Citrus Sinensis ID: 040782

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-----

MADKKLKQKRRRPDPTSDDESELPFKNILKPDQAILETLKQLFLAATTTTTAAANGASTSSSSSKPLTLSDLSLSATCREVTDLSLSAVQSTIETLILQIARSILAGNGFSFQVPSRASSNQLYVPELDRIVLKDKTTLRPFASLSTVRKSTITVKILSLIHQLCLRNIHVTKRDLFYTDVKLFQDQTQSDAVLDDVACILGCTRSSLNVIAAEKGVVVGRLIFSDNGDMIDCTKMGMGGKAIPPNIDRVGDMQSDAMFILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFLRKMKMELKLPVLALVDSDPYGLKILSVYGCGSKNMSYDSANLTTPDIKWLGIRPSDLDKYKIPEQCRLPMTEQDIKTGKDLLEEDFVKKNPGWVEELNLMVKTKQKAEIQALSSFGFQYLSEVYLPLKLQQKDWL

cccHHHHHHHccccccccccccccccccccccHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHcccccEEEEcccccccccccccccEEEEccccEEEEcccHHHHHHHHHHHHHHHHHHHHHHccccccccEEEEccccccccHHHHHHHHHHHHHHHcccccccccEEccccEEEEEEEEEEcccEEEccccccccEEcccccccccccccccEEEEEEEEHHHHHHHHHccccccccEEEEEEcccccHHHHHHHHHHHHcccccEEEEEcccccccEEEEEEccccccccccccccccccEEEEEccccccccccccccccccccHHHHHHHHHHHccccccccHHHHHHHHHHHHcccEEEEHHHHHccccccHHcHHHHHHHccccc

cccccccHccccccccccHHHHHHHHHHccccHHHHHHHHHHHHHHHccccccccccccccccccccccccccccHHHHHHHcccHHHHHHHHHHHHHHHHHHHHcccccEEEEcccccccEEEcccccEEEEcccccEEEcccHHHHHHHHHHHHHHHHHHHHHHccccccHHEEEEcccHHcccHHHHHHHHHHHHHHHcccHHHccccEccccEEEEEEEEEEcccEEEccccccccEEccccHHHcEEEEcccEEEEEEEcHHHHHHHHHccHHHcccEEEEEccccccHHHHHHHHHHHHHccccEEEEEccccccEEEEEEEEHccHHHHHHHHcccccccEEEEEcHHHHHHccccccccccccHHHHHHHHHHHccccccccHHHHHHHHHHHHcccHHHHHHHHHccccHHHHHHcHHHHHccccc

madkklkqkrrrpdptsddeselpfknilkPDQAILETLKQLFLAATTTttaaangastssssskpltlsdlslsatCREVTDLSLSAVQSTIETLILQIARSILagngfsfqvpsrassnqlyvpeldrivlkdkttlrpfaslstVRKSTITVKILSLIHQLCLRnihvtkrdlfytdvklfqdqtqsdavLDDVACILGCTRSSLNVIAAEKGVVVGRLifsdngdmidctkmgmggkaippnidrvgdmQSDAMFILLVEKDAAYIRLAEdrfynrfpciivtakgqpdVATRLFLRKMKMELKLPvlalvdsdpyglkILSVygcgsknmsydsanlttpdikwlgirpsdldkykipeqcrlpmteqdiKTGKDLLEedfvkknpgwvEELNLMVKTKQKAEIQALSSFGFQYLSevylplklqqkdwl

madkklkqkrrrpdptsddeselpfkniLKPDQAILETLKQLFLAATTTTTaaangastssssskpltLSDLSLSATCREVTDLSLSAVQSTIETLILQIARSILAGNGFSFQVPsrassnqlyvPELDRivlkdkttlrpfaslstvrkstITVKILSLIHQLCLRNIHVTKRDLFYTDVKLFQDQTQSDAVLDDVACILGCTRSSLNVIAAEKGVVVGRLIFSDNGDMIDCTKMGMGGKAIPPNIDRVGDMQSDAMFILLVEKDAAYIRLAEDRFYNRFPCiivtakgqpDVATRLFLRKMKMELKLPVlalvdsdpygLKILSVYGCGSKNMSYDSANLTTPDIKWLGIRPSDLDKYKIPEQCRLPMTEQDIKTGKDLLEEDFVKKNPGWVEELNLMVKTKQKAEIQALSSFGFQYLSEvylplklqqkdwl

MADKKLKQKRRRPDPTSDDESELPFKNILKPDQAILETLKQlflaatttttaaangastssssskpltlsdlslsATCREVTDLSLSAVQSTIETLILQIARSILAGNGFSFQVPSRASSNQLYVPELDRIVLKDKTTLRPFASLSTVRKSTITVKILSLIHQLCLRNIHVTKRDLFYTDVKLFQDQTQSDAVLDDVACILGCTRSSLNVIAAEKGVVVGRLIFSDNGDMIDCTKMGMGGKAIPPNIDRVGDMQSDAMFILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFLRKMKMELKLPVLALVDSDPYGLKILSVYGCGSKNMSYDSANLTTPDIKWLGIRPSDLDKYKIPEQCRLPMTEQDIKTGKDLLEEDFVKKNPGWVEELNLMVKTKQKAEIQALSSFGFQYLSEVYLPLKLQQKDWL

***************************ILKPDQAILETLKQLFLAATTT************************LSATCREVTDLSLSAVQSTIETLILQIARSILAGNGFSFQVPSRASSNQLYVPELDRIVLKDKTTLRPFASLSTVRKSTITVKILSLIHQLCLRNIHVTKRDLFYTDVKLFQDQTQSDAVLDDVACILGCTRSSLNVIAAEKGVVVGRLIFSDNGDMIDCTKMGMGGKAIPPNIDRVGDMQSDAMFILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFLRKMKMELKLPVLALVDSDPYGLKILSVYGCGSKNMSYDSANLTTPDIKWLGIRPSDLDKYKIPEQCRLPMTEQDIKTGKDLLEEDFVKKNPGWVEELNLMVKTKQKAEIQALSSFGFQYLSEVYLPLKL******

****************************************************************************************VQSTIETLILQIARSILAGNGFSFQVPSRASSNQLYVPELDRIV*************STVRKSTITVKILSLIHQLCLRNIHVTKRDLFYTDVKLFQDQTQSDAVLDDVACILGCTRSSLNVIAAEKGVVVGRLIFSDNGDMIDCTKMGMGGKAIPPNIDRVGDMQSDAMFILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFLRKMKMELKLPVLALVDSDPYGLKILSVYGCGSKNMSYDSANLTTPDIKWLGIRPSDLDKYKIPEQCRLPMTEQDIKTGKDLLEEDFVKKNPGWVEELNLMVKTKQKAEIQALSSFGFQYLSEVYLPLKLQQKDWL

*********************ELPFKNILKPDQAILETLKQLFLAATTTT******************LSDLSLSATCREVTDLSLSAVQSTIETLILQIARSILAGNGFSFQVPSRASSNQLYVPELDRIVLKDKTTLRPFASLSTVRKSTITVKILSLIHQLCLRNIHVTKRDLFYTDVKLFQDQTQSDAVLDDVACILGCTRSSLNVIAAEKGVVVGRLIFSDNGDMIDCTKMGMGGKAIPPNIDRVGDMQSDAMFILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFLRKMKMELKLPVLALVDSDPYGLKILSVYGCGSKNMSYDSANLTTPDIKWLGIRPSDLDKYKIPEQCRLPMTEQDIKTGKDLLEEDFVKKNPGWVEELNLMVKTKQKAEIQALSSFGFQYLSEVYLPLKLQQKDWL

********************SELPFKNILKPDQAILETLKQLFLAATT**********************D*SLSATCREVTDLSLSAVQSTIETLILQIARSILAGNGFSFQVPSRASSNQLYVPELDRIVLKDKTTLRPFASLSTVRKSTITVKILSLIHQLCLRNIHVTKRDLFYTDVKLFQDQTQSDAVLDDVACILGCTRSSLNVIAAEKGVVVGRLIFSDNGDMIDCTKMGMGGKAIPPNIDRVGDMQSDAMFILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFLRKMKMELKLPVLALVDSDPYGLKILSVYGCGSKNMSYDSANLTTPDIKWLGIRPSDLDKYKIPEQCRLPMTEQDIKTGKDLLEEDFVKKNPGWVEELNLMVKTKQKAEIQALSSFGFQYLSEVYLPLKLQQ*D*L

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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		435	2.2.26 [Sep-21-2011]
Q9LZ03		427	DNA topoisomerase 6 subun	yes	no	0.951	0.969	0.880	0.0
Q9Y5K1		396	Meiotic recombination pro	yes	no	0.804	0.883	0.371	4e-68
Q9WTK8		396	Meiotic recombination pro	yes	no	0.804	0.883	0.377	4e-67
Q9M4A2		362	Meiotic recombination pro	no	no	0.639	0.767	0.405	4e-58
Q9YE67		389	Type 2 DNA topoisomerase	yes	no	0.763	0.853	0.342	9e-58
A2BLE8		387	Type 2 DNA topoisomerase	yes	no	0.772	0.868	0.326	4e-52
Q9M4A1		383	Meiotic recombination pro	no	no	0.721	0.819	0.341	1e-50
O05208		389	Type 2 DNA topoisomerase	N/A	no	0.777	0.868	0.323	1e-49
Q971T1		387	Type 2 DNA topoisomerase	yes	no	0.788	0.886	0.312	1e-47
Q8U0K9		382	Type 2 DNA topoisomerase	yes	no	0.788	0.897	0.292	4e-43

>sp\|Q9LZ03\|TOP6A_ARATH DNA topoisomerase 6 subunit A OS=Arabidopsis thaliana GN=TOP6A PE=1 SV=1	Back alignment and function desciption

 Score =  746 bits (1927), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 367/417 (88%), Positives = 393/417 (94%), Gaps = 3/417 (0%)

Query: 19  DESELPFKNILKPDQAILETLKQLFLAATTTTTAAANGASTSSSSSKPLTLSDLSLSATC 78
           +  ELPFK+IL+ D  I E LK      +++  AAA     SSSSSKPLTL+DLSLS++C
Sbjct: 14  EAEELPFKSILESDDVITELLKSYI---SSSIKAAAGAGGASSSSSKPLTLADLSLSSSC 70

Query: 79  REVTDLSLSAVQSTIETLILQIARSILAGNGFSFQVPSRASSNQLYVPELDRIVLKDKTT 138
           REV DLSLS+VQ+ IET+I+QIARSILAG+GFSF VPSRA+SNQLYVPELDRIVLKDK+T
Sbjct: 71  REVADLSLSSVQTEIETVIVQIARSILAGDGFSFSVPSRAASNQLYVPELDRIVLKDKST 130

Query: 139 LRPFASLSTVRKSTITVKILSLIHQLCLRNIHVTKRDLFYTDVKLFQDQTQSDAVLDDVA 198
           LRPFAS+S+VRK+TIT +IL+LIHQLCLRNIHVTKRDLFYTDVKLFQDQTQSDAVLDDV+
Sbjct: 131 LRPFASVSSVRKTTITTRILALIHQLCLRNIHVTKRDLFYTDVKLFQDQTQSDAVLDDVS 190

Query: 199 CILGCTRSSLNVIAAEKGVVVGRLIFSDNGDMIDCTKMGMGGKAIPPNIDRVGDMQSDAM 258
           C+LGCTRSSLNVIAAEKGVVVGRLIFSDNGDMIDCTKMGMGGKAIPPNIDRVGDMQSDAM
Sbjct: 191 CMLGCTRSSLNVIAAEKGVVVGRLIFSDNGDMIDCTKMGMGGKAIPPNIDRVGDMQSDAM 250

Query: 259 FILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFLRKMKMELKLPVLALVDSD 318
           FILLVEKDAAY+RLAEDRFYNRFPCIIVTAKGQPDVATRLFLRKMKMELKLPVLALVDSD
Sbjct: 251 FILLVEKDAAYMRLAEDRFYNRFPCIIVTAKGQPDVATRLFLRKMKMELKLPVLALVDSD 310

Query: 319 PYGLKILSVYGCGSKNMSYDSANLTTPDIKWLGIRPSDLDKYKIPEQCRLPMTEQDIKTG 378
           PYGLKILSVYGCGSKNMSYDSANLTTPDIKWLGIRPSDLDKYKIPEQCRLPMTEQDIKTG
Sbjct: 311 PYGLKILSVYGCGSKNMSYDSANLTTPDIKWLGIRPSDLDKYKIPEQCRLPMTEQDIKTG 370

Query: 379 KDLLEEDFVKKNPGWVEELNLMVKTKQKAEIQALSSFGFQYLSEVYLPLKLQQKDWL 435
           KD+LEEDFVKKNPGWVEELNLMVKTKQKAEIQALSSFGFQYLSEVYLPLKLQQ+DWL
Sbjct: 371 KDMLEEDFVKKNPGWVEELNLMVKTKQKAEIQALSSFGFQYLSEVYLPLKLQQQDWL 427

Component of the DNA topoisomerase VI involved in chromatin organization and progression of endoreduplication cycles. Relaxes both positive and negative superturns and exhibits a strong decatenase activity. Involved in cell-elongation processes.
Arabidopsis thaliana (taxid: 3702)

>sp\|Q9Y5K1\|SPO11_HUMAN Meiotic recombination protein SPO11 OS=Homo sapiens GN=SPO11 PE=2 SV=1	Back alignment and function description

>sp\|Q9WTK8\|SPO11_MOUSE Meiotic recombination protein SPO11 OS=Mus musculus GN=Spo11 PE=2 SV=2	Back alignment and function description

>sp\|Q9M4A2\|SPO11_ARATH Meiotic recombination protein SPO11-1 OS=Arabidopsis thaliana GN=SPO11-1 PE=1 SV=1	Back alignment and function description

>sp\|Q9YE67\|TOP6A_AERPE Type 2 DNA topoisomerase 6 subunit A OS=Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1) GN=top6A PE=3 SV=2	Back alignment and function description

>sp\|A2BLE8\|TOP6A_HYPBU Type 2 DNA topoisomerase 6 subunit A OS=Hyperthermus butylicus (strain DSM 5456 / JCM 9403) GN=top6A PE=3 SV=1	Back alignment and function description

>sp\|Q9M4A1\|SPO12_ARATH Meiotic recombination protein SPO11-2 OS=Arabidopsis thaliana GN=SPO11-2 PE=1 SV=1	Back alignment and function description

>sp\|O05208\|TOP6A_SULSH Type 2 DNA topoisomerase 6 subunit A OS=Sulfolobus shibatae GN=top6A PE=1 SV=1	Back alignment and function description

>sp\|Q971T1\|TOP6A_SULTO Type 2 DNA topoisomerase 6 subunit A OS=Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) GN=top6A PE=3 SV=1	Back alignment and function description

>sp\|Q8U0K9\|TOP6A_PYRFU Type 2 DNA topoisomerase 6 subunit A OS=Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) GN=top6A 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		435
225439757		420	PREDICTED: DNA topoisomerase 6 subunit A	0.965	1.0	0.834	0.0
15241959		427	DNA topoisomerase 6 subunit A [Arabidops	0.951	0.969	0.880	0.0
297741485		471	unnamed protein product [Vitis vinifera]	0.965	0.891	0.834	0.0
449448703		420	PREDICTED: DNA topoisomerase 6 subunit A	0.965	1.0	0.841	0.0
255568446		421	meiotic recombination protein spo11, put	0.967	1.0	0.855	0.0
356537457		419	PREDICTED: DNA topoisomerase 6 subunit A	0.963	1.0	0.827	0.0
356548204		417	PREDICTED: DNA topoisomerase 6 subunit A	0.958	1.0	0.822	0.0
224069320		423	predicted protein [Populus trichocarpa]	0.951	0.978	0.845	0.0
302807688		415	hypothetical protein SELMODRAFT_122380 [	0.947	0.992	0.698	1e-175
302810679		415	hypothetical protein SELMODRAFT_125304 [	0.910	0.954	0.712	1e-174

>gi\|225439757\|ref\|XP_002274790.1\| PREDICTED: DNA topoisomerase 6 subunit A-like [Vitis vinifera]	Back alignment and taxonomy information

 Score =  748 bits (1931), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 363/435 (83%), Positives = 397/435 (91%), Gaps = 15/435 (3%)

Query: 1   MADKKLKQKRRRPDPTSDDESELPFKNILKPDQAILETLKQLFLAATTTTTAAANGASTS 60
           MADKK   KRRR DP+  D+  LPF+N LK D+ IL+TLK L       ++++++GA+ +
Sbjct: 1   MADKK---KRRRTDPSDSDQQHLPFRNSLKSDEIILQTLKDL------CSSSSSDGATGT 51

Query: 61  SSSSKPLTLSDLSLSATCREVTDLSLSAVQSTIETLILQIARSILAGNGFSFQVPSRASS 120
                 LTLSDL L++TCREV DLSLS+VQSTIETLIL++  SIL+G GFSF VPSR+S+
Sbjct: 52  ------LTLSDLGLASTCREVADLSLSSVQSTIETLILRLTHSILSGQGFSFSVPSRSSA 105

Query: 121 NQLYVPELDRIVLKDKTTLRPFASLSTVRKSTITVKILSLIHQLCLRNIHVTKRDLFYTD 180
           NQLYVPELDRIVLKDK++LRPFA++STVRKS +T +IL LIHQLC +NIHVTKRDLFYTD
Sbjct: 106 NQLYVPELDRIVLKDKSSLRPFANVSTVRKSAVTTRILQLIHQLCTKNIHVTKRDLFYTD 165

Query: 181 VKLFQDQTQSDAVLDDVACILGCTRSSLNVIAAEKGVVVGRLIFSDNGDMIDCTKMGMGG 240
           VKLFQDQTQSD+VLDDV+C+LGCTRSSLNVIA+EKGVVVGRLIFSDNGDMIDCTKMGMGG
Sbjct: 166 VKLFQDQTQSDSVLDDVSCMLGCTRSSLNVIASEKGVVVGRLIFSDNGDMIDCTKMGMGG 225

Query: 241 KAIPPNIDRVGDMQSDAMFILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFL 300
           KAIPPNIDRVGDMQSDA+FILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFL
Sbjct: 226 KAIPPNIDRVGDMQSDALFILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFL 285

Query: 301 RKMKMELKLPVLALVDSDPYGLKILSVYGCGSKNMSYDSANLTTPDIKWLGIRPSDLDKY 360
           RKMK ELKLPVLALVDSDPYGLKILSVYGCGSKNMSYDSANLTTPDIKWLGIRPSDLDKY
Sbjct: 286 RKMKTELKLPVLALVDSDPYGLKILSVYGCGSKNMSYDSANLTTPDIKWLGIRPSDLDKY 345

Query: 361 KIPEQCRLPMTEQDIKTGKDLLEEDFVKKNPGWVEELNLMVKTKQKAEIQALSSFGFQYL 420
            IPEQCRLPMTEQDIKTGKDLLEEDFVKKNPGWVEELNLMVKTKQKAEIQALSSFGFQYL
Sbjct: 346 SIPEQCRLPMTEQDIKTGKDLLEEDFVKKNPGWVEELNLMVKTKQKAEIQALSSFGFQYL 405

Query: 421 SEVYLPLKLQQKDWL 435
           SEVYLPLKLQQ+DWL
Sbjct: 406 SEVYLPLKLQQQDWL 420

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15241959|ref|NP_195902.1| DNA topoisomerase 6 subunit A [Arabidopsis thaliana] gi|297806215|ref|XP_002870991.1| hypothetical protein ARALYDRAFT_487058 [Arabidopsis lyrata subsp. lyrata] gi|75335684|sp|Q9LZ03.1|TOP6A_ARATH RecName: Full=DNA topoisomerase 6 subunit A; Short=AtTOP6A; AltName: Full=Meiotic recombination protein SPO11-3; Short=AtSPO11-3; AltName: Full=Protein BRASSINOSTEROID INSENSITIVE 5; AltName: Full=Protein ROOT HAIRLESS 2 gi|15488539|gb|AAL01152.1|AF323679_1 putative topoisomerase VI subunit A [Arabidopsis thaliana] gi|7413557|emb|CAB86036.1| meiosis specific-like protein [Arabidopsis thaliana] gi|12331186|emb|CAC24689.1| topoisomerase 6 subunit A [Arabidopsis thaliana] gi|114213517|gb|ABI54341.1| At5g02820 [Arabidopsis thaliana] gi|297316828|gb|EFH47250.1| hypothetical protein ARALYDRAFT_487058 [Arabidopsis lyrata subsp. lyrata] gi|332003139|gb|AED90522.1| DNA topoisomerase 6 subunit A [Arabidopsis thaliana]

Back alignment and taxonomy information

>gi\|297741485\|emb\|CBI32617.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|449448703\|ref\|XP_004142105.1\| PREDICTED: DNA topoisomerase 6 subunit A-like [Cucumis sativus] gi\|449521501\|ref\|XP_004167768.1\| PREDICTED: DNA topoisomerase 6 subunit A-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|255568446\|ref\|XP_002525197.1\| meiotic recombination protein spo11, putative [Ricinus communis] gi\|223535494\|gb\|EEF37163.1\| meiotic recombination protein spo11, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|356537457\|ref\|XP_003537243.1\| PREDICTED: DNA topoisomerase 6 subunit A-like [Glycine max]	Back alignment and taxonomy information

>gi\|356548204\|ref\|XP_003542493.1\| PREDICTED: DNA topoisomerase 6 subunit A-like [Glycine max]	Back alignment and taxonomy information

>gi\|224069320\|ref\|XP_002326329.1\| predicted protein [Populus trichocarpa] gi\|222833522\|gb\|EEE71999.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|302807688\|ref\|XP_002985538.1\| hypothetical protein SELMODRAFT_122380 [Selaginella moellendorffii] gi\|300146744\|gb\|EFJ13412.1\| hypothetical protein SELMODRAFT_122380 [Selaginella moellendorffii]	Back alignment and taxonomy information

>gi\|302810679\|ref\|XP_002987030.1\| hypothetical protein SELMODRAFT_125304 [Selaginella moellendorffii] gi\|300145195\|gb\|EFJ11873.1\| hypothetical protein SELMODRAFT_125304 [Selaginella moellendorffii]	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		435
TAIR\|locus:2151221		427	RHL2 "ROOT HAIRLESS 2" [Arabid	0.979	0.997	0.825	2.4e-186
UNIPROTKB\|E2RT15		396	SPO11 "Uncharacterized protein	0.804	0.883	0.383	4.1e-65
UNIPROTKB\|Q9Y5K1		396	SPO11 "Meiotic recombination p	0.804	0.883	0.371	1.1e-64
MGI\|MGI:1349669		396	Spo11 "SPO11 meiotic protein c	0.804	0.883	0.377	2.3e-64
UNIPROTKB\|E1BMM6		395	SPO11 "Uncharacterized protein	0.802	0.883	0.374	9.7e-64
UNIPROTKB\|A5GFN5		395	SPO11 "Uncharacterized protein	0.802	0.883	0.374	8.8e-63
ZFIN\|ZDB-GENE-040426-1900		383	spo11 "SPO11 meiotic protein c	0.816	0.926	0.359	2.1e-61
RGD\|1306454		371	Spo11 "SPO11 meiotic protein c	0.740	0.867	0.373	8.1e-60
UNIPROTKB\|A5GFN4		357	SPO11 "SPO11 meiotic protein c	0.666	0.812	0.404	1.7e-59
UNIPROTKB\|Q5TCH7		354	SPO11 "Meiotic recombination p	0.659	0.810	0.397	2.7e-59

TAIR\|locus:2151221 RHL2 "ROOT HAIRLESS 2" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1807 (641.2 bits), Expect = 2.4e-186, P = 2.4e-186
 Identities = 360/436 (82%), Positives = 384/436 (88%)

Query:     1 MADKKLKQKRRRPDPTSDDESE-LPFKNILKPDQAILETLKQXXXXXXXXXXXXXXXXXX 59
             MADKK   KR+R   + DDE+E LPFK+IL+ D  I E LK                   
Sbjct:     1 MADKK---KRKR---SKDDEAEELPFKSILESDDVITELLKSYISSSIKAAAGAGGASSS 54

Query:    60 XXXXXXXXXXXXXXXXATCREVTDLSLSAVQSTIETLILQIARSILAGNGFSFQVPSRAS 119
                             ++CREV DLSLS+VQ+ IET+I+QIARSILAG+GFSF VPSRA+
Sbjct:    55 SSKPLTLADLSLS---SSCREVADLSLSSVQTEIETVIVQIARSILAGDGFSFSVPSRAA 111

Query:   120 SNQLYVPELDRIVLKDKTTLRPFASLSTVRKSTITVKILSLIHQLCLRNIHVTKRDLFYT 179
             SNQLYVPELDRIVLKDK+TLRPFAS+S+VRK+TIT +IL+LIHQLCLRNIHVTKRDLFYT
Sbjct:   112 SNQLYVPELDRIVLKDKSTLRPFASVSSVRKTTITTRILALIHQLCLRNIHVTKRDLFYT 171

Query:   180 DVKLFQDQTQSDAVLDDVACILGCTRSSLNVIAAEKGVVVGRLIFSDNGDMIDCTKMGMG 239
             DVKLFQDQTQSDAVLDDV+C+LGCTRSSLNVIAAEKGVVVGRLIFSDNGDMIDCTKMGMG
Sbjct:   172 DVKLFQDQTQSDAVLDDVSCMLGCTRSSLNVIAAEKGVVVGRLIFSDNGDMIDCTKMGMG 231

Query:   240 GKAIPPNIDRVGDMQSDAMFILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLF 299
             GKAIPPNIDRVGDMQSDAMFILLVEKDAAY+RLAEDRFYNRFPCIIVTAKGQPDVATRLF
Sbjct:   232 GKAIPPNIDRVGDMQSDAMFILLVEKDAAYMRLAEDRFYNRFPCIIVTAKGQPDVATRLF 291

Query:   300 LRKMKMELKLPVLALVDSDPYGLKILSVYGCGSKNMSYDSANLTTPDIKWLGIRPSDLDK 359
             LRKMKMELKLPVLALVDSDPYGLKILSVYGCGSKNMSYDSANLTTPDIKWLGIRPSDLDK
Sbjct:   292 LRKMKMELKLPVLALVDSDPYGLKILSVYGCGSKNMSYDSANLTTPDIKWLGIRPSDLDK 351

Query:   360 YKIPEQCRLPMTEQDIKTGKDLLEEDFVKKNPGWVEELNLMVKTKQKAEIQALSSFGFQY 419
             YKIPEQCRLPMTEQDIKTGKD+LEEDFVKKNPGWVEELNLMVKTKQKAEIQALSSFGFQY
Sbjct:   352 YKIPEQCRLPMTEQDIKTGKDMLEEDFVKKNPGWVEELNLMVKTKQKAEIQALSSFGFQY 411

Query:   420 LSEVYLPLKLQQKDWL 435
             LSEVYLPLKLQQ+DWL
Sbjct:   412 LSEVYLPLKLQQQDWL 427

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0003824 "catalytic activity" evidence=IEA

GO:0003918 "DNA topoisomerase type II (ATP-hydrolyzing) activity" evidence=IEA;ISS;TAS

GO:0005524 "ATP binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0005694 "chromosome" evidence=IEA

GO:0006259 "DNA metabolic process" evidence=IEA;ISS

GO:0006265 "DNA topological change" evidence=IEA;ISS

GO:0005515 "protein binding" evidence=IPI

GO:0042802 "identical protein binding" evidence=IPI

GO:0009957 "epidermal cell fate specification" evidence=IMP

UNIPROTKB\|E2RT15 SPO11 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|Q9Y5K1 SPO11 "Meiotic recombination protein SPO11" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

MGI\|MGI:1349669 Spo11 "SPO11 meiotic protein covalently bound to DSB homolog (S. cerevisiae)" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

UNIPROTKB\|E1BMM6 SPO11 "Uncharacterized protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|A5GFN5 SPO11 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-040426-1900 spo11 "SPO11 meiotic protein covalently bound to DSB homolog (S. cerevisiae)" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

RGD\|1306454 Spo11 "SPO11 meiotic protein covalently bound to DSB homolog (S. cerevisiae)" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|A5GFN4 SPO11 "SPO11 meiotic protein covalently bound to DSB-like (S. cerevisiae)" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

UNIPROTKB\|Q5TCH7 SPO11 "Meiotic recombination protein SPO11" [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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9WTK8	SPO11_MOUSE	No assigned EC number	0.3774	0.8045	0.8838	yes	no
Q9LZ03	TOP6A_ARATH	No assigned EC number	0.8800	0.9517	0.9695	yes	no
Q9Y5K1	SPO11_HUMAN	No assigned EC number	0.3718	0.8045	0.8838	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	5.99.1.3	LOW CONFIDENCE prediction!
3rd Layer	5.99.1	LOW CONFIDENCE prediction!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00023062001	SubName- Full=Chromosome chr8 scaffold_29, whole genome shotgun sequence; (453 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00024669001	SubName- Full=Chromosome chr6 scaffold_3, whole genome shotgun sequence; (673 aa)	•	•		•		•	0.974
	GSVIVG00024178001	RecName- Full=Proliferating cell nuclear antigen;; This protein is an auxiliary protein of DNA [...] (266 aa)			•			•	0.604
	GSVIVG00022496001	SubName- Full=Chromosome chr14 scaffold_27, whole genome shotgun sequence; (330 aa)				•		•	0.592
	GSVIVG00033522001	RecName- Full=DNA topoisomerase; EC=5.99.1.2; (847 aa)						•	0.585
	GSVIVG00031663001	SubName- Full=Chromosome chr5 scaffold_58, whole genome shotgun sequence; (1093 aa)					•	•	0.528
	GSVIVG00006020001	RecName- Full=DNA topoisomerase; EC=5.99.1.2; (914 aa)						•	0.521
	GSVIVG00017942001	SubName- Full=Chromosome chr17 scaffold_16, whole genome shotgun sequence; (552 aa)	•						0.496
	GSVIVG00033901001	SubName- Full=Chromosome undetermined scaffold_71, whole genome shotgun sequence; (396 aa)	•					•	0.490
	GSVIVG00027588001	SubName- Full=Chromosome chr19 scaffold_4, whole genome shotgun sequence; (491 aa)				•	•	•	0.486
	GSVIVG00017611001	SubName- Full=Chromosome chr17 scaffold_16, whole genome shotgun sequence; (224 aa)	•	•					0.440

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		435
PRK04342		367	PRK04342, PRK04342, DNA topoisomerase VI subunit A	2e-97
COG1697		356	COG1697, COG1697, DNA topoisomerase VI, subunit A	1e-93
cd00223		160	cd00223, TOPRIM_TopoIIB_SPO, TOPRIM_TopoIIB_SPO: t	4e-70
PLN00060		384	PLN00060, PLN00060, meiotic recombination protein	2e-66
pfam04406		68	pfam04406, TP6A_N, Type IIB DNA topoisomerase	1e-22
cd00188		83	cd00188, TOPRIM, Topoisomerase-primase domain	2e-07

>gnl\|CDD\|235287 PRK04342, PRK04342, DNA topoisomerase VI subunit A; Provisional	Back alignment and domain information

 Score =  296 bits (759), Expect = 2e-97
 Identities = 132/351 (37%), Positives = 197/351 (56%), Gaps = 10/351 (2%)

Query: 93  IETLILQIARSILAGNGFSFQVPSRASSNQLYVPELDRIVLKDKTTLRPFASLSTVRKST 152
           +  L  +I   I  G     ++P R  SN  Y  +   +VL DK + R F ++   +K  
Sbjct: 18  LRELAEKIYEDIEKGKRPVLEIPKRTLSNIEYDEKKGLLVLGDKKSKRSFLNVKQAKKFM 77

Query: 153 ITVKILSLIHQLCLRNIHVTKRDLFY----TDVKL----FQDQTQSDAVLDDVACILGCT 204
            TV +   I +L   N   T R+L+Y        L    F DQ +SDAV++D+   LG  
Sbjct: 78  QTVLMAEFIKELLEENKSSTLRELYYMSKHWIPGLKENTFDDQDESDAVIEDLEVALGVL 137

Query: 205 RSSLNVIAAEKGVVVGRLIFSDNGDMIDCTKMGMGGKAIPPNIDRVGDMQSDAMFILLVE 264
           R  L++   E G VVG L   D  D IDC+K+G GG +IPPN+D +  +  DA F+L VE
Sbjct: 138 REELHIRPEEDGSVVGPLRIRDGTDEIDCSKLGEGGYSIPPNVDNIEFVDVDADFVLAVE 197

Query: 265 KDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFLRKMKMELKLPVLALVDSDPYGLKI 324
           K   + RL E+ F+ ++  I+V  KGQP  ATR F++++  EL LPV    D DP+G  I
Sbjct: 198 KGGMFQRLVEEGFWKKYNAILVHLKGQPARATRRFIKRLNEELGLPVYVFTDGDPWGYYI 257

Query: 325 LSVYGCGSKNMSYDSANLTTPDIKWLGIRPSDLDKYKIPEQCRLPMTEQDIKTGKDLLEE 384
            SV   GS  +++ S  L TPD K++G+ PSD+ +Y   +   + + + DIK  K+LL  
Sbjct: 258 YSVVKYGSIKLAHLSERLATPDAKFIGVTPSDIVEY-ERDLPTIKLKDSDIKRAKELLNY 316

Query: 385 DFVKKNPGWVEELNLMVKTKQKAEIQALSSFGFQYLSEVYLPLKLQQKDWL 435
            + +    W +E+NL +K  +KAE QAL+S G +++++ YLP KL++KDWL
Sbjct: 317 PWFQT-DFWQKEINLFLKIGKKAEQQALASKGLKFVTDEYLPEKLEEKDWL 366

Length = 367

>gnl\|CDD\|224611 COG1697, COG1697, DNA topoisomerase VI, subunit A [DNA replication, recombination, and repair]	Back alignment and domain information

>gnl\|CDD\|173774 cd00223, TOPRIM_TopoIIB_SPO, TOPRIM_TopoIIB_SPO: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IIB family of DNA topoisomerases and Spo11	Back alignment and domain information

>gnl\|CDD\|177691 PLN00060, PLN00060, meiotic recombination protein SPO11-2; Provisional	Back alignment and domain information

>gnl\|CDD\|190973 pfam04406, TP6A_N, Type IIB DNA topoisomerase	Back alignment and domain information

>gnl\|CDD\|173773 cd00188, TOPRIM, Topoisomerase-primase domain	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		435
PRK04342		367	DNA topoisomerase VI subunit A; Provisional	100.0
PLN00060		384	meiotic recombination protein SPO11-2; Provisional	100.0
KOG2795		372	consensus Catalytic subunit of the meiotic double	100.0
COG1697		356	DNA topoisomerase VI, subunit A [DNA replication,	100.0
cd00223		160	TOPRIM_TopoIIB_SPO TOPRIM_TopoIIB_SPO: topoisomera	100.0
PF04406		68	TP6A_N: Type IIB DNA topoisomerase; InterPro: IPR0	99.8
PF09983		181	DUF2220: Uncharacterized protein conserved in bact	99.64
PF09664		152	DUF2399: Protein of unknown function C-terminus (D	99.39
TIGR02679		385	conserved hypothetical protein TIGR02679. Members	98.69
cd00188		83	TOPRIM Topoisomerase-primase domain. This is a nuc	96.65
COG4924		386	Uncharacterized protein conserved in bacteria [Fun	91.86
TIGR00334		174	5S_RNA_mat_M5 ribonuclease M5. This family of orth	88.05
cd01026		97	TOPRIM_OLD TOPRIM_OLD: topoisomerase-primase (TOPR	82.56

>PRK04342 DNA topoisomerase VI subunit A; Provisional	Back alignment and domain information

Probab=100.00  E-value=8.9e-95  Score=737.79  Aligned_cols=351  Identities=37%  Similarity=0.617  Sum_probs=341.1

Q ss_pred             cCChHHHHHHHHHHHHHHHHHHHcCCCceEEeccCCCCCcccccCCCeEEecCCccccccCChhhHHHHHHHHHHHHHHH
Q 040782           83 DLSLSAVQSTIETLILQIARSILAGNGFSFQVPSRASSNQLYVPELDRIVLKDKTTLRPFASLSTVRKSTITVKILSLIH  162 (435)
Q Consensus        83 ~~~~~ev~~rIe~~~~~i~~~i~~g~~~~~~ip~R~~~n~~~~~~~~~~~l~~~~~~r~~~~~~~~~k~a~~~~vl~~i~  162 (435)
                      ..++++++++||++++++++++.+|+.|++++|+|+.+|..||++.+.+++|++.+.|+|.|++++++|+++++|++++|
T Consensus         8 ~~~~~~~~~~i~~l~~~~~~~~~~g~~p~~~ip~r~~~n~~~d~~~~~~~~~~~~~~r~~~~~~~a~~f~~~~~vl~~i~   87 (367)
T PRK04342          8 KEDREKALKKLRELAEKIYEDIEKGKRPVLEIPKRTLSNIEYDEKKGLLVLGDKKSKRSFLNVKQAKKFMQTVLMAEFIK   87 (367)
T ss_pred             cccHHHHHHHHHHHHHHHHHHHhcCCCCEEecccccccceEEccccCeEeeCCCceEEecCCHHHHHHHHHHHHHHHHHH
Confidence            44689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhcCCcccceeeecCCcc--------ccCchHHHHHHHHHHHHHhcCCCCccceEecCCceEEEEEEEeeCCceEEee
Q 040782          163 QLCLRNIHVTKRDLFYTDVK--------LFQDQTQSDAVLDDVACILGCTRSSLNVIAAEKGVVVGRLIFSDNGDMIDCT  234 (435)
Q Consensus       163 ~ll~~~~~~TkRdiYY~~~~--------lF~~Q~~vd~~I~di~~~l~~~R~~L~I~as~KGlv~G~l~~~~~g~~id~~  234 (435)
                      ++|.+|+++|+|||||++++        +|++|++||++|+|||+++|++|++|||+|++||+|+|++++..+++.|||+
T Consensus        88 ~~l~~~~~~T~RdiYY~~~~~~~~~~~~~F~~Q~~~d~~I~dl~~~l~~~R~~L~I~a~~KGlv~G~i~i~~~~~~id~~  167 (367)
T PRK04342         88 ELLEENKSSTLRELYYMSKHWIPGLKENTFDDQDESDAVIEDLEVALGVLREELHIRPEEDGSVVGPLRIRDGTDEIDCS  167 (367)
T ss_pred             HHHHcCCccchhhhcccCcccccccccccCCCHHHHHHHHHHHHHHHCCCHHHCCeeECCCeEEEeceEEEECCcEEEEe
Confidence            99999999999999999876        6999999999999999999999999999999999999999999988999999


Q ss_pred             ccCCCccccCCCcccccccccCccEEEEEechhHHHHHHHccccCCCCeEEEecCCcCChHHHHHHHHHhhccCCcEEEE
Q 040782          235 KMGMGGKAIPPNIDRVGDMQSDAMFILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFLRKMKMELKLPVLAL  314 (435)
Q Consensus       235 ~~~~~g~~Ip~~i~~i~~i~~~a~~VLvVEKeAvF~rL~~~~~~~~~~~ILITgKGyPD~aTR~fL~~L~~~~~lPv~~L  314 (435)
                      .++.+|+.||++++.++++.++|+|||||||+|+|++|++++|+++++|||||||||||++||+||++|++++++|||+|
T Consensus       168 ~~g~~~~~ip~~~~~i~~i~~~a~~VLvVEK~avF~rL~~~~~~~~~~~IlItgkG~Pd~~TR~fl~~L~~~~~lpv~~l  247 (367)
T PRK04342        168 KLGEGGYSIPPNVDNIEFVDVDADFVLAVEKGGMFQRLVEEGFWKKYNAILVHLKGQPARATRRFIKRLNEELGLPVYVF  247 (367)
T ss_pred             ccCCCceeCCCchhhheeeccCCCEEEEEechHHHHHHHHhCcccccCEEEEECCCCCCHHHHHHHHHHHHhcCCCEEEE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCchhhHHHHHHhcCCcccccccCCCCCCCceecccCcccccccCCCcccccCCCHHHHHHHHHhhccccccCChHHH
Q 040782          315 VDSDPYGLKILSVYGCGSKNMSYDSANLTTPDIKWLGIRPSDLDKYKIPEQCRLPMTEQDIKTGKDLLEEDFVKKNPGWV  394 (435)
Q Consensus       315 vD~DP~Gi~I~~tYk~GS~~~a~~s~~l~~P~l~wLGv~~sDl~~y~~~~~~~lpLt~rD~k~~~~lL~~~~~~~~~~w~  394 (435)
                      ||+||||++||++|||||++++|+++.+++|+++|+||+++|+.+| +|..+.+|||++|++++++||++|+++ ++.|+
T Consensus       248 ~D~DP~G~~I~~tyk~GS~~~a~~s~~l~~P~~kwlGl~~sDi~~~-~~~~~~~~Lt~~D~~~l~~lL~~~~~~-~~~w~  325 (367)
T PRK04342        248 TDGDPWGYYIYSVVKYGSIKLAHLSERLATPDAKFIGVTPSDIVEY-ERDLPTIKLKDSDIKRAKELLNYPWFQ-TDFWQ  325 (367)
T ss_pred             ECCCccHHHHHHHHHhCchhhhhhhhhccCCCCEEecCcHHHHHhh-ccccccCCCCHHHHHHHHHHhcCcccc-CHHHH
Confidence            9999999999999999999999999999999999999999999998 666788999999999999999999985 67899


Q ss_pred             HHHHHHHHcCCeeeeehhhhcCcccchhchHHhhhccCCCC
Q 040782          395 EELNLMVKTKQKAEIQALSSFGFQYLSEVYLPLKLQQKDWL  435 (435)
Q Consensus       395 ~EL~~ML~~~~KaEiEaL~~~g~~fl~~~YLp~Kl~~~~~i  435 (435)
                      +||+.|++.|+|+|||||++.|++|++++|||+||++++||
T Consensus       326 ~El~~ml~~~~KaEiEal~~~~~~~~~~~Ylp~Ki~~~~~i  366 (367)
T PRK04342        326 KEINLFLKIGKKAEQQALASKGLKFVTDEYLPEKLEEKDWL  366 (367)
T ss_pred             HHHHHHHHhCCceeeehhhhcChhhhHHHHHHHHHhcCCCC
Confidence            99999999999999999999999999999999999999997

>PLN00060 meiotic recombination protein SPO11-2; Provisional	Back alignment and domain information

>KOG2795 consensus Catalytic subunit of the meiotic double strand break transesterase [Replication, recombination and repair]	Back alignment and domain information

>COG1697 DNA topoisomerase VI, subunit A [DNA replication, recombination, and repair]	Back alignment and domain information

>cd00223 TOPRIM_TopoIIB_SPO TOPRIM_TopoIIB_SPO: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IIB family of DNA topoisomerases and Spo11	Back alignment and domain information

>PF04406 TP6A_N: Type IIB DNA topoisomerase; InterPro: IPR013049 This entry represents the N-terminal domain found in Spo11, a meiotic recombination protein found in eukaryotes, and in subunit A of topoisomerase VI, a type IIB topoisomerase found predominantly in archaea [, ]	Back alignment and domain information

>PF09983 DUF2220: Uncharacterized protein conserved in bacteria C-term(DUF2220); InterPro: IPR024534 This is a domain of unknown function that is found predominantly in hypothetical bacterial proteins	Back alignment and domain information

>PF09664 DUF2399: Protein of unknown function C-terminus (DUF2399); InterPro: IPR024465 This domain is found in archaeal, bacterial and eukaryotic proteins	Back alignment and domain information

>TIGR02679 conserved hypothetical protein TIGR02679	Back alignment and domain information

>cd00188 TOPRIM Topoisomerase-primase domain	Back alignment and domain information

>COG4924 Uncharacterized protein conserved in bacteria [Function unknown]	Back alignment and domain information

>TIGR00334 5S_RNA_mat_M5 ribonuclease M5	Back alignment and domain information

>cd01026 TOPRIM_OLD TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family	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		435
2zbk_A		389	Crystal Structure Of An Intact Type Ii Dna Topoisom		1e-50
1d3y_A		301	Structure Of The Dna Topoisomerase Vi A Subunit Len		2e-41
2q2e_A		369	Crystal Structure Of The Topoisomerase Vi Holoenzym		1e-35

>pdb|2ZBK|A Chain A, Crystal Structure Of An Intact Type Ii Dna Topoisomerase: Insights Into Dna Transfer Mechanisms Length = 389

Back alignment and structure

Iteration: 1

Score = 197 bits (500), Expect = 1e-50, Method: Compositional matrix adjust. Identities = 118/365 (32%), Positives = 195/365 (53%), Gaps = 27/365 (7%) Query: 97 ILQIARSILAGNGFSFQVPSRASSNQLYVPELDRIVLKDKTTLRPFASLSTVRKSTITVK 156 L + + G ++P R SN +Y + ++L +K R F L+ ++ TV Sbjct: 25 FLNLVEQLKKGEPLVMEIPMRTLSNAIYDEKRKLLLLGEKKLRRNFLDLNEAKRFMQTVL 84 Query: 157 ILSLIHQLCLRNIHVTKRDLFY-----------------TDVKLFQDQTQSDAVLDDVAC 199 + S+I+ + + + T RDL+Y ++ + +Q +SD+V+ D+ Sbjct: 85 MASIIYDALVSDEYPTIRDLYYRGKHSLLLKSIEGNKIVSEENTWDEQKESDSVIVDIEV 144 Query: 200 ILGCTRSSLNVIAAEKGVVVGRLIFSDNGDMIDCTKMGMGGKAIPPNIDRVGDMQSDAMF 259 R + +++ EKG VVG L D+ID +K G G AI P D + + DA F Sbjct: 145 FTSLLREEMLILSKEKGKVVGNLRIRSGNDVIDLSKTGHGAYAIEPTPDLIDFIDVDAEF 204 Query: 260 ILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFLRKMKMELKLPVLALVDSDP 319 +L+VEKDA + +L F+ ++ I++T+ GQPD ATR F+R++ ELKLPV L D+DP Sbjct: 205 VLVVEKDAVFQQLHRAGFWKQYKSILITSAGQPDRATRRFVRRLNEELKLPVYILTDADP 264 Query: 320 YGLKILSVYGCGSKNMSYDSANLTTPDIKWLGIRPSDL-----DKYKIPEQCR----LPM 370 YG I SV+ GS ++SY+S L TPD K+LG+ D+ K + E R + Sbjct: 265 YGWYIFSVFRIGSISLSYESERLATPDAKFLGVSMGDIFGNSRKKPYLSEAERKNYIIKA 324 Query: 371 TEQDIKTGKDLLEEDFVKKNPGWVEELNLMVKTKQKAEIQALSSFGFQYLSEVYLPLKLQ 430 + DIK +++ ++ K W EE+N ++ K K EI+A++S G ++L+ Y+P K+ Sbjct: 325 KDADIKRAEEIKNYEWF-KTKAWQEEINTFLQRKAKLEIEAMASKGLKFLAFQYIPEKIT 383 Query: 431 QKDWL 435 KD++ Sbjct: 384 NKDYI 388

PyMOL of 2zbk

>pdb|1D3Y|A Chain A, Structure Of The Dna Topoisomerase Vi A Subunit Length = 301

Back alignment and structure

>pdb|2Q2E|A Chain A, Crystal Structure Of The Topoisomerase Vi Holoenzyme From Methanosarcina Mazei Length = 369

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		435
2zbk_A		389	Type II DNA topoisomerase VI subunit A; DNA bindin	1e-110
2q2e_A		369	Type II DNA topoisomerase VI subunit A; DNA-bindin	1e-109
1d3y_A		301	DNA topoisomerase VI A subunit; DNA binding protei	1e-91
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-09

>2zbk_A Type II DNA topoisomerase VI subunit A; DNA binding protein, decatenation, ATPase, drug design, DNA-binding, magnesium, metal-binding; HET: RDC; 3.56A {Sulfolobus shibatae} Length = 389	Back alignment and structure

 Score =  330 bits (846), Expect = e-110
 Identities = 117/387 (30%), Positives = 198/387 (51%), Gaps = 27/387 (6%)

Query: 75  SATCREVTDLSLSAVQSTIETLILQIARSILAGNGFSFQVPSRASSNQLYVPELDRIVLK 134
           S    +V   +     + +    L +   +  G     ++P R  SN +Y  +   ++L 
Sbjct: 3   SEFISKVDKEARRKAANILRDKFLNLVEQLKKGEPLVMEIPMRTLSNAIYDEKRKLLLLG 62

Query: 135 DKTTLRPFASLSTVRKSTITVKILSLIHQLCLRNIHVTKRDLFY---------------- 178
           +K   R F  L+  ++   TV + S+I+   + + + T RDL+Y                
Sbjct: 63  EKKLRRNFLDLNEAKRFMQTVLMASIIYDALVSDEYPTIRDLYYRGKHSLLLKSIEGNKI 122

Query: 179 -TDVKLFQDQTQSDAVLDDVACILGCTRSSLNVIAAEKGVVVGRLIFSDNGDMIDCTKMG 237
            ++   + +Q +SD+V+ D+       R  + +++ EKG VVG L      D+ID +K G
Sbjct: 123 VSEENTWDEQKESDSVIVDIEVFTSLLREEMLILSKEKGKVVGNLRIRSGNDVIDLSKTG 182

Query: 238 MGGKAIPPNIDRVGDMQSDAMFILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATR 297
            G  AI P  D +  +  DA F+L+VEKDA + +L    F+ ++  I++T+ GQPD ATR
Sbjct: 183 HGAYAIEPTPDLIDFIDVDAEFVLVVEKDAVFQQLHRAGFWKQYKSILITSAGQPDRATR 242

Query: 298 LFLRKMKMELKLPVLALVDSDPYGLKILSVYGCGSKNMSYDSANLTTPDIKWLGIRPSDL 357
            F+R++  ELKLPV  L D+DPYG  I SV+  GS ++SY+S  L TPD K+LG+   D+
Sbjct: 243 RFVRRLNEELKLPVYILTDADPYGWYIFSVFRIGSISLSYESERLATPDAKFLGVSMGDI 302

Query: 358 DKYKIP---------EQCRLPMTEQDIKTGKDLLEEDFVKKNPGWVEELNLMVKTKQKAE 408
                          +   +   + DIK  +++   ++  K   W EE+N  ++ K K E
Sbjct: 303 FGNSRKKPYLSEAERKNYIIKAKDADIKRAEEIKNYEWF-KTKAWQEEINTFLQRKAKLE 361

Query: 409 IQALSSFGFQYLSEVYLPLKLQQKDWL 435
           I+A++S G ++L+  Y+P K+  KD++
Sbjct: 362 IEAMASKGLKFLAFQYIPEKITNKDYI 388

PyMOL of 2zbk

>2q2e_A Type II DNA topoisomerase VI subunit A; DNA-binding, SPO11, ATPase; 4.00A {Methanosarcina mazei} Length = 369	Back alignment and structure

>1d3y_A DNA topoisomerase VI A subunit; DNA binding protein, SPO11 homolog; HET: DNA; 2.00A {Methanocaldococcus jannaschii} SCOP: e.12.1.1 Length = 301	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		435
2zbk_A		389	Type II DNA topoisomerase VI subunit A; DNA bindin	100.0
2q2e_A		369	Type II DNA topoisomerase VI subunit A; DNA-bindin	100.0
1d3y_A		301	DNA topoisomerase VI A subunit; DNA binding protei	100.0

>2zbk_A Type II DNA topoisomerase VI subunit A; DNA binding protein, decatenation, ATPase, drug design, DNA-binding, magnesium, metal-binding; HET: RDC; 3.56A {Sulfolobus shibatae}	Back alignment and structure

Probab=100.00  E-value=2.9e-89  Score=701.29  Aligned_cols=351  Identities=32%  Similarity=0.544  Sum_probs=309.7

Q ss_pred             hhcCChHHHHHHHHHHHHHHH----HHHHcCCCceEEeccCCCCCcccccCCCeEEecCCccccccCChhhHHHHHHHHH
Q 040782           81 VTDLSLSAVQSTIETLILQIA----RSILAGNGFSFQVPSRASSNQLYVPELDRIVLKDKTTLRPFASLSTVRKSTITVK  156 (435)
Q Consensus        81 ~~~~~~~ev~~rIe~~~~~i~----~~i~~g~~~~~~ip~R~~~n~~~~~~~~~~~l~~~~~~r~~~~~~~~~k~a~~~~  156 (435)
                      ..+..+++++++||+++.+++    +++.+|+.|.+++|+|+.+|+.||++.+.+.+|++.+.|+|.+++++++|+++++
T Consensus         5 ~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~p~~~~p~r~~~n~~~d~~~~~~~~~~~~~~r~~~~~~~~~~f~~~~~   84 (389)
T 2zbk_A            5 FISKVDKEARRKAANILRDKFLNLVEQLKKGEPLVMEIPMRTLSNAIYDEKRKLLLLGEKKLRRNFLDLNEAKRFMQTVL   84 (389)
T ss_dssp             -----CCCHHHHHHHHTTHHHHHHHCCCCCSSCCEECCCC---------------------CCEETTSSTTHHHHHHHHH
T ss_pred             hcccChHHHHHHHHHHHHHHHHHHHHHHhCCCCCEEeccccCcCceeeccccceEEecCceeEEecCCHHHHHHHHHHHH
Confidence            345567889999999999999    9999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhcCCcccceeeecCCcc-----------------ccCchHHHHHHHHHHHHHhcCCCCccceEecCCceEE
Q 040782          157 ILSLIHQLCLRNIHVTKRDLFYTDVK-----------------LFQDQTQSDAVLDDVACILGCTRSSLNVIAAEKGVVV  219 (435)
Q Consensus       157 vl~~i~~ll~~~~~~TkRdiYY~~~~-----------------lF~~Q~~vd~~I~di~~~l~~~R~~L~I~as~KGlv~  219 (435)
                      |+++||++|.+|+++|+|||||++++                 +|++|++||++|+|||++||++|++|||+|++||+|+
T Consensus        85 vl~~i~~~l~~~~~~T~RdiYY~~~~~~~~~~~~~~~~~~~~~~F~~Q~~~d~~I~di~~~l~~~R~~L~I~a~~kGlv~  164 (389)
T 2zbk_A           85 MASIIYDALVSDEYPTIRDLYYRGKHSLLLKSIEGNKIVSEENTWDEQKESDSVIVDIEVFTSLLREEMLILSKEKGKVV  164 (389)
T ss_dssp             HTHHHHHHHHTTCCCCHHHHHSCCSCSCCSCCCC-------CCSCCSHHHHHHHHHHHHHHHSCCHHHHTCCCCCCCCBE
T ss_pred             HHHHHHHHHHcCCccchHHhhccCcccccccccccccccchhhhcCCHHHHHHHHHHHHHHHCCChhhcceEecCCcEEE
Confidence            99999999999999999999999999                 9999999999999999999999999999999999999


Q ss_pred             EEEEEeeCCceEEeeccCCCccccCCCcccccccccCccEEEEEechhHHHHHHHccccCCCCeEEEecCCcCChHHHHH
Q 040782          220 GRLIFSDNGDMIDCTKMGMGGKAIPPNIDRVGDMQSDAMFILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLF  299 (435)
Q Consensus       220 G~l~~~~~g~~id~~~~~~~g~~Ip~~i~~i~~i~~~a~~VLvVEKeAvF~rL~~~~~~~~~~~ILITgKGyPD~aTR~f  299 (435)
                      |+++|..+|.+|||+.++.+|++||++++.++.+.+++++||||||+|+|++|++++|+.+.+|||||||||||++||+|
T Consensus       165 G~l~i~~~~~~id~~~~g~~g~~Ip~~~~~i~~i~~~a~~VLvVEK~avF~rL~~~~~~~~~~~ilIt~kG~Pd~aTR~f  244 (389)
T 2zbk_A          165 GNLRIRSGNDVIDLSKTGHGAYAIEPTPDLIDFIDVDAEFVLVVEKDAVFQQLHRAGFWKQYKSILITSAGQPDRATRRF  244 (389)
T ss_dssp             ESEEEEETTEEEESSCCTTCCBCCCSCCSSEEEEEECCSCEEEESCHHHHHHHHTTTHHHHTTCEEEECCSSCCTTHHHH
T ss_pred             eeeEEEeCCcEEEeecCCCCceeCCccHHHhhccccCccEEEEEecHHHHHHHHHhCcCccCCEEEEECCCCCCHHHHHH
Confidence            99999989999999998889999999999999989999999999999999999999999889999999999999999999


Q ss_pred             HHHHhhccCCcEEEEecCCchhhHHHHHHhcCCcccccccCCCCCCCceecccCcccccccCCCcccccCCCHHH-----
Q 040782          300 LRKMKMELKLPVLALVDSDPYGLKILSVYGCGSKNMSYDSANLTTPDIKWLGIRPSDLDKYKIPEQCRLPMTEQD-----  374 (435)
Q Consensus       300 L~~L~~~~~lPv~~LvD~DP~Gi~I~~tYk~GS~~~a~~s~~l~~P~l~wLGv~~sDl~~y~~~~~~~lpLt~rD-----  374 (435)
                      |++|++++++|||+|+|+||||++|+++|+|||.+++|+++.+++|+++|+||+++|+.+|.+|.   .|||++|     
T Consensus       245 L~~L~~~~~lpv~~l~D~DP~Gi~I~~tyk~GS~~~a~~~~~l~~P~l~~lG~~~~di~~~~~~~---~~Lt~~Dr~~~~  321 (389)
T 2zbk_A          245 VRRLNEELKLPVYILTDADPYGWYIFSVFRIGSISLSYESERLATPDAKFLGVSMGDIFGNSRKK---PYLSEAERKNYI  321 (389)
T ss_dssp             HHHHHHHSCCCEEEECCSSHHHHHHHHHHTSCSCC-----CCCSCSSCEECCCCHHHHHCCSSSC---CSSCHHHHHHHC
T ss_pred             HHHHHHhcCCCEEEEecCChhhhhhHHHHhhcchhhhhhhhcccCCceEEcCCcHHHHHhccccc---ccCChhhhhhHH
Confidence            99999999999999999999999999999999999999999999999999999999999998764   6999999     


Q ss_pred             HHHHHHhhccc-------cccCChHHHHHHHHHHHcCCeeeeehhhhcCcccchhchHHhhhccCCCC
Q 040782          375 IKTGKDLLEED-------FVKKNPGWVEELNLMVKTKQKAEIQALSSFGFQYLSEVYLPLKLQQKDWL  435 (435)
Q Consensus       375 ~k~~~~lL~~~-------~~~~~~~w~~EL~~ML~~~~KaEiEaL~~~g~~fl~~~YLp~Kl~~~~~i  435 (435)
                      +++++++|++|       +++ ++.|++||++|++.|+|+|||||+++|++|++++|||+||+++|||
T Consensus       322 ~k~l~~ll~~~~~~~~~~~~~-~~~w~~el~~Ml~~~~KaE~Eal~~~g~~fl~~~yl~~Ki~~~~~i  388 (389)
T 2zbk_A          322 IKAKDADIKRAEEIKNYEWFK-TKAWQEEINTFLQRKAKLEIEAMASKGLKFLAFQYIPEKITNKDYI  388 (389)
T ss_dssp             EECCHHHHHHHHHHTTSTTTT-TTTTTHHHHHHHHHCEECCHHHHHTTCTHHHHHTHHHHHHHHTCSB
T ss_pred             HHHHHHHHhchhhcccchhcc-CHHHHHHHHHHHHhCceeeeHHhhhcCchhhHHHHHHHHHhcCCCc
Confidence            89999999998       774 6789999999999999999999999999999999999999999997

PyMOL of 2zbk

>2q2e_A Type II DNA topoisomerase VI subunit A; DNA-binding, SPO11, ATPase; 4.00A {Methanosarcina mazei}	Back alignment and structure

>1d3y_A DNA topoisomerase VI A subunit; DNA binding protein, SPO11 homolog; HET: DNA; 2.00A {Methanocaldococcus jannaschii} SCOP: e.12.1.1	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	E-value
Query		435
d1d3ya_		298	e.12.1.1 (A:) DNA topoisomerase IV, alpha subunit	3e-97

>d1d3ya_ e.12.1.1 (A:) DNA topoisomerase IV, alpha subunit {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 298	Back information, alignment and structure


class: Multi-domain proteins (alpha and beta)
fold: DNA topoisomerase IV, alpha subunit
superfamily: DNA topoisomerase IV, alpha subunit
family: DNA topoisomerase IV, alpha subunit
domain: DNA topoisomerase IV, alpha subunit
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score =  291 bits (746), Expect = 3e-97
 Identities = 97/299 (32%), Positives = 152/299 (50%), Gaps = 16/299 (5%)

Query: 149 RKSTITVKILSLIHQLCLRNIHVTKRDLFYTDVKL----FQDQTQSDAVLDDVACILGCT 204
           +    T K+L    QL   +   T R+ +Y         F DQ  S+ V++D+   LG  
Sbjct: 3   KIFAQTTKMLEFAKQLLETDDFSTLREAYYVSKNWGEARFDDQQASNNVIEDLEAALGVL 62

Query: 205 RSSLNVIAAEKGVVVG-----RLIFSDNGDMIDCTKMGMGGKAIPPNIDRVGDMQSDAMF 259
           R  L  I  E G  V           +   ++DCTK+G G   IP ++ ++ ++++DA F
Sbjct: 63  REHLGFIPEEDGSSVVGPLKIIEETPEGELVVDCTKLGTGAYNIPNDVTKL-NLETDADF 121

Query: 260 ILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFLRKMKMELKLPVLALVDSDP 319
           IL +E    + RL  +RF+++  CI+V+ KG P  ATR F++++  E  LPVL   D DP
Sbjct: 122 ILAIETSGMFARLNAERFWDKHNCILVSLKGVPARATRRFIKRLHEEHDLPVLVFTDGDP 181

Query: 320 YGLKI-LSVYGCGSKNMSYDSANLTTPDIKWLGIRPSDLDKYKIPEQCRLPMTEQDIKTG 378
           YG          GS    + +  L+ P  + +G+ P D+  Y +P     P+ EQDIK  
Sbjct: 182 YGYLNIYRTLKVGSGKAIHLADKLSIPAARLIGVTPQDIIDYDLPTH---PLKEQDIKRI 238

Query: 379 KDLL-EEDFVKKNPGWVEELNLMVKTKQKAEIQALSSFGFQYLSEVYLPLKLQQKD-WL 435
           KD L  +DFV+  P W + L  M+    +AE Q+L+ +G +Y+   YLP K++ +  WL
Sbjct: 239 KDGLKNDDFVRSFPEWQKALKQMLDMGVRAEQQSLAKYGLKYVVNTYLPEKIKDESTWL 297

PyMOL of d1d3ya_

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		435
d1d3ya_		298	DNA topoisomerase IV, alpha subunit {Archaeon Meth	100.0
d2fcja1		114	Hypothetical protein RBSTP2199 {Bacillus stearothe	83.48

>d1d3ya_ e.12.1.1 (A:) DNA topoisomerase IV, alpha subunit {Archaeon Methanococcus jannaschii [TaxId: 2190]}	Back information, alignment and structure

class: Multi-domain proteins (alpha and beta)
fold: DNA topoisomerase IV, alpha subunit
superfamily: DNA topoisomerase IV, alpha subunit
family: DNA topoisomerase IV, alpha subunit
domain: DNA topoisomerase IV, alpha subunit
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=100.00  E-value=2.4e-79  Score=606.51  Aligned_cols=285  Identities=34%  Similarity=0.646  Sum_probs=252.7

Q ss_pred             hHHHHHHHHHHHHHHHHHhhcCCcccceeeecCCccc----cCchHHHHHHHHHHHHHhcCCCCccceEecCCceEE-EE
Q 040782          147 TVRKSTITVKILSLIHQLCLRNIHVTKRDLFYTDVKL----FQDQTQSDAVLDDVACILGCTRSSLNVIAAEKGVVV-GR  221 (435)
Q Consensus       147 ~~~k~a~~~~vl~~i~~ll~~~~~~TkRdiYY~~~~l----F~~Q~~vd~~I~di~~~l~~~R~~L~I~as~KGlv~-G~  221 (435)
                      +|+|||++++||+++|++|.+|+++|+|||||+|+++    |++|++||++|+|||++||++|++|||+|++||+|+ |+
T Consensus         1 ~a~kfa~~l~vl~~i~~~l~~~~~~T~RdiYY~~~~l~~~~F~~Q~~vd~~I~di~~~l~~~R~~L~v~as~KGlv~~g~   80 (298)
T d1d3ya_           1 QAKIFAQTTKMLEFAKQLLETDDFSTLREAYYVSKNWGEARFDDQQASNNVIEDLEAALGVLREHLGFIPEEDGSSVVGP   80 (298)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHTTCCEEHHHHHHHGGGSGGGCCSSHHHHHHHHHHHHHHHTCCGGGGTEECSSCCCEEESS
T ss_pred             ChHHHHHHHHHHHHHHHHHHcCCcceeHHheeeccccccccCCCHHHHHHHHHHHHHHHCCCHHHCCeEecCCCeEEeCc
Confidence            5899999999999999999999999999999999999    999999999999999999999999999999999875 66


Q ss_pred             EEEee-C---CceEEeeccCCCccccCCCcccccccccCccEEEEEechhHHHHHHHccccCCCCeEEEecCCcCChHHH
Q 040782          222 LIFSD-N---GDMIDCTKMGMGGKAIPPNIDRVGDMQSDAMFILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATR  297 (435)
Q Consensus       222 l~~~~-~---g~~id~~~~~~~g~~Ip~~i~~i~~i~~~a~~VLvVEKeAvF~rL~~~~~~~~~~~ILITgKGyPD~aTR  297 (435)
                      +.+.. +   +.++||+..+.+++.+|...+.+ .+.++|+|||||||||+|++|++++++.+.|||+||||||||++||
T Consensus        81 ~~~~~~~~~~~~~id~~~~~~~~~~~~~~~~~~-~~~~~a~~vLVVEKeavF~rL~~~~~~~~~~~ilitgkGyPd~~TR  159 (298)
T d1d3ya_          81 LKIIEETPEGELVVDCTKLGTGAYNIPNDVTKL-NLETDADFILAIETSGMFARLNAERFWDKHNCILVSLKGVPARATR  159 (298)
T ss_dssp             CEEEEEETTEEEEEETTSCTTSEEECCSCCTTC-EEECCCSEEEEESCHHHHHHHHHTTHHHHTTEEEEECCSSCCHHHH
T ss_pred             EEEEEecCCCceEEEcccccCCCccCcccccee-eeeccCcEEEEEeehhHHHHHHhcCcccccceeeeccCCCCCHHHH
Confidence            77653 2   34799988766666666555444 4678999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhccCCcEEEEecCCchhh-HHHHHHhcCCcccccccCCCCCCCceecccCcccccccCCCcccccCCCHHHHH
Q 040782          298 LFLRKMKMELKLPVLALVDSDPYGL-KILSVYGCGSKNMSYDSANLTTPDIKWLGIRPSDLDKYKIPEQCRLPMTEQDIK  376 (435)
Q Consensus       298 ~fL~~L~~~~~lPv~~LvD~DP~Gi-~I~~tYk~GS~~~a~~s~~l~~P~l~wLGv~~sDl~~y~~~~~~~lpLt~rD~k  376 (435)
                      +||++|++++++|+|+|+|+||||+ .||++|+|||.+++|+++.+++|+++|+|++++|+..++.+.   .|||++|++
T Consensus       160 ~fL~~L~~~~~lp~~~l~D~Dp~G~~~I~~~yk~GS~~~~~~~~~~~~p~l~wlG~~~~d~~~~~~~~---~~Lt~~D~k  236 (298)
T d1d3ya_         160 RFIKRLHEEHDLPVLVFTDGDPYGYLNIYRTLKVGSGKAIHLADKLSIPAARLIGVTPQDIIDYDLPT---HPLKEQDIK  236 (298)
T ss_dssp             HHHHHHHHHHTCCEEEECCBSHHHHHTHHHHHHC---------CTTCCTTCEEEESCHHHHHHTTCCC---EECCHHHHH
T ss_pred             HHHHHHhhccCCCEEEEEcCCcchHHHHHHHHHHHhhhcccccccccCCCCEEeeccHHHHhhccccc---CccchhHHH
Confidence            9999999999999999999999996 589999999999999999999999999999999999888654   599999999


Q ss_pred             HHHHhhccccc-cCChHHHHHHHHHHHcCCeeeeehhhhcCcccchhchHHhhhccCC-CC
Q 040782          377 TGKDLLEEDFV-KKNPGWVEELNLMVKTKQKAEIQALSSFGFQYLSEVYLPLKLQQKD-WL  435 (435)
Q Consensus       377 ~~~~lL~~~~~-~~~~~w~~EL~~ML~~~~KaEiEaL~~~g~~fl~~~YLp~Kl~~~~-~i  435 (435)
                      +++++|++|.+ ..+++|++||++|++.|+|||||||++.|++|++++|||+||++.+ ||
T Consensus       237 ~~~~ll~~~~~~~~~~~w~~EL~~ml~~~~KaEiEal~~~~~~f~~~~Yl~~Ki~~~~~~i  297 (298)
T d1d3ya_         237 RIKDGLKNDDFVRSFPEWQKALKQMLDMGVRAEQQSLAKYGLKYVVNTYLPEKIKDESTWL  297 (298)
T ss_dssp             HHHHHHHHCHHHHTCHHHHHHHHHHHHHTEEBCGGGGGGGCTTHHHHTHHHHHHHCGGGCC
T ss_pred             HHHHHhcChhhhhcCHHHHHHHHHHHHhCCeEEEehhhhcCCcccHHHHHHHHHHhcCCCC
Confidence            99999999964 4568899999999999999999999999999999999999998765 97

PyMOL of d1d3ya_

>d2fcja1 c.136.1.1 (A:1-114) Hypothetical protein RBSTP2199 {Bacillus stearothermophilus [TaxId: 1422]}	Back information, alignment and structure