFSSLGSLD---EKWM-AELSSSMSSGFSEDKTP-LG  227 (437)
Q Consensus       154 LV~SvPG~h~g~~~~~~G~~~L~~~l~~~~~~~-~~~~~~i~~Q~SSiGsl~---~~wl-~~f~~sl~~~~~~~~~~-~~  227 (437)
                      ||+||||+|.|.++.+|||+||+++|++++... ..++++|+||+||||+++   .+|| ++|..+|.+...+.+.+ ..
T Consensus       210 LVaSvPG~h~~~~~~~~G~~~L~~~L~~~~~~~~~~~~~~i~~Q~SSIGslg~~~~~Wl~~~f~~sl~~~~~~~~~~~~~  289 (464)
T 1jy1_A          210 LIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKS  289 (464)
T ss_dssp             EEEECSEEEEGGGGGGSHHHHHHHHHHHHC-----CCSCCEEEECSCBCCCCSSTTTTTTTTHHHHHTCCC---------
T ss_pred             EEEeCCcCCcCCcchhhhHHHHHHHHHHhccCCCccCCCcEEEEeecccccCcchhHHHHHHHHHHhhhhcccccccccC
Confidence            999999999999999999999999999987642 235789999999999997   4899 68999997753222111 13


Q ss_pred             CCCcEEEccCchhhhcCcccccCCccccCCCccch-hHHHHHHHhhhcCCCCCCCCCCCcceeeEeecC--CceeEEEEe
Q 013748          228 IGEPLIVWPTVEDVRCSLEGYAAGNAIPSPQKNVD-KDFLKKYWAKWKASHTGRSRAMPHIKTFARYNG--QKLAWFLLT  304 (437)
Q Consensus       228 ~~~~~iifPT~~~V~~S~~G~~~gg~i~~~~~~~~-~~~l~~~~~~w~~~~~~R~~~~PH~K~y~r~~~--~~~~W~llt  304 (437)
                      .++++|||||+||||+|.+||.+|||||++.++++ +.|++++||+|+++.++|+++|||||+|+|++.  ..++|+|||
T Consensus       290 ~~~~~iifPT~e~Vr~S~~G~~~ggsi~~~~~~~~~~~~l~~~l~~w~~~~~~R~~a~pHiKty~r~~~~~~~~~W~llt  369 (464)
T 1jy1_A          290 SVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVT  369 (464)
T ss_dssp             CCCEEEECCBHHHHHTSSSCGGGGGGSCCCHHHHTTCGGGGGGEECCCCGGGTCTTSCBCCEEEEEECTTSSEEEEEEEE
T ss_pred             CCceEEEcCCHHHHHhcccccCCcceeeccchhhhhhhhhHHHHHHhccCccCCCCcCCceeeEEecCCCCCeecEEEEc
Confidence            46799999999999999999999999999866554 469999999999999999999999999999985  479999999


Q ss_pred             ccccchhhhhccccCCceeeeeeeeeeeEEcCCcccCCCccccccCCCCcccccCCccchhhccceeeeeecCCCCCCCC
Q 013748          305 SANLSKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCGFSCTSNIVPSEIKSGSTETSQIQKTKLVTLTWHGSSDAGA  384 (437)
Q Consensus       305 SaNLS~aAWG~~~k~~~ql~i~nyElGVl~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  384 (437)
                      |||||+||||+++++++||+||||||||||+|..+++. .++...                    +..      +.   .
T Consensus       370 SaNLSkaAWG~~~k~~~~l~I~nyElGVl~~P~~~~~~-~~~~~~--------------------~~~------~~---~  419 (464)
T 1jy1_A          370 SANLSKAAWGALEKNGTQLMIRSYELGVLFLPSALGLD-SFKVKQ--------------------KFF------AG---S  419 (464)
T ss_dssp             SCCBSHHHHCEEETTTTEEEECSBEEEEEECGGGGTCS-CEEEC------------------------------------
T ss_pred             cccCCHHHhCccccCCCceeEeeeeeeEEEeccccccc-ccccCc--------------------ccc------cc---c
Confidence            99999999999999999999999999999999876432 111100                    000      00   0


Q ss_pred             CCcccccccccCCCCCCCCCCCCCceecCCCCCc-cCCCCCCccc
Q 013748          385 SSEVVYLPVPYELPPQRYSSEDVPWSWDKRYTKK-DVYGQVWPRH  428 (437)
Q Consensus       385 ~~~~~~~~vPy~lP~~~Y~~~D~Pw~~~~~y~~~-D~~G~~w~~~  428 (437)
                      ....+.|||||++|++||+++|+||+++++|.+| |++|++|++.
T Consensus       420 ~~~~~~~~vPy~lP~~~Y~~~D~Pw~~~~~~~~~~D~~G~~w~p~  464 (464)
T 1jy1_A          420 QEPMATFPVPYDLPPELYGSKDRPWIWNIPYVKAPDTHGNMWVPS  464 (464)
T ss_dssp             ----CEECCSSCSSCCBCCTTCCBCCTTSCBCSSCCTTSCCBCCC
T ss_pred             cCcccceeecCCCCCcCCCCCCCCeeCCCCCCCcccCCcCcCCCC
Confidence            1224689999999999999999999999999997 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

>3hsi_A Phosphatidylserine synthase; CDP- diacylglycerol--serine O-phosphatidyltransferase, structura genomics, PSI-2; HET: MSE; 2.20A {Haemophilus influenzae}	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

>1byr_A Protein (endonuclease); phosphodiesterase,; 2.00A {Salmonella typhimurium} SCOP: d.136.1.1 PDB: 1bys_A	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		437
d1jy1a2		258	d.136.1.3 (A:351-608) Tyrosyl-DNA phosphodiesteras	3e-87
d1q32a1		215	d.136.1.3 (A:79-293) Tyrosyl-DNA phosphodiesterase	4e-51
d1q32a2		237	d.136.1.3 (A:302-538) Tyrosyl-DNA phosphodiesteras	5e-41
d1jy1a1		206	d.136.1.3 (A:145-350) Tyrosyl-DNA phosphodiesteras	4e-38

>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 =  264 bits (676), Expect = 3e-87
 Identities = 120/285 (42%), Positives = 160/285 (56%), Gaps = 40/285 (14%)

Query: 152 VRLIASVPGYHTGSSLKKWGHMKLRTVLQECTFEKGF-KKSPLVYQFSSLGSL---DEKW 207
           V LI S PG   GS    WGH +L+ +L++        +  P+V QFSS+GSL   + KW
Sbjct: 2   VYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKW 61

Query: 208 M-AELSSSMSSGFSEDKTPLGIGEPL-IVWPTVEDVRCSLEGYAAGNAIPSPQKNVDK-D 264
           + +E   SM +   E KTP     PL +++P+VE+VR SLEGY AG ++P   +  +K +
Sbjct: 62  LCSEFKESMLTLGKESKTPGKSSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQN 121

Query: 265 FLKKYWAKWKASHTGRSRAMPHIKTFARYN--GQKLAWFLLTSANLSKAAWGALQKNNSQ 322
           +L  Y+ KW A  +GRS AMPHIKT+ R +    K+AWFL+TSANLSKAAWGAL+KN +Q
Sbjct: 122 WLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQ 181

Query: 323 LMIRSYELGVLILPSAKRHGCGFSCTSNIVPSEIKSGSTETSQIQKTKLVTLTWHGSSDA 382
           LMIRSYELGVL LPSA                                L +        A
Sbjct: 182 LMIRSYELGVLFLPSA------------------------------LGLDSFKVKQKFFA 211

Query: 383 GASSEVVYLPVPYELPPQRYSSEDVPWSWDKRYTK-KDVYGQVWP 426
           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

>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

>d1jy1a1 d.136.1.3 (A:145-350) Tyrosyl-DNA phosphodiesterase TDP1 {Human (Homo sapiens) [TaxId: 9606]} Length = 206	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		437
d1jy1a2		258	Tyrosyl-DNA phosphodiesterase TDP1 {Human (Homo sa	100.0
d1q32a2		237	Tyrosyl-DNA phosphodiesterase TDP1 {Baker's yeast	100.0
d1q32a1		215	Tyrosyl-DNA phosphodiesterase TDP1 {Baker's yeast	100.0
d1jy1a1		206	Tyrosyl-DNA phosphodiesterase TDP1 {Human (Homo sa	100.0
d1byra_		152	Nuclease Nuc {Salmonella typhimurium [TaxId: 90371	92.44
d1v0wa2		246	Phospholipase D {Streptomyces sp. [TaxId: 1931]}	85.56

>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=5.2e-72  Score=540.03  Aligned_cols=247  Identities=47%  Similarity=0.838  Sum_probs=201.7

Q ss_pred             ceEEEEccCCCCCCCcchhhcHHHHHHHHHhcccc-CCCcccCeEEEecCCCCCc---hHHH-HHHHHhccCCCCCCCCC
Q 013748          151 AVRLIASVPGYHTGSSLKKWGHMKLRTVLQECTFE-KGFKKSPLVYQFSSLGSLD---EKWM-AELSSSMSSGFSEDKTP  225 (437)
Q Consensus       151 ~v~LV~SvPG~h~g~~~~~~G~~~L~~~l~~~~~~-~~~~~~~i~~Q~SSiGsl~---~~wl-~~f~~sl~~~~~~~~~~  225 (437)
                      +|+||+||||+|.|.++.+|||+||+++|+++++. ...++.+|+||+||||||+   .+|| ++|..+|.....+.+.+
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            68999999999999999999999999999998764 3345789999999999997   3799 78988887654433322


Q ss_pred             -CCCCCcEEEccCchhhhcCcccccCCccccCCCccch-hHHHHHHHhhhcCCCCCCCCCCCcceeeEeecC--CceeEE
Q 013748          226 -LGIGEPLIVWPTVEDVRCSLEGYAAGNAIPSPQKNVD-KDFLKKYWAKWKASHTGRSRAMPHIKTFARYNG--QKLAWF  301 (437)
Q Consensus       226 -~~~~~~~iifPT~~~V~~S~~G~~~gg~i~~~~~~~~-~~~l~~~~~~w~~~~~~R~~~~PH~K~y~r~~~--~~~~W~  301 (437)
                       ....+++|||||+||||+|.+|+.+|||||++.++++ +.|++++||+|.++.++|++++||||||+|+++  +.++|+
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             2345789999999999999999999999999977766 479999999999999999999999999999986  579999


Q ss_pred             EEeccccchhhhhccccCCceeeeeeeeeeeEEcCCcccCCCccccccCCCCcccccCCccchhhccceeeeeecCCCCC
Q 013748          302 LLTSANLSKAAWGALQKNNSQLMIRSYELGVLILPSAKRHGCGFSCTSNIVPSEIKSGSTETSQIQKTKLVTLTWHGSSD  381 (437)
Q Consensus       302 lltSaNLS~aAWG~~~k~~~ql~i~nyElGVl~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  381 (437)
                      ||||||||+||||+++++++||+||||||||||+|..+... .|.....                             ..
T Consensus       161 lltSaNLSkaAWG~~~~~~~~l~I~nyElGVL~~p~~~~~~-~~~~~~~-----------------------------~~  210 (258)
T d1jy1a2         161 LVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSALGLD-SFKVKQK-----------------------------FF  210 (258)
T ss_dssp             EEESCCBSHHHHCEEETTTTEEEECSBEEEEEECGGGGTCS-CEEEC---------------------------------
T ss_pred             EEccccCCHHHhCcccCCCCeEEeecceeEEEEcccccCCC-ccccccc-----------------------------cc
Confidence            99999999999999999999999999999999998865322 1211100                             00


Q ss_pred             CCCCCcccccccccCCCCCCCCCCCCCceecCCCCC-ccCCCCCCcc
Q 013748          382 AGASSEVVYLPVPYELPPQRYSSEDVPWSWDKRYTK-KDVYGQVWPR  427 (437)
Q Consensus       382 ~~~~~~~~~~~vPy~lP~~~Y~~~D~Pw~~~~~y~~-~D~~G~~w~~  427 (437)
                      ....+..+.|||||+||++||+++|+|||+|++|.+ ||++|++|++
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            001133467999999999999999999999999975 9999999987

PyMOL of d1jy1a2

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

>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

>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