Citrus Sinensis ID: 029346

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190----
Protein Sequence
MTNTESNFFIVLCLISSAIRICIITNTVSNFFIVIRLIREGAANRTCENKIVILLREIRCKLKKSVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYLPSKFRAEDWL
Secondary Structure (PSIPRED)
ccccEEEccEEEEEEcHHHHHHHHHccccccccEEEEEEccccccccHHHHHHHHHHHHHHHcccEEEEEcccccccHHHHHHHHccccccccccccccccEEEEcccccccccccccccccccccHHHHHHHHHHHHccccHHHHcccHHHHHHHHHHHHHccEEEEEEHHHccccccHHccHHHHHcccccc
Secondary Structure Prediction (SSPRO)
ccccEcccEEEEEEEcHHHHHHHHHcccHHcccEEEEEccccccHHHHHHHHHHHHHHHHHccccEEEEEccccccHEEEEEEEHccHHHHHHHHcccccccEEEEEcHHHHHHccccccccccccHHHHHHHHHHHcccccHHHHcccHHHHHHHHHHHHcccHHHHHHHHHccccHHHHHHcHHHHHccccc
Coil and Loop (DISEMBL)
MTNTESNFFIVLCLISSAIRICIITNTVSNFFIVIRLIREGAANRTCENKIVILLREIRCKLKKsvlgsfdcnpygiHILTVYMFgsknmagrnlrlavpnikwlglfpsdlekynipklcrQILSKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANkylpskfraedwl
Flexible Loop (DISEMBL)
MTNTESNFFIVLCLISSAIRICIITNTVSNFFIVIRLIregaanrtceNKIVILLREIRCKLKKSVlgsfdcnpYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANkylpskfraedwl
Low Complexity Region (SEG)
MTNTESNFFIVLCLISSAIRICIITNTVSNFFIVIRLIREGAANRTCENKIVILLREIRCKLKKSVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYLPSKFRAEDWL
Disordered region (IsUnstruct)
******NFFIVLCLISSAIRICIITNTVSNFFIVIRLIREGAANRTCENKIVILLREIRCKLKKSVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDISKLKTFLEKGDLVAFVRSNASW***************IEALDMYEYKYLANKYLP*********
Disordered Region (DISOPRED)
**NTESNFFIVLCLISSAIRICIITNTVSNFFIVIRLIREGAANRTCENKIVILLREIRCKLKKSVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYLPSKFRAEDWL
Disordered Region (DISEMBL)
MTNTESNFFIVLCLISSAIRICIITNTVSNFFIVIRLIREGAANRTCENKIVILLREIRCKLKKSVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYLPSKFRAEDWL
Disordered Region (DISPRO)
MTNTESNFFIVLCLISSAIRICIITNTVSNFFIVIRLIREGAANRTCENKIVILLREIRCKLKKSVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYLPSKFRA*D*L
Transmembrane Helix (TMHMM)
iiiiiiHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MTNTESNFFIVLCLISSAIRICIITNTVSNFFIVIRLIREGAANRTCENKIVILLREIRCKLKKSVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDISKLKTFLEKGDLVAFVRSxxxxxxxxxxxxxxxxxxxxxALDMYEYKYLANKYLPSKFRAEDWL
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	194	2.2.26 [Sep-21-2011]
Q9LZ03	427	DNA topoisomerase 6 subun	yes	no	0.711	0.323	0.450	3e-30
Q9WTK8	396	Meiotic recombination pro	yes	no	0.618	0.303	0.395	3e-21
Q9M4A2	362	Meiotic recombination pro	no	no	0.695	0.372	0.413	8e-21
Q9Y5K1	396	Meiotic recombination pro	yes	no	0.618	0.303	0.387	1e-19
O27089	353	Type 2 DNA topoisomerase	yes	no	0.556	0.305	0.338	3e-12
Q57815	369	Type 2 DNA topoisomerase	yes	no	0.608	0.319	0.341	9e-12
Q971T1	387	Type 2 DNA topoisomerase	yes	no	0.706	0.354	0.295	2e-08
Q9YE67	389	Type 2 DNA topoisomerase	yes	no	0.706	0.352	0.3	3e-08
A2BLE8	387	Type 2 DNA topoisomerase	yes	no	0.628	0.315	0.3	4e-08
Q22236	425	Meiotic recombination pro	yes	no	0.613	0.28	0.274	6e-08

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

 Score =  131 bits (329), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 64/142 (45%), Positives = 92/142 (64%), Gaps = 4/142 (2%)

Query: 53  ILLREIRCKLKKSVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDL 112
           + LR+++ +LK  VL   D +PYG+ IL+VY  GSKNM+  +  L  P+IKWLG+ PSDL
Sbjct: 290 LFLRKMKMELKLPVLALVDSDPYGLKILSVYGCGSKNMSYDSANLTTPDIKWLGIRPSDL 349

Query: 113 EKYNIPKLCRQILSKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALD 172
           +KY IP+ CR  +++ DI   K  LE+     FV+ N  W +EL  M K  +KAEI+AL 
Sbjct: 350 DKYKIPEQCRLPMTEQDIKTGKDMLEED----FVKKNPGWVEELNLMVKTKQKAEIQALS 405

Query: 173 MYEYKYLANKYLPSKFRAEDWL 194
            + ++YL+  YLP K + +DWL
Sbjct: 406 SFGFQYLSEVYLPLKLQQQDWL 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|Q9WTK8|SPO11_MOUSE Meiotic recombination protein SPO11 OS=Mus musculus GN=Spo11 PE=2 SV=2

 Score =  101 bits (252), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 49/124 (39%), Positives = 74/124 (59%), Gaps = 4/124 (3%)

Query: 71  DCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDI 130
           D +PYGI I+ +Y +GS +M+     L +P I+WLGL PSD+++ NIPK     L+K D 
Sbjct: 277 DADPYGIEIMCIYKYGSMSMSFEAHNLTIPTIRWLGLLPSDIQRLNIPKDSLIPLTKHDQ 336

Query: 131 SKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYLPSKFRA 190
            KL + L++     ++     W+KEL+ M+    KAEI+AL +    YL+  YLP+K R 
Sbjct: 337 MKLDSILKR----PYITYQPLWKKELEMMADSKMKAEIQALTLLSSDYLSRVYLPNKLRF 392

Query: 191 EDWL 194
             W+
Sbjct: 393 GGWI 396

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

Mus musculus (taxid: 10090)

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

 Score =  100 bits (248), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 57/138 (41%), Positives = 75/138 (54%), Gaps = 3/138 (2%)

Query: 54  LLREIRCKLKKSVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLE 113
            LR +  KL   V    DC+PYG  IL  Y FGS  MA     L  P++KWLG FPSD E
Sbjct: 224 FLRLLMEKLHLPVHCLVDCDPYGFEILATYRFGSMQMAYDIESLRAPDMKWLGAFPSDSE 283

Query: 114 KYNIPKLCRQILSKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDM 173
            Y++PK C   L+++D  + +  L +  L    R    W  EL+ M K G K EIEAL +
Sbjct: 284 VYSVPKQCLLPLTEEDKKRTEAMLLRCYL---KREMPQWRLELETMLKRGVKFEIEALSV 340

Query: 174 YEYKYLANKYLPSKFRAE 191
           +   +L+  Y+PSK R E
Sbjct: 341 HSLSFLSEVYIPSKIRRE 358

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 = 96.3 bits (238), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 48/124 (38%), Positives = 71/124 (57%), Gaps = 4/124 (3%)

Query: 71  DCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDI 130
           D +P+GI I+ +Y +GS +M+     L VP I+WLGL PSDL++ N+PK     L+K D 
Sbjct: 277 DADPHGIEIMCIYKYGSMSMSFEAHHLTVPAIRWLGLLPSDLKRLNVPKDSLIPLTKRDQ 336

Query: 131 SKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYLPSKFRA 190
            KL + L +     +V     W KE++ M+    KAEI+AL      YL+  YLP+K + 
Sbjct: 337 MKLDSILRR----PYVTCQPFWRKEMEIMADSKMKAEIQALTFLSSDYLSRVYLPNKLKF 392

Query: 191 EDWL 194
             W+
Sbjct: 393 GGWI 396

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

Homo sapiens (taxid: 9606)

>sp|O27089|TOP6A_METTH Type 2 DNA topoisomerase 6 subunit A OS=Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) GN=top6A PE=3 SV=1

 Score = 72.0 bits (175), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 42/124 (33%), Positives = 66/124 (53%), Gaps = 16/124 (12%)

Query: 71  DCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDI 130
           D +P+G HI  V + GS  +A  N +LA P+ K+LG+  SD+  Y++P      L   D+
Sbjct: 238 DGDPWGFHIAMVIISGSAKLAHVNHQLATPDAKFLGVTASDIINYDLPT---DPLKDVDV 294

Query: 131 SKLKTFLE----KGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYLPS 186
            +LK  L+    +GD          W+ E++KM   G+KAE ++   Y  +Y+ + YLP 
Sbjct: 295 VRLKELLQDPRYRGDF---------WKTEIKKMLTIGKKAEQQSFSKYGLEYVVDTYLPE 345

Query: 187 KFRA 190
           K  A
Sbjct: 346 KLEA 349

Relaxes both positive and negative superturns and exhibits a strong decatenase activity.

Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) (taxid: 187420)

EC: 5

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: .

EC: 3

>sp|Q57815|TOP6A_METJA Type 2 DNA topoisomerase 6 subunit A OS=Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) GN=top6A PE=1 SV=1

 Score = 70.1 bits (170), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 43/126 (34%), Positives = 67/126 (53%), Gaps = 8/126 (6%)

Query: 71  DCNPYG-IHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDD 129
           D +PYG ++I      GS        +L++P  + +G+ P D+  Y++P      L + D
Sbjct: 249 DGDPYGYLNIYRTLKVGSGKAIHLADKLSIPAARLIGVTPQDIIDYDLPT---HPLKEQD 305

Query: 130 ISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYLPSKFR 189
           I ++K  L+  D   FVRS   W+K L++M   G +AE ++L  Y  KY+ N YLP K +
Sbjct: 306 IKRIKDGLKNDD---FVRSFPEWQKALKQMLDMGVRAEQQSLAKYGLKYVVNTYLPEKIK 362

Query: 190 AED-WL 194
            E  WL
Sbjct: 363 DESTWL 368

Relaxes both positive and negative superturns and exhibits a strong decatenase activity.

Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (taxid: 243232)

EC: 5

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: .

EC: 3

>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

 Score = 58.9 bits (141), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 44/149 (29%), Positives = 78/149 (52%), Gaps = 12/149 (8%)

Query: 54  LLREIRCKLKKSVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDL- 112
            +R +  +LK  V    D +PYG +I +V+  GS +++  + RLA PN K+LG+  +D+ 
Sbjct: 242 FVRRLNEELKLPVYILTDADPYGWYIYSVFRIGSISLSYESERLATPNAKFLGVSMTDIF 301

Query: 113 -EKYNIPKLCRQ------ILSKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEK 165
            +    P L  Q      I +KD  + +K   E  +   F     +W+ E++    +  K
Sbjct: 302 GDSNKKPYLSEQERRNYIIKAKD--ADIKRATEIKNYQWF--KTKAWQHEIEIFLNKKSK 357

Query: 166 AEIEALDMYEYKYLANKYLPSKFRAEDWL 194
            EIEA+     K+LA +Y+P K +++D++
Sbjct: 358 LEIEAMASKGLKFLAFQYIPEKIKSKDYI 386

Relaxes both positive and negative superturns and exhibits a strong decatenase activity.

Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) (taxid: 273063)

EC: 5

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: .

EC: 3

>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

 Score = 58.2 bits (139), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 45/150 (30%), Positives = 69/150 (46%), Gaps = 13/150 (8%)

Query: 54  LLREIRCKLKKSVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLE 113
            +R +  +LK  V    D +PYG +I +VY  GS  ++  + RLA P  K+LG+  +D+ 
Sbjct: 243 FVRRLHEELKLPVYIITDSDPYGWYIYSVYKVGSITLSYESERLATPKAKFLGVQMTDIF 302

Query: 114 KY--NIPKLCRQILSK-------DDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGE 164
            Y    P L      K        DI + K  L      +++  N  W  E++   K   
Sbjct: 303 GYRGKKPYLSEAERKKFMIKATDKDIKRAKELLN----YSWIGKNRRWNVEIRLFLKHLV 358

Query: 165 KAEIEALDMYEYKYLANKYLPSKFRAEDWL 194
           K EIEA+     K+ A +Y+P K    DW+
Sbjct: 359 KLEIEAIASKGLKFFAYQYIPEKIETGDWI 388

Relaxes both positive and negative superturns and exhibits a strong decatenase activity.

Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1) (taxid: 272557)

EC: 5

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: .

EC: 3

>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

 Score = 57.8 bits (138), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 39/130 (30%), Positives = 65/130 (50%), Gaps = 8/130 (6%)

Query: 71  DCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNI--PKLCRQ----I 124
           D +PYG +I +V+  GS  ++  + RLA PN +++G+  +D+  Y    P L  Q     
Sbjct: 259 DADPYGWYIYSVFKIGSITLSYESERLATPNARFIGVSMTDIFGYKSKKPYLTEQERRNF 318

Query: 125 LSKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYL 184
           + K   + +K   E  +   F      W+ E+    ++  K EIEA+     ++LA+KYL
Sbjct: 319 IIKAKEADIKRAYELKNYKWF--QTKKWQIEIDIFLEKKAKLEIEAMTSKGLRFLADKYL 376

Query: 185 PSKFRAEDWL 194
           P K    DW+
Sbjct: 377 PEKIETGDWI 386

Relaxes both positive and negative superturns and exhibits a strong decatenase activity.

Hyperthermus butylicus (strain DSM 5456 / JCM 9403) (taxid: 415426)

EC: 5

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: .

EC: 3

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

 Score = 57.4 bits (137), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 36/131 (27%), Positives = 64/131 (48%), Gaps = 12/131 (9%)

Query: 54  LLREIRCKLKKSVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLE 113
           +L+ +  K K  + G FD +P+GI I   Y +G            VP I+W+GLFP+D  
Sbjct: 238 VLKMLSEKRKFPIYGLFDADPHGIEIYLTYKYGPTKEFAEGRGAFVPTIEWIGLFPTDFH 297

Query: 114 KYNIPKLCRQILSKDDISKLKTFLEK----GDLVAFVRSNASWEKELQKMSKEGEKAEIE 169
           ++ I +     L + D  K++  + +    G++V          +EL  M +   K E+E
Sbjct: 298 RFTIDQSQCLPLVRTDFVKIEKMIPRSIQLGEIVV--------TRELDWMIQNKFKMELE 349

Query: 170 ALDMYEYKYLA 180
           +++M   +Y+A
Sbjct: 350 SINMCGQEYMA 360

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

Caenorhabditis elegans (taxid: 6239)

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	194
168022302	413	predicted protein [Physcomitrella patens	0.938	0.440	0.389	4e-30
326521994	441	predicted protein [Hordeum vulgare subsp	0.958	0.421	0.381	4e-30
27476077	830	Hypothetical protein [Oryza sativa Japon	0.958	0.224	0.371	1e-29
125543392	830	hypothetical protein OsI_11065 [Oryza sa	0.958	0.224	0.371	1e-29
195647934	436	RHL2 [Zea mays]	0.958	0.426	0.371	2e-29
226497286	436	uncharacterized protein LOC100273699 [Ze	0.958	0.426	0.371	2e-29
297600747	442	Os03g0284800 [Oryza sativa Japonica Grou	0.958	0.420	0.371	2e-29
242041321	436	hypothetical protein SORBIDRAFT_01g03878	0.958	0.426	0.371	2e-29
194697080	200	unknown [Zea mays] gi|414866233|tpg|DAA4	0.958	0.93	0.371	2e-29
125585844	526	hypothetical protein OsJ_10402 [Oryza sa	0.958	0.353	0.371	2e-29

>gi|168022302|ref|XP_001763679.1| predicted protein [Physcomitrella patens subsp. patens] gi|162685172|gb|EDQ71569.1| predicted protein [Physcomitrella patens subsp. patens]

 Score =  136 bits (342), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 74/190 (38%), Positives = 110/190 (57%), Gaps = 8/190 (4%)

Query: 5   ESNFFIVLCLISSAIRICIITNTVSNFFIVIRLIREGAANRTCENKIVILLREIRCKLKK 64
           ES+   +L +   A  + +  +   N F  + L  +G  +        + L++++  LK 
Sbjct: 232 ESDALFILLVEKDAAFMRLAEDRFYNRFPCVILTAKGQPDVATR----LFLKKMKTDLKL 287

Query: 65  SVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQI 124
            VLG  D +PYG+ IL+VYM GSKNM+  +  L  P+IKWLG+ PSDL KY IP+ CR  
Sbjct: 288 PVLGLVDSDPYGLKILSVYMSGSKNMSYDSSNLTTPDIKWLGVRPSDLNKYKIPEQCRLP 347

Query: 125 LSKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYL 184
           +S  DI   K  LE+     F++ + +W KEL+ M K  EKAEI+AL  + ++YL+  YL
Sbjct: 348 MSDQDIKTGKDMLEED----FIKKDKNWVKELELMVKTKEKAEIQALSSFGFQYLSEVYL 403

Query: 185 PSKFRAEDWL 194
           P K + EDW+
Sbjct: 404 PLKLQQEDWI 413

Source: Physcomitrella patens subsp. patens

Species: Physcomitrella patens

Genus: Physcomitrella

Family: Funariaceae

Order: Funariales

Class: Bryopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|326521994|dbj|BAK04125.1| predicted protein [Hordeum vulgare subsp. vulgare]

 Score =  136 bits (342), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 74/194 (38%), Positives = 110/194 (56%), Gaps = 8/194 (4%)

Query: 1   MTNTESNFFIVLCLISSAIRICIITNTVSNFFIVIRLIREGAANRTCENKIVILLREIRC 60
           ++  ES+   +L +   A  + +  +   N F  I L  +G  +        + LR ++ 
Sbjct: 256 VSGIESDALFILLVEKDAAFMRLAEDRFYNRFPCIILTAKGQPDVATR----LFLRRLKV 311

Query: 61  KLKKSVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKL 120
           +LK  VL   D +PYG+ IL+VYM GSKNM+  +  L  P+IKWLG+ PSDL+KY +P+ 
Sbjct: 312 ELKLPVLALVDSDPYGLKILSVYMCGSKNMSYDSANLTTPDIKWLGVRPSDLDKYRVPEQ 371

Query: 121 CRQILSKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLA 180
           CR  +S  DI   K  LE+     FV+ N  W KEL+ M +  +KAEI+AL  + ++YL 
Sbjct: 372 CRLPMSDHDIKVGKEMLEED----FVKQNEGWVKELETMLRTKQKAEIQALSSFGFQYLT 427

Query: 181 NKYLPSKFRAEDWL 194
             YLP K + EDW+
Sbjct: 428 EVYLPLKLQQEDWI 441

Source: Hordeum vulgare subsp. vulgare

Species: Hordeum vulgare

Genus: Hordeum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|27476077|gb|AAO17008.1| Hypothetical protein [Oryza sativa Japonica Group] gi|108707550|gb|ABF95345.1| DNA topoisomerase VIA, putative, expressed [Oryza sativa Japonica Group]

 Score =  134 bits (338), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 72/194 (37%), Positives = 110/194 (56%), Gaps = 8/194 (4%)

Query: 1   MTNTESNFFIVLCLISSAIRICIITNTVSNFFIVIRLIREGAANRTCENKIVILLREIRC 60
           ++  ES+   +L +   A  + +  +   N F  I L  +G  +        + LR ++ 
Sbjct: 645 VSGIESDALFILLVEKDAAFMRLAEDRFYNRFPCIILTAKGQPDVATR----LFLRRLKV 700

Query: 61  KLKKSVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKL 120
           +LK  VL   D +PYG+ IL+VYM GSKNM+  +  L  P+IKWLG+ PSDL+KY +P+ 
Sbjct: 701 ELKLPVLALVDSDPYGLKILSVYMCGSKNMSYDSANLTTPDIKWLGVRPSDLDKYRVPEQ 760

Query: 121 CRQILSKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLA 180
           CR  ++  DI   K  LE+     FV+ N  W KEL+ M +  +KAEI+AL  + ++YL 
Sbjct: 761 CRLPMTDHDIKVGKELLEED----FVKQNEGWVKELETMLRTRQKAEIQALSSFGFQYLT 816

Query: 181 NKYLPSKFRAEDWL 194
             YLP K + +DW+
Sbjct: 817 EVYLPLKLQQQDWI 830

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|125543392|gb|EAY89531.1| hypothetical protein OsI_11065 [Oryza sativa Indica Group]

 Score =  134 bits (338), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 72/194 (37%), Positives = 110/194 (56%), Gaps = 8/194 (4%)

Query: 1   MTNTESNFFIVLCLISSAIRICIITNTVSNFFIVIRLIREGAANRTCENKIVILLREIRC 60
           ++  ES+   +L +   A  + +  +   N F  I L  +G  +        + LR ++ 
Sbjct: 645 VSGIESDALFILLVEKDAAFMRLAEDRFYNRFPCIILTAKGQPDVATR----LFLRRLKV 700

Query: 61  KLKKSVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKL 120
           +LK  VL   D +PYG+ IL+VYM GSKNM+  +  L  P+IKWLG+ PSDL+KY +P+ 
Sbjct: 701 ELKLPVLALVDSDPYGLKILSVYMCGSKNMSYDSANLTTPDIKWLGVRPSDLDKYRVPEQ 760

Query: 121 CRQILSKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLA 180
           CR  ++  DI   K  LE+     FV+ N  W KEL+ M +  +KAEI+AL  + ++YL 
Sbjct: 761 CRLPMTDHDIKVGKELLEED----FVKQNEGWVKELETMLRTRQKAEIQALSSFGFQYLT 816

Query: 181 NKYLPSKFRAEDWL 194
             YLP K + +DW+
Sbjct: 817 EVYLPLKLQQQDWI 830

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|195647934|gb|ACG43435.1| RHL2 [Zea mays]

 Score =  134 bits (337), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 72/194 (37%), Positives = 110/194 (56%), Gaps = 8/194 (4%)

Query: 1   MTNTESNFFIVLCLISSAIRICIITNTVSNFFIVIRLIREGAANRTCENKIVILLREIRC 60
           ++  ES+   +L +   A  + +  +   N F  I L  +G  +        + LR ++ 
Sbjct: 251 VSGIESDALFILLVEKDAAFMRLAEDRFYNRFPCIILTAKGQPDVATR----LFLRRLKV 306

Query: 61  KLKKSVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKL 120
           +LK  VL   D +PYG+ IL+VYM GSKNM+  +  L  P+IKWLG+ PSDL+KY +P+ 
Sbjct: 307 ELKLPVLALVDSDPYGLKILSVYMCGSKNMSYDSANLTTPDIKWLGVRPSDLDKYRVPEQ 366

Query: 121 CRQILSKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLA 180
           CR  ++  DI   K  LE+     FV+ N  W KEL+ M +  +KAEI+AL  + ++YL 
Sbjct: 367 CRLPMTDHDIKVGKELLEED----FVKQNEGWVKELETMLRTKQKAEIQALSSFGFQYLT 422

Query: 181 NKYLPSKFRAEDWL 194
             YLP K + +DW+
Sbjct: 423 EVYLPLKLQEQDWI 436

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|226497286|ref|NP_001141583.1| uncharacterized protein LOC100273699 [Zea mays] gi|194705154|gb|ACF86661.1| unknown [Zea mays] gi|414866232|tpg|DAA44789.1| TPA: RHL2 [Zea mays]

 Score =  134 bits (337), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 72/194 (37%), Positives = 110/194 (56%), Gaps = 8/194 (4%)

Query: 1   MTNTESNFFIVLCLISSAIRICIITNTVSNFFIVIRLIREGAANRTCENKIVILLREIRC 60
           ++  ES+   +L +   A  + +  +   N F  I L  +G  +        + LR ++ 
Sbjct: 251 VSGIESDALFILLVEKDAAFMRLAEDRFYNRFPCIILTAKGQPDVATR----LFLRRLKV 306

Query: 61  KLKKSVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKL 120
           +LK  VL   D +PYG+ IL+VYM GSKNM+  +  L  P+IKWLG+ PSDL+KY +P+ 
Sbjct: 307 ELKLPVLALVDSDPYGLKILSVYMCGSKNMSYDSANLTTPDIKWLGVRPSDLDKYRVPEQ 366

Query: 121 CRQILSKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLA 180
           CR  ++  DI   K  LE+     FV+ N  W KEL+ M +  +KAEI+AL  + ++YL 
Sbjct: 367 CRLPMTDHDIKVGKELLEED----FVKQNEGWVKELETMLRTKQKAEIQALSSFGFQYLT 422

Query: 181 NKYLPSKFRAEDWL 194
             YLP K + +DW+
Sbjct: 423 EVYLPLKLQEQDWI 436

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297600747|ref|NP_001049765.2| Os03g0284800 [Oryza sativa Japonica Group] gi|150371045|dbj|BAF65346.1| topoisomerase Spo11 [Oryza sativa Japonica Group] gi|255674417|dbj|BAF11679.2| Os03g0284800 [Oryza sativa Japonica Group]

 Score =  134 bits (337), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 72/194 (37%), Positives = 110/194 (56%), Gaps = 8/194 (4%)

Query: 1   MTNTESNFFIVLCLISSAIRICIITNTVSNFFIVIRLIREGAANRTCENKIVILLREIRC 60
           ++  ES+   +L +   A  + +  +   N F  I L  +G  +        + LR ++ 
Sbjct: 257 VSGIESDALFILLVEKDAAFMRLAEDRFYNRFPCIILTAKGQPDVATR----LFLRRLKV 312

Query: 61  KLKKSVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKL 120
           +LK  VL   D +PYG+ IL+VYM GSKNM+  +  L  P+IKWLG+ PSDL+KY +P+ 
Sbjct: 313 ELKLPVLALVDSDPYGLKILSVYMCGSKNMSYDSANLTTPDIKWLGVRPSDLDKYRVPEQ 372

Query: 121 CRQILSKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLA 180
           CR  ++  DI   K  LE+     FV+ N  W KEL+ M +  +KAEI+AL  + ++YL 
Sbjct: 373 CRLPMTDHDIKVGKELLEED----FVKQNEGWVKELETMLRTRQKAEIQALSSFGFQYLT 428

Query: 181 NKYLPSKFRAEDWL 194
             YLP K + +DW+
Sbjct: 429 EVYLPLKLQQQDWI 442

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242041321|ref|XP_002468055.1| hypothetical protein SORBIDRAFT_01g038780 [Sorghum bicolor] gi|241921909|gb|EER95053.1| hypothetical protein SORBIDRAFT_01g038780 [Sorghum bicolor]

 Score =  134 bits (336), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 72/194 (37%), Positives = 110/194 (56%), Gaps = 8/194 (4%)

Query: 1   MTNTESNFFIVLCLISSAIRICIITNTVSNFFIVIRLIREGAANRTCENKIVILLREIRC 60
           ++  ES+   +L +   A  + +  +   N F  I L  +G  +        + LR ++ 
Sbjct: 251 VSGIESDALFILLVEKDAAFMRLAEDRFYNRFPCIILTAKGQPDVATR----LFLRRLKV 306

Query: 61  KLKKSVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKL 120
           +LK  VL   D +PYG+ IL+VYM GSKNM+  +  L  P+IKWLG+ PSDL+KY +P+ 
Sbjct: 307 ELKLPVLALVDSDPYGLKILSVYMCGSKNMSYDSANLTTPDIKWLGVRPSDLDKYRVPEQ 366

Query: 121 CRQILSKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLA 180
           CR  ++  DI   K  LE+     FV+ N  W KEL+ M +  +KAEI+AL  + ++YL 
Sbjct: 367 CRLPMTDHDIKVGKELLEED----FVKQNEGWVKELEMMLRTKQKAEIQALSSFGFQYLT 422

Query: 181 NKYLPSKFRAEDWL 194
             YLP K + +DW+
Sbjct: 423 EVYLPLKLQEQDWI 436

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|194697080|gb|ACF82624.1| unknown [Zea mays] gi|414866233|tpg|DAA44790.1| TPA: hypothetical protein ZEAMMB73_994877 [Zea mays]

 Score =  134 bits (336), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 72/194 (37%), Positives = 110/194 (56%), Gaps = 8/194 (4%)

Query: 1   MTNTESNFFIVLCLISSAIRICIITNTVSNFFIVIRLIREGAANRTCENKIVILLREIRC 60
           ++  ES+   +L +   A  + +  +   N F  I L  +G  +        + LR ++ 
Sbjct: 15  VSGIESDALFILLVEKDAAFMRLAEDRFYNRFPCIILTAKGQPDVATR----LFLRRLKV 70

Query: 61  KLKKSVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKL 120
           +LK  VL   D +PYG+ IL+VYM GSKNM+  +  L  P+IKWLG+ PSDL+KY +P+ 
Sbjct: 71  ELKLPVLALVDSDPYGLKILSVYMCGSKNMSYDSANLTTPDIKWLGVRPSDLDKYRVPEQ 130

Query: 121 CRQILSKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLA 180
           CR  ++  DI   K  LE+     FV+ N  W KEL+ M +  +KAEI+AL  + ++YL 
Sbjct: 131 CRLPMTDHDIKVGKELLEED----FVKQNEGWVKELETMLRTKQKAEIQALSSFGFQYLT 186

Query: 181 NKYLPSKFRAEDWL 194
             YLP K + +DW+
Sbjct: 187 EVYLPLKLQEQDWI 200

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|125585844|gb|EAZ26508.1| hypothetical protein OsJ_10402 [Oryza sativa Japonica Group]

 Score =  134 bits (336), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 72/194 (37%), Positives = 110/194 (56%), Gaps = 8/194 (4%)

Query: 1   MTNTESNFFIVLCLISSAIRICIITNTVSNFFIVIRLIREGAANRTCENKIVILLREIRC 60
           ++  ES+   +L +   A  + +  +   N F  I L  +G  +        + LR ++ 
Sbjct: 341 VSGIESDALFILLVEKDAAFMRLAEDRFYNRFPCIILTAKGQPDVATR----LFLRRLKV 396

Query: 61  KLKKSVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKL 120
           +LK  VL   D +PYG+ IL+VYM GSKNM+  +  L  P+IKWLG+ PSDL+KY +P+ 
Sbjct: 397 ELKLPVLALVDSDPYGLKILSVYMCGSKNMSYDSANLTTPDIKWLGVRPSDLDKYRVPEQ 456

Query: 121 CRQILSKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLA 180
           CR  ++  DI   K  LE+     FV+ N  W KEL+ M +  +KAEI+AL  + ++YL 
Sbjct: 457 CRLPMTDHDIKVGKELLEED----FVKQNEGWVKELETMLRTRQKAEIQALSSFGFQYLT 512

Query: 181 NKYLPSKFRAEDWL 194
             YLP K + +DW+
Sbjct: 513 EVYLPLKLQQQDWI 526

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

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	194
TAIR|locus:2151221	427	RHL2 "ROOT HAIRLESS 2" [Arabid	0.711	0.323	0.450	1.2e-28
TAIR|locus:2090044	362	ATSPO11-1 [Arabidopsis thalian	0.690	0.370	0.416	3.9e-21
MGI|MGI:1349669	396	Spo11 "SPO11 meiotic protein c	0.618	0.303	0.395	2.6e-20
RGD|1306454	371	Spo11 "SPO11 meiotic protein c	0.618	0.323	0.379	1.9e-19
UNIPROTKB|Q5TCH7	354	SPO11 "Meiotic recombination p	0.618	0.338	0.387	9e-19
UNIPROTKB|Q9Y5K1	396	SPO11 "Meiotic recombination p	0.618	0.303	0.387	1.7e-18
UNIPROTKB|A5GFN4	357	SPO11 "SPO11 meiotic protein c	0.618	0.336	0.387	2.1e-18
UNIPROTKB|A5GFN5	395	SPO11 "Uncharacterized protein	0.618	0.303	0.387	3.7e-18
UNIPROTKB|E1BMM6	395	SPO11 "Uncharacterized protein	0.618	0.303	0.379	4.8e-18
UNIPROTKB|E2RT15	396	SPO11 "Uncharacterized protein	0.644	0.315	0.372	8.1e-18

TAIR|locus:2151221 RHL2 "ROOT HAIRLESS 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 319 (117.4 bits), Expect = 1.2e-28, P = 1.2e-28
 Identities = 64/142 (45%), Positives = 92/142 (64%)

Query:    53 ILLREIRCKLKKSVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDL 112
             + LR+++ +LK  VL   D +PYG+ IL+VY  GSKNM+  +  L  P+IKWLG+ PSDL
Sbjct:   290 LFLRKMKMELKLPVLALVDSDPYGLKILSVYGCGSKNMSYDSANLTTPDIKWLGIRPSDL 349

Query:   113 EKYNIPKLCRQILSKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALD 172
             +KY IP+ CR  +++ DI   K  LE+     FV+ N  W +EL  M K  +KAEI+AL 
Sbjct:   350 DKYKIPEQCRLPMTEQDIKTGKDMLEED----FVKKNPGWVEELNLMVKTKQKAEIQALS 405

Query:   173 MYEYKYLANKYLPSKFRAEDWL 194
              + ++YL+  YLP K + +DWL
Sbjct:   406 SFGFQYLSEVYLPLKLQQQDWL 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

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

 Score = 248 (92.4 bits), Expect = 3.9e-21, P = 3.9e-21
 Identities = 57/137 (41%), Positives = 75/137 (54%)

Query:    55 LREIRCKLKKSVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEK 114
             LR +  KL   V    DC+PYG  IL  Y FGS  MA     L  P++KWLG FPSD E 
Sbjct:   225 LRLLMEKLHLPVHCLVDCDPYGFEILATYRFGSMQMAYDIESLRAPDMKWLGAFPSDSEV 284

Query:   115 YNIPKLCRQILSKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMY 174
             Y++PK C   L+++D  + +  L +  L    R    W  EL+ M K G K EIEAL ++
Sbjct:   285 YSVPKQCLLPLTEEDKKRTEAMLLRCYLK---REMPQWRLELETMLKRGVKFEIEALSVH 341

Query:   175 EYKYLANKYLPSKFRAE 191
                +L+  Y+PSK R E
Sbjct:   342 SLSFLSEVYIPSKIRRE 358

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

MGI|MGI:1349669 Spo11 "SPO11 meiotic protein covalently bound to DSB homolog (S. cerevisiae)" [Mus musculus (taxid:10090)]

 Score = 243 (90.6 bits), Expect = 2.6e-20, P = 2.6e-20
 Identities = 49/124 (39%), Positives = 74/124 (59%)

Query:    71 DCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDI 130
             D +PYGI I+ +Y +GS +M+     L +P I+WLGL PSD+++ NIPK     L+K D 
Sbjct:   277 DADPYGIEIMCIYKYGSMSMSFEAHNLTIPTIRWLGLLPSDIQRLNIPKDSLIPLTKHDQ 336

Query:   131 SKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYLPSKFRA 190
              KL + L++     ++     W+KEL+ M+    KAEI+AL +    YL+  YLP+K R 
Sbjct:   337 MKLDSILKR----PYITYQPLWKKELEMMADSKMKAEIQALTLLSSDYLSRVYLPNKLRF 392

Query:   191 EDWL 194
               W+
Sbjct:   393 GGWI 396

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

GO:0001541 "ovarian follicle development" evidence=IMP

GO:0003677 "DNA binding" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

GO:0006259 "DNA metabolic process" evidence=IEA

GO:0007126 "meiosis" evidence=IEA

GO:0007129 "synapsis" evidence=IMP

GO:0007131 "reciprocal meiotic recombination" evidence=IMP

GO:0007141 "male meiosis I" evidence=IMP

GO:0007286 "spermatid development" evidence=IMP

GO:0016787 "hydrolase activity" evidence=IEA

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

RGD|1306454 Spo11 "SPO11 meiotic protein covalently bound to DSB homolog (S. cerevisiae)" [Rattus norvegicus (taxid:10116)]

 Score = 234 (87.4 bits), Expect = 1.9e-19, P = 1.9e-19
 Identities = 47/124 (37%), Positives = 73/124 (58%)

Query:    71 DCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDI 130
             D +PYGI I+ +Y +GS +M+     L VP I+WLGL PSD+++ NIPK     L++ D 
Sbjct:   252 DADPYGIEIMCIYKYGSMSMSFEAHNLTVPTIRWLGLLPSDIKRLNIPKDSLIPLTRRDQ 311

Query:   131 SKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYLPSKFRA 190
              KL + L +     ++  +  W+KE++ ++    KAEI+AL      YL+  YLP+K R 
Sbjct:   312 MKLDSILRR----PYITYHPFWKKEMEMLADSKTKAEIQALSFLSSDYLSRVYLPNKLRF 367

Query:   191 EDWL 194
               W+
Sbjct:   368 GGWI 371

GO:0000238 "zygotene" evidence=ISO

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

GO:0001541 "ovarian follicle development" evidence=ISO

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;ISO

GO:0007141 "male meiosis I" evidence=ISO

GO:0007286 "spermatid development" evidence=ISO

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

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

 Score = 227 (85.0 bits), Expect = 9.0e-19, P = 9.0e-19
 Identities = 48/124 (38%), Positives = 71/124 (57%)

Query:    71 DCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDI 130
             D +P+GI I+ +Y +GS +M+     L VP I+WLGL PSDL++ N+PK     L+K D 
Sbjct:   235 DADPHGIEIMCIYKYGSMSMSFEAHHLTVPAIRWLGLLPSDLKRLNVPKDSLIPLTKRDQ 294

Query:   131 SKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYLPSKFRA 190
              KL + L +     +V     W KE++ M+    KAEI+AL      YL+  YLP+K + 
Sbjct:   295 MKLDSILRR----PYVTCQPFWRKEMEIMADSKMKAEIQALTFLSSDYLSRVYLPNKLKF 350

Query:   191 EDWL 194
               W+
Sbjct:   351 GGWI 354

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 = 227 (85.0 bits), Expect = 1.7e-18, P = 1.7e-18
 Identities = 48/124 (38%), Positives = 71/124 (57%)

Query:    71 DCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDI 130
             D +P+GI I+ +Y +GS +M+     L VP I+WLGL PSDL++ N+PK     L+K D 
Sbjct:   277 DADPHGIEIMCIYKYGSMSMSFEAHHLTVPAIRWLGLLPSDLKRLNVPKDSLIPLTKRDQ 336

Query:   131 SKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYLPSKFRA 190
              KL + L +     +V     W KE++ M+    KAEI+AL      YL+  YLP+K + 
Sbjct:   337 MKLDSILRR----PYVTCQPFWRKEMEIMADSKMKAEIQALTFLSSDYLSRVYLPNKLKF 392

Query:   191 EDWL 194
               W+
Sbjct:   393 GGWI 396

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

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

 Score = 224 (83.9 bits), Expect = 2.1e-18, P = 2.1e-18
 Identities = 48/124 (38%), Positives = 71/124 (57%)

Query:    71 DCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDI 130
             D +P+GI I+ +Y +GS  M+     L VP I+WLGL PSD+++ NIPK     L+K D 
Sbjct:   238 DADPHGIEIMCIYKYGSMAMSFEAHNLTVPAIRWLGLLPSDIKRLNIPKGTLIPLTKRDQ 297

Query:   131 SKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYLPSKFRA 190
              KL + L++     +V     W KE++ M+    KAEI+AL      YL+  YLP+K + 
Sbjct:   298 MKLDSILKR----PYVACQPFWRKEMEIMADSKMKAEIQALTFLSSDYLSRVYLPNKLKF 353

Query:   191 EDWL 194
               W+
Sbjct:   354 GGWI 357

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 = 224 (83.9 bits), Expect = 3.7e-18, P = 3.7e-18
 Identities = 48/124 (38%), Positives = 71/124 (57%)

Query:    71 DCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDI 130
             D +P+GI I+ +Y +GS  M+     L VP I+WLGL PSD+++ NIPK     L+K D 
Sbjct:   276 DADPHGIEIMCIYKYGSMAMSFEAHNLTVPAIRWLGLLPSDIKRLNIPKGTLIPLTKRDQ 335

Query:   131 SKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYLPSKFRA 190
              KL + L++     +V     W KE++ M+    KAEI+AL      YL+  YLP+K + 
Sbjct:   336 MKLDSILKR----PYVACQPFWRKEMEIMADSKMKAEIQALTFLSSDYLSRVYLPNKLKF 391

Query:   191 EDWL 194
               W+
Sbjct:   392 GGWI 395

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

 Score = 223 (83.6 bits), Expect = 4.8e-18, P = 4.8e-18
 Identities = 47/124 (37%), Positives = 71/124 (57%)

Query:    71 DCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDI 130
             D +P+GI I+ +Y +GS  M+     L VP I+WLGL PSD+++ NIPK     L+K D 
Sbjct:   276 DADPHGIEIMCIYKYGSMAMSFEAHNLTVPAIRWLGLLPSDIKRLNIPKGTLIPLTKRDQ 335

Query:   131 SKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYLPSKFRA 190
              KL + L++     ++     W KE++ M+    KAEI+AL      YL+  YLP+K + 
Sbjct:   336 MKLDSILKR----PYITCQPFWRKEMEIMADSKMKAEIQALTFLSSDYLSRVYLPNKLKF 391

Query:   191 EDWL 194
               W+
Sbjct:   392 GGWI 395

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

 Score = 221 (82.9 bits), Expect = 8.1e-18, P = 8.1e-18
 Identities = 48/129 (37%), Positives = 72/129 (55%)

Query:    66 VLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQIL 125
             V    D +P+GI I+ +Y +GS  M+     L VP I+WLGL PSD+++ NIP+     L
Sbjct:   272 VFALVDADPHGIEIMCIYKYGSMAMSFEAHNLTVPAIRWLGLLPSDIKRLNIPRDTLIPL 331

Query:   126 SKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYLP 185
             +K D  KL + L++     +V     W KE++ M+    KAEI+AL      YL+  YLP
Sbjct:   332 TKRDQMKLDSVLKR----PYVTCQPFWRKEMEIMADSKMKAEIQALTFLSSDYLSRVYLP 387

Query:   186 SKFRAEDWL 194
             +K +   W+
Sbjct:   388 NKLKFGGWI 396

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	JGI126981	hypothetical protein (413 aa)
		(Physcomitrella patens)
Predicted Functional Partners:
	JGI146513	hypothetical protein (677 aa)	•		•		•		•		0.983
	JGI135715	hypothetical protein (813 aa)	•						•		0.840
	JGI145288	hypothetical protein (216 aa)	•		•	•					0.674
	JGI142435	hypothetical protein (448 aa)	•								0.646
	JGI228008	hypothetical protein (869 aa)							•		0.630
	JGI155610	hypothetical protein (915 aa)							•		0.612
	JGI162696	hypothetical protein; This protein is an auxiliary protein of DNA polymerase delta and is invol [...] (263 aa)							•		0.587
	JGI200726	hypothetical protein (349 aa)					•		•		0.538
	JGI30474	hypothetical protein (493 aa)					•	•	•		0.524
	JGI138531	hypothetical protein (312 aa)							•		0.510

---

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	194
cd00223	160	cd00223, TOPRIM_TopoIIB_SPO, TOPRIM_TopoIIB_SPO: t	1e-29
COG1697	356	COG1697, COG1697, DNA topoisomerase VI, subunit A	1e-22
PRK04342	367	PRK04342, PRK04342, DNA topoisomerase VI subunit A	3e-22
PLN00060	384	PLN00060, PLN00060, meiotic recombination protein	1e-11

>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

 Score =  106 bits (267), Expect = 1e-29
 Identities = 57/168 (33%), Positives = 84/168 (50%), Gaps = 27/168 (16%)

Query: 30  NFFIVI-------RLIREGAANRTCENKIVI------------LLREIRCKLKKSVLGSF 70
           +F +V+       RLI EG   R   N I+I             LR +  +L   V    
Sbjct: 1   DFVLVVEKEAVFQRLIEEGFHER--NNCILITGKGYPDRATRRFLRRLHEELDLPVYILV 58

Query: 71  DCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDI 130
           D +PYGI IL  Y +GS  +A  +  LA P+++WLGL PSD+ +  +P L    LS+ D+
Sbjct: 59  DGDPYGISILLTYKYGSIKLAYESESLATPDLRWLGLRPSDIIR--LPDLPLLPLSERDL 116

Query: 131 SKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKY 178
            + K+ L +       +    W++ELQ M K G+KAEIEAL     ++
Sbjct: 117 KRAKSLLRRP----RFKELPEWKRELQLMLKLGKKAEIEALASCGLEF 160

This subgroup contains proteins similar to Sulfolobus shibatae topoisomerase VI (TopoVI) and Saccharomyces cerevisiae meiotic recombination factor: Spo11. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. TopoVI enzymes are heterotetramers found in archaea and plants. Spo11 plays a role in generating the double strand breaks that initiate homologous recombination during meiosis. S. shibatae TopoVI relaxes both positive and negative supercoils, and in addition has a strong decatenase activity. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD. For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. Length = 160

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

 Score = 92.8 bits (231), Expect = 1e-22
 Identities = 53/169 (31%), Positives = 84/169 (49%), Gaps = 21/169 (12%)

Query: 36  RLIREGAANRTCENKIVI------------LLREIRCKLKKSVLGSFDCNPYGIHILTVY 83
           RL+ EG   +  EN I++             L+ +  +L   V    D +PYG +I +VY
Sbjct: 197 RLVEEGFWEK--ENAILVTLKGQPDRATRRFLKRLNEELDLPVYVFTDGDPYGWYIYSVY 254

Query: 84  MFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDISKLKTFLEKGDLV 143
            +GS  +A  + RLA P+ K+LG+   D+ +YN+P+     L   DI +LK  L      
Sbjct: 255 KYGSIKLAHESERLATPDAKFLGVTMQDIVEYNLPQ--TDKLKDRDIKRLKELLR---DP 309

Query: 144 AFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYLPSKFRAED 192
            F +    W++EL+ + K G+KAE +AL     +++A  YLP K     
Sbjct: 310 RFQKE--FWKEELKLLLKIGKKAEQQALASKGLEFVAKTYLPEKIEELK 356

Length = 356

>gnl|CDD|235287 PRK04342, PRK04342, DNA topoisomerase VI subunit A; Provisional

 Score = 91.9 bits (229), Expect = 3e-22
 Identities = 51/171 (29%), Positives = 82/171 (47%), Gaps = 20/171 (11%)

Query: 36  RLIREGAANRTCENKIVI------------LLREIRCKLKKSVLGSFDCNPYGIHILTVY 83
           RL+ EG   +   N I++             ++ +  +L   V    D +P+G +I +V 
Sbjct: 204 RLVEEGFWKK--YNAILVHLKGQPARATRRFIKRLNEELGLPVYVFTDGDPWGYYIYSVV 261

Query: 84  MFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDISKLKTFLEKGDLV 143
            +GS  +A  + RLA P+ K++G+ PSD+ +Y    L    L   DI + K  L      
Sbjct: 262 KYGSIKLAHLSERLATPDAKFIGVTPSDIVEY-ERDLPTIKLKDSDIKRAKELLNYPW-- 318

Query: 144 AFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYLPSKFRAEDWL 194
            F      W+KE+    K G+KAE +AL     K++ ++YLP K   +DWL
Sbjct: 319 -FQTDF--WQKEINLFLKIGKKAEQQALASKGLKFVTDEYLPEKLEEKDWL 366

Length = 367

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

 Score = 62.2 bits (151), Expect = 1e-11
 Identities = 45/122 (36%), Positives = 61/122 (50%), Gaps = 10/122 (8%)

Query: 66  VLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQIL 125
           +L   D NP G+ IL  Y FGS  M     R A  N+KWLGL   DL+   IP      L
Sbjct: 266 ILALVDWNPAGLAILCTYKFGSIGMGLEAYRYAC-NVKWLGLRGDDLQL--IPPEAFVEL 322

Query: 126 SKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYLP 185
              D+   K+ L       F+++   + +EL  M + G++AEIEAL  + Y YL  KY+ 
Sbjct: 323 KPRDLQIAKSLLSS----KFLQNR--YREELTLMVQTGKRAEIEALYSHGYDYLG-KYVA 375

Query: 186 SK 187
            K
Sbjct: 376 RK 377

Length = 384

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	194
PLN00060	384	meiotic recombination protein SPO11-2; Provisional	100.0
KOG2795	372	consensus Catalytic subunit of the meiotic double	100.0
PRK04342	367	DNA topoisomerase VI subunit A; Provisional	100.0
COG1697	356	DNA topoisomerase VI, subunit A [DNA replication,	100.0
cd00223	160	TOPRIM_TopoIIB_SPO TOPRIM_TopoIIB_SPO: topoisomera	100.0
PF09983	181	DUF2220: Uncharacterized protein conserved in bact	98.56
PF09664	152	DUF2399: Protein of unknown function C-terminus (D	98.13
TIGR02679	385	conserved hypothetical protein TIGR02679. Members	93.79
cd00188	83	TOPRIM Topoisomerase-primase domain. This is a nuc	93.1
COG3593	581	Predicted ATP-dependent endonuclease of the OLD fa	81.63

>PLN00060 meiotic recombination protein SPO11-2; Provisional

Probab=100.00  E-value=4.8e-54  Score=386.01  Aligned_cols=179  Identities=30%  Similarity=0.452  Sum_probs=163.7

Q ss_pred             ccceEEeeecc------cccccccee--eeeccccEEEEEccchhhhhhchhHH-------------------HHHHHHH
Q 029346            6 SNFFIVLCLIS------SAIRICIIT--NTVSNFFIVIRLIREGAANRTCENKI-------------------VILLREI   58 (194)
Q Consensus         6 ~~~~~~~c~ip------~~~~~~~i~--~i~~~a~~VLVVEKdavF~~L~~~~f-------------------R~fl~~L   58 (194)
                      .|-..++|..+      +|.+++.++  ++.++|+|||||||||||+||++++|                   |+||++|
T Consensus       178 ~~~~~idcs~~g~~G~~Ip~~~~~i~~~~i~s~a~~VLVVEKeavF~rL~e~~~~~~~~cILITgKGyPD~aTR~fL~~L  257 (384)
T PLN00060        178 PNEEPVDCSILGISGHAITGDLNLLSNLILSSDARYIIVVEKDAIFQRLAEDRFFNHIPCILITAKGYPDLATRFILHRL  257 (384)
T ss_pred             cCCcEEEeeccCCCceeCCCcHHHhhhcccccCccEEEEEecHHHHHHHHHhhhhhhCCEEEEecCCCCCHHHHHHHHHH
Confidence            34567888753      455666555  46799999999999999999999987                   9999999


Q ss_pred             Hhhc-CCcEEEEecCCcchhHHHHHHhhCCcccccccCCcCCCCeeEeeCCccccccccCCccccccCCHHHHHHHHHHH
Q 029346           59 RCKL-KKSVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDISKLKTFL  137 (194)
Q Consensus        59 ~~~~-~lpi~~L~D~DP~Gi~I~~tYk~GS~~~~~~~~~~~~p~l~wlGv~~sdl~~~~~~~~~~~~Lt~rD~~~~~~ll  137 (194)
                      ++++ ++|+|+|||+||||++|++||||||.+++|+++.++|| ++|+|++++|+..  +|.++++|||+||++++++||
T Consensus       258 ~~~~p~lPv~~LvD~DP~Gi~I~~tYkyGS~~~a~es~~la~~-i~WLGl~~sDi~~--l~~~~~i~Lt~rD~~~~~~lL  334 (384)
T PLN00060        258 SQTFPNLPILALVDWNPAGLAILCTYKFGSIGMGLEAYRYACN-VKWLGLRGDDLQL--IPPEAFVELKPRDLQIAKSLL  334 (384)
T ss_pred             HHhcCCCCEEEEECCCcchHHHHHHhhcCchhhhhcccccccC-CeEecCCHHHHhc--CCHhhcCCCCHHHHHHHHHHh
Confidence            9996 89999999999999999999999999999999999986 9999999999984  888899999999999999999


Q ss_pred             hcCCcchhccCcHHHHHHHHHHHHhCCeeeEeeeccccccchhhchhHhhhccCCCC
Q 029346          138 EKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYLPSKFRAEDWL  194 (194)
Q Consensus       138 ~~~~~~~~~~~~~~~~~EL~~ml~~~~KaEieal~~~g~~~l~~~Yl~~Ki~~~~~~  194 (194)
                      ++    |+++  ..|++||++|++.++|||||||++.|.+|+++ |||+||.++||+
T Consensus       335 ~~----~~~~--~~w~~EL~~Ml~~~~KaEiEAL~~~g~~fl~~-Ylp~Ki~~~~~i  384 (384)
T PLN00060        335 SS----KFLQ--NRYREELTLMVQTGKRAEIEALYSHGYDYLGK-YVARKIVQGDYI  384 (384)
T ss_pred             hC----hhHH--HHHHHHHHHHHHhCcchhhHhHHhcChHHHHH-HHHHHHhcCCcC
Confidence            99    7885  39999999999999999999999999999995 999999999997

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

Probab=100.00  E-value=2.4e-54  Score=381.39  Aligned_cols=186  Identities=35%  Similarity=0.545  Sum_probs=178.8

Q ss_pred             cccceEEeee------ccccccccceeeeeccccEEEEEccchhhhhhchhHH--------------------HHHHHHH
Q 029346            5 ESNFFIVLCL------ISSAIRICIITNTVSNFFIVIRLIREGAANRTCENKI--------------------VILLREI   58 (194)
Q Consensus         5 ~~~~~~~~c~------ip~~~~~~~i~~i~~~a~~VLVVEKdavF~~L~~~~f--------------------R~fl~~L   58 (194)
                      |-|-..++|+      -|+|+|++.|..+.++|+||||||||||||||+++.|                    |.|||+|
T Consensus       161 ~~ng~~id~~~~~~~~~~lp~d~~~i~~i~tdA~~IlIVEKeavFqrL~~d~~~~~~~~~ilITgKGyPD~~TR~fLkkL  240 (372)
T KOG2795|consen  161 EENGDVIDCTESGGGPKALPPDIDDISNITTDAKFILIVEKEAVFQRLAEDNFFNTFNRCILITGKGYPDIATRLFLKKL  240 (372)
T ss_pred             EcCCcEEEeccCCCCCccCCCCHHHHhhhhccceEEEEEehHHHHHHHHHHHHHhhcCCeEEEecCCCCcHHHHHHHHHH
Confidence            5577889999      7899999999999999999999999999999999977                    9999999


Q ss_pred             HhhcCCcEEEEecCCcchhHHHHHHhhCCcccccccCCcCCCCeeEeeCCccccccccCCccccccCCHHHHHHHHHHHh
Q 029346           59 RCKLKKSVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDISKLKTFLE  138 (194)
Q Consensus        59 ~~~~~lpi~~L~D~DP~Gi~I~~tYk~GS~~~~~~~~~~~~p~l~wlGv~~sdl~~~~~~~~~~~~Lt~rD~~~~~~ll~  138 (194)
                      .+++++|++||||||||||+|+++|||||.+|+|+++++++|+++|+|++|+|+..++.|+++++||+++|.+++++||+
T Consensus       241 ~~~~~lpv~~LvDaDP~Gi~I~~~Yk~GS~~ms~e~~~~~~p~I~wiGl~psD~~~~n~~k~~~lpL~~~D~k~i~~lL~  320 (372)
T KOG2795|consen  241 EEKLKLPVYGLVDADPYGIEILLTYKYGSKSMSYESHGLTVPTIRWIGLLPSDLEVKNIPKDQLLPLNKRDIKKIKDLLA  320 (372)
T ss_pred             HHHhCCCEEEEeecCCcceEEEEEeeeCccccccccccccCCcceEEeechhhhhhcCCchheeecccHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCcchhccCcHHHHHHHHHHHHhCCeeeEeeeccccccchhhchhHhhhccCCCC
Q 029346          139 KGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYLPSKFRAEDWL  194 (194)
Q Consensus       139 ~~~~~~~~~~~~~~~~EL~~ml~~~~KaEieal~~~g~~~l~~~Yl~~Ki~~~~~~  194 (194)
                      +    ..++.++.|++||++|++.++||||||+..+|.+|+.+.|+|.|+..++|+
T Consensus       321 ~----~~l~~~p~~r~el~~ml~~~~KaEieal~~~~~~~~~~~yia~k~~~~~~~  372 (372)
T KOG2795|consen  321 R----LILQKEPVVREELERMLKNKVKAEIEALSFFGSDYLSRVYIARKLERISSL  372 (372)
T ss_pred             h----hhcccChhHHHHHHHHHhcchhhhhhhhhhcchHHHhhhhhhHHHhhcccC
Confidence            9    577778899999999999999999999999999999999999999999985

>PRK04342 DNA topoisomerase VI subunit A; Provisional

Probab=100.00  E-value=8.4e-52  Score=370.92  Aligned_cols=179  Identities=28%  Similarity=0.443  Sum_probs=168.2

Q ss_pred             EEeeec------cccccccceeeeeccccEEEEEccchhhhhhchhHH-------------------HHHHHHHHhhcCC
Q 029346           10 IVLCLI------SSAIRICIITNTVSNFFIVIRLIREGAANRTCENKI-------------------VILLREIRCKLKK   64 (194)
Q Consensus        10 ~~~c~i------p~~~~~~~i~~i~~~a~~VLVVEKdavF~~L~~~~f-------------------R~fl~~L~~~~~l   64 (194)
                      .++|.-      .+|.+++.|+++.++|++||||||+|+|++|++++|                   |+||++|++++++
T Consensus       163 ~id~~~~g~~~~~ip~~~~~i~~i~~~a~~VLvVEK~avF~rL~~~~~~~~~~~IlItgkG~Pd~~TR~fl~~L~~~~~l  242 (367)
T PRK04342        163 EIDCSKLGEGGYSIPPNVDNIEFVDVDADFVLAVEKGGMFQRLVEEGFWKKYNAILVHLKGQPARATRRFIKRLNEELGL  242 (367)
T ss_pred             EEEEeccCCCceeCCCchhhheeeccCCCEEEEEechHHHHHHHHhCcccccCEEEEECCCCCCHHHHHHHHHHHHhcCC
Confidence            567754      556678889989999999999999999999999866                   9999999999999


Q ss_pred             cEEEEecCCcchhHHHHHHhhCCcccccccCCcCCCCeeEeeCCccccccccCCccccccCCHHHHHHHHHHHhcCCcch
Q 029346           65 SVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDISKLKTFLEKGDLVA  144 (194)
Q Consensus        65 pi~~L~D~DP~Gi~I~~tYk~GS~~~~~~~~~~~~p~l~wlGv~~sdl~~~~~~~~~~~~Lt~rD~~~~~~ll~~~~~~~  144 (194)
                      |+|+|+|+||||++|+++|++||.+++|+++.++||+++|+|++++|+.++ +|..+.+|||++|++++++||++    |
T Consensus       243 pv~~l~D~DP~G~~I~~tyk~GS~~~a~~s~~l~~P~~kwlGl~~sDi~~~-~~~~~~~~Lt~~D~~~l~~lL~~----~  317 (367)
T PRK04342        243 PVYVFTDGDPWGYYIYSVVKYGSIKLAHLSERLATPDAKFIGVTPSDIVEY-ERDLPTIKLKDSDIKRAKELLNY----P  317 (367)
T ss_pred             CEEEEECCCccHHHHHHHHHhCchhhhhhhhhccCCCCEEecCcHHHHHhh-ccccccCCCCHHHHHHHHHHhcC----c
Confidence            999999999999999999999999999999999999999999999999987 67788999999999999999999    7


Q ss_pred             hccCcHHHHHHHHHHHHhCCeeeEeeeccccccchhhchhHhhhccCCCC
Q 029346          145 FVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYLPSKFRAEDWL  194 (194)
Q Consensus       145 ~~~~~~~~~~EL~~ml~~~~KaEieal~~~g~~~l~~~Yl~~Ki~~~~~~  194 (194)
                      +++ .++|++||++|++.|+|||||||++.|.+|++++|||+||.+++|+
T Consensus       318 ~~~-~~~w~~El~~ml~~~~KaEiEal~~~~~~~~~~~Ylp~Ki~~~~~i  366 (367)
T PRK04342        318 WFQ-TDFWQKEINLFLKIGKKAEQQALASKGLKFVTDEYLPEKLEEKDWL  366 (367)
T ss_pred             ccc-CHHHHHHHHHHHHhCCceeeehhhhcChhhhHHHHHHHHHhcCCCC
Confidence            774 6899999999999999999999999999999999999999999997

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

Probab=100.00  E-value=7e-49  Score=345.06  Aligned_cols=172  Identities=30%  Similarity=0.460  Sum_probs=163.5

Q ss_pred             eeeccccccccceeeeeccccEEEEEccchhhhhhchhHH-------------------HHHHHHHHhhcCCcEEEEecC
Q 029346           12 LCLISSAIRICIITNTVSNFFIVIRLIREGAANRTCENKI-------------------VILLREIRCKLKKSVLGSFDC   72 (194)
Q Consensus        12 ~c~ip~~~~~~~i~~i~~~a~~VLVVEKdavF~~L~~~~f-------------------R~fl~~L~~~~~lpi~~L~D~   72 (194)
                      +|+||  ++++.|+++.++|+|||||||+||||||++++|                   |+||++|.+++++||++|+|+
T Consensus       166 ~y~Ip--~~~d~I~f~~~da~~VlvVEk~avf~rLv~e~~~~k~nailVt~KGqP~raTRrflkrL~eel~lpv~vftDg  243 (356)
T COG1697         166 GYLIP--PDVDVIEFVDTDAKFVLVVEKDAVFQRLVEEGFWEKENAILVTLKGQPDRATRRFLKRLNEELDLPVYVFTDG  243 (356)
T ss_pred             CCcCC--CChhheeeccccceEEEEEechHHHHHHHHhhhhhhcCeEEEecCCCccHHHHHHHHHHHHHhCCCEEEEecC
Confidence            46776  789999999999999999999999999999988                   999999999999999999999


Q ss_pred             CcchhHHHHHHhhCCcccccccCCcCCCCeeEeeCCccccccccCCccccccCCHHHHHHHHHHHhcCCcchhccCcHHH
Q 029346           73 NPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDISKLKTFLEKGDLVAFVRSNASW  152 (194)
Q Consensus        73 DP~Gi~I~~tYk~GS~~~~~~~~~~~~p~l~wlGv~~sdl~~~~~~~~~~~~Lt~rD~~~~~~ll~~~~~~~~~~~~~~~  152 (194)
                      ||||++||++|+|||.+.||+++.+++|.++++||+++|+..++.|  +..+|+++|+++++++++.    |+++.+. |
T Consensus       244 DPyG~~Iy~~~k~GS~k~ah~se~latp~akflGv~~~DI~~ynl~--~t~~l~~~Dik~lk~ll~~----~~f~~~~-W  316 (356)
T COG1697         244 DPYGWYIYSVYKYGSIKLAHESERLATPDAKFLGVTMQDIVEYNLP--QTDKLKDRDIKRLKELLRD----PRFQKEF-W  316 (356)
T ss_pred             CCCEEEEEEEEEecchhhhhcchhhcCCcceeeeccHHHHhhcccc--ccccchhhhHHHHHHHhcc----ccccchh-H
Confidence            9999999999999999999999999999999999999999999987  5669999999999999999    8997555 9


Q ss_pred             HHHHHHHHHhCCeeeEeeeccccccchhhchhHhhhccCC
Q 029346          153 EKELQKMSKEGEKAEIEALDMYEYKYLANKYLPSKFRAED  192 (194)
Q Consensus       153 ~~EL~~ml~~~~KaEieal~~~g~~~l~~~Yl~~Ki~~~~  192 (194)
                      ++||+.|++.++||||||++++|.+|++..|||+||.+.+
T Consensus       317 ~~el~~~l~i~kK~E~qAla~kgl~~v~~~ylpeki~e~~  356 (356)
T COG1697         317 KEELKLLLKIGKKAEQQALASKGLEFVAKTYLPEKIEELK  356 (356)
T ss_pred             HHHHHHHHHHhHHHHHHHHHhcChHHhHHhhhHHHHhccC
Confidence            9999999999999999999999999999999999998753

>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

Probab=100.00  E-value=1.2e-40  Score=267.37  Aligned_cols=141  Identities=35%  Similarity=0.560  Sum_probs=129.9

Q ss_pred             cEEEEEccchhhhhhchhHH-------------------HHHHHHHHhhcCCcEEEEecCCcchhHHHHHHhhCCccccc
Q 029346           32 FIVIRLIREGAANRTCENKI-------------------VILLREIRCKLKKSVLGSFDCNPYGIHILTVYMFGSKNMAG   92 (194)
Q Consensus        32 ~~VLVVEKdavF~~L~~~~f-------------------R~fl~~L~~~~~lpi~~L~D~DP~Gi~I~~tYk~GS~~~~~   92 (194)
                      ++||||||+|||++|+++++                   |.||++|+++.++|+|+++|+||||++|+++|++||.+++|
T Consensus         1 ~~ilvVEk~avf~~L~~~~~~~~~~~ilit~kG~P~~~tr~~l~~L~~~~~~~~~~l~D~DP~Gi~I~~~y~~gs~~~~~   80 (160)
T cd00223           1 DFVLVVEKEAVFQRLIEEGFHERNNCILITGKGYPDRATRRFLRRLHEELDLPVYILVDGDPYGISILLTYKYGSIKLAY   80 (160)
T ss_pred             CEEEEEecHHHHHHHHHcCccccCCEEEEEcCCcCCHHHHHHHHHHHHhhCCCEEEEECCCcchhhhhHHHHhCcccccc
Confidence            58999999999999999754                   99999999988999999999999999999999999999999


Q ss_pred             ccCCcCCCCeeEeeCCccccccccCCccccccCCHHHHHHHHHHHhcCCcchhccCcHHHHHHHHHHHHhCCeeeEeeec
Q 029346           93 RNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALD  172 (194)
Q Consensus        93 ~~~~~~~p~l~wlGv~~sdl~~~~~~~~~~~~Lt~rD~~~~~~ll~~~~~~~~~~~~~~~~~EL~~ml~~~~KaEieal~  172 (194)
                      +...+++|+++|+|++++|+.+  ++..+.+|||++|++++++++++    +....+++|++|+++|++.|+|+||||+.
T Consensus        81 ~~~~~~~~~l~~~G~~~~d~~~--~~~~~~~~Ls~~d~~~l~~ll~~----~~~~~~~~~~~el~~ml~~~~K~E~Eal~  154 (160)
T cd00223          81 ESESLATPDLRWLGLRPSDIIR--LPDLPLLPLSERDLKRAKSLLRR----PRFKELPEWKRELQLMLKLGKKAEIEALA  154 (160)
T ss_pred             ccccccCCCcEEccCCHHHHhh--ccccccCCCCHHHHHHHHHHHhc----cccccCHHHHHHHHHHHHhCCeeeehhHh
Confidence            9999999999999999999975  45678899999999999999999    45445789999999999999999999999


Q ss_pred             cccccc
Q 029346          173 MYEYKY  178 (194)
Q Consensus       173 ~~g~~~  178 (194)
                      +.|.+|
T Consensus       155 ~~~~~~  160 (160)
T cd00223         155 SCGLEF  160 (160)
T ss_pred             hcCCCC
Confidence            887653

This subgroup contains proteins similar to Sulfolobus shibatae topoisomerase VI (TopoVI) and Saccharomyces cerevisiae meiotic recombination factor: Spo11. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. TopoVI enzymes are heterotetramers found in archaea and plants. Spo11 plays a role in generating the double strand breaks that initiate homologous recombination during meiosis. S. shibatae TopoVI relaxes both positive and negative supercoils, and in addition has a strong decatenase activity. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspart

>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

Probab=98.56  E-value=4e-08  Score=80.57  Aligned_cols=128  Identities=20%  Similarity=0.113  Sum_probs=85.5

Q ss_pred             ccceeeeeccccEEEEEccchhhhhhchh---------HH-----HHHHHHHHhhcCCcEEEEecCCcchhHHHHHHhhC
Q 029346           21 ICIITNTVSNFFIVIRLIREGAANRTCEN---------KI-----VILLREIRCKLKKSVLGSFDCNPYGIHILTVYMFG   86 (194)
Q Consensus        21 ~~~i~~i~~~a~~VLVVEKdavF~~L~~~---------~f-----R~fl~~L~~~~~lpi~~L~D~DP~Gi~I~~tYk~G   86 (194)
                      ++.+..+...++.|||||..+.|.++.+.         ||     +.|++.+..   .|++.++|-||+|+.|+...+.-
T Consensus        33 ~~~l~~~~~~~~~vliVEN~~tf~~~~~~~~~~~Iyg~G~~~~~~~~~~~~~~~---~~~~ywGDiD~~G~~I~~~lr~~  109 (181)
T PF09983_consen   33 LEELEILSLPPRRVLIVENLTTFYSLPELPNGLVIYGGGFAISSSRRFLKWLQP---KPVYYWGDIDPGGLRILERLRRK  109 (181)
T ss_pred             HHHHHhccCCCCEEEEEeCHHHHHHHHhcCCeEEEECCCcCcHHHHHHHhhcCC---CceEEeccCCHhHHHHHHHHHHh
Confidence            45566667789999999999999999853         33     666664433   39999999999999999988762


Q ss_pred             CcccccccCCcCCCCeeEeeCCccccccccCCccccccCCHHHHHHHHHHHhcCCcchhccCcHHHHHHHHHHHHhCCee
Q 029346           87 SKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKA  166 (194)
Q Consensus        87 S~~~~~~~~~~~~p~l~wlGv~~sdl~~~~~~~~~~~~Lt~rD~~~~~~ll~~~~~~~~~~~~~~~~~EL~~ml~~~~Ka  166 (194)
                                  +|.++-.-+....+.++ .. ....+.+....+.+.. |+.    +   ....|+.=++.|+..+++.
T Consensus       110 ------------~p~~~p~~Md~~~l~~~-~~-~~~~~~~~~~~~~l~~-L~~----~---e~~~~~~l~~~~l~~~~ri  167 (181)
T PF09983_consen  110 ------------FPELKPLLMDEETLERY-QD-RYGKEPSEPYRRKLPR-LTD----E---EYALFRELIEEMLEEGKRI  167 (181)
T ss_pred             ------------CCCccccccCHHHHHHH-HH-hcCCCCCccccccchh-cCH----H---HHHHHHHHHHHHHhcCCee
Confidence                        24444455555555543 11 1111224444444444 333    1   1345665666689999999


Q ss_pred             eEeeecc
Q 029346          167 EIEALDM  173 (194)
Q Consensus       167 Eieal~~  173 (194)
                      |+|++..
T Consensus       168 EQE~I~~  174 (181)
T PF09983_consen  168 EQERIPW  174 (181)
T ss_pred             eeccccH
Confidence            9999973

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

Probab=98.13  E-value=2.6e-06  Score=68.33  Aligned_cols=121  Identities=17%  Similarity=0.131  Sum_probs=80.9

Q ss_pred             cceeeeeccccEEEEEccchhhhhhchh-HH----------------HHHHHHHHhhcCCcEEEEecCCcchhHHHHHHh
Q 029346           22 CIITNTVSNFFIVIRLIREGAANRTCEN-KI----------------VILLREIRCKLKKSVLGSFDCNPYGIHILTVYM   84 (194)
Q Consensus        22 ~~i~~i~~~a~~VLVVEKdavF~~L~~~-~f----------------R~fl~~L~~~~~lpi~~L~D~DP~Gi~I~~tYk   84 (194)
                      ..+..+.+....|.|||+-+||.++++. +.                +.||.+|.. .+.++++-+|+||.|+.|+...+
T Consensus         9 ~~~~~~~~~~~~V~VvENp~Vf~~~~~~~~~~~~pLVCt~G~p~~A~~~LL~~L~~-~g~~l~y~GDfDp~Gl~IA~~l~   87 (152)
T PF09664_consen    9 SRVPRIWPPSGRVYVVENPAVFSALADELGASCPPLVCTSGQPSAAARRLLDRLAA-AGARLYYSGDFDPEGLRIANRLI   87 (152)
T ss_pred             hccccccCCCCEEEEEecHHHHHHHHHhcCCCCCeEEEcCCcHHHHHHHHHHHHHh-CCCEEEEecCCCHHHHHHHHHHH
Confidence            3344455666679999999999999987 11                999999954 58999999999999999999987


Q ss_pred             hCCcccccccCCcCCCCeeEeeCCccccccccCCccccccCCHHHHHHHHHHHhcCCcchhccCcHHHHHHHHHHHHhCC
Q 029346           85 FGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGE  164 (194)
Q Consensus        85 ~GS~~~~~~~~~~~~p~l~wlGv~~sdl~~~~~~~~~~~~Lt~rD~~~~~~ll~~~~~~~~~~~~~~~~~EL~~ml~~~~  164 (194)
                      .-     +.    +.|   | -+.+.|+... +   ...+++.+..+ +.++  .    |+.      +.=...|.+.|+
T Consensus        88 ~r-----~~----~~~---W-rm~~~dY~~~-~---~~~~~~~~~l~-l~~v--~----p~~------~~L~~~m~~~~~  137 (152)
T PF09664_consen   88 QR-----YG----ARP---W-RMDAEDYLAA-L---SAEPLSGRRLK-LPNV--A----PWL------PELAEAMRERGR  137 (152)
T ss_pred             HH-----hC----Ccc---c-cCCHHHHHHh-c---cccCCCCCcCC-cccC--C----hhc------HHHHHHHHHhCc
Confidence            41     00    122   2 3445555321 1   22255555544 3333  1    222      233346999999


Q ss_pred             eeeEeeecc
Q 029346          165 KAEIEALDM  173 (194)
Q Consensus       165 KaEieal~~  173 (194)
                      +++.|++..
T Consensus       138 a~~QE~l~~  146 (152)
T PF09664_consen  138 AVYQEALLD  146 (152)
T ss_pred             eeeHHHHHH
Confidence            999999874

Its function is unknown.

>TIGR02679 conserved hypothetical protein TIGR02679

Probab=93.79  E-value=0.085  Score=48.35  Aligned_cols=52  Identities=12%  Similarity=-0.003  Sum_probs=43.5

Q ss_pred             EEEEEccchhhhhhchh------------HH-----HHHHHHHHhhcCCcEEEEecCCcchhHHHHHHhh
Q 029346           33 IVIRLIREGAANRTCEN------------KI-----VILLREIRCKLKKSVLGSFDCNPYGIHILTVYMF   85 (194)
Q Consensus        33 ~VLVVEKdavF~~L~~~------------~f-----R~fl~~L~~~~~lpi~~L~D~DP~Gi~I~~tYk~   85 (194)
                      .|.|||-=+||..+++.            |+     +.||.+|... +.++++=.|.||-||.|+..-+.
T Consensus       252 ~V~vvENp~vf~~~~~~~~~~~~~lIct~G~p~~a~~~LL~~L~~~-g~~l~YhGDfD~~Gi~Ia~~L~~  320 (385)
T TIGR02679       252 RVYVVENPNVLAIALDRLGPRCAPLVCTDGQPNAAQIKLLDLLAAA-GARLYYHGDFDWPGLRIANGLIR  320 (385)
T ss_pred             eEEEEecHHHHHHHHHhcCCCCceEEECCCcchHHHHHHHHHHHhc-CCeEEEecCCChhHHHHHHHHHH
Confidence            59999999999999884            33     9999999875 45566669999999999988763

Members of this protein belong to a conserved gene four-gene neighborhood found sporadically in a phylogenetically broad range of bacteria: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria).

>cd00188 TOPRIM Topoisomerase-primase domain

Probab=93.10  E-value=0.24  Score=32.88  Aligned_cols=47  Identities=15%  Similarity=-0.033  Sum_probs=32.7

Q ss_pred             cEEEEEccchhhhhhchhHH-------------HHHHHHHHhhc--CCcEEEEecCCcchhH
Q 029346           32 FIVIRLIREGAANRTCENKI-------------VILLREIRCKL--KKSVLGSFDCNPYGIH   78 (194)
Q Consensus        32 ~~VLVVEKdavF~~L~~~~f-------------R~fl~~L~~~~--~lpi~~L~D~DP~Gi~   78 (194)
                      +.|++||.++....|.+.++             ......+....  ..+++.++|.|+.|..
T Consensus         1 ~~viivEg~~d~~~l~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~v~i~~D~D~~g~~   62 (83)
T cd00188           1 KKLIIVEGPSDALALAQAGGYGGAVVALGGHALNKTRELLKRLLGEAKEVIIATDADREGEA   62 (83)
T ss_pred             CEEEEEecHHHHHHHHHHcCCCEEEEEEccEEcHHHHHHHHHHhcCCCEEEEEcCCChhHHH
Confidence            36889999998887776533             21233333322  4899999999999983

This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.

>COG3593 Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]

Probab=81.63  E-value=2.2  Score=41.29  Aligned_cols=53  Identities=11%  Similarity=-0.059  Sum_probs=41.6

Q ss_pred             ccEEEEEccch---hhhhhchhH------------------HHHHHHHHHhhcCCcEEEEecCCcchhHHHHHHh
Q 029346           31 FFIVIRLIREG---AANRTCENK------------------IVILLREIRCKLKKSVLGSFDCNPYGIHILTVYM   84 (194)
Q Consensus        31 a~~VLVVEKda---vF~~L~~~~------------------fR~fl~~L~~~~~lpi~~L~D~DP~Gi~I~~tYk   84 (194)
                      |+.||.||=+|   +.+.|+...                  |..|++ +.+..++++++++|+||.|...-.+-+
T Consensus       396 Ar~vIlVEG~aE~ill~~la~~~~~~L~~~gi~VI~~~gs~~k~f~k-f~~~~gI~~~vitD~D~~g~~~~~~~~  469 (581)
T COG3593         396 ARGVILVEGEAEVILLPELARQCGIDLEKEGIIVIEFAGSGLKPFIK-FAEAMGIRVHVITDGDEAGKKYEATVR  469 (581)
T ss_pred             hceeEEEeccchhhhHHHHHHHhccccccCcEEEEeecccCcHHHHH-HhhccCceEEEEecCCcccchhhhhhh
Confidence            67899999876   356555431                  189998 888889999999999999998776655

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	194
1d3y_A	301	Structure Of The Dna Topoisomerase Vi A Subunit Len		9e-13
2zbk_A	389	Crystal Structure Of An Intact Type Ii Dna Topoisom		2e-07
2q2e_A	369	Crystal Structure Of The Topoisomerase Vi Holoenzym		3e-05

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

Iteration: 1
 Score = 69.7 bits (169), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 43/126 (34%), Positives = 67/126 (53%), Gaps = 8/126 (6%)
Query: 71  DCNPYG-IHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDD 129
           D +PYG ++I      GS        +L++P  + +G+ P D+  Y++P      L + D
Sbjct: 181 DGDPYGYLNIYRTLKVGSGKAIHLADKLSIPAARLIGVTPQDIIDYDLPT---HPLKEQD 237
Query: 130 ISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYLPSKFR 189
           I ++K  L+  D   FVRS   W+K L++M   G +AE ++L  Y  KY+ N YLP K +
Sbjct: 238 IKRIKDGLKNDD---FVRSFPEWQKALKQMLDMGVRAEQQSLAKYGLKYVVNTYLPEKIK 294
Query: 190 AED-WL 194
            E  WL
Sbjct: 295 DESTWL 300

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

Iteration: 1
 Score = 52.0 bits (123), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 42/149 (28%), Positives = 77/149 (51%), Gaps = 12/149 (8%)
Query: 54  LLREIRCKLKKSVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLG-----LF 108
            +R +  +LK  V    D +PYG +I +V+  GS +++  + RLA P+ K+LG     +F
Sbjct: 244 FVRRLNEELKLPVYILTDADPYGWYIFSVFRIGSISLSYESERLATPDAKFLGVSMGDIF 303
Query: 109 PSDLEKYNIPKLCRQ---ILSKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEK 165
            +  +K  + +  R+   I +KD  + +K   E  +   F     +W++E+    +   K
Sbjct: 304 GNSRKKPYLSEAERKNYIIKAKD--ADIKRAEEIKNYEWF--KTKAWQEEINTFLQRKAK 359
Query: 166 AEIEALDMYEYKYLANKYLPSKFRAEDWL 194
            EIEA+     K+LA +Y+P K   +D++
Sbjct: 360 LEIEAMASKGLKFLAFQYIPEKITNKDYI 388

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 31/119 (26%), Positives = 58/119 (48%), Gaps = 8/119 (6%)
Query: 71  DCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDI 130
           D +P+   I     +G+   A  +  +A P  K+LGL PSD+ +Y   +L    L++ D+
Sbjct: 254 DGDPWSYRIYASVAYGAIKSAHLSEFMATPAAKFLGLQPSDIVEY---ELSTDKLTEQDV 310
Query: 131 SKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYLPSKFR 189
           S L++ L           +  W++++Q     G+KAE +A       ++   YLP++ +
Sbjct: 311 SALRSELSDPRF-----ESDYWKEQIQLQLDIGKKAEQQAFAGKGLDFVTEVYLPNRLK 364

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	194
2q2e_A	369	Type II DNA topoisomerase VI subunit A; DNA-bindin	5e-32
2zbk_A	389	Type II DNA topoisomerase VI subunit A; DNA bindin	1e-28
1d3y_A	301	DNA topoisomerase VI A subunit; DNA binding protei	4e-28
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-04

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

 Score =  117 bits (294), Expect = 5e-32
 Identities = 40/213 (18%), Positives = 82/213 (38%), Gaps = 29/213 (13%)

Query: 1   MTNTESNFFIVLCLISSAIRICIITNTVSNFFIVI-------RLIREGAANRTCENKIVI 53
             + + +       I   +         ++  I I       RL+  G       N I++
Sbjct: 167 NIHCQKDVGEGGYQIPFNVENIEFQKHDASMIIAIETGGMYARLMENGFDEA--YNAILV 224

Query: 54  ------------LLREIRCKLKKSVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPN 101
                       +++ +  +L   V    D +P+   I     +G+   A  +  +A P 
Sbjct: 225 HLKGQPARSTRRIIKRMNEELGIPVAVFTDGDPWSYRIYASVAYGAIKSAHLSEFMATPA 284

Query: 102 IKWLGLFPSDLEKYNIPKLCRQILSKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSK 161
            K+LGL PSD+ +Y +       L++ D+S L++ L           +  W++++Q    
Sbjct: 285 AKFLGLQPSDIVEYELST---DKLTEQDVSALRSELSDP-----RFESDYWKEQIQLQLD 336

Query: 162 EGEKAEIEALDMYEYKYLANKYLPSKFRAEDWL 194
            G+KAE +A       ++   YLP++ +    +
Sbjct: 337 IGKKAEQQAFAGKGLDFVTEVYLPNRLKEMGMI 369

>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 =  108 bits (271), Expect = 1e-28
 Identities = 37/150 (24%), Positives = 67/150 (44%), Gaps = 14/150 (9%)

Query: 54  LLREIRCKLKKSVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLE 113
            +R +  +LK  V    D +PYG +I +V+  GS +++  + RLA P+ K+LG+   D+ 
Sbjct: 244 FVRRLNEELKLPVYILTDADPYGWYIFSVFRIGSISLSYESERLATPDAKFLGVSMGDIF 303

Query: 114 KYNIP---------KLCRQILSKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGE 164
             +           K         DI + +                +W++E+    +   
Sbjct: 304 GNSRKKPYLSEAERKNYIIKAKDADIKRAEEIKNYEWF-----KTKAWQEEINTFLQRKA 358

Query: 165 KAEIEALDMYEYKYLANKYLPSKFRAEDWL 194
           K EIEA+     K+LA +Y+P K   +D++
Sbjct: 359 KLEIEAMASKGLKFLAFQYIPEKITNKDYI 388

>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 =  106 bits (264), Expect = 4e-28
 Identities = 44/143 (30%), Positives = 72/143 (50%), Gaps = 8/143 (5%)

Query: 54  LLREIRCKLKKSVLGSFDCNPYG-IHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDL 112
            ++ +  +    VL   D +PYG ++I      GS        +L++P  + +G+ P D+
Sbjct: 164 FIKRLHEEHDLPVLVFTDGDPYGYLNIYRTLKVGSGKAIHLADKLSIPAARLIGVTPQDI 223

Query: 113 EKYNIPKLCRQILSKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALD 172
             Y++P      L + DI ++K  L+  D   FVRS   W+K L++M   G +AE ++L 
Sbjct: 224 IDYDLPTHP---LKEQDIKRIKDGLKNDD---FVRSFPEWQKALKQMLDMGVRAEQQSLA 277

Query: 173 MYEYKYLANKYLPSKFR-AEDWL 194
            Y  KY+ N YLP K +    WL
Sbjct: 278 KYGLKYVVNTYLPEKIKDESTWL 300

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

 Score = 40.2 bits (93), Expect = 3e-04
 Identities = 14/79 (17%), Positives = 29/79 (36%), Gaps = 12/79 (15%)

Query: 108 FPSDLEKYNIPKLCRQILSK---DDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGE 164
           F  + +  ++  + + ILSK   D I   K  +     + +          L    +E  
Sbjct: 29  FVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWT---------LLSKQEEMV 79

Query: 165 KAEIEALDMYEYKYLANKY 183
           +  +E +    YK+L +  
Sbjct: 80  QKFVEEVLRINYKFLMSPI 98

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	194
1d3y_A	301	DNA topoisomerase VI A subunit; DNA binding protei	100.0
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 DNA topoisomerase VI A subunit; DNA binding protein, SPO11 homolog; HET: DNA; 2.00A {Methanocaldococcus jannaschii} SCOP: e.12.1.1

Probab=100.00  E-value=5.8e-52  Score=362.23  Aligned_cols=178  Identities=25%  Similarity=0.461  Sum_probs=155.3

Q ss_pred             eEEeee------ccccccccceeeeeccccEEEEEccchhhhhhchhHH-------------------HHHHHHHHhhcC
Q 029346            9 FIVLCL------ISSAIRICIITNTVSNFFIVIRLIREGAANRTCENKI-------------------VILLREIRCKLK   63 (194)
Q Consensus         9 ~~~~c~------ip~~~~~~~i~~i~~~a~~VLVVEKdavF~~L~~~~f-------------------R~fl~~L~~~~~   63 (194)
                      ..++|.      +++|.+++.++. .++|+||||||||||||||++++|                   |+||++|+++++
T Consensus        95 ~~id~~~~~~~g~~Ip~~~~~i~~-~~~a~~VLvVEK~avF~rL~~~~~~~~~~~ilIt~kGyPd~aTR~fl~~L~~~~~  173 (301)
T 1d3y_A           95 LVVDCTKLGTGAYNIPNDVTKLNL-ETDADFILAIETSGMFARLNAERFWDKHNCILVSLKGVPARATRRFIKRLHEEHD  173 (301)
T ss_dssp             EEEETTSCTTSEEECCSCCTTCEE-ECCCSEEEEESCHHHHHHHHHTTHHHHTTEEEEECCSSCCHHHHHHHHHHHHHHT
T ss_pred             cEEEeecCCCCceecCccHHhhee-ccCccEEEEEechHHHHHHHHhcccccCCEEEEECCCCCCHHHHHHHHHHHHhcC
Confidence            367774      356667888887 899999999999999999999977                   999999999999


Q ss_pred             CcEEEEecCCcchh-HHHHHHhhCCcccccccCCcCCCCeeEeeCCccccccccCCccccccCCHHHHHHHHHHHhcCCc
Q 029346           64 KSVLGSFDCNPYGI-HILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDISKLKTFLEKGDL  142 (194)
Q Consensus        64 lpi~~L~D~DP~Gi-~I~~tYk~GS~~~~~~~~~~~~p~l~wlGv~~sdl~~~~~~~~~~~~Lt~rD~~~~~~ll~~~~~  142 (194)
                      +|+|+|+|+||||+ +|+++|++||.+++|+++.++||+++|+|++++|+.++++|   .+|||++|++++++|+++   
T Consensus       174 lpv~~l~D~DP~G~~~I~~tyk~GS~~~~~~~~~l~~p~~~wlGv~~sdi~~~~~~---~~~Lt~~D~~~l~~ll~~---  247 (301)
T 1d3y_A          174 LPVLVFTDGDPYGYLNIYRTLKVGSGKAIHLADKLSIPAARLIGVTPQDIIDYDLP---THPLKEQDIKRIKDGLKN---  247 (301)
T ss_dssp             CCEEEECCBSHHHHHTHHHHHHC---------CTTCCTTCEEEESCHHHHHHTTCC---CEECCHHHHHHHHHHHHH---
T ss_pred             CCEEEEecCChHHHHHHHHHHHhCchhhccccccccCCccEEcCCCHHHHHhcccc---cCcCCHHHHHHHHHHhhC---
Confidence            99999999999999 99999999999999999999999999999999999988875   569999999999999999   


Q ss_pred             chhcc-CcHHHHHHHHHHHHhCCeeeEeeeccccccchhhchhHhhhccCC-CC
Q 029346          143 VAFVR-SNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYLPSKFRAED-WL  194 (194)
Q Consensus       143 ~~~~~-~~~~~~~EL~~ml~~~~KaEieal~~~g~~~l~~~Yl~~Ki~~~~-~~  194 (194)
                       |+++ ..++|++||++|++.|+||||||+++.|.+|++++|||+||++++ ||
T Consensus       248 -~~~~~~~~~w~~el~~ml~~~~KaEieal~~~g~~f~~~~yl~~Ki~~~~~~~  300 (301)
T 1d3y_A          248 -DDFVRSFPEWQKALKQMLDMGVRAEQQSLAKYGLKYVVNTYLPEKIKDESTWL  300 (301)
T ss_dssp             -CHHHHTCHHHHHHHHHHHHHTEEBCGGGGGGGCTTHHHHTHHHHHHHCGGGCC
T ss_pred             -ccccCcHHHHHHHHHHHHHhCCEEEEehhhhcCccchHHHHHHHHHhcCCcCC
Confidence             6774 235699999999999999999999999999999999999999999 97

>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=100.00  E-value=4.7e-47  Score=341.26  Aligned_cols=178  Identities=23%  Similarity=0.348  Sum_probs=158.9

Q ss_pred             eEEeeec------cccccccceeeeeccccEEEEEccchhhhhhchhHH-------------------HHHHHHHHhhcC
Q 029346            9 FIVLCLI------SSAIRICIITNTVSNFFIVIRLIREGAANRTCENKI-------------------VILLREIRCKLK   63 (194)
Q Consensus         9 ~~~~c~i------p~~~~~~~i~~i~~~a~~VLVVEKdavF~~L~~~~f-------------------R~fl~~L~~~~~   63 (194)
                      ..++|.-      .+|.+++.|+.+.+++++||||||+|||++|++++|                   |+||++|+++++
T Consensus       174 ~~id~~~~g~~g~~Ip~~~~~i~~i~~~a~~VLvVEK~avF~rL~~~~~~~~~~~ilIt~kG~Pd~aTR~fL~~L~~~~~  253 (389)
T 2zbk_A          174 DVIDLSKTGHGAYAIEPTPDLIDFIDVDAEFVLVVEKDAVFQQLHRAGFWKQYKSILITSAGQPDRATRRFVRRLNEELK  253 (389)
T ss_dssp             EEEESSCCTTCCBCCCSCCSSEEEEEECCSCEEEESCHHHHHHHHTTTHHHHTTCEEEECCSSCCTTHHHHHHHHHHHSC
T ss_pred             cEEEeecCCCCceeCCccHHHhhccccCccEEEEEecHHHHHHHHHhCcCccCCEEEEECCCCCCHHHHHHHHHHHHhcC
Confidence            4577752      445678889988999999999999999999999876                   999999999999


Q ss_pred             CcEEEEecCCcchhHHHHHHhhCCcccccccCCcCCCCeeEeeCCccccccccCCccccccCCHHH-----HHHHHHHHh
Q 029346           64 KSVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDD-----ISKLKTFLE  138 (194)
Q Consensus        64 lpi~~L~D~DP~Gi~I~~tYk~GS~~~~~~~~~~~~p~l~wlGv~~sdl~~~~~~~~~~~~Lt~rD-----~~~~~~ll~  138 (194)
                      +|+|+++|+||||+.|++||++||.+++|+++.+++|+++|+|++++|+.++++|.   .|||++|     +++++++++
T Consensus       254 lpv~~l~D~DP~Gi~I~~tyk~GS~~~a~~~~~l~~P~l~~lG~~~~di~~~~~~~---~~Lt~~Dr~~~~~k~l~~ll~  330 (389)
T 2zbk_A          254 LPVYILTDADPYGWYIFSVFRIGSISLSYESERLATPDAKFLGVSMGDIFGNSRKK---PYLSEAERKNYIIKAKDADIK  330 (389)
T ss_dssp             CCEEEECCSSHHHHHHHHHHTSCSCC-----CCCSCSSCEECCCCHHHHHCCSSSC---CSSCHHHHHHHCEECCHHHHH
T ss_pred             CCEEEEecCChhhhhhHHHHhhcchhhhhhhhcccCCceEEcCCcHHHHHhccccc---ccCChhhhhhHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999887754   6999999     889999998


Q ss_pred             cCCcch-------hccCcHHHHHHHHHHHHhCCeeeEeeeccccccchhhchhHhhhccCCCC
Q 029346          139 KGDLVA-------FVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYLPSKFRAEDWL  194 (194)
Q Consensus       139 ~~~~~~-------~~~~~~~~~~EL~~ml~~~~KaEieal~~~g~~~l~~~Yl~~Ki~~~~~~  194 (194)
                      +    |       ++. .++|++||++|++.|+|+||||+.++|.+|++++|||+||.++|||
T Consensus       331 ~----~~~~~~~~~~~-~~~w~~el~~Ml~~~~KaE~Eal~~~g~~fl~~~yl~~Ki~~~~~i  388 (389)
T 2zbk_A          331 R----AEEIKNYEWFK-TKAWQEEINTFLQRKAKLEIEAMASKGLKFLAFQYIPEKITNKDYI  388 (389)
T ss_dssp             H----HHHHTTSTTTT-TTTTTHHHHHHHHHCEECCHHHHHTTCTHHHHHTHHHHHHHHTCSB
T ss_pred             c----hhhcccchhcc-CHHHHHHHHHHHHhCceeeeHHhhhcCchhhHHHHHHHHHhcCCCc
Confidence            8    5       553 6789999999999999999999999999999999999999999996

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

Probab=100.00  E-value=1.9e-46  Score=335.37  Aligned_cols=170  Identities=22%  Similarity=0.360  Sum_probs=149.6

Q ss_pred             ccccccceeeeeccccEEEEEccchhhhhhchhHH-------------------HHHHHHHHhhcCCcEEEEecCCcchh
Q 029346           17 SAIRICIITNTVSNFFIVIRLIREGAANRTCENKI-------------------VILLREIRCKLKKSVLGSFDCNPYGI   77 (194)
Q Consensus        17 ~~~~~~~i~~i~~~a~~VLVVEKdavF~~L~~~~f-------------------R~fl~~L~~~~~lpi~~L~D~DP~Gi   77 (194)
                      +|.+++.++.+.+++++||||||+|||++|++++|                   |+||++|++++++|+|+++|+||||+
T Consensus       181 Ip~~~~~i~~i~~~~~~VlvVEk~avF~~L~~~~~~~~~~~ilIt~kG~Pd~atR~~L~~L~~~~~~pv~~l~D~Dp~Gi  260 (369)
T 2q2e_A          181 IPFNVENIEFQKHDASMIIAIETGGMYARLMENGFDEAYNAILVHLKGQPARSTRRIIKRMNEELGIPVAVFTDGDPWSY  260 (369)
T ss_dssp             CCSCSSSCCCCCCCCCCEEEECCTTHHHHHHHSCCTTTTCCCEEECCSSCCHHHHHHHHHHTTSSCCCEEEECCSSHHHH
T ss_pred             CCccHHHhhcccCCccEEEEEechHHHHHHHHhccCccCCEEEEECCCCCCHHHHHHHHHHHHhcCCcEEEEecCChhHH
Confidence            44477888888899999999999999999998755                   99999999988999999999999999


Q ss_pred             HHHHHHhhCCcccccccCCcCCCCeeEeeCCccccccccCCccccccCCHHHHHHHHHHHhcCCcchhccCcHHHHHHHH
Q 029346           78 HILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDISKLKTFLEKGDLVAFVRSNASWEKELQ  157 (194)
Q Consensus        78 ~I~~tYk~GS~~~~~~~~~~~~p~l~wlGv~~sdl~~~~~~~~~~~~Lt~rD~~~~~~ll~~~~~~~~~~~~~~~~~EL~  157 (194)
                      .|++||+|||.+++|++..+++|+++|+|++++|+.++++|   ..|||++|++++++++++    |+++ ++.|++|++
T Consensus       261 ~I~~tyk~GS~~~~~~~~~l~~p~~~~lgm~~~d~~~~~~~---~~~Lt~~D~k~l~~ll~~----~~~~-~~~w~~el~  332 (369)
T 2q2e_A          261 RIYASVAYGAIKSAHLSEFMATPAAKFLGLQPSDIVEYELS---TDKLTEQDVSALRSELSD----PRFE-SDYWKEQIQ  332 (369)
T ss_dssp             TTTHHHHSCC--------CCCCTTCBCCSSCTTTTTSSCCC---CCCCCHHHHHHHTTTTSS----CSSC-CTTTTHHHH
T ss_pred             HHHHHHhccchhhhhhhcccCCCccEECCCCHHHHHhcccc---cCCCCHHHHHHHHHHhhC----cccC-CHHHHHHHH
Confidence            99999999999999999999999999999999999988775   469999999999999999    6665 678999999


Q ss_pred             HHHHhCCeeeEeeeccccccchhhchhHhhhccCCCC
Q 029346          158 KMSKEGEKAEIEALDMYEYKYLANKYLPSKFRAEDWL  194 (194)
Q Consensus       158 ~ml~~~~KaEieal~~~g~~~l~~~Yl~~Ki~~~~~~  194 (194)
                      +|++.|+|+||||+.+.|.+|++++|||+||++++||
T Consensus       333 ~ml~~~~K~EqEal~~~g~~~~~~~yl~~Ki~~~~~~  369 (369)
T 2q2e_A          333 LQLDIGKKAEQQAFAGKGLDFVTEVYLPNRLKEMGMI  369 (369)
T ss_dssp             HHHHHCCCCCSGGGGGGCTTSTTTTHHHHHHHSCC--
T ss_pred             HHHHhCcEeeehhhhhcCchhhHHHHHHHHHhcCCcC
Confidence            9999999999999999999999999999999999997

---

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	194
d1d3ya_	298	e.12.1.1 (A:) DNA topoisomerase IV, alpha subunit	4e-33

>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 =  117 bits (295), Expect = 4e-33
 Identities = 51/220 (23%), Positives = 86/220 (39%), Gaps = 32/220 (14%)

Query: 1   MTNTESNFFIVLCLISSAIRICIITNTVSNFF-----IVIRLIREGAANRTCENKIVI-- 53
           +  T     +V C         I  +            ++ +   G   R    +     
Sbjct: 84  IEETPEGELVVDCTKLGTGAYNIPNDVTKLNLETDADFILAIETSGMFARLNAERFWDKH 143

Query: 54  -----------------LLREIRCKLKKSVLGSFDCNPYG-IHILTVYMFGSKNMAGRNL 95
                             ++ +  +    VL   D +PYG ++I      GS        
Sbjct: 144 NCILVSLKGVPARATRRFIKRLHEEHDLPVLVFTDGDPYGYLNIYRTLKVGSGKAIHLAD 203

Query: 96  RLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDISKLKTFLEKGDLVAFVRSNASWEKE 155
           +L++P  + +G+ P D+  Y++P      L + DI ++K  L+  D   FVRS   W+K 
Sbjct: 204 KLSIPAARLIGVTPQDIIDYDLPTHP---LKEQDIKRIKDGLKNDD---FVRSFPEWQKA 257

Query: 156 LQKMSKEGEKAEIEALDMYEYKYLANKYLPSKFRAED-WL 194
           L++M   G +AE ++L  Y  KY+ N YLP K + E  WL
Sbjct: 258 LKQMLDMGVRAEQQSLAKYGLKYVVNTYLPEKIKDESTWL 297

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	194
d1d3ya_	298	DNA topoisomerase IV, alpha subunit {Archaeon Meth	100.0

>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=100.00  E-value=3.2e-50  Score=348.67  Aligned_cols=178  Identities=28%  Similarity=0.504  Sum_probs=149.1

Q ss_pred             EEeeec------cccccccceeeeeccccEEEEEccchhhhhhchhHH-------------------HHHHHHHHhhcCC
Q 029346           10 IVLCLI------SSAIRICIITNTVSNFFIVIRLIREGAANRTCENKI-------------------VILLREIRCKLKK   64 (194)
Q Consensus        10 ~~~c~i------p~~~~~~~i~~i~~~a~~VLVVEKdavF~~L~~~~f-------------------R~fl~~L~~~~~l   64 (194)
                      .++|.-      +++...+.+ .+.++|+||||||||||||+|++++|                   |+||++|++++++
T Consensus        93 ~id~~~~~~~~~~~~~~~~~~-~~~~~a~~vLVVEKeavF~rL~~~~~~~~~~~ilitgkGyPd~~TR~fL~~L~~~~~l  171 (298)
T d1d3ya_          93 VVDCTKLGTGAYNIPNDVTKL-NLETDADFILAIETSGMFARLNAERFWDKHNCILVSLKGVPARATRRFIKRLHEEHDL  171 (298)
T ss_dssp             EEETTSCTTSEEECCSCCTTC-EEECCCSEEEEESCHHHHHHHHHTTHHHHTTEEEEECCSSCCHHHHHHHHHHHHHHTC
T ss_pred             EEEcccccCCCccCcccccee-eeeccCcEEEEEeehhHHHHHHhcCcccccceeeeccCCCCCHHHHHHHHHHhhccCC
Confidence            567753      233334444 47899999999999999999999876                   9999999999999


Q ss_pred             cEEEEecCCcchh-HHHHHHhhCCcccccccCCcCCCCeeEeeCCccccccccCCccccccCCHHHHHHHHHHHhcCCcc
Q 029346           65 SVLGSFDCNPYGI-HILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDISKLKTFLEKGDLV  143 (194)
Q Consensus        65 pi~~L~D~DP~Gi-~I~~tYk~GS~~~~~~~~~~~~p~l~wlGv~~sdl~~~~~~~~~~~~Lt~rD~~~~~~ll~~~~~~  143 (194)
                      |+|+|+|+||||+ .|+++|+|||.+++|+++.+++|+++|+|++++|+..++++   .+|||++|++++.++++++   
T Consensus       172 p~~~l~D~Dp~G~~~I~~~yk~GS~~~~~~~~~~~~p~l~wlG~~~~d~~~~~~~---~~~Lt~~D~k~~~~ll~~~---  245 (298)
T d1d3ya_         172 PVLVFTDGDPYGYLNIYRTLKVGSGKAIHLADKLSIPAARLIGVTPQDIIDYDLP---THPLKEQDIKRIKDGLKND---  245 (298)
T ss_dssp             CEEEECCBSHHHHHTHHHHHHC---------CTTCCTTCEEEESCHHHHHHTTCC---CEECCHHHHHHHHHHHHHC---
T ss_pred             CEEEEEcCCcchHHHHHHHHHHHhhhcccccccccCCCCEEeeccHHHHhhcccc---cCccchhHHHHHHHHhcCh---
Confidence            9999999999995 68999999999999999999999999999999999887764   4599999999999999993   


Q ss_pred             hhccCcHHHHHHHHHHHHhCCeeeEeeeccccccchhhchhHhhhccCC-CC
Q 029346          144 AFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYLPSKFRAED-WL  194 (194)
Q Consensus       144 ~~~~~~~~~~~EL~~ml~~~~KaEieal~~~g~~~l~~~Yl~~Ki~~~~-~~  194 (194)
                      .+...+++|++||++|++.|+|||||||++.|.+|++++|||+||++++ ||
T Consensus       246 ~~~~~~~~w~~EL~~ml~~~~KaEiEal~~~~~~f~~~~Yl~~Ki~~~~~~i  297 (298)
T d1d3ya_         246 DFVRSFPEWQKALKQMLDMGVRAEQQSLAKYGLKYVVNTYLPEKIKDESTWL  297 (298)
T ss_dssp             HHHHTCHHHHHHHHHHHHHTEEBCGGGGGGGCTTHHHHTHHHHHHHCGGGCC
T ss_pred             hhhhcCHHHHHHHHHHHHhCCeEEEehhhhcCCcccHHHHHHHHHHhcCCCC
Confidence            2444578999999999999999999999999999999999999998765 97