Citrus Sinensis ID: 043133

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-
Protein Sequence
FCKSILKDITERRSLSISINQFRNYCKNLDAHCSCSYDFPQGQEILTLEKQCHARRIDILLSVLLIVQKLLQENIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNINVVGTSLELLILPRYVN
Secondary Structure (PSIPRED)
cHHHHHHHHHcccccEEEEEcccccccccccccccccccccccEEEEEccccHHHHHHHHHHHHHHHHHHHHccccccccEEEcccccccccHHHHHHHHHHHHHHHcccccccccEEccccEEEcccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHcccccEEEEccccccccccccccccccccccccEEEEcccccHHHHHHHHHHHHHHHHHHHHcccEccccEEEEccHHHccccHHHHHHHHHHHHHHcccccccEEEEEcccEEEEccccc
Coil and Loop (DISEMBL)
FCKSILKDITERRSLSISINQFRNYCKnldahcscsydfpqgqEILTLEKQCHARRIDILLSVLLIVQKLLQENIHmskrdiyymhpslyseqsIVDQAINDICILLQCSRHNINVVGTSLELLILPRYVN
Flexible Loop (DISEMBL)
fcksilkditerrslsiSINQFRNYCKNLDAHCSCSYDFPQGQEILTLEKQCHARRIDILLSVLLIVQKLLQENIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNInvvgtslellilpryvn
Low Complexity Region (SEG)
FCKSILKDITERRSLSISINQFRNYCKNLDAHCSCSYDFPQGQEILTLEKQCHARRIDillsvllivqkllqENIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNINVVGTSLELLILPRYVN
Disordered region (IsUnstruct)
********ITERRSLSISINQFRNYCKNLDAHCSCSYDFPQGQEILTLEKQCHARRIDILLSVLLIVQKLLQENIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNINVVGTSLELLILPRY**
Disordered Region (DISOPRED)
FCKSILKDITERRSLSISINQFRNYCK*************************HARRIDILLSVLLIVQKLLQENIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNINVVGTSLELLILPRYVN
Disordered Region (DISEMBL)
FCKSILKDITERRSLSISINQFRNYCKNLDAHCSCSYDFPQGQEILTLEKQCHARRIDILLSVLLIVQKLLQENIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNINVVGTSLELLILPRYVN
Disordered Region (DISPRO)
FCKSILKDITERRSLSISINQFRNYCKNLDAHCSCSYDFPQGQEILTLEKQCHARRIDILLSVLLIVQKLLQENIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNINVVGTSLELLILPRYVN
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
FCKSILKDITERRSLSISINQFRNYCKNLDAHCSCSYDFPQGQEILTLEKQCHARRIDILLSVLLIVQKLLQENIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNINVVGTSLELLILPRYVN
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	131	2.2.26 [Sep-21-2011]
Q9M4A2	362	Meiotic recombination pro	yes	no	0.954	0.345	0.632	3e-40
Q9Y5K1	396	Meiotic recombination pro	yes	no	0.541	0.179	0.380	2e-09
Q9WTK8	396	Meiotic recombination pro	yes	no	0.534	0.176	0.371	2e-08
Q9LZ03	427	DNA topoisomerase 6 subun	no	no	0.488	0.149	0.312	1e-06
Q22236	425	Meiotic recombination pro	yes	no	0.473	0.145	0.370	0.0003
P40384	345	Meiotic recombination pro	yes	no	0.503	0.191	0.333	0.0003

>sp|Q9M4A2|SPO11_ARATH Meiotic recombination protein SPO11-1 OS=Arabidopsis thaliana GN=SPO11-1 PE=1 SV=1

 Score =  163 bits (412), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 79/125 (63%), Positives = 95/125 (76%)

Query: 1   FCKSILKDITERRSLSISINQFRNYCKNLDAHCSCSYDFPQGQEILTLEKQCHARRIDIL 60
           F +S++ D+ E RS  ISINQFRNYC N +A C CS D P+GQEI TL+K+    RID+L
Sbjct: 20  FTQSVVVDLAEGRSPKISINQFRNYCMNPEADCLCSSDKPKGQEIFTLKKEPQTYRIDML 79

Query: 61  LSVLLIVQKLLQENIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNINVVGTS 120
           L VLLIVQ+LLQEN H SKRDIYYMHPS +  QSIVD+AI DICIL QCSR+N+NVV   
Sbjct: 80  LRVLLIVQQLLQENRHASKRDIYYMHPSAFKAQSIVDRAIGDICILFQCSRYNLNVVSVG 139

Query: 121 LELLI 125
             L++
Sbjct: 140 NGLVM 144

Required for meiotic recombination. Mediates DNA cleavage that forms the double-strand breaks (DSB) that initiate meiotic recombination.
Arabidopsis thaliana (taxid: 3702)

>sp|Q9Y5K1|SPO11_HUMAN Meiotic recombination protein SPO11 OS=Homo sapiens GN=SPO11 PE=2 SV=1

 Score = 61.2 bits (147), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 27/71 (38%), Positives = 48/71 (67%)

Query: 54  ARRIDILLSVLLIVQKLLQENIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHN 113
           A++  ++L +L ++ KL+Q N + +KRDIYY    L+  Q++VD  INDI  +L+ SR +
Sbjct: 108 AQKFSLILKILSMIYKLVQSNTYATKRDIYYTDSQLFGNQTVVDNIINDISCMLKVSRRS 167

Query: 114 INVVGTSLELL 124
           ++++ TS  L+
Sbjct: 168 LHILSTSKGLI 178

Required for meiotic recombination. Mediates DNA cleavage that forms the double-strand breaks (DSB) that initiate meiotic recombination.

Homo sapiens (taxid: 9606)

>sp|Q9WTK8|SPO11_MOUSE Meiotic recombination protein SPO11 OS=Mus musculus GN=Spo11 PE=2 SV=2

 Score = 57.8 bits (138), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 26/70 (37%), Positives = 46/70 (65%)

Query: 55  RRIDILLSVLLIVQKLLQENIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNI 114
           ++  ++L VL ++ KL+Q + + +KRDIYY    L+  Q+ VD AI+DI  +L+  R ++
Sbjct: 109 KKFALILKVLSMIYKLIQSDTYATKRDIYYTDSQLFGNQAAVDSAIDDISCMLKVPRRSL 168

Query: 115 NVVGTSLELL 124
           +V+ TS  L+
Sbjct: 169 HVLSTSKGLI 178

Required for meiotic recombination. Mediates DNA cleavage that forms the double-strand breaks (DSB) that initiate meiotic recombination.

Mus musculus (taxid: 10090)

>sp|Q9LZ03|TOP6A_ARATH DNA topoisomerase 6 subunit A OS=Arabidopsis thaliana GN=TOP6A PE=1 SV=1

 Score = 52.0 bits (123), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 20/64 (31%), Positives = 40/64 (62%)

Query: 55  RRIDILLSVLLIVQKLLQENIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNI 114
           R+  I   +L ++ +L   NIH++KRD++Y    L+ +Q+  D  ++D+  +L C+R ++
Sbjct: 141 RKTTITTRILALIHQLCLRNIHVTKRDLFYTDVKLFQDQTQSDAVLDDVSCMLGCTRSSL 200

Query: 115 NVVG 118
           NV+ 
Sbjct: 201 NVIA 204

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|Q22236|SPO11_CAEEL Meiotic recombination protein spo-11 OS=Caenorhabditis elegans GN=spo-11 PE=3 SV=1

 Score = 43.9 bits (102), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 23/62 (37%), Positives = 37/62 (59%)

Query: 56  RIDILLSVLLIVQKLLQENIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNIN 115
           ++D  L  L  V  LL+ +   +KR++YY H ++Y  Q  +D +I  IC LL  SR N+N
Sbjct: 91  KLDRDLHCLHQVYDLLENDKRSTKRELYYEHKAVYGNQKYLDSSIKSICELLNESRANLN 150

Query: 116 VV 117
           ++
Sbjct: 151 IL 152

Required for meiotic recombination. Mediates DNA cleavage that forms the double-strand breaks (DSB) that initiate meiotic recombination.

Caenorhabditis elegans (taxid: 6239)

>sp|P40384|REC12_SCHPO Meiotic recombination protein rec12 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rec12 PE=1 SV=2

 Score = 43.5 bits (101), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 22/66 (33%), Positives = 38/66 (57%)

Query: 60  LLSVLLIVQKLLQENIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNINVVGT 119
           L  VL  V + +  +  ++KRDIYY    L+  Q++VD+ + DI   + CSR ++NV  +
Sbjct: 74  LFRVLDCVHEAVISDTVITKRDIYYRDVDLFKRQTVVDELLGDISNTIGCSRSDLNVEAS 133

Query: 120 SLELLI 125
           +  L+ 
Sbjct: 134 AKGLVF 139

Required for crossover recombination and chiasmatic segregation of chromosomes during meiosis I. Also involved in the faithful equational segregation of chromosomes during meiosis II.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	131
255563518	373	meiotic recombination protein spo11, put	0.954	0.335	0.632	1e-41
224061220	365	predicted protein [Populus trichocarpa]	0.931	0.334	0.647	4e-40
297834134	362	predicted protein [Arabidopsis lyrata su	0.954	0.345	0.64	7e-39
13383478	362	AtSPO11-1 [Arabidopsis thaliana]	0.954	0.345	0.632	2e-38
15231162	362	meiotic recombination protein SPO11-1 [A	0.954	0.345	0.632	2e-38
357494931	452	Meiotic recombination protein SPO11 [Med	0.916	0.265	0.583	2e-35
356499439	367	PREDICTED: meiotic recombination protein	0.954	0.340	0.552	9e-34
10172604	357	DNA topoisomerase VI, subunit A [Arabido	0.824	0.302	0.598	6e-32
225461890	361	PREDICTED: meiotic recombination protein	0.954	0.346	0.616	1e-31
296089901	415	unnamed protein product [Vitis vinifera]	0.916	0.289	0.633	1e-31

>gi|255563518|ref|XP_002522761.1| meiotic recombination protein spo11, putative [Ricinus communis] gi|223537999|gb|EEF39612.1| meiotic recombination protein spo11, putative [Ricinus communis]

 Score =  174 bits (440), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 79/125 (63%), Positives = 106/125 (84%)

Query: 1   FCKSILKDITERRSLSISINQFRNYCKNLDAHCSCSYDFPQGQEILTLEKQCHARRIDIL 60
           F KS+++D++  +S +I I++FRNYC N +A+C C  D P+GQEILTL+K+C+ARRID++
Sbjct: 20  FTKSLVRDVSVGKSPAIFIDKFRNYCTNPEANCFCISDLPKGQEILTLKKECNARRIDVM 79

Query: 61  LSVLLIVQKLLQENIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNINVVGTS 120
           L VL+IVQ+LLQEN H SKRDIYYMHPS++S+QS+VDQAINDICI+LQCSRHN+NVV   
Sbjct: 80  LRVLVIVQQLLQENKHGSKRDIYYMHPSVFSDQSVVDQAINDICIILQCSRHNLNVVSVG 139

Query: 121 LELLI 125
             L++
Sbjct: 140 TGLVM 144

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224061220|ref|XP_002300376.1| predicted protein [Populus trichocarpa] gi|222847634|gb|EEE85181.1| predicted protein [Populus trichocarpa]

 Score =  169 bits (428), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 79/122 (64%), Positives = 104/122 (85%)

Query: 4   SILKDITERRSLSISINQFRNYCKNLDAHCSCSYDFPQGQEILTLEKQCHARRIDILLSV 63
           S++K+++E RS +I I++FRNYC + +++C CS D P+GQ++LTL +QCHA RID+LL V
Sbjct: 20  SLVKELSEGRSPNICIHKFRNYCTDPNSNCLCSSDLPKGQQVLTLTRQCHACRIDVLLRV 79

Query: 64  LLIVQKLLQENIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNINVVGTSLEL 123
           L+IVQKLLQEN H SKRDIYYMHPS++SEQS+VD+AINDICILLQCSRHN+NVV     L
Sbjct: 80  LVIVQKLLQENRHGSKRDIYYMHPSVFSEQSVVDRAINDICILLQCSRHNLNVVSVGNGL 139

Query: 124 LI 125
           ++
Sbjct: 140 VM 141

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297834134|ref|XP_002884949.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297330789|gb|EFH61208.1| predicted protein [Arabidopsis lyrata subsp. lyrata]

 Score =  164 bits (416), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 80/125 (64%), Positives = 97/125 (77%)

Query: 1   FCKSILKDITERRSLSISINQFRNYCKNLDAHCSCSYDFPQGQEILTLEKQCHARRIDIL 60
           F +SI++D+ E RS  ISIN+FRNYC N +A C CS D P+GQEILTLE++    RID+L
Sbjct: 20  FTRSIVEDLAEGRSPKISINRFRNYCINPEADCLCSSDTPKGQEILTLERKPQTYRIDML 79

Query: 61  LSVLLIVQKLLQENIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNINVVGTS 120
           L VLLIVQ+LLQEN H SKRDIYYMHPS +  QSIVD+AI DICIL QCSR+N+NVV   
Sbjct: 80  LRVLLIVQQLLQENRHASKRDIYYMHPSAFKAQSIVDRAIGDICILFQCSRYNLNVVSVG 139

Query: 121 LELLI 125
             L++
Sbjct: 140 NGLVM 144

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|13383478|gb|AAK21002.1| AtSPO11-1 [Arabidopsis thaliana]

 Score =  163 bits (413), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 79/125 (63%), Positives = 97/125 (77%)

Query: 1   FCKSILKDITERRSLSISINQFRNYCKNLDAHCSCSYDFPQGQEILTLEKQCHARRIDIL 60
           F +S+++D+ E RS  ISI+QFRNYC N +A C CS D P+GQEILTL+K+    RID+L
Sbjct: 20  FTQSVVEDLAEGRSPKISISQFRNYCMNPEADCLCSSDKPKGQEILTLKKEPQTYRIDML 79

Query: 61  LSVLLIVQKLLQENIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNINVVGTS 120
           L VLLIVQ+LLQEN H SKRDIYYMHPS +  QSIVD+AI DICIL QCSR+N+NVV   
Sbjct: 80  LRVLLIVQQLLQENRHASKRDIYYMHPSAFKAQSIVDRAIGDICILFQCSRYNLNVVSVG 139

Query: 121 LELLI 125
             L++
Sbjct: 140 NGLVM 144

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15231162|ref|NP_187923.1| meiotic recombination protein SPO11-1 [Arabidopsis thaliana] gi|75335900|sp|Q9M4A2.1|SPO11_ARATH RecName: Full=Meiotic recombination protein SPO11-1; Short=AtSPO11-1 gi|7270975|emb|CAB81544.1| putative topoisomerase VIA [Arabidopsis thaliana] gi|114050705|gb|ABI49502.1| At3g13170 [Arabidopsis thaliana] gi|332641783|gb|AEE75304.1| meiotic recombination protein SPO11-1 [Arabidopsis thaliana]

 Score =  163 bits (412), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 79/125 (63%), Positives = 95/125 (76%)

Query: 1   FCKSILKDITERRSLSISINQFRNYCKNLDAHCSCSYDFPQGQEILTLEKQCHARRIDIL 60
           F +S++ D+ E RS  ISINQFRNYC N +A C CS D P+GQEI TL+K+    RID+L
Sbjct: 20  FTQSVVVDLAEGRSPKISINQFRNYCMNPEADCLCSSDKPKGQEIFTLKKEPQTYRIDML 79

Query: 61  LSVLLIVQKLLQENIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNINVVGTS 120
           L VLLIVQ+LLQEN H SKRDIYYMHPS +  QSIVD+AI DICIL QCSR+N+NVV   
Sbjct: 80  LRVLLIVQQLLQENRHASKRDIYYMHPSAFKAQSIVDRAIGDICILFQCSRYNLNVVSVG 139

Query: 121 LELLI 125
             L++
Sbjct: 140 NGLVM 144

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357494931|ref|XP_003617754.1| Meiotic recombination protein SPO11 [Medicago truncatula] gi|355519089|gb|AET00713.1| Meiotic recombination protein SPO11 [Medicago truncatula]

 Score =  153 bits (387), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 70/120 (58%), Positives = 95/120 (79%)

Query: 1   FCKSILKDITERRSLSISINQFRNYCKNLDAHCSCSYDFPQGQEILTLEKQCHARRIDIL 60
           F +S+L ++T R+S  I I++F+N+C   D++C C  D P G+E+LTL K+ H RR+D++
Sbjct: 38  FTRSLLVNLTNRKSPIILIDRFKNHCTLSDSNCFCGSDLPVGKEVLTLCKETHVRRLDVM 97

Query: 61  LSVLLIVQKLLQENIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNINVVGTS 120
           L VL+IVQKLLQEN H SKRDIYYMHPS++ +QS+VD AINDIC+L+QCSRHN+NVV   
Sbjct: 98  LRVLVIVQKLLQENKHSSKRDIYYMHPSVFLDQSVVDHAINDICVLMQCSRHNLNVVSAG 157

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356499439|ref|XP_003518548.1| PREDICTED: meiotic recombination protein SPO11-1-like [Glycine max]

 Score =  147 bits (372), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 69/125 (55%), Positives = 97/125 (77%)

Query: 1   FCKSILKDITERRSLSISINQFRNYCKNLDAHCSCSYDFPQGQEILTLEKQCHARRIDIL 60
           F +++L D+T  RS  I I++FR+YC   +++C C+ D P G+E+LTL ++ HA R+ ++
Sbjct: 26  FTRALLADLTNGRSPLILIDRFRSYCTLSNSNCFCASDLPCGKELLTLRRKSHAHRLAVM 85

Query: 61  LSVLLIVQKLLQENIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNINVVGTS 120
           L V+LIVQKLLQEN H SKRDIYY +PS++ +QS+VDQAINDICIL+QCSRHN+NVV   
Sbjct: 86  LRVMLIVQKLLQENKHSSKRDIYYTYPSVFLDQSVVDQAINDICILMQCSRHNLNVVSAG 145

Query: 121 LELLI 125
             L++
Sbjct: 146 NGLIM 150

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|10172604|dbj|BAB01408.1| DNA topoisomerase VI, subunit A [Arabidopsis thaliana]

 Score =  142 bits (357), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 70/117 (59%), Positives = 84/117 (71%), Gaps = 9/117 (7%)

Query: 1   FCKSILKDITERRSLSISINQFRNYCKNLDAHCSCSYDFPQGQEILTLEKQCHARRIDIL 60
           F +S++ D+ E RS  ISINQFRNYC N +A C CS D P+GQEI TL+K+    RI   
Sbjct: 20  FTQSVVVDLAEGRSPKISINQFRNYCMNPEADCLCSSDKPKGQEIFTLKKEPQTYRI--- 76

Query: 61  LSVLLIVQKLLQENIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNINVV 117
                 VQ+LLQEN H SKRDIYYMHPS +  QSIVD+AI DICIL QCSR+N+NV+
Sbjct: 77  ------VQQLLQENRHASKRDIYYMHPSAFKAQSIVDRAIGDICILFQCSRYNLNVI 127

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225461890|ref|XP_002264649.1| PREDICTED: meiotic recombination protein SPO11-1-like [Vitis vinifera]

 Score =  141 bits (355), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 77/125 (61%), Positives = 102/125 (81%)

Query: 1   FCKSILKDITERRSLSISINQFRNYCKNLDAHCSCSYDFPQGQEILTLEKQCHARRIDIL 60
           F +SIL D++  +S  + I++FRNYC +   +C CS D  +G+EILTL+++CHARR+D+L
Sbjct: 20  FTRSILDDLSIGKSPVVLIDRFRNYCTDNTGNCCCSSDLSKGKEILTLQRECHARRLDVL 79

Query: 61  LSVLLIVQKLLQENIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNINVVGTS 120
           L VLLIVQ+LLQEN H SKRDIYYMHPS++S+QS+VD+AINDICILLQCSRHN+NVV   
Sbjct: 80  LRVLLIVQQLLQENRHGSKRDIYYMHPSVFSDQSVVDRAINDICILLQCSRHNLNVVSVG 139

Query: 121 LELLI 125
             L++
Sbjct: 140 KGLVM 144

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296089901|emb|CBI39720.3| unnamed protein product [Vitis vinifera]

 Score =  140 bits (354), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 76/120 (63%), Positives = 99/120 (82%)

Query: 1   FCKSILKDITERRSLSISINQFRNYCKNLDAHCSCSYDFPQGQEILTLEKQCHARRIDIL 60
           F +SIL D++  +S  + I++FRNYC +   +C CS D  +G+EILTL+++CHARR+D+L
Sbjct: 20  FTRSILDDLSIGKSPVVLIDRFRNYCTDNTGNCCCSSDLSKGKEILTLQRECHARRLDVL 79

Query: 61  LSVLLIVQKLLQENIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNINVVGTS 120
           L VLLIVQ+LLQEN H SKRDIYYMHPS++S+QS+VD+AINDICILLQCSRHN+NVV   
Sbjct: 80  LRVLLIVQQLLQENRHGSKRDIYYMHPSVFSDQSVVDRAINDICILLQCSRHNLNVVSVG 139

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	131
TAIR|locus:2090044	362	ATSPO11-1 [Arabidopsis thalian	0.954	0.345	0.544	8.8e-31
UNIPROTKB|Q5TCH6	270	SPO11 "Meiotic recombination p	0.389	0.188	0.411	1.6e-06
UNIPROTKB|Q5TCH7	354	SPO11 "Meiotic recombination p	0.389	0.144	0.411	2.9e-06
UNIPROTKB|Q9Y5K1	396	SPO11 "Meiotic recombination p	0.389	0.128	0.411	3.5e-06
ZFIN|ZDB-GENE-040426-1900	383	spo11 "SPO11 meiotic protein c	0.343	0.117	0.355	4.9e-06
UNIPROTKB|E1BMM6	395	SPO11 "Uncharacterized protein	0.389	0.129	0.392	1.2e-05
UNIPROTKB|E2RT14	322	SPO11 "Uncharacterized protein	0.389	0.158	0.392	1.4e-05
UNIPROTKB|E2RT15	396	SPO11 "Uncharacterized protein	0.389	0.128	0.392	2e-05
UNIPROTKB|A5GFN4	357	SPO11 "SPO11 meiotic protein c	0.389	0.142	0.372	2.1e-05
UNIPROTKB|A5GFN5	395	SPO11 "Uncharacterized protein	0.389	0.129	0.372	2.5e-05

TAIR|locus:2090044 ATSPO11-1 [Arabidopsis thaliana (taxid:3702)]

 Score = 339 (124.4 bits), Expect = 8.8e-31, P = 8.8e-31
 Identities = 68/125 (54%), Positives = 82/125 (65%)

Query:     1 FCKSILKDITERRSLSISINQFRNYCKNLDAHCSCSYDFPQGQEILTLEKQCHARRIDXX 60
             F +S++ D+ E RS  ISINQFRNYC N +A C CS D P+GQEI TL+K+    RID  
Sbjct:    20 FTQSVVVDLAEGRSPKISINQFRNYCMNPEADCLCSSDKPKGQEIFTLKKEPQTYRIDML 79

Query:    61 XXXXXXXXXXXXENIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNINVVGTS 120
                         EN H SKRDIYYMHPS +  QSIVD+AI DICIL QCSR+N+NVV   
Sbjct:    80 LRVLLIVQQLLQENRHASKRDIYYMHPSAFKAQSIVDRAIGDICILFQCSRYNLNVVSVG 139

Query:   121 LELLI 125
               L++
Sbjct:   140 NGLVM 144

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

GO:0003824 "catalytic activity" evidence=IEA

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

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=ISS

GO:0007129 "synapsis" evidence=RCA;IMP

GO:0007131 "reciprocal meiotic recombination" evidence=RCA;IMP

GO:0034090 "maintenance of meiotic sister chromatid cohesion" evidence=IGI

GO:0042138 "meiotic DNA double-strand break formation" evidence=IGI;RCA

GO:0000706 "meiotic DNA double-strand break processing" evidence=IGI

GO:0051026 "chiasma assembly" evidence=IMP

GO:0000724 "double-strand break repair via homologous recombination" evidence=RCA

GO:0006302 "double-strand break repair" evidence=RCA

GO:0006312 "mitotic recombination" evidence=RCA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=RCA

GO:0007059 "chromosome segregation" evidence=RCA

GO:0007062 "sister chromatid cohesion" evidence=RCA

GO:0007140 "male meiosis" evidence=RCA

GO:0010212 "response to ionizing radiation" evidence=RCA

GO:0010332 "response to gamma radiation" evidence=RCA

GO:0016444 "somatic cell DNA recombination" evidence=RCA

GO:0031048 "chromatin silencing by small RNA" evidence=RCA

GO:0032204 "regulation of telomere maintenance" evidence=RCA

GO:0032504 "multicellular organism reproduction" evidence=RCA

GO:0033044 "regulation of chromosome organization" evidence=RCA

GO:0043247 "telomere maintenance in response to DNA damage" evidence=RCA

GO:0043687 "post-translational protein modification" evidence=RCA

GO:0045132 "meiotic chromosome segregation" evidence=RCA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA

UNIPROTKB|Q5TCH6 SPO11 "Meiotic recombination protein SPO11" [Homo sapiens (taxid:9606)]

 Score = 115 (45.5 bits), Expect = 1.6e-06, P = 1.6e-06
 Identities = 21/51 (41%), Positives = 34/51 (66%)

Query:    74 NIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNINVVGTSLELL 124
             N + +KRDIYY    L+  Q++VD  INDI  +L+ SR +++++ TS  L+
Sbjct:   106 NTYATKRDIYYTDSQLFGNQTVVDNIINDISCMLKVSRRSLHILSTSKGLI 156

GO:0003677 "DNA binding" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

GO:0007131 "reciprocal meiotic recombination" evidence=IEA

UNIPROTKB|Q5TCH7 SPO11 "Meiotic recombination protein SPO11" [Homo sapiens (taxid:9606)]

 Score = 115 (45.5 bits), Expect = 2.9e-06, P = 2.9e-06
 Identities = 21/51 (41%), Positives = 34/51 (66%)

Query:    74 NIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNINVVGTSLELL 124
             N + +KRDIYY    L+  Q++VD  INDI  +L+ SR +++++ TS  L+
Sbjct:    90 NTYATKRDIYYTDSQLFGNQTVVDNIINDISCMLKVSRRSLHILSTSKGLI 140

GO:0003677 "DNA binding" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

GO:0007131 "reciprocal meiotic recombination" evidence=IEA

UNIPROTKB|Q9Y5K1 SPO11 "Meiotic recombination protein SPO11" [Homo sapiens (taxid:9606)]

 Score = 115 (45.5 bits), Expect = 3.5e-06, P = 3.5e-06
 Identities = 21/51 (41%), Positives = 34/51 (66%)

Query:    74 NIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNINVVGTSLELL 124
             N + +KRDIYY    L+  Q++VD  INDI  +L+ SR +++++ TS  L+
Sbjct:   128 NTYATKRDIYYTDSQLFGNQTVVDNIINDISCMLKVSRRSLHILSTSKGLI 178

GO:0005524 "ATP binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0000238 "zygotene" evidence=IEA

GO:0000781 "chromosome, telomeric region" evidence=IEA

GO:0001541 "ovarian follicle development" evidence=IEA

GO:0007131 "reciprocal meiotic recombination" evidence=IEA

GO:0007141 "male meiosis I" evidence=IEA

GO:0007286 "spermatid development" evidence=IEA

GO:0034502 "protein localization to chromosome" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0007283 "spermatogenesis" evidence=TAS

GO:0007292 "female gamete generation" evidence=TAS

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

 Score = 97 (39.2 bits), Expect = 4.9e-06, Sum P(2) = 4.9e-06
 Identities = 16/45 (35%), Positives = 30/45 (66%)

Query:    76 HMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNINVVGTS 120
             + +KRDIYY  P L+  Q ++D  ++DI  +L+  R +++++ TS
Sbjct:   117 YATKRDIYYNDPQLFGSQRMLDSIVDDISCMLKVPRRSLHILATS 161

GO:0003677 "DNA binding" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

GO:0006259 "DNA metabolic process" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|E1BMM6 SPO11 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 110 (43.8 bits), Expect = 1.2e-05, P = 1.2e-05
 Identities = 20/51 (39%), Positives = 33/51 (64%)

Query:    74 NIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNINVVGTSLELL 124
             N + +KRDIYY    L+  Q++VD  INDI  +L+  R +++++ TS  L+
Sbjct:   128 NTYATKRDIYYTDSQLFGNQTVVDNIINDISCMLKVPRRSLHILSTSKGLI 178

GO:0034502 "protein localization to chromosome" evidence=IEA

GO:0007286 "spermatid development" evidence=IEA

GO:0007141 "male meiosis I" evidence=IEA

GO:0007131 "reciprocal meiotic recombination" evidence=IEA

GO:0001541 "ovarian follicle development" evidence=IEA

GO:0000781 "chromosome, telomeric region" evidence=IEA

GO:0000238 "zygotene" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|E2RT14 SPO11 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 108 (43.1 bits), Expect = 1.4e-05, P = 1.4e-05
 Identities = 20/51 (39%), Positives = 33/51 (64%)

Query:    74 NIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNINVVGTSLELL 124
             N + +KRDIYY    L+  Q++VD  INDI  +L+  R +++++ TS  L+
Sbjct:   128 NTYATKRDIYYTDSQLFGNQTVVDNIINDISCMLKVPRMSLHILSTSKGLI 178

GO:0007131 "reciprocal meiotic recombination" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|E2RT15 SPO11 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 108 (43.1 bits), Expect = 2.0e-05, P = 2.0e-05
 Identities = 20/51 (39%), Positives = 33/51 (64%)

Query:    74 NIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNINVVGTSLELL 124
             N + +KRDIYY    L+  Q++VD  INDI  +L+  R +++++ TS  L+
Sbjct:   128 NTYATKRDIYYTDSQLFGNQTVVDNIINDISCMLKVPRMSLHILSTSKGLI 178

GO:0034502 "protein localization to chromosome" evidence=IEA

GO:0007286 "spermatid development" evidence=IEA

GO:0007141 "male meiosis I" evidence=IEA

GO:0007131 "reciprocal meiotic recombination" evidence=IEA

GO:0001541 "ovarian follicle development" evidence=IEA

GO:0000781 "chromosome, telomeric region" evidence=IEA

GO:0000238 "zygotene" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|A5GFN4 SPO11 "SPO11 meiotic protein covalently bound to DSB-like (S. cerevisiae)" [Sus scrofa (taxid:9823)]

 Score = 107 (42.7 bits), Expect = 2.1e-05, P = 2.1e-05
 Identities = 19/51 (37%), Positives = 32/51 (62%)

Query:    74 NIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNINVVGTSLELL 124
             N + +KRDIYY    L+  Q++VD  IND+  +L+  R ++++  TS  L+
Sbjct:    90 NTYATKRDIYYTDSQLFGNQTVVDNIINDVSCMLKVPRRSLHIFSTSKGLI 140

GO:0034502 "protein localization to chromosome" evidence=IEA

GO:0007286 "spermatid development" evidence=IEA

GO:0007141 "male meiosis I" evidence=IEA

GO:0007131 "reciprocal meiotic recombination" evidence=IEA

GO:0001541 "ovarian follicle development" evidence=IEA

GO:0000781 "chromosome, telomeric region" evidence=IEA

GO:0000238 "zygotene" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|A5GFN5 SPO11 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 107 (42.7 bits), Expect = 2.5e-05, P = 2.5e-05
 Identities = 19/51 (37%), Positives = 32/51 (62%)

Query:    74 NIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNINVVGTSLELL 124
             N + +KRDIYY    L+  Q++VD  IND+  +L+  R ++++  TS  L+
Sbjct:   128 NTYATKRDIYYTDSQLFGNQTVVDNIINDVSCMLKVPRRSLHIFSTSKGLI 178

GO:0007131 "reciprocal meiotic recombination" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

---

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

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	131
pfam04406	68	pfam04406, TP6A_N, Type IIB DNA topoisomerase	2e-18
COG1697	356	COG1697, COG1697, DNA topoisomerase VI, subunit A	1e-08
PLN00060	384	PLN00060, PLN00060, meiotic recombination protein	0.003

>gnl|CDD|190973 pfam04406, TP6A_N, Type IIB DNA topoisomerase

 Score = 73.3 bits (181), Expect = 2e-18
 Identities = 23/64 (35%), Positives = 40/64 (62%)

Query: 54  ARRIDILLSVLLIVQKLLQENIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHN 113
           A++    L VL  +++LL+E+   +KRDIYY +  L+  QS  D+ I D+ +LL   R +
Sbjct: 5   AKKFAQTLYVLEFIKELLEEDKSSTKRDIYYTNKHLFGSQSESDRIIEDLEVLLGLPRED 64

Query: 114 INVV 117
           +N++
Sbjct: 65  LNII 68

Type II DNA topoisomerases are ubiquitous enzymes that catalyze the ATP-dependent transport of one DNA duplex through a second DNA segment via a transient double-strand break. Type II DNA topoisomerases are now subdivided into two sub-families, type IIA and IIB DNA topoisomerases. TP6A_N is present in type IIB topoisomerase and is thought to be involved in DNA binding owing to its sequence similarity to E. coli catabolite activator protein (CAP). Length = 68

>gnl|CDD|224611 COG1697, COG1697, DNA topoisomerase VI, subunit A [DNA replication, recombination, and repair]

 Score = 51.2 bits (123), Expect = 1e-08
 Identities = 19/68 (27%), Positives = 37/68 (54%), Gaps = 4/68 (5%)

Query: 53  HARRIDILLSVLLIVQKLLQENIHMSKRDIYYMHPSL----YSEQSIVDQAINDICILLQ 108
            AR++   L +L  +++LL+     + R+IYY+   +    + +QS  D+ I DI + L 
Sbjct: 68  GARKLAQTLLMLDFIKELLELGKTSTLREIYYISKHVEVFKFDDQSESDRLIEDIEVTLG 127

Query: 109 CSRHNINV 116
            SR ++ +
Sbjct: 128 LSREDLGI 135

Length = 356

>gnl|CDD|177691 PLN00060, PLN00060, meiotic recombination protein SPO11-2; Provisional

 Score = 36.0 bits (83), Expect = 0.003
 Identities = 22/84 (26%), Positives = 46/84 (54%), Gaps = 4/84 (4%)

Query: 46  LTLEKQCHARRIDILLSVLLIVQKLLQENIHMSKRDIYYM----HPSLYSEQSIVDQAIN 101
            +L K   A+    +  V+ +  ++L E   +++R+++Y      P  +S Q  V+Q + 
Sbjct: 87  RSLTKAGSAKAFVRVWKVMEMCYQILGEGKLVTQRELFYKLLCDSPEYFSCQRHVNQTVQ 146

Query: 102 DICILLQCSRHNINVVGTSLELLI 125
           D+  LL+CSR+++ ++ +S   LI
Sbjct: 147 DVVSLLRCSRYSLGIMASSRGALI 170

Length = 384

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	131
PRK04342	367	DNA topoisomerase VI subunit A; Provisional	100.0
COG1697	356	DNA topoisomerase VI, subunit A [DNA replication,	99.97
PLN00060	384	meiotic recombination protein SPO11-2; Provisional	99.95
KOG2795	372	consensus Catalytic subunit of the meiotic double	99.95
PF04406	68	TP6A_N: Type IIB DNA topoisomerase; InterPro: IPR0	99.93

>PRK04342 DNA topoisomerase VI subunit A; Provisional

Probab=100.00  E-value=3.1e-33  Score=233.09  Aligned_cols=122  Identities=20%  Similarity=0.317  Sum_probs=114.1

Q ss_pred             CHHHHHHHHhcCCcceEEEecccCcccCCCCCceeEEeCCCCeEEEe-------ecchhhHHHHHHHHHHHHHHHHHHhc
Q 043133            1 FCKSILKDITERRSLSISINQFRNYCKNLDAHCSCSYDFPQGQEILT-------LEKQCHARRIDILLSVLLIVQKLLQE   73 (131)
Q Consensus         1 ~~~~i~~~l~~g~~P~i~l~~r~~~~~n~~~~~~~~yd~~~g~~~l~-------~~~~~~~~kf~~~l~vl~~i~~ll~~   73 (131)
                      +++++++++++|+.|.|++|+|+.+  |      +.||+..|.++++       +.+..+++||+++++||+++|++|++
T Consensus        21 l~~~~~~~~~~g~~p~~~ip~r~~~--n------~~~d~~~~~~~~~~~~~~r~~~~~~~a~~f~~~~~vl~~i~~~l~~   92 (367)
T PRK04342         21 LAEKIYEDIEKGKRPVLEIPKRTLS--N------IEYDEKKGLLVLGDKKSKRSFLNVKQAKKFMQTVLMAEFIKELLEE   92 (367)
T ss_pred             HHHHHHHHHhcCCCCEEeccccccc--c------eEEccccCeEeeCCCceEEecCCHHHHHHHHHHHHHHHHHHHHHHc
Confidence            3789999999999999999998655  9      9999999887764       56799999999999999999999999


Q ss_pred             CCccceeeeeccCCC--------CCCchHHHHHHHHHHHHHhcCCccccceeecCCceEEeecee
Q 043133           74 NIHMSKRDIYYMHPS--------LYSEQSIVDQAINDICILLQCSRHNINVVGTSLELLILPRYV  130 (131)
Q Consensus        74 ~~~~T~RdiYY~~~~--------lF~~Q~~vd~~I~di~~~l~~~R~~L~i~a~~KGlv~G~i~~  130 (131)
                      |+++|+|||||++++        +|++|++||++|+|||+++|++|++|||+|++||+|+|++.+
T Consensus        93 ~~~~T~RdiYY~~~~~~~~~~~~~F~~Q~~~d~~I~dl~~~l~~~R~~L~I~a~~KGlv~G~i~i  157 (367)
T PRK04342         93 NKSSTLRELYYMSKHWIPGLKENTFDDQDESDAVIEDLEVALGVLREELHIRPEEDGSVVGPLRI  157 (367)
T ss_pred             CCccchhhhcccCcccccccccccCCCHHHHHHHHHHHHHHHCCCHHHCCeeECCCeEEEeceEE
Confidence            999999999999876        599999999999999999999999999999999999999875

>COG1697 DNA topoisomerase VI, subunit A [DNA replication, recombination, and repair]

Probab=99.97  E-value=8.7e-31  Score=215.56  Aligned_cols=122  Identities=23%  Similarity=0.340  Sum_probs=115.4

Q ss_pred             CHHHHHHHHhcCCcceEEEecccCcccCCCCCceeEEeCCCCeEEEe-------ecchhhHHHHHHHHHHHHHHHHHHhc
Q 043133            1 FCKSILKDITERRSLSISINQFRNYCKNLDAHCSCSYDFPQGQEILT-------LEKQCHARRIDILLSVLLIVQKLLQE   73 (131)
Q Consensus         1 ~~~~i~~~l~~g~~P~i~l~~r~~~~~n~~~~~~~~yd~~~g~~~l~-------~~~~~~~~kf~~~l~vl~~i~~ll~~   73 (131)
                      |+..+++|+++|+.|.+.+|.|+++  |      +.||++.+.++++       +.++.++++|+++++++++|++++..
T Consensus        17 ~~~~~~~~l~~~~~p~~~vp~r~~s--n------~~~d~~~~~~~lg~r~~~r~~~~v~~a~k~~q~l~~~~~i~e~l~~   88 (356)
T COG1697          17 FAHKIYEQLEKGQIPIVEVPTRTKS--N------IIYDEESDHIVLGDRKSERSFLTVKGARKLAQTLLMLDFIKELLEL   88 (356)
T ss_pred             HHHHHHHHHhcCCCCceeccccccc--c------cccCccccceeccccccchhhhhHHHHHHHHHHHHHHHHHHHHHhc
Confidence            5789999999999999999999988  9      9999999998885       56799999999999999999999999


Q ss_pred             CCccceeeeecc--CCCCCC--chHHHHHHHHHHHHHhcCCccccceeecCCceEEeecee
Q 043133           74 NIHMSKRDIYYM--HPSLYS--EQSIVDQAINDICILLQCSRHNINVVGTSLELLILPRYV  130 (131)
Q Consensus        74 ~~~~T~RdiYY~--~~~lF~--~Q~~vd~~I~di~~~l~~~R~~L~i~a~~KGlv~G~i~~  130 (131)
                      |+++|+|||||.  +..+|.  +|++||++|+||+..+|++||+|||.|++||+|+||+.+
T Consensus        89 ~~~~TlReiYY~~~~~~~~k~~~Q~esd~lieDie~~~gl~Re~l~i~p~ekG~V~G~l~I  149 (356)
T COG1697          89 GKTSTLREIYYISKHVEVFKFDDQSESDRLIEDIEVTLGLSREDLGIRPEEKGLVYGPLRI  149 (356)
T ss_pred             CCCccHHHHhhhccCcccccccchhHHHHHHHHHHHHhccCHHHcCCCcccCceEEcceEE
Confidence            999999999999  666787  999999999999999999999999999999999999976

>PLN00060 meiotic recombination protein SPO11-2; Provisional

Probab=99.95  E-value=2.7e-28  Score=204.33  Aligned_cols=121  Identities=20%  Similarity=0.256  Sum_probs=103.1

Q ss_pred             HHHHHHHHhcCCcce--EEEecccCcccCCCCCceeEEeCCC------------CeEEEeecchhhHHHHHHHHHHHHHH
Q 043133            2 CKSILKDITERRSLS--ISINQFRNYCKNLDAHCSCSYDFPQ------------GQEILTLEKQCHARRIDILLSVLLIV   67 (131)
Q Consensus         2 ~~~i~~~l~~g~~P~--i~l~~r~~~~~n~~~~~~~~yd~~~------------g~~~l~~~~~~~~~kf~~~l~vl~~i   67 (131)
                      +..++.+|.+|+.+.  +++|+|++.  |      +.|.+.-            .....++.+.++++||+++++||+++
T Consensus        37 ~~~~~~~l~~~~~~~~~~~~~~r~~~--n------~~~~~~~~~~~~~~~~l~~~~~~r~~~~~~~a~kf~~~~~vl~~i  108 (384)
T PLN00060         37 VLNFLAALNSPDPAISDLPLISRNCS--N------VLLRRGLLQGDVSSIFLSHLFCKRSLTKAGSAKAFVRVWKVMEMC  108 (384)
T ss_pred             HHHHHHHHhcCCCccceecccccccc--c------ccccccccccccceeeeccceeeEecCCHHHHHHHHHHHHHHHHH
Confidence            567888999985444  777886644  7      6666532            11112366789999999999999999


Q ss_pred             HHHHhcCCccceeeeecc----CCCCCCchHHHHHHHHHHHHHhcCCccccceeecCCceEEeecee
Q 043133           68 QKLLQENIHMSKRDIYYM----HPSLYSEQSIVDQAINDICILLQCSRHNINVVGTSLELLILPRYV  130 (131)
Q Consensus        68 ~~ll~~~~~~T~RdiYY~----~~~lF~~Q~~vd~~I~di~~~l~~~R~~L~i~a~~KGlv~G~i~~  130 (131)
                      |++|.+|+++|+|||||+    ++++|++|++||++|+|||++++++|++|||+|++||+|+|++.+
T Consensus       109 ~~~l~~~~~~TkRdiYY~~~~~~~~lF~~Q~~vd~~I~Di~~~l~~~R~~L~I~a~~KGlV~G~l~i  175 (384)
T PLN00060        109 YQILGEGKLVTQRELFYKLLCDSPEYFSCQRHVNQTVQDVVSLLRCSRYSLGIMASSRGALIGRLVL  175 (384)
T ss_pred             HHHHHcCCccchHHhhcccccCChhhcCCHHHHHHHHHHHHHHHCCCHHHCCeEecCCceEEeeeEE
Confidence            999999999999999999    889999999999999999999999999999999999999999865

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

Probab=99.95  E-value=2.9e-28  Score=201.62  Aligned_cols=127  Identities=31%  Similarity=0.471  Sum_probs=106.0

Q ss_pred             CHHHHHHHHhcCCcceEEEecccCc--ccCCCCCceeEEeCCCCeEEEeecchhhHHHHHHHHHHHHHHHHHHhcCCccc
Q 043133            1 FCKSILKDITERRSLSISINQFRNY--CKNLDAHCSCSYDFPQGQEILTLEKQCHARRIDILLSVLLIVQKLLQENIHMS   78 (131)
Q Consensus         1 ~~~~i~~~l~~g~~P~i~l~~r~~~--~~n~~~~~~~~yd~~~g~~~l~~~~~~~~~kf~~~l~vl~~i~~ll~~~~~~T   78 (131)
                      |...++.++++.+.+++++++|..+  +.|+.-.+.+.++.+......   ....+++|+++|++|++||++++.|+++|
T Consensus        31 ~v~~~~~~l~r~~~~sls~~~r~~~n~~~~~~l~~~~~~~~~~~~~~~---~~~~~~~~~~llrvL~~V~ell~~~~~~T  107 (372)
T KOG2795|consen   31 FVLSVLVQLARPEGFSLSVINRKRSNSLSSPDLDTLVSKSHNTLRFTF---SSKKAKKFAILLRVLEIVHELLELGKRVT  107 (372)
T ss_pred             HHHHHHHHhhcccCCcccchhhhhcCCccCcchhhhhcccccccceee---ccccchHHHHHHHHHHHHHHHHHcCCcee
Confidence            4567889999877777777776544  444444555667666443211   13348999999999999999999999999


Q ss_pred             eeeeeccCCCCCCchHHHHHHHHHHHHHhcCCccccceeecCCceEEeecee
Q 043133           79 KRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNINVVGTSLELLILPRYV  130 (131)
Q Consensus        79 ~RdiYY~~~~lF~~Q~~vd~~I~di~~~l~~~R~~L~i~a~~KGlv~G~i~~  130 (131)
                      +|||||+|+.+|++|.+||++++|||++|+|+|.+|||.|++||+|+|++.+
T Consensus       108 kRdiyY~dv~lF~~Qs~Vd~~l~dI~~~l~~SR~sLnI~a~~KGLV~G~l~~  159 (372)
T KOG2795|consen  108 KRDIYYMDVDLFRRQSVVDRLLDDICCLLKCSRYSLNILAASKGLVAGRLRF  159 (372)
T ss_pred             eeeeeecCHHHHhhHHHHHHHHHHHHHHhcCChhcCCeeeecCceEEeeEEE
Confidence            9999999999999999999999999999999999999999999999999875

>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 [, ]

Probab=99.93  E-value=8.1e-27  Score=152.66  Aligned_cols=68  Identities=49%  Similarity=0.734  Sum_probs=61.7

Q ss_pred             chhhHHHHHHHHHHHHHHHHHHhcCCccceeeeeccCCCCCCchHHHHHHHHHHHHHhcCCcccccee
Q 043133           50 KQCHARRIDILLSVLLIVQKLLQENIHMSKRDIYYMHPSLYSEQSIVDQAINDICILLQCSRHNINVV  117 (131)
Q Consensus        50 ~~~~~~kf~~~l~vl~~i~~ll~~~~~~T~RdiYY~~~~lF~~Q~~vd~~I~di~~~l~~~R~~L~i~  117 (131)
                      |+++++||++++++|+.+|+++.+|+++|+|||||+++++|++|++||++|+|||.+|+++|++|||+
T Consensus         1 n~~~~~k~a~~l~vl~~i~~~l~~~~~~T~RdiYY~~~~lF~~Q~~vd~~i~di~~~l~~~R~~L~Iv   68 (68)
T PF04406_consen    1 NVKSARKFAQLLRVLAIIHELLQNNKTSTKRDIYYRNVSLFKSQREVDRAIDDICCLLGVSREDLNIV   68 (68)
T ss_dssp             -TCHHHHHHHHHHHHHHHHHHHHTT--EEHHHHHHHCSCS-SSHHHHHHHHHHHHHHHTS-GGGGTEE
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHcCCccchHHHHHhchhhccCHHHHHHHHHHHHHHHCCCHHHcCCC
Confidence            46789999999999999999999999999999999999999999999999999999999999999996

These two types of proteins share structural homology. Spo11 is a meiosis-specific protein that is responsible for the initiation of recombination through the formation of DNA double-strand breaks by a type II DNA topoisomerase-like activity. Spo11 acts in conjunction with several other proteins, including Rec102 in yeast, to bring about meiotic recombination []. DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. They can be divided into two classes: type I enzymes (5.99.1.2 from EC, topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC, topoisomerases II, IV and VI) break double-strand DNA []. Topoisomerase VI is a type IIB enzymes that assembles as a heterotetramer, consisting of two A subunits required for DNA cleavage and two B subunits required for ATP hydrolysis. The B subunit is structurally similar to the ATPase domain of type IIA topoisomerases, but the A subunit is distinct, and instead shares homology with the Spo11 protein. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003824 catalytic activity, 0005524 ATP binding, 0006259 DNA metabolic process, 0005694 chromosome; PDB: 1D3Y_B 2ZBK_A 2Q2E_A.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	131
1d3y_A	301	DNA topoisomerase VI A subunit; DNA binding protei	3e-13
2q2e_A	369	Type II DNA topoisomerase VI subunit A; DNA-bindin	6e-13
2zbk_A	389	Type II DNA topoisomerase VI subunit A; DNA bindin	2e-11

>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

 Score = 63.7 bits (154), Expect = 3e-13
 Identities = 12/72 (16%), Positives = 29/72 (40%), Gaps = 4/72 (5%)

Query: 53  HARRIDILLSVLLIVQKLLQENIHMSKRDIYYMHPSL----YSEQSIVDQAINDICILLQ 108
            A+       +L   ++LL+ +   + R+ YY+  +     + +Q   +  I D+   L 
Sbjct: 4   QAKIFAQTTKMLEFAKQLLETDDFSTLREAYYVSKNWGEARFDDQQASNNVIEDLEAALG 63

Query: 109 CSRHNINVVGTS 120
             R ++  +   
Sbjct: 64  VLREHLGFIPEE 75

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

 Score = 63.4 bits (153), Expect = 6e-13
 Identities = 20/126 (15%), Positives = 44/126 (34%), Gaps = 8/126 (6%)

Query: 1   FCKSILKDITERRSLSISINQF--RNYCKNLDAHCSCSYDFPQGQEILTLEKQCHARRID 58
             + I     E    S+S+      N   + ++      D    +   T++      +  
Sbjct: 23  IAEKIYNQFEEEVVPSVSLPSRTKANLEYSDESDVWVYGDRESERSAKTVKGAFQLLKT- 81

Query: 59  ILLSVLLIVQKLLQENIHMSKRDIYYMHP----SLYSEQSIVDQAINDICILLQCSRHNI 114
              +   ++ + L  N   + R++YY+      + + EQ   D+ I D+ IL    R   
Sbjct: 82  -TYATDFLINEHLARNRGSTLRELYYISEGWDYAKFKEQGESDRLIEDLEILTSLQREYF 140

Query: 115 NVVGTS 120
           ++    
Sbjct: 141 HMRPEE 146

>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

 Score = 58.8 bits (141), Expect = 2e-11
 Identities = 19/135 (14%), Positives = 42/135 (31%), Gaps = 22/135 (16%)

Query: 1   FCKSILKDITERRSLSISINQ--FRNYCKNLDAHCSCSYDFPQGQEILTLEKQCHARRID 58
              ++++ + +   L + I      N   +         +    +  L       A+R  
Sbjct: 24  KFLNLVEQLKKGEPLVMEIPMRTLSNAIYDEKRKLLLLGEKKLRRNFLD---LNEAKRFM 80

Query: 59  ILLSVLLIVQKLLQENIHMSKRDIYYMH-----------------PSLYSEQSIVDQAIN 101
             + +  I+   L  + + + RD+YY                    + + EQ   D  I 
Sbjct: 81  QTVLMASIIYDALVSDEYPTIRDLYYRGKHSLLLKSIEGNKIVSEENTWDEQKESDSVIV 140

Query: 102 DICILLQCSRHNINV 116
           DI +     R  + +
Sbjct: 141 DIEVFTSLLREEMLI 155

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	131
2zbk_A	389	Type II DNA topoisomerase VI subunit A; DNA bindin	99.97
2q2e_A	369	Type II DNA topoisomerase VI subunit A; DNA-bindin	99.97
1d3y_A	301	DNA topoisomerase VI A subunit; DNA binding protei	99.92
3vxv_A	69	Methyl-CPG-binding domain protein 4; methyl CPG bi	85.81

>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}

Probab=99.97  E-value=7.9e-33  Score=230.89  Aligned_cols=121  Identities=17%  Similarity=0.189  Sum_probs=97.8

Q ss_pred             HHHHH----HHHhcCCcceEEEecccCcccCCCCCceeEEeCCCCeEEEe-------ecchhhHHHHHHHHHHHHHHHHH
Q 043133            2 CKSIL----KDITERRSLSISINQFRNYCKNLDAHCSCSYDFPQGQEILT-------LEKQCHARRIDILLSVLLIVQKL   70 (131)
Q Consensus         2 ~~~i~----~~l~~g~~P~i~l~~r~~~~~n~~~~~~~~yd~~~g~~~l~-------~~~~~~~~kf~~~l~vl~~i~~l   70 (131)
                      +.+++    +++++|+.|.|++|+|+.+  |      +.||+..|.++++       +.+.++++||+++++||++||++
T Consensus        21 ~~~~~~~~~~~~~~~~~p~~~~p~r~~~--n------~~~d~~~~~~~~~~~~~~r~~~~~~~~~~f~~~~~vl~~i~~~   92 (389)
T 2zbk_A           21 LRDKFLNLVEQLKKGEPLVMEIPMRTLS--N------AIYDEKRKLLLLGEKKLRRNFLDLNEAKRFMQTVLMASIIYDA   92 (389)
T ss_dssp             TTHHHHHHHCCCCCSSCCEECCCC-----------------------------CCEETTSSTTHHHHHHHHHHTHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCEEeccccCcC--c------eeeccccceEEecCceeEEecCCHHHHHHHHHHHHHHHHHHHH
Confidence            34555    9999999999999998855  9      9999999988774       55789999999999999999999


Q ss_pred             HhcCCccceeeeeccCCC-----------------CCCchHHHHHHHHHHHHHhcCCccccceeecCCceEEeecee
Q 043133           71 LQENIHMSKRDIYYMHPS-----------------LYSEQSIVDQAINDICILLQCSRHNINVVGTSLELLILPRYV  130 (131)
Q Consensus        71 l~~~~~~T~RdiYY~~~~-----------------lF~~Q~~vd~~I~di~~~l~~~R~~L~i~a~~KGlv~G~i~~  130 (131)
                      |.+|+++|+|||||++++                 +|++|++||++|+|||++||++|++|||+|++||+|+||+.+
T Consensus        93 l~~~~~~T~RdiYY~~~~~~~~~~~~~~~~~~~~~~F~~Q~~~d~~I~di~~~l~~~R~~L~I~a~~kGlv~G~l~i  169 (389)
T 2zbk_A           93 LVSDEYPTIRDLYYRGKHSLLLKSIEGNKIVSEENTWDEQKESDSVIVDIEVFTSLLREEMLILSKEKGKVVGNLRI  169 (389)
T ss_dssp             HHTTCCCCHHHHHSCCSCSCCSCCCC-------CCSCCSHHHHHHHHHHHHHHHSCCHHHHTCCCCCCCCBEESEEE
T ss_pred             HHcCCccchHHhhccCcccccccccccccccchhhhcCCHHHHHHHHHHHHHHHCCChhhcceEecCCcEEEeeeEE
Confidence            999999999999999999                 999999999999999999999999999999999999999875

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

Probab=99.97  E-value=1.2e-32  Score=228.23  Aligned_cols=122  Identities=17%  Similarity=0.166  Sum_probs=98.7

Q ss_pred             CHHHHHHHHhcCCcceEEEecccCcccCCCCCceeEEeCCCCeEEEe-------ecchhhHHHHHHHHHHHHHH-HHHHh
Q 043133            1 FCKSILKDITERRSLSISINQFRNYCKNLDAHCSCSYDFPQGQEILT-------LEKQCHARRIDILLSVLLIV-QKLLQ   72 (131)
Q Consensus         1 ~~~~i~~~l~~g~~P~i~l~~r~~~~~n~~~~~~~~yd~~~g~~~l~-------~~~~~~~~kf~~~l~vl~~i-~~ll~   72 (131)
                      ++.+++++|++|+.|.|++|+|+.+  |      +.||++.|.++++       +.+.++++||+++++||++| |+++.
T Consensus        23 ~~~~~~~~l~~~~~p~~~i~~r~~~--n------~~~d~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~vl~~i~~~~l~   94 (369)
T 2q2e_A           23 IAEKIYNQFEEEVVPSVSLPSRTKA--N------LEYSDESDVWVYGDRESERSAKTVKGAFQLLKTTYATDFLINEHLA   94 (369)
T ss_dssp             HHHHHHHTTHHHHTTSCCCCC--------------------------------CCSSTHHHHHHHCC-HHHHHHTTTSST
T ss_pred             HHHHHHHHHhcCCCCeEEeeccccC--c------eeecccCCeeeecCceeeEecCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3678999999999999999998755  8      9999999987774       45688999999999999999 99999


Q ss_pred             cCCccceeeeeccCC----CCCCchHHHHHHHHHHHHHhcCCccccceeecCCc-eEEeecee
Q 043133           73 ENIHMSKRDIYYMHP----SLYSEQSIVDQAINDICILLQCSRHNINVVGTSLE-LLILPRYV  130 (131)
Q Consensus        73 ~~~~~T~RdiYY~~~----~lF~~Q~~vd~~I~di~~~l~~~R~~L~i~a~~KG-lv~G~i~~  130 (131)
                      +|+++|+|||||+++    ++|++|++||++|+|||++||++|++|||+|++|| +|+||+.+
T Consensus        95 ~~~~~T~RdiYY~~~~~~~~lF~~Q~~~d~~I~di~~~l~~~R~~L~I~a~~kG~lv~G~l~i  157 (369)
T 2q2e_A           95 RNRGSTLRELYYISEGWDYAKFKEQGESDRLIEDLEILTSLQREYFHMRPEEDGATMFGPIEI  157 (369)
T ss_dssp             TCCCEEHHHHHHHTSSSTTSCCSCTTTHHHHHHHHHHHSCCCGGGGTEECSSCCCCEECSCCC
T ss_pred             cCCccchHHhhccCcccchhhccCHHHHHHHHHHHHHHHCCCHHHcceeccCCceEEEEeEEE
Confidence            999999999999999    99999999999999999999999999999999999 99999875

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

Probab=99.92  E-value=1.2e-25  Score=181.90  Aligned_cols=81  Identities=16%  Similarity=0.263  Sum_probs=76.6

Q ss_pred             chhhHHHHHHHHHHHHHHHHHHhcCCccceeeeeccCC----CCCCchHHHHHHHHHHHHHhcCCccccceeecCCc-eE
Q 043133           50 KQCHARRIDILLSVLLIVQKLLQENIHMSKRDIYYMHP----SLYSEQSIVDQAINDICILLQCSRHNINVVGTSLE-LL  124 (131)
Q Consensus        50 ~~~~~~kf~~~l~vl~~i~~ll~~~~~~T~RdiYY~~~----~lF~~Q~~vd~~I~di~~~l~~~R~~L~i~a~~KG-lv  124 (131)
                      +.++++||+++++||+++|++|++|+++|+|||||+++    ++|++|++||++|+|||++|+++|++|||+|++|| +|
T Consensus         1 ~~~~~~~~~~~~~vl~~i~~~l~~~~~~T~RdiYY~~~~~~~~~F~~Q~~~d~~i~di~~~l~~~R~~L~i~a~~kG~lv   80 (301)
T 1d3y_A            1 TVNQAKIFAQTTKMLEFAKQLLETDDFSTLREAYYVSKNWGEARFDDQQASNNVIEDLEAALGVLREHLGFIPEEDGSSV   80 (301)
T ss_dssp             ---CHHHHHHHHHHHHHHHHHHHTTCCEEHHHHHHHGGGSGGGCCSSHHHHHHHHHHHHHHHTCCGGGGTEECSSCCCEE
T ss_pred             ChHHHHHHHHHHHHHHHHHHHHHcCCccchhhhhccCCccchhhccCHHHHHHHHHHHHHHHCCCHHHCCeeeCCCceEE
Confidence            35789999999999999999999999999999999998    89999999999999999999999999999999999 99


Q ss_pred             Eeecee
Q 043133          125 ILPRYV  130 (131)
Q Consensus       125 ~G~i~~  130 (131)
                      +|++.+
T Consensus        81 ~G~l~i   86 (301)
T 1d3y_A           81 VGPLKI   86 (301)
T ss_dssp             ESSCEE
T ss_pred             EeeeEE
Confidence            999875

>3vxv_A Methyl-CPG-binding domain protein 4; methyl CPG binding domain, protein-DNA complex, versatIle BA recognition, hydrolase-DNA complex; HET: DNA 5CM; 2.00A {Mus musculus} PDB: 3vxx_A* 3vyb_A* 3vyq_A*

Probab=85.81  E-value=0.45  Score=30.17  Aligned_cols=48  Identities=10%  Similarity=0.127  Sum_probs=35.8

Q ss_pred             CCccceeeeeccCCC--CCCchHHHHHHHHHHHHHhcCCccccceeecCCc
Q 043133           74 NIHMSKRDIYYMHPS--LYSEQSIVDQAINDICILLQCSRHNINVVGTSLE  122 (131)
Q Consensus        74 ~~~~T~RdiYY~~~~--lF~~Q~~vd~~I~di~~~l~~~R~~L~i~a~~KG  122 (131)
                      |....+.|+||.+|.  -|.+-.++.+.+.+-... +++.+++.-.+.+||
T Consensus        20 G~s~gk~DvyY~sP~Gkk~RSk~ev~~yL~~~~~~-~l~~~~FdF~~p~~~   69 (69)
T 3vxv_A           20 GKTAGKFDVYFISPQGLKFRSKRSLANYLLKNGET-FLKPEDFNFTVLPKG   69 (69)
T ss_dssp             STTTTCEEEEEECTTSCEECSHHHHHHHHHHHCCC-CCCGGGSCCCCCCC-
T ss_pred             CCCCCcceEEEEcCCCCEeeCHHHHHHHHHhCCCC-CCCHHHcceeCCCCC
Confidence            455668899999986  699999999999886432 567777776666554

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	131
d1d3ya_	298	e.12.1.1 (A:) DNA topoisomerase IV, alpha subunit	6e-16

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

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 = 70.0 bits (171), Expect = 6e-16
 Identities = 12/77 (15%), Positives = 30/77 (38%), Gaps = 4/77 (5%)

Query: 53  HARRIDILLSVLLIVQKLLQENIHMSKRDIYYMHPSL----YSEQSIVDQAINDICILLQ 108
            A+       +L   ++LL+ +   + R+ YY+  +     + +Q   +  I D+   L 
Sbjct: 1   QAKIFAQTTKMLEFAKQLLETDDFSTLREAYYVSKNWGEARFDDQQASNNVIEDLEAALG 60

Query: 109 CSRHNINVVGTSLELLI 125
             R ++  +       +
Sbjct: 61  VLREHLGFIPEEDGSSV 77

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	131
d1d3ya_	298	DNA topoisomerase IV, alpha subunit {Archaeon Meth	99.92

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

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=99.92  E-value=6.2e-26  Score=181.44  Aligned_cols=77  Identities=17%  Similarity=0.266  Sum_probs=73.4

Q ss_pred             hHHHHHHHHHHHHHHHHHHhcCCccceeeeeccCCCC----CCchHHHHHHHHHHHHHhcCCccccceeecCCceEE-ee
Q 043133           53 HARRIDILLSVLLIVQKLLQENIHMSKRDIYYMHPSL----YSEQSIVDQAINDICILLQCSRHNINVVGTSLELLI-LP  127 (131)
Q Consensus        53 ~~~kf~~~l~vl~~i~~ll~~~~~~T~RdiYY~~~~l----F~~Q~~vd~~I~di~~~l~~~R~~L~i~a~~KGlv~-G~  127 (131)
                      +|+|||++++||+++|++|++|+++|+|||||+++++    |++|++||++|+|||++|||+|++|||+|++||+|+ |+
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 55


Q ss_pred             ce
Q 043133          128 RY  129 (131)
Q Consensus       128 i~  129 (131)
                      +.
T Consensus        81 ~~   82 (298)
T d1d3ya_          81 LK   82 (298)
T ss_dssp             CE
T ss_pred             EE
Confidence            44