Citrus Sinensis ID: 048704

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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-------200-------210-------220
Protein Sequence
MAPLKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICFH
Secondary Structure (PSIPRED)
cccccEEEEEcccHHHHHHHHHHcccccEEEccccEEEEEEEEEcccccEEEEEEEccccccccccccccccccccccccccccEEEEcccccHHHHHHHHHHHcccccEEEEEEccccHHHHHHHHHHHHccccccccccEEEEEEccccHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccEEEEEcccccEEEcc
Secondary Structure Prediction (SSPRO)
ccccEEEEEEccHHHHHHHHHHHccccccccccccEEEEEEEEEccccEEEEEEEEEEcEEcccccHHHcccccccHHHHccccEEEEccccHHHHHHHHHHHHccccEEEEEEccccccHHHHHHHHHHHHHHHccccccEEEEEEccccHHHHHHHHHccccccccHHHHHHHHHHHcHEEHHcccHHHHHHHHHcccccccHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
MAPLKVLMVAEKPSIALSIATVLSggklytrkastevhefdgmflgshaYIKVTSVVGhvfrldfppayqdwnasnpldlfqapvhkaesnpkvhICRHLNQEARGCGHLVLWLdcdregeniCFEVIEctgfqvndaRRKVHRARFSSVTEKDILKAMGnlvepnrnealavdARQEIDLKVGVAFTRFQTtyfqgkygnlDSRFISLVFSSLFLICFH
Flexible Loop (DISEMBL)
MAPLKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIEctgfqvndarrKVHRarfssvtekdILKAmgnlvepnrNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICFH
Low Complexity Region (SEG)
MAPLKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICFH
Disordered region (IsUnstruct)
*****VLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF*
Disordered Region (DISOPRED)
*APLKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAPVHKAESNPKV**CRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICFH
Disordered Region (DISEMBL)
MAPLKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICFH
Disordered Region (DISPRO)
**PLKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF*
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHi
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAPLKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICFH
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	220	2.2.26 [Sep-21-2011]
O95985	862	DNA topoisomerase 3-beta-	yes	no	0.927	0.236	0.554	4e-60
Q9Z321	862	DNA topoisomerase 3-beta-	yes	no	0.927	0.236	0.545	5e-60
O96651	875	DNA topoisomerase 3-beta	yes	no	0.922	0.232	0.502	4e-54
Q13472	1001	DNA topoisomerase 3-alpha	no	no	0.859	0.188	0.433	2e-35
O70157	1003	DNA topoisomerase 3-alpha	no	no	0.859	0.188	0.418	3e-34
Q9NG98	1250	DNA topoisomerase 3-alpha	no	no	0.863	0.152	0.401	3e-34
Q8T2T7	828	DNA topoisomerase 3 OS=Di	yes	no	0.854	0.227	0.388	4e-34
O61660	759	DNA topoisomerase 3 OS=Ca	no	no	0.890	0.258	0.333	4e-27
O60126	622	DNA topoisomerase 3 OS=Sc	yes	no	0.918	0.324	0.350	5e-25
P13099	656	DNA topoisomerase 3 OS=Sa	yes	no	0.868	0.291	0.341	9e-25

>sp|O95985|TOP3B_HUMAN DNA topoisomerase 3-beta-1 OS=Homo sapiens GN=TOP3B PE=1 SV=1

 Score =  231 bits (588), Expect = 4e-60,   Method: Compositional matrix adjust.
 Identities = 117/211 (55%), Positives = 146/211 (69%), Gaps = 7/211 (3%)

Query: 6   VLMVAEKPSIALSIATVLSGGKLYTRKA---STEVHEFDGMFLGSHAYIKVTSVVGHVFR 62
           VLMVAEKPS+A SIA +LS G L + K    +  VHE+ G F G     K+TSV GHV  
Sbjct: 4   VLMVAEKPSLAQSIAKILSRGSLSSHKGLNGACSVHEYTGTFAGQPVRFKMTSVCGHVMT 63

Query: 63  LDFPPAYQDWNASNPLDLF-QAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGE 121
           LDF   Y  W+  +P +LF QAP  K E+NPK+++ + L  E RGC ++VLWLDCD+EGE
Sbjct: 64  LDFLGKYNKWDKVDPAELFSQAPTEKKEANPKLNMVKFLQVEGRGCDYIVLWLDCDKEGE 123

Query: 122 NICFEVIECTGFQVNDA---RRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQE 178
           NICFEV++     +N A    + V RARFSS+T+ DI  AM  L EP+ NEAL+VDARQE
Sbjct: 124 NICFEVLDAVLPVMNKAHGGEKTVFRARFSSITDTDICNAMACLGEPDHNEALSVDARQE 183

Query: 179 IDLKVGVAFTRFQTTYFQGKYGNLDSRFISL 209
           +DL++G AFTRFQT YFQGKYG+LDS  IS 
Sbjct: 184 LDLRIGCAFTRFQTKYFQGKYGDLDSSLISF 214

Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand than undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone (By similarity). Possesses negatively supercoiled DNA relaxing activity.
Homo sapiens (taxid: 9606)
EC: 5EC: .EC: 9EC: 9EC: .EC: 1EC: .EC: 2

>sp|Q9Z321|TOP3B_MOUSE DNA topoisomerase 3-beta-1 OS=Mus musculus GN=Top3b PE=2 SV=1

 Score =  230 bits (587), Expect = 5e-60,   Method: Compositional matrix adjust.
 Identities = 115/211 (54%), Positives = 148/211 (70%), Gaps = 7/211 (3%)

Query: 6   VLMVAEKPSIALSIATVLSGGKLYTRKA---STEVHEFDGMFLGSHAYIKVTSVVGHVFR 62
           VLMVAEKPS+A SIA +LS G + + K    +  VH++ G F G   + K+TSV GHV  
Sbjct: 4   VLMVAEKPSLAQSIAKILSRGNMSSHKGLNGACSVHKYTGTFAGQPVHFKMTSVCGHVMT 63

Query: 63  LDFPPAYQDWNASNPLDLF-QAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGE 121
           LDF   Y  W+  +P +LF QAP  K E+NPK+++ + L  E RGC ++VLWLDCD+EGE
Sbjct: 64  LDFLGKYNKWDKVDPAELFSQAPTEKKEANPKLNMVKFLQVEGRGCDYVVLWLDCDKEGE 123

Query: 122 NICFEVIECTGFQVNDA---RRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQE 178
           NICFEV++     +N+A    + V RARFSS+T+ DI  AM  L EP+ NEAL+VDARQE
Sbjct: 124 NICFEVLDAVLPVMNNAHNGEKTVFRARFSSITDTDICNAMTRLSEPDHNEALSVDARQE 183

Query: 179 IDLKVGVAFTRFQTTYFQGKYGNLDSRFISL 209
           +DL++G AFTRFQT YFQGKYG+LDS  IS 
Sbjct: 184 LDLRIGCAFTRFQTKYFQGKYGDLDSSLISF 214

Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand than undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone (By similarity). Possesses negatively supercoiled DNA relaxing activity.

Mus musculus (taxid: 10090)

EC: 5

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: .

EC: 2

>sp|O96651|TOP3B_DROME DNA topoisomerase 3-beta OS=Drosophila melanogaster GN=Top3beta PE=2 SV=2

 Score =  211 bits (536), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 105/209 (50%), Positives = 142/209 (67%), Gaps = 6/209 (2%)

Query: 6   VLMVAEKPSIALSIATVLSGGKLYTRKAS---TEVHEFDGMFLGSHA-YIKVTSVVGHVF 61
           VLMVAEKPS+A S+A +LS G+   ++ +      HE+ G F    + + ++TSV GHV 
Sbjct: 4   VLMVAEKPSLAASLAGILSNGRCTAKRGTGNGCSTHEWTGNFRNEGSVHFRMTSVCGHVM 63

Query: 62  RLDFPPAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGE 121
            LDF   Y  W+  +P+ LF     K E+NPK ++ + L  EARGC +LVLWLDCD+EGE
Sbjct: 64  SLDFNKKYNCWDKVDPIQLFGCATEKKETNPKQNMRKFLAHEARGCDYLVLWLDCDKEGE 123

Query: 122 NICFEVIECTGFQVND--ARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEI 179
           NICFEV++     +N+  + +  +RA FS++TEKDI KAM  L  PN NEA +VDARQE+
Sbjct: 124 NICFEVMDAVKHVINNVYSDQVTYRAHFSAITEKDIKKAMETLGHPNENEAKSVDARQEL 183

Query: 180 DLKVGVAFTRFQTTYFQGKYGNLDSRFIS 208
           DL++G AFTRFQT +FQ +YG+LDS  IS
Sbjct: 184 DLRIGCAFTRFQTKFFQDRYGDLDSSLIS 212

Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand than undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone (By similarity). Weakly relaxes negative supercoils and displays a distinct preference for binding single-stranded DNA.

Drosophila melanogaster (taxid: 7227)

EC: 5

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: .

EC: 2

>sp|Q13472|TOP3A_HUMAN DNA topoisomerase 3-alpha OS=Homo sapiens GN=TOP3A PE=1 SV=1

 Score =  149 bits (376), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 85/196 (43%), Positives = 116/196 (59%), Gaps = 7/196 (3%)

Query: 5   KVLMVAEKPSIALSIATVLSGGKLYTRKASTE---VHEFDGMFLGSHAYIKVTSVVGHVF 61
           KVL VAEK   A  IA +LS G++  R+  ++   ++EFD    G +  + +TSV GH+ 
Sbjct: 35  KVLCVAEKNDAAKGIADLLSNGRMRRREGLSKFNKIYEFDYHLYGQNVTMVMTSVSGHLL 94

Query: 62  RLDFPPAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGE 121
             DF   ++ W + NPL LF+A + K      V I + L +E R C  LV+W DCDREGE
Sbjct: 95  AHDFQMQFRKWQSCNPLVLFEAEIEKYCPENFVDIKKTLERETRQCQALVIWTDCDREGE 154

Query: 122 NICFEVIE-CTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEID 180
           NI FE+I  C   + N    +V RARFS +T   +  A  NL EP++  + AVD RQE+D
Sbjct: 155 NIGFEIIHVCKAVKPN---LQVLRARFSEITPHAVRTACENLTEPDQRVSDAVDVRQELD 211

Query: 181 LKVGVAFTRFQTTYFQ 196
           L++G AFTRFQT   Q
Sbjct: 212 LRIGAAFTRFQTLRLQ 227

Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand than undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone (By similarity). Essential component of the RMI complex, a complex that plays an important role in the processing of homologous recombination intermediates to limit DNA crossover formation in cells.

Homo sapiens (taxid: 9606)

EC: 5

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: .

EC: 2

>sp|O70157|TOP3A_MOUSE DNA topoisomerase 3-alpha OS=Mus musculus GN=Top3a PE=1 SV=1

 Score =  145 bits (365), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 82/196 (41%), Positives = 115/196 (58%), Gaps = 7/196 (3%)

Query: 5   KVLMVAEKPSIALSIATVLSGGKLYTRKASTE---VHEFDGMFLGSHAYIKVTSVVGHVF 61
           KVL VAEK   A  IA +LS G++  ++  ++   ++EFD    G +  + +TSV GH+ 
Sbjct: 35  KVLCVAEKNDAAKGIADLLSNGRMRRKEGLSKFNKIYEFDYHLYGQNVTMIMTSVSGHLL 94

Query: 62  RLDFPPAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGE 121
             DF   ++ W + NPL LF+A + K      + I + L +E   C  LV+W DCDREGE
Sbjct: 95  AHDFQMQFRKWQSCNPLVLFEAEIEKYCPENFIDIKKTLERETHHCQALVIWTDCDREGE 154

Query: 122 NICFEVIE-CTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEID 180
           NI FE+I  C   + N    +V RARFS +T   +  A  NL EP++  + AVD RQE+D
Sbjct: 155 NIGFEIIHVCKAVKPN---LRVLRARFSEITPHAVRTACENLTEPDQRVSDAVDVRQELD 211

Query: 181 LKVGVAFTRFQTTYFQ 196
           L++G AFTRFQT   Q
Sbjct: 212 LRIGAAFTRFQTLRLQ 227

Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand than undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone. Essential component of the RMI complex, a complex that plays an important role in the processing of homologous recombination intermediates to limit DNA crossover formation in cells.

Mus musculus (taxid: 10090)

EC: 5

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: .

EC: 2

>sp|Q9NG98|TOP3A_DROME DNA topoisomerase 3-alpha OS=Drosophila melanogaster GN=Top3alpha PE=2 SV=2

 Score =  145 bits (365), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 79/197 (40%), Positives = 117/197 (59%), Gaps = 7/197 (3%)

Query: 4   LKVLMVAEKPSIALSIATVLSGGKLYTRKAST---EVHEFDGMFLGSHAYIKVTSVVGHV 60
           +K L VAEK   A +IA +LS G    R+  +   +V +F+    G +A + +TSV GH+
Sbjct: 26  MKYLNVAEKNDAAKTIAGLLSNGAAQRREGYSVYNKVFDFEAPVRGQNAKMVMTSVSGHM 85

Query: 61  FRLDFPPAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREG 120
            +L F  +Y++W   +P  LF APV K   +    I R L +E RGC  L++W DCDREG
Sbjct: 86  MQLAFQVSYKNWRTVDPRSLFDAPVKKGVGSDYEPIKRTLEREVRGCQGLIIWTDCDREG 145

Query: 121 ENICFEVIE-CTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEI 179
           ENI +E+I+ C   + N +   V+RA FS +T   + +A+  L +P++ ++ AVD R E+
Sbjct: 146 ENIGYEIIDVCRAIKPNIS---VYRATFSEITTVAVRRALQQLGQPDKRQSDAVDVRTEL 202

Query: 180 DLKVGVAFTRFQTTYFQ 196
           DL+ G A TRFQT   Q
Sbjct: 203 DLRTGAAITRFQTMRLQ 219

Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand than undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone (By similarity). Weakly relaxes negative supercoils and displays a distinct preference for binding single-stranded DNA.

Drosophila melanogaster (taxid: 7227)

EC: 5

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: .

EC: 2

>sp|Q8T2T7|TOP3_DICDI DNA topoisomerase 3 OS=Dictyostelium discoideum GN=top3 PE=3 SV=1

 Score =  144 bits (364), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 77/198 (38%), Positives = 119/198 (60%), Gaps = 10/198 (5%)

Query: 5   KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVH---EFDGMFLG-SHAYIKVTSVVGHV 60
           ++L VAEKPS A  IA +LS  +   R+  ++ +   +F    L  +   +  TSV GH+
Sbjct: 4   RILNVAEKPSAAKEIAAILSNKRATVREGFSKYNKLWDFKYNILNFNDCEMTFTSVTGHL 63

Query: 61  FRLDFPPAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREG 120
             +D    ++ W + +P+ LF AP+ K   + K  + + L +E +    L+LWLDCDREG
Sbjct: 64  MEIDVVEQFKPWASCDPIQLFDAPIRKTVPSDKEPLKKTLEREIKKADILILWLDCDREG 123

Query: 121 ENICFEVIECTGFQVNDARRK--VHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQE 178
           ENI FEV+E       +A++K   +RA FS++  ++I +A  NL +PN  +++AVD R E
Sbjct: 124 ENIAFEVLEV----CKNAKKKFEFYRAHFSAIIPREIDRACKNLAKPNEKDSIAVDTRME 179

Query: 179 IDLKVGVAFTRFQTTYFQ 196
           IDL++G AFTRFQT Y +
Sbjct: 180 IDLRIGAAFTRFQTLYLK 197

Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand than undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone.

Dictyostelium discoideum (taxid: 44689)

EC: 5

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: .

EC: 2

>sp|O61660|TOP3_CAEEL DNA topoisomerase 3 OS=Caenorhabditis elegans GN=top-3 PE=2 SV=1

 Score =  121 bits (303), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 67/201 (33%), Positives = 110/201 (54%), Gaps = 5/201 (2%)

Query: 5   KVLMVAEKPSIALSIATVLSGGKLYTRKASTE---VHEFDGMFLGSHAYIKVTSVVGHVF 61
           + L VAEK  +A  +A +LS G    R+  ++   ++  +    G    I VTSV GH+ 
Sbjct: 3   RALFVAEKNDVAKGVAAILSNGTANRREGRSKFNKIYTLNTELFGQQTAISVTSVSGHMM 62

Query: 62  RLDFPPAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGE 121
              F     +W  ++ ++LF+APV    +     I + L ++A+    LV+W DCDREGE
Sbjct: 63  NFQFHENMSNWQTASMVELFRAPVRHVVTPEMKLIEQTLREQAQRHDILVVWTDCDREGE 122

Query: 122 NICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDL 181
            I  E+++    + ++ R  + RARFS +T+  I +A  NL+  +     AVD R E+DL
Sbjct: 123 AIGAEIVKVC--RDSNRRLDIFRARFSEITKAAITRAARNLIRLDEKTVAAVDCRSELDL 180

Query: 182 KVGVAFTRFQTTYFQGKYGNL 202
           ++G AFTR QT + + ++ +L
Sbjct: 181 RIGSAFTRLQTLHLRNRFRDL 201

Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand than undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone.

Caenorhabditis elegans (taxid: 6239)

EC: 5

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: .

EC: 2

>sp|O60126|TOP3_SCHPO DNA topoisomerase 3 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=top3 PE=1 SV=2

 Score =  114 bits (285), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 74/211 (35%), Positives = 116/211 (54%), Gaps = 9/211 (4%)

Query: 4   LKVLMVAEKPSIALSIATVLSGGKLY---TRKASTEVHEFDGMFLGS--HAYIKVTSVVG 58
           ++VL VAEK SIA S+A++L GG +    TR    + ++F   F G+   + + +TSV G
Sbjct: 1   MRVLCVAEKNSIAKSVASILGGGHVRRRDTRSKYVKNYDFSFNFGGNVGSSDVTMTSVSG 60

Query: 59  HVFRLDFPPAYQDWNASNPLD-LFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCD 117
           H+    FP  Y  W +S P D LF A +  + S     +  ++ +EAR   +L +W DCD
Sbjct: 61  HLTEASFPSEYSSW-SSVPQDVLFDAQIITSVSKNAEVLADNIKKEARNAQYLYIWTDCD 119

Query: 118 REGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQ 177
           REGE+I  E+      + ++   +V RA F+++    I+ A     + ++N A AVDAR 
Sbjct: 120 REGEHIGVEISNVA--RASNPSIQVIRADFNNLERSHIISAAKRPRDVSKNAADAVDARI 177

Query: 178 EIDLKVGVAFTRFQTTYFQGKYGNLDSRFIS 208
           E+D ++G  FTR QT   Q  +  L ++ IS
Sbjct: 178 ELDFRLGAIFTRLQTIQLQKSFDILQNKIIS 208

Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand than undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone.

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

EC: 5

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: .

EC: 2

>sp|P13099|TOP3_YEAST DNA topoisomerase 3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=TOP3 PE=1 SV=1

 Score =  113 bits (283), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 73/214 (34%), Positives = 112/214 (52%), Gaps = 23/214 (10%)

Query: 4   LKVLMVAEKPSIALSIATVLSGGKLYTRKAS-TEVHEFDGMFLG-------SHAYIKVTS 55
           +KVL VAEK SIA +++ +L GG+  +R +    V  +D MF G       ++  + +TS
Sbjct: 1   MKVLCVAEKNSIAKAVSQILGGGRSTSRDSGYMYVKNYDFMFSGFPFARNGANCEVTMTS 60

Query: 56  VVGHVFRLDFPPAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLD 115
           V GH+  +DF      W      +LF AP+++  +N +  I  ++ +EAR   +L++W D
Sbjct: 61  VAGHLTGIDFSHDSHGWGKCAIQELFDAPLNEIMNNNQKKIASNIKREARNADYLMIWTD 120

Query: 116 CDREGENICFEVIECTGFQVNDARR--------KVHRARFSSVTEKDILKAMGNLVEPNR 167
           CDREGE I +E+ +       +A+R        +V+RA FS +  + IL A  N    + 
Sbjct: 121 CDREGEYIGWEIWQ-------EAKRGNRLIQNDQVYRAVFSHLERQHILNAARNPSRLDM 173

Query: 168 NEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGN 201
               AV  R EIDL+ GV FTR  T   + K  N
Sbjct: 174 KSVHAVGTRIEIDLRAGVTFTRLLTETLRNKLRN 207

Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand than undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone (By similarity). Essential for proper chromosome segregation in both meiosis and mitosis. Weakly relaxes negative supercoils and displays a distinct preference for binding single-stranded DNA. The TOP3-SGS1 protein complex may function as a eukaryotic reverse gyrase introducing positive supercoils into extrachromosomal ribosomal DNA rings.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

EC: 5

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: .

EC: 2

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	220
255550676	865	prokaryotic DNA topoisomerase, putative	0.945	0.240	0.798	1e-95
449459882	867	PREDICTED: DNA topoisomerase 3-beta-1-li	0.945	0.239	0.788	6e-92
359478029	894	PREDICTED: DNA topoisomerase 3-beta-1-li	0.922	0.227	0.785	3e-90
296089603	837	unnamed protein product [Vitis vinifera]	0.922	0.242	0.785	4e-90
449498877	864	PREDICTED: DNA topoisomerase 3-beta-1-li	0.909	0.231	0.795	1e-89
356540116	863	PREDICTED: DNA topoisomerase 3-beta-1-li	0.927	0.236	0.766	2e-88
242045216	866	hypothetical protein SORBIDRAFT_02g02900	0.931	0.236	0.759	6e-88
42569543	865	DNA topoisomerase III [Arabidopsis thali	0.931	0.236	0.756	8e-88
218202402	866	hypothetical protein OsI_31918 [Oryza sa	0.940	0.239	0.740	1e-87
115479969	866	Os09g0500600 [Oryza sativa Japonica Grou	0.940	0.239	0.740	1e-87

>gi|255550676|ref|XP_002516387.1| prokaryotic DNA topoisomerase, putative [Ricinus communis] gi|223544485|gb|EEF46004.1| prokaryotic DNA topoisomerase, putative [Ricinus communis]

 Score =  355 bits (910), Expect = 1e-95,   Method: Compositional matrix adjust.
 Identities = 166/208 (79%), Positives = 188/208 (90%)

Query: 1   MAPLKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHV 60
           MAP  VLMVAEKPSIALSIA+ LS G++ ++K  TEVHEFDGMFLG  A+ KVTSV+GH+
Sbjct: 1   MAPPVVLMVAEKPSIALSIASALSHGQMSSKKGGTEVHEFDGMFLGFQAHYKVTSVIGHI 60

Query: 61  FRLDFPPAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREG 120
           F +DFP  YQDW A++P+DLFQAP+ KAESNPKVHI RHL+QEARGCGHLVLWLDCDREG
Sbjct: 61  FSVDFPQKYQDWTANDPMDLFQAPIVKAESNPKVHIRRHLSQEARGCGHLVLWLDCDREG 120

Query: 121 ENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEID 180
           ENICFEVIECTGF +ND+RR+V+RARFSSV EKDILKAM NLV+PNR+EALAVDARQEID
Sbjct: 121 ENICFEVIECTGFHLNDSRRRVYRARFSSVAEKDILKAMDNLVQPNRDEALAVDARQEID 180

Query: 181 LKVGVAFTRFQTTYFQGKYGNLDSRFIS 208
           LKVGVAFTRFQT++FQGKYGNLDSR IS
Sbjct: 181 LKVGVAFTRFQTSFFQGKYGNLDSRVIS 208

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449459882|ref|XP_004147675.1| PREDICTED: DNA topoisomerase 3-beta-1-like [Cucumis sativus]

 Score =  342 bits (877), Expect = 6e-92,   Method: Compositional matrix adjust.
 Identities = 164/208 (78%), Positives = 180/208 (86%)

Query: 1   MAPLKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHV 60
           M    VLMVAEKPSIALSIA+ LS G++ TRK STEVHEFDG FLG HAY KVTSV+GHV
Sbjct: 1   MVAPTVLMVAEKPSIALSIASALSHGQMSTRKGSTEVHEFDGRFLGHHAYYKVTSVIGHV 60

Query: 61  FRLDFPPAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREG 120
           F +DF   +QDW +++PLDLFQA V K ESNPK HIC+HL++EARGC  LVLWLDCDREG
Sbjct: 61  FSIDFQAGFQDWKSTDPLDLFQASVIKTESNPKAHICQHLSREARGCDCLVLWLDCDREG 120

Query: 121 ENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEID 180
           ENICFEVIECTGF  N  R+KV+RARFSSVTEKDILKA+ NLVEPNRNEALAVDARQEID
Sbjct: 121 ENICFEVIECTGFGGNGTRKKVYRARFSSVTEKDILKALDNLVEPNRNEALAVDARQEID 180

Query: 181 LKVGVAFTRFQTTYFQGKYGNLDSRFIS 208
           LKVGVAFTRFQTT+FQGKYGNLDSR IS
Sbjct: 181 LKVGVAFTRFQTTFFQGKYGNLDSRLIS 208

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359478029|ref|XP_002264970.2| PREDICTED: DNA topoisomerase 3-beta-1-like [Vitis vinifera]

 Score =  337 bits (863), Expect = 3e-90,   Method: Compositional matrix adjust.
 Identities = 161/205 (78%), Positives = 180/205 (87%), Gaps = 2/205 (0%)

Query: 6   VLMVAEKPSIALSIATVLSGGKLYTRK--ASTEVHEFDGMFLGSHAYIKVTSVVGHVFRL 63
           +L VAEKPSIALSIA+ LSGG + TR+  +STEVHEF+G F GS+A  KVTSV+GHVF +
Sbjct: 32  ILQVAEKPSIALSIASALSGGHMSTRRGGSSTEVHEFNGTFRGSNAQYKVTSVIGHVFSV 91

Query: 64  DFPPAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENI 123
           DFP  YQDW  ++PLDLFQAP+ KAESNPK HI RHL+QEAR CGHLVLWLDCDREGENI
Sbjct: 92  DFPAKYQDWTVTDPLDLFQAPILKAESNPKAHIRRHLSQEARDCGHLVLWLDCDREGENI 151

Query: 124 CFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDLKV 183
           CFEV+ECTGF  N+ARR+V+RARFSSVTEKDILKAM NLVEPN +EA AVDARQEIDLKV
Sbjct: 152 CFEVVECTGFHGNEARRRVYRARFSSVTEKDILKAMDNLVEPNEDEARAVDARQEIDLKV 211

Query: 184 GVAFTRFQTTYFQGKYGNLDSRFIS 208
           GVAFTRFQT+YFQGKYGNLDSR IS
Sbjct: 212 GVAFTRFQTSYFQGKYGNLDSRVIS 236

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296089603|emb|CBI39422.3| unnamed protein product [Vitis vinifera]

 Score =  336 bits (861), Expect = 4e-90,   Method: Compositional matrix adjust.
 Identities = 161/205 (78%), Positives = 180/205 (87%), Gaps = 2/205 (0%)

Query: 6   VLMVAEKPSIALSIATVLSGGKLYTRK--ASTEVHEFDGMFLGSHAYIKVTSVVGHVFRL 63
           +L VAEKPSIALSIA+ LSGG + TR+  +STEVHEF+G F GS+A  KVTSV+GHVF +
Sbjct: 48  ILQVAEKPSIALSIASALSGGHMSTRRGGSSTEVHEFNGTFRGSNAQYKVTSVIGHVFSV 107

Query: 64  DFPPAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENI 123
           DFP  YQDW  ++PLDLFQAP+ KAESNPK HI RHL+QEAR CGHLVLWLDCDREGENI
Sbjct: 108 DFPAKYQDWTVTDPLDLFQAPILKAESNPKAHIRRHLSQEARDCGHLVLWLDCDREGENI 167

Query: 124 CFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDLKV 183
           CFEV+ECTGF  N+ARR+V+RARFSSVTEKDILKAM NLVEPN +EA AVDARQEIDLKV
Sbjct: 168 CFEVVECTGFHGNEARRRVYRARFSSVTEKDILKAMDNLVEPNEDEARAVDARQEIDLKV 227

Query: 184 GVAFTRFQTTYFQGKYGNLDSRFIS 208
           GVAFTRFQT+YFQGKYGNLDSR IS
Sbjct: 228 GVAFTRFQTSYFQGKYGNLDSRVIS 252

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449498877|ref|XP_004160658.1| PREDICTED: DNA topoisomerase 3-beta-1-like [Cucumis sativus]

 Score =  335 bits (858), Expect = 1e-89,   Method: Compositional matrix adjust.
 Identities = 159/200 (79%), Positives = 176/200 (88%)

Query: 9   VAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPA 68
           VAEKPSIALSIA+ LS G++ TRK STEVHEFDG FLG HAY KVTSV+GHVF +DF   
Sbjct: 6   VAEKPSIALSIASALSHGQMSTRKGSTEVHEFDGRFLGHHAYYKVTSVIGHVFSIDFQAG 65

Query: 69  YQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVI 128
           +QDW +++PLDLFQA V K ESNPK HIC+HL++EARGC  LVLWLDCDREGENICFEVI
Sbjct: 66  FQDWKSTDPLDLFQASVIKTESNPKAHICQHLSREARGCDCLVLWLDCDREGENICFEVI 125

Query: 129 ECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDLKVGVAFT 188
           EC+GF  N  R+KV+RARFSSVTEKDILKA+ NLVEPNRNEALAVDARQEIDLKVGVAFT
Sbjct: 126 ECSGFGGNGTRKKVYRARFSSVTEKDILKALDNLVEPNRNEALAVDARQEIDLKVGVAFT 185

Query: 189 RFQTTYFQGKYGNLDSRFIS 208
           RFQTT+FQGKYGNLDSR IS
Sbjct: 186 RFQTTFFQGKYGNLDSRLIS 205

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356540116|ref|XP_003538536.1| PREDICTED: DNA topoisomerase 3-beta-1-like [Glycine max]

 Score =  330 bits (847), Expect = 2e-88,   Method: Compositional matrix adjust.
 Identities = 161/210 (76%), Positives = 182/210 (86%), Gaps = 6/210 (2%)

Query: 1   MAPL--KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVG 58
           MAP   KVLMVAEKPSIALSIA+VLS  +++TR+ STEVHEFDG FLGS A+ +VTSV+G
Sbjct: 1   MAPPIPKVLMVAEKPSIALSIASVLSHAQMFTRRGSTEVHEFDGKFLGSPAHFRVTSVIG 60

Query: 59  HVFRLDFPPAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDR 118
           HVF +DFP  YQDW A++PLDLFQA V K ESNPK HICRHL+QEARGC +LVLWLDCDR
Sbjct: 61  HVFSVDFPGKYQDWAATDPLDLFQAQVIKNESNPKAHICRHLSQEARGCRYLVLWLDCDR 120

Query: 119 EGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQE 178
           EGENICFEVI+ TGF +ND     +RARFSSVTEKD++KA+ NLV PNR+EALAVDARQE
Sbjct: 121 EGENICFEVIKSTGFHIND----TYRARFSSVTEKDVVKALDNLVRPNRDEALAVDARQE 176

Query: 179 IDLKVGVAFTRFQTTYFQGKYGNLDSRFIS 208
           IDLKVGVAFTRFQT+YFQGKYGNLDSR IS
Sbjct: 177 IDLKVGVAFTRFQTSYFQGKYGNLDSRVIS 206

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242045216|ref|XP_002460479.1| hypothetical protein SORBIDRAFT_02g029000 [Sorghum bicolor] gi|241923856|gb|EER97000.1| hypothetical protein SORBIDRAFT_02g029000 [Sorghum bicolor]

 Score =  328 bits (842), Expect = 6e-88,   Method: Compositional matrix adjust.
 Identities = 158/208 (75%), Positives = 180/208 (86%), Gaps = 3/208 (1%)

Query: 1   MAPLKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHV 60
           MAP KVLMVAEKPSIALSIA+ LSGG++ TRK ST+VHEFDG F GS+A  KVTSV+GHV
Sbjct: 1   MAP-KVLMVAEKPSIALSIASALSGGRMSTRKGSTDVHEFDGTFQGSYANFKVTSVIGHV 59

Query: 61  FRLDFPPAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREG 120
             +DFPPAYQ+W A++PLDLF+APV ++E NPK HI RHL QEARGC +L+LWLDCDREG
Sbjct: 60  LSVDFPPAYQNWEATDPLDLFEAPVLRSECNPKAHIRRHLAQEARGCTYLILWLDCDREG 119

Query: 121 ENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEID 180
           ENIC+EVIECTG  + D  R++ RARFSSVTEKDIL AM NLV PN++EAL+VDARQEID
Sbjct: 120 ENICYEVIECTG--IPDNGRRIFRARFSSVTEKDILTAMDNLVLPNKDEALSVDARQEID 177

Query: 181 LKVGVAFTRFQTTYFQGKYGNLDSRFIS 208
           LKVGVAFTRFQT YFQGKYGNLDSR IS
Sbjct: 178 LKVGVAFTRFQTRYFQGKYGNLDSRVIS 205

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|42569543|ref|NP_180760.2| DNA topoisomerase III [Arabidopsis thaliana] gi|330253525|gb|AEC08619.1| DNA topoisomerase III [Arabidopsis thaliana]

 Score =  328 bits (842), Expect = 8e-88,   Method: Compositional matrix adjust.
 Identities = 155/205 (75%), Positives = 177/205 (86%)

Query: 4   LKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRL 63
           L+VLMVAEKPSIALSIA+VLS G++ TR+ STEVHEFDGMF G  A+ +VTSV+GHVF +
Sbjct: 5   LRVLMVAEKPSIALSIASVLSHGQMSTRRGSTEVHEFDGMFRGFKAHYRVTSVIGHVFSV 64

Query: 64  DFPPAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENI 123
           DFP  YQ+W   +P DLF AP+ K ESNPK HICRHL+ EARGC ++VLWLDCDREGENI
Sbjct: 65  DFPEKYQNWATIDPQDLFDAPIIKKESNPKAHICRHLSNEARGCSYMVLWLDCDREGENI 124

Query: 124 CFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDLKV 183
           CFEVIE TGF + D++RKV+RARFSSVTEKDI KAM NLVEPNR+EALAVDARQEIDLKV
Sbjct: 125 CFEVIESTGFDMKDSKRKVYRARFSSVTEKDISKAMDNLVEPNRDEALAVDARQEIDLKV 184

Query: 184 GVAFTRFQTTYFQGKYGNLDSRFIS 208
           GVAF+RFQT+YFQGKY NLD R IS
Sbjct: 185 GVAFSRFQTSYFQGKYQNLDCRVIS 209

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|218202402|gb|EEC84829.1| hypothetical protein OsI_31918 [Oryza sativa Indica Group]

 Score =  328 bits (841), Expect = 1e-87,   Method: Compositional matrix adjust.
 Identities = 154/208 (74%), Positives = 179/208 (86%), Gaps = 1/208 (0%)

Query: 1   MAPLKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHV 60
           MAP  VLMVAEKPSIALSIA+ LSGG++ TRK ST+VHEFDGMF GSHA+ KVTSV+GHV
Sbjct: 1   MAP-TVLMVAEKPSIALSIASALSGGRMSTRKGSTDVHEFDGMFQGSHAFFKVTSVIGHV 59

Query: 61  FRLDFPPAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREG 120
             +DFPPAYQ+W  ++P+DLF APV ++E NPK HI RHL QEARGC +LVLWLDCDREG
Sbjct: 60  LSVDFPPAYQNWEGTDPMDLFVAPVLRSECNPKAHIRRHLAQEARGCTYLVLWLDCDREG 119

Query: 121 ENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEID 180
           ENIC+EVI+CTG   ++  R++ RA+FSSVTEKDI+ AM NLV P+++EALAVDARQEID
Sbjct: 120 ENICYEVIDCTGIPKSEVGRRIFRAKFSSVTEKDIMDAMNNLVLPSKDEALAVDARQEID 179

Query: 181 LKVGVAFTRFQTTYFQGKYGNLDSRFIS 208
           LKVGVAFTRFQT YFQGKYGNLDSR IS
Sbjct: 180 LKVGVAFTRFQTRYFQGKYGNLDSRVIS 207

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115479969|ref|NP_001063578.1| Os09g0500600 [Oryza sativa Japonica Group] gi|113631811|dbj|BAF25492.1| Os09g0500600 [Oryza sativa Japonica Group] gi|215695029|dbj|BAG90220.1| unnamed protein product [Oryza sativa Japonica Group]

 Score =  328 bits (841), Expect = 1e-87,   Method: Compositional matrix adjust.
 Identities = 154/208 (74%), Positives = 179/208 (86%), Gaps = 1/208 (0%)

Query: 1   MAPLKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHV 60
           MAP  VLMVAEKPSIALSIA+ LSGG++ TRK ST+VHEFDGMF GSHA+ KVTSV+GHV
Sbjct: 1   MAP-TVLMVAEKPSIALSIASALSGGRMSTRKGSTDVHEFDGMFQGSHAFFKVTSVIGHV 59

Query: 61  FRLDFPPAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREG 120
             +DFPPAYQ+W  ++P+DLF APV ++E NPK HI RHL QEARGC +LVLWLDCDREG
Sbjct: 60  LSVDFPPAYQNWEGTDPMDLFVAPVLRSECNPKAHIRRHLAQEARGCTYLVLWLDCDREG 119

Query: 121 ENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEID 180
           ENIC+EVI+CTG   ++  R++ RA+FSSVTEKDI+ AM NLV P+++EALAVDARQEID
Sbjct: 120 ENICYEVIDCTGIPKSEVGRRIFRAKFSSVTEKDIMDAMNNLVLPSKDEALAVDARQEID 179

Query: 181 LKVGVAFTRFQTTYFQGKYGNLDSRFIS 208
           LKVGVAFTRFQT YFQGKYGNLDSR IS
Sbjct: 180 LKVGVAFTRFQTRYFQGKYGNLDSRVIS 207

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	220
TAIR|locus:2045517	865	AT2G32000 [Arabidopsis thalian	0.931	0.236	0.756	2.5e-81
ZFIN|ZDB-GENE-070705-37	862	top3b "topoisomerase (DNA) III	0.922	0.235	0.561	5.4e-57
UNIPROTKB|Q5ZK71	862	TOP3B "DNA topoisomerase" [Gal	0.922	0.235	0.557	9.1e-57
UNIPROTKB|E1BQG8	863	TOP3B "DNA topoisomerase" [Gal	0.922	0.235	0.557	9.3e-57
UNIPROTKB|F1RL05	859	TOP3B "DNA topoisomerase" [Sus	0.922	0.236	0.547	1.6e-55
UNIPROTKB|C9JEI7	246	TOP3B "DNA topoisomerase 3-bet	0.922	0.825	0.557	1.8e-55
RGD|1309468	862	Top3b "topoisomerase (DNA) III	0.922	0.235	0.547	2.1e-55
MGI|MGI:1333803	862	Top3b "topoisomerase (DNA) III	0.922	0.235	0.547	3.6e-55
UNIPROTKB|E2R770	862	TOP3B "DNA topoisomerase" [Can	0.922	0.235	0.547	4.6e-55
UNIPROTKB|O95985	862	TOP3B "DNA topoisomerase 3-bet	0.922	0.235	0.557	4.6e-55

TAIR|locus:2045517 AT2G32000 [Arabidopsis thaliana (taxid:3702)]

 Score = 816 (292.3 bits), Expect = 2.5e-81, P = 2.5e-81
 Identities = 155/205 (75%), Positives = 177/205 (86%)

Query:     4 LKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRL 63
             L+VLMVAEKPSIALSIA+VLS G++ TR+ STEVHEFDGMF G  A+ +VTSV+GHVF +
Sbjct:     5 LRVLMVAEKPSIALSIASVLSHGQMSTRRGSTEVHEFDGMFRGFKAHYRVTSVIGHVFSV 64

Query:    64 DFPPAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENI 123
             DFP  YQ+W   +P DLF AP+ K ESNPK HICRHL+ EARGC ++VLWLDCDREGENI
Sbjct:    65 DFPEKYQNWATIDPQDLFDAPIIKKESNPKAHICRHLSNEARGCSYMVLWLDCDREGENI 124

Query:   124 CFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDLKV 183
             CFEVIE TGF + D++RKV+RARFSSVTEKDI KAM NLVEPNR+EALAVDARQEIDLKV
Sbjct:   125 CFEVIESTGFDMKDSKRKVYRARFSSVTEKDISKAMDNLVEPNRDEALAVDARQEIDLKV 184

Query:   184 GVAFTRFQTTYFQGKYGNLDSRFIS 208
             GVAF+RFQT+YFQGKY NLD R IS
Sbjct:   185 GVAFSRFQTSYFQGKYQNLDCRVIS 209

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

GO:0003916 "DNA topoisomerase activity" evidence=IEA

GO:0003917 "DNA topoisomerase type I activity" evidence=IEA;ISS

GO:0005576 "extracellular region" evidence=ISM

GO:0005694 "chromosome" evidence=IEA

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

GO:0006268 "DNA unwinding involved in replication" evidence=ISS

GO:0048573 "photoperiodism, flowering" evidence=RCA

ZFIN|ZDB-GENE-070705-37 top3b "topoisomerase (DNA) III beta" [Danio rerio (taxid:7955)]

 Score = 589 (212.4 bits), Expect = 5.4e-57, P = 5.4e-57
 Identities = 118/210 (56%), Positives = 150/210 (71%)

Query:     6 VLMVAEKPSIALSIATVLSGGKLYTRKA---STEVHEFDGMFLGSHAYIKVTSVVGHVFR 62
             VLMVAEKPS+A SIA +LS G   TRK    +  VHE+ G F G +   K+TSV GHV  
Sbjct:     4 VLMVAEKPSLAQSIAKILSKGSCSTRKGLNGACSVHEYMGSFTGQNVRFKMTSVCGHVMS 63

Query:    63 LDFPPAYQDWNASNPLDLF-QAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGE 121
             LDF   Y +W+  +P +LF +AP  K E+NPK+++ + L  EA+GC ++VLWLDCD+EGE
Sbjct:    64 LDFIGKYNNWDKVDPAELFSKAPTEKKEANPKLNMVKFLQVEAKGCDYVVLWLDCDKEGE 123

Query:   122 NICFEVIECTGFQVNDA---RRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQE 178
             NICFEV++     +N      R V+RA+FSS+T+ DI  AM  L EPN+NEAL+VDARQE
Sbjct:   124 NICFEVLDAIQPVMNKPYGNERTVYRAKFSSITDTDICNAMNRLGEPNKNEALSVDARQE 183

Query:   179 IDLKVGVAFTRFQTTYFQGKYGNLDSRFIS 208
             +DL++G AFTRFQT YFQGKYGNLDS  IS
Sbjct:   184 LDLRIGCAFTRFQTKYFQGKYGNLDSSLIS 213

GO:0003677 "DNA binding" evidence=IEA

GO:0003916 "DNA topoisomerase activity" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

GO:0006265 "DNA topological change" evidence=IEA

GO:0003917 "DNA topoisomerase type I activity" evidence=IEA

GO:0016853 "isomerase activity" evidence=IEA

UNIPROTKB|Q5ZK71 TOP3B "DNA topoisomerase" [Gallus gallus (taxid:9031)]

 Score = 587 (211.7 bits), Expect = 9.1e-57, P = 9.1e-57
 Identities = 117/210 (55%), Positives = 149/210 (70%)

Query:     6 VLMVAEKPSIALSIATVLSGGKLYTRKAST---EVHEFDGMFLGSHAYIKVTSVVGHVFR 62
             VLMVAEKPS+A SIA +LS G + +RK       VHE+ G F+G  A+ K+TSV GHV  
Sbjct:     4 VLMVAEKPSLAQSIAKILSRGNMSSRKGLNGVCSVHEYTGSFIGQSAHFKMTSVCGHVMT 63

Query:    63 LDFPPAYQDWNASNPLDLF-QAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGE 121
             LDF   Y  W+  +P +LF +AP  K E+NPK+ + + L  E RGC  +VLWLDCD+EGE
Sbjct:    64 LDFIGKYNSWDKVDPAELFSKAPTEKKEANPKLTMVKFLQVEGRGCDSIVLWLDCDKEGE 123

Query:   122 NICFEVIECTGFQVNDA---RRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQE 178
             NICFEV++     +N +    R ++RA+FSS+T+ DI  AM +L EPN NEAL+VDARQE
Sbjct:   124 NICFEVLDAVLPVMNKSPSTERMIYRAKFSSITDTDICNAMNHLGEPNLNEALSVDARQE 183

Query:   179 IDLKVGVAFTRFQTTYFQGKYGNLDSRFIS 208
             +DL++G AFTRFQT YFQGKYGNLDS  IS
Sbjct:   184 LDLRIGCAFTRFQTKYFQGKYGNLDSSLIS 213

GO:0005694 "chromosome" evidence=IEA

GO:0006265 "DNA topological change" evidence=IEA

GO:0003917 "DNA topoisomerase type I activity" evidence=IEA

UNIPROTKB|E1BQG8 TOP3B "DNA topoisomerase" [Gallus gallus (taxid:9031)]

 Score = 587 (211.7 bits), Expect = 9.3e-57, P = 9.3e-57
 Identities = 117/210 (55%), Positives = 149/210 (70%)

Query:     6 VLMVAEKPSIALSIATVLSGGKLYTRKAST---EVHEFDGMFLGSHAYIKVTSVVGHVFR 62
             VLMVAEKPS+A SIA +LS G + +RK       VHE+ G F+G  A+ K+TSV GHV  
Sbjct:     4 VLMVAEKPSLAQSIAKILSRGNMSSRKGLNGVCSVHEYTGSFIGQSAHFKMTSVCGHVMT 63

Query:    63 LDFPPAYQDWNASNPLDLF-QAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGE 121
             LDF   Y  W+  +P +LF +AP  K E+NPK+ + + L  E RGC  +VLWLDCD+EGE
Sbjct:    64 LDFIGKYNSWDKVDPAELFSKAPTEKKEANPKLTMVKFLQVEGRGCDSIVLWLDCDKEGE 123

Query:   122 NICFEVIECTGFQVNDA---RRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQE 178
             NICFEV++     +N +    R ++RA+FSS+T+ DI  AM +L EPN NEAL+VDARQE
Sbjct:   124 NICFEVLDAVLPVMNKSPSTERMIYRAKFSSITDTDICNAMNHLGEPNLNEALSVDARQE 183

Query:   179 IDLKVGVAFTRFQTTYFQGKYGNLDSRFIS 208
             +DL++G AFTRFQT YFQGKYGNLDS  IS
Sbjct:   184 LDLRIGCAFTRFQTKYFQGKYGNLDSSLIS 213

GO:0006265 "DNA topological change" evidence=IEA

GO:0000793 "condensed chromosome" evidence=IEA

GO:0007059 "chromosome segregation" evidence=IEA

GO:0003917 "DNA topoisomerase type I activity" evidence=IEA

UNIPROTKB|F1RL05 TOP3B "DNA topoisomerase" [Sus scrofa (taxid:9823)]

 Score = 576 (207.8 bits), Expect = 1.6e-55, P = 1.6e-55
 Identities = 115/210 (54%), Positives = 148/210 (70%)

Query:     6 VLMVAEKPSIALSIATVLSGGKLYTRKA---STEVHEFDGMFLGSHAYIKVTSVVGHVFR 62
             VLMVAEKPS+A SIA +LS G + + K    +  VHE+ G F G   + K+TSV GHV  
Sbjct:     4 VLMVAEKPSLAQSIARILSRGNMSSHKGLNGTCSVHEYTGTFAGQPVHFKMTSVCGHVMT 63

Query:    63 LDFPPAYQDWNASNPLDLF-QAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGE 121
             LDF   Y  W+  +P +LF QAP  K E+NPK+++ + L  E +GC ++VLWLDCD+EGE
Sbjct:    64 LDFLGKYNKWDKVDPAELFSQAPTEKKEANPKLNMVKFLQVEGKGCDYIVLWLDCDKEGE 123

Query:   122 NICFEVIECTGFQVNDAR---RKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQE 178
             NICFEV++     +N A    + V RARFSS+T+ DI  AM +L EP+ NEAL+VDARQE
Sbjct:   124 NICFEVLDAVLPVMNQAHGSEKTVFRARFSSITDTDICNAMAHLGEPDHNEALSVDARQE 183

Query:   179 IDLKVGVAFTRFQTTYFQGKYGNLDSRFIS 208
             +DL++G AFTRFQT YFQGKYG+LDS  IS
Sbjct:   184 LDLRIGCAFTRFQTKYFQGKYGDLDSSLIS 213

GO:0007059 "chromosome segregation" evidence=IEA

GO:0000793 "condensed chromosome" evidence=IEA

GO:0003917 "DNA topoisomerase type I activity" evidence=IEA

GO:0006265 "DNA topological change" evidence=IEA

UNIPROTKB|C9JEI7 TOP3B "DNA topoisomerase 3-beta-1" [Homo sapiens (taxid:9606)]

 Score = 572 (206.4 bits), Expect = 1.8e-55, P = 1.8e-55
 Identities = 117/210 (55%), Positives = 146/210 (69%)

Query:     6 VLMVAEKPSIALSIATVLSGGKLYTRKA---STEVHEFDGMFLGSHAYIKVTSVVGHVFR 62
             VLMVAEKPS+A SIA +LS G L + K    +  VHE+ G F G     K+TSV GHV  
Sbjct:     4 VLMVAEKPSLAQSIAKILSRGSLSSHKGLNGACSVHEYTGTFAGQPVRFKMTSVCGHVMT 63

Query:    63 LDFPPAYQDWNASNPLDLF-QAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGE 121
             LDF   Y  W+  +P +LF QAP  K E+NPK+++ + L  E RGC ++VLWLDCD+EGE
Sbjct:    64 LDFLGKYNKWDKVDPAELFSQAPTEKKEANPKLNMVKFLQVEGRGCDYIVLWLDCDKEGE 123

Query:   122 NICFEVIECTGFQVNDAR---RKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQE 178
             NICFEV++     +N A    + V RARFSS+T+ DI  AM  L EP+ NEAL+VDARQE
Sbjct:   124 NICFEVLDAVLPVMNKAHGGEKTVFRARFSSITDTDICNAMACLGEPDHNEALSVDARQE 183

Query:   179 IDLKVGVAFTRFQTTYFQGKYGNLDSRFIS 208
             +DL++G AFTRFQT YFQGKYG+LDS  IS
Sbjct:   184 LDLRIGCAFTRFQTKYFQGKYGDLDSSLIS 213

GO:0003917 "DNA topoisomerase type I activity" evidence=IEA

GO:0006265 "DNA topological change" evidence=IEA

GO:0000793 "condensed chromosome" evidence=IEA

GO:0007059 "chromosome segregation" evidence=IEA

RGD|1309468 Top3b "topoisomerase (DNA) III beta" [Rattus norvegicus (taxid:10116)]

 Score = 575 (207.5 bits), Expect = 2.1e-55, P = 2.1e-55
 Identities = 115/210 (54%), Positives = 148/210 (70%)

Query:     6 VLMVAEKPSIALSIATVLSGGKLYTRKA---STEVHEFDGMFLGSHAYIKVTSVVGHVFR 62
             VLMVAEKPS+A SIA +LS G + + K    +  VH++ G F G   + K+TSV GHV  
Sbjct:     4 VLMVAEKPSLAQSIAKILSRGNMSSHKGLNGACSVHKYTGTFAGQPVHFKMTSVCGHVMT 63

Query:    63 LDFPPAYQDWNASNPLDLF-QAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGE 121
             LDF   Y  W+  +P +LF QAP  K E+NPK+++ + L  E RGC ++VLWLDCD+EGE
Sbjct:    64 LDFLGKYNKWDKVDPAELFSQAPTEKKEANPKLNMVKFLQVEGRGCDYVVLWLDCDKEGE 123

Query:   122 NICFEVIECTGFQVNDAR---RKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQE 178
             NICFEV++     +N+A    + V RARFSS+T+ DI  AM  L EP+ NEAL+VDARQE
Sbjct:   124 NICFEVLDAVLPVLNNAHNGEKTVFRARFSSITDTDICNAMTRLTEPDHNEALSVDARQE 183

Query:   179 IDLKVGVAFTRFQTTYFQGKYGNLDSRFIS 208
             +DL++G AFTRFQT YFQGKYG+LDS  IS
Sbjct:   184 LDLRIGCAFTRFQTKYFQGKYGDLDSSLIS 213

GO:0000793 "condensed chromosome" evidence=IEA;ISO

GO:0003917 "DNA topoisomerase type I activity" evidence=IEA

GO:0006265 "DNA topological change" evidence=IEA

GO:0007059 "chromosome segregation" evidence=IEA;ISO

MGI|MGI:1333803 Top3b "topoisomerase (DNA) III beta" [Mus musculus (taxid:10090)]

 Score = 573 (206.8 bits), Expect = 3.6e-55, P = 3.6e-55
 Identities = 115/210 (54%), Positives = 148/210 (70%)

Query:     6 VLMVAEKPSIALSIATVLSGGKLYTRKA---STEVHEFDGMFLGSHAYIKVTSVVGHVFR 62
             VLMVAEKPS+A SIA +LS G + + K    +  VH++ G F G   + K+TSV GHV  
Sbjct:     4 VLMVAEKPSLAQSIAKILSRGNMSSHKGLNGACSVHKYTGTFAGQPVHFKMTSVCGHVMT 63

Query:    63 LDFPPAYQDWNASNPLDLF-QAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGE 121
             LDF   Y  W+  +P +LF QAP  K E+NPK+++ + L  E RGC ++VLWLDCD+EGE
Sbjct:    64 LDFLGKYNKWDKVDPAELFSQAPTEKKEANPKLNMVKFLQVEGRGCDYVVLWLDCDKEGE 123

Query:   122 NICFEVIECTGFQVNDAR---RKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQE 178
             NICFEV++     +N+A    + V RARFSS+T+ DI  AM  L EP+ NEAL+VDARQE
Sbjct:   124 NICFEVLDAVLPVMNNAHNGEKTVFRARFSSITDTDICNAMTRLSEPDHNEALSVDARQE 183

Query:   179 IDLKVGVAFTRFQTTYFQGKYGNLDSRFIS 208
             +DL++G AFTRFQT YFQGKYG+LDS  IS
Sbjct:   184 LDLRIGCAFTRFQTKYFQGKYGDLDSSLIS 213

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000793 "condensed chromosome" evidence=IDA

GO:0003677 "DNA binding" evidence=IEA

GO:0003916 "DNA topoisomerase activity" evidence=IEA

GO:0003917 "DNA topoisomerase type I activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

GO:0006265 "DNA topological change" evidence=IEA

GO:0007059 "chromosome segregation" evidence=IMP

GO:0016853 "isomerase activity" evidence=IEA

UNIPROTKB|E2R770 TOP3B "DNA topoisomerase" [Canis lupus familiaris (taxid:9615)]

 Score = 572 (206.4 bits), Expect = 4.6e-55, P = 4.6e-55
 Identities = 115/210 (54%), Positives = 145/210 (69%)

Query:     6 VLMVAEKPSIALSIATVLSGGKLYTRKA---STEVHEFDGMFLGSHAYIKVTSVVGHVFR 62
             VLMVAEKPS+A SIA +LS G + + K    +  VHE+ G F G     K+TSV GHV  
Sbjct:     4 VLMVAEKPSLAQSIAKILSRGNMSSHKGLNGTCSVHEYSGTFAGQPVRFKMTSVCGHVMT 63

Query:    63 LDFPPAYQDWNASNPLDLF-QAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGE 121
             LDF   Y  W+  +P +LF QAP  K E+NPK+++ + L  E +GC ++VLWLDCD+EGE
Sbjct:    64 LDFLGKYNKWDKVDPAELFSQAPTEKKEANPKLNMVKFLQVEGKGCDYIVLWLDCDKEGE 123

Query:   122 NICFEVIECTGFQVN---DARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQE 178
             NICFEV++     +N      + V RARFSS+T+ DI  AM  L EP+ NEAL+VDARQE
Sbjct:   124 NICFEVLDAVLPVMNPTHSGEKTVFRARFSSITDTDICAAMARLGEPDHNEALSVDARQE 183

Query:   179 IDLKVGVAFTRFQTTYFQGKYGNLDSRFIS 208
             +DL++G AFTRFQT YFQGKYGNLDS  IS
Sbjct:   184 LDLRIGCAFTRFQTKYFQGKYGNLDSSLIS 213

GO:0007059 "chromosome segregation" evidence=IEA

GO:0000793 "condensed chromosome" evidence=IEA

GO:0003917 "DNA topoisomerase type I activity" evidence=IEA

GO:0006265 "DNA topological change" evidence=IEA

UNIPROTKB|O95985 TOP3B "DNA topoisomerase 3-beta-1" [Homo sapiens (taxid:9606)]

 Score = 572 (206.4 bits), Expect = 4.6e-55, P = 4.6e-55
 Identities = 117/210 (55%), Positives = 146/210 (69%)

Query:     6 VLMVAEKPSIALSIATVLSGGKLYTRKA---STEVHEFDGMFLGSHAYIKVTSVVGHVFR 62
             VLMVAEKPS+A SIA +LS G L + K    +  VHE+ G F G     K+TSV GHV  
Sbjct:     4 VLMVAEKPSLAQSIAKILSRGSLSSHKGLNGACSVHEYTGTFAGQPVRFKMTSVCGHVMT 63

Query:    63 LDFPPAYQDWNASNPLDLF-QAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGE 121
             LDF   Y  W+  +P +LF QAP  K E+NPK+++ + L  E RGC ++VLWLDCD+EGE
Sbjct:    64 LDFLGKYNKWDKVDPAELFSQAPTEKKEANPKLNMVKFLQVEGRGCDYIVLWLDCDKEGE 123

Query:   122 NICFEVIECTGFQVNDAR---RKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQE 178
             NICFEV++     +N A    + V RARFSS+T+ DI  AM  L EP+ NEAL+VDARQE
Sbjct:   124 NICFEVLDAVLPVMNKAHGGEKTVFRARFSSITDTDICNAMACLGEPDHNEALSVDARQE 183

Query:   179 IDLKVGVAFTRFQTTYFQGKYGNLDSRFIS 208
             +DL++G AFTRFQT YFQGKYG+LDS  IS
Sbjct:   184 LDLRIGCAFTRFQTKYFQGKYGDLDSSLIS 213

GO:0006265 "DNA topological change" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003917 "DNA topoisomerase type I activity" evidence=IEA

GO:0000793 "condensed chromosome" evidence=IEA

GO:0007059 "chromosome segregation" evidence=IEA

GO:0003677 "DNA binding" evidence=TAS

GO:0003916 "DNA topoisomerase activity" evidence=TAS

GO:0005634 "nucleus" evidence=TAS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	220
cd03362	151	cd03362, TOPRIM_TopoIA_TopoIII, TOPRIM_TopoIA_Topo	7e-49
cd01028	142	cd01028, TOPRIM_TopoIA, TOPRIM_TopoIA: topoisomera	2e-43
PRK07219	822	PRK07219, PRK07219, DNA topoisomerase I; Validated	6e-41
COG0550	570	COG0550, TopA, Topoisomerase IA [DNA replication,	3e-35
PRK07220	740	PRK07220, PRK07220, DNA topoisomerase I; Validated	8e-26
PRK14973	936	PRK14973, PRK14973, DNA topoisomerase I; Provision	2e-18
smart00436	89	smart00436, TOP1Bc, Bacterial DNA topoisomeraes I	3e-13
PRK05776	670	PRK05776, PRK05776, DNA topoisomerase I; Provision	2e-12
TIGR01057	618	TIGR01057, topA_arch, DNA topoisomerase I, archaea	2e-11
TIGR01056	660	TIGR01056, topB, DNA topoisomerase III, bacteria a	2e-10
PRK08173	862	PRK08173, PRK08173, DNA topoisomerase III; Validat	8e-08
PRK07726	658	PRK07726, PRK07726, DNA topoisomerase III; Provisi	2e-07
PRK14724	987	PRK14724, PRK14724, DNA topoisomerase III; Provisi	9e-07
cd03363	123	cd03363, TOPRIM_TopoIA_TopoI, TOPRIM_TopoIA_TopoI:	3e-06
cd00186	381	cd00186, TOP1Ac, DNA Topoisomerase, subtype IA; DN	6e-06
smart00493	75	smart00493, TOPRIM, topoisomerases, DnaG-type prim	1e-05
TIGR01051	610	TIGR01051, topA_bact, DNA topoisomerase I, bacteri	2e-05
pfam01131	365	pfam01131, Topoisom_bac, DNA topoisomerase	3e-05
TIGR01054	1171	TIGR01054, rgy, reverse gyrase	4e-04
PRK06599	675	PRK06599, PRK06599, DNA topoisomerase I; Validated	0.001
cd00188	83	cd00188, TOPRIM, Topoisomerase-primase domain	0.002
pfam01751	86	pfam01751, Toprim, Toprim domain	0.004

>gnl|CDD|173782 cd03362, TOPRIM_TopoIA_TopoIII, TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III

 Score =  156 bits (397), Expect = 7e-49
 Identities = 57/160 (35%), Positives = 76/160 (47%), Gaps = 11/160 (6%)

Query: 5   KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLD 64
            VL++AEKPS+A +IA +L GG     K        +G          VT   GH+  LD
Sbjct: 1   MVLIIAEKPSVAKAIAKILGGGSKKKGKGRYYEFYGEG------GGYVVTWASGHLLELD 54

Query: 65  FPPAYQDWNASNPLD--LFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGEN 122
           FP  Y  W+   PL+  LF AP        K    + L + A+    +V+  D DREGE 
Sbjct: 55  FPEEYDPWDKVWPLEDPLFPAPFKLKVDKGKKKQFKVLKKLAKRADEIVIATDADREGEL 114

Query: 123 ICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNL 162
           I  E++E         R+ V RA FSS+T K I +A  NL
Sbjct: 115 IGREILEYAK---CVKRKPVKRAWFSSLTPKAIRRAFKNL 151

Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. 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 = 151

>gnl|CDD|173778 cd01028, TOPRIM_TopoIA, TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IA family of DNA topoisomerases (TopoIA)

 Score =  142 bits (360), Expect = 2e-43
 Identities = 54/158 (34%), Positives = 75/158 (47%), Gaps = 16/158 (10%)

Query: 5   KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLD 64
           KVL++AEKPS A +IA +L  G           +   G +        VT+ VGH+  L 
Sbjct: 1   KVLIIAEKPSKAKTIAKILGKGS-----KKKGFYGEGGGY-------VVTASVGHLLELP 48

Query: 65  FPPAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENIC 124
           FP  Y DW+   PL+LF           K    + L + A+    +VL  D DREGE I 
Sbjct: 49  FPEEYVDWDKDWPLELFPFEPKYVVIPDKKKQLKALKKLAKKADEIVLATDPDREGELIA 108

Query: 125 FEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNL 162
           +E++E     +    + V RA FS +T K I +A  NL
Sbjct: 109 WEILE----VLKCDNKPVKRAWFSEITPKAIREAFKNL 142

This subgroup contains proteins similar to the Type I DNA topoisomerases: E. coli topisomerases I and III, eukaryotic topoisomerase III and, ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA. These enzymes cleave one strand of the DNA duplex, covalently link to the 5' phosphoryl end of the DNA break and allow the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. 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 = 142

>gnl|CDD|235971 PRK07219, PRK07219, DNA topoisomerase I; Validated

 Score =  147 bits (374), Expect = 6e-41
 Identities = 67/186 (36%), Positives = 89/186 (47%), Gaps = 10/186 (5%)

Query: 6   VLMVAEKPSIALSIATVLSGGKLYT-RKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLD 64
            L++AEK + A  IA +LSGGK    R      +EF+           V  + GH+  +D
Sbjct: 2   ELIIAEKNNAARRIADILSGGKAKKKRVNGVPYYEFER----KGEKWIVIGLSGHIVTVD 57

Query: 65  FPPAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENIC 124
           FP  Y DW   +P +L  A   K  +         L + A+    +++  D DREGE I 
Sbjct: 58  FPEEYGDWRDVDPAELIDADPVKKITKQN--YINALKKLAKDADEIIIATDYDREGELIG 115

Query: 125 FEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDLKVG 184
            E        V      V RARFSS+T+K+I KA  N  E + N A A +ARQ IDL  G
Sbjct: 116 KEAYHILRE-VCQV--PVKRARFSSLTKKEIRKAFENPDEIDFNLADAGEARQIIDLYWG 172

Query: 185 VAFTRF 190
            A TRF
Sbjct: 173 AALTRF 178

Length = 822

>gnl|CDD|223624 COG0550, TopA, Topoisomerase IA [DNA replication, recombination, and repair]

 Score =  130 bits (329), Expect = 3e-35
 Identities = 54/194 (27%), Positives = 75/194 (38%), Gaps = 29/194 (14%)

Query: 5   KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLD 64
           K L++ E PS A +IA  L  G                          VT+ VGH+  L 
Sbjct: 1   KRLIIVESPSKAKTIAKYLGKG------------------------YVVTASVGHLRDLP 36

Query: 65  FPPAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENIC 124
           FP  Y+ W   +        + K     KV     L + A+    + L  D DREGE I 
Sbjct: 37  FPEEYKGWVDVDLPIFEPKYIIKPGKKKKVVK--KLKKLAKKADEVYLATDPDREGEAIG 94

Query: 125 FEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDLKVG 184
           + ++E           KV R  FS +T+K IL A  N  E + N   A  AR+ +D  VG
Sbjct: 95  WHILEVLK---LKNPSKVKRVVFSEITKKAILSAFKNPREIDMNLVDAQLARRILDRLVG 151

Query: 185 VAFTRFQTTYFQGK 198
              +R      +  
Sbjct: 152 YNLSRLLWKKLKRG 165

Length = 570

>gnl|CDD|180892 PRK07220, PRK07220, DNA topoisomerase I; Validated

 Score =  104 bits (261), Expect = 8e-26
 Identities = 59/186 (31%), Positives = 91/186 (48%), Gaps = 11/186 (5%)

Query: 7   LMVAEKPSIALSIATVLSGGKLYTRKAS-TEVHEFDGMFLGSHAYIKVTSVVGHVFRLDF 65
           L++ EK   A  IA +L+  K    + S  +V+ ++     +     V  + GH+  +DF
Sbjct: 3   LIITEKNIAARRIAQILAPKKPKKTRVSGVDVYRYED----NGDDTVVVGLSGHIVNIDF 58

Query: 66  PPAYQDWNASNPLDLFQAPVHKAESNPK-VHICRHLNQEARGCGHLVLWLDCDREGENIC 124
           P  Y +W   +  DL  A +    +  K V   + L +EA     + +  D DREGE I 
Sbjct: 59  PKEYNNWQKVDARDLIDAEIITTPTQKKIVTALKKLGKEA---DRVTIATDYDREGELIG 115

Query: 125 FEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDLKVG 184
            E +     +VN    K  R R+S++T+K+I +A  N VE + N A A  +RQ IDL  G
Sbjct: 116 VEAL-NIIKKVNPDI-KFDRVRYSAITKKEIERAFSNPVEVDFNLADAGHSRQVIDLVWG 173

Query: 185 VAFTRF 190
            A TR+
Sbjct: 174 AALTRY 179

Length = 740

>gnl|CDD|184936 PRK14973, PRK14973, DNA topoisomerase I; Provisional

 Score = 83.0 bits (205), Expect = 2e-18
 Identities = 55/191 (28%), Positives = 86/191 (45%), Gaps = 22/191 (11%)

Query: 7   LMVAEKPSIALSIATVLSGGK--LYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLD 64
           L++AEK   A  IA +L+G       +      + FD           V  + GHV  +D
Sbjct: 3   LIIAEKNIAANRIAQILAGKTKVQVKKDGGVSTYSFDDTV--------VVGLRGHVVEVD 54

Query: 65  FPPAYQDWNASN--PLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGEN 122
           F P Y +W +    P  L  A   K  +  K  I   + + A+    + +  D D EGE 
Sbjct: 55  FEPGYTNWRSEEHTPRSLIDADTIKKPTEKK--IVGLIQKLAKKADRVTIATDFDTEGEL 112

Query: 123 I---CFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEI 179
           I    +E++     +V      + RARFS++T+++I+ A     + +   A A +ARQ I
Sbjct: 113 IGKEAYELVRAVNPKV-----PIDRARFSAITKEEIVTAFAEPTDLDFALAAAGEARQII 167

Query: 180 DLKVGVAFTRF 190
           DL  G + TRF
Sbjct: 168 DLIWGASLTRF 178

Length = 936

>gnl|CDD|214662 smart00436, TOP1Bc, Bacterial DNA topoisomeraes I ATP-binding domain

 Score = 62.6 bits (153), Expect = 3e-13
 Identities = 17/55 (30%), Positives = 28/55 (50%)

Query: 142 VHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQ 196
           + R  FS +T+K I +A+ N  E + N   A  AR+ +D  +G   +R  T   +
Sbjct: 1   IKRIEFSEITKKAIREALKNPREIDENLVNAQLARRILDRLIGFNLSRLLTKKLR 55

Extension of TOPRIM in Bacterial DNA topoisomeraes I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase beta subunit. Length = 89

>gnl|CDD|235602 PRK05776, PRK05776, DNA topoisomerase I; Provisional

 Score = 65.8 bits (161), Expect = 2e-12
 Identities = 46/193 (23%), Positives = 77/193 (39%), Gaps = 28/193 (14%)

Query: 5   KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRL- 63
            +L++AEKP  A  IA  LS   +  R                   I V    GH+F L 
Sbjct: 2   YILVIAEKPKAARKIAEALSEKPIRCRIYGVPYWIVKRD----GKKIVVAPAAGHLFGLH 57

Query: 64  ----DFPPAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWL---DC 116
                FP    +W           P+++ +   K +  ++    +    +   ++   D 
Sbjct: 58  TKSKGFPVFDYEW----------KPLYEIDKGSK-YTKKYYELLSSLSKYADEFINACDY 106

Query: 117 DREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDAR 176
           D EG  I + +I+  G    D ++   R +FS++T+ DI +A  NL   +     A  AR
Sbjct: 107 DIEGSVIGYLIIKYLG----DPKK-AKRMKFSALTKSDIRRAFRNLETLDYEMINAGIAR 161

Query: 177 QEIDLKVGVAFTR 189
            E+D   G+  +R
Sbjct: 162 HELDWLWGINVSR 174

Length = 670

>gnl|CDD|233253 TIGR01057, topA_arch, DNA topoisomerase I, archaeal

 Score = 62.2 bits (151), Expect = 2e-11
 Identities = 48/187 (25%), Positives = 79/187 (42%), Gaps = 22/187 (11%)

Query: 9   VAEKPSIALSIATVLSGGKLYTRK---ASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDF 65
           +AEKP +A  IA  LS G++  +            DG        I V S VGH+F L  
Sbjct: 1   IAEKPKVAAKIAGALSDGRVLKKSEYGVPYWEVRRDG------KKIIVASAVGHLFGL-- 52

Query: 66  PPAYQDWNASNPL-DLFQAPVHKAESNPKV--HICRHLNQEARGCGHLVLWLDCDREGEN 122
              +       P+ D+   P+ + +          + L++ A+G    +   D D EGE 
Sbjct: 53  ---HPKSRGGYPVFDIEWVPIFEFDKGKGYVSKYIKALSKLAKGADEYINACDYDIEGEV 109

Query: 123 ICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDLK 182
           I F+ ++           +  R +FS++T++DI +A  N  E +     A  AR  +D  
Sbjct: 110 IGFKALKYFC-----GVERAKRMKFSTLTKQDIRRAYANPEEIDYGMVDAGMARHILDWY 164

Query: 183 VGVAFTR 189
            G+  +R
Sbjct: 165 WGINLSR 171

This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent [DNA metabolism, DNA replication, recombination, and repair]. Length = 618

>gnl|CDD|233252 TIGR01056, topB, DNA topoisomerase III, bacteria and conjugative plasmid

 Score = 59.5 bits (144), Expect = 2e-10
 Identities = 54/198 (27%), Positives = 79/198 (39%), Gaps = 26/198 (13%)

Query: 5   KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLD 64
             L++ EKPS A  +ATVL+           +  + +G          VT  VGH+  L 
Sbjct: 1   MTLVLCEKPSQARDLATVLA-----------KKKKGNGYLEIGVGGF-VTWAVGHLVELA 48

Query: 65  FPPAY----QDWNASN-PL--DLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCD 117
            P  Y    ++W   + PL  + +Q  V          I R L +       +V+  D D
Sbjct: 49  EPEEYDEKYKNWRTYDLPLEPEDWQLVVSDKTKKQFNVIKRILKENK--VDEVVIATDPD 106

Query: 118 REGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVD--A 175
           REGE I  E+++         +  + R   SS+ +  I KA  NL   +  E L     A
Sbjct: 107 REGELIAREILDYLKVT---DKVTIKRLWISSLVDSSIRKAFKNLRPKSETEGLYKSGVA 163

Query: 176 RQEIDLKVGVAFTRFQTT 193
           R   D  VG+  TR  T 
Sbjct: 164 RARADWLVGINLTRAFTK 181

This model describes topoisomerase III from bacteria and its equivalents encoded on plasmids. The gene is designated topB if found in the bacterial chromosome, traE on conjugative plasmid RP4, etc. These enzymes are involved in the control of DNA topology. DNA topoisomerase III belongs to the type I topoisomerases, which are ATP-independent [DNA metabolism, DNA replication, recombination, and repair]. Length = 660

>gnl|CDD|236172 PRK08173, PRK08173, DNA topoisomerase III; Validated

 Score = 51.6 bits (124), Expect = 8e-08
 Identities = 62/205 (30%), Positives = 90/205 (43%), Gaps = 41/205 (20%)

Query: 5   KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRL- 63
           K L++AEKPS+A  IA  L G   +T+    E  E       S  Y+ ++S VGH+  + 
Sbjct: 3   KALIIAEKPSVANDIARALGG---FTKH--DEYFE-------SDEYV-LSSAVGHLLEIA 49

Query: 64  ---DFPPAYQDWNASN-PL-----DLFQAPVHKAESNPKVHICRHLNQEAR--GCGHLVL 112
              ++      W+ ++ P+     DL   P+ K ES  KV     L +  +      L+ 
Sbjct: 50  APEEYEVKRGKWSFAHLPVIPPHFDL--NPIAKTESRLKV-----LTKLIKRKDVTRLIN 102

Query: 113 WLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALA 172
             D  REGE I F +I     Q   A++ V R    S+T + I     NL      + LA
Sbjct: 103 ACDAGREGELI-FRLIA----QHAKAKKPVKRLWLQSMTPQAIRDGFANLRSDEDMQPLA 157

Query: 173 VDA---RQEIDLKVGVAFTRFQTTY 194
            DA   R E D  VG+  TR  T +
Sbjct: 158 -DAARCRSEADWLVGINGTRAMTAF 181

Length = 862

>gnl|CDD|236078 PRK07726, PRK07726, DNA topoisomerase III; Provisional

 Score = 50.5 bits (122), Expect = 2e-07
 Identities = 60/204 (29%), Positives = 85/204 (41%), Gaps = 43/204 (21%)

Query: 5   KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLD 64
             L +AEKPS+   IA VL       +K        DG   G+     VT  +GH+  L 
Sbjct: 1   MRLFIAEKPSVGRDIADVLKP----HKKG-------DGYIEGNGYI--VTWAIGHLLELA 47

Query: 65  FP----PAYQDWNASNPLDLFQAPVH-KAESNPKV----HICRHLNQEARGCGHLVLWLD 115
            P      Y+ W      DL   P   K     K     ++ + L ++A     +V+  D
Sbjct: 48  EPEAYDERYKRWRLE---DLPIIPEKWKLVVKKKTAKQFNVVKKLLKQA---TEIVIATD 101

Query: 116 CDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRN------E 169
            DREGE I  E+++  G      R+ + R   SS+T+K I +A  NL +P +        
Sbjct: 102 ADREGELIAREILDYCGV-----RKPIKRLWISSLTDKAIKRAFANL-KPGKETIPLYYS 155

Query: 170 ALAVDARQEIDLKVGVAFTRFQTT 193
           AL   AR   D  VG+  TR  T 
Sbjct: 156 AL---ARSRADWLVGINMTRAYTL 176

Length = 658

>gnl|CDD|237803 PRK14724, PRK14724, DNA topoisomerase III; Provisional

 Score = 48.8 bits (116), Expect = 9e-07
 Identities = 61/206 (29%), Positives = 86/206 (41%), Gaps = 32/206 (15%)

Query: 4   LKVLMVAEKPSIALSIATVLS--GGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVF 61
            K L++AEKPS+A  I   L+   GK        E H+       S +Y+ VTS VGH+ 
Sbjct: 1   TKTLVIAEKPSVAQDIVRALTPVAGKF-------EKHD---EHFESDSYV-VTSAVGHLV 49

Query: 62  RLDFPPAYQ----DWNASN----PLDLFQAPVHKAES--NPKVHICRHLNQEARGCGHLV 111
            +  P  +      W+ +N    P      PV K ++  N  V + +      +    LV
Sbjct: 50  EIQAPEEFDVKRGKWSFANLPVIPPYFDLKPVDKTKTRLNAVVKLAKR-----KDVTELV 104

Query: 112 LWLDCDREGENICFEVIE-CTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEA 170
              D  REGE I F +IE   G       + V R    S+T + I     NL    + + 
Sbjct: 105 NACDAGREGELI-FRLIEQYAGGAKGGLGKPVKRLWLQSMTPQAIRDGFDNLRSDAQMQG 163

Query: 171 LAVDA--RQEIDLKVGVAFTRFQTTY 194
           LA  A  R E D  VG+  TR  T +
Sbjct: 164 LASAARSRSEADWLVGINGTRAMTAF 189

Length = 987

>gnl|CDD|173783 cd03363, TOPRIM_TopoIA_TopoI, TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I

 Score = 44.5 bits (106), Expect = 3e-06
 Identities = 32/118 (27%), Positives = 51/118 (43%), Gaps = 13/118 (11%)

Query: 44  FLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQE 103
           +LG   Y  V + VGH+ R D P         +  D    P +      K  + + L + 
Sbjct: 18  YLGKE-YE-VLASVGHI-R-DLPKKGLG---VDGEDDGFEPKYVVIPGKKKVV-KELKKL 69

Query: 104 ARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGN 161
           A+    + L  D DREGE I + + E    + N     V R  F+ +T++ I +A+ N
Sbjct: 70  AKKADEIYLATDPDREGEAIAWHLAEVLKLKKN-----VKRVVFNEITKEAIKEALKN 122

Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. 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 = 123

>gnl|CDD|238110 cd00186, TOP1Ac, DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases

 Score = 45.7 bits (109), Expect = 6e-06
 Identities = 10/33 (30%), Positives = 14/33 (42%)

Query: 168 NEALAVDARQEIDLKVGVAFTRFQTTYFQGKYG 200
           N   A  AR+ +D  VG   +R  T   + K  
Sbjct: 2   NLVNAQLARRILDRLVGFNLSRLLTKKLRRKGV 34

Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand. Length = 381

>gnl|CDD|214695 smart00493, TOPRIM, topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins

 Score = 41.9 bits (99), Expect = 1e-05
 Identities = 21/125 (16%), Positives = 37/125 (29%), Gaps = 56/125 (44%)

Query: 5   KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLD 64
           KVL++ E P+ A+++                                 V ++ GH+    
Sbjct: 1   KVLIIVEGPADAIALEKAGGKR------------------------GNVVALGGHLL--- 33

Query: 65  FPPAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENIC 124
                                            + L + A+    ++L  D DREGE I 
Sbjct: 34  ----------------------------SKEQIKLLKKLAKKA-EVILATDPDREGEAIA 64

Query: 125 FEVIE 129
           +E+ E
Sbjct: 65  WELAE 69

Length = 75

>gnl|CDD|233249 TIGR01051, topA_bact, DNA topoisomerase I, bacterial

 Score = 44.3 bits (105), Expect = 2e-05
 Identities = 35/133 (26%), Positives = 55/133 (41%), Gaps = 11/133 (8%)

Query: 52  KVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLV 111
           +V + +GH+  L       D         F+       S  K  + + L   A+    + 
Sbjct: 22  EVEASMGHIRDLPKSRLGVDIEKD-----FEP--EYVVSKGKKKVVKELKTLAKKADEVY 74

Query: 112 LWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEAL 171
           L  D DREGE I + + E    +    +R V    F+ +T+K I  A+ N  E + N   
Sbjct: 75  LATDPDREGEAIAWHLAEVLKPKDPVYKRIV----FNEITKKAIRAALKNPREIDMNLVN 130

Query: 172 AVDARQEIDLKVG 184
           A  AR+ +D  VG
Sbjct: 131 AQQARRILDRLVG 143

This model describes DNA topoisomerase I among the members of bacteria. DNA topoisomerase I transiently cleaves one DNA strand and thus relaxes negatively supercoiled DNA during replication, transcription and recombination events [DNA metabolism, DNA replication, recombination, and repair]. Length = 610

>gnl|CDD|216317 pfam01131, Topoisom_bac, DNA topoisomerase

 Score = 43.7 bits (104), Expect = 3e-05
 Identities = 11/35 (31%), Positives = 17/35 (48%)

Query: 164 EPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGK 198
           E + N   A +AR+ +D  +G   +R  T  F  K
Sbjct: 1   EEDENLVDAQEARRILDRLIGFNLSRALTLKFNNK 35

This subfamily of topoisomerase is divided on the basis that these enzymes preferentially relax negatively supercoiled DNA, from a 5' phospho- tyrosine linkage in the enzyme-DNA covalent intermediate and has high affinity for single stranded DNA. Length = 365

>gnl|CDD|233251 TIGR01054, rgy, reverse gyrase

 Score = 40.6 bits (95), Expect = 4e-04
 Identities = 52/207 (25%), Positives = 80/207 (38%), Gaps = 44/207 (21%)

Query: 6   VLMVAEKPSIALSIATVLSGGKLYTRK-ASTEVHEFDGMFLGSHAYIKVTSVVGHVFRL- 63
            L+V E P+ A +IA     GK   RK   + V+E   + +G    + +T+  GHVF L 
Sbjct: 603 ALLVVESPNKARTIARFF--GKPSVRKIGGSVVYE---VPVGDL-ILMITASGGHVFDLV 656

Query: 64  -------------DFPPAYQDWNASNPLDLFQAPVHKAESNPK------------VHICR 98
                         + P Y   +     D         ES PK            + I R
Sbjct: 657 TDKGFHGVLVENGRYVPVYT--SIKRCRDCGYQFTEDRESCPKCGSENIEDSKSIIEILR 714

Query: 99  HLNQEARGCGHLVLWLDCDREGENICFEV-IECTGFQVNDARRKVHRARFSSVTEKDILK 157
            L  E      + +  D D EGE I +++ +  + +  N     V RA F  VT + IL+
Sbjct: 715 ELAHEVD---EVFIGTDPDTEGEKIGWDLALLLSPYNPN-----VKRAEFHEVTRRAILE 766

Query: 158 AMGNLVEPNRNEALAVDARQEIDLKVG 184
           A+ +    + N   A   R+  D  +G
Sbjct: 767 ALESPRSVDENLVKAQVVRRIEDRWIG 793

This model describes reverse gyrase, found in both archaeal and bacterial thermophiles. This enzyme, a fusion of a type I topoisomerase domain and a helicase domain, introduces positive supercoiling to increase the melting temperature of DNA double strands. Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA [DNA metabolism, DNA replication, recombination, and repair]. Length = 1171

>gnl|CDD|235840 PRK06599, PRK06599, DNA topoisomerase I; Validated

 Score = 39.5 bits (93), Expect = 0.001
 Identities = 39/142 (27%), Positives = 64/142 (45%), Gaps = 12/142 (8%)

Query: 44  FLGSHAYIKVTSVVGHVFRLDFPPAYQDWNAS-NPLDLFQAPVHKAESNPKVHICRHLNQ 102
           +LG   Y KV +  GHV R D P          +P + F AP ++     +  +   L +
Sbjct: 20  YLGK-DY-KVLASFGHV-R-DLPKK----KGGVDPDNDF-APKYEIIEGKEKVV-DALKK 69

Query: 103 EARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNL 162
            A+    + L  D DREGE I + + E          + V R  F+ +T+K + +A+ N 
Sbjct: 70  AAKKADAVYLATDPDREGEAIAWHIAEVLKEAKLK-DKNVKRVVFNEITKKAVQEAIENP 128

Query: 163 VEPNRNEALAVDARQEIDLKVG 184
            + + +   A  AR+ +D  VG
Sbjct: 129 RDIDMDLVDAQQARRALDYLVG 150

Length = 675

>gnl|CDD|173773 cd00188, TOPRIM, Topoisomerase-primase domain

 Score = 35.5 bits (82), Expect = 0.002
 Identities = 23/136 (16%), Positives = 35/136 (25%), Gaps = 56/136 (41%)

Query: 5   KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLD 64
           K L++ E PS AL++A     G                          V ++ GH     
Sbjct: 1   KKLIIVEGPSDALALAQAGGYG------------------------GAVVALGGHALN-- 34

Query: 65  FPPAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENIC 124
                                              L +       +++  D DREGE I 
Sbjct: 35  ------------------------------KTRELLKRLLGEAKEVIIATDADREGEAIA 64

Query: 125 FEVIECTGFQVNDARR 140
             ++E         RR
Sbjct: 65  LRLLELLKSLGKKVRR 80

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. Length = 83

>gnl|CDD|216679 pfam01751, Toprim, Toprim domain

 Score = 34.9 bits (81), Expect = 0.004
 Identities = 23/124 (18%), Positives = 38/124 (30%), Gaps = 54/124 (43%)

Query: 6   VLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDF 65
            L++ E PS A+++                          G      V +  GH   L+ 
Sbjct: 1   ELIIVEGPSDAIALE----------------------KAGGVLGGA-VVATSGHALDLE- 36

Query: 66  PPAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICF 125
                                        HI + L +  +G   ++L  D DREGE I  
Sbjct: 37  -----------------------------HI-KELKKALKGAKEVILATDPDREGEAIAL 66

Query: 126 EVIE 129
           +++E
Sbjct: 67  KLLE 70

This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesises the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyze the relaxation of DNA supercoiling by causing transient double strand breaks. Length = 86

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	220
PRK08173	862	DNA topoisomerase III; Validated	100.0
PRK07726	658	DNA topoisomerase III; Provisional	100.0
PRK14724	987	DNA topoisomerase III; Provisional	100.0
PRK07220	740	DNA topoisomerase I; Validated	100.0
PRK14973	936	DNA topoisomerase I; Provisional	100.0
PRK07219	822	DNA topoisomerase I; Validated	100.0
TIGR01056	660	topB DNA topoisomerase III, bacteria and conjugati	100.0
TIGR01057	618	topA_arch DNA topoisomerase I, archaeal. This mode	100.0
PRK05776	670	DNA topoisomerase I; Provisional	100.0
PRK09401	1176	reverse gyrase; Reviewed	100.0
TIGR01051	610	topA_bact DNA topoisomerase I, bacterial. This mod	100.0
PRK06599	675	DNA topoisomerase I; Validated	100.0
COG0550	570	TopA Topoisomerase IA [DNA replication, recombinat	100.0
PRK05582	650	DNA topoisomerase I; Validated	100.0
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	100.0
PRK06319	860	DNA topoisomerase I/SWI domain fusion protein; Val	100.0
PRK08780	780	DNA topoisomerase I; Provisional	100.0
PRK07561	859	DNA topoisomerase I subunit omega; Validated	100.0
PRK14701	1638	reverse gyrase; Provisional	100.0
KOG1956	758	consensus DNA topoisomerase III alpha [Replication	100.0
KOG1957	555	consensus DNA topoisomerase III beta [Replication,	100.0
cd03362	151	TOPRIM_TopoIA_TopoIII TOPRIM_TopoIA_TopoIII: The t	100.0
cd01028	142	TOPRIM_TopoIA TOPRIM_TopoIA: topoisomerase-primase	100.0
PTZ00407	805	DNA topoisomerase IA; Provisional	100.0
cd03361	170	TOPRIM_TopoIA_RevGyr TopoIA_RevGyr : The topoisome	100.0
cd03363	123	TOPRIM_TopoIA_TopoI TOPRIM_TopoIA_TopoI: The topoi	100.0
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	100.0
smart00436	89	TOP1Bc Bacterial DNA topoisomeraes I ATP-binding d	99.94
PF01751	100	Toprim: Toprim domain; InterPro: IPR006171 This is	99.94
smart00493	76	TOPRIM topoisomerases, DnaG-type primases, OLD fam	98.95
cd01025	112	TOPRIM_recR TOPRIM_recR: topoisomerase-primase (TO	98.49
cd00188	83	TOPRIM Topoisomerase-primase domain. This is a nuc	98.06
PRK00076	196	recR recombination protein RecR; Reviewed	97.88
cd01027	81	TOPRIM_RNase_M5_like TOPRIM_ RNase M5_like: The to	97.44
PRK13844	200	recombination protein RecR; Provisional	97.01
TIGR00615	195	recR recombination protein RecR. This family is ba	96.94
COG0353	198	RecR Recombinational DNA repair protein (RecF path	96.67
PF13662	81	Toprim_4: Toprim domain; PDB: 1EQN_E 1DD9_A 3B39_B	95.66
COG1658	127	Small primase-like proteins (Toprim domain) [DNA r	95.13
PRK04031	408	DNA primase; Provisional	94.97
PF09664	152	DUF2399: Protein of unknown function C-terminus (D	94.89
TIGR00334	174	5S_RNA_mat_M5 ribonuclease M5. This family of orth	94.38
COG4026	290	Uncharacterized protein containing TOPRIM domain,	92.91
PRK04017	132	hypothetical protein; Provisional	89.96
cd03364	79	TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The top	82.67
cd01029	79	TOPRIM_primases TOPRIM_primases: The topoisomerase	81.38

>PRK08173 DNA topoisomerase III; Validated

Probab=100.00  E-value=6e-58  Score=450.93  Aligned_cols=189  Identities=26%  Similarity=0.320  Sum_probs=160.8

Q ss_pred             CceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCC----CCCccCCCCC
Q 048704            4 LKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAY----QDWNASNPLD   79 (220)
Q Consensus         4 ~~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y----~~w~~~~p~~   79 (220)
                      |++||||||||+|++||++||..   +++        +|||+|+  +|+||||+|||++|++|++|    +.|+..    
T Consensus         2 m~~LiIAEKPs~Ak~Ia~~Lg~~---~k~--------~gy~e~~--~~~Vtwa~GHL~el~~Pe~Y~~~~~~W~~~----   64 (862)
T PRK08173          2 SKALIIAEKPSVANDIARALGGF---TKH--------DEYFESD--EYVLSSAVGHLLEIAAPEEYEVKRGKWSFA----   64 (862)
T ss_pred             CCEEEEEeCHHHHHHHHHHhCCC---cCC--------CCeEeCC--cEEEEeeccccccCCCchhccccccccccc----
Confidence            57899999999999999999852   232        5788887  89999999999999999987    356542    


Q ss_pred             CCCCCceec-----cCCCcHHHHHHHHHHh--ccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCH
Q 048704           80 LFQAPVHKA-----ESNPKVHICRHLNQEA--RGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTE  152 (220)
Q Consensus        80 l~~~p~~~~-----~~~~~~~~~~~lk~~~--~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~  152 (220)
                        ++|++|.     ....+.++++.|++++  +++|+||||||||||||+|+|+|+++++.     +++++|+||||+|+
T Consensus        65 --~LPi~p~~f~~~~~~~~~~q~~~ik~l~k~~~~d~Ii~AtD~dREGElI~~~I~~~~~~-----~kpv~Rlw~sslt~  137 (862)
T PRK08173         65 --HLPVIPPHFDLNPIAKTESRLKVLTKLIKRKDVTRLINACDAGREGELIFRLIAQHAKA-----KKPVKRLWLQSMTP  137 (862)
T ss_pred             --ccCCCCccccccccccHHHHHHHHHHHHhhCCCCEEEECCCCChhHHHHHHHHHHHhCC-----CCCeEEEEEccCCH
Confidence              3444432     2334678999999999  46999999999999999999999999986     57999999999999


Q ss_pred             HHHHHHHhcCCCCC--cchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704          153 KDILKAMGNLVEPN--RNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF  219 (220)
Q Consensus       153 ~~I~~A~~nl~~~~--~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~  219 (220)
                      ++|++||+||+|++  .+|++||+||+++|||||||+||++|+..++. ++  ..++|+||||||||.+
T Consensus       138 ~aI~~a~~nl~~~~~~~~L~~aa~aR~~aDwlvG~N~TR~~T~~~~~~-g~--~~~lSvGRVQTPtL~l  203 (862)
T PRK08173        138 QAIRDGFANLRSDEDMQPLADAARCRSEADWLVGINGTRAMTAFNSKG-GG--FFLTTVGRVQTPTLSI  203 (862)
T ss_pred             HHHHHHHhcCCCchhhHHHHHHHHHHHHHHHHhhHHHhHHHHHhHhhc-CC--ccccccccchhhHHHH
Confidence            99999999999997  49999999999999999999999999865432 21  2479999999999975

>PRK07726 DNA topoisomerase III; Provisional

Probab=100.00  E-value=3.5e-56  Score=429.35  Aligned_cols=187  Identities=28%  Similarity=0.374  Sum_probs=161.2

Q ss_pred             eEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCC----CCCccCCCCCCC
Q 048704            6 VLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAY----QDWNASNPLDLF   81 (220)
Q Consensus         6 ~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y----~~w~~~~p~~l~   81 (220)
                      +||||||||+|++||++||..   +++        +|||+|+  +++|||+.|||++|++|++|    +.|+..      
T Consensus         2 ~LiIaEKPs~Ak~Ia~~L~~~---~~~--------~g~~~g~--~~~Vt~~~GHl~~L~~p~~y~~~~~~W~~~------   62 (658)
T PRK07726          2 RLFIAEKPSVGRDIADVLKPH---KKG--------DGYIEGN--GYIVTWAIGHLLELAEPEAYDERYKRWRLE------   62 (658)
T ss_pred             eEEEEeCHHHHHHHHHHhCCc---cCC--------CCeEeCC--CEEEEechhhhccCCCchhcccccCccccc------
Confidence            799999999999999999852   222        5788887  89999999999999999876    456532      


Q ss_pred             CCCceec-----cCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHH
Q 048704           82 QAPVHKA-----ESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDIL  156 (220)
Q Consensus        82 ~~p~~~~-----~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~  156 (220)
                      ++|+.|.     ...++.++++.|++++++||+||||||||||||+|||+|+++++.     +++++|+|||++|+++|+
T Consensus        63 ~lpi~p~~~~~~~~~~~~~~~~~ik~l~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~-----~~~v~Rl~~sslt~~~I~  137 (658)
T PRK07726         63 DLPIIPEKWKLVVKKKTAKQFNVVKKLLKQATEIVIATDADREGELIAREILDYCGV-----RKPIKRLWISSLTDKAIK  137 (658)
T ss_pred             cCCCCcccceeeeccchHHHHHHHHHHHhhCCeEEEcCCCCccccHHHHHHHHHhCC-----CCCeEEEEEccCCHHHHH
Confidence            3454442     134567899999999999999999999999999999999999996     579999999999999999


Q ss_pred             HHHhcCCCCC--cchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704          157 KAMGNLVEPN--RNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF  219 (220)
Q Consensus       157 ~A~~nl~~~~--~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~  219 (220)
                      +||+||+|++  .+|++||+||+++||+||||+||++|+.+++.  ++ +.++|+||||||||.+
T Consensus       138 ~A~~nl~~~~~~~~l~~aa~aR~~~D~liG~nlSr~~t~~~~~~--g~-~~~lS~GRVQTPtL~l  199 (658)
T PRK07726        138 RAFANLKPGKETIPLYYSALARSRADWLVGINMTRAYTLLGRKA--GY-NGVLSVGRVQTPTLAL  199 (658)
T ss_pred             HHHHhcCCchhhHHHHHHHHHHHHHHHHhhhhHhHHHHHHHhhc--CC-CcceeecccccchhHH
Confidence            9999999985  59999999999999999999999999987643  22 3589999999999975

>PRK14724 DNA topoisomerase III; Provisional

Probab=100.00  E-value=8.1e-56  Score=440.29  Aligned_cols=196  Identities=27%  Similarity=0.332  Sum_probs=160.6

Q ss_pred             CceEEEEeChHHHHHHHHHcCC--CCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCC----CCccCCC
Q 048704            4 LKVLMVAEKPSIALSIATVLSG--GKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQ----DWNASNP   77 (220)
Q Consensus         4 ~~~LiIaEKPs~Ak~ia~~L~~--~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~----~w~~~~p   77 (220)
                      |++||||||||+|++||++|++  +.+ ++.        +|||+|+  +|+||||+|||++|++|++|.    .|+..  
T Consensus         1 Mk~LiIAEKPSvAk~IA~aL~~~~g~~-~k~--------~gy~eg~--~~~Vtwa~GHL~eL~~Pe~y~~~~~~W~~~--   67 (987)
T PRK14724          1 TKTLVIAEKPSVAQDIVRALTPVAGKF-EKH--------DEHFESD--SYVVTSAVGHLVEIQAPEEFDVKRGKWSFA--   67 (987)
T ss_pred             CCEEEEEeCHHHHHHHHHHhhhccCCC-cCC--------CceecCC--CEEEEecccccccCCChhhcccccCCcccc--
Confidence            5789999999999999999952  112 222        5788887  899999999999999999873    56543  


Q ss_pred             CCCCCCCceec-----cCCCcHHHHHHHHHHh--ccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCc
Q 048704           78 LDLFQAPVHKA-----ESNPKVHICRHLNQEA--RGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSV  150 (220)
Q Consensus        78 ~~l~~~p~~~~-----~~~~~~~~~~~lk~~~--~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~ssl  150 (220)
                          ++|++|.     ....+.++++.|++++  +++|+||||||||||||+|+|+|++++++.+.+.+++++|+|||++
T Consensus        68 ----~LPiiP~~f~~~~~~~~k~q~~~Ik~l~k~~~~~~II~AtD~DREGElI~~~I~~~~~~~~~~~~kpv~Rlw~ssl  143 (987)
T PRK14724         68 ----NLPVIPPYFDLKPVDKTKTRLNAVVKLAKRKDVTELVNACDAGREGELIFRLIEQYAGGAKGGLGKPVKRLWLQSM  143 (987)
T ss_pred             ----ccccCCccceeeeccchHHHHHHHHHHHhhCCCCeEEECCCCCcchhHHHHHHHHHhCcccccCCCceEEEEEccC
Confidence                3555543     2344578999999999  4678999999999999999999999998621111379999999999


Q ss_pred             CHHHHHHHHhcCCCCCc--chHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704          151 TEKDILKAMGNLVEPNR--NEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF  219 (220)
Q Consensus       151 t~~~I~~A~~nl~~~~~--~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~  219 (220)
                      |+++|++||+||+++++  +|++||+||+++|||||||+||++|+..+.. +++  .++|+||||||||.+
T Consensus       144 T~~aI~~af~nlr~~~~~~~L~~Aa~aR~~aDwLvG~N~SR~~T~~~~~~-~~~--~~lSvGRVQTPtL~l  211 (987)
T PRK14724        144 TPQAIRDGFDNLRSDAQMQGLASAARSRSEADWLVGINGTRAMTAFNSRD-GGF--FLTTVGRVQTPTLSL  211 (987)
T ss_pred             CHHHHHHHHhCCCCchhhhhHHHHHHHHHHHHHHhHHHHhHHHHHHHHhc-CCc--ceeccccchhHHHHH
Confidence            99999999999999984  9999999999999999999999999854322 221  378999999999975

>PRK07220 DNA topoisomerase I; Validated

Probab=100.00  E-value=1.3e-55  Score=429.66  Aligned_cols=202  Identities=29%  Similarity=0.369  Sum_probs=171.8

Q ss_pred             eEEEEeChHHHHHHHHHcCCCCcc-cccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCCC
Q 048704            6 VLMVAEKPSIALSIATVLSGGKLY-TRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAP   84 (220)
Q Consensus         6 ~LiIaEKPs~Ak~ia~~L~~~~~~-~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~p   84 (220)
                      .||||||||+|++||++||++..+ .+..++++|+|.  .+|+  +++|+|+.|||++|++|++|++|..|++..+|+.+
T Consensus         2 ~LiIaEKPs~Ak~Ia~~Lg~~~~~~~~~~g~~~y~~~--~~g~--~~~v~~~~GHl~~l~~P~~y~~w~~~~~~~l~~~~   77 (740)
T PRK07220          2 HLIITEKNIAARRIAQILAPKKPKKTRVSGVDVYRYE--DNGD--DTVVVGLSGHIVNIDFPKEYNNWQKVDARDLIDAE   77 (740)
T ss_pred             eEEEEeCHHHHHHHHHHhCCCCccccccCCcceeEEe--cCCC--CEEEEEeCcccccCCCCccccccCCCChhHcCCcc
Confidence            599999999999999999854322 234566666553  1455  89999999999999999999889888766676655


Q ss_pred             ceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcCCC
Q 048704           85 VHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVE  164 (220)
Q Consensus        85 ~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl~~  164 (220)
                      +..  ...+.++++.|++++++||+||||||||||||+|||+|+++++..+  +.++++|+|||++|+++|++||+||++
T Consensus        78 ~~~--~~~~~~~~~~lk~l~k~ad~viiAtD~DREGE~I~~~i~~~l~~~~--~~~~~~R~~fs~iT~~~I~~A~~n~~~  153 (740)
T PRK07220         78 IIT--TPTQKKIVTALKKLGKEADRVTIATDYDREGELIGVEALNIIKKVN--PDIKFDRVRYSAITKKEIERAFSNPVE  153 (740)
T ss_pred             eEe--cCCHHHHHHHHHHHHhcCCEEEECCCCCccHHHHHHHHHHHHHhcC--CCCceEEEEEccCCHHHHHHHHhCCCC
Confidence            443  2456889999999999999999999999999999999999998642  246999999999999999999999999


Q ss_pred             CCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704          165 PNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF  219 (220)
Q Consensus       165 ~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~  219 (220)
                      +|.+|++||+|||++||+||||+||++|+.+++..    +.++|+||||||||.|
T Consensus       154 ~d~~l~~A~~aR~~~D~lvG~nlSr~~t~~~~~~~----~~~lS~GRVQtptL~l  204 (740)
T PRK07220        154 VDFNLADAGHSRQVIDLVWGAALTRYISLAAGRLG----KMFLSVGRVQSPTLAL  204 (740)
T ss_pred             CChhHHHHHHHHHHHHHHhchhcCHHHHHHHHhhC----CccccccccchhhhHH
Confidence            99999999999999999999999999999876421    2479999999999975

>PRK14973 DNA topoisomerase I; Provisional

Probab=100.00  E-value=1.8e-54  Score=427.83  Aligned_cols=198  Identities=27%  Similarity=0.358  Sum_probs=167.5

Q ss_pred             eEEEEeChHHHHHHHHHcCCCCc--ccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCC--CCCCC
Q 048704            6 VLMVAEKPSIALSIATVLSGGKL--YTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASN--PLDLF   81 (220)
Q Consensus         6 ~LiIaEKPs~Ak~ia~~L~~~~~--~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~--p~~l~   81 (220)
                      .||||||||+|++||++||++..  .++.+++.+|.|     +   +.+|||+.|||++|++++.|++|+..+  |..++
T Consensus         2 ~LiIAEKPSvAk~IA~~L~~~~~~~~k~~g~~~~y~~-----~---~~~vt~~~GHLl~l~y~~~yk~W~~~~LPP~~l~   73 (936)
T PRK14973          2 HLIIAEKNIAANRIAQILAGKTKVQVKKDGGVSTYSF-----D---DTVVVGLRGHVVEVDFEPGYTNWRSEEHTPRSLI   73 (936)
T ss_pred             EEEEEcCHHHHHHHHHHhCCCCccccccCCCcceEEe-----C---CCEEEEEcccceecccCcccCCCccccCChhhcc
Confidence            49999999999999999986421  234456655543     3   348999999999999999999998753  34455


Q ss_pred             CCCceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhc
Q 048704           82 QAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGN  161 (220)
Q Consensus        82 ~~p~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~n  161 (220)
                      +.++.+  ...+.++++.|++++++||.||||||||||||+|+|+|+++++..+  ++++++|+|||++|+++|++||+|
T Consensus        74 ~~~~~~--~~~~kk~~~~Ik~l~k~ad~IiiAtD~DREGE~I~~~i~e~~~~~~--~~~~v~R~~fs~iT~~~I~~A~~n  149 (936)
T PRK14973         74 DADTIK--KPTEKKIVGLIQKLAKKADRVTIATDFDTEGELIGKEAYELVRAVN--PKVPIDRARFSAITKEEIVTAFAE  149 (936)
T ss_pred             Ccceee--cCchHHHHHHHHHHHHhCCEEEECCCCCcchHHHHHHHHHHhhhcc--CCCceEEEEEccCCHHHHHHHHhC
Confidence            555433  2346789999999999999999999999999999999999998643  257999999999999999999999


Q ss_pred             CCCCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704          162 LVEPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF  219 (220)
Q Consensus       162 l~~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~  219 (220)
                      +++++.+|++||+||+++||++|||+||++|+.++..+    +.++|+||||||||.|
T Consensus       150 l~~~d~~l~~A~~aR~~~D~lvG~nlSr~lt~~~~~g~----~~~lS~GRVQTPtL~l  203 (936)
T PRK14973        150 PTDLDFALAAAGEARQIIDLIWGASLTRFISLAAHRGG----DNILSVGRVQSPTLAM  203 (936)
T ss_pred             CCCCcHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhcCC----CcceeeccccchHHHH
Confidence            99999999999999999999999999999999876321    3589999999999976

>PRK07219 DNA topoisomerase I; Validated

Probab=100.00  E-value=3.8e-54  Score=423.70  Aligned_cols=202  Identities=35%  Similarity=0.415  Sum_probs=166.5

Q ss_pred             eEEEEeChHHHHHHHHHcCCCCcc-cccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCCC
Q 048704            6 VLMVAEKPSIALSIATVLSGGKLY-TRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAP   84 (220)
Q Consensus         6 ~LiIaEKPs~Ak~ia~~L~~~~~~-~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~p   84 (220)
                      +||||||||+|++||++|+++..+ ++..++++|+|.+  +|+  +|+|||+.|||++|++|++|++|+..+|..+++.+
T Consensus         2 ~LiIaEKps~Ak~Ia~~L~~g~~~~~~~~g~~~~~~~~--~g~--~~~v~~~~GHl~~l~~p~~y~~w~~~~l~~l~~~~   77 (822)
T PRK07219          2 ELIIAEKNNAARRIADILSGGKAKKKRVNGVPYYEFER--KGE--KWIVIGLSGHIVTVDFPEEYGDWRDVDPAELIDAD   77 (822)
T ss_pred             EEEEEeCHHHHHHHHHHhcCCCcccccCCCcceEEecC--CCC--eEEEEEecCcccccCCchhcCCcCcCChhhccccc
Confidence            799999999999999999654332 3445666776632  354  89999999999999999999999876544334333


Q ss_pred             ceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcCCC
Q 048704           85 VHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVE  164 (220)
Q Consensus        85 ~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl~~  164 (220)
                      +.+  ...+.++++.|++++++||+||||||||||||+|||+|++++....   .++++|+|||++|+++|++||+||++
T Consensus        78 ~~~--~~~~~~~~~~lk~l~~~ad~iiiAtD~DREGE~I~~ei~~i~~~~~---~~~v~R~~fs~iT~~~I~~A~~n~~~  152 (822)
T PRK07219         78 PVK--KITKQNYINALKKLAKDADEIIIATDYDREGELIGKEAYHILREVC---QVPVKRARFSSLTKKEIRKAFENPDE  152 (822)
T ss_pred             eee--cCCHHHHHHHHHHHHhcCCEEEEcCCCChhHHHHHHHHHHHHHhcC---CCceeEEEEccCCHHHHHHHHhCccc
Confidence            222  2356789999999999999999999999999999966655555321   57999999999999999999999999


Q ss_pred             CCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704          165 PNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF  219 (220)
Q Consensus       165 ~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~  219 (220)
                      +|.+|++||+||+++||+||||+||++|+.+++.+.   ..++|+||||||||.|
T Consensus       153 ~d~~l~~a~~aR~~~D~lvG~nlSr~lt~~~~~~g~---~~~lS~GRVQtPtL~l  204 (822)
T PRK07219        153 IDFNLADAGEARQIIDLYWGAALTRFLSLSVRQLGR---WDFLSVGRVQTPTLAF  204 (822)
T ss_pred             CCHHHHHHHHHHHHHHHHhhhhhCHHHHHHHHhccc---cCccccccccchhhHH
Confidence            999999999999999999999999999998864311   2589999999999976

>TIGR01056 topB DNA topoisomerase III, bacteria and conjugative plasmid

Probab=100.00  E-value=1.2e-53  Score=411.33  Aligned_cols=189  Identities=26%  Similarity=0.311  Sum_probs=159.9

Q ss_pred             eEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceec-CCcceEEEEccccceecccCCCCC----CCCccCCCCCC
Q 048704            6 VLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFL-GSHAYIKVTSVVGHVFRLDFPPAY----QDWNASNPLDL   80 (220)
Q Consensus         6 ~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~-g~~~~~~vt~~~GHl~~l~~p~~y----~~w~~~~p~~l   80 (220)
                      .||||||||+|++||++||.+   +++        +|||+ |+  +|+|+|+.|||++|++|++|    ++|+..+    
T Consensus         2 ~LiIaEKPs~Ak~Ia~~L~~~---~~~--------~gy~e~g~--~~~V~~~~GHl~~L~~p~~~~~~~~~W~~~~----   64 (660)
T TIGR01056         2 TLVLCEKPSQARDLATVLAKK---KKG--------NGYLEIGV--GGFVTWAVGHLVELAEPEEYDEKYKNWRTYD----   64 (660)
T ss_pred             eEEEEeCHHHHHHHHHHhCCC---cCC--------CCcEEECC--cEEEEeCchhhhcCCChhhcccccCccccCC----
Confidence            699999999999999999863   222        57787 77  89999999999999988754    5676533    


Q ss_pred             CCCCcee-----ccCCCcHHHHHHHHHHhc--cCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHH
Q 048704           81 FQAPVHK-----AESNPKVHICRHLNQEAR--GCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEK  153 (220)
Q Consensus        81 ~~~p~~~-----~~~~~~~~~~~~lk~~~~--~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~  153 (220)
                        +|+.|     .....+.++++.|+++++  +||.||+|||||||||+|||+|+++++..   +..+++|+|||++|++
T Consensus        65 --lp~~p~~f~~~~~~~~~~~~~~ik~l~k~~~ad~Ii~AtDpDREGE~I~~~i~~~l~~~---~~~~v~Ri~f~~iT~~  139 (660)
T TIGR01056        65 --LPLEPEDWQLVVSDKTKKQFNVIKRILKENKVDEVVIATDPDREGELIAREILDYLKVT---DKVTIKRLWISSLVDS  139 (660)
T ss_pred             --CCcccccceeeeccchHHHHHHHHHHhhhcCCCEEEECCCCCcchHHHHHHHHHHhCCC---CCCceEEEEeccCCHH
Confidence              33322     123457889999999999  99999999999999999999999999862   1248999999999999


Q ss_pred             HHHHHHhcCCCC--CcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704          154 DILKAMGNLVEP--NRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF  219 (220)
Q Consensus       154 ~I~~A~~nl~~~--~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~  219 (220)
                      +|++||+||+++  +.+|++||+||+++||++|||+||++|+.++..  ++ +.++|+||||||||.+
T Consensus       140 ~I~~A~~n~~~~~~~~~l~~a~~aR~~~D~lvG~nlSr~lt~~~~~~--g~-~~~lS~GRVQtptL~l  204 (660)
T TIGR01056       140 SIRKAFKNLRPKSETEGLYKSGVARARADWLVGINLTRAFTKLGREA--GN-DGVLSVGRVQTPTLAM  204 (660)
T ss_pred             HHHHHHHcCCCchhhhhHHHHHHHHHHHHHHHHHhHhHHHHHhhhhc--CC-CCceecccchhhhhHH
Confidence            999999999997  569999999999999999999999999987643  22 3479999999999975

This model describes topoisomerase III from bacteria and its equivalents encoded on plasmids. The gene is designated topB if found in the bacterial chromosome, traE on conjugative plasmid RP4, etc. These enzymes are involved in the control of DNA topology. DNA topoisomerase III belongs to the type I topoisomerases, which are ATP-independent.

>TIGR01057 topA_arch DNA topoisomerase I, archaeal

Probab=100.00  E-value=1.5e-53  Score=408.82  Aligned_cols=196  Identities=25%  Similarity=0.277  Sum_probs=159.6

Q ss_pred             EEeChHHHHHHHHHcCCCCc-ccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCCCcee
Q 048704            9 VAEKPSIALSIATVLSGGKL-YTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAPVHK   87 (220)
Q Consensus         9 IaEKPs~Ak~ia~~L~~~~~-~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~p~~~   87 (220)
                      ||||||+|++||++||.+.. .++++++++|+|+  ++|+  +++||||.|||++|++|++ .+|..|+   +-.+|+.+
T Consensus         1 iAEKPs~A~~ia~~l~~~~~~~~~~~g~~y~~~~--~~g~--~~~Vt~~~GHl~~l~~p~~-~~~~~w~---~~~lP~~~   72 (618)
T TIGR01057         1 IAEKPKVAAKIAGALSDGRVLKKSEYGVPYWEVR--RDGK--KIIVASAVGHLFGLHPKSR-GGYPVFD---IEWVPIFE   72 (618)
T ss_pred             CCCChHHHHHHHHHhCCCCcccccCCCceEEEEe--cCCC--eEEEEEeccccccCCCccc-cCCCCCC---cccCceee
Confidence            79999999999999987421 1334454455543  2365  8999999999999999986 2333322   22466665


Q ss_pred             ccC--CCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcCCCC
Q 048704           88 AES--NPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEP  165 (220)
Q Consensus        88 ~~~--~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl~~~  165 (220)
                      ...  ..+.++++.|++++++||+||||||||||||+|+|+|+++++.     .++++|+|||++|+++|++||+||++.
T Consensus        73 ~~~~~~~~~~~~~~ik~l~~~~d~ii~AtD~DREGE~I~~~i~~~~~~-----~~~v~Rl~~~~lt~~~I~~a~~nl~~~  147 (618)
T TIGR01057        73 FDKGKGYVSKYIKALSKLAKGADEYINACDYDIEGEVIGFKALKYFCG-----VERAKRMKFSTLTKQDIRRAYANPEEI  147 (618)
T ss_pred             ecCCcccHHHHHHHHHHHHhcCCEEEECCCCCccHHHHHHHHHHHhcc-----CCCceEEEEccCCHHHHHHHHhCcccC
Confidence            421  1235899999999999999999999999999999999999975     368999999999999999999999988


Q ss_pred             CcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704          166 NRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF  219 (220)
Q Consensus       166 ~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~  219 (220)
                      +.+|++||+||+++||++|||+||++|+.++...+  .+.++|+||||||||.|
T Consensus       148 ~~~l~~a~~aR~~~D~liG~n~Sr~~t~~~~~~~~--~~~~lS~GRVQtPtL~l  199 (618)
T TIGR01057       148 DYGMVDAGMARHILDWYWGINLSRALMEAIRAAAG--RWVILSAGRVQGPTLAF  199 (618)
T ss_pred             CHhHHHHHHHHHHHHHHHhhhhhHHHHHHhhccCC--CcccccccccchhHHHH
Confidence            88999999999999999999999999998764322  13589999999999975

This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent.

>PRK05776 DNA topoisomerase I; Provisional

Probab=100.00  E-value=1.5e-52  Score=404.16  Aligned_cols=199  Identities=25%  Similarity=0.288  Sum_probs=159.5

Q ss_pred             ceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCC-CCCCcc-CCCCCCCC
Q 048704            5 KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPA-YQDWNA-SNPLDLFQ   82 (220)
Q Consensus         5 ~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~-y~~w~~-~~p~~l~~   82 (220)
                      ++||||||||+|++||++||.+...++.+++.+|+|.  ++|+  +|+|+|+.|||++|++|+. |..+.. +.|  .|.
T Consensus         2 ~~LiIaEKPs~Ak~Ia~~Lg~~~~~~~~~g~~~~e~~--~~g~--~~~V~~~~GHl~~L~~~~~~~~~~~~~~~p--~~~   75 (670)
T PRK05776          2 YILVIAEKPKAARKIAEALSEKPIRCRIYGVPYWIVK--RDGK--KIVVAPAAGHLFGLHTKSKGFPVFDYEWKP--LYE   75 (670)
T ss_pred             CEEEEEcCHHHHHHHHHHhCCCccccccCCCceEEEe--cCCC--CEEEEEecccCccCCCcccCCCCCCcCccc--ceE
Confidence            5899999999999999999853323343455555552  2355  8999999999999998874 321110 011  111


Q ss_pred             CCceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcC
Q 048704           83 APVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNL  162 (220)
Q Consensus        83 ~p~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl  162 (220)
                        +.+. ...++++++.|++++++||+||||||||||||+|||||+++++.     .++++|+|||++|+++|++||+|+
T Consensus        76 --~~~~-~~~~~~~~~~lk~l~k~ad~iiiAtD~DREGE~I~~~i~~~~~~-----~~~v~R~~fs~iT~~~I~~A~~n~  147 (670)
T PRK05776         76 --IDKG-SKYTKKYYELLSSLSKYADEFINACDYDIEGSVIGYLIIKYLGD-----PKKAKRMKFSALTKSDIRRAFRNL  147 (670)
T ss_pred             --eccC-cccHHHHHHHHHHHHhcCCEEEECCCCChhHHHHHHHHHHHhCC-----CCCeeEEEEccCCHHHHHHHHhCc
Confidence              1110 12245899999999999999999999999999999999999984     468999999999999999999999


Q ss_pred             CCCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704          163 VEPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF  219 (220)
Q Consensus       163 ~~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~  219 (220)
                      +++|.+|++||+||+++|||+|||+||++|+.+++..+  ...++|+||||||||.|
T Consensus       148 ~~~d~~l~~A~~aR~~lD~lvG~nlSr~lt~~~~~~~g--~~~~lS~GRVQsptL~l  202 (670)
T PRK05776        148 ETLDYEMINAGIARHELDWLWGINVSRALMSSVRDASG--KRVILSAGRVQSPTLKY  202 (670)
T ss_pred             cccchhHHHHHHHHHHHHHHHhHHHhHHHHHHhhhhcC--CccceecceecCchhhH
Confidence            99999999999999999999999999999998864332  13479999999999975

>PRK09401 reverse gyrase; Reviewed

Probab=100.00  E-value=8.3e-51  Score=410.23  Aligned_cols=200  Identities=23%  Similarity=0.258  Sum_probs=164.6

Q ss_pred             CceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCC-CC-CCC
Q 048704            4 LKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASN-PL-DLF   81 (220)
Q Consensus         4 ~~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~-p~-~l~   81 (220)
                      +++||||||||+|++||++||.++ .++.+++++|++..   |+ ..++|||+.|||++|..|++|.+|...+ |+ +.+
T Consensus       601 k~~LiIaEkPskAk~IA~~lg~~~-~r~~g~~~~ye~~~---~~-~~~~Vt~s~GHl~dL~~~~~y~g~~~~~~p~~P~y  675 (1176)
T PRK09401        601 KTTLLIVESPTKARTIANFFGRPS-RRRIGGLVVYETVT---GD-RILTITASKGHVYDLTTEIGYYGVLVKDGGFVPVY  675 (1176)
T ss_pred             CCEEEEEcCHHHHHHHHHHhCCCc-cccCCCceeEEEec---CC-cEEEEEEeccccccCCCccccCcccccCCccccee
Confidence            579999999999999999998642 33456666666422   33 1348999999999999999998897643 21 111


Q ss_pred             C------------------CCceecc-CCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcE
Q 048704           82 Q------------------APVHKAE-SNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKV  142 (220)
Q Consensus        82 ~------------------~p~~~~~-~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v  142 (220)
                      .                  +|...+. ..++.++++.|++++++||+||||||||||||+|||+|+++++..    ++++
T Consensus       676 ~~~k~c~~~g~~f~~~~~~~~~c~~~~~~~k~~~~~~Lr~l~~~~d~IiiAtDpDrEGE~Ia~~i~~~l~~~----~~~i  751 (1176)
T PRK09401        676 DTIKRCRDCGYQFTDESDKCPRCGSTNIEDKEEIIEALRELALEVDEVLIATDPDTEGEKIAWDLYLLLSPY----NSNI  751 (1176)
T ss_pred             eeeccccccccccccccccccccccccCCCHHHHHHHHHHHHhcCCEEEEccCcChhHHHHHHHHHHHhccc----CCCE
Confidence            0                  1111100 145678999999999999999999999999999999999999953    5789


Q ss_pred             EEEEecCcCHHHHHHHHhcCCCCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704          143 HRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF  219 (220)
Q Consensus       143 ~R~~~sslt~~~I~~A~~nl~~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~  219 (220)
                      +|+|||++|+++|++||+|++++|.+|++||.||+++||++|||+||++|+.++       +..+|+||||||||.+
T Consensus       752 ~R~~f~eiT~~aI~~A~~n~r~~~~~l~~A~~aRr~~D~~iG~~lSr~l~~~~~-------~~~lSaGRVQTPtL~~  821 (1176)
T PRK09401        752 KRIEFHEVTRKAILEALRNPRDVNENLVKAQIVRRIEDRWIGFELSQKLQKKFG-------KRNLSAGRVQTPVLGW  821 (1176)
T ss_pred             EEEEeecCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-------ccCccccccccchhhh
Confidence            999999999999999999999999999999999999999999999999998764       2359999999999975

>TIGR01051 topA_bact DNA topoisomerase I, bacterial

Probab=100.00  E-value=2.7e-51  Score=392.51  Aligned_cols=169  Identities=25%  Similarity=0.278  Sum_probs=147.6

Q ss_pred             EEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCCCce
Q 048704            7 LMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAPVH   86 (220)
Q Consensus         7 LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~p~~   86 (220)
                      ||||||||+|++||++||.                        +++||||.|||++|+.|+.+..|+..     | .| .
T Consensus         1 LiIaEkps~a~~Ia~~lg~------------------------~~~Vt~~~GHl~~l~~~~~~~~~~~~-----~-~~-~   49 (610)
T TIGR01051         1 LVIVESPAKAKTIKKYLGD------------------------EYEVEASMGHIRDLPKSRLGVDIEKD-----F-EP-E   49 (610)
T ss_pred             CEEEeChHHHHHHHHHhCC------------------------CCEEEeccCeeccCCCcccCCChhhc-----C-ce-e
Confidence            7999999999999999974                        57899999999999888666667531     2 12 1


Q ss_pred             eccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcE-EEEEecCcCHHHHHHHHhcCCCC
Q 048704           87 KAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKV-HRARFSSVTEKDILKAMGNLVEP  165 (220)
Q Consensus        87 ~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v-~R~~~sslt~~~I~~A~~nl~~~  165 (220)
                      .....++.++++.|++++++||+||||||||||||+|+|+|+++++.     .+++ +|+|||++|+++|++||+||+++
T Consensus        50 ~~~~~~~~~~~~~i~~l~~~~d~ii~AtD~DrEGE~I~~~i~~~~~~-----~~~~~~Rl~~s~lt~~~I~~a~~~l~~~  124 (610)
T TIGR01051        50 YVVSKGKKKVVKELKTLAKKADEVYLATDPDREGEAIAWHLAEVLKP-----KDPVYKRIVFNEITKKAIRAALKNPREI  124 (610)
T ss_pred             EEEcccHHHHHHHHHHHHhcCCEEEECCCCCcchhHHHHHHHHHhCC-----CCCCceEEEEccCCHHHHHHHHhCcccc
Confidence            12234678899999999999999999999999999999999999996     3455 99999999999999999999999


Q ss_pred             CcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704          166 NRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF  219 (220)
Q Consensus       166 ~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~  219 (220)
                      +.+|++||.||+++||++|||+||++|+.++        ..+|+||||||||.|
T Consensus       125 ~~~l~~aa~aR~~~D~liG~n~Tr~~t~~~~--------~~lSvGRVQtPtL~l  170 (610)
T TIGR01051       125 DMNLVNAQQARRILDRLVGYTLSPLLWKKVA--------KGLSAGRVQSVALRL  170 (610)
T ss_pred             chhHHHHHHHHHHHHHHHhHhhhHHHHHhhc--------CCCCcceehHHHHHH
Confidence            9999999999999999999999999998542        249999999999975

This model describes DNA topoisomerase I among the members of bacteria. DNA topoisomerase I transiently cleaves one DNA strand and thus relaxes negatively supercoiled DNA during replication, transcription and recombination events.

>PRK06599 DNA topoisomerase I; Validated

Probab=100.00  E-value=1.1e-50  Score=392.31  Aligned_cols=176  Identities=24%  Similarity=0.242  Sum_probs=148.5

Q ss_pred             CceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCC
Q 048704            4 LKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQA   83 (220)
Q Consensus         4 ~~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~   83 (220)
                      |++||||||||+|++||++||.                        +|+|+||.|||++|..|  +..|...+   .|. 
T Consensus         2 ~~~LiIaEKPs~ak~Ia~~lg~------------------------~~~V~~~~GHl~~l~~~--~~~~~~~~---~~~-   51 (675)
T PRK06599          2 AKKLVIVESPAKAKTIKKYLGK------------------------DYKVLASFGHVRDLPKK--KGGVDPDN---DFA-   51 (675)
T ss_pred             CCeEEEEeCHHHHHHHHHHcCC------------------------CCEEEecccchhcCCcc--ccCCCccc---CCC-
Confidence            3789999999999999999974                        67899999999999543  33554322   222 


Q ss_pred             CceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcCC
Q 048704           84 PVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLV  163 (220)
Q Consensus        84 p~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl~  163 (220)
                       +.....+++.++++.|++++++||+||||||||||||+|||+|+++++... ...++++|+|||++|+++|++||+|++
T Consensus        52 -~~~~~~~~~~~~~~~ik~l~~~~d~iiiAtD~DrEGE~I~~~i~~~~~~~~-~~~~~v~Rl~~s~lt~~~I~~a~~n~~  129 (675)
T PRK06599         52 -PKYEIIEGKEKVVDALKKAAKKADAVYLATDPDREGEAIAWHIAEVLKEAK-LKDKNVKRVVFNEITKKAVQEAIENPR  129 (675)
T ss_pred             -ceEEECCcHHHHHHHHHHHHhhCCEEEECCCCCcchHHHHHHHHHHHHhhc-CCCCCeeEEEEccCCHHHHHHHHhCcc
Confidence             111223457889999999999999999999999999999999999995100 015789999999999999999999999


Q ss_pred             CCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704          164 EPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF  219 (220)
Q Consensus       164 ~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~  219 (220)
                      +++.+|++||+||+++||++|||+||++|+.++        ..+|+||||||||.+
T Consensus       130 ~~~~~l~~a~~aR~~~D~liG~n~tr~~t~~~~--------~~lS~GRVQtPtL~l  177 (675)
T PRK06599        130 DIDMDLVDAQQARRALDYLVGFKLSPLLWKKVR--------RGLSAGRVQSVALRL  177 (675)
T ss_pred             cCCHHHHHHHHHHHHHHHHhhhhhCHHHHHhcc--------CCCccceeHHHHhHH
Confidence            999999999999999999999999999998763        249999999999975

>COG0550 TopA Topoisomerase IA [DNA replication, recombination, and repair]

Probab=100.00  E-value=1.3e-50  Score=383.08  Aligned_cols=178  Identities=30%  Similarity=0.355  Sum_probs=154.3

Q ss_pred             ceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCCC
Q 048704            5 KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAP   84 (220)
Q Consensus         5 ~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~p   84 (220)
                      +.|||||||++||+||++||.                        +|+|+|+.|||++|.+|++++.|...+.. .|...
T Consensus         1 ~~LiIvEsPskAk~Ia~~Lg~------------------------~~~V~as~GHi~dl~~~~~~~~~~~~~~~-~~~~~   55 (570)
T COG0550           1 KRLIIVESPSKAKTIAKYLGK------------------------GYVVTASVGHLRDLPFPEEYKGWVDVDLP-IFEPK   55 (570)
T ss_pred             CeEEEEeCHHHHHHHHHhcCC------------------------CcEEEEcccccccCCChhhccCCcCCccc-ccccc
Confidence            469999999999999999986                        58999999999999999998888764311 11111


Q ss_pred             ceeccCCC-cHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcCC
Q 048704           85 VHKAESNP-KVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLV  163 (220)
Q Consensus        85 ~~~~~~~~-~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl~  163 (220)
                      +.  .... +.++++.|+.++++||.||||||||||||+|||||+++++..+   ..+++|||||++|+++|++||+|++
T Consensus        56 ~~--~~~~~k~~~v~~lk~~ak~ad~v~lAtD~DREGE~I~~~i~~~l~~~~---~~~~~R~~F~eiT~~aI~~A~~~p~  130 (570)
T COG0550          56 YI--IKPGKKKKVVKKLKKLAKKADEVYLATDPDREGEAIGWHILEVLKLKN---PSKVKRVVFSEITKKAILSAFKNPR  130 (570)
T ss_pred             ee--ccchhhHHHHHHHHHHhccCCEEEECCCCCcchHHHHHHHHHHhCccC---CCceeEEEEecCCHHHHHHHHhCch
Confidence            11  1122 6888999999999999999999999999999999999999842   1479999999999999999999999


Q ss_pred             CCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704          164 EPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF  219 (220)
Q Consensus       164 ~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~  219 (220)
                      ..|.+|++|++||+++|||+|+|+||++|+.+++       .++|+||||||||.+
T Consensus       131 ~id~~lv~A~~aR~~lD~lvG~~lSr~l~~~~~~-------~~LSaGRVQSpaL~l  179 (570)
T COG0550         131 EIDMNLVDAQLARRILDRLVGYNLSRLLWKKLKR-------GVLSAGRVQSPALRL  179 (570)
T ss_pred             hhchHHHHHHHHHHHHHHHhhhhhhHHHHHhhcc-------CCCCCccccchhhhh
Confidence            9999999999999999999999999999998753       179999999999975

>PRK05582 DNA topoisomerase I; Validated

Probab=100.00  E-value=9.9e-51  Score=391.28  Aligned_cols=173  Identities=23%  Similarity=0.273  Sum_probs=146.3

Q ss_pred             CceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCC
Q 048704            4 LKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQA   83 (220)
Q Consensus         4 ~~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~   83 (220)
                      |++||||||||+|++||++||.                        +|+|+||.|||++|..| .+.    .+|.+.+. 
T Consensus         2 m~~LiIaEkps~a~~ia~~lg~------------------------~~~V~~~~GHl~~l~~~-~~~----~~~~~~~~-   51 (650)
T PRK05582          2 MKKLVIVESPAKAKTIEKYLGK------------------------NYKVVASMGHIRDLPKS-QLG----IDIENNFE-   51 (650)
T ss_pred             CCeEEEEeCHHHHHHHHHHcCC------------------------CCEEEeccCchhcCCCc-cCC----CCcccCCc-
Confidence            4789999999999999999964                        68999999999999865 210    11111111 


Q ss_pred             CceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcCC
Q 048704           84 PVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLV  163 (220)
Q Consensus        84 p~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl~  163 (220)
                      |.. .....+.++++.|++++++||+||||||||||||+|||+|+++++..    .++++|+|||++|+++|++||+||+
T Consensus        52 ~~~-~~~~~~~~~~~~ik~l~~~~d~ii~AtD~DrEGE~I~~~i~~~~~~~----~~~~~R~~~s~lt~~~I~~a~~nl~  126 (650)
T PRK05582         52 PKY-ITIRGKGPVIKELKKAAKKAKKVYLATDPDREGEAIAWHLAHILGLD----EKEKNRIVFNEITKDAIKNAFKNPR  126 (650)
T ss_pred             eee-EECCcHHHHHHHHHHHHhcCCEEEECCCCCcchHHHHHHHHHHhCCC----CCCceEEEEcccCHHHHHHHHhCcc
Confidence            110 11235678999999999999999999999999999999999999862    3678999999999999999999999


Q ss_pred             CCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704          164 EPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF  219 (220)
Q Consensus       164 ~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~  219 (220)
                      +++.+|++||+||+++||++|||+||++|+.++        ..+|+||||||||.+
T Consensus       127 ~~~~~l~~a~~aR~~~D~liG~n~tr~~t~~~~--------~~ls~GRVQtPtL~l  174 (650)
T PRK05582        127 KIDMNLVDAQQARRILDRLVGYKLSPLLWKKVK--------KGLSAGRVQSVALKL  174 (650)
T ss_pred             cccHHHHHHHHHHHHHHHHhhhhcCHHHHHhhc--------CCCccccchHhHHHH
Confidence            999999999999999999999999999998653        249999999999975

>TIGR01054 rgy reverse gyrase

Probab=100.00  E-value=1.8e-49  Score=400.63  Aligned_cols=200  Identities=23%  Similarity=0.254  Sum_probs=163.4

Q ss_pred             CceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCC-CC-CC-
Q 048704            4 LKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASN-PL-DL-   80 (220)
Q Consensus         4 ~~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~-p~-~l-   80 (220)
                      +++|||||||++|++||++||.++ .++.+++.+|+|.+   |+ ..++|||+.|||++|..|+.|.+|...+ |+ +. 
T Consensus       601 k~~LiIvEsP~kAk~Ia~~lg~~~-~r~~~g~~~yE~~~---g~-~~~~Vtas~GHl~dL~~~~~~~g~~~~~~~f~P~y  675 (1171)
T TIGR01054       601 KTALLVVESPNKARTIARFFGKPS-VRKIGGSVVYEVPV---GD-LILMITASGGHVFDLVTDKGFHGVLVENGRYVPVY  675 (1171)
T ss_pred             CceEEEEcChHHHHHHHHHhCCCc-ccccCCcceEEEec---CC-eeEEEEEeCceeeeCCCccccCcccccCCcccccc
Confidence            579999999999999999998743 23336667777643   33 2459999999999999998777776532 11 11 


Q ss_pred             ------------CC-----CCceec-cCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcE
Q 048704           81 ------------FQ-----APVHKA-ESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKV  142 (220)
Q Consensus        81 ------------~~-----~p~~~~-~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v  142 (220)
                                  |+     +|-..+ ...++.++++.|++++++||+||||||||||||+|||+|+++++..    ++++
T Consensus       676 ~~~k~~~~~~~~f~~~~~~~p~~~~~~~~~k~~~~~~lr~l~~~~d~ViiATDpDrEGE~Ia~~i~~~l~~~----~~~i  751 (1171)
T TIGR01054       676 TSIKRCRDCGYQFTEDRESCPKCGSENIEDSKSIIEILRELAHEVDEVFIGTDPDTEGEKIGWDLALLLSPY----NPNV  751 (1171)
T ss_pred             cccccCCchhhhccccccccccccccccccHHHHHHHHHHHHhcCCEEEECCCCCccHHHHHHHHHHHhccc----CCCe
Confidence                        10     111100 1245688999999999999999999999999999999999999753    5689


Q ss_pred             EEEEecCcCHHHHHHHHhcCCCCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704          143 HRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF  219 (220)
Q Consensus       143 ~R~~~sslt~~~I~~A~~nl~~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~  219 (220)
                      +|+|||++|+++|++||+|++++|.+|++||.||+++||++|||+||++|+.++       +..+|+||||||||.+
T Consensus       752 ~R~~f~eiT~~aI~~A~~n~r~~~~~L~~A~~aRr~~D~liG~~lSr~lt~~~~-------~~~lSaGRVQTPtL~l  821 (1171)
T TIGR01054       752 KRAEFHEVTRRAILEALESPRSVDENLVKAQVVRRIEDRWIGFTLSQKLWEAFN-------KRWLSAGRVQTPVLGW  821 (1171)
T ss_pred             EEEEEccCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhhhhCHHHHHhhc-------CCCcccceecchhhHH
Confidence            999999999999999999999999999999999999999999999999998653       2469999999999965

Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.

>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated

Probab=100.00  E-value=3.3e-49  Score=389.71  Aligned_cols=174  Identities=22%  Similarity=0.271  Sum_probs=151.3

Q ss_pred             CceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCC
Q 048704            4 LKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQA   83 (220)
Q Consensus         4 ~~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~   83 (220)
                      |+.|||||||++|++|+++||.                        +|+|+|+.|||++|  |+.+.+|...++   |. 
T Consensus         2 ~~~LvIvEsP~kak~I~~~Lg~------------------------~~~V~as~GHl~dL--p~~~~~~~~~~~---f~-   51 (860)
T PRK06319          2 KKSLIIVESPAKIKTLQKLLGE------------------------GFIFASSLGHIVDL--PAKEFGIDIEND---FE-   51 (860)
T ss_pred             CCeEEEEeCHHHHHHHHHHhCC------------------------CCEEEecccCcccC--CcccCCcCCCCC---CC-
Confidence            3789999999999999999975                        68999999999999  666556764322   22 


Q ss_pred             CceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcCC
Q 048704           84 PVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLV  163 (220)
Q Consensus        84 p~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl~  163 (220)
                      |.. ....++.++++.|++++++||.||||||||||||+|+|||+++++.     +++++|+|||++|+++|++||+|++
T Consensus        52 p~y-~~~~~k~~~~~~ik~~~k~ad~iilAtDpDREGE~I~~~i~~~l~~-----~~~v~Rv~f~~iT~~aI~~A~~~~~  125 (860)
T PRK06319         52 PDY-QILPDKEEVINKICKLAKKCDVVYLSPDPDREGEAIAWHIANQLPK-----NTKIQRISFNAITKGAVTEALKHPR  125 (860)
T ss_pred             cce-EECccHHHHHHHHHHHHHhCCEEEECCCCCcchHHHHHHHHHHcCC-----CCCeeEEEEccCCHHHHHHHHhCcc
Confidence            211 1234678999999999999999999999999999999999999975     5799999999999999999999999


Q ss_pred             CCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704          164 EPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF  219 (220)
Q Consensus       164 ~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~  219 (220)
                      ++|.+|++|++||+++|||||||+||++|+.++..      ..+|+||||||||.+
T Consensus       126 ~~d~~l~~A~~aR~~lD~lvG~nlSr~l~~~~~~~------~~lSaGRVQsp~L~l  175 (860)
T PRK06319        126 EIDMALVNAQQARRLLDRIVGYKISPILSRKLQRR------SGVSAGRVQSVALKL  175 (860)
T ss_pred             ccCHHHHHHHHHHHHHHHHhhhhcCHHHHHhhccC------CCCcCCccchhhhHH
Confidence            99999999999999999999999999999887531      249999999999964

>PRK08780 DNA topoisomerase I; Provisional

Probab=100.00  E-value=1.9e-49  Score=387.89  Aligned_cols=177  Identities=23%  Similarity=0.210  Sum_probs=149.2

Q ss_pred             CceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCC
Q 048704            4 LKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQA   83 (220)
Q Consensus         4 ~~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~   83 (220)
                      |+.|||||||++|++|+++||.                        +|+|+|+.|||++|..|+.+-     +|...|..
T Consensus         2 ~~~LiIvEsPskAk~I~~~Lg~------------------------~y~V~as~GHi~dL~~~~~~v-----d~~~~f~~   52 (780)
T PRK08780          2 SKHLVIVESPAKAKTINKYLGK------------------------DFTVLASYGHVRDLVPKEGAV-----DPENGFAM   52 (780)
T ss_pred             CCeEEEEeCHHHHHHHHHHcCC------------------------CCEEEeccCCcccCCCcccCC-----ChhhCCce
Confidence            3789999999999999999975                        689999999999998876541     11111221


Q ss_pred             CceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcCC
Q 048704           84 PVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLV  163 (220)
Q Consensus        84 p~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl~  163 (220)
                      .+.  ...++.++++.|++++++||.||+|||||||||+|+|||+++++..+..+.++++|+|||++|+++|++||+|++
T Consensus        53 ~y~--~~~~k~~~~~~lk~~~k~ad~vilAtD~DREGE~Ia~~i~~~l~~~~~~~~~~v~Ri~f~eiT~~aI~~A~~n~r  130 (780)
T PRK08780         53 RYD--LIDKNEKHVEAIAKAAKSADDLYLATDPDREGEAISWHLAEILKERGLLKDKPMQRVVFTEITPRAIKEAMAKPR  130 (780)
T ss_pred             EEE--EcCchHHHHHHHHHHHHhCCEEEECCCCCcccHHHHHHHHHHhcccccCCCCceEEEEEccCCHHHHHHHHhCCC
Confidence            111  124567899999999999999999999999999999999999974211124689999999999999999999999


Q ss_pred             CCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704          164 EPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF  219 (220)
Q Consensus       164 ~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~  219 (220)
                      ++|++|++|++||+++|||+|||+||++|..++        ..+|+||||||||.+
T Consensus       131 ~~d~~l~~A~~aRr~lD~lvG~~lSr~l~~~~~--------~~lSaGRVQspaL~l  178 (780)
T PRK08780        131 DIASDLVDAQQARRALDYLVGFNLSPLLWRKIQ--------RGLSAGRVQSPALRM  178 (780)
T ss_pred             cCcHhHHHHHHHHHHHHHhcCeeecHHHHHhhC--------CCCcccccHHHHHHH
Confidence            999999999999999999999999999998663        249999999999975

>PRK07561 DNA topoisomerase I subunit omega; Validated

Probab=100.00  E-value=5.7e-49  Score=388.33  Aligned_cols=177  Identities=26%  Similarity=0.259  Sum_probs=150.5

Q ss_pred             ceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCC-----CCCCccC----
Q 048704            5 KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPA-----YQDWNAS----   75 (220)
Q Consensus         5 ~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~-----y~~w~~~----   75 (220)
                      +.|||||||++|++|+++||.                        +|+|+|++|||++|..|+.     |+.|...    
T Consensus         2 ~~LvIvEkP~kak~I~~~Lg~------------------------~~~V~~s~GHi~dL~~~~~~~~~~~k~~~w~~l~i   57 (859)
T PRK07561          2 KSLVIVESPAKAKTINKYLGS------------------------DYVVKASVGHIRDLPTSASSVPAKEKGALWARMGV   57 (859)
T ss_pred             CEEEEEeCHHHHHHHHHHcCC------------------------CCEEEeccCChhhCCCccccChhhhhhchHhhcCc
Confidence            579999999999999999974                        6899999999999998544     4433311    


Q ss_pred             CCCCCCCCCceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHH
Q 048704           76 NPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDI  155 (220)
Q Consensus        76 ~p~~l~~~p~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I  155 (220)
                      +|.+.|..  ......+++++++.|++++++||+||||||||||||+|+|||+++++..    +++++|+|||++|+++|
T Consensus        58 ~~~~~f~~--~y~~~~~k~~~~~~lk~~~k~ad~iilAtD~DREGE~I~~~i~~~l~~~----~~~v~Ri~f~~iT~~aI  131 (859)
T PRK07561         58 DPDHDFEA--LYEVLPGKEKVVSELKKAAKDADELYLATDPDREGEAIAWHLLEVLGGD----DVPVKRVVFNEITKNAI  131 (859)
T ss_pred             CcccCcce--eEEECccHHHHHHHHHHHHhcCCEEEECCCCCccchHHHHHHHHHhCCC----CCCeEEEEEccCCHHHH
Confidence            12222221  1122346789999999999999999999999999999999999999842    57999999999999999


Q ss_pred             HHHHhcCCCCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704          156 LKAMGNLVEPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF  219 (220)
Q Consensus       156 ~~A~~nl~~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~  219 (220)
                      ++||+|++++|.+|++|++||+++|||||||+||++|..++        ..+|+||||||||.+
T Consensus       132 ~~A~~n~~~~~~~l~~A~~aRr~lD~lvG~~lS~~l~~~~~--------~~lSaGRVQsp~L~l  187 (859)
T PRK07561        132 QEAFENPRELDINLVNAQQARRFLDRLVGYMVSPLLWKKIA--------RGLSAGRVQSVAVRL  187 (859)
T ss_pred             HHHHhCcccCCHHHHHHHHHHHHHHHHhhhhcCHHHHHhhc--------cCCCcccchhhhhHH
Confidence            99999999999999999999999999999999999998653        249999999999975

>PRK14701 reverse gyrase; Provisional

Probab=100.00  E-value=2.5e-48  Score=400.07  Aligned_cols=200  Identities=20%  Similarity=0.216  Sum_probs=162.5

Q ss_pred             CceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCC-------
Q 048704            4 LKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASN-------   76 (220)
Q Consensus         4 ~~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~-------   76 (220)
                      +++||||||||+|++||++||.++ .++.+++.+|++..   |+ +.++|||+.|||++|..|++|.+|...+       
T Consensus       580 ~~~LiIaEkPs~Ak~IA~~lg~~~-~r~~g~~~~ye~~~---g~-~~~~Vtas~GHl~dL~~~~~~~g~~~~~~~f~P~y  654 (1638)
T PRK14701        580 KSALMIVESPNKARTIANFFGQPS-VRKIGDLVAYEVSI---GD-HMLIITASGGHVFDLVTNEGFHGVLINNNLFIPIY  654 (1638)
T ss_pred             CCeEEEEeChHHHHHHHHHhCCCc-cccCCCcceEEEec---CC-cEEEEEEecceeccCCCccccCccccccCccCCcc
Confidence            579999999999999999998643 33356777776532   32 3689999999999999888775554321       


Q ss_pred             --------CCCCCCCCc----eec----cCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCC
Q 048704           77 --------PLDLFQAPV----HKA----ESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARR  140 (220)
Q Consensus        77 --------p~~l~~~p~----~~~----~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~  140 (220)
                              +..+|+.+.    .|.    ...++.++++.|++++++||+||||||||||||+|||+|++++...    ++
T Consensus       655 ~~~k~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~lr~l~~~ad~viiatD~DrEGE~I~~~i~~~~~~~----~~  730 (1638)
T PRK14701        655 DSIKRCRDCGHQFTDWEDKGVCPRCGSKNVDDAKENIKAMRELAHEVDEILIGTDPDTEGEKIAWDIRNVLAPY----GP  730 (1638)
T ss_pred             cccccCCCchhhccccccccccccccccccccHHHHHHHHHHHHHhCCeEEECCCCChhhHHHHHHHHHHhccC----CC
Confidence                    112222110    110    1134577899999999999999999999999999999999998643    57


Q ss_pred             cEEEEEecCcCHHHHHHHHhcCCCCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704          141 KVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF  219 (220)
Q Consensus       141 ~v~R~~~sslt~~~I~~A~~nl~~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~  219 (220)
                      +++|+|||++|+++|++||+|++++|++|++||.||+++||++|||+||++|..++       +..+|+||||||||.|
T Consensus       731 ~i~R~~fs~lT~~aI~~A~~nlr~~d~~l~~A~~aRr~~D~~iG~nlSr~l~~~~~-------~~~lS~GRVQTPtL~~  802 (1638)
T PRK14701        731 NIKRIEFHEVTRRAILKAIKEARDIDENRVKAQIVRRIEDRWIGFELSQKLWEVFE-------DRNLSAGRVQTPVLGW  802 (1638)
T ss_pred             CeeEEEEccCCHHHHHHHHhCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHhcc-------CCceeecccccchhhh
Confidence            89999999999999999999999999999999999999999999999999998753       2359999999999975

>KOG1956 consensus DNA topoisomerase III alpha [Replication, recombination and repair]

Probab=100.00  E-value=3e-48  Score=360.46  Aligned_cols=214  Identities=40%  Similarity=0.622  Sum_probs=195.9

Q ss_pred             CceEEEEeChHHHHHHHHHcCCCCccccc---CCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCC
Q 048704            4 LKVLMVAEKPSIALSIATVLSGGKLYTRK---ASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDL   80 (220)
Q Consensus         4 ~~~LiIaEKPs~Ak~ia~~L~~~~~~~~~---~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l   80 (220)
                      |+.|++|||+|+|+.+|.+|++|+...+.   .++.+|+|+..+.|.+++.++|++.|||+++++|.+|..|..++|.++
T Consensus         1 ~~vl~vAekn~~ak~va~il~~g~~~~re~rSk~~kiy~f~~~~~g~~~~~~mtsvsghl~~~~f~~~~s~w~s~~~~~l   80 (758)
T KOG1956|consen    1 MRVLCVAEKNSIAKSVASILSGGTVRRREGRSKYNKIYDFDFNLFGQNCDVTMTSVSGHLTEADFPSEYSKWQSCPPDEL   80 (758)
T ss_pred             CCcccccccchhhhhhhhhcCCCCcCCccchhhhhhhhhhhhhhcCCcceeEEeeccccccccCCcccccceeecCHHHH
Confidence            47899999999999999999998765554   477888887666688899999999999999999999999999999899


Q ss_pred             CCCCceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHh
Q 048704           81 FQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMG  160 (220)
Q Consensus        81 ~~~p~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~  160 (220)
                      |+.|+......+.+.+.+.|+++++.||.+|||||||||||+|||||++.|+..++  ...|.|++||+||+.+|+.|.+
T Consensus        81 f~a~~~~~~~~~~~~i~~~ir~eAr~ad~LviwtDcDREGE~Ig~eI~~v~~~~~~--~~~V~RA~Fs~it~~~I~sA~~  158 (758)
T KOG1956|consen   81 FDAPVIKSVPENAKDIAKTIREEARRADYLVIWTDCDREGENIGWEIIDVCRAVKR--LLQVRRARFSEITRSAIKSAAR  158 (758)
T ss_pred             hhhhhhhcCchhhhHHHHHHHHHHhhcceEEEeccCCccchhhhHHHHHHHHhhCc--cceeehhhhhcccHHHHHHHHh
Confidence            99998877667778899999999999999999999999999999999999998753  5679999999999999999999


Q ss_pred             cCCCCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704          161 NLVEPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF  219 (220)
Q Consensus       161 nl~~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~  219 (220)
                      ||+++|+.+++|.+||+++|++||..|||++|+.+++++.-+...++|+|+||.|||-|
T Consensus       159 nlreid~~~v~AvdaR~ELDlrIGa~FTRlqT~~L~r~f~~~~~~viSyG~cQfpTLgf  217 (758)
T KOG1956|consen  159 NLREIDEKLVHAVDARIELDLRIGAAFTRLQTLLLRRKFPILGEQVISYGPCQFPTLGF  217 (758)
T ss_pred             CccccchHHHHHHHHHHHHHHHhhhhHHHHHhHHHHhhhhhhhccccccccccCcceee
Confidence            99999999999999999999999999999999999988764556899999999999987

>KOG1957 consensus DNA topoisomerase III beta [Replication, recombination and repair]

Probab=100.00  E-value=9.2e-45  Score=326.57  Aligned_cols=198  Identities=56%  Similarity=0.871  Sum_probs=184.9

Q ss_pred             CceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCC
Q 048704            4 LKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQA   83 (220)
Q Consensus         4 ~~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~   83 (220)
                      +..|+||||||.|..||++|+.|..++++|...+++|+|.|.|.+..+.||++.||++.|++|+.|++|...+|-+||..
T Consensus         2 ~tvlmvaekpsla~sia~ils~g~~s~~kg~csvhe~~g~f~g~~~~fk~tsvcghvmsldf~~kyn~w~~vdp~elf~a   81 (555)
T KOG1957|consen    2 KTVLMVAEKPSLADSIANILSNGQASKRKGWCSVHEYDGQFRGRAARFKVTSVCGHVMSLDFPPKYNNWDKVDPAELFSA   81 (555)
T ss_pred             CceeEeecCchHHHHHHHHhhCCccccccCceeeeeccccccCceeeEEEeeeeceeEeccCchhcCCccccCHHHHhCC
Confidence            37899999999999999999998888888999999999999999889999999999999999999999999999999999


Q ss_pred             CceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcCC
Q 048704           84 PVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLV  163 (220)
Q Consensus        84 p~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl~  163 (220)
                      |..+++.++|.+..+-|...++.||.+++|.|+|+|||+|.+||++..+...+.....++|++||++|+++|.+|++||.
T Consensus        82 pt~kkeanpk~~m~kfl~~eargcdy~vlwldcdkegenicfevidav~~~m~~~~~~tyra~fsaitekdi~~am~~lg  161 (555)
T KOG1957|consen   82 PTEKKEANPKMNMNKFLASEARGCDYLVLWLDCDKEGENICFEVIDAVKCVMNRSDFKTYRAHFSAITEKDIKKAMRNLG  161 (555)
T ss_pred             cchhcccCchhhHHHHHhhhccCCcEEEEEeecCCCcCeeehhhhhhhhhhhccCcceEEeeeeccccHHHHHHHHHhcC
Confidence            99988888999999999999999999999999999999999999998887665445678999999999999999999999


Q ss_pred             CCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704          164 EPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF  219 (220)
Q Consensus       164 ~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~  219 (220)
                      .+|+|.+.|.+|||++|+.|         +         .++.||+|+||||||-|
T Consensus       162 ~p~~nea~svdarqeldlri---------l---------ds~~isygpcqtptlgf  199 (555)
T KOG1957|consen  162 EPDQNEALSVDARQELDLRI---------L---------DSSLISYGPCQTPTLGF  199 (555)
T ss_pred             CCCcchhcccchhhhhhhhh---------h---------hhcceeecCCCCCccee
Confidence            99999999999999999988         1         24689999999999987

>cd03362 TOPRIM_TopoIA_TopoIII TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III

Probab=100.00  E-value=4.5e-43  Score=282.08  Aligned_cols=149  Identities=38%  Similarity=0.539  Sum_probs=120.3

Q ss_pred             ceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCC--CCC
Q 048704            5 KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLD--LFQ   82 (220)
Q Consensus         5 ~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~--l~~   82 (220)
                      ++||||||||+|++||++||++..  ++++..++  .+++++.  +++|||+.|||++|++|++|..|....+.+  +++
T Consensus         1 ~~LiIAEKPs~Ak~ia~~L~~~~~--~~~~~~~~--~~~~~~~--~~~vt~~~GHl~~l~~p~~y~~~~~~~~~~~p~~~   74 (151)
T cd03362           1 MVLIIAEKPSVAKAIAKILGGGSK--KKGKGRYY--EFYGEGG--GYVVTWASGHLLELDFPEEYDPWDKVWPLEDPLFP   74 (151)
T ss_pred             CEEEEecCHHHHHHHHHHhCCCCc--cCCccccc--ceecCCC--CEEEEEEhhHhhcccChHHhccCCCCCccccCCcC
Confidence            379999999999999999987532  22222233  3466666  899999999999999999998775433322  343


Q ss_pred             CCceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcC
Q 048704           83 APVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNL  162 (220)
Q Consensus        83 ~p~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl  162 (220)
                      .++......+++++++.|++++++||.||+|||||||||+|||+|+++++..   ++++++|||||++|+++|++||+||
T Consensus        75 ~~~~~~~~~~~~~~~~~ik~l~~~ad~ii~atD~DrEGE~I~~~i~~~~~~~---~~~~v~R~~fsslT~~~I~~A~~nl  151 (151)
T cd03362          75 APFKLKVDKGKKKQFKVLKKLAKRADEIVIATDADREGELIGREILEYAKCV---KRKPVKRAWFSSLTPKAIRRAFKNL  151 (151)
T ss_pred             CceEEEECccHHHHHHHHHHHHhCCCeEEEccCCCccccHHHHHHHHHhCCC---CCCcEEEEEEccCCHHHHHHHHhcC
Confidence            3333333456789999999999999999999999999999999999999974   2579999999999999999999986

Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. 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.

>cd01028 TOPRIM_TopoIA TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IA family of DNA topoisomerases (TopoIA)

Probab=100.00  E-value=1.9e-41  Score=269.95  Aligned_cols=142  Identities=39%  Similarity=0.535  Sum_probs=115.7

Q ss_pred             ceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCCC
Q 048704            5 KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAP   84 (220)
Q Consensus         5 ~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~p   84 (220)
                      ++||||||||+|++||++||.+.  .+++        ++++++  +++||||.|||++|++|++|..|....+..++..+
T Consensus         1 ~~LiIaEKPs~a~~ia~~L~~~~--~~~~--------~~~~~~--~~~v~~~~GHl~~l~~~~~~~~~~~~~~~~~~~~~   68 (142)
T cd01028           1 KVLIIAEKPSKAKTIAKILGKGS--KKKG--------FYGEGG--GYVVTASVGHLLELPFPEEYVDWDKDWPLELFPFE   68 (142)
T ss_pred             CEEEEEeCHHHHHHHHHHhCCCc--ccCC--------ceecCC--CEEEEEEccccccCCCcccccccccCCchhhCCCC
Confidence            47999999999999999998742  2221        245565  89999999999999999999766443222223333


Q ss_pred             ceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcC
Q 048704           85 VHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNL  162 (220)
Q Consensus        85 ~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl  162 (220)
                      +......++.++++.|++++++||+||||||||||||+|||+|+++++..    +++++|+|||++|+++|++||+||
T Consensus        69 ~~~~~~~~~~~~~~~ik~l~~~~d~iiiAtD~DrEGE~I~~~i~~~~~~~----~~~v~R~~fsslT~~~I~~A~~nl  142 (142)
T cd01028          69 PKYVVIPDKKKQLKALKKLAKKADEIVLATDPDREGELIAWEILEVLKCD----NKPVKRAWFSEITPKAIREAFKNL  142 (142)
T ss_pred             ceEEeCCcHHHHHHHHHHHHhcCCEEEEcCCCCcchHHHHHHHHHHhCCC----CCCeEEEEEccCCHHHHHHHHhCc
Confidence            33233456789999999999999999999999999999999999999972    579999999999999999999986

This subgroup contains proteins similar to the Type I DNA topoisomerases: E. coli topisomerases I and III, eukaryotic topoisomerase III and, ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA. These enzymes cleave one strand of the DNA duplex, covalently link to the 5' phosphoryl end of the DNA break and allow the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. 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 b

>PTZ00407 DNA topoisomerase IA; Provisional

Probab=100.00  E-value=3e-39  Score=313.43  Aligned_cols=197  Identities=19%  Similarity=0.208  Sum_probs=146.9

Q ss_pred             ceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeee-cceec---CCcceEEEEccccceecccCCCCCCCCccCC--CC
Q 048704            5 KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEF-DGMFL---GSHAYIKVTSVVGHVFRLDFPPAYQDWNASN--PL   78 (220)
Q Consensus         5 ~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~-~~~~~---g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~--p~   78 (220)
                      ..|+|+|+|++.-++...|+.++      -+|-|.| ++.+.   -+.+..+..++.||+|.|++-    .|+.-.  |.
T Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~   79 (805)
T PTZ00407         10 EKLVIVESPNKVIKVEGLLSDPK------VIPDWSFKQSHLRRIGTGAEKAVAMATTGHFMALKEI----TWSPQASSPA   79 (805)
T ss_pred             hheeEEecCCceEEEeecccCCC------cCCCcccccccceeeccchHHHHHHhhcccceeehhe----ecccCCCCCc
Confidence            46999999999999999998742      3445555 23332   123467888999999998643    243211  10


Q ss_pred             -------CCCCC-----Ccee--ccCCCcH--HHHH-HHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCc
Q 048704           79 -------DLFQA-----PVHK--AESNPKV--HICR-HLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRK  141 (220)
Q Consensus        79 -------~l~~~-----p~~~--~~~~~~~--~~~~-~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~  141 (220)
                             +-|+.     .+.+  .....+.  +++. .|++.+++||+||+|||||||||+|+|||+++++..+...+++
T Consensus        80 ~~~~~~~~~~~~~~~~~~f~~~y~~~~~~~~~~~i~~~i~~~ak~ad~IIlATDpDREGE~Ia~hIle~l~~~~~~~~k~  159 (805)
T PTZ00407         80 SVVGAGDEPFPSNGTLAEYTLEWELLPGRRIQETLERYIEEKADNVTEIILATDPDREGELIAVHALQTIKRLYPKLKVP  159 (805)
T ss_pred             ccCCCCCCCCCCCCceEEEEEEEEEcCCCchhHHHHHHHHHHHhcCCEEEECCCCCcchHHHHHHHHHHhchhccccCCc
Confidence                   11110     0011  1122233  5565 6999999999999999999999999999999998542212468


Q ss_pred             EEEEEecCcCHHHHHHHHhcC--CCCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704          142 VHRARFSSVTEKDILKAMGNL--VEPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF  219 (220)
Q Consensus       142 v~R~~~sslt~~~I~~A~~nl--~~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~  219 (220)
                      ++|+|||++|+++|++||+|+  ...+.+|++|++||+++|||||||+||++|...        ...+|+||||||||.|
T Consensus       160 v~Rv~FseITk~aI~~A~~nlkp~~~d~~L~~Aa~ARr~lD~LVG~nlS~~l~~~~--------~~~lSaGRVQTPtL~L  231 (805)
T PTZ00407        160 FSRAYMHSITEDGIRKAMRERHVEACDYDLANAAETRHAMDRIFGFLGSSVVRAAN--------SQMRSIGRVQTPALIL  231 (805)
T ss_pred             ceEEEEccCCHHHHHHHHhCCCCCcccHhHHHHHHHHHHHHHHhhhhhhHHHHhhc--------cCceeecccchHHHHH
Confidence            999999999999999999996  456779999999999999999999999998732        2469999999999975

>cd03361 TOPRIM_TopoIA_RevGyr TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to the ATP-dependent reverse gyrase found in archaea and thermophilic bacteria

Probab=100.00  E-value=1e-37  Score=255.69  Aligned_cols=149  Identities=26%  Similarity=0.312  Sum_probs=117.6

Q ss_pred             ceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCcc----------
Q 048704            5 KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNA----------   74 (220)
Q Consensus         5 ~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~----------   74 (220)
                      .+||||||||+|++||++||.+. .++.+++++|+|.+   ++ +.++|||+.|||++|++|++|.+|..          
T Consensus         1 ~~LiIaEKPs~Ak~Ia~~L~~~~-~~~~~~~~~~e~~~---~~-~~~~Vt~~~GHl~~l~~~~~~~~~~~~~~~~~p~~~   75 (170)
T cd03361           1 TALMIVESPNKARTIANFFGRPS-VRRLGGLVVYEVST---GD-GVLMITASGGHVYDLVTKEGGHGVVEDDGRYVPVYD   75 (170)
T ss_pred             CeEEEEeChHHHHHHHHHhCCCc-ccccCCceeEEEec---CC-eEEEEEeCCCeeecCCCccCccCccccCCcceeeee
Confidence            37999999999999999998642 34446788888743   22 36789999999999999988765322          


Q ss_pred             ----CCC-CCCCC-----CCceecc-CCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEE
Q 048704           75 ----SNP-LDLFQ-----APVHKAE-SNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVH  143 (220)
Q Consensus        75 ----~~p-~~l~~-----~p~~~~~-~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~  143 (220)
                          +.| ..+|+     +|+.... ..+++++++.|+++++++|+||+|||||||||+|+|+|+++++..    +++++
T Consensus        76 ~~~~c~pc~~lF~~~~~~cp~c~~~~~~~~~~~~~~l~~l~~~~~~iiiatD~drEGe~I~~~i~~~~~~~----~~~v~  151 (170)
T cd03361          76 SIKRCRDCGYQFTEDSDKCPRCGSENIDDKLETLEALRELALEVDEVLIATDPDTEGEKIAWDVYLALRPY----NKNIK  151 (170)
T ss_pred             EeeccCCcccccccccccCCcCCCcCCcchHHHHHHHHHHHhhCCEEEEecCCCccHHHHHHHHHHHhccC----CCCeE
Confidence                111 12332     3333222 245688999999999999999999999999999999999999863    46899


Q ss_pred             EEEecCcCHHHHHHHHhcC
Q 048704          144 RARFSSVTEKDILKAMGNL  162 (220)
Q Consensus       144 R~~~sslt~~~I~~A~~nl  162 (220)
                      |+|||++|+++|++||+||
T Consensus       152 R~~fs~it~~~I~~a~~n~  170 (170)
T cd03361         152 RAEFHEVTRRAILEALRNP  170 (170)
T ss_pred             EEEEecCCHHHHHHHHhCc
Confidence            9999999999999999986

Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. 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.

>cd03363 TOPRIM_TopoIA_TopoI TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I

Probab=100.00  E-value=2.2e-37  Score=241.31  Aligned_cols=123  Identities=27%  Similarity=0.355  Sum_probs=105.2

Q ss_pred             ceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCCC
Q 048704            5 KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAP   84 (220)
Q Consensus         5 ~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~p   84 (220)
                      |+||||||||+|++||++||.                        +|+||||.|||++|.+|++|..|.. .|   +..+
T Consensus         1 ~~LiIaEKp~~a~~ia~~Lg~------------------------~~~v~~~~GHl~~l~~p~~~~~~~~-~~---~~~~   52 (123)
T cd03363           1 KKLVIVESPAKAKTIKKYLGK------------------------EYEVLASVGHIRDLPKKGLGVDGED-DG---FEPK   52 (123)
T ss_pred             CEEEEEeCHHHHHHHHHHhCC------------------------CcEEEeccCccccCCCcccCCChhc-cC---cCce
Confidence            369999999999999999974                        5789999999999999999865432 12   1111


Q ss_pred             ceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcC
Q 048704           85 VHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNL  162 (220)
Q Consensus        85 ~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl  162 (220)
                      +  ....++.++++.|+++++++|+||+|||||||||+|+++|+++++.     +.+++|+|||++|+++|++||+||
T Consensus        53 ~--~~~~~~~~~~~~ik~l~~~~~eiiiAtD~drEGe~i~~~i~~~~~~-----~~~v~Rl~~sslt~~~I~~A~~n~  123 (123)
T cd03363          53 Y--VVIPGKKKVVKELKKLAKKADEIYLATDPDREGEAIAWHLAEVLKL-----KKNVKRVVFNEITKEAIKEALKNP  123 (123)
T ss_pred             E--EECccHHHHHHHHHHHHhcCCEEEEcCCCCcchHHHHHHHHHHcCC-----CCCeEEEEEccCCHHHHHHHHhCc
Confidence            1  1234567899999999999999999999999999999999999986     578999999999999999999986

Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. 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.

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]

Probab=100.00  E-value=5.1e-34  Score=277.10  Aligned_cols=199  Identities=23%  Similarity=0.250  Sum_probs=160.5

Q ss_pred             CceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCC-------CC----
Q 048704            4 LKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQ-------DW----   72 (220)
Q Consensus         4 ~~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~-------~w----   72 (220)
                      +..|+|+|+|++|++||+++|.++ .++-++..+|+-.-   |+ .-.+||++.||+++|...+.+-       +|    
T Consensus       617 kt~L~IVESPnKARTIA~FFgrPS-~R~~~~~~vYEv~~---gD-~vL~ItAS~GHv~DLvt~~g~hGvl~~~~~~vPvY  691 (1187)
T COG1110         617 KTALMIVESPNKARTIASFFGRPS-VRRLGGGVVYEVAI---GD-LVLTITASGGHVFDLVTEPGVHGVLVKDGKYVPVY  691 (1187)
T ss_pred             hceEEEEeCChHHHHHHHHhCCcc-eeeeCCeeEEEEec---CC-eEEEEEecCCeeEEeecccccceeeccCCceEehH
Confidence            468999999999999999999753 23337777776521   33 2468999999999997665431       11    


Q ss_pred             ---ccCC-CCCC-----CCCCceecc-CCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcE
Q 048704           73 ---NASN-PLDL-----FQAPVHKAE-SNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKV  142 (220)
Q Consensus        73 ---~~~~-p~~l-----~~~p~~~~~-~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v  142 (220)
                         +.|. -...     ..+|.+... ..++...++.|++++-.+|+|+||||||.|||-|||+|..++...    +..+
T Consensus       692 ~tIKrC~dcg~q~~~~~~~cP~Cgs~~v~d~~~~ve~lRelA~EvDeVlIgTDPDtEGEKIawDv~~~l~Py----~~ni  767 (1187)
T COG1110         692 DTIKRCRDCGEQFVDSEDKCPRCGSRNVEDKTETVEALRELALEVDEILIGTDPDTEGEKIAWDVFNYLRPY----NPNV  767 (1187)
T ss_pred             HHHHHHhhcCceeccccccCCCCCCccccccHHHHHHHHHHHhhcCEEEEcCCCCCccchhHHHHHHhhCcC----CCce
Confidence               0110 0000     124544432 356788999999999999999999999999999999999999975    6789


Q ss_pred             EEEEecCcCHHHHHHHHhcCCCCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceecc
Q 048704          143 HRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLIC  218 (220)
Q Consensus       143 ~R~~~sslt~~~I~~A~~nl~~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~  218 (220)
                      +|+.|+++|+.+|.+|++|+++.|+||+.|+..|++.|+.|||.||+.++..+.       +..+|+||||||+|-
T Consensus       768 kR~eFHEVTrrAIleAl~n~r~vd~nlVkAQiVRRIeDRWIGF~LS~~Lw~~F~-------~~nLsAGRVQTPVLG  836 (1187)
T COG1110         768 KRIEFHEVTRRAILEALKNPRDVDENLVKAQIVRRIEDRWIGFELSQKLWDVFN-------NKNLSAGRVQTPVLG  836 (1187)
T ss_pred             eEEEeeeecHHHHHHHHhCccccchhhhHHHhhhhhhhcccceeecHHHHHHhC-------ccCccccccccccce
Confidence            999999999999999999999999999999999999999999999999998763       456999999999984

>smart00436 TOP1Bc Bacterial DNA topoisomeraes I ATP-binding domain

Probab=99.94  E-value=1.5e-27  Score=175.80  Aligned_cols=71  Identities=25%  Similarity=0.257  Sum_probs=66.3

Q ss_pred             EEEEEecCcCHHHHHHHHhcCCCCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704          142 VHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF  219 (220)
Q Consensus       142 v~R~~~sslt~~~I~~A~~nl~~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~  219 (220)
                      ++|+|||++|+++|++||+|++|.+.+|++||+||+++||++|||+||++|+.+++       .++|+||||||||.+
T Consensus         1 v~R~~fs~lt~~~I~~a~~~l~~~~~~l~~a~~aR~~~D~l~G~n~Sr~~t~~~~~-------~~ls~GRVQtptL~l   71 (89)
T smart00436        1 IKRIEFSEITKKAIREALKNPREIDENLVNAQLARRILDRLIGFNLSRLLTKKLRK-------GVLSAGRVQTPTLGL   71 (89)
T ss_pred             CEEEEEecCCHHHHHHHHHCcccccHHHHHHHHHHHHHHHHHhHhhhHHHHHHhCC-------CCcceecchHHHHHH
Confidence            57999999999999999999999888999999999999999999999999998752       379999999999975

Extension of TOPRIM in Bacterial DNA topoisomeraes I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase beta subunit

>PF01751 Toprim: Toprim domain; InterPro: IPR006171 This is a conserved region from DNA primase

Probab=99.94  E-value=6.1e-27  Score=175.69  Aligned_cols=99  Identities=34%  Similarity=0.499  Sum_probs=85.6

Q ss_pred             eEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCCCc
Q 048704            6 VLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAPV   85 (220)
Q Consensus         6 ~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~p~   85 (220)
                      +|||+|||++|++|+++|++                     .  ++.|+|+.||++++..|+.|..              
T Consensus         1 ~liIvE~ps~a~~i~~~l~~---------------------~--~~~v~~~~Ghl~~~~~~~~~~~--------------   43 (100)
T PF01751_consen    1 ELIIVEKPSDAKAIAKALGG---------------------E--EYIVIATSGHLLELAKPEDYDP--------------   43 (100)
T ss_dssp             EEEEESSHHHHHHHHHHSST---------------------T--TEEEEEESSSSEESTTSSHHHC--------------
T ss_pred             CEEEEeCHHHHHHHHHHcCC---------------------C--CEEEEEeCCccccccccccccc--------------
Confidence            58999999999999999973                     1  5899999999999999988632              


Q ss_pred             eeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCc-EEEEEecCc
Q 048704           86 HKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRK-VHRARFSSV  150 (220)
Q Consensus        86 ~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~-v~R~~~ssl  150 (220)
                           ..+.+.++.|+++++++|+||+|||||||||.|+++|+++++...    .. ++|+|||++
T Consensus        44 -----~~~~~~i~~l~~~~~~~~~iiiatD~D~EGe~Ia~~i~~~~~~~~----~~~~~R~~~~~i  100 (100)
T PF01751_consen   44 -----KDKKKQIKNLKKLLKKADEIIIATDPDREGELIAWEIIELLGKNN----PKLIKRVWFSSI  100 (100)
T ss_dssp             -----HTTHHHHHHHHHHHHSCSEEEEEC-SSHHHHHHHHHHHHHHHHHS----HHHTTEEEEESS
T ss_pred             -----ccccccchhhHHHhhhccEeeecCCCChHHHHHHHHHHHHHhHhC----CCcCCEEEEecC
Confidence                 245788999999999999999999999999999999999999852    22 699999985

This corresponds to the Toprim (topoisomerase-primase) domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR/M DNA repair proteins []. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase 2.7.7.6 from EC is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division []. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases []. Type II DNA topoisomerases catalyse the relaxation of DNA supercoiling by causing transient double strand breaks.; PDB: 2ZJT_A 3IG0_A 3M4I_A 3NUH_B 1GKU_B 1GL9_C 3PWT_A 1CY4_A 1ECL_A 1CY7_A ....

>smart00493 TOPRIM topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins

Probab=98.95  E-value=7.2e-09  Score=73.03  Aligned_cols=73  Identities=29%  Similarity=0.376  Sum_probs=57.0

Q ss_pred             ceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCCC
Q 048704            5 KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAP   84 (220)
Q Consensus         5 ~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~p   84 (220)
                      +.|+|+|.|.-|..+.++++.                        +..+.++.||+..                      
T Consensus         1 ~~l~ivEg~~da~~~~~~~~~------------------------~~~~~~~~G~~~~----------------------   34 (76)
T smart00493        1 KVLIIVEGPADAIALEKAGGF------------------------GGNVVALGGHLLK----------------------   34 (76)
T ss_pred             CEEEEEcCHHHHHHHHHhcCC------------------------CEEEEEEeeeecH----------------------
Confidence            469999999999999998642                        3567777899721                      


Q ss_pred             ceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCC
Q 048704           85 VHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGF  133 (220)
Q Consensus        85 ~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~  133 (220)
                               .+.++.|++.... ++||+|+|+|+||+.+++++.+++..
T Consensus        35 ---------~~~~~~l~~~~~~-~~Iii~~D~D~~G~~~~~~i~~~l~~   73 (76)
T smart00493       35 ---------KEIIKLLKRLAKK-KEVILATDPDREGEAIAWKLAELLKP   73 (76)
T ss_pred             ---------HHHHHHHHHHhcC-CEEEEEcCCChhHHHHHHHHHHHhhh
Confidence                     2244455555544 78999999999999999999999875

>cd01025 TOPRIM_recR TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in Escherichia coli RecR

Probab=98.49  E-value=1.1e-06  Score=67.31  Aligned_cols=91  Identities=23%  Similarity=0.185  Sum_probs=61.7

Q ss_pred             ceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCCC
Q 048704            5 KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAP   84 (220)
Q Consensus         5 ~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~p   84 (220)
                      +.|||+|.|....+|.+.   +                .|+|   .|.|.  .||+--++.         ..|.   +  
T Consensus         1 ~~lcVVE~~~Dv~~iE~~---~----------------~y~G---~Y~VL--~G~ispl~g---------i~p~---~--   42 (112)
T cd01025           1 NKLCVVEEPRDVLAIEES---G----------------EYRG---LYHVL--GGLISPLDG---------IGPD---D--   42 (112)
T ss_pred             CEEEEECCHHHHHHHHhh---C----------------ccce---EEEEe--CCCcCCCCC---------CCcc---c--
Confidence            369999999999999885   2                1222   45555  677644321         1111   1  


Q ss_pred             ceeccCCCcHHHHHHHHHHhc--cCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEe
Q 048704           85 VHKAESNPKVHICRHLNQEAR--GCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARF  147 (220)
Q Consensus        85 ~~~~~~~~~~~~~~~lk~~~~--~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~  147 (220)
                                -.++.|.+.++  +.++||+||||++|||.+++.|.+.++..    ..++.|+-+
T Consensus        43 ----------l~i~~L~~ri~~~~i~EVIlA~~pt~EGe~Ta~yi~~~l~~~----~~kvsRlA~   93 (112)
T cd01025          43 ----------LNIDKLLERIAKGQVKEVILATNPTVEGEATALYIAKLLKDF----GVKVTRLAQ   93 (112)
T ss_pred             ----------cCHHHHHHHHhcCCCcEEEEecCCCchHHHHHHHHHHHHhHc----CCCeEEEEE
Confidence                      11233444443  46899999999999999999999999974    567888754

RecR participates in the RecFOR pathway of homologous recombinational repair in prokaryotes. This pathway provides a single-stranded DNA molecule coated with RecA to allow invasion of a homologous molecule. The RecFOR system directs the loading of RecA onto gapped DNA coated with SSB protein. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). In RecR sequences this glutamate in the first turn of the TOPRIM domain is semiconserved, the DXD motif is not conserved.

>cd00188 TOPRIM Topoisomerase-primase domain

Probab=98.06  E-value=7.7e-05  Score=51.40  Aligned_cols=81  Identities=27%  Similarity=0.293  Sum_probs=56.7

Q ss_pred             eEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCCCc
Q 048704            6 VLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAPV   85 (220)
Q Consensus         6 ~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~p~   85 (220)
                      .+||+|.++-+..+.+....                        +..++++.||...         |             
T Consensus         2 ~viivEg~~d~~~l~~~~~~------------------------~~~~~~~~G~~~~---------~-------------   35 (83)
T cd00188           2 KLIIVEGPSDALALAQAGGY------------------------GGAVVALGGHALN---------K-------------   35 (83)
T ss_pred             EEEEEecHHHHHHHHHHcCC------------------------CEEEEEEccEEcH---------H-------------
Confidence            68999999999999988532                        2456677777653         0             


Q ss_pred             eeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEE
Q 048704           86 HKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRAR  146 (220)
Q Consensus        86 ~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~  146 (220)
                                ....+....+....|++++|+|.+|+.+.+.+.+.....    ...+.|++
T Consensus        36 ----------~~~~~~~~~~~~~~v~i~~D~D~~g~~~~~~~~~~~~~~----~~~~~~~~   82 (83)
T cd00188          36 ----------TRELLKRLLGEAKEVIIATDADREGEAIALRLLELLKSL----GKKVRRLL   82 (83)
T ss_pred             ----------HHHHHHHHhcCCCEEEEEcCCChhHHHHHHHHHHHHHhc----CCceEEee
Confidence                      011222333336899999999999999999999988752    34555554

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.

>PRK00076 recR recombination protein RecR; Reviewed

Probab=97.88  E-value=0.00025  Score=59.44  Aligned_cols=109  Identities=22%  Similarity=0.225  Sum_probs=72.9

Q ss_pred             ceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCCC
Q 048704            5 KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAP   84 (220)
Q Consensus         5 ~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~p   84 (220)
                      .+|||+|.|.-..+|.+.   +                .|+|   .|-|..  |||--++.         ..|.   ++.
T Consensus        79 ~~icVVE~~~Dv~aiE~s---~----------------~y~G---~YhVL~--G~ispl~g---------i~p~---~l~  122 (196)
T PRK00076         79 SLICVVESPADVLAIERT---G----------------EYRG---LYHVLG--GLLSPLDG---------IGPE---DLN  122 (196)
T ss_pred             CEEEEECCHHHHHHHHhh---C----------------cCce---EEEEec--CCcCCCCC---------CCcc---ccC
Confidence            579999999999999885   2                1222   455543  66643321         1121   111


Q ss_pred             ceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEe--------cCcCHHHHH
Q 048704           85 VHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARF--------SSVTEKDIL  156 (220)
Q Consensus        85 ~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~--------sslt~~~I~  156 (220)
                              -.+.++.+ +  .++++||+||+|+.|||..+..|.+.++..    ..+|.|+-.        .-+++..+.
T Consensus       123 --------i~~L~~ri-~--~~v~EVIlA~~pt~EGe~Ta~yi~~~lk~~----~ikvtRiA~GiP~G~~ley~D~~TL~  187 (196)
T PRK00076        123 --------IDELLERL-D--GEVKEVILATNPTVEGEATAHYIARLLKPL----GVKVTRLAHGVPVGGELEYVDEGTLS  187 (196)
T ss_pred             --------HHHHHHHH-h--CCCCEEEEeCCCCchHHHHHHHHHHHHHHc----CCCeeeeeeCCCCCcceeeCCHHHHH
Confidence                    13344444 1  568999999999999999999999999863    467888643        345677788


Q ss_pred             HHHhcCCC
Q 048704          157 KAMGNLVE  164 (220)
Q Consensus       157 ~A~~nl~~  164 (220)
                      +||++.+.
T Consensus       188 ~Al~~R~~  195 (196)
T PRK00076        188 RALEGRRE  195 (196)
T ss_pred             HHHHhCcC
Confidence            88877653

>cd01027 TOPRIM_RNase_M5_like TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in Ribonuclease M5: (RNase M5) and other small primase-like proteins from bacteria and archaea

Probab=97.44  E-value=0.00043  Score=50.03  Aligned_cols=44  Identities=20%  Similarity=0.231  Sum_probs=33.3

Q ss_pred             HHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEE
Q 048704           96 ICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRAR  146 (220)
Q Consensus        96 ~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~  146 (220)
                      .++.|++.   .+.||++||+|+.|+.|.+.+.++++..    ...++|+.
T Consensus        37 ~~~~l~~~---~~~VIiltD~D~aG~~i~~~~~~~l~~~----~~~~~~~~   80 (81)
T cd01027          37 TIELIKKA---YRGVIILTDPDRKGEKIRKKLSEYLSGP----VPEIKRAF   80 (81)
T ss_pred             HHHHHHHh---CCEEEEEECCCHHHHHHHHHHHHHhccc----CCCeeecc
Confidence            34444443   6899999999999999999999999762    34466653

RNase M5 catalyzes the maturation of 5S rRNA in low G+C Gram-positive bacteria. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.

>PRK13844 recombination protein RecR; Provisional

Probab=97.01  E-value=0.014  Score=49.05  Aligned_cols=54  Identities=15%  Similarity=0.202  Sum_probs=43.5

Q ss_pred             cCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEE--------ecCcCHHHHHHHHhcCCC
Q 048704          106 GCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRAR--------FSSVTEKDILKAMGNLVE  164 (220)
Q Consensus       106 ~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~--------~sslt~~~I~~A~~nl~~  164 (220)
                      ++++||+||.|+-|||.-+..|.+.++.     ..+|.|+=        +.=+++..+.+||++.+.
T Consensus       138 ~v~EVIlAt~~t~EGe~Ta~yi~~~lk~-----~vkvtRlA~GiP~G~~ley~D~~TL~~Al~~R~~  199 (200)
T PRK13844        138 KIDEVILAISPTVEGETTAHFISQMIAK-----DIKISRIGFGVPFGGELEYLDQQTLLHAFNARTN  199 (200)
T ss_pred             CCcEEEEeCCCCccHHHHHHHHHHHhcC-----CCcEEeeeecCcCCcceeecCHHHHHHHHHhCcC
Confidence            6899999999999999999999999985     35677763        234567788888887654

>TIGR00615 recR recombination protein RecR

Probab=96.94  E-value=0.016  Score=48.65  Aligned_cols=53  Identities=17%  Similarity=0.109  Sum_probs=41.8

Q ss_pred             cCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEe--------cCcCHHHHHHHHhcC
Q 048704          106 GCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARF--------SSVTEKDILKAMGNL  162 (220)
Q Consensus       106 ~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~--------sslt~~~I~~A~~nl  162 (220)
                      ++.+||+||+|+-|||.-+..|.+.++..    ..++.|+=.        .-.++..+.+||++.
T Consensus       134 ~v~EVIlAt~~tvEGe~Ta~yi~~~lk~~----~ikvtRlA~GiP~G~~ley~D~~TL~~Al~~R  194 (195)
T TIGR00615       134 SVKEVILATNPTVEGEATALYIARLLQPF----GVKVTRIASGLPVGGDLEYADEVTLARALEGR  194 (195)
T ss_pred             CCcEEEEeCCCCchHHHHHHHHHHHhhhc----CCcEEeeeecCCCCcceeecCHHHHHHHHHcC
Confidence            58999999999999999999999999853    467877642        334577777777654

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]

Probab=96.67  E-value=0.04  Score=46.14  Aligned_cols=108  Identities=23%  Similarity=0.192  Sum_probs=69.0

Q ss_pred             ceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCCC
Q 048704            5 KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAP   84 (220)
Q Consensus         5 ~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~p   84 (220)
                      .+|+|+|-|.-..++.+.   +.            |+|       .|-|.  .|||--|+.         ..|.      
T Consensus        80 ~~icVVe~p~Dv~a~E~~---~~------------f~G-------~YhVL--~G~lspl~g---------igpe------  120 (198)
T COG0353          80 SQLCVVEEPKDVLALEKT---GE------------FRG-------LYHVL--GGLLSPLDG---------IGPE------  120 (198)
T ss_pred             ceEEEEcchHHHHHHHHh---cc------------cCe-------eEEEe--cCccCcccC---------CCcc------
Confidence            579999999999999886   21            122       35553  456532211         1111      


Q ss_pred             ceeccCCCcHHHHHHHHHHhccC--CeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEe--------cCcCHHH
Q 048704           85 VHKAESNPKVHICRHLNQEARGC--GHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARF--------SSVTEKD  154 (220)
Q Consensus        85 ~~~~~~~~~~~~~~~lk~~~~~a--d~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~--------sslt~~~  154 (220)
                               .--++.|.+.+.+-  ++||+||+|--|||.-+..|.+.++..    ..+|.|+=.        -=+++-.
T Consensus       121 ---------~l~i~~L~~Rl~~~~~~EvIlAtnpTvEGeaTA~YI~~~l~~~----~ikvtRlA~GiPvGg~lEyvD~~T  187 (198)
T COG0353         121 ---------DLNIDELLQRLAEGSIKEVILATNPTVEGEATALYIARLLKPL----GLKVTRLAQGVPVGGELEYVDEGT  187 (198)
T ss_pred             ---------cccHHHHHHHHhcCCCceEEEecCCCccchHHHHHHHHHHhhc----CCeEEEEeecCccCCceecccHHH
Confidence                     01123343434333  399999999999999999999999975    467888642        2245666


Q ss_pred             HHHHHhcCCC
Q 048704          155 ILKAMGNLVE  164 (220)
Q Consensus       155 I~~A~~nl~~  164 (220)
                      +.+||.+.++
T Consensus       188 L~~Al~~R~~  197 (198)
T COG0353         188 LSRALEGRRK  197 (198)
T ss_pred             HHHHHhcCcC
Confidence            7777766553

>PF13662 Toprim_4: Toprim domain; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A

Probab=95.66  E-value=0.017  Score=41.13  Aligned_cols=35  Identities=17%  Similarity=0.210  Sum_probs=23.7

Q ss_pred             CCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEE
Q 048704          107 CGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRA  145 (220)
Q Consensus       107 ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~  145 (220)
                      ..+||+|+|+|.+|+..+.++.+.+...    ..+++|+
T Consensus        46 ~~~Vii~~D~D~~G~~~a~~i~~~l~~~----gi~v~~v   80 (81)
T PF13662_consen   46 VKEVIIAFDNDKAGEKAAQKIAKKLLPL----GIRVTRV   80 (81)
T ss_dssp             -SEEEEEEESSHHHHHHHHHHHHHHG-------------
T ss_pred             CceEEEEeCcCHHHHHHHHHHHHHHHhh----ccccccC
Confidence            5789999999999999999999987642    3456654

>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]

Probab=95.13  E-value=0.056  Score=42.38  Aligned_cols=67  Identities=15%  Similarity=0.129  Sum_probs=45.0

Q ss_pred             HHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCC-cccCCC----Cc---EEE-EEecCcCHHHHHHHHhcCC
Q 048704           96 ICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGF-QVNDAR----RK---VHR-ARFSSVTEKDILKAMGNLV  163 (220)
Q Consensus        96 ~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~-~~~~~~----~~---v~R-~~~sslt~~~I~~A~~nl~  163 (220)
                      .++.|++.. +-..||+-||||+.||-|...+.+++.. .+....    .+   ..| .-+-++....+++|+++..
T Consensus        45 ~ie~i~~~~-~~k~VIILTD~D~~Ge~Irk~l~~~l~~~~~~~id~~~~~~~~~~~~i~gVE~~~~~~~~~~l~~~~  120 (127)
T COG1658          45 TIELIKKAQ-KYKGVIILTDPDRKGERIRKKLKEYLPGAKGAFIDREIRNKLKINGKIIGVEEASSEALRKALKEVP  120 (127)
T ss_pred             HHHHHHHhh-ccCCEEEEeCCCcchHHHHHHHHHHhcccccccccHHHhhhcccccccccceecChHHHHHHHHhCC
Confidence            344454432 3457999999999999999999999987 211100    01   222 2344777888899988877

>PRK04031 DNA primase; Provisional

Probab=94.97  E-value=0.042  Score=50.78  Aligned_cols=67  Identities=25%  Similarity=0.311  Sum_probs=47.6

Q ss_pred             HHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcCCCCCcc
Q 048704           99 HLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRN  168 (220)
Q Consensus        99 ~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl~~~~~~  168 (220)
                      .++++++ .+.||+++|+|+-|+.|.+++++.++... -.+.| .-.-.-++++++|.+||.+..|..+-
T Consensus       203 ~i~~l~k-~~~Vil~~DgD~aGe~I~k~l~~v~~~d~-VaraP-~G~dVE~ls~eeI~kAL~~~~p~~~~  269 (408)
T PRK04031        203 TIIELSK-KKTVTAFLDGDRGGELILKELLQVADIDY-VARAP-PGKEVEELTKKEIAKALRNKVPVEQY  269 (408)
T ss_pred             HHHHHhc-CCCEEEEECCCHHHHHHHHHHHhhcceeE-EecCC-CCCChhhCCHHHHHHHHHhcCCHHHH
Confidence            4556655 78999999999999999999998543110 00111 11235578899999999999987653

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

Probab=94.89  E-value=0.26  Score=39.68  Aligned_cols=74  Identities=22%  Similarity=0.222  Sum_probs=50.8

Q ss_pred             ceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCCC
Q 048704            5 KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQAP   84 (220)
Q Consensus         5 ~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~p   84 (220)
                      ..++|+|.|++-..+++.++..                       ..-++++.|+.-.                      
T Consensus        19 ~~V~VvENp~Vf~~~~~~~~~~-----------------------~~pLVCt~G~p~~----------------------   53 (152)
T PF09664_consen   19 GRVYVVENPAVFSALADELGAS-----------------------CPPLVCTSGQPSA----------------------   53 (152)
T ss_pred             CEEEEEecHHHHHHHHHhcCCC-----------------------CCeEEEcCCcHHH----------------------
Confidence            4599999999999999998652                       2233444555311                      


Q ss_pred             ceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCC
Q 048704           85 VHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGF  133 (220)
Q Consensus        85 ~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~  133 (220)
                             .....++.|   ...--.+..++|.|.||=.|+..+.+..+.
T Consensus        54 -------A~~~LL~~L---~~~g~~l~y~GDfDp~Gl~IA~~l~~r~~~   92 (152)
T PF09664_consen   54 -------AARRLLDRL---AAAGARLYYSGDFDPEGLRIANRLIQRYGA   92 (152)
T ss_pred             -------HHHHHHHHH---HhCCCEEEEecCCCHHHHHHHHHHHHHhCC
Confidence                   012223333   232337999999999999999999998875

Its function is unknown.

>TIGR00334 5S_RNA_mat_M5 ribonuclease M5

Probab=94.38  E-value=0.19  Score=41.42  Aligned_cols=71  Identities=13%  Similarity=0.100  Sum_probs=48.3

Q ss_pred             HHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcc-----cCCCCc-EEEEEecCcCHHHHHHHHhcCCCC
Q 048704           94 VHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQV-----NDARRK-VHRARFSSVTEKDILKAMGNLVEP  165 (220)
Q Consensus        94 ~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~-----~~~~~~-v~R~~~sslt~~~I~~A~~nl~~~  165 (220)
                      .+.++.|+.+. +-.-||+-||||.-||-|=..|.+++....     +....+ -.-+=+-..++++|++|++++...
T Consensus        35 ~~~i~~i~~~~-~~rgVIIfTDpD~~GekIRk~i~~~vp~~khafi~~~~a~~~~~~iGVE~As~e~I~~AL~~~~~~  111 (174)
T TIGR00334        35 DETINLIKKAQ-KKQGVIILTDPDFPGEKIRKKIEQHLPGYENCFIPKHLAKPNKKKIGVEEASVEAIIAALENVHEE  111 (174)
T ss_pred             HHHHHHHHHHh-hcCCEEEEeCCCCchHHHHHHHHHHCCCCeEEeeeHHhcCcCCCCcccCCCCHHHHHHHHHHhccc
Confidence            45566666654 345699999999999999999999876321     000000 001345567899999999999753

This family of orthologous proteins shows a weak but significant similarity to the central region of the DnaG-type DNA primase. The region of similarity is termed the Toprim (topoisomerase-primase) domain and is also shared by RecR, OLD family nucleases, and type IA and II topoisomerases.

>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]

Probab=92.91  E-value=0.19  Score=43.07  Aligned_cols=44  Identities=18%  Similarity=0.271  Sum_probs=37.3

Q ss_pred             HHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEec
Q 048704          101 NQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFS  148 (220)
Q Consensus       101 k~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~s  148 (220)
                      +..+..||-|+||||+||-|--++....+.+...    -..+.||.+.
T Consensus        52 ~raaeGADlvlIATDaD~~GReLA~kf~eeLrg~----VGhiERmK~P   95 (290)
T COG4026          52 KRAAEGADLVLIATDADRVGRELAEKFFEELRGM----VGHIERMKIP   95 (290)
T ss_pred             HHhhccCCEEEEeecCcchhHHHHHHHHHHHHHh----hhhhheeccC
Confidence            4556799999999999999999999998888764    5688888874

>PRK04017 hypothetical protein; Provisional

Probab=89.96  E-value=0.38  Score=37.94  Aligned_cols=31  Identities=23%  Similarity=0.269  Sum_probs=26.8

Q ss_pred             hccCCeEEEecCCChhHhHHHHHHHHHhCCc
Q 048704          104 ARGCGHLVLWLDCDREGENICFEVIECTGFQ  134 (220)
Q Consensus       104 ~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~  134 (220)
                      +.+...||+.||+|.-||-|...+.+.+...
T Consensus        62 a~~~r~VIILTD~D~~GekIr~~l~~~l~~~   92 (132)
T PRK04017         62 ASRGKEVIILTDFDRKGEELAKKLSEYLQGY   92 (132)
T ss_pred             HhcCCeEEEEECCCcchHHHHHHHHHHHHhC
Confidence            3467789999999999999999999988763

>cd03364 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG

Probab=82.67  E-value=3.1  Score=29.12  Aligned_cols=27  Identities=19%  Similarity=0.274  Sum_probs=23.7

Q ss_pred             CCeEEEecCCChhHhHHHHHHHHHhCC
Q 048704          107 CGHLVLWLDCDREGENICFEVIECTGF  133 (220)
Q Consensus       107 ad~ii~AtD~DrEGE~I~~~Il~~~~~  133 (220)
                      ..+||+++|.|..|+.-...+.+.+..
T Consensus        43 ~~~vii~~D~D~aG~~a~~~~~~~l~~   69 (79)
T cd03364          43 AKEVILAFDGDEAGQKAALRALELLLK   69 (79)
T ss_pred             CCeEEEEECCCHHHHHHHHHHHHHHHH
Confidence            478999999999999988888887765

Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM 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. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. E. coli DnaG is a single subunit enzyme.

>cd01029 TOPRIM_primases TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs

Probab=81.38  E-value=3.5  Score=28.48  Aligned_cols=27  Identities=19%  Similarity=0.223  Sum_probs=23.1

Q ss_pred             CCeEEEecCCChhHhHHHHHHHHHhCC
Q 048704          107 CGHLVLWLDCDREGENICFEVIECTGF  133 (220)
Q Consensus       107 ad~ii~AtD~DrEGE~I~~~Il~~~~~  133 (220)
                      ...||++.|.|..|+.....+.+.+..
T Consensus        43 ~~~vii~~D~D~~G~~~~~~~~~~~~~   69 (79)
T cd01029          43 ARTVILAFDNDEAGKKAAARALELLLA   69 (79)
T ss_pred             CCEEEEEECCCHHHHHHHHHHHHHHHH
Confidence            478999999999999888888777764

Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM 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. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. The prototypical bacterial primase. Escherichia coli DnaG is a single subunit enzyme.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	220
1i7d_A	659	Noncovalent Complex Of E.Coli Dna Topoisomerase Iii		1e-04
2o19_A	659	Structure Of E. Coli Topoisomersae Iii In Complex W		1e-04
1d6m_A	653	Crystal Structure Of E. Coli Dna Topoisomerase Iii		1e-04
1ecl_A	597	Amino Terminal 67kda Domain Of Escherichia Coli Dna		5e-04
1cy1_A	599	Complex Of E.Coli Dna Topoisomerase I With 5'ptptpt		5e-04
1mw8_X	592	Crystal Structure Of A Complex Between H365r Mutant		6e-04

>pdb|1I7D|A Chain A, Noncovalent Complex Of E.Coli Dna Topoisomerase Iii With An 8-Base Single-Stranded Dna Oligonucleotide Length = 659

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 54/195 (27%), Positives = 82/195 (42%), Gaps = 25/195 (12%)
Query: 7   LMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFP 66
           L +AEKPS+A +IA VL       RK        DG     +  + VT  +GH+     P
Sbjct: 3   LFIAEKPSLARAIADVLPKPH---RKG-------DGFIECGNGQV-VTWCIGHLLEQAQP 51
Query: 67  PAYQD----WNASNPLDLFQAPVHKAESNPKVHICRHLNQEAR---GCGHLVLWLDCDRE 119
            AY      WN +   DL   P  K +  P+  + + LN   R       +V   D DRE
Sbjct: 52  DAYDSRYARWNLA---DLPIVP-EKWQLQPRPSVTKQLNVIKRFLHEASEIVHAGDPDRE 107
Query: 120 GENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVD--ARQ 177
           G+ +  EV++       + R++V R   + +  + + +A+  L   +    L V   AR 
Sbjct: 108 GQLLVDEVLDYLQL-APEKRQQVQRCLINDLNPQAVERAIDRLRSNSEFVPLCVSALARA 166
Query: 178 EIDLKVGVAFTRFQT 192
             D   G+  TR  T
Sbjct: 167 RADWLYGINMTRAYT 181

>pdb|2O19|A Chain A, Structure Of E. Coli Topoisomersae Iii In Complex With An 8- Base Single Stranded Oligonucleotide. Frozen In Glycerol At Ph 5.5 Length = 659

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 54/195 (27%), Positives = 82/195 (42%), Gaps = 25/195 (12%)
Query: 7   LMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFP 66
           L +AEKPS+A +IA VL       RK        DG     +  + VT  +GH+     P
Sbjct: 3   LFIAEKPSLARAIADVLPKPH---RKG-------DGFIECGNGQV-VTWCIGHLLEQAQP 51
Query: 67  PAYQD----WNASNPLDLFQAPVHKAESNPKVHICRHLNQEAR---GCGHLVLWLDCDRE 119
            AY      WN +   DL   P  K +  P+  + + LN   R       +V   D DRE
Sbjct: 52  DAYDSRYARWNLA---DLPIVP-EKWQLQPRPSVTKQLNVIKRFLHEASEIVHAGDPDRE 107
Query: 120 GENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVD--ARQ 177
           G+ +  EV++       + R++V R   + +  + + +A+  L   +    L V   AR 
Sbjct: 108 GQLLVDEVLDYLQL-APEKRQQVQRCLINDLNPQAVERAIDRLRSNSEFVPLCVSALARA 166
Query: 178 EIDLKVGVAFTRFQT 192
             D   G+  TR  T
Sbjct: 167 RADWLYGINMTRAYT 181

>pdb|1D6M|A Chain A, Crystal Structure Of E. Coli Dna Topoisomerase Iii Length = 653

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 54/195 (27%), Positives = 82/195 (42%), Gaps = 25/195 (12%)
Query: 7   LMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFP 66
           L +AEKPS+A +IA VL       RK        DG     +  + VT  +GH+     P
Sbjct: 3   LFIAEKPSLARAIADVLPKPH---RKG-------DGFIECGNGQV-VTWCIGHLLEQAQP 51
Query: 67  PAYQD----WNASNPLDLFQAPVHKAESNPKVHICRHLNQEAR---GCGHLVLWLDCDRE 119
            AY      WN +   DL   P  K +  P+  + + LN   R       +V   D DRE
Sbjct: 52  DAYDSRYARWNLA---DLPIVP-EKWQLQPRPSVTKQLNVIKRFLHEASEIVHAGDPDRE 107
Query: 120 GENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVD--ARQ 177
           G+ +  EV++       + R++V R   + +  + + +A+  L   +    L V   AR 
Sbjct: 108 GQLLVDEVLDYLQL-APEKRQQVQRCLINDLNPQAVERAIDRLRSNSEFVPLCVSALARA 166
Query: 178 EIDLKVGVAFTRFQT 192
             D   G+  TR  T
Sbjct: 167 RADWLYGINMTRAYT 181

>pdb|1ECL|A Chain A, Amino Terminal 67kda Domain Of Escherichia Coli Dna Topoisomerase I (Residues 2-590 Of Mature Protein) Cloning Artifact Adds Two Residues To The Amino-Terminus Which Were Not Observed In The Experimental Electron Density (Gly-2, Ser-1) Length = 597

Iteration: 1
 Score = 41.2 bits (95), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 31/92 (33%), Positives = 43/92 (46%), Gaps = 4/92 (4%)
Query: 93  KVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTE 152
           K  +   L Q A    H+ L  D DREGE I + + E  G   +DAR    R  F+ +T+
Sbjct: 89  KEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGG--DDAR--YSRVVFNEITK 144
Query: 153 KDILKAMGNLVEPNRNEALAVDARQEIDLKVG 184
             I +A     E N +   A  AR+ +D  VG
Sbjct: 145 NAIRQAFNKPGELNIDRVNAQQARRFMDRVVG 176

>pdb|1CY1|A Chain A, Complex Of E.Coli Dna Topoisomerase I With 5'ptptpt Length = 599

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 31/92 (33%), Positives = 43/92 (46%), Gaps = 4/92 (4%)
Query: 93  KVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTE 152
           K  +   L Q A    H+ L  D DREGE I + + E  G   +DAR    R  F+ +T+
Sbjct: 91  KEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGG--DDAR--YSRVVFNEITK 146
Query: 153 KDILKAMGNLVEPNRNEALAVDARQEIDLKVG 184
             I +A     E N +   A  AR+ +D  VG
Sbjct: 147 NAIRQAFNKPGELNIDRVNAQQARRFMDRVVG 178

>pdb|1MW8|X Chain X, Crystal Structure Of A Complex Between H365r Mutant Of 67 Kda N-Terminal Fragment Of E. Coli Dna Topoisomerase I And 5'-Acttcgggatg-3' Length = 592

Iteration: 1
 Score = 40.8 bits (94), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 31/92 (33%), Positives = 43/92 (46%), Gaps = 4/92 (4%)
Query: 93  KVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTE 152
           K  +   L Q A    H+ L  D DREGE I + + E  G   +DAR    R  F+ +T+
Sbjct: 89  KEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGG--DDAR--YSRVVFNEITK 144
Query: 153 KDILKAMGNLVEPNRNEALAVDARQEIDLKVG 184
             I +A     E N +   A  AR+ +D  VG
Sbjct: 145 NAIRQAFNKPGELNIDRVNAQQARRFMDRVVG 176

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	220
1i7d_A	659	DNA topoisomerase III; decatenating enzyme, protei	2e-15
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	3e-06
1qzv_F	154	Plant photosystem I: subunit PSAF; photosynthesis,	7e-04

>1i7d_A DNA topoisomerase III; decatenating enzyme, protein-DNA complex, single-stranded DNA, isomerase/DNA complex; HET: DNA; 2.05A {Escherichia coli} SCOP: e.10.1.1 PDB: 2o5c_A* 2o54_A* 2o59_A* 2o19_A* 2o5e_A* 1d6m_A* Length = 659

 Score = 73.8 bits (182), Expect = 2e-15
 Identities = 55/213 (25%), Positives = 85/213 (39%), Gaps = 36/213 (16%)

Query: 7   LMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFP 66
           L +AEKPS+A +IA VL       RK        DG     +  + VT  +GH+     P
Sbjct: 3   LFIAEKPSLARAIADVL-PKP--HRKG-------DGFIECGNGQV-VTWCIGHLLEQAQP 51

Query: 67  ----PAYQDWNASN-PL--DLFQ-APVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDR 118
                 Y  WN ++ P+  + +Q  P         V I R L++       +V   D DR
Sbjct: 52  DAYDSRYARWNLADLPIVPEKWQLQPRPSVTKQLNV-IKRFLHE----ASEIVHAGDPDR 106

Query: 119 EGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNR------NEALA 172
           EG+ +  EV++       + R++V R   + +  + + +A+  L   N         AL 
Sbjct: 107 EGQLLVDEVLDYLQLA-PEKRQQVQRCLINDLNPQAVERAIDRL-RSNSEFVPLCVSAL- 163

Query: 173 VDARQEIDLKVGVAFTRFQT-TYFQGKYGNLDS 204
             AR   D   G+  TR  T       Y  + S
Sbjct: 164 --ARARADWLYGINMTRAYTILGRNAGYQGVLS 194

>1gku_B Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea, helicase; 2.7A {Archaeoglobus fulgidus} SCOP: c.37.1.16 c.37.1.16 e.10.1.1 PDB: 1gl9_B* Length = 1054

 Score = 46.2 bits (110), Expect = 3e-06
 Identities = 41/193 (21%), Positives = 67/193 (34%), Gaps = 33/193 (17%)

Query: 5   KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRL- 63
             L + E P+ A  I+     GK   +           + +  +    VT+ +GHV  L 
Sbjct: 506 PALFIVESPTKARQISRFF--GKPSVKVLDG--AVVYEIPMQKYVL-MVTASIGHVVDLI 560

Query: 64  ------------DFPPAYQ------DWNASNPLDLFQAPVHKAESNP-KVHICRHLNQEA 104
                        F P Y       D       D    P   +E+          L + A
Sbjct: 561 TNRGFHGVLVNGRFVPVYASIKRCRDCGYQFTEDRESCPKCGSENVDNSRSRIEALRKLA 620

Query: 105 RGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVE 164
                +++  D D EGE I +++       +      V RA F  VT + IL+A+ +L +
Sbjct: 621 HDAEFVIVGTDPDTEGEKIAWDLKN-----LLSGCGAVKRAEFHEVTRRAILEALESLRD 675

Query: 165 PNRNEALAVDARQ 177
            + N    V A+ 
Sbjct: 676 VDEN---LVKAQV 685

>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant photosynthetic reaction center, peripheral antenna; HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1 Length = 154

 Score = 38.0 bits (87), Expect = 7e-04
 Identities = 10/30 (33%), Positives = 13/30 (43%), Gaps = 3/30 (10%)

Query: 152 EKDILKAMGN---LVEPNRNEALAVDARQE 178
           EK  LK +     L   +   ALA+ A  E
Sbjct: 18  EKQALKKLQASLKLYADDSAPALAIKATME 47

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	220
1i7d_A	659	DNA topoisomerase III; decatenating enzyme, protei	100.0
1mw9_X	592	DNA topoisomerase I; decatenase enzyme, toprim dom	100.0
2gai_A	633	DNA topoisomerase I; zinc ribbon; HET: DNA; 1.70A	100.0
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	100.0
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	100.0
2fcj_A	119	Small toprim domain protein; structural genomics,	96.45
1vdd_A	228	Recombination protein RECR; helix-hairpin-helix, z	96.38
1t6t_1	118	Putative protein; structural genomics, PSI, protei	94.77
3vdp_A	212	Recombination protein RECR; zinc finger, DNA repai	94.19

>1i7d_A DNA topoisomerase III; decatenating enzyme, protein-DNA complex, single-stranded DNA, isomerase/DNA complex; HET: DNA; 2.05A {Escherichia coli} SCOP: e.10.1.1 PDB: 2o5c_A* 2o54_A* 2o59_A* 2o19_A* 2o5e_A* 1d6m_A*

Probab=100.00  E-value=6e-56  Score=425.90  Aligned_cols=197  Identities=23%  Similarity=0.275  Sum_probs=162.0

Q ss_pred             eEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceec-CCcceEEEEccccceecccCCCCC----CCCccCCCCCC
Q 048704            6 VLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFL-GSHAYIKVTSVVGHVFRLDFPPAY----QDWNASNPLDL   80 (220)
Q Consensus         6 ~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~-g~~~~~~vt~~~GHl~~l~~p~~y----~~w~~~~p~~l   80 (220)
                      .||||||||+|++||++||++  .++.        +|||+ |+  +|+|||+.|||++|++|++|    ++|+..+ .++
T Consensus         2 ~LiIaEKPs~Ak~Ia~~L~g~--~~r~--------~gy~e~g~--~~~Vt~~~GHl~~L~~p~~y~~~~k~W~~~~-lpi   68 (659)
T 1i7d_A            2 RLFIAEKPSLARAIADVLPKP--HRKG--------DGFIECGN--GQVVTWCIGHLLEQAQPDAYDSRYARWNLAD-LPI   68 (659)
T ss_dssp             EEEEESSHHHHHHHHTTSCSC--CEEE--------TTEEEETT--TEEEEECSSCSEEECCHHHHCGGGGSCCSTT-CSC
T ss_pred             EEEEEECHHHHHHHHHHhcCC--cccC--------CCcEeeCC--CEEEEeccchhhcCCCccccchhccccccCC-ccc
Confidence            699999999999999999643  2333        57787 77  89999999999999998765    5776543 112


Q ss_pred             CCCCceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHh
Q 048704           81 FQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMG  160 (220)
Q Consensus        81 ~~~p~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~  160 (220)
                      ++.++......++.++++.|++++++||.||||||||||||+|+|+|+++++...+ ++++++|+|||++|+++|++||+
T Consensus        69 ~p~~~~~~v~~~~~~~~~~lk~l~k~ad~iiiAtD~DREGE~I~~~i~~~~~~~~~-~~~~v~R~~fs~iT~~aI~~A~~  147 (659)
T 1i7d_A           69 VPEKWQLQPRPSVTKQLNVIKRFLHEASEIVHAGDPDREGQLLVDEVLDYLQLAPE-KRQQVQRCLINDLNPQAVERAID  147 (659)
T ss_dssp             CCSSCCEEECGGGHHHHHHHHHHHHHCSEEEEECCSSHHHHHHHHHHHHHTTCCHH-HHHTCEECCCSCCSHHHHHHHHT
T ss_pred             ccccceeeecccHHHHHHHHHHHHhcCCeEEEcCCCCCCCCHHHHHHHHHhCcccc-CCCceEEEEEccCCHHHHHHHHh
Confidence            11111111234568899999999999999999999999999999999999986200 13689999999999999999999


Q ss_pred             cCCCCC--cchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704          161 NLVEPN--RNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF  219 (220)
Q Consensus       161 nl~~~~--~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~  219 (220)
                      ||++++  .+|++||+||+++||+||||+||++|+.+++...   +.++|+||||||||.+
T Consensus       148 nlr~~~~~~~l~~A~~aR~~~D~lvG~n~Sr~lt~~~r~~~~---~~~lS~GRVQTPtL~l  205 (659)
T 1i7d_A          148 RLRSNSEFVPLCVSALARARADWLYGINMTRAYTILGRNAGY---QGVLSVGRVQTPVLGL  205 (659)
T ss_dssp             TCEEGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTC---CSCCCCCTTHHHHHHH
T ss_pred             CCCCcchhhhHHHHHHHHHHHHHHHHHHhHHHHHHHHhhcCC---CCceecCccccchHHH
Confidence            999997  6999999999999999999999999998775321   3589999999999975

>1mw9_X DNA topoisomerase I; decatenase enzyme, toprim domain; HET: DNA; 1.67A {Escherichia coli} SCOP: e.10.1.1 PDB: 1mw8_X* 1cy1_A* 1cy0_A* 1cy2_A* 1cy4_A* 1cy6_A* 1cy7_A* 1cy8_A* 3pwt_A* 3px7_A* 1ecl_A 1cy9_A* 1cyy_A*

Probab=100.00  E-value=5.5e-53  Score=401.67  Aligned_cols=177  Identities=25%  Similarity=0.260  Sum_probs=147.4

Q ss_pred             ceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCC---------------CCC
Q 048704            5 KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFP---------------PAY   69 (220)
Q Consensus         5 ~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p---------------~~y   69 (220)
                      +.||||||||+|++||++||.                        +|+||||+|||++|..|               ++|
T Consensus         3 k~LiIaEkPs~Ak~Ia~~Lg~------------------------~~~Vt~~~GHl~~L~~~~~~~~~~~~~~~~~p~~y   58 (592)
T 1mw9_X            3 KALVIVESPAKAKTINKYLGS------------------------DYVVKSSVGHIRDLPTSGSAAKKSADSTSTKTAKK   58 (592)
T ss_dssp             CEEEEESCHHHHHHHHTTSCT------------------------TEEEEECCSCCEESCC-------------------
T ss_pred             ceEEEEECHHHHHHHHHHhCC------------------------CcEEEeeccccccCCcccccccccccccccchhhh
Confidence            789999999999999999975                        68999999999999875               455


Q ss_pred             CC-----Ccc----CCCCCCCCCCceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCC
Q 048704           70 QD-----WNA----SNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARR  140 (220)
Q Consensus        70 ~~-----w~~----~~p~~l~~~p~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~  140 (220)
                      +.     |..    .+|.+.|...+.+  ..++.++++.|++++++||.||||||||||||+|+|+|+++++..    ++
T Consensus        59 ~~~~~~~~~~~~l~i~p~~~f~~~~~~--~~~k~~~~~~lk~l~k~ad~iiiAtD~DREGE~I~~~i~~~~~~~----~~  132 (592)
T 1mw9_X           59 PKKDERGALVNRMGVDPWHNWEAHYEV--LPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGD----DA  132 (592)
T ss_dssp             ----CHHHHHHHHTEETTTTTEECCEE--CTTCHHHHHHHHHHHHTCSEEEECCCSSHHHHHHHHHHHHHHCSC----GG
T ss_pred             chhhhcccchhcCCcCccccCceeEEE--cccHHHHHHHHHHHHhcCCeEEEcCCCCccccHHHHHHHHHhCCC----CC
Confidence            42     111    1122223222221  345789999999999999999999999999999999999999963    46


Q ss_pred             cEEEEEecCcCHHHHHHHHhcCCCCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704          141 KVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF  219 (220)
Q Consensus       141 ~v~R~~~sslt~~~I~~A~~nl~~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~  219 (220)
                      +++|+|||++|+++|++||+|+++.+.+|++|++||+++||++|||+||++|..++        ..+|+||||||||.|
T Consensus       133 ~v~R~~fs~iT~~aI~~A~~~~~~~~~~l~~A~~aR~~~D~lvG~n~Sr~l~~~~~--------~~lS~GRVQtptL~l  203 (592)
T 1mw9_X          133 RYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIA--------RGLSAGRVQSVAVRL  203 (592)
T ss_dssp             GEEECCCSSCSHHHHHHHHHSCBCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC--------TTCCCCTTHHHHHHH
T ss_pred             CeEEEEEccCCHHHHHHHHhCCccccHHHHHHHHHHHHHHHHhhHhhhHHHHhhhc--------cccccCccchhHHHH
Confidence            89999999999999999999999999999999999999999999999999998652        369999999999965

>2gai_A DNA topoisomerase I; zinc ribbon; HET: DNA; 1.70A {Thermotoga maritima} PDB: 2gaj_A*

Probab=100.00  E-value=1.3e-52  Score=401.66  Aligned_cols=171  Identities=23%  Similarity=0.272  Sum_probs=148.0

Q ss_pred             CceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCCCCCCCCC
Q 048704            4 LKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASNPLDLFQA   83 (220)
Q Consensus         4 ~~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~p~~l~~~   83 (220)
                      |+.||||||||+|++||++||.                        +|+|||+.|||++|..|+ + +|...+   .|..
T Consensus         5 mk~LvIaEkPs~Ak~Ia~~Lg~------------------------~y~Vt~s~GHl~~l~~~~-~-~~~~~~---~f~p   55 (633)
T 2gai_A            5 VKKYIVVESPAKAKTIKSILGN------------------------EYEVFASMGHIIDLPKSK-F-GVDLEK---DFEP   55 (633)
T ss_dssp             --CEEEESCHHHHHHHHHHHGG------------------------GSEEEECCSCSEESCSSS-C-CEETTT---TSEE
T ss_pred             CcEEEEEeCHHHHHHHHHHhCC------------------------CCEEEecccccccCCccC-C-CCCccc---CcCc
Confidence            6789999999999999999964                        679999999999997763 2 454322   2321


Q ss_pred             CceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHHHHHHHHhcCC
Q 048704           84 PVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLV  163 (220)
Q Consensus        84 p~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~~I~~A~~nl~  163 (220)
                      .+.  ...++.++++.|++++++|| ||||||||||||+|+|+|+++++.     +++++|+|||++|+++|++||+||+
T Consensus        56 ~~~--~~~~~~~~~~~lk~l~k~ad-iiiAtD~DREGE~I~~~i~~~~~~-----~~~v~R~~fs~iT~~aI~~a~~~~~  127 (633)
T 2gai_A           56 EFA--VIKGKEKVVEKLKDLAKKGE-LLIASDMDREGEAIAWHIARVTNT-----LGRKNRIVFSEITPRVIREAVKNPR  127 (633)
T ss_dssp             CCE--ECTTCHHHHHHHHHHHHHSC-EEECCCSSHHHHHHHHHHHHHHTC-----TTSSCBCCCSSCCHHHHHHHHHSCB
T ss_pred             eEE--ECccHHHHHHHHHHHHhhCC-EEEcCCCCcccCHHHHHHHHHcCC-----CCCeEEEEEccCCHHHHHHHHhCCC
Confidence            111  23467899999999999999 999999999999999999999986     4789999999999999999999999


Q ss_pred             CCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704          164 EPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF  219 (220)
Q Consensus       164 ~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~  219 (220)
                      +++.+|++|++||+++|||+|||+||++|+.++        ..+|+||||||||.+
T Consensus       128 ~~~~~l~~A~~aR~~~D~lvG~n~Sr~l~~~~~--------~~lS~GRVQtptL~l  175 (633)
T 2gai_A          128 EIDMKKVRAQLARRILDRIVGYSLSPVLWRNFK--------SNLSAGRVQSATLKL  175 (633)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS--------CCCTTHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHhhHHHHHhhHHHCHHHHHhhh--------cccccCccchHHHHH
Confidence            999999999999999999999999999999763        369999999999965

>1gku_B Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea, helicase; 2.7A {Archaeoglobus fulgidus} SCOP: c.37.1.16 c.37.1.16 e.10.1.1 PDB: 1gl9_B*

Probab=100.00  E-value=1.6e-51  Score=413.29  Aligned_cols=194  Identities=21%  Similarity=0.243  Sum_probs=161.0

Q ss_pred             CceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCC-CCccCCCCCCCC
Q 048704            4 LKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQ-DWNASNPLDLFQ   82 (220)
Q Consensus         4 ~~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~-~w~~~~p~~l~~   82 (220)
                      ++.||||||||+|++||++||.. ..++.+++++|+|.   .|+ +.++|||+.|||++|++|++|. .|. .+++    
T Consensus       505 ~~~LiIaEkPs~ak~ia~~Lg~~-~~~~~~~~~~ye~~---~~~-~~~~vt~~~GHl~~l~~~~~~~~~~~-~~~~----  574 (1054)
T 1gku_B          505 KPALFIVESPTKARQISRFFGKP-SVKVLDGAVVYEIP---MQK-YVLMVTASIGHVVDLITNRGFHGVLV-NGRF----  574 (1054)
T ss_dssp             EEEEEEESCHHHHHHHHGGGEEC-EEEEETTEEEEEEE---CSS-EEEEEEECCSCSEEECSSSSTTSSCC-SSSC----
T ss_pred             CCEEEEEECHHHHHHHHHHhCCC-cccCCCCceeEEee---cCC-ceEEEEEeccccccCCCchhhcCccc-ccCc----
Confidence            46899999999999999999863 23344777777653   233 2469999999999999998753 454 2211    


Q ss_pred             CCceec------------------------cCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCC
Q 048704           83 APVHKA------------------------ESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDA  138 (220)
Q Consensus        83 ~p~~~~------------------------~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~  138 (220)
                      +|+.+.                        ...++.++++.|++++++||.||||||||||||+|+|+|+++++.     
T Consensus       575 ~P~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~l~~l~~~~d~ii~atD~DrEGE~I~~~i~~~~~~-----  649 (1054)
T 1gku_B          575 VPVYASIKRCRDCGYQFTEDRESCPKCGSENVDNSRSRIEALRKLAHDAEFVIVGTDPDTEGEKIAWDLKNLLSG-----  649 (1054)
T ss_dssp             CCEEEECC------------------------CCHHHHHHHHHHHHHHHSEEEECCCSSHHHHHHHHHHHHHHTT-----
T ss_pred             CCcccccccccchhhhcccccccccccccccCccHHHHHHHHHHHHhcCCEEEECCCCChhhhHHHHHHHHHhCC-----
Confidence            233221                        123568899999999999999999999999999999999999965     


Q ss_pred             CCcEEEEEecCcCHHHHHHHHhcCCCCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceecc
Q 048704          139 RRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLIC  218 (220)
Q Consensus       139 ~~~v~R~~~sslt~~~I~~A~~nl~~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~  218 (220)
                      +++++|+|||++|+++|++||+||++++++|++||+||+++||++|||+||++|..+.       +..+|+||||||||.
T Consensus       650 ~~~~~R~~~~~it~~aI~~a~~~~~~~~~~l~~a~~aR~~~D~lvG~~~sr~l~~~~~-------~~~lS~GRVQtptL~  722 (1054)
T 1gku_B          650 CGAVKRAEFHEVTRRAILEALESLRDVDENLVKAQVVRRIEDRWIGFVLSQKLWERFN-------NRNLSAGRAQTLVLG  722 (1054)
T ss_dssp             SSEEEECCCSBCSHHHHHHHHTSCBCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTT-------CSSCCCCTTHHHHHH
T ss_pred             CCCeEEEEEccCCHHHHHHHHhCCCCCcHhHHHHHHhHHHHHHHHHHHhCHHHHHhcc-------CceeeeccccchHHH
Confidence            5799999999999999999999999999999999999999999999999999997542       357999999999997


Q ss_pred             c
Q 048704          219 F  219 (220)
Q Consensus       219 ~  219 (220)
                      |
T Consensus       723 ~  723 (1054)
T 1gku_B          723 W  723 (1054)
T ss_dssp             H
T ss_pred             H
Confidence            5

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=100.00  E-value=7.5e-51  Score=409.72  Aligned_cols=200  Identities=21%  Similarity=0.226  Sum_probs=163.0

Q ss_pred             CceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCCCCccCC-CC-CC-
Q 048704            4 LKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQDWNASN-PL-DL-   80 (220)
Q Consensus         4 ~~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~~w~~~~-p~-~l-   80 (220)
                      |++||||||||+|++||++||.+ .+++.+++.+|+|.   .|+ ..++|||+.|||++|..|++|.+|...+ ++ +. 
T Consensus       541 ~~~LvIaEkPs~Ak~ia~~Lg~~-~~~~~~~~~~ye~~---~~~-~~~~v~~~~GHl~~l~~~~~~~~~~~~~~~~~p~y  615 (1104)
T 4ddu_A          541 RSLLIIVESPTKAETLSRFLGRA-SSRKERNIIVHEAV---TGE-GVILFTATRGHVYDLVTKGGIHGVEEENGKFVPVY  615 (1104)
T ss_dssp             BCEEEEESCHHHHHHHHHHHTCC-EEEEETTEEEEEEE---ETT-EEEEEEECCSCCEEECSSSTBTTBEEETTEEECEE
T ss_pred             CCeEEEEECHHHHHHHHHHhCCC-ccccCCCceeEEEe---cCC-ceEEEEEeccccccCCCccccCccccccCCcCccc
Confidence            47999999999999999999874 22344677777652   243 1459999999999999999886554322 11 11 


Q ss_pred             ------------CC-----CCceec-cCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcE
Q 048704           81 ------------FQ-----APVHKA-ESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKV  142 (220)
Q Consensus        81 ------------~~-----~p~~~~-~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v  142 (220)
                                  |.     +|.... ...++.++++.|++++++||.||+|||||||||+|+|+|+++++..    ++++
T Consensus       616 ~~~~~~~~~~~~f~~~~~~~p~~~~~~~~~~~~~~~~lk~~~~~~d~i~~atD~DrEGE~I~~~i~~~~~~~----~~~~  691 (1104)
T 4ddu_A          616 NSLKRCRDCGYQFTEDRDECPVCSSKNIDDKTETLRALREISLEADEILVATDPDVEGEKISWDVTQYLLPS----TRSL  691 (1104)
T ss_dssp             EECEEETTTCCEECSCCSSCTTTCCSCEEEHHHHHHHHHHHTTTCSEEEECCCSSHHHHHHHHHHHHHHTTT----CSCE
T ss_pred             cccccccchhhhhccccccccccccccCccHHHHHHHHHHHHhcCCEEEECcCCchhHHHHHHHHHHHhccc----CCCe
Confidence                        11     011000 0125688999999999999999999999999999999999999853    5789


Q ss_pred             EEEEecCcCHHHHHHHHhcCCCCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704          143 HRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF  219 (220)
Q Consensus       143 ~R~~~sslt~~~I~~A~~nl~~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~  219 (220)
                      +|+|||++|+++|++||+||++++++|++|++||+++||++|||+||++|..++       +.++|+||||||||.+
T Consensus       692 ~R~~f~~it~~aI~~a~~~~~~~~~~l~~a~~aR~~~D~lvG~~~sr~l~~~~~-------~~~lS~GRVQtptL~l  761 (1104)
T 4ddu_A          692 RRIEMHEITRYGFKKARESVRFVDFNLVKAQIVRRVQDRWIGFELSGKLQKRFG-------RSNLSAGRVQSTVLGW  761 (1104)
T ss_dssp             EECCCSSSSHHHHHHHHHTCBCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-------CSCCCCCHHHHHHHHH
T ss_pred             EEEEEccCCHHHHHHHHhCCCcCchhHHHHHHHHHHHHHHHHHHHhHHHHHhhC-------CcccccCccccHHHHH
Confidence            999999999999999999999999999999999999999999999999998763       2479999999999975

>2fcj_A Small toprim domain protein; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: MES; 1.30A {Geobacillus stearothermophilus} SCOP: c.136.1.1 PDB: 2i5r_A*

Probab=96.45  E-value=0.0033  Score=47.68  Aligned_cols=66  Identities=12%  Similarity=-0.017  Sum_probs=48.2

Q ss_pred             HHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccC--CCCcEEEEEecCcCHHHHHHHHhcCCCC
Q 048704           96 ICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVND--ARRKVHRARFSSVTEKDILKAMGNLVEP  165 (220)
Q Consensus        96 ~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~--~~~~v~R~~~sslt~~~I~~A~~nl~~~  165 (220)
                      .++.|+++. +-..||+.||||+.||.|-..|.+++....-.  ++.+.   =+..+++++|++|+++....
T Consensus        40 ~l~~I~~~~-~~r~VIi~TD~D~~GekIRk~i~~~lp~~~hafi~r~~~---gVE~a~~~~I~~aL~~~~~~  107 (119)
T 2fcj_A           40 RLEELADEL-EGYDVYLLADADEAGEKLRRQFRRMFPEAEHLYIDRAYR---EVAAAPIWHLAQVLLRARFD  107 (119)
T ss_dssp             HHHHHHHHT-TTSEEEEECCSSHHHHHHHHHHHHHCTTSEEECCCTTTC---STTTSCHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHh-cCCCEEEEECCCccHHHHHHHHHHHCCCCcEEeccCCcc---CcccCCHHHHHHHHHhcccc
Confidence            345565554 35689999999999999999999988763200  11222   36688999999999998754

>1vdd_A Recombination protein RECR; helix-hairpin-helix, zinc finger, toprim, walker B ATP binding motif; 2.50A {Deinococcus radiodurans} SCOP: e.49.1.1 PDB: 2v1c_A

Probab=96.38  E-value=0.0018  Score=54.21  Aligned_cols=57  Identities=11%  Similarity=0.026  Sum_probs=47.2

Q ss_pred             ccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEE--------ecCcCHHHHHHHHhcCCCC
Q 048704          105 RGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRAR--------FSSVTEKDILKAMGNLVEP  165 (220)
Q Consensus       105 ~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~--------~sslt~~~I~~A~~nl~~~  165 (220)
                      ..+++||+||+|+-|||..++.|.+.++..    ..+|.|+-        +-=+++-.+.+||++.++.
T Consensus       132 ~~V~EVIlAtnpTvEGEaTA~YI~~~Lk~~----~vkVTRiA~GiPvGgeLEY~De~TL~~Al~~R~~~  196 (228)
T 1vdd_A          132 GQGMEVILATGTTVEGDATALYLQRLLEPL----GAAISRIAYGVPVGGSLEYTDEVTLGRALTGRQTV  196 (228)
T ss_dssp             CTTCEEEECCCSSHHHHHHHHHHHHHHTTS----SCEEEECCBCBCTTCCGGGSCHHHHHHHHHTCEEE
T ss_pred             CCCCEEEEeCCCCchHHHHHHHHHHHHHHc----CCCEEEecccCCCCcceeeccHHHHHHHHHcCccc
Confidence            578999999999999999999999999864    46788863        2345688999999987654

>1t6t_1 Putative protein; structural genomics, PSI, protein structur initiative, midwest center for structural genomics, MCSG, U function; 1.80A {Aquifex aeolicus} SCOP: c.136.1.1

Probab=94.77  E-value=0.035  Score=41.86  Aligned_cols=34  Identities=21%  Similarity=0.241  Sum_probs=28.0

Q ss_pred             HHHHhccCCeEEEecCCChhHhHHHHHHHHHhCC
Q 048704          100 LNQEARGCGHLVLWLDCDREGENICFEVIECTGF  133 (220)
Q Consensus       100 lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~  133 (220)
                      ++.+.+..+.||+.||+|+.|+.|...+.+++..
T Consensus        55 i~~l~~~~~~VIIltD~D~aGe~ir~~i~~~l~~   88 (118)
T 1t6t_1           55 VDMLEGKWEKVILLFDLDTHGERINQKMKELLSS   88 (118)
T ss_dssp             HHHHTTTCSEEEECCCSSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhCCCEEEEEECCChhHHHHHHHHHHhcCc
Confidence            3344345667999999999999999999999875

>3vdp_A Recombination protein RECR; zinc finger, DNA repair, DNA binding; 2.45A {Thermoanaerobacter tengcongensis} PDB: 3vdu_A 3ve5_D

Probab=94.19  E-value=0.074  Score=43.96  Aligned_cols=55  Identities=18%  Similarity=0.108  Sum_probs=43.0

Q ss_pred             ccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEE--------ecCcCHHHHHHHHhcCC
Q 048704          105 RGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRAR--------FSSVTEKDILKAMGNLV  163 (220)
Q Consensus       105 ~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~--------~sslt~~~I~~A~~nl~  163 (220)
                      .++++||+||+|.-|||.-+..|.+.++..    ..+|.|+=        +-=+++-.+.+||++.+
T Consensus       148 ~~v~EVIlAtnpTvEGeaTa~Yi~~~Lk~~----~vkvTRiA~GiPvGgeLEY~D~~TL~~Al~~R~  210 (212)
T 3vdp_A          148 GSVKEVILATNPDIEGEATAMYIAKLLKPF----GVKVTRIAHGIPVGGDLEYTDVVTLSKALEGRR  210 (212)
T ss_dssp             SCCSEEEECCCSSHHHHHHHHHHHHHHTTT----TCEEEECCBSBCTTCCGGGSCHHHHHHHHHTCE
T ss_pred             CCCcEEEEECCCCccHHHHHHHHHHHhhhc----CCCeeeccccCcCCcchhhccHHHHHHHHHhCc
Confidence            468999999999999999999999999974    45677753        22345777778877654

---

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	220
d1i7da_	620	e.10.1.1 (A:) DNA topoisomerase III {Escherichia c	1e-34
d1mw9x_	591	e.10.1.1 (X:) DNA topoisomerase I, 67K N-terminal	1e-25
d1gkub3	556	e.10.1.1 (B:499-1054) Topoisomerase "domain" of re	4e-25

>d1i7da_ e.10.1.1 (A:) DNA topoisomerase III {Escherichia coli [TaxId: 562]} Length = 620

class: Multi-domain proteins (alpha and beta)
fold: Prokaryotic type I DNA topoisomerase
superfamily: Prokaryotic type I DNA topoisomerase
family: Prokaryotic type I DNA topoisomerase
domain: DNA topoisomerase III
species: Escherichia coli [TaxId: 562]

 Score =  127 bits (319), Expect = 1e-34
 Identities = 47/200 (23%), Positives = 77/200 (38%), Gaps = 17/200 (8%)

Query: 7   LMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFP 66
           L +AEKPS+A +IA VL       RK    +   +G          VT  +GH+     P
Sbjct: 3   LFIAEKPSLARAIADVLPKP---HRKGDGFIECGNGQ--------VVTWCIGHLLEQAQP 51

Query: 67  PAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLN---QEARGCGHLVLWLDCDREGENI 123
            AY    A   L        K +  P+  + + LN   +       +V   D DREG+ +
Sbjct: 52  DAYDSRYARWNLADLPIVPEKWQLQPRPSVTKQLNVIKRFLHEASEIVHAGDPDREGQLL 111

Query: 124 CFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNR--NEALAVDARQEIDL 181
             EV++         R++V R   + +  + + +A+  L   +      ++  AR   D 
Sbjct: 112 VDEVLDYLQLAPEK-RQQVQRCLINDLNPQAVERAIDRLRSNSEFVPLCVSALARARADW 170

Query: 182 KVGVAFTRFQTTYFQGKYGN 201
             G+  TR  T   +     
Sbjct: 171 LYGINMTRAYTILGRNAGYQ 190

>d1mw9x_ e.10.1.1 (X:) DNA topoisomerase I, 67K N-terminal domain {Escherichia coli [TaxId: 562]} Length = 591

class: Multi-domain proteins (alpha and beta)
fold: Prokaryotic type I DNA topoisomerase
superfamily: Prokaryotic type I DNA topoisomerase
family: Prokaryotic type I DNA topoisomerase
domain: DNA topoisomerase I, 67K N-terminal domain
species: Escherichia coli [TaxId: 562]

 Score =  101 bits (253), Expect = 1e-25
 Identities = 43/195 (22%), Positives = 70/195 (35%), Gaps = 12/195 (6%)

Query: 5   KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFD---GMFLGSHAYIKVTSVVGHVF 61
           K L++ E P+ A +I   L     Y  K+S   H  D          +    ++      
Sbjct: 2   KALVIVESPAKAKTINKYLGSD--YVVKSSVG-HIRDLPTSGSAAKKSADSTSTKTAKKP 58

Query: 62  RLDFPPAYQDWNASNPLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGE 121
           + D   A  +    +P   ++A         K  +   L Q A    H+ L  D DREGE
Sbjct: 59  KKDERGALVNRMGVDPWHNWEAHYEVLPGKEK--VVSELKQLAEKADHIYLATDLDREGE 116

Query: 122 NICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDL 181
            I + + E     +     +  R  F+ +T+  I +A     E N +   A  AR+ +D 
Sbjct: 117 AIAWHLREV----IGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDR 172

Query: 182 KVGVAFTRFQTTYFQ 196
            VG   +        
Sbjct: 173 VVGYMVSPLLWKKIA 187

>d1gkub3 e.10.1.1 (B:499-1054) Topoisomerase "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 556

class: Multi-domain proteins (alpha and beta)
fold: Prokaryotic type I DNA topoisomerase
superfamily: Prokaryotic type I DNA topoisomerase
family: Prokaryotic type I DNA topoisomerase
domain: Topoisomerase "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score =  100 bits (248), Expect = 4e-25
 Identities = 38/215 (17%), Positives = 66/215 (30%), Gaps = 30/215 (13%)

Query: 5   KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRL- 63
             L + E P+ A  I+       +     +                + VT+ +GHV  L 
Sbjct: 8   PALFIVESPTKARQISRFFGKPSVKVLDGAVVYE-----IPMQKYVLMVTASIGHVVDLI 62

Query: 64  ------------DFPPAYQDWNASNPLDLFQAP-------VHKAESNPKVHICRHLNQEA 104
                        F P Y                            +        L + A
Sbjct: 63  TNRGFHGVLVNGRFVPVYASIKRCRDCGYQFTEDRESCPKCGSENVDNSRSRIEALRKLA 122

Query: 105 RGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEKDILKAMGNLVE 164
                +++  D D EGE I +++       +      V RA F  VT + IL+A+ +L +
Sbjct: 123 HDAEFVIVGTDPDTEGEKIAWDLKN-----LLSGCGAVKRAEFHEVTRRAILEALESLRD 177

Query: 165 PNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKY 199
            + N   A   R+  D  +G   ++     F  + 
Sbjct: 178 VDENLVKAQVVRRIEDRWIGFVLSQKLWERFNNRN 212

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	220
d1gkub3	556	Topoisomerase "domain" of reverse gyrase {Archaeon	100.0
d1i7da_	620	DNA topoisomerase III {Escherichia coli [TaxId: 56	100.0
d1mw9x_	591	DNA topoisomerase I, 67K N-terminal domain {Escher	100.0
d1vdda_	199	Recombination protein RecR {Deinococcus radioduran	97.24
d2fcja1	114	Hypothetical protein RBSTP2199 {Bacillus stearothe	92.75
d1t6t1_	108	Hypothetical protein aq_2086 {Aquifex aeolicus [Ta	90.96
d1nuia1	192	Primase fragment of primase-helicase protein {Bact	89.15

>d1gkub3 e.10.1.1 (B:499-1054) Topoisomerase "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Multi-domain proteins (alpha and beta)
fold: Prokaryotic type I DNA topoisomerase
superfamily: Prokaryotic type I DNA topoisomerase
family: Prokaryotic type I DNA topoisomerase
domain: Topoisomerase "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=100.00  E-value=1.9e-55  Score=413.81  Aligned_cols=199  Identities=20%  Similarity=0.208  Sum_probs=159.1

Q ss_pred             CceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCC----CCccCCCC-
Q 048704            4 LKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQ----DWNASNPL-   78 (220)
Q Consensus         4 ~~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~----~w~~~~p~-   78 (220)
                      +++||||||||+|++||++||.+.. ++.++...+  .+++.+.  .|+||||.|||++|++|++|.    +|+..... 
T Consensus         7 ~~~LiIaEKPs~ak~Ia~~Lg~~~~-k~~~~~~~~--~~~~~~~--~~~vt~~~GHl~~L~~p~~~~~~~~~~~~~p~~~   81 (556)
T d1gkub3           7 KPALFIVESPTKARQISRFFGKPSV-KVLDGAVVY--EIPMQKY--VLMVTASIGHVVDLITNRGFHGVLVNGRFVPVYA   81 (556)
T ss_dssp             EEEEEEESCHHHHHHHHGGGEECEE-EEETTEEEE--EEECSSE--EEEEEECCSCSEEECSSSSTTSSCCSSSCCCEEE
T ss_pred             CCeEEEECCHHHHHHHHHHcCCCcc-cccCCcccc--ccccCCc--eEEEEEccCccccCCCcccccccccccCcCcccc
Confidence            4679999999999999999987532 222344443  3455554  899999999999999999873    45431100 


Q ss_pred             ---C------CC--CCCcee----ccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEE
Q 048704           79 ---D------LF--QAPVHK----AESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVH  143 (220)
Q Consensus        79 ---~------l~--~~p~~~----~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~  143 (220)
                         .      .+  +.+..+    .....++++++.|++++++||.||||||||||||+|||+|+++++.     .++++
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~i~~l~k~ad~ii~AtD~DREGE~I~~~i~~~~~~-----~~~v~  156 (556)
T d1gkub3          82 SIKRCRDCGYQFTEDRESCPKCGSENVDNSRSRIEALRKLAHDAEFVIVGTDPDTEGEKIAWDLKNLLSG-----CGAVK  156 (556)
T ss_dssp             ECC------------------------CCHHHHHHHHHHHHHHHSEEEECCCSSHHHHHHHHHHHHHHTT-----SSEEE
T ss_pred             ccccccccccccccccccccccccccCccHHHHHHHHHHHHhhCCEEEECCCCCcchhHHHHHHHHHhcC-----CCCeE
Confidence               0      00  000111    1123467899999999999999999999999999999999999996     57999


Q ss_pred             EEEecCcCHHHHHHHHhcCCCCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704          144 RARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF  219 (220)
Q Consensus       144 R~~~sslt~~~I~~A~~nl~~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~  219 (220)
                      |+|||++|+++|++||+||++++++|++|+.||+.+||++|+|+||++|..++       +.++|+||||||||.|
T Consensus       157 R~~~~~~t~~~I~~a~~~l~~~~~~l~~a~~aR~~~D~~iG~~~s~~l~~~~~-------~~~lS~GRVQtPtL~l  225 (556)
T d1gkub3         157 RAEFHEVTRRAILEALESLRDVDENLVKAQVVRRIEDRWIGFVLSQKLWERFN-------NRNLSAGRAQTLVLGW  225 (556)
T ss_dssp             ECCCSBCSHHHHHHHHTSCBCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTT-------CSSCCCCTTHHHHHHH
T ss_pred             EEEehhccHHHHHhHHhhccccchhhhHHHHHHhHHHHHhcchhHHHHHHHHh-------cccccccccccchhhh
Confidence            99999999999999999999999999999999999999999999999997653       3579999999999975

>d1i7da_ e.10.1.1 (A:) DNA topoisomerase III {Escherichia coli [TaxId: 562]}

class: Multi-domain proteins (alpha and beta)
fold: Prokaryotic type I DNA topoisomerase
superfamily: Prokaryotic type I DNA topoisomerase
family: Prokaryotic type I DNA topoisomerase
domain: DNA topoisomerase III
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=1.1e-55  Score=420.22  Aligned_cols=193  Identities=23%  Similarity=0.309  Sum_probs=161.4

Q ss_pred             CceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceec-CCcceEEEEccccceecccCCCCC----CCCccCCCC
Q 048704            4 LKVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFL-GSHAYIKVTSVVGHVFRLDFPPAY----QDWNASNPL   78 (220)
Q Consensus         4 ~~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~-g~~~~~~vt~~~GHl~~l~~p~~y----~~w~~~~p~   78 (220)
                      |+ ||||||||+|++||++||.+.  ++.        +||++ |+  +|+|||+.|||++|++|++|    ++|+..   
T Consensus         1 Mk-LiIaEkPs~Ak~Ia~~Lg~~~--~~~--------~g~~~~g~--~~~Vt~~~GHl~~l~~p~~~~~~~~~w~~~---   64 (620)
T d1i7da_           1 MR-LFIAEKPSLARAIADVLPKPH--RKG--------DGFIECGN--GQVVTWCIGHLLEQAQPDAYDSRYARWNLA---   64 (620)
T ss_dssp             CE-EEEESSHHHHHHHHTTSCSCC--EEE--------TTEEEETT--TEEEEECSSCSEEECCHHHHCGGGGSCCST---
T ss_pred             Ce-EEEECCHHHHHHHHHHhCCcc--ccC--------CCceecCC--CeEEEEeCCcCcCCCCchhccccccCCccc---
Confidence            44 999999999999999998642  222        45665 55  79999999999999999765    456543   


Q ss_pred             CCCCCCceec-----cCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEecCcCHH
Q 048704           79 DLFQAPVHKA-----ESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFSSVTEK  153 (220)
Q Consensus        79 ~l~~~p~~~~-----~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~sslt~~  153 (220)
                         ++|+.|.     ...++.++++.|++++++||.||+|||||||||+|||||+++++.... .+++++|+|||++|++
T Consensus        65 ---~lp~~p~~~~~~~~~~~~k~~~~lk~l~k~ad~iilAtD~DREGE~Ia~~i~~~~~~~~~-~~~~v~R~~f~~iT~~  140 (620)
T d1i7da_          65 ---DLPIVPEKWQLQPRPSVTKQLNVIKRFLHEASEIVHAGDPDREGQLLVDEVLDYLQLAPE-KRQQVQRCLINDLNPQ  140 (620)
T ss_dssp             ---TCSCCCSSCCEEECGGGHHHHHHHHHHHHHCSEEEEECCSSHHHHHHHHHHHHHTTCCHH-HHHTCEECCCSCCSHH
T ss_pred             ---cCCCCCccceeeeCccHHHHHHHHHHHHhcCCEEEEcCCCCcchhHHHHHHHHHhccccc-cCCceEEEEeecCcHH
Confidence               3444332     234567899999999999999999999999999999999999986321 1468999999999999


Q ss_pred             HHHHHHhcCCCCCc--chHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704          154 DILKAMGNLVEPNR--NEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF  219 (220)
Q Consensus       154 ~I~~A~~nl~~~~~--~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~  219 (220)
                      +|++||+|++++++  +|++|++||+++||++|||+||++|+++++.+.   +.++|+||||||||.|
T Consensus       141 aI~~A~~n~~~~~~~~~l~~a~~aR~~~D~liG~~~Sr~~t~~~~~~~~---~~~lS~GRVQtPtL~l  205 (620)
T d1i7da_         141 AVERAIDRLRSNSEFVPLCVSALARARADWLYGINMTRAYTILGRNAGY---QGVLSVGRVQTPVLGL  205 (620)
T ss_dssp             HHHHHHTTCEEGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTC---CSCCCCCTTHHHHHHH
T ss_pred             HHHHHHHhcCCchhhhhHHHHHHHhHHHHhhcCcchhHHHHHHHhhcCC---Cccccccccccchhhh
Confidence            99999999999984  889999999999999999999999988765432   4689999999999975

>d1mw9x_ e.10.1.1 (X:) DNA topoisomerase I, 67K N-terminal domain {Escherichia coli [TaxId: 562]}

class: Multi-domain proteins (alpha and beta)
fold: Prokaryotic type I DNA topoisomerase
superfamily: Prokaryotic type I DNA topoisomerase
family: Prokaryotic type I DNA topoisomerase
domain: DNA topoisomerase I, 67K N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=1.3e-51  Score=390.19  Aligned_cols=177  Identities=26%  Similarity=0.277  Sum_probs=146.3

Q ss_pred             ceEEEEeChHHHHHHHHHcCCCCcccccCCeeeeeecceecCCcceEEEEccccceecccCCCCCC----CCccCC----
Q 048704            5 KVLMVAEKPSIALSIATVLSGGKLYTRKASTEVHEFDGMFLGSHAYIKVTSVVGHVFRLDFPPAYQ----DWNASN----   76 (220)
Q Consensus         5 ~~LiIaEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~g~~~~~~vt~~~GHl~~l~~p~~y~----~w~~~~----   76 (220)
                      |.||||||||+|++||++||.                        +|+|+||+|||++|..|+.|.    .|....    
T Consensus         2 K~LiIaEKPs~Ak~Ia~~Lg~------------------------~y~V~~~~GHl~~l~~~~~~~~~~~~~~~~~~~~~   57 (591)
T d1mw9x_           2 KALVIVESPAKAKTINKYLGS------------------------DYVVKSSVGHIRDLPTSGSAAKKSADSTSTKTAKK   57 (591)
T ss_dssp             CEEEEESCHHHHHHHHTTSCT------------------------TEEEEECCSCCEESCC-------------------
T ss_pred             CEEEEECCHHHHHHHHHHhCC------------------------CCEEEeccCceeECCCCcccccccccccccccccc
Confidence            689999999999999999975                        689999999999999998763    343211    


Q ss_pred             ----------------CCCCCCCCceeccCCCcHHHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCC
Q 048704           77 ----------------PLDLFQAPVHKAESNPKVHICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARR  140 (220)
Q Consensus        77 ----------------p~~l~~~p~~~~~~~~~~~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~  140 (220)
                                      |...|...+  ....+++++++.|++++++||.||||||||||||+|||+|+++++..    ++
T Consensus        58 ~~~~~~~~~~~~~~~~p~~~~~~~~--~~~~~~~k~~~~ik~l~k~~d~iiiAtD~DrEGE~I~~~i~~~~~~~----~~  131 (591)
T d1mw9x_          58 PKKDERGALVNRMGVDPWHNWEAHY--EVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGD----DA  131 (591)
T ss_dssp             ----CHHHHHHHHTEETTTTTEECC--EECTTCHHHHHHHHHHHHTCSEEEECCCSSHHHHHHHHHHHHHHCSC----GG
T ss_pred             cccccccccccccCcCcccCCceeE--EECCchHHHHHHHHHHHhcCCEEEECCCCCccchHHHHHHHHHhccC----CC
Confidence                            111111111  12345789999999999999999999999999999999999999873    56


Q ss_pred             cEEEEEecCcCHHHHHHHHhcCCCCCcchHHHHHHHHHHHHHHHHhhhHHHHHHhhcccCCCCCCceeeccccceeccc
Q 048704          141 KVHRARFSSVTEKDILKAMGNLVEPNRNEALAVDARQEIDLKVGVAFTRFQTTYFQGKYGNLDSRFISLVFSSLFLICF  219 (220)
Q Consensus       141 ~v~R~~~sslt~~~I~~A~~nl~~~~~~l~~A~~aR~~~D~liG~nlTR~~t~~~~~~~~~~~~~~~S~GRvQtp~l~~  219 (220)
                      +++|+|||++|+++|++||+|+.+.++++++||.||+.+||++|||+||++|+.++        ..+|+||||||||.+
T Consensus       132 ~~~R~~~~~lt~~~i~~A~~n~~~~~~~l~~a~~aR~~~D~liG~n~Sr~~t~~~~--------~~lS~GRVQtPtL~l  202 (591)
T d1mw9x_         132 RYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIA--------RGLSAGRVQSVAVRL  202 (591)
T ss_dssp             GEEECCCSSCSHHHHHHHHHSCBCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC--------TTCCCCTTHHHHHHH
T ss_pred             ceEEEEeccCCHHHHHHHHhCcccccchHHHHHHHHHHHHHHHHHhcchHHhhhhc--------cccccchhcCcceee
Confidence            89999999999999999999999999999999999999999999999999998763        359999999999975

>d1vdda_ e.49.1.1 (A:) Recombination protein RecR {Deinococcus radiodurans [TaxId: 1299]}

class: Multi-domain proteins (alpha and beta)
fold: Recombination protein RecR
superfamily: Recombination protein RecR
family: Recombination protein RecR
domain: Recombination protein RecR
species: Deinococcus radiodurans [TaxId: 1299]

Probab=97.24  E-value=0.00026  Score=56.39  Aligned_cols=58  Identities=10%  Similarity=0.031  Sum_probs=47.4

Q ss_pred             ccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEE--------ecCcCHHHHHHHHhcCCCCC
Q 048704          105 RGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRAR--------FSSVTEKDILKAMGNLVEPN  166 (220)
Q Consensus       105 ~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~--------~sslt~~~I~~A~~nl~~~~  166 (220)
                      ++..+||+||++.-|||.-+..|.+.++..    +.+|.|+=        +.-+++..+.+||++.+..+
T Consensus       132 ~~~~EiIlA~~~t~EGe~Ta~yi~~~l~~~----~ikitrlA~GiP~G~~ley~D~~TL~~Al~~R~~i~  197 (199)
T d1vdda_         132 GQGMEVILATGTTVEGDATALYLQRLLEPL----GAAISRIAYGVPVGGSLEYTDEVTLGRALTGRQTVS  197 (199)
T ss_dssp             CTTCEEEECCCSSHHHHHHHHHHHHHHTTS----SCEEEECCBCBCTTCCGGGSCHHHHHHHHHTCEEEE
T ss_pred             cCCcEEEEEecCCcchHHHHHHHHHHhhhc----CceEEeecccCCCCcchhhcCHHHHHHHHHcCccCC
Confidence            455799999999999999999999999874    46788763        34567999999999887654

>d2fcja1 c.136.1.1 (A:1-114) Hypothetical protein RBSTP2199 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: Toprim domain
superfamily: Toprim domain
family: Toprim domain
domain: Hypothetical protein RBSTP2199
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=92.75  E-value=0.091  Score=37.15  Aligned_cols=62  Identities=13%  Similarity=0.068  Sum_probs=40.5

Q ss_pred             HHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEE--EEecCcCHHHHHHHHhcC
Q 048704           97 CRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHR--ARFSSVTEKDILKAMGNL  162 (220)
Q Consensus        97 ~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R--~~~sslt~~~I~~A~~nl  162 (220)
                      ++.|.+.. +...||+++|+|..|+.++.++.+.+....   ..-+.|  --+.++..+.+.++|+..
T Consensus        41 ~~~l~~~~-~~~~Iii~~D~D~aG~~~a~~l~~~l~~~~---~~~i~~~~~~v~~~p~~~~~~~l~~~  104 (114)
T d2fcja1          41 LEELADEL-EGYDVYLLADADEAGEKLRRQFRRMFPEAE---HLYIDRAYREVAAAPIWHLAQVLLRA  104 (114)
T ss_dssp             HHHHHHHT-TTSEEEEECCSSHHHHHHHHHHHHHCTTSE---EECCCTTTCSTTTSCHHHHHHHHHHT
T ss_pred             HHHHHHHh-CCCcEEEEeCCChHHHHHHHHHHHHCCCCc---EEEecccccchhhCcHHHHHHHHHhc
Confidence            44555543 356899999999999999999999997421   000011  013466677777777654

>d1t6t1_ c.136.1.1 (1:) Hypothetical protein aq_2086 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: Toprim domain
superfamily: Toprim domain
family: Toprim domain
domain: Hypothetical protein aq 2086
species: Aquifex aeolicus [TaxId: 63363]

Probab=90.96  E-value=0.14  Score=35.93  Aligned_cols=34  Identities=21%  Similarity=0.241  Sum_probs=28.8

Q ss_pred             HHHHhccCCeEEEecCCChhHhHHHHHHHHHhCC
Q 048704          100 LNQEARGCGHLVLWLDCDREGENICFEVIECTGF  133 (220)
Q Consensus       100 lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~  133 (220)
                      +..+.+..+.||+++|.|+.|+..+..+.+.+..
T Consensus        51 ~~~l~~~~~~vii~~D~D~aG~~aa~kl~~~L~~   84 (108)
T d1t6t1_          51 VDMLEGKWEKVILLFDLDTHGERINQKMKELLSS   84 (108)
T ss_dssp             HHHHTTTCSEEEECCCSSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhcCCeEEEEeCCCHHHHHHHHHHHHHHHH
Confidence            3444566789999999999999999999998875

>d1nuia1 e.13.1.2 (A:64-255) Primase fragment of primase-helicase protein {Bacteriophage T7 [TaxId: 10760]}

class: Multi-domain proteins (alpha and beta)
fold: DNA primase core
superfamily: DNA primase core
family: Primase fragment of primase-helicase protein
domain: Primase fragment of primase-helicase protein
species: Bacteriophage T7 [TaxId: 10760]

Probab=89.15  E-value=0.28  Score=36.79  Aligned_cols=48  Identities=19%  Similarity=0.210  Sum_probs=35.8

Q ss_pred             HHHHHHHHHhccCCeEEEecCCChhHhHHHHHHHHHhCCcccCCCCcEEEEEec
Q 048704           95 HICRHLNQEARGCGHLVLWLDCDREGENICFEVIECTGFQVNDARRKVHRARFS  148 (220)
Q Consensus        95 ~~~~~lk~~~~~ad~ii~AtD~DrEGE~I~~~Il~~~~~~~~~~~~~v~R~~~s  148 (220)
                      +.+....+.++..+.||+|+|.|--|+..+.++.+.+..      ..++++.+.
T Consensus       124 ~~~~~~~~~l~~~~~Vvl~~DnD~AG~~aa~~~~~~l~~------~~~~~~~~~  171 (192)
T d1nuia1         124 KTCAANYEYFDQFEQIILMFDMDEAGRKAVEEAAQVLPA------GKVRVAVLP  171 (192)
T ss_dssp             HHHHHTHHHHTTBSCEEEECCSSHHHHHHHHHHHHHSCT------TTEEECCCS
T ss_pred             hHHhHHHHHhcCCCeEEEEcCCCHHHHHHHHHHHHHcCC------CcEEEecCC
Confidence            334444455577889999999999999999999998864      346655444