Query psy11240
Match_columns 363
No_of_seqs 204 out of 1250
Neff 4.6
Searched_HMMs 46136
Date Fri Aug 16 21:43:58 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11240.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11240hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03237 DNA topoisomerase 2; 100.0 6E-115 1E-119 959.6 26.7 342 2-355 603-1081(1465)
2 PTZ00108 DNA topoisomerase 2-l 100.0 3E-112 6E-117 939.8 24.9 341 2-354 585-1054(1388)
3 PLN03128 DNA topoisomerase 2; 100.0 4E-112 8E-117 930.1 24.5 341 2-354 578-1053(1135)
4 PHA02592 52 DNA topisomerase I 100.0 3.4E-81 7.3E-86 632.5 19.7 256 86-346 3-384 (439)
5 smart00434 TOP4c DNA Topoisome 100.0 3E-76 6.4E-81 598.0 18.0 257 89-350 1-396 (445)
6 cd00187 TOP4c DNA Topoisomeras 100.0 8.8E-73 1.9E-77 572.5 15.7 236 107-348 1-389 (445)
7 PF00521 DNA_topoisoIV: DNA gy 100.0 4.6E-72 1E-76 563.6 7.1 228 109-345 1-377 (426)
8 TIGR01061 parC_Gpos DNA topois 100.0 4.4E-70 9.6E-75 580.6 20.1 252 87-346 2-409 (738)
9 PRK05561 DNA topoisomerase IV 100.0 5.1E-70 1.1E-74 580.4 18.7 248 85-339 9-415 (742)
10 PRK05560 DNA gyrase subunit A; 100.0 2.4E-69 5.2E-74 579.8 18.9 255 85-348 4-412 (805)
11 TIGR01063 gyrA DNA gyrase, A s 100.0 7.7E-67 1.7E-71 560.1 19.5 252 87-346 2-409 (800)
12 TIGR01062 parC_Gneg DNA topois 100.0 1.2E-65 2.7E-70 545.2 18.3 239 87-332 2-392 (735)
13 PRK13979 DNA topoisomerase IV 100.0 3.3E-65 7.2E-70 554.0 18.6 267 73-352 4-432 (957)
14 COG0188 GyrA Type IIA topoisom 100.0 7.2E-65 1.6E-69 541.5 14.7 259 86-353 8-421 (804)
15 KOG0355|consensus 100.0 4.1E-65 8.9E-70 536.4 9.9 194 2-222 573-798 (842)
16 PRK09631 DNA topoisomerase IV 100.0 3.4E-61 7.5E-66 503.6 18.9 242 90-348 3-377 (635)
17 PRK12758 DNA topoisomerase IV 100.0 1.5E-60 3.2E-65 508.0 19.6 249 88-351 20-401 (869)
18 PRK09630 DNA topoisomerase IV 100.0 8.9E-60 1.9E-64 475.4 19.0 252 90-354 3-390 (479)
19 TIGR01055 parE_Gneg DNA topois 99.3 1.9E-12 4.1E-17 137.4 4.1 63 2-64 555-621 (625)
20 smart00433 TOP2c Topoisomerase 99.2 1.3E-11 2.9E-16 130.3 5.4 64 2-65 529-593 (594)
21 PRK05559 DNA topoisomerase IV 99.2 1.3E-11 2.8E-16 131.2 4.8 63 2-65 561-625 (631)
22 PRK05644 gyrB DNA gyrase subun 99.1 1E-10 2.2E-15 124.5 5.1 62 2-65 566-630 (638)
23 TIGR01058 parE_Gpos DNA topois 99.0 2.3E-10 5E-15 121.9 4.0 64 2-65 563-627 (637)
24 TIGR01059 gyrB DNA gyrase, B s 98.4 1.5E-07 3.3E-12 100.7 4.4 61 2-65 582-646 (654)
25 COG0187 GyrB Type IIA topoisom 97.4 9.3E-05 2E-09 79.0 3.3 60 2-63 563-625 (635)
26 PF00986 DNA_gyraseB_C: DNA gy 95.0 0.054 1.2E-06 42.7 5.2 60 2-62 4-65 (65)
27 PHA02569 39 DNA topoisomerase 93.3 0.067 1.4E-06 57.7 3.4 31 32-63 572-602 (602)
28 KOG0355|consensus 88.3 0.15 3.2E-06 56.6 0.1 117 95-213 81-242 (842)
29 KOG3441|consensus 69.2 5.1 0.00011 35.6 3.2 49 135-203 80-130 (149)
30 PF09996 DUF2237: Uncharacteri 32.9 43 0.00092 29.5 2.9 34 94-127 41-78 (117)
31 COG2143 Thioredoxin-related pr 30.2 2.3E+02 0.0049 26.7 7.2 68 224-297 86-157 (182)
32 TIGR03333 salvage_mtnX 2-hydro 29.3 2.6E+02 0.0056 25.4 7.6 25 263-287 1-25 (214)
33 PF12395 DUF3658: Protein of u 27.2 1.3E+02 0.0028 25.4 4.9 81 54-169 13-93 (111)
34 PTZ00109 DNA gyrase subunit b; 26.1 52 0.0011 37.7 2.9 62 3-65 836-899 (903)
35 KOG1478|consensus 24.9 77 0.0017 32.0 3.4 74 201-288 6-83 (341)
36 TIGR01488 HAD-SF-IB Haloacid D 23.9 4.6E+02 0.0099 22.3 7.8 25 263-287 1-25 (177)
37 COG2739 Uncharacterized protei 23.0 2.7E+02 0.0058 24.2 5.8 38 277-314 35-74 (105)
38 PRK13711 conjugal transfer pro 22.5 33 0.00071 29.0 0.3 14 200-213 27-40 (113)
39 COG5504 Predicted Zn-dependent 22.4 44 0.00095 33.2 1.2 21 152-172 158-180 (280)
40 PRK09552 mtnX 2-hydroxy-3-keto 22.3 3.2E+02 0.0068 24.9 6.8 25 263-287 5-29 (219)
41 PF00356 LacI: Bacterial regul 21.9 51 0.0011 24.0 1.2 31 318-348 16-46 (46)
No 1
>PLN03237 DNA topoisomerase 2; Provisional
Probab=100.00 E-value=5.9e-115 Score=959.58 Aligned_cols=342 Identities=50% Similarity=0.762 Sum_probs=332.0
Q ss_pred CCcceeeccccccCCcHHHHHHhhhhhcceeeeEEcCCCchHHHHHhcCCcchhhHHHHHHHhHHHhhhhhccCCccccc
Q psy11240 2 NTIHDVMIAGLGTSTSKEAKEYFSNMERHRILFKYSGDNDDAHIRMAFSKKLVDERKTWLTTWMEECRRRKEMGIGEDYL 81 (363)
Q Consensus 2 ~~w~iKYyKGLGTst~~eakeyF~~l~~h~~~f~~~~~~d~~~i~~aF~kk~~d~RK~Wl~~~~~~~~~~~~~~~~~~~l 81 (363)
++|+||||||||||+++|++|||+||++|++.|.|.+++|+++|+|||||+++|+||+||++|. ||+||
T Consensus 603 ~~~~IkyYKGLGe~~~~e~keyf~~~~~h~~~f~~~~~~~~~~i~laF~k~~~d~RK~Wl~~~~-----------~~~~l 671 (1465)
T PLN03237 603 TGWSIKYYKGLGTSTAKEGKEYFKNLGKHKKDFVWEDEQDGDAIELAFSKKKIEARKNWLRQYE-----------PGTHL 671 (1465)
T ss_pred CceeeEeeccCCCCCHHHHHHHHHhHHhceEEEEECCCCcHHHHHHHhCCccHHHHHHHHHhCC-----------CCccc
Confidence 4799999999999999999999999999999999999999999999999999999999999997 99999
Q ss_pred ccCcceeecHHHHHHHHHHHHHHhhccCCCCccccCCCCcceeeEeecccCCCCCceeeeeehhhhhhhccCCCCcchHH
Q psy11240 82 YTKTTKAITYTEFVNKELILFSNMDNERSIPSLCDGLKPGSRKVLFTCLKRNDRREVKVAQLAGSVAEHSAYHHGEQSLM 161 (363)
Q Consensus 82 ~d~~~~~i~~~dfinkeli~yS~~~~~RsIPsv~DGLKP~QRKILy~~~k~~~k~~~KvAql~G~Vse~~~YHHGe~Sl~ 161 (363)
|++.+.|+|+||||+|||+|||+|+.||||||+||||||||||||+||++++++++|||||+|+|+|||+|||||+|||
T Consensus 672 -d~~~~~i~~~dfinkeli~ySm~~i~RAIP~v~DGLKPvQRkILya~~k~~~~~~~KvAqlvG~V~e~~~YHHGd~Sly 750 (1465)
T PLN03237 672 -DQTQKDVKYSDFVNKELILFSMADLQRSIPSMVDGLKPGQRKILFCSFKRNFVKEAKVAQLSGYVSEHSAYHHGEQSLA 750 (1465)
T ss_pred -cCCCCcccHHHHHHHHHHHHHHHHHhccCCchhcCCCchHhHHHHHHHhcCCccccchhhhHHHHhhhccCCCcHHHHH
Confidence 8999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhccccccccccccccCCCCCccc----------eeec--CC------------------------------C-C
Q psy11240 162 STIINLAQNFVGSNNINLLQPIGQFGTFL----------FIFE--ST------------------------------N-L 198 (363)
Q Consensus 162 ~tiV~MAQdfvGSnNi~Ll~p~G~FGsr~----------Yi~t--s~------------------------------P-i 198 (363)
+|||+||||||||||+|||+|+||||||+ |||| || | |
T Consensus 751 ~tiV~MAQdfvGsnnipLl~p~GnFGSR~~gG~daAA~RYietrLs~ia~~lf~~~Dd~~l~~~n~Dg~~iEP~~y~pii 830 (1465)
T PLN03237 751 STIIGMAQDFVGSNNINLLLPNGQFGTRLQGGKDHASARYIFTRLSPITRFLFPKDDDILLDYLNEDGQSIEPTWYMPII 830 (1465)
T ss_pred HHHHHHhhccccccccceeecCCCCCCCCCCCCcccccccceechhHHHHHHhccCCccccCccCCCCcccCCceecCCC
Confidence 99999999999999999999999999986 9999 44 6 9
Q ss_pred ccccccCCCcccccc-----------------------------------------------------------------
Q psy11240 199 SGAVVNALDFGSGGW----------------------------------------------------------------- 213 (363)
Q Consensus 199 P~vLvNGa~GIgtG~----------------------------------------------------------------- 213 (363)
||||||||+||||||
T Consensus 831 P~lLVNGa~GIatG~sT~IPphNp~eVi~~i~~~i~~e~~~~~~P~~~gf~G~I~~~~~t~g~g~~~~rG~~~~~~~~~i 910 (1465)
T PLN03237 831 PTVLVNGAEGIGTGWSTFIPNYNPRDIVANIRRLLNGESMEPMHPWYRGFKGTIEKTASKEGGCTYTITGLYEEVDETTL 910 (1465)
T ss_pred cceeecCCcceecccccCCCCCCHHHHHHHHHHHhcCCCcCCCCCeecCCCceEeEhhhcCCCceEEEEEEEEEecCCeE
Confidence 999999999999999
Q ss_pred ----------c-------------------cccccccccCCCceeEEEEEeCCCCChHHHHHhHhhhccceeeeccceEE
Q psy11240 214 ----------R-------------------FESNDYKEYHTDTTVKFVVTMSPDKLHKAEMDGLHKVFKLQTTLAISSMC 264 (363)
Q Consensus 214 ----------T-------------------~~I~d~~d~~~~~~v~f~I~l~~~~~~~~~~~~L~k~fkL~~s~~~~nm~ 264 (363)
| ..|.||+|+|++++|+|+|+|+++.+++++.++|+|.|+|+++++++||+
T Consensus 911 ~ITElP~~~~t~~y~~~le~i~~~~~~~k~~~I~d~~d~s~~~~vr~vI~lk~~~~~~~~~~~L~k~~kL~~s~~~~nm~ 990 (1465)
T PLN03237 911 RITELPIRRWTDDYKEFLESLKTDNNKNKDPFIKDVKAYNDDTTVHFEVILSEENMLAAKQEGLLKKFKLTTTISTSNMH 990 (1465)
T ss_pred EEEeCCCeecchHHHHHHHHHHHHHhccCcCceeechhccCCceEEEEEEeccchhHHHHHHHHHHhhcCcceeceeEEE
Confidence 0 05889999999999999999999999999999999999999999999999
Q ss_pred EEecCCcccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchhHHHHHHhhhcceeEcccchHHHHHHHHHcC
Q psy11240 265 AFDRYGVLTKFDTTNQILKEFYAVRLEYYAKRKDYLEGVLGAEALKLTNQARFIVEKCDGDLRIENRKKKEMIAELIKRK 344 (363)
Q Consensus 265 lfd~~g~i~ky~~~~eIl~~F~~~Rl~~y~kRk~~~l~~l~~~~~~l~nk~rFI~~vi~~~i~i~~k~k~~l~~~L~~~~ 344 (363)
|||++|++++|.++.+||++||++|+++|++|+++++++++.++.+++||++||++||+|+|+|.+++|++|+++|.++|
T Consensus 991 l~d~~G~i~k~~~~~~Il~~F~~~Rl~~Y~kRk~~~~~~~~~el~k~~~k~~fI~~vi~g~i~i~~k~k~~l~~~L~~~g 1070 (1465)
T PLN03237 991 LFDSKGVIKKYDTPEQILEEFFHLRLEYYEKRKEVLLKNLEFELLKLENKVRFILAVVDGEIIVNNRKKADLVEELRQKG 1070 (1465)
T ss_pred EEcCCCCcceeCCHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCceEEccCCHHHHHHHHHHcC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCchhhhh
Q psy11240 345 YDSDPVKSWKM 355 (363)
Q Consensus 345 f~~~~~~~~k~ 355 (363)
|+++|..+|..
T Consensus 1071 f~~~~~~~~~~ 1081 (1465)
T PLN03237 1071 FTPFPKKAKSV 1081 (1465)
T ss_pred CCccchhhccc
Confidence 99999887754
No 2
>PTZ00108 DNA topoisomerase 2-like protein; Provisional
Probab=100.00 E-value=3e-112 Score=939.80 Aligned_cols=341 Identities=51% Similarity=0.799 Sum_probs=330.0
Q ss_pred CCcceeeccccccCCcHHHHHHhhhhhcceeeeEEcCCCchHHHHHhcCCcchhhHHHHHHHhHHHhhhhhccCCccccc
Q psy11240 2 NTIHDVMIAGLGTSTSKEAKEYFSNMERHRILFKYSGDNDDAHIRMAFSKKLVDERKTWLTTWMEECRRRKEMGIGEDYL 81 (363)
Q Consensus 2 ~~w~iKYyKGLGTst~~eakeyF~~l~~h~~~f~~~~~~d~~~i~~aF~kk~~d~RK~Wl~~~~~~~~~~~~~~~~~~~l 81 (363)
++|+||||||||||+++|++|||.|+++|++.|.|.++.++++|+|||+|+++++||+||.+|. ||+||
T Consensus 585 ~~~~IkyyKGLGe~~~~e~~eyf~~~~r~~i~~~~~~~~~~~~idl~fgk~~a~~RK~wi~~~~-----------~~~~~ 653 (1388)
T PTZ00108 585 KGWKIKYYKGLGTSTDKEGKEYFSNIDKHRIRFVYVDDSDDDSIDLAFSKKRVEDRKEWITNYK-----------GGTYV 653 (1388)
T ss_pred CCCccccccchhhcCHHHHHHHhcccCceEEEEecCCccHHHHHHHHhCCCChHHHHHHHHhhC-----------ccccc
Confidence 4799999999999999999999999999999999998889999999999999999999999997 89999
Q ss_pred ccCcceeecHHHHHHHHHHHHHHhhccCCCCccccCCCCcceeeEeecccCCCCCceeeeeehhhhhhhccCCCCcchHH
Q psy11240 82 YTKTTKAITYTEFVNKELILFSNMDNERSIPSLCDGLKPGSRKVLFTCLKRNDRREVKVAQLAGSVAEHSAYHHGEQSLM 161 (363)
Q Consensus 82 ~d~~~~~i~~~dfinkeli~yS~~~~~RsIPsv~DGLKP~QRKILy~~~k~~~k~~~KvAql~G~Vse~~~YHHGe~Sl~ 161 (363)
|++.+.|+|+||||+|||+|||+||.||||||+||||||||||||+||++++++++|||||+|+|||||+|||||+|||
T Consensus 654 -d~~~~~i~~~dFvnkEli~FS~~d~~RaIP~v~DGLKP~QRkILy~~~k~nl~~~~KvAql~G~V~e~~~YHHGe~Sl~ 732 (1388)
T PTZ00108 654 -DHSKKKLTYSDFVNKELILFSIADNERSIPSLVDGLKPGQRKILFACFKRNLKNEIKVAQLSGYVSEHSAYHHGEQSLQ 732 (1388)
T ss_pred -cccCceecHHHhhhHHHHHHhhhhcccCCCccccCCCchhhHHHHHHHHcCCCccchHHHHHHHHHhhccCCCChhHHH
Confidence 8999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhccccccccccccccCCCCCccc----------eeec--CC------------------------------C-C
Q psy11240 162 STIINLAQNFVGSNNINLLQPIGQFGTFL----------FIFE--ST------------------------------N-L 198 (363)
Q Consensus 162 ~tiV~MAQdfvGSnNi~Ll~p~G~FGsr~----------Yi~t--s~------------------------------P-i 198 (363)
+|||+||||||||||+|||+|+||||||+ |||| || | |
T Consensus 733 ~tiV~MAQ~fvGsnni~Ll~p~GnFGsr~~gG~daAA~RYi~trLs~~ar~lf~~~Dd~~l~y~~~Dg~~~EP~~y~pii 812 (1388)
T PTZ00108 733 QTIVGMAQNFVGSNNINLLYPCGQFGSRLQGGKDHAAARYIFTKLSKITRYIFPEEDDPILDYLEDDGQSVEPFYYVPII 812 (1388)
T ss_pred HHHHHHhcccchhccceeEecCCCcCCCCCCCCcchhhhhhhhhhhHHHHHHhcccccCccCccCCCCCccCCeeecCcc
Confidence 99999999999999999999999999995 9999 43 6 9
Q ss_pred ccccccCCCcccccc---------------------------------------------------------------c-
Q psy11240 199 SGAVVNALDFGSGGW---------------------------------------------------------------R- 214 (363)
Q Consensus 199 P~vLvNGa~GIgtG~---------------------------------------------------------------T- 214 (363)
||||||||+|||||| |
T Consensus 813 P~lLvNGa~GIatG~sT~IP~hNp~EVi~~i~~~l~~e~~~~~~P~~~gf~G~i~~~g~G~~~~rG~~~~~~~~~i~ITE 892 (1388)
T PTZ00108 813 PMVLVNGAEGIGTGFSTSIPNYNPLDIIDNLRRRLNGEEVRPLVPWYRGFKGTIERNPKGKFISKGIYEKVPDGTVEITE 892 (1388)
T ss_pred chhhccCCceeEeeeecCCCCCCHHHHHHHHHHHHcCCchhhhcCcCCCCCcEEEecCCeEEEEEEEEEEecCCeEEEEe
Confidence 999999999999999 0
Q ss_pred ----------------------cccccccccCCCceeEEEEEeCCCCChHHHHHhHhhhccceeeeccceEEEEecCCcc
Q psy11240 215 ----------------------FESNDYKEYHTDTTVKFVVTMSPDKLHKAEMDGLHKVFKLQTTLAISSMCAFDRYGVL 272 (363)
Q Consensus 215 ----------------------~~I~d~~d~~~~~~v~f~I~l~~~~~~~~~~~~L~k~fkL~~s~~~~nm~lfd~~g~i 272 (363)
..|++|+|+||+++|+|+|+|+++.++++++++|+|.|+|+++|+++||+|||++|++
T Consensus 893 LP~~~~t~~y~e~l~~~~~~~~~~I~d~~d~s~~~~v~~~I~l~~~~~~~~~~~~L~k~~kL~~s~~~~Nm~~~d~~g~i 972 (1388)
T PTZ00108 893 LPIGKWTEDYKEFLESETLKEKDVIVDYRDYSTANTVHFTVKLNDGVLEQWEEEGIEKVFKLKSTISTTNMVLFDENGKI 972 (1388)
T ss_pred CCCcccHHHHHHHHHHHHhcCCCcceeeeeccCCCceEEEEEECCCcCHHHHHHHHHHhcCCceeecceeEEEEeCCCCc
Confidence 1799999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchhHHHHHHhhhcceeEcccchHHHHHHHHHcCCCCCCchh
Q psy11240 273 TKFDTTNQILKEFYAVRLEYYAKRKDYLEGVLGAEALKLTNQARFIVEKCDGDLRIENRKKKEMIAELIKRKYDSDPVKS 352 (363)
Q Consensus 273 ~ky~~~~eIl~~F~~~Rl~~y~kRk~~~l~~l~~~~~~l~nk~rFI~~vi~~~i~i~~k~k~~l~~~L~~~~f~~~~~~~ 352 (363)
++|.++.+||++||++|+++|++|++|+|+++++++++|+|++|||++||+|+|+|.+++|++|+++|.++||++++...
T Consensus 973 ~~~~~~~~Il~~f~~~Rl~~y~kR~~~~l~~l~~~~~~l~~~~rFI~~vi~~~i~i~~~~k~~l~~~L~~~gf~~~~~~~ 1052 (1388)
T PTZ00108 973 KKYSDALDILKEFYLVRLDLYKKRKEYLLGKLERELARLSNKVRFIKHVINGELVITNAKKKDLVKELKKLGYVRFKDII 1052 (1388)
T ss_pred ceeCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCeeEEccCCHHHHHHHHHHcCCCccchhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999998754
Q ss_pred hh
Q psy11240 353 WK 354 (363)
Q Consensus 353 ~k 354 (363)
+.
T Consensus 1053 ~~ 1054 (1388)
T PTZ00108 1053 KK 1054 (1388)
T ss_pred hh
Confidence 33
No 3
>PLN03128 DNA topoisomerase 2; Provisional
Probab=100.00 E-value=3.9e-112 Score=930.10 Aligned_cols=341 Identities=51% Similarity=0.792 Sum_probs=329.9
Q ss_pred CCcceeeccccccCCcHHHHHHhhhhhcceeeeEEcCCCchHHHHHhcCCcchhhHHHHHHHhHHHhhhhhccCCccccc
Q psy11240 2 NTIHDVMIAGLGTSTSKEAKEYFSNMERHRILFKYSGDNDDAHIRMAFSKKLVDERKTWLTTWMEECRRRKEMGIGEDYL 81 (363)
Q Consensus 2 ~~w~iKYyKGLGTst~~eakeyF~~l~~h~~~f~~~~~~d~~~i~~aF~kk~~d~RK~Wl~~~~~~~~~~~~~~~~~~~l 81 (363)
++|+||||||||||+++|++|||+||++|++.|.|.+++|+++|||||+|++||+||+||++|. ||+||
T Consensus 578 ~~~~ikyyKGLGe~~~~e~~e~f~~~~~~~~~f~~~~~~~~~~i~~aF~k~~~~~RK~Wl~~~~-----------~~~~~ 646 (1135)
T PLN03128 578 KGWTIKYYKGLGTSTSEEAKEYFSNLDIHKKEFLWQSDEDGDLIDMAFSKKRVEDRKIWLNNYE-----------PGTFL 646 (1135)
T ss_pred CCccceeecccccCCHHHHHHHHHhHHHhEEEEEeCCCCcHHHHHHhcCCCcHHHHHHHHHhCC-----------CCccc
Confidence 4799999999999999999999999999999999999999999999999999999999999997 99999
Q ss_pred ccCcceeecHHHHHHHHHHHHHHhhccCCCCccccCCCCcceeeEeecccCCCCCceeeeeehhhhhhhccCCCCcchHH
Q psy11240 82 YTKTTKAITYTEFVNKELILFSNMDNERSIPSLCDGLKPGSRKVLFTCLKRNDRREVKVAQLAGSVAEHSAYHHGEQSLM 161 (363)
Q Consensus 82 ~d~~~~~i~~~dfinkeli~yS~~~~~RsIPsv~DGLKP~QRKILy~~~k~~~k~~~KvAql~G~Vse~~~YHHGe~Sl~ 161 (363)
|++.+.|+|+||||+|||+|||+|+.|||||++||||||||||||+||+++++.++|||||+|+|+|+|+|||||+|||
T Consensus 647 -d~~~~~i~~~dfi~~eli~fs~~~~~RaiP~v~DGLKPvQRkILy~~~~~~~~~~~Kva~l~G~V~e~~~YHHGd~Sl~ 725 (1135)
T PLN03128 647 -DQTGNGISYSDFINKELILFSQADLARSIPSMVDGLKPSQRKVLFACFKRNLKSEIKVAQLSGYVAEHSAYHHGEASLA 725 (1135)
T ss_pred -cCCCccccHHHHHHHHHHHHHHHHhcCCCCchhcCCCchhhHHHHHHHhcCCCccchHHHHHHHHhhccCCCCChHHHH
Confidence 8999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhccccccccccccccCCCCCccc----------eeec--CC------------------------------C-C
Q psy11240 162 STIINLAQNFVGSNNINLLQPIGQFGTFL----------FIFE--ST------------------------------N-L 198 (363)
Q Consensus 162 ~tiV~MAQdfvGSnNi~Ll~p~G~FGsr~----------Yi~t--s~------------------------------P-i 198 (363)
+|||+||||||||||+|||+|+||||||+ |||| || | |
T Consensus 726 ~tiV~mAQ~f~Gsnn~~Ll~~~GnFGSr~~~G~~aAa~RYi~~rLs~ia~~lf~~~dd~~l~y~~~Dg~~~EP~~~~p~i 805 (1135)
T PLN03128 726 STIIGMAQDFVGSNNINLLTPSGQFGTRLQGGKDAASARYIFTRLSPITRALFPKDDDVLLNYLNEDGQSIEPEWYCPII 805 (1135)
T ss_pred HHHHHHhhhccccccceeeccCCCCCCCCCCCChhhhhhHHhhhhhHHHHHHhccccccccCCcCCCccccCCceecccc
Confidence 99999999999999999999999999986 9998 43 6 9
Q ss_pred ccccccCCCcccccc-----------------------------------------------------------------
Q psy11240 199 SGAVVNALDFGSGGW----------------------------------------------------------------- 213 (363)
Q Consensus 199 P~vLvNGa~GIgtG~----------------------------------------------------------------- 213 (363)
||||||||+||||||
T Consensus 806 P~lLvNGs~GIa~G~aT~IPphN~~evi~~~~~~i~~~~~~~l~p~~~g~~G~i~~~~~tg~g~~~~~g~~~~~~~~~i~ 885 (1135)
T PLN03128 806 PMVLVNGSEGIGTGWSTFIPNYNPRDIIANIRRLLRGEELEPMHPWYRGFKGTITEVSTSRSGSYTVTGIIEQIGDTTIR 885 (1135)
T ss_pred hhhhccCCcccccccccCCCCCCHHHHHHHHHHHHcCCCHHHHHhhccCCCceEEEccccCCceEEEEEEEEEecCcEEE
Confidence 999999999999999
Q ss_pred ---------c------------------cccccccccCCCceeEEEEEeCCCCChHHHHHhHhhhccceeeeccceEEEE
Q psy11240 214 ---------R------------------FESNDYKEYHTDTTVKFVVTMSPDKLHKAEMDGLHKVFKLQTTLAISSMCAF 266 (363)
Q Consensus 214 ---------T------------------~~I~d~~d~~~~~~v~f~I~l~~~~~~~~~~~~L~k~fkL~~s~~~~nm~lf 266 (363)
| ..|+||+|+|++++|+|+|+|+++.+++++.++|+|.|+|+++|+++||+||
T Consensus 886 ItElP~~~~~~~y~~~l~~l~~~~~k~~~~I~d~~d~s~~~~v~~~i~l~~~~~~~~~~~~l~k~~~L~~~~~~~nm~l~ 965 (1135)
T PLN03128 886 ITELPVRKWTQDYKEFLEALLTGTKKKEPEIKDFKENHTDTTVHFTVTLSEEKMARALAEGLEKKFKLSTTISTSNMHLF 965 (1135)
T ss_pred EEecCCccchHHHHHHHHHHHhhhccCCcceeeeeeccCCCceEEEEEECcchhHHHHHHHHHhhcceehhcCceEEEEE
Confidence 0 1688999999999999999999999999999999999999999999999999
Q ss_pred ecCCcccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchhHHHHHHhhhcceeEcccchHHHHHHHHHcCCC
Q psy11240 267 DRYGVLTKFDTTNQILKEFYAVRLEYYAKRKDYLEGVLGAEALKLTNQARFIVEKCDGDLRIENRKKKEMIAELIKRKYD 346 (363)
Q Consensus 267 d~~g~i~ky~~~~eIl~~F~~~Rl~~y~kRk~~~l~~l~~~~~~l~nk~rFI~~vi~~~i~i~~k~k~~l~~~L~~~~f~ 346 (363)
|++|++++|.|+++||++|++||+++|+||++|++++++.++++|+||++||+++++++|+|.+++|++++++|.++||+
T Consensus 966 d~~~~i~ky~~~~~il~~f~~~R~~~y~kRk~~~l~~~~~~~~~l~~k~~fi~~v~~~~~~i~~~~k~~~~~~L~~~~f~ 1045 (1135)
T PLN03128 966 DKDGKIKKYDSPEDILEEFFHLRLDLYVKRKEVLLENLEYELKKLDNKARFILAVVKGEIVVNNRKRAELLAELEEKGFD 1045 (1135)
T ss_pred CCCCcccCCCCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHhHHHhheecceEEEcCCCHHHHHHHHHHcCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCchhhh
Q psy11240 347 SDPVKSWK 354 (363)
Q Consensus 347 ~~~~~~~k 354 (363)
+++...+.
T Consensus 1046 ~~~~~~~~ 1053 (1135)
T PLN03128 1046 KFPKTAKI 1053 (1135)
T ss_pred Ccchhhhh
Confidence 98765544
No 4
>PHA02592 52 DNA topisomerase II medium subunit; Provisional
Probab=100.00 E-value=3.4e-81 Score=632.54 Aligned_cols=256 Identities=28% Similarity=0.430 Sum_probs=242.5
Q ss_pred ceeecHHHHHHHHHHHHHHhh-ccCCCCccccCCCCcceeeEeecc---cCCCCCceeeeeehhhhhhhccCCCCcchHH
Q psy11240 86 TKAITYTEFVNKELILFSNMD-NERSIPSLCDGLKPGSRKVLFTCL---KRNDRREVKVAQLAGSVAEHSAYHHGEQSLM 161 (363)
Q Consensus 86 ~~~i~~~dfinkeli~yS~~~-~~RsIPsv~DGLKP~QRKILy~~~---k~~~k~~~KvAql~G~Vse~~~YHHGe~Sl~ 161 (363)
..+++|+||||+||+.|||++ +.|||||++||||||||||||+|+ ++++++++|||||+|+|+++ +|||||+|||
T Consensus 3 ~~~~~i~~~v~~~~i~ya~~vI~~RAiP~v~DGLKPvQRrILyam~~~~~~~~~~~~KvA~lvG~v~~~-~YHHGd~Sly 81 (439)
T PHA02592 3 LKERSLKSIVNNEALEYAMYTVEERAIPNLIDGLKPVQRFVIHRALEYAKGNKEKFDKVAAIAGGVADL-GYHHGETSAQ 81 (439)
T ss_pred ceeccHHHHHHHHHHHHHHHHhhcccCCccccCCCcchhhhhHhHHhhCCCCCCcchhhHHHHHHHhcc-cCCCchHHHH
Confidence 457999999999999999998 999999999999999999999999 55678999999999999888 9999999999
Q ss_pred HHHHHhhccccccccccccccCCCCCccc--------eeec--CC---------------------------C-Cccccc
Q psy11240 162 STIINLAQNFVGSNNINLLQPIGQFGTFL--------FIFE--ST---------------------------N-LSGAVV 203 (363)
Q Consensus 162 ~tiV~MAQdfvGSnNi~Ll~p~G~FGsr~--------Yi~t--s~---------------------------P-iP~vLv 203 (363)
+|||+||||| |||+|||+|+||||||+ |||| || | ||||||
T Consensus 82 ~tiV~MAQ~f--snn~pLl~~~GnFGs~~G~~aAA~RYte~rLs~~a~~l~~d~D~~~n~dd~~~~eP~~y~P~iP~lLv 159 (439)
T PHA02592 82 DAGALMANTW--NNNIPLLDGQGNFGSRLVQKAAAARYIFARVHDNFRKIYKDEDLAPVHEDPEHIPPAFYLPIIPMVLL 159 (439)
T ss_pred HHHHHHhhhh--ccceeeEecCCCCCCCCCCCccchhhhhcchhHHHHHHhcccCCCcCCCCCcccCCcccccCCchhhc
Confidence 9999999999 99999999999999998 9988 43 6 899999
Q ss_pred cCCCcccccc---------------------------------------------------------------c------
Q psy11240 204 NALDFGSGGW---------------------------------------------------------------R------ 214 (363)
Q Consensus 204 NGa~GIgtG~---------------------------------------------------------------T------ 214 (363)
|||+|||||| |
T Consensus 160 NG~~GIavG~sT~IPphN~~evi~~~~~~l~~~~~~~~~Pdfpg~~G~i~~tg~g~~~~rg~~~~~~~~~i~ItElP~~~ 239 (439)
T PHA02592 160 NGVSGIATGYATNILPHSPKSVIKAVLAALNGKDITEPKVQFPEFKGEVVEIEPGSYEIRGTYELNGKTKLHITEIPVKY 239 (439)
T ss_pred cCCcceeeeeecCCCCCCHHHHHHHHHHHhcCCCCCCCCCcCCCCCCeEEEcCCceEEEEEEEEEeCCCEEEEEeCCCcc
Confidence 9999999999 0
Q ss_pred ---------------cccccccccCCCceeEEEEEeCCCCChHHHHHhHhhhccceeeeccceEEEEecCCcccccCCHH
Q psy11240 215 ---------------FESNDYKEYHTDTTVKFVVTMSPDKLHKAEMDGLHKVFKLQTTLAISSMCAFDRYGVLTKFDTTN 279 (363)
Q Consensus 215 ---------------~~I~d~~d~~~~~~v~f~I~l~~~~~~~~~~~~L~k~fkL~~s~~~~nm~lfd~~g~i~ky~~~~ 279 (363)
..|++|.| |++++|+|+|+++++..++.+.++|++.|+|+++|++ ||++||++|+|++|.|+.
T Consensus 240 ~~~~~~~~i~~l~~~~~i~~i~d-s~~~~v~i~I~lk~~~~~~~~~~~L~k~~~L~~~~~~-Nm~~~d~~g~~~~~~~~~ 317 (439)
T PHA02592 240 DRETYVAVLDPLEEKGKIVSYDD-CTEDGFRFKVTLKREENEEATHEKIMKDFGLIERVSQ-NITVINENGKLKVYENAE 317 (439)
T ss_pred cHHHHHHHHHHHHhcCCcCCccc-CCCCceEEEEEECCCCCHHHHHHHHHHhcCchheeee-eEEEEecCCeeeecCCHH
Confidence 16889999 9999999999999999999999999999999999986 799999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchhHHHHHHhhhcceeEcccchHHHHHHHHHcCCC
Q psy11240 280 QILKEFYAVRLEYYAKRKDYLEGVLGAEALKLTNQARFIVEKCDGDLRIENRKKKEMIAELIKRKYD 346 (363)
Q Consensus 280 eIl~~F~~~Rl~~y~kRk~~~l~~l~~~~~~l~nk~rFI~~vi~~~i~i~~k~k~~l~~~L~~~~f~ 346 (363)
|||++|++||+++|+||++|+|+++++++++|.++++||.+||++.+.+.+++++++.+.|.+.+|.
T Consensus 318 ~Il~~f~~~R~~~~~kR~~~~l~k~~~r~~~l~~~~~fI~~vi~~~~~~~~~~~~~~~~~l~~~~~~ 384 (439)
T PHA02592 318 DLIRDFVEIRKTYVQKRIQYEIKETEEAFDLALAKAEFIKRVIAGEIVLQGKTRSELTEELSDNKDF 384 (439)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHcCCC
Confidence 9999999999999999999999999999999999999999999999999888999999999887764
No 5
>smart00434 TOP4c DNA Topoisomerase IV. Bacterial DNA topoisomerase IV, GyrA, ParC
Probab=100.00 E-value=3e-76 Score=597.98 Aligned_cols=257 Identities=32% Similarity=0.446 Sum_probs=231.5
Q ss_pred ecHHHHHHHHHHHHHHh-hccCCCCccccCCCCcceeeEeecccCCCCC-ceeeeeehhhhhhhccCC-CCcchHHHHHH
Q psy11240 89 ITYTEFVNKELILFSNM-DNERSIPSLCDGLKPGSRKVLFTCLKRNDRR-EVKVAQLAGSVAEHSAYH-HGEQSLMSTII 165 (363)
Q Consensus 89 i~~~dfinkeli~yS~~-~~~RsIPsv~DGLKP~QRKILy~~~k~~~k~-~~KvAql~G~Vse~~~YH-HGe~Sl~~tiV 165 (363)
++|+|||++||+.|||+ ++.|||||++||||||||||||+||+++++. +.||++++|++++||+|| |||+|+|+|||
T Consensus 1 ~~~~~~~~~~~i~ya~~vi~~RaiP~v~DGLKPvqRrILyam~~~~~~~~~~~~k~a~~~g~~~~~YHpHGd~Siy~aiV 80 (445)
T smart00434 1 IDIEDFINKEYLDYSMSVINGRAIPDVRDGLKPVQRRILYAMFKRGLTPDEPKVKSARGVGDVMGKYHPHGDSSLYDAIV 80 (445)
T ss_pred CCHHHHHHHHHHHHHHHHHhccCCCccccCCCchhhHHHHHHHHcCCCCCCceeEEEEEEEeeccCCCCCchHHHHHHHH
Confidence 58999999999999996 8999999999999999999999999998866 555555555555599999 99999999999
Q ss_pred HhhccccccccccccccCCCCCcc-c--------eeec--CC-------------------------------C-Ccccc
Q psy11240 166 NLAQNFVGSNNINLLQPIGQFGTF-L--------FIFE--ST-------------------------------N-LSGAV 202 (363)
Q Consensus 166 ~MAQdfvGSnNi~Ll~p~G~FGsr-~--------Yi~t--s~-------------------------------P-iP~vL 202 (363)
+||||| +||+|||+|+|||||| + |||| || | |||||
T Consensus 81 ~mAQ~f--~~n~pLl~~~GnFGs~~~g~~aAA~RYte~rLs~~a~~l~~~~d~~~v~~~~n~Dg~~~EP~~lp~~iP~lL 158 (445)
T smart00434 81 RMAQDF--SNNYPLLDGQGNFGSRLDGDDAAAMRYTETRLSPLARELLPDIDKDTVDFVPNYDGQEIEPTVLPPIIPNLL 158 (445)
T ss_pred HHhccc--ccccceEeCCCCCCCCCCCCcccchHHHHHhHHHHHHHHHhhcCcccccCCcCCCccccCCccccccCCeee
Confidence 999999 5999999999999999 4 9988 43 5 99999
Q ss_pred ccCCCcccccc--------------------------------------------------------------------c
Q psy11240 203 VNALDFGSGGW--------------------------------------------------------------------R 214 (363)
Q Consensus 203 vNGa~GIgtG~--------------------------------------------------------------------T 214 (363)
||||+|||||| |
T Consensus 159 vNGs~GIavG~aT~IpphN~~evi~~~~~~l~~~~~~~~~l~~~~~~pdF~~g~~~~~~~~~~~rg~~~~~~~~~~ivIt 238 (445)
T smart00434 159 VNGSSGIAVGMATNIPPHNLREVIDAVRRLIDNPEASIDELMMIPWGPDFPTGGEIIGPGSYVVRGKIEIEDGRNTIVIT 238 (445)
T ss_pred eecCcceeeeeecCCCCCCHHHHHHHHHHHhCCCCCCHHHHhcCCcCCCCCCeeEEecCCeEEEEEEEEEEcCCceEEEE
Confidence 99999999999 0
Q ss_pred ------------------------cccccccccC-CCceeEEEEEeCCCCChHHHHHhHhhhccceeeeccceEEEEecC
Q psy11240 215 ------------------------FESNDYKEYH-TDTTVKFVVTMSPDKLHKAEMDGLHKVFKLQTTLAISSMCAFDRY 269 (363)
Q Consensus 215 ------------------------~~I~d~~d~~-~~~~v~f~I~l~~~~~~~~~~~~L~k~fkL~~s~~~~nm~lfd~~ 269 (363)
+.|.+.+|++ ++++|+|+|+++++.++++++++|+|.|+|+++|++|||++++ +
T Consensus 239 ElP~~~~~~~~~e~I~~lv~~~ki~~i~~~~des~~~~~vrivI~lk~~~~~~~~~~~L~k~t~Lq~s~~~n~~~l~~-~ 317 (445)
T smart00434 239 ELPYQVNKAKLIEKIAELVKDKKIEGIIDVRDESHDRTGVRIVIELKRGAMAEVVLNGLYKLTKLQSTFSINMLALFD-N 317 (445)
T ss_pred eCCCcccHHHHHHHHHHHHhcCCCCcceehhhccCCCCceEEEEEECCCcCHHHHHHHHHHhcCCeeeeceeEEEEec-C
Confidence 0345556655 8899999999999999999999999999999999999999997 8
Q ss_pred CcccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchhHHHHHHhhhcceeEcccchHHHHHHHHHcCCCCCC
Q psy11240 270 GVLTKFDTTNQILKEFYAVRLEYYAKRKDYLEGVLGAEALKLTNQARFIVEKCDGDLRIENRKKKEMIAELIKRKYDSDP 349 (363)
Q Consensus 270 g~i~ky~~~~eIl~~F~~~Rl~~y~kRk~~~l~~l~~~~~~l~nk~rFI~~vi~~~i~i~~k~k~~l~~~L~~~~f~~~~ 349 (363)
|+|++| ++.|||++|+++|+++|+||++|+|++++ +..++.++.+||..++.++|+...++++++.+++++.+|.+++
T Consensus 318 g~p~~~-~l~~iL~~f~~~R~~~~~rR~~~~l~k~~-~~r~~~~~~~fi~~~~~d~ii~~ir~~~~~~~~~~~~l~~~f~ 395 (445)
T smart00434 318 GKPKKY-NLKEILKEFLDHRLEVYTRRKEYLLGKLE-AERLHILEGLFIALSIIDEIIVLIRSSKDLAKEAKELLMERFE 395 (445)
T ss_pred CeeEEe-cHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHhhcchHHHHhhccchhHHHHHHhCCccCC
Confidence 999999 66799999999999999999999999999 5556688999999999999988889999999999999999886
Q ss_pred c
Q psy11240 350 V 350 (363)
Q Consensus 350 ~ 350 (363)
.
T Consensus 396 ~ 396 (445)
T smart00434 396 L 396 (445)
T ss_pred C
Confidence 4
No 6
>cd00187 TOP4c DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA topology by catalysing the concerted breakage and rejoining of DNA strands during normal cellular growth.
Probab=100.00 E-value=8.8e-73 Score=572.51 Aligned_cols=236 Identities=35% Similarity=0.496 Sum_probs=216.6
Q ss_pred ccCCCCccccCCCCcceeeEeecccCCCC---CceeeeeehhhhhhhccCCCCcchHHHHHHHhhccccccccccccccC
Q psy11240 107 NERSIPSLCDGLKPGSRKVLFTCLKRNDR---REVKVAQLAGSVAEHSAYHHGEQSLMSTIINLAQNFVGSNNINLLQPI 183 (363)
Q Consensus 107 ~~RsIPsv~DGLKP~QRKILy~~~k~~~k---~~~KvAql~G~Vse~~~YHHGe~Sl~~tiV~MAQdfvGSnNi~Ll~p~ 183 (363)
+.|||||++||||||||||||+|++++++ +++|||||+|+|+++. |||||+|+|+|||+||||| |||+|||+|+
T Consensus 1 ~~RAiPdv~DGLKPvqRrILyam~~~~~~~~~~~~K~A~lvG~v~g~~-hpHGd~Siy~aiV~MAQ~f--s~n~pLldg~ 77 (445)
T cd00187 1 NGRALPDVRDGLKPVQRRILYAMFKRGLTPDKPEKKVARLVGDVAGKY-HPHGDSSLYDTIVRMAQDF--SNNIPLLDPQ 77 (445)
T ss_pred CCCCCCchhcCCCchHHHHHHHHHHhCCCCCCCceeehhhhhhHhhcc-CCCchHHHHHHHHHHhhhc--cccceeEeCC
Confidence 57999999999999999999999998876 9999999999997665 6699999999999999999 9999999999
Q ss_pred CCCCccc--------eeec--CC-------------------------------C-CccccccCCCcccccc--------
Q psy11240 184 GQFGTFL--------FIFE--ST-------------------------------N-LSGAVVNALDFGSGGW-------- 213 (363)
Q Consensus 184 G~FGsr~--------Yi~t--s~-------------------------------P-iP~vLvNGa~GIgtG~-------- 213 (363)
||||||+ |||| || | |||||||||+||||||
T Consensus 78 GnFGS~~Gd~aAA~RYte~rLs~~a~~l~~d~d~~~v~~~~n~Dg~~~EP~~lp~~iP~lLvNGs~GIavG~aT~IPphN 157 (445)
T cd00187 78 GNFGSRDGDDAAAMRYTETRLSPIARLLLPDIDDPTVDFVPNYDGQEVEPEVLPPIFPNLLVNGSSGIAVGMATNIPPHN 157 (445)
T ss_pred CCCCCCCCCcccchHHHhhhhhHHHHHHHhhcCccccccccCCCCCccCCccccccCCeeeeecCcceeeeeccCCCCCC
Confidence 9999998 9988 43 5 9999999999999999
Q ss_pred -------------------------------------------------------------------------c------
Q psy11240 214 -------------------------------------------------------------------------R------ 214 (363)
Q Consensus 214 -------------------------------------------------------------------------T------ 214 (363)
|
T Consensus 158 ~~evi~a~~~~l~~~~~~~~~l~~~~~~Pdfptgg~I~~~~~~~~~y~tG~g~~~~rg~~~~~~~~~~~~i~ItElP~~~ 237 (445)
T cd00187 158 LREVIDALRALIDNPEASIDELMEIIKGPDFPTGGIIEGRAGIREAYETGRGRYIIRGKYEIEDDEGRNTIEITELPYQV 237 (445)
T ss_pred HHHHHHHHHHHhcCCCCCHHHHhcCCCCCCCCCCCEEecChhHHHHhhcCCceEEEEEEEEEEccCCCceEEEEeCCCcc
Confidence 0
Q ss_pred ------------------cccccccccCCCceeEEEEEeCCCCChHHHHHhHhhhccceeeeccceEEEEecCCcccccC
Q psy11240 215 ------------------FESNDYKEYHTDTTVKFVVTMSPDKLHKAEMDGLHKVFKLQTTLAISSMCAFDRYGVLTKFD 276 (363)
Q Consensus 215 ------------------~~I~d~~d~~~~~~v~f~I~l~~~~~~~~~~~~L~k~fkL~~s~~~~nm~lfd~~g~i~ky~ 276 (363)
..|++|+|+|++++|+|+|+++++.+++.++++|++.|+|+++|++ ||++||++|+|++|
T Consensus 238 ~~~~~~e~i~~l~~~~k~~~I~~~~D~s~~~~vrivI~lk~~~~~~~~~~~L~k~t~L~~s~~~-Nm~~~~~~g~p~~~- 315 (445)
T cd00187 238 NKAKLKEKIAELVKDKKIEGISDVRDESDREGIRFVIELKRGAMAEVVLNGLYKVTKLQTTFGI-NMVAFDPNGRPKKL- 315 (445)
T ss_pred cHHHHHHHHHHHHhcCCCcccceeeeccCCCceEEEEEECCCccHHHHHHHHHHhcCCceeeee-eEEEEecCCeeEEe-
Confidence 0689999999999999999999999999999999999999999999 79999999999999
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchhHHHHHHhhhcceeEcccc---hHHHHHHHHHcCCCCC
Q psy11240 277 TTNQILKEFYAVRLEYYAKRKDYLEGVLGAEALKLTNQARFIVEKCDGDLRIENRK---KKEMIAELIKRKYDSD 348 (363)
Q Consensus 277 ~~~eIl~~F~~~Rl~~y~kRk~~~l~~l~~~~~~l~nk~rFI~~vi~~~i~i~~k~---k~~l~~~L~~~~f~~~ 348 (363)
|+.+||++|++||+++|+||++|+|+++++++|+|+|+++||..++ ..|.+.+.. |+.|++.|.++||...
T Consensus 316 ~l~~iL~~f~~~R~~~~~rR~~~~l~k~~~rl~il~g~~~~i~~id-~vi~~ir~s~~ak~~L~~~l~~~~~~~~ 389 (445)
T cd00187 316 NLKEILQEFLDHRLEVYTRRKEYELGKAEARLHILEGLLKAILNID-EVINLIRSSDEAKKALIEELEKLGFSEI 389 (445)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH-HHHHHHhccHHHHHHHHHHHHhcCCCHH
Confidence 9999999999999999999999999999999999999999999876 443433222 8999999988888753
No 7
>PF00521 DNA_topoisoIV: DNA gyrase/topoisomerase IV, subunit A; InterPro: IPR002205 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils []. Type IIA topoisomerases together manage chromosome integrity and topology in cells. Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively; this topoisomerase II forms a homodimer that is equivalent to the bacterial heterotetramer. There are four functional domains in topoisomerase II: domain 1 (N-terminal of gyrB) is an ATPase, domain 2 (C-terminal of gyrB) is responsible for subunit interactions (differs between eukaryotic and bacterial enzymes), domain 3 (N-terminal of gyrA) is responsible for the breaking-rejoining function through its capacity to form protein-DNA bridges, and domain 4 (C-terminal of gyrA) is able to non-specifically bind DNA []. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication []. Topoisomerase IV consists of two polypeptide subunits, parE and parC, where parC is homologous to gyrA and parE is homologous to gyrB. This entry represents subunit A (gyrA and parC) of bacterial gyrase and topoisomerase IV, and the equivalent C-terminal region in eukaryotic topoisomerase II composed of a single polypeptide. This subunit has DNA-binding capacity. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0005694 chromosome; PDB: 1ZVU_A 1AB4_A 1X75_A 3NUH_A 1BJT_A 1BGW_A 2RGR_A 3KSB_B 3FOE_B 2NOV_C ....
Probab=100.00 E-value=4.6e-72 Score=563.59 Aligned_cols=228 Identities=41% Similarity=0.656 Sum_probs=202.5
Q ss_pred CCCCccccCCCCcceeeEeeccc-CCC-CCceeeeeehhhhhhhccCC-CCcchHHHHHHHhhccccccccccccccCCC
Q psy11240 109 RSIPSLCDGLKPGSRKVLFTCLK-RND-RREVKVAQLAGSVAEHSAYH-HGEQSLMSTIINLAQNFVGSNNINLLQPIGQ 185 (363)
Q Consensus 109 RsIPsv~DGLKP~QRKILy~~~k-~~~-k~~~KvAql~G~Vse~~~YH-HGe~Sl~~tiV~MAQdfvGSnNi~Ll~p~G~ 185 (363)
|||||++||||||||||||+||+ ++. ++++|||||||+| ||+|| |||+|||+|||+|||||+| |+|||+|+||
T Consensus 1 RaiP~~~DGLKP~qRkil~~~~~~~~~~~~~~Kva~l~G~v--~~~YHpHGe~sl~~tiv~mAq~f~~--n~pll~~~Gn 76 (426)
T PF00521_consen 1 RAIPSVRDGLKPVQRKILYAMFKLRNPDKKEIKVAQLVGYV--MGKYHPHGESSLYDTIVRMAQDFVG--NYPLLDGQGN 76 (426)
T ss_dssp HHS-BTTTS--HHHHHHHHHHHHCCCTTSS-EEHHHHHHHH--HHHTSTSSHHHHHHHHHHCTSTTTT--SS-SEEEES-
T ss_pred CCCCccccCCChHHHHHHHHHHHHhhcccccceeeeehhhh--HhhhCCCcchhhhhhhhhhhhcccc--ccceeeCCCC
Confidence 89999999999999999999999 665 9999999999999 99999 9999999999999999977 9999999999
Q ss_pred CCccc---------eeec--CC-------------------------------C-CccccccCCCcccccc---------
Q psy11240 186 FGTFL---------FIFE--ST-------------------------------N-LSGAVVNALDFGSGGW--------- 213 (363)
Q Consensus 186 FGsr~---------Yi~t--s~-------------------------------P-iP~vLvNGa~GIgtG~--------- 213 (363)
||||+ |||| || | |||||||||+||||||
T Consensus 77 FGs~~~g~~~Aa~RYi~~rls~~~~~l~~~~d~~~l~~~~~~Dg~~~EP~~~~p~iP~vLvNG~~GIa~G~sT~Ip~hN~ 156 (426)
T PF00521_consen 77 FGSRLDGDKDAAMRYIETRLSKIARDLFPDIDDDTLDYVPNYDGSEIEPEVYPPIIPMVLVNGASGIAVGMSTNIPPHNP 156 (426)
T ss_dssp BSCTTTSCTBTTTTTCEEEE-HHHHHHCTTTTTTCS-EEEETTSSSEEESS---SS-HHHHHTEEEESSSEEEEE--B-H
T ss_pred cccccCCCCCCccceEEEechHhHHHHHhhhcccccccCcCccccccchHHhhhcCcHHhccCCcchhhhhccCCCCCCH
Confidence 99994 9999 43 6 9999999999999999
Q ss_pred --------------------------------------------------------c----c------------------
Q psy11240 214 --------------------------------------------------------R----F------------------ 215 (363)
Q Consensus 214 --------------------------------------------------------T----~------------------ 215 (363)
+ +
T Consensus 157 ~evi~~~~~~l~~~~~~l~~~~~~P~f~~~~g~i~~~~~~~~y~tg~G~~~~~~~~~~~~~~i~ITELP~~~~t~~~~e~ 236 (426)
T PF00521_consen 157 REVIDAIIRLLDGEEIELMKYIMGPDFPTFGGIIEKNGIKNIYETGRGSIEVRGKYEIEGNTIVITELPYGVWTEKYKEK 236 (426)
T ss_dssp HHHHHHHHHHHHTTT-HHCTTSSSB--TTSCEEEECHHHHHHHHHSEEEEEEEEEEEEETEEEEEEE--TT--HHHHHHH
T ss_pred HHHHHHHHHHhCCCcccccccCCCCCCCCCCceeeccchhhhhccCcceEEEeeEEEEeccEEEEEeCCccccHHHHHHH
Confidence 0 0
Q ss_pred --------c--cccccccCCCceeEEEEEeCCCCChHHHHHhHhhhccceeeeccceEEEEecCCcccccCCHHHHHHHH
Q psy11240 216 --------E--SNDYKEYHTDTTVKFVVTMSPDKLHKAEMDGLHKVFKLQTTLAISSMCAFDRYGVLTKFDTTNQILKEF 285 (363)
Q Consensus 216 --------~--I~d~~d~~~~~~v~f~I~l~~~~~~~~~~~~L~k~fkL~~s~~~~nm~lfd~~g~i~ky~~~~eIl~~F 285 (363)
. |+||+|++++ +|+|+|+++++.+++...++|++.|+|++++++|||+++|. | ++|.|+++||++|
T Consensus 237 i~~l~~~~~i~I~d~~D~Sd~-~v~ivI~lk~~~~~~~~~~~L~k~t~Lq~s~~~n~~~l~~~-~--p~~~~~~eIL~~f 312 (426)
T PF00521_consen 237 IEELVEDKKIKISDYRDESDR-GVRIVIELKRGADPEKILEGLYKKTKLQSSISTNNMVLFDN-G--PKYDSLKEILKEF 312 (426)
T ss_dssp HHHHHHTTSSTEEEEEE-BBT-BS-EEEEESTTSHHHHHHHHHHHHSTTEEEEEEETEEEETT-E--EEESSHHHHHHHH
T ss_pred HHHHhccCcchhhHHHhcCCC-ceeEEEEecCCccHHHHHHHHHHHhhhhccccchheEEecC-c--ceeCCHHHHHHHH
Confidence 3 4599999545 99999999999999999999999999999999999999996 4 7899999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhc------hhHHHHHHhhhcceeEcccchHHHHHHHHHcCC
Q psy11240 286 YAVRLEYYAKRKDYLEGVLGAEALKLT------NQARFIVEKCDGDLRIENRKKKEMIAELIKRKY 345 (363)
Q Consensus 286 ~~~Rl~~y~kRk~~~l~~l~~~~~~l~------nk~rFI~~vi~~~i~i~~k~k~~l~~~L~~~~f 345 (363)
+++|+++|+||++|+++++++++++|+ ++++||.+||++++. .++++++|+++|.+..|
T Consensus 313 ~~~R~~~~~kR~~~~l~kl~~~l~il~gl~~~~~~idfIi~vI~~s~~-~~~~k~~L~~~L~~~q~ 377 (426)
T PF00521_consen 313 YEFRLEYYQKRKQYLLEKLEERLHILEGLIKALNKIDFIIEVIRGSID-KNKAKKDLIEELSEEQA 377 (426)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHSSS-HHHHHHHHHHHHCHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhcccc-chHHHHHHHhhchHHHH
Confidence 999999999999999999999999999 999999999999999 88999999999876433
No 8
>TIGR01061 parC_Gpos DNA topoisomerase IV, A subunit, Gram-positive. Operationally, topoisomerase IV is a type II topoisomerase required for the decatenation of chromosome segregation. Not every bacterium has both a topo II and a topo IV. The topo IV families of the Gram-positive bacteria and the Gram-negative bacteria appear not to represent a single clade among the type II topoisomerases, and are represented by separate models for this reason.
Probab=100.00 E-value=4.4e-70 Score=580.63 Aligned_cols=252 Identities=18% Similarity=0.286 Sum_probs=233.4
Q ss_pred eeecHHHHHHHHHHHHHHhh-ccCCCCccccCCCCcceeeEeecccCC---CCCceeeeeehhhhhhhccCC-CCcchHH
Q psy11240 87 KAITYTEFVNKELILFSNMD-NERSIPSLCDGLKPGSRKVLFTCLKRN---DRREVKVAQLAGSVAEHSAYH-HGEQSLM 161 (363)
Q Consensus 87 ~~i~~~dfinkeli~yS~~~-~~RsIPsv~DGLKP~QRKILy~~~k~~---~k~~~KvAql~G~Vse~~~YH-HGe~Sl~ 161 (363)
..+++++.++++++.||||+ ..|||||++||||||||||||+|++++ +++++||||+||+| +|+|| |||+|+|
T Consensus 2 ~~~~~~~~~~~~~l~ya~~vi~~RalP~~~DGlKPvqRril~~m~~~~~~~~~~~~K~A~~vG~v--~g~YHpHGd~siy 79 (738)
T TIGR01061 2 FNKPLEEVFGESFGKYAKYIIQDRALPDIRDGLKPVQRRILYAMFQDGNTFDKPYKKSARTVGEI--MGKYHPHGDSSIY 79 (738)
T ss_pred cccCHHHHHHHHHHHhHHHHHhhccCCccccCCCchhhhhhHhHHhcCCCCCCCceeeeeehhhh--hhccCCCchHHHH
Confidence 46799999999999999995 999999999999999999999999987 58999999999999 89999 9999999
Q ss_pred HHHHHhhccccccccccccccCCCCCccc--------eeec--CC-------------------------------C-Cc
Q psy11240 162 STIINLAQNFVGSNNINLLQPIGQFGTFL--------FIFE--ST-------------------------------N-LS 199 (363)
Q Consensus 162 ~tiV~MAQdfvGSnNi~Ll~p~G~FGsr~--------Yi~t--s~-------------------------------P-iP 199 (363)
+|||+||||| |||+|||+|+|||||++ |||| || | ||
T Consensus 80 ~a~v~maq~f--~~~~pli~~~GnFGs~~gd~~Aa~RYte~rl~~~a~~~~~~~d~~~v~~~~n~d~~~~EP~~lp~~~P 157 (738)
T TIGR01061 80 DAMVRMSQDW--KNNWTLVEMHGNNGSIDGDNAAAMRYTEARLSLIASELLKDIDKKTVSFIPNFDDSEKEPTVLPALFP 157 (738)
T ss_pred HHHHHHhhhc--cccceeEeCCCCCCCCCCCcchhhHHHhhhhhHHHHHHhhccCccccccccCCCCCccccccccccCC
Confidence 9999999999 99999999999999998 8888 43 4 99
Q ss_pred cccccCCCcccccc------------------------------------------------------------------
Q psy11240 200 GAVVNALDFGSGGW------------------------------------------------------------------ 213 (363)
Q Consensus 200 ~vLvNGa~GIgtG~------------------------------------------------------------------ 213 (363)
|||||||+||||||
T Consensus 158 ~lLvNGs~GIavG~aT~Ipphn~~evi~~~~~~i~~~~~~~~~l~~~~~~pdfptGg~i~~~~~i~~~y~tg~G~~~~rg 237 (738)
T TIGR01061 158 NLLINGATGIAAGYATNIPPHNLNEVIDALIYRIDHPNCSVDKLMEIVKGPDFPTGGIIQGEDGISKAYETGKGKFIIRA 237 (738)
T ss_pred ceeecCCcceeeeeecCCCCCCHHHHHHHHHHHhcCCCCChHHhcccccCCCCCCCcEEECchhhHHheecCCceEEEEE
Confidence 99999999999999
Q ss_pred ----------------c------------------------cccccccccCCCceeEEEEEeCCCCChHHHHHhHhhhcc
Q psy11240 214 ----------------R------------------------FESNDYKEYHTDTTVKFVVTMSPDKLHKAEMDGLHKVFK 253 (363)
Q Consensus 214 ----------------T------------------------~~I~d~~d~~~~~~v~f~I~l~~~~~~~~~~~~L~k~fk 253 (363)
| ++|.+|+|+|++++|||+|+++++..++.+++.|++.|+
T Consensus 238 ~~~~e~~~~~~~~i~ItEiP~~~~~~~~~~~i~~l~~~~~~~~i~~~~Des~~~~vrivi~lk~~~~~~~~~~~l~k~t~ 317 (738)
T TIGR01061 238 KIEIEVNKNGLNQIVITEIPYETNKANIVKKIEEIIFDNKVAGIEEVRDESDRNGIRIIIELKKDANAEKILNFLFKHTD 317 (738)
T ss_pred EEEEEEcCCCCcEEEEEecCCccCHHHHHHHHHHHHhcCCccccceeeeccCCCceEEEEEECCCCCHHHHHHHHHHhcc
Confidence 0 168999999999999999999999999999999999999
Q ss_pred ceeeeccceEEEEecCCcccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchhHHHHHHhhhcceeE--ccc
Q psy11240 254 LQTTLAISSMCAFDRYGVLTKFDTTNQILKEFYAVRLEYYAKRKDYLEGVLGAEALKLTNQARFIVEKCDGDLRI--ENR 331 (363)
Q Consensus 254 L~~s~~~~nm~lfd~~g~i~ky~~~~eIl~~F~~~Rl~~y~kRk~~~l~~l~~~~~~l~nk~rFI~~vi~~~i~i--~~k 331 (363)
|+++|++ ||++|+. |.| ++.++.+||++|++||+++|+||++|+|+++++++|+|++.++|+. +|++.|.| ..+
T Consensus 318 l~~~~~~-n~~~~~~-~~p-~~~~l~~il~~~~~~R~~~~~rr~~~~l~k~~~r~~il~g~~~~~~-~id~~i~iir~~~ 393 (738)
T TIGR01061 318 LQINYNF-NMVAIAN-RTP-IQVGLLSYLDAYIKHCHEVIINRSKYELEKASKRLEIVEGLIKAIS-IIDEIIKLIRSSE 393 (738)
T ss_pred Ccceeee-eEEEEEC-Ccc-eECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-hhhhHhHHHHcCC
Confidence 9999997 6999995 566 5679999999999999999999999999999999999999999997 89999988 456
Q ss_pred chHHHHHHHHHc-CCC
Q psy11240 332 KKKEMIAELIKR-KYD 346 (363)
Q Consensus 332 ~k~~l~~~L~~~-~f~ 346 (363)
+++++.+.|.+. +|.
T Consensus 394 ~~~~~~~~l~~~f~~~ 409 (738)
T TIGR01061 394 DKSDAKENLIDNFKFT 409 (738)
T ss_pred CHHHHHHHHHHhcCCC
Confidence 788899999776 554
No 9
>PRK05561 DNA topoisomerase IV subunit A; Validated
Probab=100.00 E-value=5.1e-70 Score=580.41 Aligned_cols=248 Identities=22% Similarity=0.339 Sum_probs=224.0
Q ss_pred cceeecHHHHHHHHHHHHHHhh-ccCCCCccccCCCCcceeeEeecccCC---CCCceeeeeehhhhhhhccCC-CCcch
Q psy11240 85 TTKAITYTEFVNKELILFSNMD-NERSIPSLCDGLKPGSRKVLFTCLKRN---DRREVKVAQLAGSVAEHSAYH-HGEQS 159 (363)
Q Consensus 85 ~~~~i~~~dfinkeli~yS~~~-~~RsIPsv~DGLKP~QRKILy~~~k~~---~k~~~KvAql~G~Vse~~~YH-HGe~S 159 (363)
.+..++|++||+++|+.|||++ +.|||||++||||||||||||+|++++ +++++||||+||+| +|+|| |||+|
T Consensus 9 ~i~~~~~~~~~~~~~l~ya~~vi~~RalP~~~DGlKPvqRrily~m~~~~~~~~~~~~K~A~~vG~v--~g~YHPHGd~s 86 (742)
T PRK05561 9 GIEDLPLEEFLEERYLRYAMYVIMDRALPDVRDGLKPVQRRILYAMSELGLTPDAKFKKSARVVGDV--LGKYHPHGDSS 86 (742)
T ss_pred cceEeeHHHHHHHHHHHHHHHHhhcccCCchhcCCCCchhhhhHhHHhcCCCcCCCceeehhhhhhH--hhccCCCcHHH
Confidence 4778999999999999999997 999999999999999999999999987 68999999999999 58999 99999
Q ss_pred HHHHHHHhhccccccccccccccCCCCCccc--------eeec--CC-------------------------------C-
Q psy11240 160 LMSTIINLAQNFVGSNNINLLQPIGQFGTFL--------FIFE--ST-------------------------------N- 197 (363)
Q Consensus 160 l~~tiV~MAQdfvGSnNi~Ll~p~G~FGsr~--------Yi~t--s~-------------------------------P- 197 (363)
+|+|||+||||| |||+|||+|+||||||+ |||| || |
T Consensus 87 iy~a~v~maQ~f--~~~~pli~~~GnFGs~~g~~~Aa~RYte~rl~~~~~~l~~~~d~~~v~~~~n~d~~~~EP~~lp~~ 164 (742)
T PRK05561 87 IYDAMVRMAQDF--SYRYPLVDGQGNFGSIDGDPAAAMRYTEARLSPIAELLLEEIDEGTVDFVPNFDGTLKEPTVLPAR 164 (742)
T ss_pred HHHHHHHHhhhc--cccccccccCCCCCCCCCCcHHHHHHHHHhhhHHHHHHhhhcCccccccccCCCCcccCccccccc
Confidence 999999999999 99999999999999998 8888 43 4
Q ss_pred CccccccCCCcccccc----------------------------------------------------------------
Q psy11240 198 LSGAVVNALDFGSGGW---------------------------------------------------------------- 213 (363)
Q Consensus 198 iP~vLvNGa~GIgtG~---------------------------------------------------------------- 213 (363)
+||||||||+||||||
T Consensus 165 ~P~lLvNG~~GIavG~aT~ipphn~~evi~~~~~~i~~~~~~~~~l~~~~~gpdFptGg~ii~~~~~i~~~y~tg~G~~~ 244 (742)
T PRK05561 165 FPNLLLNGATGIAVGMATDIPPHNLREVIDAAIHLIDNPDATLEELMEFVPGPDFPTGGEIITGRDGIRKAYETGRGSIR 244 (742)
T ss_pred cchhhccCCcchhhhhhcCCCCCCHHHHHHHHHHHHhCCCCChHHHhhcccCCCCCCCcEEEeCchhHHHHhhcCCceEE
Confidence 9999999999999999
Q ss_pred -------------------c------------------------cccccccccCCCce-eEEEEEeCCC-CChHHHHHhH
Q psy11240 214 -------------------R------------------------FESNDYKEYHTDTT-VKFVVTMSPD-KLHKAEMDGL 248 (363)
Q Consensus 214 -------------------T------------------------~~I~d~~d~~~~~~-v~f~I~l~~~-~~~~~~~~~L 248 (363)
| .+|.|++|+|++++ |||+|+++++ ..++.+++.|
T Consensus 245 ~r~~~~~~~~~~~~~~i~itEiP~~~~~~~~~~~i~~l~~~~~~~~i~~~~d~s~~~~~~r~~i~~k~~~~~~~~~~~~l 324 (742)
T PRK05561 245 VRARWEIEDLAGGRWQIVITELPYQVSKAKLIEQIAELMNAKKLPGIADVRDESDRENPVRIVIEPKSNRVDPEALMNHL 324 (742)
T ss_pred EEEEEEEEecCCCCceEEEEeCCCcccHHHHHHHHHHHHhcCCccccccceeccCCCCCEEEEEEECCCcCCHHHHHHHH
Confidence 0 06899999999988 9999999999 6778899999
Q ss_pred hhhccceeeeccceEEEEecCCcccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchhHHHHHHhhhcceeE
Q psy11240 249 HKVFKLQTTLAISSMCAFDRYGVLTKFDTTNQILKEFYAVRLEYYAKRKDYLEGVLGAEALKLTNQARFIVEKCDGDLRI 328 (363)
Q Consensus 249 ~k~fkL~~s~~~~nm~lfd~~g~i~ky~~~~eIl~~F~~~Rl~~y~kRk~~~l~~l~~~~~~l~nk~rFI~~vi~~~i~i 328 (363)
++.|+|+++|++ ||++||++|+| ++.++.+||++|++||+++|+||++|+|+++++++|+|++....+. .++..|.+
T Consensus 325 ~k~t~l~~~~~~-n~~~~d~~~~p-~~~~l~~il~~f~~~R~~~~~rr~~~~l~k~~~r~~~l~g~~~~~~-~id~vI~i 401 (742)
T PRK05561 325 FATTDLESSYRV-NMNAIGLDGRP-RVKGLKEILSEWLDHRREVVTRRSQFRLDKVEKRLHILEGLLIAFL-NIDEVIRI 401 (742)
T ss_pred HHhcCcceeeee-eEEEEccCCEE-EECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-hHHHHHHH
Confidence 999999999999 79999999999 5579999999999999999999999999999999999999665443 35666665
Q ss_pred ccc---chHHHHHH
Q psy11240 329 ENR---KKKEMIAE 339 (363)
Q Consensus 329 ~~k---~k~~l~~~ 339 (363)
.+. .++.|++.
T Consensus 402 ir~s~~ak~~l~~~ 415 (742)
T PRK05561 402 IRESDEPKANLMAR 415 (742)
T ss_pred HhcCccHHHHHHHH
Confidence 444 45555544
No 10
>PRK05560 DNA gyrase subunit A; Validated
Probab=100.00 E-value=2.4e-69 Score=579.77 Aligned_cols=255 Identities=21% Similarity=0.321 Sum_probs=228.7
Q ss_pred cceeecHHHHHHHHHHHHHHhh-ccCCCCccccCCCCcceeeEeecccCCC---CCceeeeeehhhhhhhccCC-CCcch
Q psy11240 85 TTKAITYTEFVNKELILFSNMD-NERSIPSLCDGLKPGSRKVLFTCLKRND---RREVKVAQLAGSVAEHSAYH-HGEQS 159 (363)
Q Consensus 85 ~~~~i~~~dfinkeli~yS~~~-~~RsIPsv~DGLKP~QRKILy~~~k~~~---k~~~KvAql~G~Vse~~~YH-HGe~S 159 (363)
.+..+++++||+++|+.|||++ +.|||||++||||||||||||+|+++++ ++++|||||+|+| +++|| |||+|
T Consensus 4 ~i~~~~~~~~~~~~~~~ya~~~i~~RaiP~~~DGlKPvqRril~~~~~~~~~~~~~~~K~a~~~G~v--~~~YHpHGd~s 81 (805)
T PRK05560 4 RIIPVNIEDEMKRSYLDYAMSVIVGRALPDVRDGLKPVHRRILYAMNELGNTPDKPYKKSARIVGDV--MGKYHPHGDSA 81 (805)
T ss_pred ceeEeeHHHHHHHHHHHHHHHHhhhccCCchhcCCCcchhHHHHHHHhhCCCCCCCceeehhhhhhH--HhhcCCCchHH
Confidence 4678999999999999999997 9999999999999999999999999864 6699999999999 57999 99999
Q ss_pred HHHHHHHhhccccccccccccccCCCCCccc--------eeec--CC-------------------------------C-
Q psy11240 160 LMSTIINLAQNFVGSNNINLLQPIGQFGTFL--------FIFE--ST-------------------------------N- 197 (363)
Q Consensus 160 l~~tiV~MAQdfvGSnNi~Ll~p~G~FGsr~--------Yi~t--s~-------------------------------P- 197 (363)
+|+|||+||||| |||+|||+|+|||||++ |||| || |
T Consensus 82 ~~~a~v~maq~f--~~~~pll~~~GnfGs~~g~~~Aa~RY~e~rl~~~~~~~~~~~d~~~~~~~~n~d~~~~EP~~~p~~ 159 (805)
T PRK05560 82 VYDALVRMAQDF--SMRYPLVDGQGNFGSIDGDPAAAMRYTEARMSKIAHELLADIDKETVDFVPNYDGSEQEPTVLPAR 159 (805)
T ss_pred HHHHHHHHhhhc--cccceeEeCCCCCCCCCCCchhhhHHHHhhhhHHHHHHHhhcCccccccccCCCCcccCccccccc
Confidence 999999999999 99999999999999997 9988 43 5
Q ss_pred CccccccCCCcccccc----------------------------------------------------------------
Q psy11240 198 LSGAVVNALDFGSGGW---------------------------------------------------------------- 213 (363)
Q Consensus 198 iP~vLvNGa~GIgtG~---------------------------------------------------------------- 213 (363)
+||||||||+||||||
T Consensus 160 ~P~~LvNG~~GIa~G~at~ip~hn~~evi~~~~~~l~~~~~~~~~l~~~~~gpdfptgg~i~~~~~~~~~~~~g~g~~~~ 239 (805)
T PRK05560 160 FPNLLVNGSSGIAVGMATNIPPHNLGEVIDACLALIDNPDITIEELMEIIPGPDFPTGGIILGRSGIREAYRTGRGSIVM 239 (805)
T ss_pred CCeeeecCCcceeeeeecCCCCCCHHHHHHHHHHHhcCCCCCHHHHhhcCCCCCCCCccEEECccchhhheecCCceEEE
Confidence 9999999999999999
Q ss_pred -----------------c------------------------cccccccccCCCceeEEEEEeCCCCChHHHHHhHhhhc
Q psy11240 214 -----------------R------------------------FESNDYKEYHTDTTVKFVVTMSPDKLHKAEMDGLHKVF 252 (363)
Q Consensus 214 -----------------T------------------------~~I~d~~d~~~~~~v~f~I~l~~~~~~~~~~~~L~k~f 252 (363)
| ..|+|++|+|++++|+|+|+++++.+++.+++.|++.|
T Consensus 240 ~~~~~~~~~~~~~~i~iteiP~~~~~~~~~~~i~~~~~~~~~~~i~~~~d~s~~~~~~~~i~~~~~~~~~~~~~~l~~~~ 319 (805)
T PRK05560 240 RAKAEIEEIKGREAIIVTEIPYQVNKARLIEKIAELVKEKKIEGISDLRDESDRDGMRIVIELKRDAVPEVVLNNLYKHT 319 (805)
T ss_pred EEEEEEEecCCCcEEEEEeCCCccCHHHHHHHHHHHHhcCCCCccccchhcCCCCceEEEEEECCCCCHHHHHHHHHHhc
Confidence 0 05889999999999999999999999999999999999
Q ss_pred cceeeeccceEEEEecCCcccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchhHHHHHHhhhcceeE--cc
Q psy11240 253 KLQTTLAISSMCAFDRYGVLTKFDTTNQILKEFYAVRLEYYAKRKDYLEGVLGAEALKLTNQARFIVEKCDGDLRI--EN 330 (363)
Q Consensus 253 kL~~s~~~~nm~lfd~~g~i~ky~~~~eIl~~F~~~Rl~~y~kRk~~~l~~l~~~~~~l~nk~rFI~~vi~~~i~i--~~ 330 (363)
+|+++|++| |++++ +|+| +|.++.+||++|++||+++|++|++|+|+++++++|+|+|.++|+. .++..|.+ ..
T Consensus 320 ~l~~~~~~n-~~~~~-~~~~-~~~~~~~il~~~~~~r~~~~~~r~~~~l~~~~~~~~~l~g~~~~~~-~~d~vI~iir~s 395 (805)
T PRK05560 320 QLQTSFGIN-MLALV-DGQP-KLLNLKEILEAFLEHRKEVITRRTRFELRKAEERAHILEGLLIALD-NIDEVIALIRAS 395 (805)
T ss_pred CCeeeeeee-EEEEE-CCEe-EECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-hhHHHHHHHHcC
Confidence 999999995 66666 4665 5679999999999999999999999999999999999999999864 45555544 34
Q ss_pred cchHHHHHHHHHcCCCCC
Q psy11240 331 RKKKEMIAELIKRKYDSD 348 (363)
Q Consensus 331 k~k~~l~~~L~~~~f~~~ 348 (363)
++++++.+.|.+. |...
T Consensus 396 ~~~~~~~~~L~~~-f~~~ 412 (805)
T PRK05560 396 PTPAEAKEGLMER-FGLS 412 (805)
T ss_pred CCHHHHHHHHHHh-cCCC
Confidence 6788999999774 6544
No 11
>TIGR01063 gyrA DNA gyrase, A subunit. This model describes the common type II DNA topoisomerase (DNA gyrase). Two apparently independently arising families, one in the Proteobacteria and one in Gram-positive lineages, are both designated toposisomerase IV.
Probab=100.00 E-value=7.7e-67 Score=560.06 Aligned_cols=252 Identities=21% Similarity=0.334 Sum_probs=225.8
Q ss_pred eeecHHHHHHHHHHHHHHhh-ccCCCCccccCCCCcceeeEeecccCCC---CCceeeeeehhhhhhhccCC-CCcchHH
Q psy11240 87 KAITYTEFVNKELILFSNMD-NERSIPSLCDGLKPGSRKVLFTCLKRND---RREVKVAQLAGSVAEHSAYH-HGEQSLM 161 (363)
Q Consensus 87 ~~i~~~dfinkeli~yS~~~-~~RsIPsv~DGLKP~QRKILy~~~k~~~---k~~~KvAql~G~Vse~~~YH-HGe~Sl~ 161 (363)
..+++++.|.+.++.|||++ .+|||||++||||||||||||+|+++++ ++++||||+||+| +|+|| |||+|+|
T Consensus 2 ~~~~~~~~~~~~~~~ya~~vi~~RaiP~~~DGlKPvqRril~~~~~~~~~~~~~~~K~a~~~G~v--~~~YHpHGd~s~~ 79 (800)
T TIGR01063 2 VPVNIEEEMKRSYLDYAMSVIVSRALPDVRDGLKPVHRRILYAMYELGLTPDKPYKKSARIVGDV--MGKYHPHGDSAIY 79 (800)
T ss_pred eeecHHHHHHHHHHHHHHHHHhhccCCchhcCCCchhhhhhHhHHhhCCCCCCCceeehhhhhhH--hhccCCCchHHHH
Confidence 46899999999999999995 9999999999999999999999999865 5599999999999 59999 9999999
Q ss_pred HHHHHhhccccccccccccccCCCCCccc--------eeec--CC-------------------------------C-Cc
Q psy11240 162 STIINLAQNFVGSNNINLLQPIGQFGTFL--------FIFE--ST-------------------------------N-LS 199 (363)
Q Consensus 162 ~tiV~MAQdfvGSnNi~Ll~p~G~FGsr~--------Yi~t--s~-------------------------------P-iP 199 (363)
+|||+||||| |||+|||+|+|||||++ |||| || | ||
T Consensus 80 ~a~v~maq~f--~~~~pl~~~~GnfGs~~g~~~Aa~RY~e~rls~~~~~~~~~~d~~~v~~~~n~d~~~~EP~~lp~~~P 157 (800)
T TIGR01063 80 DTLVRMAQDF--SLRYPLVDGQGNFGSIDGDPPAAMRYTEARLTKIAEELLRDIDKETVDFVPNYDGSEQEPTVLPSRFP 157 (800)
T ss_pred HHHHHHhhhc--cccceeeecCCCCCCCCCCchhhHHHHHhhhhHHHHHHhhccCccccccccCCCCcccCccccccccc
Confidence 9999999999 99999999999999987 9988 43 4 99
Q ss_pred cccccCCCcccccc------------------------------------------------------------------
Q psy11240 200 GAVVNALDFGSGGW------------------------------------------------------------------ 213 (363)
Q Consensus 200 ~vLvNGa~GIgtG~------------------------------------------------------------------ 213 (363)
|||||||+||||||
T Consensus 158 ~lLvNG~~GIa~G~at~ip~hn~~evi~~~~~~~~~~~~~~~~l~~~~~gpdfp~gg~i~~~~g~~~~y~~g~g~~~~~~ 237 (800)
T TIGR01063 158 NLLVNGSSGIAVGMATNIPPHNLGEIIDALLAYIDNPDISIQELLEVIKGPDFPTGGIILGRSGIRSAYETGRGSIVIRA 237 (800)
T ss_pred hheecCCcceeeeeecCCCCCCHHHHHHHHHHHhcCCCCChHHHHhcCCCCCCCCccEEECccchhhhhccCCceEEEEE
Confidence 99999999999999
Q ss_pred ----------------c------------------------cccccccccCCCceeEEEEEeCCCCChHHHHHhHhhhcc
Q psy11240 214 ----------------R------------------------FESNDYKEYHTDTTVKFVVTMSPDKLHKAEMDGLHKVFK 253 (363)
Q Consensus 214 ----------------T------------------------~~I~d~~d~~~~~~v~f~I~l~~~~~~~~~~~~L~k~fk 253 (363)
| ..|+||+|+|++++|+|+|+++++..++.+++.|+|.|+
T Consensus 238 ~~~~~~~~~~~~~i~IteiP~~~~~~~~~~~i~~~~~~~~~~~i~~~~d~s~~~~~~~~i~~k~~~~~~~~~~~l~k~t~ 317 (800)
T TIGR01063 238 RAEIEEDSKGREAIIVTEIPYQVNKARLIEKIAELVREKKIEGISDIRDESDREGIRIVIELKRDAVAEVVLNNLYKQTQ 317 (800)
T ss_pred EEEEEeccCCCcEEEEEecCCcccHHHHHHHHHHHHhcCCCCccccceecCCCCceEEEEEeCCCCCHHHHHHHHHHhcc
Confidence 0 068999999999999999999999999999999999999
Q ss_pred ceeeeccceEEEEecCCcccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchhHHHHHHhhhcceeE--ccc
Q psy11240 254 LQTTLAISSMCAFDRYGVLTKFDTTNQILKEFYAVRLEYYAKRKDYLEGVLGAEALKLTNQARFIVEKCDGDLRI--ENR 331 (363)
Q Consensus 254 L~~s~~~~nm~lfd~~g~i~ky~~~~eIl~~F~~~Rl~~y~kRk~~~l~~l~~~~~~l~nk~rFI~~vi~~~i~i--~~k 331 (363)
|+++|++ ||++|+ +|.| ++.++.+||++|++||+++|++|++|+|+++++++|+|++.++.+ ..++..|.+ ..+
T Consensus 318 l~~~~~~-n~~~~~-~~~~-~~~~~~~il~~~~~~r~~~~~~r~~~~l~~~~~~~~~~~g~~~~~-~~~d~vi~~ir~~~ 393 (800)
T TIGR01063 318 LQVSFGI-NMLALV-KGLP-KVLNLKELLEAFVEHRKDVITRRTIFELRKAEERAHILEGLLIAL-DNIDEVIALIRASQ 393 (800)
T ss_pred cceeeee-eEEEEE-CCEe-eECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HhhhHHHHHHHhCC
Confidence 9999999 688898 4666 567999999999999999999999999999999999999998844 334444433 346
Q ss_pred chHHHHHHHHHc-CCC
Q psy11240 332 KKKEMIAELIKR-KYD 346 (363)
Q Consensus 332 ~k~~l~~~L~~~-~f~ 346 (363)
+++++.+.|.+. +|.
T Consensus 394 ~~~~~~~~L~~~~~~~ 409 (800)
T TIGR01063 394 NTEEAKTRLVERFSLS 409 (800)
T ss_pred CHHHHHHHHHHhcCCC
Confidence 788999999765 443
No 12
>TIGR01062 parC_Gneg DNA topoisomerase IV, A subunit, proteobacterial. Operationally, topoisomerase IV is a type II topoisomerase required for the decatenation of chromosome segregation. Not every bacterium has both a topo II and a topo IV. The topo IV families of the Gram-positive bacteria and the Gram-negative bacteria appear not to represent a single clade among the type II topoisomerases, and are represented by separate models for this reason.
Probab=100.00 E-value=1.2e-65 Score=545.18 Aligned_cols=239 Identities=19% Similarity=0.248 Sum_probs=215.5
Q ss_pred eeecHHHHHHHHHHHHHHhh-ccCCCCccccCCCCcceeeEeecccCC---CCCceeeeeehhhhhhhccCC-CCcchHH
Q psy11240 87 KAITYTEFVNKELILFSNMD-NERSIPSLCDGLKPGSRKVLFTCLKRN---DRREVKVAQLAGSVAEHSAYH-HGEQSLM 161 (363)
Q Consensus 87 ~~i~~~dfinkeli~yS~~~-~~RsIPsv~DGLKP~QRKILy~~~k~~---~k~~~KvAql~G~Vse~~~YH-HGe~Sl~ 161 (363)
..+++++|++++|+.|||++ ..|||||++||||||||||||+|++++ ..++.||||++|+| +++|| |||+|+|
T Consensus 2 ~~~~~~~~~~~~yl~ya~~vi~~RalP~v~DGLKPvqRrilyam~~~~l~~~~~~~K~Ar~vG~v--~gkyHPHGd~s~y 79 (735)
T TIGR01062 2 ENIDLGNFTEEAYLNYSMYVIMDRALPFIGDGLKPVQRRIVYAMSELGLNANAKYKKSARTVGDV--LGKYHPHGDSACY 79 (735)
T ss_pred ccccHHHHHHHHHHHHHHHHhhcccCCchhcCCCcchhhhhHhHHhcCCCcCCCceeehhhHHHH--HhhcCCCchHHHH
Confidence 46899999999999999997 699999999999999999999999986 46788999999999 67999 9999999
Q ss_pred HHHHHhhccccccccccccccCCCCCccc---------eeec--CC------------------------------C--C
Q psy11240 162 STIINLAQNFVGSNNINLLQPIGQFGTFL---------FIFE--ST------------------------------N--L 198 (363)
Q Consensus 162 ~tiV~MAQdfvGSnNi~Ll~p~G~FGsr~---------Yi~t--s~------------------------------P--i 198 (363)
+|||+||||| |||+||++|+||||||+ |||| +| | +
T Consensus 80 ~a~V~mAQ~f--s~~~pLvdg~GnFGs~dg~~~~AAmRYte~rl~~~a~~ll~~~d~~~v~~~~n~Dg~~~EP~~lp~~~ 157 (735)
T TIGR01062 80 EAMVLMAQPF--SYRYPLVDGQGNWGAPDDPKSFAAMRYTESRLSKISELLLEELGQGTVDFRPNFDGTLLEPVILPARL 157 (735)
T ss_pred HHHHHHhhhc--ccCceeEecCCCCCCCCCCChhHhHHHHHhhhHHHHHHHhhccCccccccccCCCCCccCCccccccc
Confidence 9999999999 99999999999999998 8887 43 4 9
Q ss_pred ccccccCCCcccccc-----------------------------------------------------------------
Q psy11240 199 SGAVVNALDFGSGGW----------------------------------------------------------------- 213 (363)
Q Consensus 199 P~vLvNGa~GIgtG~----------------------------------------------------------------- 213 (363)
||||||||+||||||
T Consensus 158 P~lLvNG~~GIavGmaT~IpphN~~ev~~a~~~~i~~~~~~~~~l~~~~~gPDfptgG~ii~~~~~i~~~y~tg~G~~~~ 237 (735)
T TIGR01062 158 PNILLNGTTGIAVGMATDIPPHNLHELADAALYLIDNPKAGLDDILNIVQGPDFPTEAEIIDKAEEIRKIYETGRGSFRM 237 (735)
T ss_pred chhhhcCCcceEeeeecCCCCCCHHHHHHHHHHHHhCCCCCHHHHhhhccCCCCCCCcEEecCchhHHHHhccCCceEEE
Confidence 999999999999999
Q ss_pred -------------c------------------------cccccccccCCC-ceeEEEEEeC-CCCChHHHHHhHhhhccc
Q psy11240 214 -------------R------------------------FESNDYKEYHTD-TTVKFVVTMS-PDKLHKAEMDGLHKVFKL 254 (363)
Q Consensus 214 -------------T------------------------~~I~d~~d~~~~-~~v~f~I~l~-~~~~~~~~~~~L~k~fkL 254 (363)
| .+|.|++|+|++ ++|||+|+++ ++..++.+++.|++.|+|
T Consensus 238 r~~~~~e~~~ivItelP~~v~~~~~~e~i~~~~~~kk~~~i~d~~Des~~~~~vr~vi~~k~~~~~~~~~~~~L~~~t~L 317 (735)
T TIGR01062 238 RARWKKEDGQIVISALPHQISKSKVIEQIAIQMKDKKLPMISDIRDESDHENPIRVVIVPRSNRVDPDIVMEHLFATTDL 317 (735)
T ss_pred EEEEEEECCeEEEEeCCCcccHHHHHHHHHHHHhcCCCcceeehhhcCCCcCcEEEEEEECCCCCCHHHHHHHHHHhcCC
Confidence 0 058999999997 5899999998 457778899999999999
Q ss_pred eeeeccceEEEEecCCcccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchhHHHHHHhhhcceeEcccc
Q psy11240 255 QTTLAISSMCAFDRYGVLTKFDTTNQILKEFYAVRLEYYAKRKDYLEGVLGAEALKLTNQARFIVEKCDGDLRIENRK 332 (363)
Q Consensus 255 ~~s~~~~nm~lfd~~g~i~ky~~~~eIl~~F~~~Rl~~y~kRk~~~l~~l~~~~~~l~nk~rFI~~vi~~~i~i~~k~ 332 (363)
+++|++ ||++++.+|+|+.+ ++.+||++|++||+++|+||++|+|+++++++|+|++... +...||+.|.|.+..
T Consensus 318 ~~~~~~-n~~~i~~~~~p~~~-~l~~il~~~~~~R~~~~~rR~~~~l~k~~~rl~il~Gl~i-a~~~iDevI~iIR~s 392 (735)
T TIGR01062 318 EKSYRL-NMNMIGLDNVPAVK-NLLEILQEWLVFRRNTVIRRLTYRLNKVLQRLHILEGLRI-AFLNIDEVIEIIREE 392 (735)
T ss_pred eeeecc-cEEEEEeCCeeeEC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHhHHHHHHHHHcC
Confidence 999999 47777777998875 9999999999999999999999999999999999999854 445588888886543
No 13
>PRK13979 DNA topoisomerase IV subunit A; Provisional
Probab=100.00 E-value=3.3e-65 Score=553.99 Aligned_cols=267 Identities=19% Similarity=0.292 Sum_probs=232.2
Q ss_pred ccCCcccccccCcceeecHHHHHHHHHHHHHHhh-ccCCCCccccCCCCcceeeEeecccCC---CCCceeeeeehhhhh
Q psy11240 73 EMGIGEDYLYTKTTKAITYTEFVNKELILFSNMD-NERSIPSLCDGLKPGSRKVLFTCLKRN---DRREVKVAQLAGSVA 148 (363)
Q Consensus 73 ~~~~~~~~l~d~~~~~i~~~dfinkeli~yS~~~-~~RsIPsv~DGLKP~QRKILy~~~k~~---~k~~~KvAql~G~Vs 148 (363)
+.++|+ +..+..+++++.|.++++.||||+ ..|||||++||||||||||||+|++++ +++++||||++|+|
T Consensus 4 ~~~~~~----~~~i~~~~~~~~~~~~yl~Ya~~vi~~RAlPd~rDGLKPvqRrILyam~~~~~~~~~~~~K~A~ivG~v- 78 (957)
T PRK13979 4 KIVIPK----DNNIIKIPLEEAMPENYLPYAVEVAKDRALPDVRDGLKPVHRRILYGAYMLKAFPDKPYYKSARIVGDI- 78 (957)
T ss_pred cccCcC----cCceeeecHHHHHHHHHHHhHHHHHHhhcCCccccCCCchHhHHHHHHHHcCCCCCCCceeehhhHHhH-
Confidence 445553 456889999999999999999995 999999999999999999999999876 78999999999999
Q ss_pred hhccCC-CCcchHHHHHHHhhccccccccccccccCCCCCccc--------eeec--CC---------------------
Q psy11240 149 EHSAYH-HGEQSLMSTIINLAQNFVGSNNINLLQPIGQFGTFL--------FIFE--ST--------------------- 196 (363)
Q Consensus 149 e~~~YH-HGe~Sl~~tiV~MAQdfvGSnNi~Ll~p~G~FGsr~--------Yi~t--s~--------------------- 196 (363)
+++|| |||+|+|+|||+||||| |||+|||+|+|||||++ |||| ||
T Consensus 79 -~g~YHPHGd~siy~alvrmaQ~f--~~~~plidg~GnFGs~dgd~~AA~RYte~rl~~~a~~~~~d~d~~~v~~~~n~d 155 (957)
T PRK13979 79 -LGKYHPHGDSSVYDAMVILAQDF--TTRMPLIDGHGNWGSIDGDSAAAMRYTEARLTPIAMEMLRDIDKDVVNMVDNYS 155 (957)
T ss_pred -HhccCCCchHHHHHHHHHHhhhc--cccceeEeCCCCCCCCCCCchhhhhhhhhcchHHHHHHhhccCccccccccCCC
Confidence 67999 99999999999999999 99999999999999998 8888 43
Q ss_pred ---------C--CccccccCCCcccccc----------------------------------------------------
Q psy11240 197 ---------N--LSGAVVNALDFGSGGW---------------------------------------------------- 213 (363)
Q Consensus 197 ---------P--iP~vLvNGa~GIgtG~---------------------------------------------------- 213 (363)
| +||||||||+||||||
T Consensus 156 ~~~~EP~vlp~~~P~lLvNG~~GIavG~aT~Ipphnl~evi~a~~~~i~~~~~~~~~l~~~~~gpDfptGg~i~~~~~i~ 235 (957)
T PRK13979 156 DSEKEPEVLPARYPNLLVNGAFGIAVGLATNIPPHNLKEVIDGTLAYIDNNEITTKELMNYIKGPDLPTGGILIGKKSLL 235 (957)
T ss_pred CCeeccccccccCCceeecCCcceeeeeecCCCCCCHHHHHHHHHHHhcCCCCCHHHHhhhccCCCCCCCeEEECchhHH
Confidence 4 9999999999999999
Q ss_pred ------------------------------c----------------------------cccccccccCCCceeEEEEEe
Q psy11240 214 ------------------------------R----------------------------FESNDYKEYHTDTTVKFVVTM 235 (363)
Q Consensus 214 ------------------------------T----------------------------~~I~d~~d~~~~~~v~f~I~l 235 (363)
| ..|.|++|+|+++++||+|++
T Consensus 236 ~~y~tg~G~~~~r~k~~~e~~~~~~~~ivitEiPy~~~~~~~~~~i~~l~~~~~~~~~~~~i~~~~desd~~g~rivi~l 315 (957)
T PRK13979 236 SAYETGEGKVTLRAKTKIEKLENGRLGIVITEFPYRRNKAKLLQTISEMTADKKHSKALENISDIRDESDRNGIRAVIEF 315 (957)
T ss_pred HHhhcCCCCEEEEEEEEEEEcCCCceEEEEEccCCcccHHHHHHHHHHHHhcccccccCccccchhhccCCCceEEEEEE
Confidence 0 037899999999999999999
Q ss_pred CCCCC---hHHHHHhHhhhccceeeeccceEEEEecCCcccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q psy11240 236 SPDKL---HKAEMDGLHKVFKLQTTLAISSMCAFDRYGVLTKFDTTNQILKEFYAVRLEYYAKRKDYLEGVLGAEALKLT 312 (363)
Q Consensus 236 ~~~~~---~~~~~~~L~k~fkL~~s~~~~nm~lfd~~g~i~ky~~~~eIl~~F~~~Rl~~y~kRk~~~l~~l~~~~~~l~ 312 (363)
+++.. ++.+++.|+++|+||++|++ ||++++ +|+|+++ ++.+||++|++||+++|+||++|+|+++++++|+|+
T Consensus 316 k~~~~~~~~~~v~~~L~~~t~l~~~~~~-n~~~~~-~~~p~~~-~l~~il~~~~~~r~~~~~rr~~~~l~k~~~r~~i~e 392 (957)
T PRK13979 316 KKSADEDVAEKVLKYLYKKTDLQCNISF-NMVALA-DGKPETM-GLKTMLKHYVEHQKEVVTRRTKKELEIAEKRFHIVE 392 (957)
T ss_pred CCCCCcccHHHHHHHHHHhCCCeeEeee-eEEEEE-CCEEEEc-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99865 47889999999999999999 688888 8999996 999999999999999999999999999999999999
Q ss_pred hhHHHHHHhhhcceeE--cccchHHHHHHHHHcCCCCCCchh
Q psy11240 313 NQARFIVEKCDGDLRI--ENRKKKEMIAELIKRKYDSDPVKS 352 (363)
Q Consensus 313 nk~rFI~~vi~~~i~i--~~k~k~~l~~~L~~~~f~~~~~~~ 352 (363)
+...-+ ..||..|.+ ..+.+++..+.|.+. |.-...+|
T Consensus 393 Gl~~a~-~~id~vi~~ir~s~~~~~a~~~l~~~-f~~s~~qa 432 (957)
T PRK13979 393 GFIKAI-GIMDEIIKTIRSSKSKKDASENLIEK-FGFTDEQA 432 (957)
T ss_pred HHHHHH-HhHHHHHHHHHcCCCHHHHHHHHHHH-hCCCHHHH
Confidence 876532 344554444 345678888888553 55434333
No 14
>COG0188 GyrA Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair]
Probab=100.00 E-value=7.2e-65 Score=541.53 Aligned_cols=259 Identities=23% Similarity=0.364 Sum_probs=231.1
Q ss_pred ceeecHHHHHHHHHHHHHHhh-ccCCCCccccCCCCcceeeEeecccCC---CCCceeeeeehhhhhhhccCC-CCcchH
Q psy11240 86 TKAITYTEFVNKELILFSNMD-NERSIPSLCDGLKPGSRKVLFTCLKRN---DRREVKVAQLAGSVAEHSAYH-HGEQSL 160 (363)
Q Consensus 86 ~~~i~~~dfinkeli~yS~~~-~~RsIPsv~DGLKP~QRKILy~~~k~~---~k~~~KvAql~G~Vse~~~YH-HGe~Sl 160 (363)
+..++++++|+++|+.||||+ ..||||+|+||||||||||||+|++.+ ++++.|||++||.| +|+|| |||+|+
T Consensus 8 i~~v~i~~e~~~syl~YAmsVIv~RALPdVRDGLKPVqRRILYaM~e~gl~~d~~~kKsAriVGdv--mGkyHPHGDssi 85 (804)
T COG0188 8 IEPIDIEDEMKRSYLDYAMSVIVGRALPDVRDGLKPVQRRILYAMFELGLTPDKKYKKSARIVGDV--MGKYHPHGDSSI 85 (804)
T ss_pred cccccHHHHHHHHHHHHHHHHHhhccCCccccCCccHHHHHHHHHHHcCCCCCCCchhhhhhHHhh--cccCCCCCchHH
Confidence 679999999999999999996 669999999999999999999999975 78999999999999 99999 999999
Q ss_pred HHHHHHhhccccccccccccccCCCCCccc--------eeec--CC------------------------------C--C
Q psy11240 161 MSTIINLAQNFVGSNNINLLQPIGQFGTFL--------FIFE--ST------------------------------N--L 198 (363)
Q Consensus 161 ~~tiV~MAQdfvGSnNi~Ll~p~G~FGsr~--------Yi~t--s~------------------------------P--i 198 (363)
|||||+||||| |+|+||++|||||||++ |+++ || | +
T Consensus 86 YdalVRMAQdf--s~RypLVdgqGNFGSiDgD~aAAMRYTEaRLs~ia~elL~di~kdtVdf~~NyDg~~~EP~VLPa~~ 163 (804)
T COG0188 86 YDALVRMAQDF--SLRYPLVDGQGNFGSIDGDPAAAMRYTEARLSKIAEELLEDIDKDTVDFVPNYDGSEKEPEVLPARF 163 (804)
T ss_pred HHHHHHHhhhh--hhcCcceecCCCCCCCCCChHHHHHHHHhhchHHHHHHHhccccCeeecccCCCCCccCCccccccC
Confidence 99999999999 99999999999999999 7777 54 6 9
Q ss_pred ccccccCCCcccccc-----------------------------------------------------------------
Q psy11240 199 SGAVVNALDFGSGGW----------------------------------------------------------------- 213 (363)
Q Consensus 199 P~vLvNGa~GIgtG~----------------------------------------------------------------- 213 (363)
||||||||+||||||
T Consensus 164 PnLLvNGssGIAVGmATnIPPHNl~Evida~~~li~np~~~~~~lm~~i~GPDFPTgg~I~g~~~I~~aY~tGrG~i~vR 243 (804)
T COG0188 164 PNLLVNGSSGIAVGMATNIPPHNLGEVIDALIALIDNPDATIDELMEIIKGPDFPTGGIIIGRSGIREAYETGRGSIRVR 243 (804)
T ss_pred CeeEeccCCceecceecCCCCCCHHHHHHHHHHHHcCCCCchhhhhhccCCCCCCCcceEecchhhHHHHccCCceEEEE
Confidence 999999999999999
Q ss_pred -----------------c------------------------cccccccccCCCceeEEEEEeCCCCChHHHHHhHhhhc
Q psy11240 214 -----------------R------------------------FESNDYKEYHTDTTVKFVVTMSPDKLHKAEMDGLHKVF 252 (363)
Q Consensus 214 -----------------T------------------------~~I~d~~d~~~~~~v~f~I~l~~~~~~~~~~~~L~k~f 252 (363)
| ..|.+.+|+|+++++||+|+++++..++.+++.|||.+
T Consensus 244 a~~~iE~~~~gr~~IvItEiPyqvnka~lie~Iaelv~~kki~gis~vrDEsdr~giRivIelk~~~~~~~vln~Lfk~T 323 (804)
T COG0188 244 AKAEIEDTKNGREQIVITEIPYQVNKAKLIEKIAELVKEKKIEGISDIRDESDREGIRIVIELKRDAVAEVVLNNLFKLT 323 (804)
T ss_pred EEEEEEecCCCceEEEEEecCccccHHHHHHHHHHHHhcCCccCcccccccccCCCeEEEEEECCccchHHHHHHHHHhc
Confidence 0 06888999999999999999999998889999999999
Q ss_pred cceeeeccceEEEEecCCcccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchhHHHHHHhhhcceeEccc-
Q psy11240 253 KLQTTLAISSMCAFDRYGVLTKFDTTNQILKEFYAVRLEYYAKRKDYLEGVLGAEALKLTNQARFIVEKCDGDLRIENR- 331 (363)
Q Consensus 253 kL~~s~~~~nm~lfd~~g~i~ky~~~~eIl~~F~~~Rl~~y~kRk~~~l~~l~~~~~~l~nk~rFI~~vi~~~i~i~~k- 331 (363)
.||++|+.| |+++.. |+|+ +.++.+||++|++||++++++|++|+|+++++++|+|++...++. .|+..|.+.+.
T Consensus 324 ~LQ~~f~~n-m~ai~~-~~P~-~~~L~~iL~~~~~hr~~vi~rR~~~~L~Ka~~R~hileGl~~a~~-~iDevI~iIr~s 399 (804)
T COG0188 324 DLQTSFNVN-MLALVN-GRPK-VLNLKEILSEFLEHRLEVVTRRTEYELNKAEERLHILEGLLIALL-NIDEVIEIIRES 399 (804)
T ss_pred hHHhhhCce-eEEecC-Ccce-ecCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-hhHHHHHHHHcC
Confidence 999999995 777764 7775 569999999999999999999999999999999999999999885 46677666443
Q ss_pred -chHHHHHHHHHcCCCCCCchhh
Q psy11240 332 -KKKEMIAELIKRKYDSDPVKSW 353 (363)
Q Consensus 332 -~k~~l~~~L~~~~f~~~~~~~~ 353 (363)
.+.+..+.|.++ |.....+|.
T Consensus 400 ~~~~~a~~~L~~~-f~lse~Qa~ 421 (804)
T COG0188 400 KDKPEAKEELMAR-FGLSEKQAE 421 (804)
T ss_pred CCchHHHHHHHHH-cCCcHHHHH
Confidence 335666677555 776666654
No 15
>KOG0355|consensus
Probab=100.00 E-value=4.1e-65 Score=536.36 Aligned_cols=194 Identities=63% Similarity=0.945 Sum_probs=181.0
Q ss_pred CCcceeeccccccCCcHHHHHHhhhhhcceeeeEEcCCCchHHHHHhcCCcchhhHHHHHHHhHHHhhhhhccCCccccc
Q psy11240 2 NTIHDVMIAGLGTSTSKEAKEYFSNMERHRILFKYSGDNDDAHIRMAFSKKLVDERKTWLTTWMEECRRRKEMGIGEDYL 81 (363)
Q Consensus 2 ~~w~iKYyKGLGTst~~eakeyF~~l~~h~~~f~~~~~~d~~~i~~aF~kk~~d~RK~Wl~~~~~~~~~~~~~~~~~~~l 81 (363)
++|+|||||||||||++||+|||+||++|++.|.|+++.|+++|+|||+|+++|+||+||.+++ | .|+
T Consensus 573 ~~~~ikyykglgts~~~e~keyf~~~~~h~~~F~~~~~~d~~~i~~af~k~k~~~rk~wL~~~~-----------~-~~~ 640 (842)
T KOG0355|consen 573 KSWKIKYYKGLGTSTSKEAKEYFSDLDRHRILFKYDGGIDDEAIDMAFSKKKIDARKEWLRKYM-----------P-EYL 640 (842)
T ss_pred cccceEEeecCCcccHHHHHHHhcCcchheEEEeccCcchHHHHhhhcccccHHHHHHHHHHHh-----------H-Hhc
Confidence 5899999999999999999999999999999999999999999999999999999999999998 4 778
Q ss_pred ccCcceeecHHHHHHHHHHHHHHhhccCCCCccccCCCCcceeeEeecccCCCCCceeeeeehhhhhhhccCCCCcchHH
Q psy11240 82 YTKTTKAITYTEFVNKELILFSNMDNERSIPSLCDGLKPGSRKVLFTCLKRNDRREVKVAQLAGSVAEHSAYHHGEQSLM 161 (363)
Q Consensus 82 ~d~~~~~i~~~dfinkeli~yS~~~~~RsIPsv~DGLKP~QRKILy~~~k~~~k~~~KvAql~G~Vse~~~YHHGe~Sl~ 161 (363)
| +.+..++|+||+ +|||+||++| |||||+||||||||||||+|||+|++.|+|||||||+|||+++|||||+||.
T Consensus 641 ~-~~~~~v~~sdf~-~elilf~~~~---sIp~~~dglkpgqRkv~~~~~k~n~~~E~Kv~ql~g~v~~~s~yhhge~sl~ 715 (842)
T KOG0355|consen 641 Y-KTTKFVTISDFV-KELILFSNAD---SIPSLVDGLKPGQRKVLFTCFKRNDKREVKVAQLAGSVAEMSAYHHGEQSLM 715 (842)
T ss_pred c-cccceeEHHHHH-HHHHHHHhcc---ccHhHHhccCccchhhhhhhhhhcCCCceeEeeecchHHHHHHhhcccHhHH
Confidence 6 899999999999 9999999999 9999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhccccccccccccccCCCCCccceeec--CC-----------------------------C-CccccccCCCcc
Q psy11240 162 STIINLAQNFVGSNNINLLQPIGQFGTFLFIFE--ST-----------------------------N-LSGAVVNALDFG 209 (363)
Q Consensus 162 ~tiV~MAQdfvGSnNi~Ll~p~G~FGsr~Yi~t--s~-----------------------------P-iP~vLvNGa~GI 209 (363)
+|||||||+||| =.=-|+-|||| || | +||||||||+||
T Consensus 716 ~ti~~l~q~~~g----------kdaa~~ryi~t~l~~~tr~~f~~~dd~ll~~~~~~~~~vep~y~pi~p~vlvngaegi 785 (842)
T KOG0355|consen 716 STIVNLAQDFVG----------KDAASARYIFTKLSPLTRLLFPPADDLLLKYLNEDGQRVEPEYCPIIPMVLVNGAEGI 785 (842)
T ss_pred HHHHHHHHhhcC----------CcchhhHHHHHhcChhhhhcCCCCchhHhhhhccCCcCcCcccccceeEEEeeccccc
Confidence 999999999999 01112239999 44 8 999999999999
Q ss_pred ccccccccccccc
Q psy11240 210 SGGWRFESNDYKE 222 (363)
Q Consensus 210 gtG~T~~I~d~~d 222 (363)
||||+..|..|.+
T Consensus 786 GtGws~~i~n~n~ 798 (842)
T KOG0355|consen 786 GTGWSTFIPNYNP 798 (842)
T ss_pred cCCccccCCCCCH
Confidence 9999878877743
No 16
>PRK09631 DNA topoisomerase IV subunit A; Provisional
Probab=100.00 E-value=3.4e-61 Score=503.59 Aligned_cols=242 Identities=17% Similarity=0.300 Sum_probs=215.9
Q ss_pred cHHHHHHHHHHHHHHhh-ccCCCCccccCCCCcceeeEeecccCCCCCceeeeeehhhhhhhccCC-CCcchHHHHHHHh
Q psy11240 90 TYTEFVNKELILFSNMD-NERSIPSLCDGLKPGSRKVLFTCLKRNDRREVKVAQLAGSVAEHSAYH-HGEQSLMSTIINL 167 (363)
Q Consensus 90 ~~~dfinkeli~yS~~~-~~RsIPsv~DGLKP~QRKILy~~~k~~~k~~~KvAql~G~Vse~~~YH-HGe~Sl~~tiV~M 167 (363)
++++.+.++++.||||+ .+|||||++||||||||||||+|++++++++.|||+++|+| + +|| |||+|+|+|||+|
T Consensus 3 ~i~~~~~~~fl~YA~~VI~~RAlP~v~DGLKPvqRrIL~am~~~~~~~~~K~A~ivG~v--~-~YHPHGd~SiydalV~m 79 (635)
T PRK09631 3 DIKTLFKDNFLQYASYVIKDRAIPDVIDGLKPVQRRILHSLFEMHDGKFHKVANVVGNT--M-KYHPHGDASIYEALVNL 79 (635)
T ss_pred cHHHHHHHHHHhhhHHhhhhccCCchhhCCCcchhhhhHhhhhccCCCceeeeeecccc--c-ccCCCchHHHHHHHHHh
Confidence 67899999999999995 99999999999999999999999999999999999999999 5 999 9999999999999
Q ss_pred hccccccccccccccCCCCCccc---------eeec--CC-----------------------------C-CccccccCC
Q psy11240 168 AQNFVGSNNINLLQPIGQFGTFL---------FIFE--ST-----------------------------N-LSGAVVNAL 206 (363)
Q Consensus 168 AQdfvGSnNi~Ll~p~G~FGsr~---------Yi~t--s~-----------------------------P-iP~vLvNGa 206 (363)
|| |+|||+|+|||||++ |||| || | +||||||||
T Consensus 80 aq------~~~Lid~qGnFGs~l~Gd~aAA~RYte~rLs~~a~~~~~~~~~v~~~~n~Dg~~~EP~~lp~~~P~lLvNGa 153 (635)
T PRK09631 80 AN------KDLFIDKQGNFGNLFTGDPASAARYIECRLTPLAKEVLYNKEITEYEPSYDGRNNEPLCLPAKIPVILIQGA 153 (635)
T ss_pred cC------CcceeecCCCCCCCCCCChhhhHHHHHHhhhHHHHHHhcCcCcccCCcCCCCCccCCccccccCceeeecCC
Confidence 99 589999999999994 8888 43 4 999999999
Q ss_pred Ccccccc-----------------------------------------------------------------cc------
Q psy11240 207 DFGSGGW-----------------------------------------------------------------RF------ 215 (363)
Q Consensus 207 ~GIgtG~-----------------------------------------------------------------T~------ 215 (363)
+|||||| |.
T Consensus 154 ~GIavG~aT~IpphN~~evi~a~~~~l~~~~~~~~PdFptGgii~~~~Y~tG~G~~~~r~~~~~~~~~~ivItEiP~~~~ 233 (635)
T PRK09631 154 EGIAVGMATKILPHNFNEILQAVKSELLGESFALYPDFPTGGIVDVSEYADGNGKVLVRAKIETKDEKTIVIREIPFGTT 233 (635)
T ss_pred cceeeeeecCCCCCCHHHHHHHHHHHhcCCCccccCCCCCCcEEEeeeeecCCceEEEEEEEEEecCCEEEEEeCCCccc
Confidence 9999999 00
Q ss_pred -----------------ccccccccCCCceeEEEEEeCCCCChHHHHHhHhhhccceeeeccceEEEEecCCcccccCCH
Q psy11240 216 -----------------ESNDYKEYHTDTTVKFVVTMSPDKLHKAEMDGLHKVFKLQTTLAISSMCAFDRYGVLTKFDTT 278 (363)
Q Consensus 216 -----------------~I~d~~d~~~~~~v~f~I~l~~~~~~~~~~~~L~k~fkL~~s~~~~nm~lfd~~g~i~ky~~~ 278 (363)
.|++++|++++ +|+|+|+++++..++.+.++|+++|+||++|++|||+++| |+|+ +.++
T Consensus 234 ~~~li~~i~~~~~~~ki~I~~i~D~s~~-~v~i~i~l~~~~~~~~~~~~Lyk~t~lq~s~~~n~~~i~~--~~p~-~~~l 309 (635)
T PRK09631 234 TESLIASIEKAARKGKIKISSINDYTAE-NVEIEIKLPRGVYASEVIEALYAYTDCEVSISVNLLVIKD--RYPV-IYTV 309 (635)
T ss_pred HHHHHHHHHHHHHcCCCccceeEeCCCC-cEEEEEEECCCCCHHHHHHHHHHhcCceeEeeeeEEEEEC--CcCc-CCCH
Confidence 48899999775 6999999999999999999999999999999999999987 5664 4799
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HhchhHHHHHHhhhcceeEcccchHHHHHHHHHcCCCCC
Q psy11240 279 NQILKEFYAVRLEYYAKRKDYLEGVLGAEAL--KLTNQARFIVEKCDGDLRIENRKKKEMIAELIKRKYDSD 348 (363)
Q Consensus 279 ~eIl~~F~~~Rl~~y~kRk~~~l~~l~~~~~--~l~nk~rFI~~vi~~~i~i~~k~k~~l~~~L~~~~f~~~ 348 (363)
.+||++|++||.+++++|.+|.|.++++++| +|++- ||.+.|++.|.+. +..+++++.+ +....|+
T Consensus 310 ~~il~~~~~~r~~vl~rr~~~~l~k~~~r~h~~~legl--~i~~~i~~~i~~~-~~~~~v~~~i-~~~~~~~ 377 (635)
T PRK09631 310 TDIIKFHAEHLQKVLKMELELERAKLLEKIFAKTLEQI--FIEERIYKRIETI-SSEEDVISIV-LSELKPF 377 (635)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHhhhH--HhhhhHHHHHHhh-cCHHHHHHHH-Hhccchh
Confidence 9999999999999999999999999999999 57765 7778888888765 5556666655 4445554
No 17
>PRK12758 DNA topoisomerase IV subunit A; Provisional
Probab=100.00 E-value=1.5e-60 Score=508.00 Aligned_cols=249 Identities=18% Similarity=0.273 Sum_probs=221.9
Q ss_pred eecHHHHHHHHHHHHHHhh-ccCCCCccccCCCCcceeeEeecccCCCCCceeeeeehhhhhhhccCC-CCcchHHHHHH
Q psy11240 88 AITYTEFVNKELILFSNMD-NERSIPSLCDGLKPGSRKVLFTCLKRNDRREVKVAQLAGSVAEHSAYH-HGEQSLMSTII 165 (363)
Q Consensus 88 ~i~~~dfinkeli~yS~~~-~~RsIPsv~DGLKP~QRKILy~~~k~~~k~~~KvAql~G~Vse~~~YH-HGe~Sl~~tiV 165 (363)
..++++.+.++++.||||+ +.|||||++||||||||||||+|+++++++++||||++|+| + +|| |||+|+|+|||
T Consensus 20 ~~~l~~~~~~~fLdYA~yVI~~RAiP~v~DGLKPvQRRIL~am~~~~~~~~~KvA~ivG~v--~-~YHPHGD~SiydaiV 96 (869)
T PRK12758 20 LTHVSGMYKNWFLDYASYVILERAVPHIEDGLKPVQRRILHSMKEMDDGRYNKVANVVGHT--M-QYHPHGDASIGDALV 96 (869)
T ss_pred cccHHHHHHHHHHhhhHhhhhcccCCchhcCCCcchhhhhHhhhhcCCCCceeEeeeehhh--h-ccCCCchHHHHHHHH
Confidence 4689999999999999995 99999999999999999999999999999999999999999 4 999 99999999999
Q ss_pred HhhccccccccccccccCCCCCccc---------eeec--CC----------------------------C--Ccccccc
Q psy11240 166 NLAQNFVGSNNINLLQPIGQFGTFL---------FIFE--ST----------------------------N--LSGAVVN 204 (363)
Q Consensus 166 ~MAQdfvGSnNi~Ll~p~G~FGsr~---------Yi~t--s~----------------------------P--iP~vLvN 204 (363)
+|||+ | +||+|+|||||++ |||| || | +||||||
T Consensus 97 ~MAQ~-----~-~Lid~qGNFGsi~~Gd~aAA~RYieaRLs~~a~~~l~~~~~vd~~~nyDg~~~EP~~LP~k~P~lLvN 170 (869)
T PRK12758 97 QLGQK-----D-LLIDTQGNWGNILTGDGAAAPRYIEARLSKFALEVVFNPKTTEWQLSYDGRKKEPVTLPVKFPLLLAQ 170 (869)
T ss_pred HHhCc-----C-cEEeccCCCCCCCCCCcccchhhHhhhhhHHHHHHcCCccccCCCcCCCCcccccccccCcCceeeec
Confidence 99997 3 5999999999994 9988 43 6 9999999
Q ss_pred CCCcccccc-------------------------------------------------------------------cc--
Q psy11240 205 ALDFGSGGW-------------------------------------------------------------------RF-- 215 (363)
Q Consensus 205 Ga~GIgtG~-------------------------------------------------------------------T~-- 215 (363)
||+|||||| |.
T Consensus 171 Gs~GIAvG~aT~IpPHN~~Evida~~~~l~~~~~~~~PDFpTGgii~~~~y~~G~~~G~i~vrgkie~~~~~~ivItEiP 250 (869)
T PRK12758 171 GAEGIAVGLSTKILPHNFNELIDASIAYLKGKEFKLYPDFPTGGIIDVSNYNDGERGGRVRVRAKIEKLDKKTLVITEIP 250 (869)
T ss_pred cCcceeeccccCCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCcEEEeeecccCccceEEEEEEEEEEcCCCEEEEEecC
Confidence 999999999 00
Q ss_pred ---------------------ccccccccCCCceeEEEEEeCCCCChHHHHHhHhhhccceeeeccceEEEEecCCcccc
Q psy11240 216 ---------------------ESNDYKEYHTDTTVKFVVTMSPDKLHKAEMDGLHKVFKLQTTLAISSMCAFDRYGVLTK 274 (363)
Q Consensus 216 ---------------------~I~d~~d~~~~~~v~f~I~l~~~~~~~~~~~~L~k~fkL~~s~~~~nm~lfd~~g~i~k 274 (363)
.|++++|+++ .+|+|+|+|+++..++.++++|+++|+||+++++|||+++| |+| +
T Consensus 251 y~~~t~~lie~I~~~~~~~ki~I~di~D~s~-~~vrivI~lk~~~~~~~~~~~Ly~~T~lq~s~s~n~~vi~d--~~P-~ 326 (869)
T PRK12758 251 YGTTTSSLIDSILKANDKGKIKIKKVEDNTA-ADVEILVHLAPGVSPDKTIDALYAFTDCEVSISPNACVIID--NKP-H 326 (869)
T ss_pred CcccHHHHHHHHHHHHhcCCCceeeeEecCC-CceEEEEEeCCCCCHHHHHHHHHhhcCceeEeeeeEEEEEC--Cee-e
Confidence 4678877654 67999999999999999999999999999999999888887 665 6
Q ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchhHHHHHHhhhcceeEcccchHHHHHHHHHcCCCCCCch
Q psy11240 275 FDTTNQILKEFYAVRLEYYAKRKDYLEGVLGAEALKLTNQARFIVEKCDGDLRIENRKKKEMIAELIKRKYDSDPVK 351 (363)
Q Consensus 275 y~~~~eIl~~F~~~Rl~~y~kRk~~~l~~l~~~~~~l~nk~rFI~~vi~~~i~i~~k~k~~l~~~L~~~~f~~~~~~ 351 (363)
|.++.|||++|++||.+++++|.+|+|+++++++|++.-+.-||...|-..|+ ..+.++++++.| ..+|.|+...
T Consensus 327 ~~~l~eiL~~~~~~r~~vl~rr~~~~l~k~~er~hi~~le~i~i~d~Ii~~Ir-~s~~~~~a~~~l-~~~~~p~~~~ 401 (869)
T PRK12758 327 FLGVSDILRRSTDHTVSLLKQELEIRLSELEEQWHFASLEKIFIEERIYKEIE-EAETWEAVIEAI-DKGLEPFKKQ 401 (869)
T ss_pred ECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHhhhHHHHHHH-cCCCHHHHHHHH-HHhcccchhh
Confidence 78999999999999999999999999999999999977777787665556655 567888999888 5578876544
No 18
>PRK09630 DNA topoisomerase IV subunit A; Provisional
Probab=100.00 E-value=8.9e-60 Score=475.41 Aligned_cols=252 Identities=20% Similarity=0.269 Sum_probs=223.4
Q ss_pred cHHHHHHHHHHHHHHhh-ccCCCCccccCCCCcceeeEeecccCCCCCceeeeeehhhhhhhccCCCCcchHHHHHHHhh
Q psy11240 90 TYTEFVNKELILFSNMD-NERSIPSLCDGLKPGSRKVLFTCLKRNDRREVKVAQLAGSVAEHSAYHHGEQSLMSTIINLA 168 (363)
Q Consensus 90 ~~~dfinkeli~yS~~~-~~RsIPsv~DGLKP~QRKILy~~~k~~~k~~~KvAql~G~Vse~~~YHHGe~Sl~~tiV~MA 168 (363)
++++.+.+.++.|||++ ++|||||++||||||||||||+|+++++++++||||++|+| |+.|||||+|+|+|||+||
T Consensus 3 ~i~~~~~~~fl~YA~yVI~~RAIPdv~DGLKPVQRRILyam~~~~~~~~~KvA~ivG~~--m~yhpHGDaSiydAlV~MA 80 (479)
T PRK09630 3 DVSDLFKTHFMHYASYVILERAIPHILDGLKPVQRRLLWTLFRMDDGKMHKVANIAGRT--MALHPHGDAPIVEALVVLA 80 (479)
T ss_pred cHHHHHHHHHHhhhHHHhhcccCCccccCCCCchhhhhhhhhhcCCCCceeeeeehhcc--cccCCCchHHHHHHHHHhc
Confidence 57889999999999995 99999999999999999999999999999999999999998 7755599999999999999
Q ss_pred ccccccccccccccCCCCCccc---------eeec--CC-----------------------------C-CccccccCCC
Q psy11240 169 QNFVGSNNINLLQPIGQFGTFL---------FIFE--ST-----------------------------N-LSGAVVNALD 207 (363)
Q Consensus 169 QdfvGSnNi~Ll~p~G~FGsr~---------Yi~t--s~-----------------------------P-iP~vLvNGa~ 207 (363)
| |+|||+|+||||||+ |||| || | +||||||||+
T Consensus 81 Q------n~~LId~qGNFGSrl~Gd~aAA~RYiEaRLs~~a~~il~~~~~v~~~~nyDg~~~EP~~lP~~iP~LLvNGa~ 154 (479)
T PRK09630 81 N------KGYLIDTQGNFGNPLTGDPHAAARYIEARLSPLAKEVLFNTDLMTFHDSYDGREKEPDILPAKLPLLLLHGVD 154 (479)
T ss_pred c------CceeeeCCCCCCCCCCCCcchhHHHHHHhhHHHHHHHhcCcCcccccccCCCcccCCcccCCcCCeecccCCc
Confidence 8 579999999999985 9988 43 4 9999999999
Q ss_pred cccccc-----------------------------------------------------------------cc-------
Q psy11240 208 FGSGGW-----------------------------------------------------------------RF------- 215 (363)
Q Consensus 208 GIgtG~-----------------------------------------------------------------T~------- 215 (363)
|||||| |.
T Consensus 155 GIAvG~AT~IpPHNl~Evida~i~~L~~~~~~~~PDFptGG~I~~~~Y~tG~G~~~vrgk~~~~~~~~ivItEIPy~~~t 234 (479)
T PRK09630 155 GIAVGMTTKIFPHNFCELLEAQIAILNDQPFTLLPDFPSGGTMDASEYQDGLGSITLRASIDIINDKTLLIKEICPSTTT 234 (479)
T ss_pred eeeeccccCCCCCCHHHHHHHHHHHhCCCCCcCCcCCCCCcEEEEeecccCCceEEEEEEEEEecCCEEEEEeCCCcccH
Confidence 999999 00
Q ss_pred ----------------ccccccccCCCceeEEEEEeCCCCChHHHHHhHhhhccceeeeccceEEEEecCCcccccCCHH
Q psy11240 216 ----------------ESNDYKEYHTDTTVKFVVTMSPDKLHKAEMDGLHKVFKLQTTLAISSMCAFDRYGVLTKFDTTN 279 (363)
Q Consensus 216 ----------------~I~d~~d~~~~~~v~f~I~l~~~~~~~~~~~~L~k~fkL~~s~~~~nm~lfd~~g~i~ky~~~~ 279 (363)
.|++|+|+|++ +|+|+|+++++.+++.+++.||++|.||++|++|++++. +|+|+. .++.
T Consensus 235 ~~lie~I~~l~~~gki~I~~i~D~s~~-~v~i~I~Lk~~~~~~~vl~~Ly~~T~lq~s~~~n~~~i~--~~~P~~-~~l~ 310 (479)
T PRK09630 235 ETLIRSIENAAKRGIIKIDSIQDFSTD-LPHIEIKLPKGIYAKDLLRPLFTHTECQVILTSRPTAIY--QNKPVE-TSIS 310 (479)
T ss_pred HHHHHHHHHHHhcCCCccceeeccCCC-CceEEEEECCCCCHHHHHHHHHhhCchhhhccceEEEEE--CCcccc-cCHH
Confidence 46999999887 699999999999999999999999999999999755555 488866 5999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchhHHHHHHhhhccee-----Ecc-cchHHHHHHHHHcCCCCCCchhh
Q psy11240 280 QILKEFYAVRLEYYAKRKDYLEGVLGAEALKLTNQARFIVEKCDGDLR-----IEN-RKKKEMIAELIKRKYDSDPVKSW 353 (363)
Q Consensus 280 eIl~~F~~~Rl~~y~kRk~~~l~~l~~~~~~l~nk~rFI~~vi~~~i~-----i~~-k~k~~l~~~L~~~~f~~~~~~~~ 353 (363)
+||+...++...+.+++.+..+.+++++++-.+-..-||+..|...++ ++. .+.+++++.+ ..|+.|+-....
T Consensus 311 ~il~~~~~~~~~~l~~eLe~~~~~l~~~~~~~sle~ifie~riy~~~~~~~~~~e~~~~~~~~~~~i-~~~l~p~~~~~~ 389 (479)
T PRK09630 311 EILRLHTETLQGYLKKELLILEDSLSREHYHKTLEYIFIKHKLYDTVREMLSKRKTSPSSSDLHNAV-LEALTPFLDTLP 389 (479)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhccCCHHHHHHHH-HHhcCcchhhcc
Confidence 999999999999999999999999999999999889999999988873 444 4566666665 889999866544
Q ss_pred h
Q psy11240 354 K 354 (363)
Q Consensus 354 k 354 (363)
+
T Consensus 390 r 390 (479)
T PRK09630 390 T 390 (479)
T ss_pred C
Confidence 3
No 19
>TIGR01055 parE_Gneg DNA topoisomerase IV, B subunit, proteobacterial. This protein is active as an alpha(2)beta(2) heterotetramer.
Probab=99.28 E-value=1.9e-12 Score=137.44 Aligned_cols=63 Identities=19% Similarity=0.264 Sum_probs=57.4
Q ss_pred CCcceeeccccccCCcHHHHHHhhhhh-cceeeeEEcCCC---chHHHHHhcCCcchhhHHHHHHHh
Q psy11240 2 NTIHDVMIAGLGTSTSKEAKEYFSNME-RHRILFKYSGDN---DDAHIRMAFSKKLVDERKTWLTTW 64 (363)
Q Consensus 2 ~~w~iKYyKGLGTst~~eakeyF~~l~-~h~~~f~~~~~~---d~~~i~~aF~kk~~d~RK~Wl~~~ 64 (363)
++|+|+||||||||+++|++|||.|.+ +|.+.|.+++.. .+++|+|+|+++++++||+||.+.
T Consensus 555 ~~~~i~ryKGLGe~~~~~~~e~~~~p~~r~l~~v~~~~~~~~~~~~~~~~lmg~~~~~~Rk~~i~~~ 621 (625)
T TIGR01055 555 GKPNVQRFKGLGEMNPAQLRETTMDPNTRRLVQLTLDDVQDQRVDKIMDMLLAKKRSEDRFNWLQEK 621 (625)
T ss_pred CCcceeEecccchhhHHHHHHHhhCccceecccccccchhhhhHHHHHHHHhCCCCCchhHHHHHhc
Confidence 369999999999999999999999998 778999997654 489999999999999999999865
No 20
>smart00433 TOP2c TopoisomeraseII. Eukaryotic DNA topoisomerase II, GyrB, ParE
Probab=99.19 E-value=1.3e-11 Score=130.27 Aligned_cols=64 Identities=27% Similarity=0.315 Sum_probs=58.2
Q ss_pred CCcceeeccccccCCcHHHHHHhhhhhcceeeeEEcCCCchH-HHHHhcCCcchhhHHHHHHHhH
Q psy11240 2 NTIHDVMIAGLGTSTSKEAKEYFSNMERHRILFKYSGDNDDA-HIRMAFSKKLVDERKTWLTTWM 65 (363)
Q Consensus 2 ~~w~iKYyKGLGTst~~eakeyF~~l~~h~~~f~~~~~~d~~-~i~~aF~kk~~d~RK~Wl~~~~ 65 (363)
++|+|+||||||+++++|++|||.|.++|++.+.+.++.++. .|.++|.++++++||+||.++.
T Consensus 529 ~~~~i~ryKGLGe~~~~~~~e~~~~p~~r~l~~v~~~d~~~~~~~~~~l~g~~~~~Rk~~i~~~~ 593 (594)
T smart00433 529 SKYEIQRYKGLGEMNADQLWETTMDPERRTLLFVTLDDADEADLIFSALMGDKVEPRKEWIEENA 593 (594)
T ss_pred CCccceeccccccCCHHHHHHHhcCccceeEEEEEcCchhhHHHHHHHHcCCCchHHHHHHHhhC
Confidence 369999999999999999999999999999999998765544 8999999999999999998763
No 21
>PRK05559 DNA topoisomerase IV subunit B; Reviewed
Probab=99.19 E-value=1.3e-11 Score=131.16 Aligned_cols=63 Identities=16% Similarity=0.234 Sum_probs=56.5
Q ss_pred CCcceeeccccccCCcHHHHHHhhhhh-cceeeeEEcC-CCchHHHHHhcCCcchhhHHHHHHHhH
Q psy11240 2 NTIHDVMIAGLGTSTSKEAKEYFSNME-RHRILFKYSG-DNDDAHIRMAFSKKLVDERKTWLTTWM 65 (363)
Q Consensus 2 ~~w~iKYyKGLGTst~~eakeyF~~l~-~h~~~f~~~~-~~d~~~i~~aF~kk~~d~RK~Wl~~~~ 65 (363)
++|+|+||||||+++++|++|||.|.+ +|+++|.+++ +.++++++|+|++ ++++||+||.+.-
T Consensus 561 ~~~~i~ryKGLGe~~~~~~~e~~~~p~~r~l~~v~~~d~~~~~~~~~~l~g~-~~~~Rk~~i~~~~ 625 (631)
T PRK05559 561 GKPEIQRFKGLGEMNPDQLWETTMDPETRRLVRVTIDDAEETEKLVDMLMGK-KAEPRREWIEENG 625 (631)
T ss_pred CCCCceEeCchhhcCHHHHHHHhhCccceeEEEEEccchhhHHHHHHHHhCC-CchHHHHHHHHhh
Confidence 479999999999999999999999998 6689999864 4578999999999 7999999998763
No 22
>PRK05644 gyrB DNA gyrase subunit B; Validated
Probab=99.07 E-value=1e-10 Score=124.55 Aligned_cols=62 Identities=19% Similarity=0.173 Sum_probs=52.4
Q ss_pred CCcceeeccccccCCcHHHHHHhhhhhcceeeeEEcCCCchHHHHHhcCC---cchhhHHHHHHHhH
Q psy11240 2 NTIHDVMIAGLGTSTSKEAKEYFSNMERHRILFKYSGDNDDAHIRMAFSK---KLVDERKTWLTTWM 65 (363)
Q Consensus 2 ~~w~iKYyKGLGTst~~eakeyF~~l~~h~~~f~~~~~~d~~~i~~aF~k---k~~d~RK~Wl~~~~ 65 (363)
++|+||||||||||+++|++|||.|.+.| .-+.+. .+|.+.++++|++ +++++||+||.++-
T Consensus 566 ~~~~i~ryKGLGe~~~~~~~e~~~~~~~r-~~~~v~-~~d~~~~~~~f~~lmg~~~~~Rk~~i~~~~ 630 (638)
T PRK05644 566 PKYGIQRYKGLGEMNPEQLWETTMDPETR-TLLQVT-IEDAAEADEIFSILMGDDVEPRREFIEENA 630 (638)
T ss_pred CCCceeEecCccccCHHHHHHHhcCccce-eeeeec-cccHHHHHHHHHHHhCCCChHHHHHHHHhh
Confidence 47999999999999999999999998544 445553 4577889999994 88999999998874
No 23
>TIGR01058 parE_Gpos DNA topoisomerase IV, B subunit, Gram-positive. Operationally, topoisomerase IV is a type II topoisomerase required for the decatenation step of chromosome segregation. Not every bacterium has both a topo II and a topo IV. The topo IV families of the Gram-positive bacteria and the Gram-negative bacteria appear not to represent a single clade among the type II topoisomerases, and are represented by separate models for this reason.
Probab=98.99 E-value=2.3e-10 Score=121.93 Aligned_cols=64 Identities=17% Similarity=0.159 Sum_probs=59.4
Q ss_pred CCcceeeccccccCCcHHHHHHhhhh-hcceeeeEEcCCCchHHHHHhcCCcchhhHHHHHHHhH
Q psy11240 2 NTIHDVMIAGLGTSTSKEAKEYFSNM-ERHRILFKYSGDNDDAHIRMAFSKKLVDERKTWLTTWM 65 (363)
Q Consensus 2 ~~w~iKYyKGLGTst~~eakeyF~~l-~~h~~~f~~~~~~d~~~i~~aF~kk~~d~RK~Wl~~~~ 65 (363)
++|+|+||||||+++++|++|||.|. .||++++.+++..+.+.|.++|..+++++||+||.+.-
T Consensus 563 ~~~~i~ryKGLGem~~~~l~ettm~p~~r~l~~v~~~d~~~~~~~~~~lmg~~~~~Rk~~i~~~~ 627 (637)
T TIGR01058 563 KNYTLQRYKGLGEMNADQLWETTMNPETRTLVRVKIDDLARAERQINTLMGDKVEPRKKWIEANI 627 (637)
T ss_pred CCCCceEECchhhhhHHHHHHHhhCcccceeeEEehhhhhhHHHHHHHHcCCCchHHHHHHHHhh
Confidence 57999999999999999999999999 79999999988778899999999999999999998753
No 24
>TIGR01059 gyrB DNA gyrase, B subunit. This model describes the common type II DNA topoisomerase (DNA gyrase). Two apparently independently arising families, one in the Proteobacteria and one in Gram-positive lineages, are both designated toposisomerase IV. Proteins scoring above the noise cutoff for this model and below the trusted cutoff for topoisomerase IV models probably should be designated GyrB.
Probab=98.43 E-value=1.5e-07 Score=100.70 Aligned_cols=61 Identities=20% Similarity=0.207 Sum_probs=54.1
Q ss_pred CCcceeeccccccCCcHHHHHHhhhhh-cceeeeEEcCCCchHHHHHhcC---CcchhhHHHHHHHhH
Q psy11240 2 NTIHDVMIAGLGTSTSKEAKEYFSNME-RHRILFKYSGDNDDAHIRMAFS---KKLVDERKTWLTTWM 65 (363)
Q Consensus 2 ~~w~iKYyKGLGTst~~eakeyF~~l~-~h~~~f~~~~~~d~~~i~~aF~---kk~~d~RK~Wl~~~~ 65 (363)
++|.|+||||||++++++++|||.|.. ||.+++.+. |...++.+|+ ++++++||+||..+-
T Consensus 582 ~~~~IqryKGLGem~~~~l~ettmdp~~R~l~~v~l~---d~~~~~~~f~~lmg~~~~~Rk~~I~~~~ 646 (654)
T TIGR01059 582 KGIEIQRYKGLGEMNADQLWETTMDPESRTLLKVTIE---DAVEADRIFSTLMGDEVEPRREFIEANA 646 (654)
T ss_pred CCcceeeeCchhhcCHHHHHHHhcCcccceeeeeecc---hHHHHHHHHHHHhCCCchHHHHHHHHhh
Confidence 479999999999999999999999976 999999984 3457889999 788999999998874
No 25
>COG0187 GyrB Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), B subunit [DNA replication, recombination, and repair]
Probab=97.41 E-value=9.3e-05 Score=78.99 Aligned_cols=60 Identities=20% Similarity=0.226 Sum_probs=49.4
Q ss_pred CCcceeeccccccCCcHHHHHHhhhhhcceeeeEEcCCCchHHHHHhcCCcc---hhhHHHHHHH
Q psy11240 2 NTIHDVMIAGLGTSTSKEAKEYFSNMERHRILFKYSGDNDDAHIRMAFSKKL---VDERKTWLTT 63 (363)
Q Consensus 2 ~~w~iKYyKGLGTst~~eakeyF~~l~~h~~~f~~~~~~d~~~i~~aF~kk~---~d~RK~Wl~~ 63 (363)
++|+|.+|||||++.+++..|+|.|.+.|++.++-.. |...+|.+|+... ++.||+|+..
T Consensus 563 ~~~~IqRyKGLGEMnp~QLwETTmdP~~R~L~~V~i~--da~~ad~~f~~LMGd~ve~Rr~fIe~ 625 (635)
T COG0187 563 KGYEIQRYKGLGEMNPDQLWETTMDPETRRLLQVTIE--DADEADEIFSTLMGDKVEPRRNFIEE 625 (635)
T ss_pred CCceeEeecccCCCCHHHHHHhccCccceeEEEEEcc--cHHHHHHHHHHHcCCCchHHHHHHHH
Confidence 4899999999999999999999999999999888764 4455999998754 5556666654
No 26
>PF00986 DNA_gyraseB_C: DNA gyrase B subunit, carboxyl terminus The Prosite motif does not match this Pfam entry.; InterPro: IPR002288 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils []. Type IIA topoisomerases together manage chromosome integrity and topology in cells. Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively; this topoisomerase II forms a homodimer that is equivalent to the bacterial heterotetramer. There are four functional domains in topoisomerase II: domain 1 (N-terminal of gyrB) is an ATPase, domain 2 (C-terminal of gyrB) is responsible for subunit interactions, domain 3 (N-terminal of gyrA) is responsible for the breaking-rejoining function through its capacity to form protein-DNA bridges, and domain 4 (C-terminal of gyrA) is able to non-specifically bind DNA []. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication []. Topoisomerase IV consists of two polypeptide subunits, parE and parC, where parC is homologous to gyrA and parE is homologous to gyrB. This entry represents the C-terminal region (C-terminal part of domain 2) of subunit B found in topoisomerase II (gyrB) and topoisomerase IV (parE), which are primarily of bacterial origin. It does not include the topoisomerase II enzymes composed of a single polypeptide, as are found in most eukaryotes. This region is involved in subunit interaction, which accounts for the difference between subunit B and single polypeptide topoisomerase II. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0005694 chromosome; PDB: 3LTN_D 3RAF_C 3FOF_C 3RAE_C 3KSA_D 3RAD_C 3FOE_D 3KSB_D 3K9F_D 2XCT_D ....
Probab=95.00 E-value=0.054 Score=42.65 Aligned_cols=60 Identities=18% Similarity=0.244 Sum_probs=44.7
Q ss_pred CCcceeeccccccCCcHHHHHHhhhh-hcceeeeEEcCC-CchHHHHHhcCCcchhhHHHHHH
Q psy11240 2 NTIHDVMIAGLGTSTSKEAKEYFSNM-ERHRILFKYSGD-NDDAHIRMAFSKKLVDERKTWLT 62 (363)
Q Consensus 2 ~~w~iKYyKGLGTst~~eakeyF~~l-~~h~~~f~~~~~-~d~~~i~~aF~kk~~d~RK~Wl~ 62 (363)
+++.|-=|||||-.++++-+|..=|= .|..++-...+. ..++++++-..+ .++.||+||.
T Consensus 4 ~~~~I~RfKGLGEM~p~qL~eTTmdP~~R~L~~V~i~d~~~~~~~~~~LMG~-~v~~Rr~fIe 65 (65)
T PF00986_consen 4 KKVEIQRFKGLGEMNPDQLWETTMDPETRRLIRVTIEDAEEADELFEMLMGK-NVEPRREFIE 65 (65)
T ss_dssp TTTEEEESSSGGGS-HHHHHHHHTSTTTTEEEEEEHCCHHHHHHHHHHHHSS-THHHHHHHHH
T ss_pred CCceeEEecccccCCHHHHHHHccCccceEEEEEEECCHHHHHHHHHHHcCC-CcHHHHHHhC
Confidence 46889999999999999999986553 455566665421 345677777788 6999999984
No 27
>PHA02569 39 DNA topoisomerase II large subunit; Provisional
Probab=93.29 E-value=0.067 Score=57.67 Aligned_cols=31 Identities=23% Similarity=0.281 Sum_probs=27.0
Q ss_pred eeeEEcCCCchHHHHHhcCCcchhhHHHHHHH
Q psy11240 32 ILFKYSGDNDDAHIRMAFSKKLVDERKTWLTT 63 (363)
Q Consensus 32 ~~f~~~~~~d~~~i~~aF~kk~~d~RK~Wl~~ 63 (363)
+.|.+.++.++++++|||++ ++++||+||.+
T Consensus 572 l~~~~~~d~~~~~~~~l~g~-~~~~Rk~wi~~ 602 (602)
T PHA02569 572 YDVVVLPDDWKELFEMLFGD-DADLRKDWMSQ 602 (602)
T ss_pred cEEEecCchHHHHHHHHhCC-CchHHHHHhhC
Confidence 66777777799999999998 69999999964
No 28
>KOG0355|consensus
Probab=88.34 E-value=0.15 Score=56.62 Aligned_cols=117 Identities=13% Similarity=-0.081 Sum_probs=83.3
Q ss_pred HHHHHHHHHHhhccCCC-----CccccCCCCcceeeEeecccCCCCCceeeeeehhhhhhh-ccCC-CCcchHHHHHHHh
Q psy11240 95 VNKELILFSNMDNERSI-----PSLCDGLKPGSRKVLFTCLKRNDRREVKVAQLAGSVAEH-SAYH-HGEQSLMSTIINL 167 (363)
Q Consensus 95 inkeli~yS~~~~~RsI-----Psv~DGLKP~QRKILy~~~k~~~k~~~KvAql~G~Vse~-~~YH-HGe~Sl~~tiV~M 167 (363)
|++|--.=|+++|.+-| |...++++|..+.+|+|+.+-++..-.=.---.||+|+. ..+| |+..-.++.-++|
T Consensus 81 i~~e~~~isv~nnGkGIPv~~H~~ek~yvpelifg~Lltssny~d~ekK~tggrngygakLcniFs~~f~~Et~d~~~~~ 160 (842)
T KOG0355|consen 81 IDKEKNEISVYNNGKGIPVTIHKVEKVYVPELIFGNLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFTVETADREYKM 160 (842)
T ss_pred EccCCCEEEEEeCCCcceeeecccccccchHHHHhhhhhccccCCCccccccCCCccceeeeeeccccceeeeeehHhHH
Confidence 44444344555665555 567799999999999999987653322223345555555 5688 9999999999999
Q ss_pred hccccccccccccccCCCCCccc----eeec--CC------------------------------C--CccccccCCCcc
Q psy11240 168 AQNFVGSNNINLLQPIGQFGTFL----FIFE--ST------------------------------N--LSGAVVNALDFG 209 (363)
Q Consensus 168 AQdfvGSnNi~Ll~p~G~FGsr~----Yi~t--s~------------------------------P--iP~vLvNGa~GI 209 (363)
||-+ +-.-|+...++++++.. |+.+ +| | +|.-+-|++.++
T Consensus 161 ~~kQ--~w~~nm~~~~~~~i~~~~~~~yTkitF~PDl~~F~m~eLD~Div~l~~rr~~d~a~~~~~vkv~ln~~~~~~~~ 238 (842)
T KOG0355|consen 161 AFKQ--TWINNMTRDEEPKIVPSTDEDYTKITFSPDLEKFKMKELDDDIVALMARRAYDLAGSVKSVKVELNGKNIPVKG 238 (842)
T ss_pred HHHH--hhhcCCcccCCceeecCCCCCcceEEeCcChHhcCchhhcchHHHhHHhhhhhhcccccceeeeecCCCCccch
Confidence 9877 44556778999999998 7665 55 3 566667777777
Q ss_pred cccc
Q psy11240 210 SGGW 213 (363)
Q Consensus 210 gtG~ 213 (363)
..+|
T Consensus 239 f~~y 242 (842)
T KOG0355|consen 239 FYDY 242 (842)
T ss_pred HHHH
Confidence 7776
No 29
>KOG3441|consensus
Probab=69.19 E-value=5.1 Score=35.65 Aligned_cols=49 Identities=31% Similarity=0.498 Sum_probs=36.3
Q ss_pred CCceeeeeehhhhhhhccCC-CCcchHHHHHHHhhccccccccccccccCCC-CCccceeecCCCCccccc
Q psy11240 135 RREVKVAQLAGSVAEHSAYH-HGEQSLMSTIINLAQNFVGSNNINLLQPIGQ-FGTFLFIFESTNLSGAVV 203 (363)
Q Consensus 135 k~~~KvAql~G~Vse~~~YH-HGe~Sl~~tiV~MAQdfvGSnNi~Ll~p~G~-FGsr~Yi~ts~PiP~vLv 203 (363)
+...|-|-++|.| .|- ||- .-.-|||+-|+|-.|| .|+|. ..|||+.|-
T Consensus 80 kGQmkKa~vVGh~----~~~k~~~------------P~fDsNniVLiddnGnPlGtRI----~~PIPT~Lr 130 (149)
T KOG3441|consen 80 KGQMKKAYVVGHV----HYRKHGV------------PVFDSNNIVLIDDNGNPLGTRI----TAPIPTKLR 130 (149)
T ss_pred ecceeeeEEEEee----ccCCCCC------------cccCCCcEEEECCCCCcccceE----eccCcHHHH
Confidence 5567778899966 566 773 2224999999999998 68887 126888876
No 30
>PF09996 DUF2237: Uncharacterized protein conserved in bacteria (DUF2237); InterPro: IPR018714 This family of hypothetical proteins has no known function.; PDB: 2LQ3_A 3USH_B.
Probab=32.87 E-value=43 Score=29.48 Aligned_cols=34 Identities=38% Similarity=0.592 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHh---hccCCCCcc-ccCCCCcceeeEe
Q psy11240 94 FVNKELILFSNM---DNERSIPSL-CDGLKPGSRKVLF 127 (363)
Q Consensus 94 finkeli~yS~~---~~~RsIPsv-~DGLKP~QRKILy 127 (363)
.|.+|++.||.+ |..-..|.. .-|||||+|=-|=
T Consensus 41 ~vT~eFL~fs~~~GNDL~tP~P~~~FpGLkpGd~WClC 78 (117)
T PF09996_consen 41 VVTEEFLEFSKSRGNDLSTPRPEFGFPGLKPGDRWCLC 78 (117)
T ss_dssp E--HHHHHHHHHCCS-SSSSCCCGTBSS--TT-ECCE-
T ss_pred hhCHHHHHHHHHhCCCCCCCCccCCCCCCCCCCceEec
Confidence 356899999998 344455554 4799999996553
No 31
>COG2143 Thioredoxin-related protein [Posttranslational modification, protein turnover, chaperones]
Probab=30.23 E-value=2.3e+02 Score=26.66 Aligned_cols=68 Identities=24% Similarity=0.322 Sum_probs=43.8
Q ss_pred CCCceeEEEEEeCCCCChHHHHHhHhhhccceeeeccceEEEEecCCc----ccccCCHHHHHHHHHHHHHHHHHHHH
Q psy11240 224 HTDTTVKFVVTMSPDKLHKAEMDGLHKVFKLQTTLAISSMCAFDRYGV----LTKFDTTNQILKEFYAVRLEYYAKRK 297 (363)
Q Consensus 224 ~~~~~v~f~I~l~~~~~~~~~~~~L~k~fkL~~s~~~~nm~lfd~~g~----i~ky~~~~eIl~~F~~~Rl~~y~kRk 297 (363)
++.++|.|.+..+...++ .+.|...|+.+++ .+.+.||.+|+ |+-|..+++.|.--=-+-.+.|++-+
T Consensus 86 ~~skpv~f~~g~kee~~s---~~ELa~kf~vrst---PtfvFfdk~Gk~Il~lPGY~ppe~Fl~vlkYVa~g~ykd~~ 157 (182)
T COG2143 86 SYSKPVLFKVGDKEEKMS---TEELAQKFAVRST---PTFVFFDKTGKTILELPGYMPPEQFLAVLKYVADGKYKDTK 157 (182)
T ss_pred ccCcceEeecCceeeeec---HHHHHHHhccccC---ceEEEEcCCCCEEEecCCCCCHHHHHHHHHHHHHHHHhhhc
Confidence 334556666655544444 2467777888754 67999999985 67788888876654444555555433
No 32
>TIGR03333 salvage_mtnX 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase. Members of this family are the methionine salvage enzyme MnxX, a member of the HAD-superfamily hydrolases, subfamily IB (see TIGR01488). Members are found in Bacillus subtilis and related species, paired with MtnW (TIGR03332). In most species that recycle methionine from methylthioadenosine, the single protein MtnC replaces the MtnW/MtnX pair. In B. subtilis, mtnX was first known as ykrX.
Probab=29.28 E-value=2.6e+02 Score=25.41 Aligned_cols=25 Identities=28% Similarity=0.348 Sum_probs=19.4
Q ss_pred EEEEecCCcccccCCHHHHHHHHHH
Q psy11240 263 MCAFDRYGVLTKFDTTNQILKEFYA 287 (363)
Q Consensus 263 m~lfd~~g~i~ky~~~~eIl~~F~~ 287 (363)
+++||=+|.|.+-++...+++.|..
T Consensus 1 ~~~fDFDgTit~~d~~~~~~~~~~~ 25 (214)
T TIGR03333 1 FIICDFDGTITNNDNIISIMKQFAP 25 (214)
T ss_pred CEEeccCCCCCcchhHHHHHHHhCc
Confidence 3678888999888888888877754
No 33
>PF12395 DUF3658: Protein of unknown function ; InterPro: IPR022123 This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with PF08874 from PFAM. There are two completely conserved residues (D and R) that may be functionally important.
Probab=27.20 E-value=1.3e+02 Score=25.42 Aligned_cols=81 Identities=20% Similarity=0.212 Sum_probs=49.5
Q ss_pred hhhHHHHHHHhHHHhhhhhccCCcccccccCcceeecHHHHHHHHHHHHHHhhccCCCCccccCCCCcceeeEeecccCC
Q psy11240 54 VDERKTWLTTWMEECRRRKEMGIGEDYLYTKTTKAITYTEFVNKELILFSNMDNERSIPSLCDGLKPGSRKVLFTCLKRN 133 (363)
Q Consensus 54 ~d~RK~Wl~~~~~~~~~~~~~~~~~~~l~d~~~~~i~~~dfinkeli~yS~~~~~RsIPsv~DGLKP~QRKILy~~~k~~ 133 (363)
+++|......|.. .++.+-|=...-+..+..++. ||++.-++. ..
T Consensus 13 ~~~~~~l~~eW~~----L~~~n~~LR~w~~g~i~sv~e-d~yD~~Il~------------------------------~~ 57 (111)
T PF12395_consen 13 AEERQRLANEWEE----LKEENAPLRIWENGKIVSVPE-DYYDDFILE------------------------------QA 57 (111)
T ss_pred HHHHHHHHHHHHH----HHhCCCceEEEECCeEEecCh-HHhhHHHHh------------------------------cC
Confidence 4566666666653 222233323333667888887 888888776 22
Q ss_pred CCCceeeeeehhhhhhhccCCCCcchHHHHHHHhhc
Q psy11240 134 DRREVKVAQLAGSVAEHSAYHHGEQSLMSTIINLAQ 169 (363)
Q Consensus 134 ~k~~~KvAql~G~Vse~~~YHHGe~Sl~~tiV~MAQ 169 (363)
...+.|+|+++|.|..+..-.=||.=+.-=|=.|++
T Consensus 58 ~~~~~~~arvIg~vl~~~~~~i~D~f~~~Ri~~Li~ 93 (111)
T PF12395_consen 58 PDEFQKAARVIGEVLGHSDQGIGDWFLEYRIRELIS 93 (111)
T ss_pred CccccHHHHHHHHHHHhcCcCCChHHHHHHHHHHHH
Confidence 357889999999994443223555555555555665
No 34
>PTZ00109 DNA gyrase subunit b; Provisional
Probab=26.15 E-value=52 Score=37.74 Aligned_cols=62 Identities=18% Similarity=0.128 Sum_probs=43.1
Q ss_pred CcceeeccccccCCcHHHHHHhhhh-hcceeeeEEcC-CCchHHHHHhcCCcchhhHHHHHHHhH
Q psy11240 3 TIHDVMIAGLGTSTSKEAKEYFSNM-ERHRILFKYSG-DNDDAHIRMAFSKKLVDERKTWLTTWM 65 (363)
Q Consensus 3 ~w~iKYyKGLGTst~~eakeyF~~l-~~h~~~f~~~~-~~d~~~i~~aF~kk~~d~RK~Wl~~~~ 65 (363)
++.|.=|||||-..+++-.|-==|= .|.+++-...+ ...++++++-..++ +..||+||.+.-
T Consensus 836 ~~~iqRfKGLGEM~~~qLweTTMdP~~R~L~rv~v~d~~~a~~~~~~LMG~~-~~~Rk~fI~~n~ 899 (903)
T PTZ00109 836 HYEIQRFKGLGEMMADQLWETTMDPKKRILIRITVSDAMRASELIFLLMGED-VQSRKQFIFENS 899 (903)
T ss_pred cccceeeccHhhhhHHHHHHhhhChhhceeeeeeHHHHHHHHHHHHHHhCCC-ChhhHHHHHhhc
Confidence 5788889999999998887653332 33344444322 13457788888877 899999998653
No 35
>KOG1478|consensus
Probab=24.86 E-value=77 Score=31.99 Aligned_cols=74 Identities=12% Similarity=0.142 Sum_probs=44.6
Q ss_pred ccccCC-Cccccccc-cccccccccCCCceeEEEEEeCCCCChHHH--HHhHhhhccceeeeccceEEEEecCCcccccC
Q psy11240 201 AVVNAL-DFGSGGWR-FESNDYKEYHTDTTVKFVVTMSPDKLHKAE--MDGLHKVFKLQTTLAISSMCAFDRYGVLTKFD 276 (363)
Q Consensus 201 vLvNGa-~GIgtG~T-~~I~d~~d~~~~~~v~f~I~l~~~~~~~~~--~~~L~k~fkL~~s~~~~nm~lfd~~g~i~ky~ 276 (363)
+||.|| +|||.|-. -++.. +|++|++.|-+.-..+++++ -+.|...+.= +++..+ .|+.|-.
T Consensus 6 alITGanSglGl~i~~RLl~~-----~De~~~ltl~ltcR~~~kae~vc~~lk~f~p~-~~i~~~-yvlvD~s------- 71 (341)
T KOG1478|consen 6 ALITGANSGLGLAICKRLLAE-----DDENVRLTLCLTCRNMSKAEAVCAALKAFHPK-STIEVT-YVLVDVS------- 71 (341)
T ss_pred EEEecCCCcccHHHHHHHHhc-----cCCceeEEEEEEeCChhHHHHHHHHHHHhCCC-ceeEEE-EEEEehh-------
Confidence 688887 78888762 23322 45578888877777777654 4566555543 355664 7888843
Q ss_pred CHHHHHHHHHHH
Q psy11240 277 TTNQILKEFYAV 288 (363)
Q Consensus 277 ~~~eIl~~F~~~ 288 (363)
|....+....+.
T Consensus 72 Nm~Sv~~A~~di 83 (341)
T KOG1478|consen 72 NMQSVFRASKDI 83 (341)
T ss_pred hHHHHHHHHHHH
Confidence 444444444443
No 36
>TIGR01488 HAD-SF-IB Haloacid Dehalogenase superfamily, subfamily IB, phosphoserine phosphatase-like. Subfamily IA includes the enzyme phosphoserine phosphatase (TIGR00338) as well as three hypothetical equivalogs. Many members of these hypothetical equivalogs have been annotated as PSPase-like or PSPase-family proteins. In particular, the hypothetical equivalog which appears to be most closely related to PSPase contains only Archaea (while TIGR00338 contains only eukaryotes and bacteria) of which some are annotated as PSPases. Although this is a reasonable conjecture, none of these sequences has sufficient evidence for this assignment. If such should be found, this model should be retired while the PSPase model should be broadened to include these sequences.
Probab=23.86 E-value=4.6e+02 Score=22.32 Aligned_cols=25 Identities=28% Similarity=0.461 Sum_probs=18.8
Q ss_pred EEEEecCCcccccCCHHHHHHHHHH
Q psy11240 263 MCAFDRYGVLTKFDTTNQILKEFYA 287 (363)
Q Consensus 263 m~lfd~~g~i~ky~~~~eIl~~F~~ 287 (363)
+++||=+|.|..-++..++++.+..
T Consensus 1 l~~fD~DgTl~~~~s~~~~~~~~~~ 25 (177)
T TIGR01488 1 LAIFDFDGTLTRQDSLIDLLAKLLG 25 (177)
T ss_pred CEEecCccccccchhhHHHHHHHhC
Confidence 3678888888777676777777765
No 37
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.95 E-value=2.7e+02 Score=24.19 Aligned_cols=38 Identities=18% Similarity=0.211 Sum_probs=35.3
Q ss_pred CHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHhchh
Q psy11240 277 TTNQILKEFYAVRLEYYA--KRKDYLEGVLGAEALKLTNQ 314 (363)
Q Consensus 277 ~~~eIl~~F~~~Rl~~y~--kRk~~~l~~l~~~~~~l~nk 314 (363)
|..||-++|==-|-.+|. ||..-+|...++.++..+..
T Consensus 35 Sl~EIAee~~VSRqAIyDnIKr~~~~L~~YE~KL~l~~k~ 74 (105)
T COG2739 35 SLSEIAEEFNVSRQAIYDNIKRTEKILEDYEEKLKLYEKY 74 (105)
T ss_pred cHHHHHHHhCccHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 899999999999999998 99999999999999998854
No 38
>PRK13711 conjugal transfer protein TrbJ; Provisional
Probab=22.54 E-value=33 Score=29.00 Aligned_cols=14 Identities=7% Similarity=-0.021 Sum_probs=12.6
Q ss_pred cccccCCCcccccc
Q psy11240 200 GAVVNALDFGSGGW 213 (363)
Q Consensus 200 ~vLvNGa~GIgtG~ 213 (363)
.+|+-|.+|||||-
T Consensus 27 vlliagisgiatgi 40 (113)
T PRK13711 27 VLLIAGISGIATGI 40 (113)
T ss_pred EEEEeccccceeeE
Confidence 57889999999998
No 39
>COG5504 Predicted Zn-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=22.45 E-value=44 Score=33.22 Aligned_cols=21 Identities=29% Similarity=0.597 Sum_probs=19.2
Q ss_pred cCCCCcchHHHHHH--Hhhcccc
Q psy11240 152 AYHHGEQSLMSTII--NLAQNFV 172 (363)
Q Consensus 152 ~YHHGe~Sl~~tiV--~MAQdfv 172 (363)
.||||+.||-++|| +||++||
T Consensus 158 ~~~eg~vtLle~lV~EGLAE~av 180 (280)
T COG5504 158 DYGEGSVTLLEALVMEGLAEHAV 180 (280)
T ss_pred ccCCCceeHHHHHHHHHHHHHHH
Confidence 78899999999998 8999985
No 40
>PRK09552 mtnX 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase; Reviewed
Probab=22.28 E-value=3.2e+02 Score=24.90 Aligned_cols=25 Identities=28% Similarity=0.282 Sum_probs=19.4
Q ss_pred EEEEecCCcccccCCHHHHHHHHHH
Q psy11240 263 MCAFDRYGVLTKFDTTNQILKEFYA 287 (363)
Q Consensus 263 m~lfd~~g~i~ky~~~~eIl~~F~~ 287 (363)
+++||=+|.|...++...+++.|..
T Consensus 5 ~vifDfDgTi~~~d~~~~~~~~~~~ 29 (219)
T PRK09552 5 QIFCDFDGTITNNDNIIAIMKKFAP 29 (219)
T ss_pred EEEEcCCCCCCcchhhHHHHHHhCH
Confidence 6889999998888777777777643
No 41
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=21.92 E-value=51 Score=23.97 Aligned_cols=31 Identities=10% Similarity=0.305 Sum_probs=24.8
Q ss_pred HHHhhhcceeEcccchHHHHHHHHHcCCCCC
Q psy11240 318 IVEKCDGDLRIENRKKKEMIAELIKRKYDSD 348 (363)
Q Consensus 318 I~~vi~~~i~i~~k~k~~l~~~L~~~~f~~~ 348 (363)
+..++++.=.|....++.+.+.++++||.|+
T Consensus 16 VSr~ln~~~~vs~~tr~rI~~~a~~lgY~pN 46 (46)
T PF00356_consen 16 VSRVLNGPPRVSEETRERILEAAEELGYRPN 46 (46)
T ss_dssp HHHHHTTCSSSTHHHHHHHHHHHHHHTB-SS
T ss_pred HHHHHhCCCCCCHHHHHHHHHHHHHHCCCCC
Confidence 4566778767777899999999999999984
Done!