Query 010553
Match_columns 507
No_of_seqs 207 out of 1407
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 01:52:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010553.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010553hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0187 GyrB Type IIA topoisom 100.0 2E-168 4E-173 1328.5 51.6 495 1-507 140-635 (635)
2 TIGR01058 parE_Gpos DNA topois 100.0 1E-154 3E-159 1266.9 51.5 486 1-500 138-630 (637)
3 PTZ00109 DNA gyrase subunit b; 100.0 3E-154 7E-159 1268.6 51.9 494 1-499 273-901 (903)
4 PRK05644 gyrB DNA gyrase subun 100.0 2E-149 4E-154 1230.5 53.1 494 2-507 142-638 (638)
5 PRK05559 DNA topoisomerase IV 100.0 9E-149 2E-153 1224.5 51.6 483 1-500 141-628 (631)
6 PRK14939 gyrB DNA gyrase subun 100.0 6E-147 1E-151 1214.9 49.3 495 1-507 141-756 (756)
7 smart00433 TOP2c Topoisomerase 100.0 1E-146 3E-151 1202.9 51.0 485 1-498 105-594 (594)
8 TIGR01055 parE_Gneg DNA topois 100.0 2E-146 4E-151 1202.6 50.5 482 2-498 135-623 (625)
9 TIGR01059 gyrB DNA gyrase, B s 100.0 9E-145 2E-149 1200.6 52.7 495 2-507 135-654 (654)
10 PHA02569 39 DNA topoisomerase 100.0 2E-136 5E-141 1116.2 46.4 438 2-495 154-602 (602)
11 PTZ00108 DNA topoisomerase 2-l 100.0 2E-133 5E-138 1150.5 47.8 469 1-503 168-654 (1388)
12 PLN03128 DNA topoisomerase 2; 100.0 3E-130 7E-135 1117.5 48.8 471 1-503 160-647 (1135)
13 PLN03237 DNA topoisomerase 2; 100.0 7E-127 1E-131 1091.9 47.8 463 1-503 185-672 (1465)
14 KOG0355 DNA topoisomerase type 100.0 2.7E-93 5.9E-98 768.2 25.7 466 2-498 161-637 (842)
15 cd03366 TOPRIM_TopoIIA_GyrB TO 100.0 1E-60 2.3E-65 409.6 11.5 114 288-402 1-114 (114)
16 cd01030 TOPRIM_TopoIIA_like TO 100.0 2E-59 4.2E-64 404.0 10.7 115 288-402 1-115 (115)
17 cd03365 TOPRIM_TopoIIA TOPRIM_ 100.0 4.2E-56 9E-61 385.6 8.7 115 288-402 1-120 (120)
18 cd00822 TopoII_Trans_DNA_gyras 100.0 1.6E-43 3.5E-48 331.8 20.3 170 90-260 1-171 (172)
19 PF00204 DNA_gyraseB: DNA gyra 100.0 4.1E-42 8.8E-47 323.1 20.3 168 91-260 1-172 (173)
20 cd03481 TopoIIA_Trans_ScTopoII 100.0 2.1E-32 4.6E-37 250.9 14.4 145 91-247 2-149 (153)
21 PF00986 DNA_gyraseB_C: DNA gy 99.9 2.5E-27 5.4E-32 183.8 6.0 63 432-494 3-65 (65)
22 PF01751 Toprim: Toprim domain 99.2 7.8E-12 1.7E-16 107.0 3.5 97 289-400 1-98 (100)
23 cd00329 TopoII_MutL_Trans MutL 98.8 1.3E-08 2.8E-13 86.9 7.5 100 93-210 2-106 (107)
24 PRK00095 mutL DNA mismatch rep 98.5 4.2E-06 9E-11 93.7 17.1 193 2-232 120-326 (617)
25 PRK14939 gyrB DNA gyrase subun 97.8 1.7E-06 3.7E-11 97.8 -3.5 48 437-485 575-623 (756)
26 PRK04184 DNA topoisomerase VI 96.2 0.79 1.7E-05 50.6 21.5 99 119-233 353-461 (535)
27 TIGR00585 mutl DNA mismatch re 94.6 0.83 1.8E-05 47.0 14.2 149 26-203 138-301 (312)
28 cd00188 TOPRIM Topoisomerase-p 92.9 0.12 2.6E-06 40.6 3.6 71 289-385 2-72 (83)
29 TIGR01052 top6b DNA topoisomer 92.2 0.41 8.9E-06 52.2 7.6 98 119-232 348-455 (488)
30 cd00823 TopoIIB_Trans TopoIIB_ 89.3 4.1 8.8E-05 37.4 10.0 89 119-222 33-127 (151)
31 PF09239 Topo-VIb_trans: Topoi 87.8 4.7 0.0001 37.3 9.5 89 119-222 42-136 (160)
32 PRK04017 hypothetical protein; 80.7 0.51 1.1E-05 42.5 0.0 29 359-387 64-92 (132)
33 PRK14867 DNA topoisomerase VI 74.5 30 0.00065 39.4 11.6 99 119-233 498-614 (659)
34 TIGR01052 top6b DNA topoisomer 72.4 47 0.001 36.6 12.2 45 28-76 162-206 (488)
35 PRK14868 DNA topoisomerase VI 69.7 44 0.00096 38.6 11.5 103 119-233 542-655 (795)
36 COG1389 DNA topoisomerase VI, 66.8 73 0.0016 34.7 11.7 100 119-234 357-465 (538)
37 COG1658 Small primase-like pro 65.0 5.9 0.00013 35.5 2.8 25 357-381 52-76 (127)
38 PF10691 DUF2497: Protein of u 63.7 16 0.00035 29.5 4.8 33 214-246 34-67 (73)
39 cd01027 TOPRIM_RNase_M5_like T 61.6 1.1 2.4E-05 36.8 -2.2 27 360-386 45-71 (81)
40 cd01028 TOPRIM_TopoIA TOPRIM_T 55.8 9.4 0.0002 34.5 2.6 25 360-384 91-115 (142)
41 PF13662 Toprim_4: Toprim doma 53.5 2.1 4.6E-05 34.7 -1.9 18 360-377 46-63 (81)
42 PRK04031 DNA primase; Provisio 45.1 18 0.00039 38.5 3.0 53 359-428 209-262 (408)
43 cd03363 TOPRIM_TopoIA_TopoI TO 42.9 18 0.00038 32.1 2.2 24 361-384 74-97 (123)
44 PF14484 FISNA: Fish-specific 40.5 16 0.00035 29.5 1.4 13 287-299 30-42 (73)
45 TIGR00334 5S_RNA_mat_M5 ribonu 39.4 23 0.0005 33.5 2.5 23 359-381 46-68 (174)
46 cd03362 TOPRIM_TopoIA_TopoIII 34.2 36 0.00079 31.0 2.9 25 360-384 99-123 (151)
47 PRK14867 DNA topoisomerase VI 27.7 84 0.0018 35.9 4.9 44 27-74 167-210 (659)
48 PF11169 DUF2956: Protein of u 26.2 1.4E+02 0.003 25.8 4.7 24 203-232 18-41 (103)
49 cd01026 TOPRIM_OLD TOPRIM_OLD: 26.0 25 0.00055 29.4 0.3 58 290-375 6-70 (97)
50 smart00493 TOPRIM topoisomeras 24.8 54 0.0012 25.5 2.0 20 361-380 48-67 (76)
51 cd03361 TOPRIM_TopoIA_RevGyr T 24.1 57 0.0012 30.6 2.3 25 360-384 119-143 (170)
52 cd06404 PB1_aPKC PB1 domain is 23.2 3.4E+02 0.0073 22.6 6.3 67 32-103 4-72 (83)
53 cd00818 IleRS_core catalytic c 22.8 2.8E+02 0.0061 28.8 7.4 97 334-449 90-206 (338)
54 KOG4174 Uncharacterized conser 20.1 7.7E+02 0.017 25.0 9.3 64 334-400 104-189 (282)
No 1
>COG0187 GyrB Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), B subunit [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.7e-168 Score=1328.46 Aligned_cols=495 Identities=53% Similarity=0.900 Sum_probs=469.2
Q ss_pred CEEEEEecCCCCCCcceeeecCCCCCCCCCeEEEEEeCccccccccCCCHHHHHHHHHHHhccCCCcEEEEeecCCCCCC
Q 010553 1 MEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEK 80 (507)
Q Consensus 1 k~y~q~F~~G~~~~~l~~~~~~~~~~~~~GT~V~F~PD~~iF~~~~~fd~~~l~~Rl~elA~Ln~Gl~I~l~der~~~~~ 80 (507)
++|+|+|++|++++++++++. +.++++||+|+||||++||++ ..|++++|++|||++|||||||+|.|+|+|....
T Consensus 140 k~y~q~f~~G~~~~~l~~ig~--~~~~~~GT~V~F~PD~~iF~~-~~f~~~~l~~RlrelA~L~~gl~I~l~d~r~~~~- 215 (635)
T COG0187 140 KIYRQRFERGVPVTPLEVIGS--TDTKKTGTKVRFKPDPEIFGE-TEFDYEILKRRLRELAFLNKGVKITLTDERTGEE- 215 (635)
T ss_pred EEEEEEEeCCCcCCCceeccc--CCCCCCccEEEEEcChHhcCC-cccCHHHHHHHHHHHhccCCCCEEEEEeccCCcc-
Confidence 579999999999999998821 245679999999999999986 5899999999999999999999999999997631
Q ss_pred CcceeEecCCCHHHHHHHHhcCCCCCCc-eeEEEEeccceEEEEeeeecCCCCCceeeeeeCceecCCCCcchhhHHHHH
Q 010553 81 NQYNEYFFAGGLEEYVQWLNTDKKPLHD-VVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASL 159 (507)
Q Consensus 81 ~~~~~f~~~~Gl~~yv~~l~~~~~~~~~-~i~~~~~~~~~~veval~~s~~~~~~~~~SFvN~I~T~~GGTHv~g~~~al 159 (507)
.. .|||++||.+||++++.+++++++ ++++.++.+++.|||||||+ ++|+++++||||||+|++||||++||++||
T Consensus 216 -~~-~~~y~~Gl~~yv~~l~~~k~~l~~~~~~~~~~~~~~~vEvA~q~~-d~~~e~~~SFvNnI~T~eGGTH~~Gfr~al 292 (635)
T COG0187 216 -KK-EFHYEGGLKDYVEYLNKGKTPLHEEIFYFNGEKDGIAVEVALQWN-DGYSENILSFVNNIPTREGGTHEAGFRSAL 292 (635)
T ss_pred -cc-eeecccHHHHHHHHHhcCCCccccCceecccCccceEEEEEEEEe-cCCceEEEEeecCccCCCCchHHHHHHHHH
Confidence 22 599999999999999999999996 66667777889999999999 899999999999999999999999999999
Q ss_pred HHHHHHHHHhccCCCCcCCCCCHHhHhcccEEEEEEeecCCCCCCccccccCChhhHhhhhHhhHHHHHHHHhhChHHHH
Q 010553 160 TRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLD 239 (507)
Q Consensus 160 ~~~in~~~kk~~~~k~~~~~i~~~diregL~~vvsv~i~nP~FegQTK~kL~n~~v~~~v~~~v~~~l~~~l~~n~~~~~ 239 (507)
+|+||+|+++++++|+++ ++++||||||++||||+||||+|+||||+||+|++++.+|++++.+.|..||++||.+|+
T Consensus 293 tr~in~y~~~~~~~k~~~--l~g~Diregl~aviSvki~~PqFegQTK~KL~n~e~~~~V~~~v~~~~~~~l~enp~~a~ 370 (635)
T COG0187 293 TRAINEYAKKKNLLKEGD--LTGDDIREGLTAVISVKIPDPQFEGQTKEKLGNSEVRSIVEKLVSEAFSLFLEENPQEAK 370 (635)
T ss_pred HHHHHHHHHHhCcCcccC--CCHHHHhhccEEEEEEECCCCCcCcccccccccHHHHHHHHHHHHHHHHHHHHHChHHHH
Confidence 999999999999988766 999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhccccccCCCCCCCCCCCCCCCCCceEEEeecCCCCCcccccCCCCceEeeccCCc
Q 010553 240 SILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGK 319 (507)
Q Consensus 240 ~I~~~~~~~~k~r~aakkar~~~~~k~~~~~~~lpgKL~Dc~~~~~~~~eL~lvEGDSA~gsak~gRdr~~qailPLrGK 319 (507)
.|+++++.+++||+||++||+.+|+|+.++...|||||+||++++|++|||||||||||||||||||||+||||||||||
T Consensus 371 ~i~~k~i~aa~aR~aarkare~~R~k~~~~~~~LpGKLadC~skd~~~~ELfiVEGDSAGGSAKqgRdR~~QAILPLRGK 450 (635)
T COG0187 371 KIVEKAIAAAKAREAARKARELTRRKSALDIPGLPGKLADCTSKDPEKSELFLVEGDSAGGSAKQGRDREFQAILPLRGK 450 (635)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhcccccCCCCCcCcccccCCcccceEEEEecCCcchhhhhccCccceEEecccCc
Confidence 99999999999999999999999999988999999999999999999999999999999999999999999999999999
Q ss_pred cccccccCHHHHhhCcchHHHHHHhcCCccCCcCcccccccceEEEeecCCCCChhhHHHHHHHHHHHHHHHhhcCcEEE
Q 010553 320 ILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYV 399 (507)
Q Consensus 320 iLNv~ka~~~ki~~N~Ei~~li~alG~~~~~~~~~~~~LRY~kiiImtDaD~DG~HI~~Llltff~~~~p~Li~~G~v~~ 399 (507)
|||||+|+.++|++|+||++|++|||||++ .+||+++||||||||||||||||+|||+|||||||||||+||+.||||+
T Consensus 451 iLNVeka~~~kil~N~EI~~ii~AlG~g~~-~~fd~~~LRY~kIiIMTDADvDGaHIrtLLlTfFyr~m~~LIe~G~vyi 529 (635)
T COG0187 451 ILNVEKARLDKILKNEEIQTIITALGTGIG-KDFDLEKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMPPLIENGHVYI 529 (635)
T ss_pred chhhhhccHhhhhhhHHHHHHHHHhCCCCC-CCCChhhCccCcEEEEecCCCChHHHHHHHHHHHHHHhHHHHHcCcEEE
Confidence 999999999999999999999999999995 4599999999999999999999999999999999999999999999999
Q ss_pred ecCCeEEEEeCCEEEEEeCHHHHHHHHHhCCCCCCccceeeeccCCCChhhHHhhhcCcCcceEEeeccccHHHHHHHHH
Q 010553 400 GVPPLYKVERGKQVQYCYDDAELKKVKSSFPSNALYSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFS 479 (507)
Q Consensus 400 ~~tPl~kv~~gk~~~~~y~~~e~~~~~~~~~~~~~~~i~ryKGLGe~~~~~l~et~~~p~~r~l~~v~~~d~~~~~~~f~ 479 (507)
|+||||||++|+++.|+|||.|++..+.++...++|+||||||||||||+|||||||||++|+|.+|+++|+.+|+++|+
T Consensus 530 A~PPLYkv~~~k~~~Y~~~d~E~~~~~~~~~~~~~~~IqRyKGLGEMnp~QLwETTmdP~~R~L~~V~i~da~~ad~~f~ 609 (635)
T COG0187 530 AQPPLYKVKKGKKTFYAYDDEELEKLLERLGKKKGYEIQRYKGLGEMNPDQLWETTMDPETRRLLQVTIEDADEADEIFS 609 (635)
T ss_pred EcCceEEEEcCCceeEeCCHHHHHHHHHHhcccCCceeEeecccCCCCHHHHHHhccCccceeEEEEEcccHHHHHHHHH
Confidence 99999999999999999999999999988743258999999999999999999999999999999999999999999999
Q ss_pred HhcCCCchHHHHHHHhccccCCccCCCC
Q 010553 480 SLMGARVDTRKELIQNAANLVNLDHLDI 507 (507)
Q Consensus 480 ~lmg~~~~~Rk~~i~~~~~~~~~~~~d~ 507 (507)
+|||+++++||+||++|+..+ .++||
T Consensus 610 ~LMGd~ve~Rr~fIe~na~~~--~~~di 635 (635)
T COG0187 610 TLMGDKVEPRRNFIEENALFV--ENLDI 635 (635)
T ss_pred HHcCCCchHHHHHHHHHhhhh--hhccC
Confidence 999999999999999999964 56665
No 2
>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=100.00 E-value=1.2e-154 Score=1266.87 Aligned_cols=486 Identities=45% Similarity=0.763 Sum_probs=457.6
Q ss_pred CEEEEEecCC-CCCCcceeeecCCCCCCCCCeEEEEEeCccccccccCCCHHHHHHHHHHHhccCCCcEEEEeecCCCCC
Q 010553 1 MEYHQKYSRG-KPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPE 79 (507)
Q Consensus 1 k~y~q~F~~G-~~~~~l~~~~~~~~~~~~~GT~V~F~PD~~iF~~~~~fd~~~l~~Rl~elA~Ln~Gl~I~l~der~~~~ 79 (507)
+.|+|+|++| .|+.+++++ +.+.++||+|+||||++||++ ..|++++|.+||+++|||||||+|+|+|+|.+
T Consensus 138 k~~~q~f~~Gg~~~~~l~~~----~~~~~~GT~V~F~PD~~iF~~-~~f~~d~l~~RlrelA~Ln~GL~I~l~der~~-- 210 (637)
T TIGR01058 138 QIYQQRFENGGKIVQSLKKI----GTTKKTGTLVHFHPDPTIFKT-TQFNSNIIKERLKESAFLLKKLKLTFTDKRTN-- 210 (637)
T ss_pred EEEEEEEecCCcCcCCcccc----cCCCCCceEEEEEeCHHHcCC-CccCHHHHHHHHHHHhccCCCcEEEEEecCCC--
Confidence 4699999997 788888776 556779999999999999974 57999999999999999999999999999854
Q ss_pred CCcceeEecCCCHHHHHHHHhcCCCCCCceeEEEEeccceEEEEeeeecCCCCCceeeeeeCceecCCCCcchhhHHHHH
Q 010553 80 KNQYNEYFFAGGLEEYVQWLNTDKKPLHDVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASL 159 (507)
Q Consensus 80 ~~~~~~f~~~~Gl~~yv~~l~~~~~~~~~~i~~~~~~~~~~veval~~s~~~~~~~~~SFvN~I~T~~GGTHv~g~~~al 159 (507)
..++|||++||.+|+++++.+++++++++++.++.+++.||||++|+ ++|+++++||||||+|++|||||+||++||
T Consensus 211 --~~~~f~~~~Gl~~yv~~l~~~k~~l~~~i~~~~~~~~~~vevAl~~~-~~~~e~~~SFvN~I~T~~GGTHv~g~~~aL 287 (637)
T TIGR01058 211 --KTTVFFYENGLVDFVDYINETKETLSQVTYFEGEKNGIEVEVAFQFN-DGDSENILSFANSVKTKEGGTHENGFKLAI 287 (637)
T ss_pred --ceEEEEcCcCHHHHHHHhcCCCCcCCccEEEEEEECCcEEEEEEEEc-CCCCeEEEEeECCccCCCCCcHHHHHHHHH
Confidence 34579999999999999998887777788888877789999999998 688889999999999999999999999999
Q ss_pred HHHHHHHHHhccCCCCcCCCCCHHhHhcccEEEEEEeecCC--CCCCccccccCChhhHhhhhHhhHHHHHHHHhhChHH
Q 010553 160 TRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNP--EFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDV 237 (507)
Q Consensus 160 ~~~in~~~kk~~~~k~~~~~i~~~diregL~~vvsv~i~nP--~FegQTK~kL~n~~v~~~v~~~v~~~l~~~l~~n~~~ 237 (507)
+++||+|+++++++|+++.+++++|||+||++||||++++| +|+||||++|+|++++.+|++++.+.|..||++||..
T Consensus 288 tr~in~~~~~~~~lK~~~~~i~~~diregL~~vIsvki~~pnP~FegQTK~kL~n~~v~~~v~~~v~e~l~~~l~~np~~ 367 (637)
T TIGR01058 288 TDVINSYARKYNLLKEKDKNLEGSDIREGLSAIISVRIPEELIQFEGQTKSKLFSPEARNVVDEIVQDHLFFFLEENNND 367 (637)
T ss_pred HHHHHHHHHHhchhccccccCChhhHhhccEEEEEEecCCCcccccCcccccccChhHHHHHHHHHHHHHHHHHHHCHHH
Confidence 99999999999988877789999999999999999999755 9999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhc--cccccCCCCCCCCCCCCCCCCCceEEEeecCCCCCcccccCCCCceEeec
Q 010553 238 LDSILSKSLSALKAALAAKRARDLVRQK--SVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILP 315 (507)
Q Consensus 238 ~~~I~~~~~~~~k~r~aakkar~~~~~k--~~~~~~~lpgKL~Dc~~~~~~~~eL~lvEGDSA~gsak~gRdr~~qailP 315 (507)
++.|+++++.++++|+||+++|++.|+| +......|||||+||++++|++|||||||||||||||||||||+||||||
T Consensus 368 a~~Iiek~~~~a~aR~aa~~ar~~~r~~~k~~~~~~~lpgKL~dc~~~~~~~~eLfivEGDSAggsak~gRdr~~qailP 447 (637)
T TIGR01058 368 AKLLIDKAIKARDAKEAAKKAREEKKSGKKPKKEKGILSGKLTPAQSKNPAKNELFLVEGDSAGGSAKQGRDRKFQAILP 447 (637)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccCCCCcccccccCCCCCccEEEEEecCccccccccccccceEEEec
Confidence 9999999999999999999999999874 35566679999999999999999999999999999999999999999999
Q ss_pred cCCccccccccCHHHHhhCcchHHHHHHhcCCccCCcCcccccccceEEEeecCCCCChhhHHHHHHHHHHHHHHHhhcC
Q 010553 316 LRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEG 395 (507)
Q Consensus 316 LrGKiLNv~ka~~~ki~~N~Ei~~li~alG~~~~~~~~~~~~LRY~kiiImtDaD~DG~HI~~Llltff~~~~p~Li~~G 395 (507)
|||||||||+++.++|++|+||++|++|||||+ +++||+++||||||||||||||||+|||||||||||||||+||++|
T Consensus 448 LRGKiLNv~ka~~~ki~~N~Ei~~l~~alG~~~-g~~~~~~~LRY~kIiImTDADvDGsHIr~LLltff~r~~p~Li~~G 526 (637)
T TIGR01058 448 LRGKVLNVEKAKLADILKNEEINTIIFCIGTGI-GADFSIKDLKYDKIIIMTDADTDGAHIQVLLLTFFYRYMRPLIELG 526 (637)
T ss_pred cCCcccccccCCHHHHhcchHHHHHHHHhCCCc-CccCCccccccceEEEEeCCCCCcchhHHHHHHHHHHhCHhhccCC
Confidence 999999999999999999999999999999999 5679999999999999999999999999999999999999999999
Q ss_pred cEEEecCCeEEEEeC--CEEEEEeCHHHHHHHHHhCCCCCCccceeeeccCCCChhhHHhhhcCcCcceEEeeccccHHH
Q 010553 396 CIYVGVPPLYKVERG--KQVQYCYDDAELKKVKSSFPSNALYSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAE 473 (507)
Q Consensus 396 ~v~~~~tPl~kv~~g--k~~~~~y~~~e~~~~~~~~~~~~~~~i~ryKGLGe~~~~~l~et~~~p~~r~l~~v~~~d~~~ 473 (507)
|||+|+||||||++| ++++||||++|+++|++++ ++|+||||||||||+|+|||||||||++|+|.+|+++|+..
T Consensus 527 ~v~~~~~Pl~kv~~~~~~~~~y~~~~~e~~~~~~~~---~~~~i~ryKGLGem~~~~l~ettm~p~~r~l~~v~~~d~~~ 603 (637)
T TIGR01058 527 HVYIALPPLYKLSKKDGKKVKYAWSDLELESVKKKL---KNYTLQRYKGLGEMNADQLWETTMNPETRTLVRVKIDDLAR 603 (637)
T ss_pred eEEEecCCEEEEEeCCCceEEEeCCHHHHHHHHHhc---CCCCceEECchhhhhHHHHHHHhhCcccceeeEEehhhhhh
Confidence 999999999999984 6788999999999999874 47999999999999999999999999999999999999999
Q ss_pred HHHHHHHhcCCCchHHHHHHHhccccC
Q 010553 474 ANVVFSSLMGARVDTRKELIQNAANLV 500 (507)
Q Consensus 474 ~~~~f~~lmg~~~~~Rk~~i~~~~~~~ 500 (507)
++.+|++|||+++++||+||++|+..+
T Consensus 604 ~~~~~~~lmg~~~~~Rk~~i~~~~~~~ 630 (637)
T TIGR01058 604 AERQINTLMGDKVEPRKKWIEANINFS 630 (637)
T ss_pred HHHHHHHHcCCCchHHHHHHHHhhhhh
Confidence 999999999999999999999999765
No 3
>PTZ00109 DNA gyrase subunit b; Provisional
Probab=100.00 E-value=3.3e-154 Score=1268.59 Aligned_cols=494 Identities=43% Similarity=0.718 Sum_probs=458.4
Q ss_pred CEEEEEecCCCCCCcceeeecCCCCC-CCCCeEEEEEeC-ccccccccC-------------CCHHHHHHHHHHHhccCC
Q 010553 1 MEYHQKYSRGKPVTTLTCHVLPVDSK-DRQGTRIRFWPD-KQVFTTAIQ-------------FDHNTIAGRIRELAFLNP 65 (507)
Q Consensus 1 k~y~q~F~~G~~~~~l~~~~~~~~~~-~~~GT~V~F~PD-~~iF~~~~~-------------fd~~~l~~Rl~elA~Ln~ 65 (507)
++|+|+|++|+++.|++++ +++ +++||+|+|||| ++||+++.. |++++|.+||+++|||||
T Consensus 273 K~y~q~F~rG~~v~pLkvi----g~~~~~tGT~VtF~PD~~~IF~~~~~~~~~~~~~~~~~~F~~d~L~~RLrElAfLNp 348 (903)
T PTZ00109 273 KIYSIELSKGKVTKPLSVF----SCPLKKRGTTIHFLPDYKHIFKTHHQHTETEEEEGCKNGFNLDLIKNRIHELSYLNP 348 (903)
T ss_pred EEEEEEeCCCcccCCcccc----CCcCCCCceEEEEEeCcchhcCccccccccccccccccccCHHHHHHHHHHHhccCC
Confidence 4799999999999999877 444 679999999999 999975333 899999999999999999
Q ss_pred CcEEEEeecCCCCCC--CcceeEecCCCHHHHHHHHhcCCCCCC-c--eeEEEEeccceEEEEeeeecCCCCCceeeeee
Q 010553 66 KLTIALRKEDSDPEK--NQYNEYFFAGGLEEYVQWLNTDKKPLH-D--VVGFRKDVDGITIDLALQWCSDAYSDTMLGYA 140 (507)
Q Consensus 66 Gl~I~l~der~~~~~--~~~~~f~~~~Gl~~yv~~l~~~~~~~~-~--~i~~~~~~~~~~veval~~s~~~~~~~~~SFv 140 (507)
||+|+|+|+|...+. ...++|+|++||.+||++++.++++++ + ++++.++.+++.|||||+|++++|+++++|||
T Consensus 349 GL~I~L~DeR~~~~~~~~~~e~f~~egGi~dfv~~ln~~k~~l~~~~~~I~~~g~~~~i~VEVAlq~s~~~y~e~i~SFV 428 (903)
T PTZ00109 349 GLTFYLVDERIANENNFYPYETIKHEGGTREFLEELIKDKTPLYKDINIISIRGVIKNVNVEVSLSWSLESYTALIKSFA 428 (903)
T ss_pred CcEEEEEecCccccCCcceEEEEEecCCHHHHHHHhcCCCCccCCCCceEEEEeeecCeEEEEEEEecCCCCceEEEEEE
Confidence 999999999864210 134679999999999999999888886 3 68888877789999999998557889999999
Q ss_pred CceecCCCCcchhhHHHHHHHHHHHHHHhccCCCCcCCCCCHHhHhcccEEEEEEeecCCCCCCccccccCChhhHhhhh
Q 010553 141 NSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVD 220 (507)
Q Consensus 141 N~I~T~~GGTHv~g~~~al~~~in~~~kk~~~~k~~~~~i~~~diregL~~vvsv~i~nP~FegQTK~kL~n~~v~~~v~ 220 (507)
|+|+|+ |||||+||++||+++||.|+++++++|+++.+++++||||||++||||+++||+|+||||++|+|++++.+|+
T Consensus 429 NnI~T~-GGTHv~Gfr~ALTr~In~y~kk~~llK~k~~~i~gedIREGLtavISvki~~PqFeGQTK~KLgn~~vk~~ve 507 (903)
T PTZ00109 429 NNVSTT-AGTHIDGFKYAITRCVNGNIKKNGYFKGNFVNIPGEFIREGMTAIISVKLNGAEFDGQTKTKLGNHLLKTILE 507 (903)
T ss_pred CCccCC-CCCHHHHHHHHHHHHHHHHHHHhCcccccCCCCCHHHHhhccEEEEEEeccCCcccCcccccccCHHHHHHHH
Confidence 999999 9999999999999999999999999887778999999999999999999999999999999999999999999
Q ss_pred HhhHHHHHHHHhhChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccc-cCCCCCCCCCCCCCCCCCceEEEeecCCCC
Q 010553 221 QSVQEYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDLVRQKSVLR-SSSLPGKLADCSSTTPEESEIFIVEGDSAG 299 (507)
Q Consensus 221 ~~v~~~l~~~l~~n~~~~~~I~~~~~~~~k~r~aakkar~~~~~k~~~~-~~~lpgKL~Dc~~~~~~~~eL~lvEGDSA~ 299 (507)
.++.+.|..||++||++++.|+++++++++||++||+||++.|+|+... ...|||||+||+++++++||||||||||||
T Consensus 508 ~iv~e~L~~~l~~np~~a~~I~~Ka~~a~~AreaAk~arel~R~K~~~~~~~~lPgKL~DC~s~d~~~~ELfIVEGDSAg 587 (903)
T PTZ00109 508 SIVFEQLSEILEFEPNLLLAIYNKSLAAKKAFEEAKAAKDLIRQKNNQYYSTILPGKLVDCISDDIERNELFIVEGESAA 587 (903)
T ss_pred HHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHhhHHHhhhhhcccccCCCCCcccccccCCCcccEEEEEcccCCC
Confidence 9999999999999999999999999999999999999999999987763 366999999999999999999999999999
Q ss_pred CcccccCCCCceEeeccCCccccccccC-HHHHhhCcchHHHHHHhcCCccCC---cCcc--------------------
Q 010553 300 GSAKQGRDRRFQAILPLRGKILNVERKD-EAAMYKNEEIQNLIRALGLGVKGE---DFKK-------------------- 355 (507)
Q Consensus 300 gsak~gRdr~~qailPLrGKiLNv~ka~-~~ki~~N~Ei~~li~alG~~~~~~---~~~~-------------------- 355 (507)
|||||||||+|||||||||||||||+++ .++|++|+||++||+|||||++.. +||+
T Consensus 588 GSAKqgRdR~~QAILPLRGKILNVeka~~~~kil~N~EI~~Li~alG~gig~~~~~~~dl~~~~~~~~~~~~~~~~~~~~ 667 (903)
T PTZ00109 588 GNAKQARNREFQAVLPLKGKILNIEKIKNNKKVFENSEIKLLITSIGLSVNPVTWRQYDLSHGTKASKDESVQNNNSTLT 667 (903)
T ss_pred cccccccCccceeecccCCceehhcccccHHHHHhcHHHHHHHHHhCCCCCcccccccCccccccccccccccccccccc
Confidence 9999999999999999999999999995 999999999999999999999542 6888
Q ss_pred --------cccccceEEEeecCCCCChhhHHHHHHHHHHHHHHHhhcCcEEEecCCeEEEEeC------------CEEEE
Q 010553 356 --------EALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKVERG------------KQVQY 415 (507)
Q Consensus 356 --------~~LRY~kiiImtDaD~DG~HI~~Llltff~~~~p~Li~~G~v~~~~tPl~kv~~g------------k~~~~ 415 (507)
++||||||||||||||||+|||+|||||||||||+||++||||+|+||||||++| |+++|
T Consensus 668 ~~~~~~~~~~LRYgKIIIMTDADVDGsHIrtLLLTff~r~~p~Lie~G~vyia~pPLyki~~~~~~~~~~~~~~~k~~~y 747 (903)
T PTZ00109 668 KKKNSLFDTPLRYGKIILLTDADVDGEHLRILLLTLLYRFCPSLYEHGRVYVACPPLYRITNNRMKQFNVSTKNSKKYIY 747 (903)
T ss_pred ccccccccccCCcCeEEEEeCCCCChhHHHHHHHHHHHHhCHHhhhCCEEEEecCCEEEEEecCcccccccccccceeEE
Confidence 9999999999999999999999999999999999999999999999999999985 77889
Q ss_pred EeCHHHHHHHHHhCC-----------------------------------------------------------------
Q 010553 416 CYDDAELKKVKSSFP----------------------------------------------------------------- 430 (507)
Q Consensus 416 ~y~~~e~~~~~~~~~----------------------------------------------------------------- 430 (507)
+|||+|++.+++++.
T Consensus 748 ~~sd~el~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 827 (903)
T PTZ00109 748 TWSDEELNVLIKLLNKDYSSKETTRSVEEKGNAPDLDNEYEDEKLDNKNMRENNVDEVELKTELGTNVADTEQTDELDIN 827 (903)
T ss_pred eCCHHHHHHHHHHhhccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence 999999999997651
Q ss_pred ----C-CCCccceeeeccCCCChhhHHhhhcCcCcceEEeeccccHHHHHHHHHHhcCCCchHHHHHHHhcccc
Q 010553 431 ----S-NALYSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQNAANL 499 (507)
Q Consensus 431 ----~-~~~~~i~ryKGLGe~~~~~l~et~~~p~~r~l~~v~~~d~~~~~~~f~~lmg~~~~~Rk~~i~~~~~~ 499 (507)
. .++++||||||||||+|+|||||||||++|+|+||+++|+..|+++|++|||+++++||+||.+|+..
T Consensus 828 ~~~~~~~~~~~iqRfKGLGEM~~~qLweTTMdP~~R~L~rv~v~d~~~a~~~~~~LMG~~~~~Rk~fI~~n~~~ 901 (903)
T PTZ00109 828 KAFFKFSKHYEIQRFKGLGEMMADQLWETTMDPKKRILIRITVSDAMRASELIFLLMGEDVQSRKQFIFENSPA 901 (903)
T ss_pred ccccccCCcccceeeccHhhhhHHHHHHhhhChhhceeeeeeHHHHHHHHHHHHHHhCCCChhhHHHHHhhccc
Confidence 0 13689999999999999999999999999999999999999999999999999999999999999874
No 4
>PRK05644 gyrB DNA gyrase subunit B; Validated
Probab=100.00 E-value=1.7e-149 Score=1230.46 Aligned_cols=494 Identities=55% Similarity=0.922 Sum_probs=464.5
Q ss_pred EEEEEecCCCCCCcceeeecCCCCCCCCCeEEEEEeCccccccccCCCHHHHHHHHHHHhccCCCcEEEEeecCCCCCCC
Q 010553 2 EYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKN 81 (507)
Q Consensus 2 ~y~q~F~~G~~~~~l~~~~~~~~~~~~~GT~V~F~PD~~iF~~~~~fd~~~l~~Rl~elA~Ln~Gl~I~l~der~~~~~~ 81 (507)
.|+|+|++|+++.+++.+ +++.++||+|+|+||+++|+ ...|+++.|.+|++++|+|||||+|.|++++.+. .
T Consensus 142 ~~~~~~~~G~~~~~~~~~----~~~~~~GT~I~F~Pd~~~F~-~~~~e~~~i~~rl~~~A~l~pgl~i~l~~er~~~--~ 214 (638)
T PRK05644 142 IYYQEYERGVPVTPLEVI----GETDETGTTVTFKPDPEIFE-TTEFDYDTLATRLRELAFLNKGLKITLTDEREGE--E 214 (638)
T ss_pred EEEEEEECCeEccCcccc----CCcCCCCcEEEEEECHHHcC-CcccCHHHHHHHHHHHHhhCCCcEEEEEeccCCC--c
Confidence 599999999998888766 44567999999999999996 4679999999999999999999999999998542 1
Q ss_pred cceeEecCCCHHHHHHHHhcCCCCCC-ceeEEEEeccceEEEEeeeecCCCCCceeeeeeCceecCCCCcchhhHHHHHH
Q 010553 82 QYNEYFFAGGLEEYVQWLNTDKKPLH-DVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLT 160 (507)
Q Consensus 82 ~~~~f~~~~Gl~~yv~~l~~~~~~~~-~~i~~~~~~~~~~veval~~s~~~~~~~~~SFvN~I~T~~GGTHv~g~~~al~ 160 (507)
..++|+|++||.+|+++++.++++++ +++++.++.++++|||||+|+ ++|+++++||||+|+|++|||||+||+++|+
T Consensus 215 ~~~~f~~~~Gl~dyv~~l~~~~~~~~~~~i~~~~~~~~~~veval~~~-~~~~~~~~SFvN~I~T~~GGTHv~g~~~al~ 293 (638)
T PRK05644 215 KEETFHYEGGIKEYVEYLNRNKEPLHEEPIYFEGEKDGIEVEVAMQYN-DGYSENILSFANNINTHEGGTHEEGFKTALT 293 (638)
T ss_pred ceeEEEcCCCHHHHHHHHhcCCCcCCCCCeEEEeeccCeEEEEEEEec-CCCceEEEEEECcccCCCCCCHHHHHHHHHH
Confidence 35679999999999999998888886 578887776778999999999 6788899999999999999999999999999
Q ss_pred HHHHHHHHhccCCCCcCCCCCHHhHhcccEEEEEEeecCCCCCCccccccCChhhHhhhhHhhHHHHHHHHhhChHHHHH
Q 010553 161 RTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDS 240 (507)
Q Consensus 161 ~~in~~~kk~~~~k~~~~~i~~~diregL~~vvsv~i~nP~FegQTK~kL~n~~v~~~v~~~v~~~l~~~l~~n~~~~~~ 240 (507)
++||+|+++++++|+++.+++++|||+||++||||+|+||+|+||||++|+|++++.+|++++.+.|..||++||+.++.
T Consensus 294 ~~l~~~~~k~~~~Kk~~~~i~~~dIregl~~vVsv~i~nP~F~gQTKekL~~~~v~~~v~~~v~~~l~~~l~~n~~~~~~ 373 (638)
T PRK05644 294 RVINDYARKNKLLKEKDDNLTGEDVREGLTAVISVKHPEPQFEGQTKTKLGNSEVRGIVDSVVSEALSEFLEENPNVAKK 373 (638)
T ss_pred HHHHHHHHHhCcccccCCCCChhHHhhceEEEEEEecCCCcccCcccccccCHHHHHHHHHHHHHHHHHHHHHChHHHHH
Confidence 99999999988887767899999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhccccccCCCCCCCCCCCCCCCCCceEEEeecCCCCCcccccCCCCceEeeccCCcc
Q 010553 241 ILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKI 320 (507)
Q Consensus 241 I~~~~~~~~k~r~aakkar~~~~~k~~~~~~~lpgKL~Dc~~~~~~~~eL~lvEGDSA~gsak~gRdr~~qailPLrGKi 320 (507)
|+++++.++++|++++++|+..|+|+......|||||+||++++|++|||||||||||||||++||||+|||||||||||
T Consensus 374 I~~~~~~~a~~r~~a~~~k~~~r~k~~~~~~~lpgKL~dc~~~~~~~~eLflvEGDSA~gsak~grdr~~qailPLrGKi 453 (638)
T PRK05644 374 IVEKAILAARAREAARKARELTRRKSALESSSLPGKLADCSSKDPEESELYIVEGDSAGGSAKQGRDRRFQAILPLRGKI 453 (638)
T ss_pred HHHHHHHHHHHHHHHHHhHHHhhcccccccCCCCchhcccccCCCCccEEEEEecCCCccccccccCccceeecccCCce
Confidence 99999999999999999999998888877789999999999999999999999999999999999999999999999999
Q ss_pred ccccccCHHHHhhCcchHHHHHHhcCCccCCcCcccccccceEEEeecCCCCChhhHHHHHHHHHHHHHHHhhcCcEEEe
Q 010553 321 LNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVG 400 (507)
Q Consensus 321 LNv~ka~~~ki~~N~Ei~~li~alG~~~~~~~~~~~~LRY~kiiImtDaD~DG~HI~~Llltff~~~~p~Li~~G~v~~~ 400 (507)
||||+++.++|++|+||++|++|||||+ +++||+++|||||||||||||+||+|||+|||||||||||+||++||||+|
T Consensus 454 LNv~~a~~~ki~~N~Ei~~l~~alG~~~-~~~~~~~~LRY~kiiImtDaD~DG~HI~~Llltff~~~~p~Li~~G~l~~~ 532 (638)
T PRK05644 454 LNVEKARLDKILKNEEIRALITALGTGI-GDDFDISKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGYVYIA 532 (638)
T ss_pred eccccCCHHHHHhCHHHHHHHHHhCCCC-CCcCChhhCccCeEEEEeCCCCCchHHHHHHHHHHHHhCHHhccCCeEEEe
Confidence 9999999999999999999999999999 567999999999999999999999999999999999999999999999999
Q ss_pred cCCeEEEEeCCEEEEEeCHHHHHHHHHhCCC--CCCccceeeeccCCCChhhHHhhhcCcCcceEEeeccccHHHHHHHH
Q 010553 401 VPPLYKVERGKQVQYCYDDAELKKVKSSFPS--NALYSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVF 478 (507)
Q Consensus 401 ~tPl~kv~~gk~~~~~y~~~e~~~~~~~~~~--~~~~~i~ryKGLGe~~~~~l~et~~~p~~r~l~~v~~~d~~~~~~~f 478 (507)
+||||||++||++ ||||++||++|+++++. .++|+||||||||||+|+|+|||||||++|.|.+|+++|.+.++++|
T Consensus 533 ~~Pl~kv~~gk~~-~~~~~~e~~~~~~~~~~~~~~~~~i~ryKGLGe~~~~~~~e~~~~~~~r~~~~v~~~d~~~~~~~f 611 (638)
T PRK05644 533 QPPLYKIKKGGKE-YAYSDEELDEILAELKLKGNPKYGIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIF 611 (638)
T ss_pred cCCEEEEEeCCeE-eecCHHHHHHHHHHhccccCCCCceeEecCccccCHHHHHHHhcCccceeeeeeccccHHHHHHHH
Confidence 9999999999988 99999999999988753 35799999999999999999999999999999999999999999999
Q ss_pred HHhcCCCchHHHHHHHhccccCCccCCCC
Q 010553 479 SSLMGARVDTRKELIQNAANLVNLDHLDI 507 (507)
Q Consensus 479 ~~lmg~~~~~Rk~~i~~~~~~~~~~~~d~ 507 (507)
++|||+++++||+||.+|+.. +++||+
T Consensus 612 ~~lmg~~~~~Rk~~i~~~~~~--~~~~d~ 638 (638)
T PRK05644 612 SILMGDDVEPRREFIEENAKY--VRNLDI 638 (638)
T ss_pred HHHhCCCChHHHHHHHHhhhh--HhhccC
Confidence 999999999999999999974 466775
No 5
>PRK05559 DNA topoisomerase IV subunit B; Reviewed
Probab=100.00 E-value=9.5e-149 Score=1224.49 Aligned_cols=483 Identities=43% Similarity=0.771 Sum_probs=454.3
Q ss_pred CEEEEEecCCCCCCcceeeecCCCCC--CCCCeEEEEEeCccccccccCCCHHHHHHHHHHHhccCCCcEEEEeecCCCC
Q 010553 1 MEYHQKYSRGKPVTTLTCHVLPVDSK--DRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDP 78 (507)
Q Consensus 1 k~y~q~F~~G~~~~~l~~~~~~~~~~--~~~GT~V~F~PD~~iF~~~~~fd~~~l~~Rl~elA~Ln~Gl~I~l~der~~~ 78 (507)
+.|.|+|++|+++.+++.+ +.. ..+||+|+|+||+++|+ ...++++.|.+||+++|+|||||+|.|+|++ .
T Consensus 141 ~~~~~~f~~G~~~~~l~~~----~~~~~~~~GT~V~f~PD~~iF~-~~~~~~~~i~~~l~~~A~lnpgl~i~l~d~~-~- 213 (631)
T PRK05559 141 KVYRQRFEGGDPVGPLEVV----GTAGKRKTGTRVRFWPDPKIFD-SPKFSPERLKERLRSKAFLLPGLTITLNDER-E- 213 (631)
T ss_pred eEEEEEEECCcCccCcccc----ccccCCCCCcEEEEEECHHHcC-CcccCHHHHHHHHHHHHhhCCCeEEEEEeCC-c-
Confidence 3599999999999988766 333 67999999999999996 4579999999999999999999999999987 2
Q ss_pred CCCcceeEecCCCHHHHHHHHhcCCCCCCc--eeEEEEeccceEEEEeeeecCCCCCceeeeeeCceecCCCCcchhhHH
Q 010553 79 EKNQYNEYFFAGGLEEYVQWLNTDKKPLHD--VVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVK 156 (507)
Q Consensus 79 ~~~~~~~f~~~~Gl~~yv~~l~~~~~~~~~--~i~~~~~~~~~~veval~~s~~~~~~~~~SFvN~I~T~~GGTHv~g~~ 156 (507)
.+.|+|++||.+|+.+++.+++++++ +++++++.++..|||||+|+ ++|+++++||||||+|++|||||+||+
T Consensus 214 ----~~~f~~~~gl~~~v~~~~~~~~~i~~~~~i~~~~~~~~~~veval~~~-~~~~~~~~SFvN~I~T~~GGTHv~g~~ 288 (631)
T PRK05559 214 ----RQTFHYENGLKDYLAELNEGKETLPEEFVGSFEGEAEGEAVEWALQWT-DEGGENIESYVNLIPTPQGGTHENGFR 288 (631)
T ss_pred ----eEEEECCccHHHHHHHHhCCCCccCCCCceEEeeeeccceEEEEEEec-CCCCeEEEEEECcccCCCCCCHHHHHH
Confidence 45799999999999999988778874 78888877789999999998 678889999999999999999999999
Q ss_pred HHHHHHHHHHHHhccCCCCcCCCCCHHhHhcccEEEEEEeecCCCCCCccccccCChhhHhhhhHhhHHHHHHHHhhChH
Q 010553 157 ASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPD 236 (507)
Q Consensus 157 ~al~~~in~~~kk~~~~k~~~~~i~~~diregL~~vvsv~i~nP~FegQTK~kL~n~~v~~~v~~~v~~~l~~~l~~n~~ 236 (507)
+||+++||+|+++++++| ++.+++++|||+||++||||+|+||+|+||||++|+|++++.+|++++.+.|..||++||.
T Consensus 289 ~al~~~in~~~~~~~l~k-~~~~l~~~diregl~~vvsvki~~P~FegQTK~kL~n~~v~~~v~~~v~~~l~~~l~~n~~ 367 (631)
T PRK05559 289 EGLLKAVREFAEKRNLLP-KGKKLEGEDVREGLAAVLSVKIPEPQFEGQTKEKLGSREARRFVSGVVKDAFDLWLNQNPE 367 (631)
T ss_pred HHHHHHHHHHHHHhCccc-cccCCChhhHhhceEEEEEEEcCCCcccCcccccccCHhHhhhhhhHHHHHHHHHHHHChH
Confidence 999999999999999887 6789999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccCCCCCCCCCCCCCCCCCceEEEeecCCCCCcccccCCCCceEeecc
Q 010553 237 VLDSILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPL 316 (507)
Q Consensus 237 ~~~~I~~~~~~~~k~r~aakkar~~~~~k~~~~~~~lpgKL~Dc~~~~~~~~eL~lvEGDSA~gsak~gRdr~~qailPL 316 (507)
+++.|+++++.++++|++ ++|++.|+|+... ..|||||+||++++|++|||||||||||||||+|||||+|||||||
T Consensus 368 ~a~~ii~k~~~~a~ar~~--~~~~~~r~k~~~~-~~lpgKL~dc~~~~~~~~eL~lvEGDSAggsak~grdr~~qailPL 444 (631)
T PRK05559 368 LAEKLAEKAIKAAQARLR--AAKKVKRKKKTSG-PALPGKLADCTSQDPERTELFLVEGDSAGGSAKQARDREFQAILPL 444 (631)
T ss_pred HHHHHHHHHHHHHHHHHH--HHHHHhhhccccC-CCCCCcCcccccCCCCCCEEEEEeCCCCccccccccCccceeeccc
Confidence 999999999999999997 4788888887766 7899999999999999999999999999999999999999999999
Q ss_pred CCccccccccCHHHHhhCcchHHHHHHhcCCccCCcCcccccccceEEEeecCCCCChhhHHHHHHHHHHHHHHHhhcCc
Q 010553 317 RGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGC 396 (507)
Q Consensus 317 rGKiLNv~ka~~~ki~~N~Ei~~li~alG~~~~~~~~~~~~LRY~kiiImtDaD~DG~HI~~Llltff~~~~p~Li~~G~ 396 (507)
|||||||++|+.+||++|+||++|++|||||+ +++||+++||||||||||||||||+|||||||||||||||+||++||
T Consensus 445 RGKiLNv~~a~~~ki~~N~Ei~~l~~alG~~~-~~~~~~~~LRY~kIiImTDaDvDGsHI~~Llltff~~~~p~Li~~G~ 523 (631)
T PRK05559 445 RGKILNTWEASLDDVLANEEIHDIIVAIGIGP-GDSFDLEDLRYGKIIIMTDADVDGAHIATLLLTFFYRHFPPLVEAGH 523 (631)
T ss_pred CCeecccccCCHHHHhcChhHHHHHHHhCCCC-CCccCccccccCeEEEEeCCCCCcchhHHHHHHHHHHhCHhhccCCe
Confidence 99999999999999999999999999999999 57899999999999999999999999999999999999999999999
Q ss_pred EEEecCCeEEEEeCCEEEEEeCHHHHHHHHHhCC-CCCCccceeeeccCCCChhhHHhhhcCcCcceEEeeccccHHHHH
Q 010553 397 IYVGVPPLYKVERGKQVQYCYDDAELKKVKSSFP-SNALYSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEAN 475 (507)
Q Consensus 397 v~~~~tPl~kv~~gk~~~~~y~~~e~~~~~~~~~-~~~~~~i~ryKGLGe~~~~~l~et~~~p~~r~l~~v~~~d~~~~~ 475 (507)
||+|+||||||++||+++|||||+|+++|+++++ ..++|+||||||||||+|+|||||||||++|+|.+|+++|++.++
T Consensus 524 v~~~~~Pl~kv~~gk~~~y~~~~~e~~~~~~~~~~~~~~~~i~ryKGLGe~~~~~~~e~~~~p~~r~l~~v~~~d~~~~~ 603 (631)
T PRK05559 524 VYIALPPLYRVDKGKKKIYALDEEEKEELLKKLGKKGGKPEIQRFKGLGEMNPDQLWETTMDPETRRLVRVTIDDAEETE 603 (631)
T ss_pred EEEecCCEEEEEcCCceEEecCHHHHHHHHHHhcccCCCCCceEeCchhhcCHHHHHHHhhCccceeEEEEEccchhhHH
Confidence 9999999999999999999999999999998863 235799999999999999999999999999999999999998899
Q ss_pred HHHHHhcCCCchHHHHHHHhccccC
Q 010553 476 VVFSSLMGARVDTRKELIQNAANLV 500 (507)
Q Consensus 476 ~~f~~lmg~~~~~Rk~~i~~~~~~~ 500 (507)
++|++|||+++++||+||++|+..+
T Consensus 604 ~~~~~l~g~~~~~Rk~~i~~~~~~~ 628 (631)
T PRK05559 604 KLVDMLMGKKAEPRREWIEENGDFA 628 (631)
T ss_pred HHHHHHhCCCchHHHHHHHHhhhhh
Confidence 9999999999999999999999754
No 6
>PRK14939 gyrB DNA gyrase subunit B; Provisional
Probab=100.00 E-value=6.4e-147 Score=1214.91 Aligned_cols=495 Identities=48% Similarity=0.827 Sum_probs=465.4
Q ss_pred CEEEEEecCCCCCCcceeeecCCCCCCCCCeEEEEEeCccccccccCCCHHHHHHHHHHHhccCCCcEEEEeecCCCCCC
Q 010553 1 MEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEK 80 (507)
Q Consensus 1 k~y~q~F~~G~~~~~l~~~~~~~~~~~~~GT~V~F~PD~~iF~~~~~fd~~~l~~Rl~elA~Ln~Gl~I~l~der~~~~~ 80 (507)
+.|+|+|++|+++.|++.+ +++.++||+|+|+||+++|+ ...|++++|.+||+++|||||||+|+|+|+|.+
T Consensus 141 k~~~q~f~~G~~~~~l~~~----g~~~~~GT~V~F~PD~~iF~-~~~~~~~~i~~rl~elA~lnpgl~i~l~der~~--- 212 (756)
T PRK14939 141 KIHEQEFEHGVPVAPLKVV----GETDKTGTEVRFWPSPEIFE-NTEFDYDILAKRLRELAFLNSGVRIRLKDERDG--- 212 (756)
T ss_pred eEEEEEEecCccccCcccc----CCcCCCCcEEEEEECHHHcC-CcccCHHHHHHHHHHHhhcCCCCEEEEeccCCC---
Confidence 3699999999999998877 55678999999999999996 457999999999999999999999999999964
Q ss_pred CcceeEecCCCHHHHHHHHhcCCCCCC-ceeEEEEeccceEEEEeeeecCCCCCceeeeeeCceecCCCCcchhhHHHHH
Q 010553 81 NQYNEYFFAGGLEEYVQWLNTDKKPLH-DVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASL 159 (507)
Q Consensus 81 ~~~~~f~~~~Gl~~yv~~l~~~~~~~~-~~i~~~~~~~~~~veval~~s~~~~~~~~~SFvN~I~T~~GGTHv~g~~~al 159 (507)
..++|+|++||.+|+++++.++.+++ +++++.++.+++.||||+||+ ++|+++++||||||+|++|||||+||++||
T Consensus 213 -~~~~f~~egGi~~fv~~l~~~~~~~~~~~i~~~~~~~~~~veval~~~-~~~~e~~~SFvN~I~T~~GGTHv~gf~~al 290 (756)
T PRK14939 213 -KEEEFHYEGGIKAFVEYLNRNKTPLHPNIFYFSGEKDGIGVEVALQWN-DSYQENVLCFTNNIPQRDGGTHLAGFRAAL 290 (756)
T ss_pred -ceeEEEeCChHHHHHHHHhcCCCcCCCCceEEEeeeCCeEEEEEEEEc-CCCceeEEEEECcccCCCCCCHHHHHHHHH
Confidence 35689999999999999998888887 578888887889999999999 789899999999999999999999999999
Q ss_pred HHHHHHHHHhccCCCCcCCCCCHHhHhcccEEEEEEeecCCCCCCccccccCChhhHhhhhHhhHHHHHHHHhhChHHHH
Q 010553 160 TRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLD 239 (507)
Q Consensus 160 ~~~in~~~kk~~~~k~~~~~i~~~diregL~~vvsv~i~nP~FegQTK~kL~n~~v~~~v~~~v~~~l~~~l~~n~~~~~ 239 (507)
+++||+|++++++.|+++.+++++||||||++||||+++||+|+||||++|+|++++.+|++++.+.|..||++||..++
T Consensus 291 tr~in~y~~~~~l~K~~~~~l~~~diregl~~vvsvki~~P~FegQTK~kL~n~ev~~~v~~~v~e~l~~~l~~np~~a~ 370 (756)
T PRK14939 291 TRTINNYIEKEGLAKKAKVSLTGDDAREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNEKLSEFLEENPNEAK 370 (756)
T ss_pred HHHHHHHHHHhCcccccCCCCCHhHHhhceEEEEEEecCCCcccCchhccccCHHHHHHHHHHHHHHHHHHHHHChHHHH
Confidence 99999999998888877789999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhccccccCCCCCCCCCCCCCCCCCceEEEeecCCCCCcccccCCCCceEeeccCCc
Q 010553 240 SILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGK 319 (507)
Q Consensus 240 ~I~~~~~~~~k~r~aakkar~~~~~k~~~~~~~lpgKL~Dc~~~~~~~~eL~lvEGDSA~gsak~gRdr~~qailPLrGK 319 (507)
.|+++++.+++||+||++||++.|||+.++...|||||+||+++||++|||||||||||||||||||||+||||||||||
T Consensus 371 ~ii~k~~~aa~aR~aa~kar~~~rrK~~~~~~~lpgKL~Dc~~~d~~~~eLfivEGDSAgGsAk~gRdr~~qailPLRGK 450 (756)
T PRK14939 371 IIVGKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRDRKFQAILPLKGK 450 (756)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccccccccCCCCCCccccccCCCCceEEEEEeCCCCccccccccCccceeccccCCc
Confidence 99999999999999999999999999988888999999999999999999999999999999999999999999999999
Q ss_pred cccccccCHHHHhhCcchHHHHHHhcCCccCCcCcccccccceEEEeecCCCCChhhHHHHHHHHHHHHHHHhhcCcEEE
Q 010553 320 ILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYV 399 (507)
Q Consensus 320 iLNv~ka~~~ki~~N~Ei~~li~alG~~~~~~~~~~~~LRY~kiiImtDaD~DG~HI~~Llltff~~~~p~Li~~G~v~~ 399 (507)
|||||+|+.+||++|+||++||+|||||++.++||+++||||||||||||||||+|||||||||||||||+||++||||+
T Consensus 451 iLNveka~~~kil~N~Ei~~li~alG~gig~~~fd~~~LRY~kIiIMTDADvDGsHIrtLLltff~r~~p~Lie~G~vyi 530 (756)
T PRK14939 451 ILNVEKARFDKMLSSQEIGTLITALGCGIGRDEFNPDKLRYHKIIIMTDADVDGSHIRTLLLTFFYRQMPELIERGHLYI 530 (756)
T ss_pred cchhccCCHHHHhcCHHHHHHHHHhCCCCCcccCChhhCCcCeEEEEcCCCCCchHHHHHHHHHHHHhChhhccCCeEEE
Confidence 99999999999999999999999999999546899999999999999999999999999999999999999999999999
Q ss_pred ecCCeEEEEeCCEEEEEeCHHHHHHHHHhCCC------------------------------------------------
Q 010553 400 GVPPLYKVERGKQVQYCYDDAELKKVKSSFPS------------------------------------------------ 431 (507)
Q Consensus 400 ~~tPl~kv~~gk~~~~~y~~~e~~~~~~~~~~------------------------------------------------ 431 (507)
|+||||||++||++.||||++|+++|+.+++.
T Consensus 531 a~pPLykv~~gk~~~y~~~~~e~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~ 610 (756)
T PRK14939 531 AQPPLYKVKKGKQEQYLKDDEALDDYLIELALEGATLHLADGPAISGEALEKLVKEYRAVRKIIDRLERRYPRAVLEALI 610 (756)
T ss_pred ecCcEEEEecCCeeEecCCHHHHHHHHHHhCcCCceeecCCCCcccHHHHHHHHHHHHHHHHHHhHHhccccHHHHHHHH
Confidence 99999999999999999999999999765310
Q ss_pred ------------------------------------------------------------------------CCCcccee
Q 010553 432 ------------------------------------------------------------------------NALYSIQR 439 (507)
Q Consensus 432 ------------------------------------------------------------------------~~~~~i~r 439 (507)
.++..|||
T Consensus 611 ~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ell~~v~~~gr~g~~Iqr 690 (756)
T PRK14939 611 YAPALDLDDLADEAAVAALDADFLTSAEYRRLVELAEKLRGLIEEGAYLERGERKQPVSSFEEALDWLLAEARKGLSIQR 690 (756)
T ss_pred hccccchhhhcchhhhhhcchhhhcCHHHHHHHHHHHHHHHHhccCcEEEcCCcceecCCHHHHHHHHHhhhccCccccc
Confidence 00122899
Q ss_pred eeccCCCChhhHHhhhcCcCcceEEeeccccHHHHHHHHHHhcCCCchHHHHHHHhccccCCccCCCC
Q 010553 440 FKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQNAANLVNLDHLDI 507 (507)
Q Consensus 440 yKGLGe~~~~~l~et~~~p~~r~l~~v~~~d~~~~~~~f~~lmg~~~~~Rk~~i~~~~~~~~~~~~d~ 507 (507)
|||||||+|+|+|+|||||.+|++.++.++|+..++++|+.|||+.+++||+||+.++.. +++||+
T Consensus 691 ~KgLgEM~~eqL~eTtmdp~~R~l~~v~led~~~a~~~f~~lMg~~ve~rr~fI~~~a~~--v~~LD~ 756 (756)
T PRK14939 691 YKGLGEMNPEQLWETTMDPENRRLLQVTIEDAIAADEIFTTLMGDEVEPRREFIEENALN--VANLDV 756 (756)
T ss_pred cccHHHhHHHHHHHHhhChhheeeeeeehhhHHHHHHHHHHHhcCCcchhHHHHHHhhhh--HhhcCC
Confidence 999999999999999999999999999999999999999999999999999999999983 466875
No 7
>smart00433 TOP2c TopoisomeraseII. Eukaryotic DNA topoisomerase II, GyrB, ParE
Probab=100.00 E-value=1.2e-146 Score=1202.86 Aligned_cols=485 Identities=49% Similarity=0.812 Sum_probs=452.0
Q ss_pred CEEEEEecC-CCCCCcceeeecCCCCCCCCCeEEEEEeCccccccccCCCHHHHHHHHHHHhccCCCcEEEEeecCCCCC
Q 010553 1 MEYHQKYSR-GKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPE 79 (507)
Q Consensus 1 k~y~q~F~~-G~~~~~l~~~~~~~~~~~~~GT~V~F~PD~~iF~~~~~fd~~~l~~Rl~elA~Ln~Gl~I~l~der~~~~ 79 (507)
+.|+|+|++ |.++.++++. +.+.++||+|+|+||+++|.....++++.|.+|++++|+|||||+|.|+|++..
T Consensus 105 ~~~~~~~~~~G~~~~~~~~~----~~~~~~GT~V~F~Pd~~~F~~~~~~~~~~i~~rl~~~A~l~pgl~i~l~der~~-- 178 (594)
T smart00433 105 KEYKQSFSNNGKPLSEPKII----GDTKKDGTKVTFKPDLEIFGMTTDDDFELLKRRLRELAFLNKGVKITLNDERSD-- 178 (594)
T ss_pred cEEEEEEeCCCeECccceec----CCCCCCCcEEEEEECHHHhCCcccchHHHHHHHHHHHHhcCCCcEEEEeccCCC--
Confidence 359999987 8888877665 445679999999999999975447899999999999999999999999999854
Q ss_pred CCcceeEecCCCHHHHHHHHhcCCCCCC-ceeEEEEeccceEEEEeeeecCCCCCceeeeeeCceecCCCCcchhhHHHH
Q 010553 80 KNQYNEYFFAGGLEEYVQWLNTDKKPLH-DVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKAS 158 (507)
Q Consensus 80 ~~~~~~f~~~~Gl~~yv~~l~~~~~~~~-~~i~~~~~~~~~~veval~~s~~~~~~~~~SFvN~I~T~~GGTHv~g~~~a 158 (507)
..++|+|++||.+|+++++.++++++ +++++.++.+++.|||||+|+ ++|+++++||||+|+|++|||||+||+++
T Consensus 179 --~~~~f~~~~Gl~~yv~~~~~~~~~~~~~~i~~~~~~~~~~veval~~~-~~~~~~~~SFvN~I~T~~GGTHv~g~~~a 255 (594)
T smart00433 179 --EEETFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQYT-DGYSENIVSFVNNIATTEGGTHENGFKDA 255 (594)
T ss_pred --cceEEECCCCHHHHHHHHhCCCCcccCCCeEEEEEeCCcEEEEEEEcc-CCCCcEEEEEECCccCCCCCcHHHHHHHH
Confidence 35679999999999999998887776 577777777788999999999 67888999999999999999999999999
Q ss_pred HHHHHHHHHHhccCCCCcCCCCCHHhHhcccEEEEEEeecCCCCCCccccccCChhhHhhhhHhhHHHHHHHHhhChHHH
Q 010553 159 LTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVL 238 (507)
Q Consensus 159 l~~~in~~~kk~~~~k~~~~~i~~~diregL~~vvsv~i~nP~FegQTK~kL~n~~v~~~v~~~v~~~l~~~l~~n~~~~ 238 (507)
|+++||+|++++++.|+ .+++++|||+||++||||+++||+|+||||++|+|++++.+|++++++.|..||++||..+
T Consensus 256 l~~~i~~~~~~~~~~k~--~~i~~~diregl~~vIsvki~~P~FegQTK~kL~n~~~~~~v~~~v~~~l~~~l~~n~~~a 333 (594)
T smart00433 256 LTRVINEYAKKKKKLKE--KNIKGEDVREGLTAFISVKIPEPQFEGQTKEKLGTSEVRFGVEKIVSECLLSFLEENPVEA 333 (594)
T ss_pred HHHHHHHHHHHhCcccc--CCCChhhHhhCeEEEEEEEEchheecccccccccChhHHHHHHHHHHHHHHHHHHHCHHHH
Confidence 99999999999887764 7899999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhccccccCCCCCCCCCCCCCCCCCceEEEeecCCCCCcccccCCCCceEeeccCC
Q 010553 239 DSILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRG 318 (507)
Q Consensus 239 ~~I~~~~~~~~k~r~aakkar~~~~~k~~~~~~~lpgKL~Dc~~~~~~~~eL~lvEGDSA~gsak~gRdr~~qailPLrG 318 (507)
+.|+++++.++++|++|+++|++.|+| ..+...|||||+||+++++++|||||||||||||||++||||+|||||||||
T Consensus 334 ~~ii~k~~~~a~ar~~a~~~~~~~r~k-~~~~~~l~~KL~dc~~~~~~~~eL~ivEGDSA~gsak~grdr~~qailPLrG 412 (594)
T smart00433 334 SKIVEKVLLAAKARAAAKKARELTRKK-KLSKISLPGKLADASSAGPKKCELFLVEGDSAGGSAKSGRDRDFQAILPLRG 412 (594)
T ss_pred HHHHHHHHHHHHHHHHHHHhHHHhccc-ccccccccccccccccCCCCCcEEEEEecCCCccccccccCccceeecccCC
Confidence 999999999999999999999999888 6677889999999999999999999999999999999999999999999999
Q ss_pred ccccccccCHHHHhhCcchHHHHHHhcCCccCCcCcccccccceEEEeecCCCCChhhHHHHHHHHHHHHHHHhhcCcEE
Q 010553 319 KILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIY 398 (507)
Q Consensus 319 KiLNv~ka~~~ki~~N~Ei~~li~alG~~~~~~~~~~~~LRY~kiiImtDaD~DG~HI~~Llltff~~~~p~Li~~G~v~ 398 (507)
||||||+++.++|++|+||++|++|||||+ +++||+++||||||||||||||||+|||||||||||||||+||++||||
T Consensus 413 KiLNv~~~~~~ki~~N~Ei~~li~alG~~~-~~~~~~~~LRY~kIiImtDaDvDG~HI~~Llltff~r~~p~Li~~G~vy 491 (594)
T smart00433 413 KLLNVEKASLDKILKNEEIQALITALGLGI-GKDFDIEKLRYGKIIIMTDADVDGSHIKGLLLTFFYRYMPPLIEAGFVY 491 (594)
T ss_pred eecchhhccHHHHhhCHHHHHHHHHhCCCc-CcccCccccccceEEEEeCCCCCcchhHHHHHHHHHHhChhhhhCCeEE
Confidence 999999999999999999999999999999 5679999999999999999999999999999999999999999999999
Q ss_pred EecCCeEEEEeCCE--EEEEeCHHHHHHHHHhCCC-CCCccceeeeccCCCChhhHHhhhcCcCcceEEeeccccHHHHH
Q 010553 399 VGVPPLYKVERGKQ--VQYCYDDAELKKVKSSFPS-NALYSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEAN 475 (507)
Q Consensus 399 ~~~tPl~kv~~gk~--~~~~y~~~e~~~~~~~~~~-~~~~~i~ryKGLGe~~~~~l~et~~~p~~r~l~~v~~~d~~~~~ 475 (507)
+|+||||||++|++ +.+||+++|+++|+..... .++|+||||||||||+|+|+|||||||++|+|.+|+++|+..++
T Consensus 492 ~~~~Pl~ki~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~ryKGLGe~~~~~~~e~~~~p~~r~l~~v~~~d~~~~~ 571 (594)
T smart00433 492 IAIPPLYKVTKGKKKYVYSFYSLDEYEKWLETKGGNKSKYEIQRYKGLGEMNADQLWETTMDPERRTLLFVTLDDADEAD 571 (594)
T ss_pred EecCCEEEEEeCCcceEEeehhhHHHHHHHHhhhccCCCccceeccccccCCHHHHHHHhcCccceeEEEEEcCchhhHH
Confidence 99999999999986 5678888899999865331 45799999999999999999999999999999999999998888
Q ss_pred HHHHHhcCCCchHHHHHHHhccc
Q 010553 476 VVFSSLMGARVDTRKELIQNAAN 498 (507)
Q Consensus 476 ~~f~~lmg~~~~~Rk~~i~~~~~ 498 (507)
.+|++|||+++++||+||.+|++
T Consensus 572 ~~~~~l~g~~~~~Rk~~i~~~~~ 594 (594)
T smart00433 572 LIFSALMGDKVEPRKEWIEENAP 594 (594)
T ss_pred HHHHHHcCCCchHHHHHHHhhCC
Confidence 99999999999999999999874
No 8
>TIGR01055 parE_Gneg DNA topoisomerase IV, B subunit, proteobacterial. This protein is active as an alpha(2)beta(2) heterotetramer.
Probab=100.00 E-value=1.9e-146 Score=1202.57 Aligned_cols=482 Identities=32% Similarity=0.552 Sum_probs=442.4
Q ss_pred EEEEEecCCCCCCcceeeecCCCCC--CCCCeEEEEEeCccccccccCCCHHHHHHHHHHHhccCCCcEEEEeecCCCCC
Q 010553 2 EYHQKYSRGKPVTTLTCHVLPVDSK--DRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPE 79 (507)
Q Consensus 2 ~y~q~F~~G~~~~~l~~~~~~~~~~--~~~GT~V~F~PD~~iF~~~~~fd~~~l~~Rl~elA~Ln~Gl~I~l~der~~~~ 79 (507)
.|+|+|++|+++.+++++ ++. ..+||+|+|+||+++|+. ..|+++.|.+||+++|||||||+|.|+|+|..
T Consensus 135 ~~~~~~~~G~~~~~~~~i----~~~~~~~~GT~V~F~PD~~~F~~-~~~e~~~i~~~l~~lA~lnpgi~~~l~der~~-- 207 (625)
T TIGR01055 135 LYSIAFENGAKVTDLISA----GTCGKRLTGTSVHFTPDPEIFDS-LHFSVSRLYHILRAKAVLCRGVEIEFEDEVNN-- 207 (625)
T ss_pred EEEEEEECCeEccccccc----cccCCCCCCeEEEEEECHHHCCC-CccCHHHHHHHHHHHHhhCCCcEEEEeecCCC--
Confidence 599999999998888766 333 459999999999999974 57999999999999999999999999999854
Q ss_pred CCcceeEecCCCHHHHHHHHhcCCCCCCce-eEEEEeccceEEEEeeeecCCCCCceeeeeeCceecCCCCcchhhHHHH
Q 010553 80 KNQYNEYFFAGGLEEYVQWLNTDKKPLHDV-VGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKAS 158 (507)
Q Consensus 80 ~~~~~~f~~~~Gl~~yv~~l~~~~~~~~~~-i~~~~~~~~~~veval~~s~~~~~~~~~SFvN~I~T~~GGTHv~g~~~a 158 (507)
..+.|+|++||.+||++++.++++++++ +......+++.++|||+|+.++++++++||||||+|++|||||+||++|
T Consensus 208 --~~~~f~~~~Gi~~yv~~l~~~~~~~~~~~~~~~~~~~~~~ve~al~~~~~~~~~~~~SFvN~I~T~~GGTHv~gf~~a 285 (625)
T TIGR01055 208 --TKALWNYPDGLKDYLSEAVNGDNTLPPKPFSGNFEGDDEAVEWALLWLPEGGELFMESYVNLIPTPQGGTHVNGLRQG 285 (625)
T ss_pred --ceeEEecCchHHHHHHHHhcCCCCCCCCceEEEEeeCCceEEEEEEEecCCCCEEEEEeeccccCCCCCCHHHHHHHH
Confidence 2457999999999999998877777643 3333334677899999998555778899999999999999999999999
Q ss_pred HHHHHHHHHHhccCCCCcCCCCCHHhHhcccEEEEEEeecCCCCCCccccccCChhhHhhhhHhhHHHHHHHHhhChHHH
Q 010553 159 LTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVL 238 (507)
Q Consensus 159 l~~~in~~~kk~~~~k~~~~~i~~~diregL~~vvsv~i~nP~FegQTK~kL~n~~v~~~v~~~v~~~l~~~l~~n~~~~ 238 (507)
|+++||+|++++++.|+ +.+++++|||+||++||||+++||+|+||||++|+|++++.+|++++.+.|..||++||..+
T Consensus 286 lt~~in~~~~~~~~~kk-~~~i~~~diregl~~vVsvki~~P~FegQTK~kL~n~~v~~~v~~~v~~~l~~~l~~n~~~a 364 (625)
T TIGR01055 286 LLDALREFCEMRNNLPR-GVKLTAEDIWDRCSYVLSIKMQDPQFAGQTKERLSSRQVAKFVSGVIKDAFDLWLNQNVQLA 364 (625)
T ss_pred HHHHHHHHHHHhCcccc-cCCCCHHHHhhccEEEEEEeccCCcccCcccccccCHHHHHHHHHHHHHHHHHHHHHCHHHH
Confidence 99999999998887654 57899999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhccccccCCCCCCCCCCCCCCCCCceEEEeecCCCCCcccccCCCCceEeeccCC
Q 010553 239 DSILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRG 318 (507)
Q Consensus 239 ~~I~~~~~~~~k~r~aakkar~~~~~k~~~~~~~lpgKL~Dc~~~~~~~~eL~lvEGDSA~gsak~gRdr~~qailPLrG 318 (507)
+.|+++++.++++|+ ++||+..| |+.++...|||||+||++++|++|||||||||||||||+|||||+|||||||||
T Consensus 365 ~~i~~k~~~~a~ar~--~~a~~~~r-k~~~~~~~lpgKL~dc~~~~~~~~eLfivEGDSA~gsak~grdr~~qailPLRG 441 (625)
T TIGR01055 365 EHLAEHAISSAQRRK--RAAKKVVR-KKLTSGPALPGKLADCTRQDLEGTELFLVEGDSAGGSAKQARDREYQAILPLWG 441 (625)
T ss_pred HHHHHHHHHHHHHHH--HHHHHHhh-cccccCCCCCccccccccCCCCceEEEEEecCCCCccccccCCcceeEEeccCC
Confidence 999999999999997 77888766 446677889999999999999999999999999999999999999999999999
Q ss_pred ccccccccCHHHHhhCcchHHHHHHhcCCccCCcCcccccccceEEEeecCCCCChhhHHHHHHHHHHHHHHHhhcCcEE
Q 010553 319 KILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIY 398 (507)
Q Consensus 319 KiLNv~ka~~~ki~~N~Ei~~li~alG~~~~~~~~~~~~LRY~kiiImtDaD~DG~HI~~Llltff~~~~p~Li~~G~v~ 398 (507)
||||||+++.+||++|+||++|++|||||++ ++ ++++||||||||||||||||+|||||||||||||||+||++||||
T Consensus 442 KiLNv~ka~~~ki~~N~Ei~~li~alG~g~~-~~-~~~~LRY~kiiImTDADvDG~HI~~LLltff~r~~p~Li~~G~vy 519 (625)
T TIGR01055 442 KILNTWEVSLDKVLNSQEIHDIEVALGIDPD-SN-DLSQLRYGKICILADADSDGLHIATLLCALFFLHFPKLVEEGHVY 519 (625)
T ss_pred ceeecccCCHHHhhcCHHHHHHHHHhCCCcc-cc-cccccccceEEEEeCCCCCcchhHHHHHHHHHHhCHhhccCCeEE
Confidence 9999999999999999999999999999995 44 599999999999999999999999999999999999999999999
Q ss_pred EecCCeEEEEeCCEEEEEeCHHHHHHHHHhCCC-CCCccceeeeccCCCChhhHHhhhcCcCcceEEeeccccHHH--HH
Q 010553 399 VGVPPLYKVERGKQVQYCYDDAELKKVKSSFPS-NALYSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAE--AN 475 (507)
Q Consensus 399 ~~~tPl~kv~~gk~~~~~y~~~e~~~~~~~~~~-~~~~~i~ryKGLGe~~~~~l~et~~~p~~r~l~~v~~~d~~~--~~ 475 (507)
+|+||||||++||+++|+|+|.|++++++++++ .++|+||||||||||+|+|||||||||++|+|.+|+++|++. ++
T Consensus 520 ~~~~Pl~kv~~gk~~~y~~~e~e~~~~~~~~~~~~~~~~i~ryKGLGe~~~~~~~e~~~~p~~r~l~~v~~~~~~~~~~~ 599 (625)
T TIGR01055 520 VAKPPLYRIDLSKEVYYALDEEEKEKLLYKLKKKKGKPNVQRFKGLGEMNPAQLRETTMDPNTRRLVQLTLDDVQDQRVD 599 (625)
T ss_pred EEeCCEEEEecCCceEEcCCHHHHHHHHHhhcccCCCcceeEecccchhhHHHHHHHhhCccceecccccccchhhhhHH
Confidence 999999999999999999999999999876543 247999999999999999999999999999999999999864 89
Q ss_pred HHHHHhcCCC-chHHHHHHHhccc
Q 010553 476 VVFSSLMGAR-VDTRKELIQNAAN 498 (507)
Q Consensus 476 ~~f~~lmg~~-~~~Rk~~i~~~~~ 498 (507)
++|++|||++ +++||+||++|+.
T Consensus 600 ~~~~~lmg~~~~~~Rk~~i~~~~~ 623 (625)
T TIGR01055 600 KIMDMLLAKKRSEDRFNWLQEKGD 623 (625)
T ss_pred HHHHHHhCCCCCchhHHHHHhccc
Confidence 9999999999 9999999999986
No 9
>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=100.00 E-value=9e-145 Score=1200.57 Aligned_cols=495 Identities=51% Similarity=0.896 Sum_probs=465.4
Q ss_pred EEEEEecCCCCCCcceeeecCCCCCCCCCeEEEEEeCccccccccCCCHHHHHHHHHHHhccCCCcEEEEeecCCCCCCC
Q 010553 2 EYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKN 81 (507)
Q Consensus 2 ~y~q~F~~G~~~~~l~~~~~~~~~~~~~GT~V~F~PD~~iF~~~~~fd~~~l~~Rl~elA~Ln~Gl~I~l~der~~~~~~ 81 (507)
.|+|+|++|+++.++++. +.+..+||+|+|+|||++|. +..++++.|.+|++++|+|||||+|.|+++|.+. .
T Consensus 135 ~~~~~~~~G~~~~~l~~~----~~~~~~GT~V~F~pdp~~F~-~~~~e~~~i~~rl~~~A~l~pgl~i~l~~er~~~--~ 207 (654)
T TIGR01059 135 IYRQEFERGIPLGPLEVV----GETKKTGTTVRFWPDPEIFE-TTEFDFDILAKRLRELAFLNSGVKISLEDERDGK--G 207 (654)
T ss_pred EEEEEEeCCCcccCceec----cCCCCCCcEEEEEEChHHhC-CcccCHHHHHHHHHHhhccCCCeEEEEEeecCCC--C
Confidence 599999999999988766 45667999999999999997 5679999999999999999999999999998531 2
Q ss_pred cceeEecCCCHHHHHHHHhcCCCCCC-ceeEEEEeccceEEEEeeeecCCCCCceeeeeeCceecCCCCcchhhHHHHHH
Q 010553 82 QYNEYFFAGGLEEYVQWLNTDKKPLH-DVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLT 160 (507)
Q Consensus 82 ~~~~f~~~~Gl~~yv~~l~~~~~~~~-~~i~~~~~~~~~~veval~~s~~~~~~~~~SFvN~I~T~~GGTHv~g~~~al~ 160 (507)
..++|+|++||.+|+++++.++++++ +++++.++.++++|||||+|+ ++|+++++||||+|+|++|||||+||++||+
T Consensus 208 ~~~~f~~~~Gl~~yv~~l~~~~~~l~~~~i~~~~~~~~~~veva~~~~-~~~~~~~~SFvN~I~T~~GGTHv~g~~~al~ 286 (654)
T TIGR01059 208 KSVTFHYEGGIKSFVKYLNRNKEPLHEEIIYIKGEKEGIEVEVALQWN-DGYSENILSFVNNINTREGGTHLEGFRSALT 286 (654)
T ss_pred ceeEEEcCCcHHHHHHHHhcCCCcCCCCCeEEEecccCeEEEEEEEec-CCCceeEEEEECcccCCCCCcHHHHHHHHHH
Confidence 35689999999999999988887876 578888776789999999999 6788899999999999999999999999999
Q ss_pred HHHHHHHHhccCCCCcCCCCCHHhHhcccEEEEEEeecCCCCCCccccccCChhhHhhhhHhhHHHHHHHHhhChHHHHH
Q 010553 161 RTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDS 240 (507)
Q Consensus 161 ~~in~~~kk~~~~k~~~~~i~~~diregL~~vvsv~i~nP~FegQTK~kL~n~~v~~~v~~~v~~~l~~~l~~n~~~~~~ 240 (507)
++||+|+++++++|+++.+++++|||+||++||||+|+||+|+||||++|+|++++.+|.+++.+.|..||++||+.++.
T Consensus 287 ~~i~~~~~~~~l~K~~~~~i~~~diregl~~vvsv~i~~P~F~gQTK~kL~~~~v~~~v~~~v~~~l~~~l~~n~~~a~~ 366 (654)
T TIGR01059 287 RVINSYAKNNKLLKESKPNLTGEDIREGLTAVISVKVPDPQFEGQTKTKLGNSEVRSIVESLVYEKLTEFFEENPQEAKA 366 (654)
T ss_pred HHHHHHHHHhCcccccCCCCCHHHHhhccEEEEEEecCCCcccCcccccccChhHHHHHHHHHHHHHHHHHHhChHHHHH
Confidence 99999999999888777899999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhccccccCCCCCCCCCCCCCCCCCceEEEeecCCCCCcccccCCCCceEeeccCCcc
Q 010553 241 ILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKI 320 (507)
Q Consensus 241 I~~~~~~~~k~r~aakkar~~~~~k~~~~~~~lpgKL~Dc~~~~~~~~eL~lvEGDSA~gsak~gRdr~~qailPLrGKi 320 (507)
|+++++.++++|++++++|++.|+|+......|||||+||++++|++|||||||||||||||++||||+|||||||||||
T Consensus 367 iv~k~~~~a~~r~~a~~~k~~~r~k~~~~~~~lpgKL~dc~~~~~~~~eL~lvEGDSA~gsak~gRd~~~qai~PLrGKi 446 (654)
T TIGR01059 367 IVEKAILAAQAREAARKARELTRRKSALDSGGLPGKLADCSSKDPSKSELYIVEGDSAGGSAKQGRDRKFQAILPLRGKI 446 (654)
T ss_pred HHHHHHHHHHHHHHHHHhHHHhhcccccccCCCCcCccCcccCCCCCCEEEEEecCCCCcccccccccccccccccCCcc
Confidence 99999999999999999999999988877788999999999999999999999999999999999999999999999999
Q ss_pred ccccccCHHHHhhCcchHHHHHHhcCCccCCcCcccccccceEEEeecCCCCChhhHHHHHHHHHHHHHHHhhcCcEEEe
Q 010553 321 LNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVG 400 (507)
Q Consensus 321 LNv~ka~~~ki~~N~Ei~~li~alG~~~~~~~~~~~~LRY~kiiImtDaD~DG~HI~~Llltff~~~~p~Li~~G~v~~~ 400 (507)
||||+++.++|++|+||++|++|||||+ +++||+++|||||||||||||+||+||++|||||||||||+||++||||+|
T Consensus 447 LNv~~~~~~ki~~n~Ei~~l~~~lG~~~-~~~~~~~~LrY~kiiImtDaD~DG~HI~~Lll~ff~~~~p~Li~~g~~~~~ 525 (654)
T TIGR01059 447 LNVEKARLDKILSNQEIGAIITALGCGI-GKDFDLEKLRYHKIIIMTDADVDGSHIRTLLLTFFYRYMRPLIENGYVYIA 525 (654)
T ss_pred chhccCCHHHHhhChHHHHHHHHhCCCc-cccccccccccceEEEEeCCCCCcchhHHHHHHHHHHhcHhhccCCeEEEe
Confidence 9999999999999999999999999999 578999999999999999999999999999999999999999999999999
Q ss_pred cCCeEEEEeCCEE---------------------EEEeCHHHHHHHHHhCC---CCCCccceeeeccCCCChhhHHhhhc
Q 010553 401 VPPLYKVERGKQV---------------------QYCYDDAELKKVKSSFP---SNALYSIQRFKGLGEMMPVQLWETTL 456 (507)
Q Consensus 401 ~tPl~kv~~gk~~---------------------~~~y~~~e~~~~~~~~~---~~~~~~i~ryKGLGe~~~~~l~et~~ 456 (507)
+||||||++||++ .||||++|+++|++.++ ..++|+||||||||||+|+|+|||||
T Consensus 526 ~~Pl~kv~~g~~~~~~~~~~~~~~~~~~~~~~~e~Y~~dd~e~e~~l~~l~~~~~~~~~~IqryKGLGem~~~~l~ettm 605 (654)
T TIGR01059 526 QPPLYKVKKGKKERYIKDDKEKELVGEALEDLRALYIYSDKEKEEAKTQIPVHEGRKGIEIQRYKGLGEMNADQLWETTM 605 (654)
T ss_pred cCCEEEEEeCCeeeecccchhhhccccccccccceecCCHHHHHHHHHhccccccCCCcceeeeCchhhcCHHHHHHHhc
Confidence 9999999999988 89999999999998763 13579999999999999999999999
Q ss_pred CcCcceEEeeccccHHHHHHHHHHhcCCCchHHHHHHHhccccCCccCCCC
Q 010553 457 NPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQNAANLVNLDHLDI 507 (507)
Q Consensus 457 ~p~~r~l~~v~~~d~~~~~~~f~~lmg~~~~~Rk~~i~~~~~~~~~~~~d~ 507 (507)
||++|+|.+++++|...++++|++|||+++++||+||.+++.. +++||+
T Consensus 606 dp~~R~l~~v~l~d~~~~~~~f~~lmg~~~~~Rk~~I~~~~~~--~~~ld~ 654 (654)
T TIGR01059 606 DPESRTLLKVTIEDAVEADRIFSTLMGDEVEPRREFIEANALD--VKNLDV 654 (654)
T ss_pred CcccceeeeeecchHHHHHHHHHHHhCCCchHHHHHHHHhhhh--HhhcCC
Confidence 9999999999999999999999999999999999999999973 455775
No 10
>PHA02569 39 DNA topoisomerase II large subunit; Provisional
Probab=100.00 E-value=2.4e-136 Score=1116.16 Aligned_cols=438 Identities=29% Similarity=0.468 Sum_probs=396.5
Q ss_pred EEEEEecCCCCCCcceeeecCCCCCCCCCeEEEEEeCccccccccCCC---HHHHHHHHHHHhccCCCcEEEEeecCCCC
Q 010553 2 EYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFD---HNTIAGRIRELAFLNPKLTIALRKEDSDP 78 (507)
Q Consensus 2 ~y~q~F~~G~~~~~l~~~~~~~~~~~~~GT~V~F~PD~~iF~~~~~fd---~~~l~~Rl~elA~Ln~Gl~I~l~der~~~ 78 (507)
.|+|+|++|+++.+++ . +++.++||+|+||||++||++ ..|+ +++|.+||+|+|||||||+|+|+|+|.+
T Consensus 154 ~~~q~f~~G~~~~~~~-~----~~~~~~GT~V~F~PD~~iF~~-~~~~~~~~~~l~~Rl~elA~Ln~Gl~I~l~der~~- 226 (602)
T PHA02569 154 EVTVNCSNGAENISWS-T----KPGKGKGTSVTFIPDFSHFEV-NGLDQQYLDIILDRLQTLAVVFPDIKFTFNGKKVS- 226 (602)
T ss_pred EEEEEecCCcccCCcc-c----CCCCCCccEEEEEECHHHhCC-CccCccHHHHHHHHHHHHhcCCCCCEEEEEecCCC-
Confidence 6999999999988875 3 455679999999999999975 4576 7899999999999999999999999842
Q ss_pred CCCcceeEecCCCHHHHHHHHhcCCCCCCceeEEEEeccceEEEEeeeecCCCCCceeeeeeCceecCCCCcchhhHHHH
Q 010553 79 EKNQYNEYFFAGGLEEYVQWLNTDKKPLHDVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKAS 158 (507)
Q Consensus 79 ~~~~~~~f~~~~Gl~~yv~~l~~~~~~~~~~i~~~~~~~~~~veval~~s~~~~~~~~~SFvN~I~T~~GGTHv~g~~~a 158 (507)
+||.+||++++. ++++++. + .|+||++|+.++| +++||||||+|++|||||+||++|
T Consensus 227 -----------~g~~~yv~~~~~------~~i~~~~--~--~veva~~~~~~~~--~~~SFvN~I~T~~GGTHv~gf~~a 283 (602)
T PHA02569 227 -----------GKFKKYAKQFGD------DTIVQEN--D--NVSIALAPSPDGF--RQLSFVNGLHTKNGGHHVDCVMDD 283 (602)
T ss_pred -----------CCHHHHHHHhCC------CCeEEec--C--cEEEEEEecCCCc--EEEEEECcccCCCCCCHHHHHHHH
Confidence 699999999953 2455532 2 5899999984566 479999999999999999999999
Q ss_pred HHHHHHHHHHhccCCCCcCCCCCHHhHhcccEEEEEEe-ecCCCCCCccccccCCh--hhHhhhhHhhHHHHHHHHhhCh
Q 010553 159 LTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVR-VPNPEFEGQTKTRLGNP--EVRKVVDQSVQEYLTEYLELHP 235 (507)
Q Consensus 159 l~~~in~~~kk~~~~k~~~~~i~~~diregL~~vvsv~-i~nP~FegQTK~kL~n~--~v~~~v~~~v~~~l~~~l~~n~ 235 (507)
|+++||+|+++. ++.+++++||||||++||||+ ++||+|+||||++|+|+ +++..| +++.+.|..||++||
T Consensus 284 ltr~in~~~~kk-----~~~~l~~~diregL~avVsvk~i~~P~FegQTK~kL~~~~~~~~~~v-~~~~~~l~~~l~~n~ 357 (602)
T PHA02569 284 ICEELIPMIKKK-----HKIEVTKARVKECLTIVLFVRNMSNPRFDSQTKERLTSPFGEIRNHI-DLDYKKIAKQILKTE 357 (602)
T ss_pred HHHHHHHHHHhc-----ccCCCCHHHHHhCCEEEEEEeccCCCcccCcccccccCChHHhccce-eehHHHHHHHHHHCH
Confidence 999999999762 236799999999999999998 99999999999999999 689999 999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH---HHHhhcccc-ccCCCCCCCCCCCCCCCCCceEEEeecCCCCCcccccCCCCce
Q 010553 236 DVLDSILSKSLSALKAALAAKRAR---DLVRQKSVL-RSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQ 311 (507)
Q Consensus 236 ~~~~~I~~~~~~~~k~r~aakkar---~~~~~k~~~-~~~~lpgKL~Dc~~~~~~~~eL~lvEGDSA~gsak~gRdr~~q 311 (507)
.+++.|+++++.++++|+|+++++ ++.|+|... ..+.|||| |++|||||||||||||||+|||||+||
T Consensus 358 ~~~~~i~~~a~~~~~ar~a~~~~k~~k~~~r~k~~~~~~a~lpGk--------~~~~eL~ivEGDSAggsAk~~RdR~~q 429 (602)
T PHA02569 358 AIIMPIIEAALARKLAAEKAAETKAAKKAKKAKVAKHIKANLIGK--------DAETTLFLTEGDSAIGYLIEVRDEELH 429 (602)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhccccccccCCCCCC--------CCCceEEEEecCCCCcccccccCccce
Confidence 999999999999999999886443 566666544 36778888 789999999999999999999999999
Q ss_pred EeeccCCccccccccCHHHHhhCcchHHHHHHhcCCccCCcCcccccccceEEEeecCCCCC-hhhHHHHHHHHHHHHHH
Q 010553 312 AILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDG-AHIRTLLLTFFYRYQKT 390 (507)
Q Consensus 312 ailPLrGKiLNv~ka~~~ki~~N~Ei~~li~alG~~~~~~~~~~~~LRY~kiiImtDaD~DG-~HI~~Llltff~~~~p~ 390 (507)
||||||||||||++|+.+||++|+||++|++|||||+ +++|+ +|||||||||||||||| ||||||||||||| ||+
T Consensus 430 aIlPLRGKiLNV~ka~~~ki~~N~Ei~~li~alG~g~-g~~~~--~LRY~kIiImTDADvDG~sHIr~LLltff~~-~p~ 505 (602)
T PHA02569 430 GGYPLRGKVLNTWGMSYADILKNKELFDICAITGLVL-GEKAE--NMNYKNIAIMTDADVDGKGSIYPLLLAFFSR-WPE 505 (602)
T ss_pred eecccCCcccchhhCCHHHhhcchhHHHHHHHhCCCc-Ccccc--ccccCcEEEEecCCCcchHHHHHHHHHHHHh-chh
Confidence 9999999999999999999999999999999999999 45674 99999999999999999 9999999999999 999
Q ss_pred HhhcCcEEEecCCeEEEEeCCEEEEEeCHHHHHHHHHhCCCCCCccceeeeccCCCChhhHHhhhcCcCcceEEeecccc
Q 010553 391 LFDEGCIYVGVPPLYKVERGKQVQYCYDDAELKKVKSSFPSNALYSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIED 470 (507)
Q Consensus 391 Li~~G~v~~~~tPl~kv~~gk~~~~~y~~~e~~~~~~~~~~~~~~~i~ryKGLGe~~~~~l~et~~~p~~r~l~~v~~~d 470 (507)
||++||||+|+||||||++||+++||||++||++|++++ ++|+||||||||||+|+|+|||||||+ |.+++++|
T Consensus 506 Li~~G~v~~~~~Pl~kv~~gk~~~~~~~~~e~~~~~~~~---~~~~i~~yKGLGe~~~~~~~e~~~~p~---l~~~~~~d 579 (602)
T PHA02569 506 LFEQGRIRFVKTPVIIAQVGKETKWFYSLDEFEKAKDSL---KKWSIRYIKGLGSLRKSEYRRVINNPV---YDVVVLPD 579 (602)
T ss_pred hccCCeEEEecCCEEEEEcCCeeEEecCHHHHHHHHHhc---CCcceEEeccCCCCCHHHHHHHhcCcc---cEEEecCc
Confidence 999999999999999999999999999999999999865 479999999999999999999999998 77888888
Q ss_pred HHHHHHHHHHhcCCCchHHHHHHHh
Q 010553 471 AAEANVVFSSLMGARVDTRKELIQN 495 (507)
Q Consensus 471 ~~~~~~~f~~lmg~~~~~Rk~~i~~ 495 (507)
. ++++|++|||+++++||+||.+
T Consensus 580 ~--~~~~~~~l~g~~~~~Rk~wi~~ 602 (602)
T PHA02569 580 D--WKELFEMLFGDDADLRKDWMSQ 602 (602)
T ss_pred h--HHHHHHHHhCCCchHHHHHhhC
Confidence 4 7899999999999999999974
No 11
>PTZ00108 DNA topoisomerase 2-like protein; Provisional
Probab=100.00 E-value=2.4e-133 Score=1150.46 Aligned_cols=469 Identities=25% Similarity=0.349 Sum_probs=417.7
Q ss_pred CEEEEEecCCCCCCcceeeecCCCCC-C-CCCeEEEEEeCccccccccCCCHHH---HHHHHHHHhccCCCcEEEEeecC
Q 010553 1 MEYHQKYSRGKPVTTLTCHVLPVDSK-D-RQGTRIRFWPDKQVFTTAIQFDHNT---IAGRIRELAFLNPKLTIALRKED 75 (507)
Q Consensus 1 k~y~q~F~~G~~~~~l~~~~~~~~~~-~-~~GT~V~F~PD~~iF~~~~~fd~~~---l~~Rl~elA~Ln~Gl~I~l~der 75 (507)
+.|+|+|++||.+...+++ +++ . ++||+|+||||++||++ ..||+++ |.+||+++|||||||+|+|+|+|
T Consensus 168 k~y~q~f~~Gm~~~~~p~i----~~~~~~~~GT~VtF~PD~~iF~~-~~fd~d~~~ll~~Rl~dlA~ln~GLkI~lnder 242 (1388)
T PTZ00108 168 KKFKMTWTDNMSKKSEPRI----TSYDGKKDYTKVTFYPDYAKFGM-TEFDDDMLRLLKKRVYDLAGCFGKLKVYLNGER 242 (1388)
T ss_pred CEEEEEecCCCcCCCCCcc----CCCCCCCCceEEEEEeCHHHcCC-CccChHHHHHHHHHHHHHhcCCCCcEEEEeCcc
Confidence 5799999999744333344 332 3 79999999999999985 4799998 99999999999999999999987
Q ss_pred CCCCCCcceeEecCCCHHHHHHHH---hcCCCCCCceeE-EEEeccceEEEEeeeecCCCCCceeeeeeCceecCCCCcc
Q 010553 76 SDPEKNQYNEYFFAGGLEEYVQWL---NTDKKPLHDVVG-FRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTH 151 (507)
Q Consensus 76 ~~~~~~~~~~f~~~~Gl~~yv~~l---~~~~~~~~~~i~-~~~~~~~~~veval~~s~~~~~~~~~SFvN~I~T~~GGTH 151 (507)
. |+.+|++++ +.+..+.+++++ +.++.++.+|||||+|++ ++++++||||||+|++||||
T Consensus 243 ~--------------gi~~F~~y~~ly~~~~~~~~~~~~~~~~~~~~~~~eVal~~s~--~~~~~~SFVN~I~T~~GGTH 306 (1388)
T PTZ00108 243 I--------------AIKSFKDYVDLYLPDGEEGKKPPYPFVYTSVNGRWEVVVSLSD--GQFQQVSFVNSICTTKGGTH 306 (1388)
T ss_pred c--------------cHHHHHHHHHhhccCCccCCCCceeeeccccCceEEEEEEEeC--CCceEEEEEcccccCCCCCH
Confidence 4 455555554 555555544444 556666789999999994 56789999999999999999
Q ss_pred hhhHHHHHHHHHHHHHHhccCCCCcCCCCCHHhHhcccEEEEEEeecCCCCCCccccccCChhhHhhhhHhhHHHHHHHH
Q 010553 152 IEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYL 231 (507)
Q Consensus 152 v~g~~~al~~~in~~~kk~~~~k~~~~~i~~~diregL~~vvsv~i~nP~FegQTK~kL~n~~v~~~v~~~v~~~l~~~l 231 (507)
|+||+++|+++|++|++++ |+++.+++++|||+||++||||+|+||+|+||||++|+|++++.++.+.+.+.|..||
T Consensus 307 v~g~~~alt~~i~~~~k~k---kk~~~~i~~~dIregl~~~Vs~~i~nP~FdsQTKekL~~~~~~~~~~~~v~e~l~~~l 383 (1388)
T PTZ00108 307 VNYILDQLISKLQEKAKKK---KKKGKEIKPNQIKNHLWVFVNCLIVNPSFDSQTKETLTTKPSKFGSTCELSEKLIKYV 383 (1388)
T ss_pred HHHHHHHHHHHHHHHHHHh---cccCCCCCHHHHHhCcEEEEEEecCCCccCCcccccccChhhHHHHHHHHHHHHHHHH
Confidence 9999999999999999873 3345789999999999999999999999999999999999999999999999999999
Q ss_pred hhChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccCCCCCCCCCCC---CCCCCCceEEEeecCCCCCccccc---
Q 010553 232 ELHPDVLDSILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLADCS---STTPEESEIFIVEGDSAGGSAKQG--- 305 (507)
Q Consensus 232 ~~n~~~~~~I~~~~~~~~k~r~aakkar~~~~~k~~~~~~~lpgKL~Dc~---~~~~~~~eL~lvEGDSA~gsak~g--- 305 (507)
+++ .|+++++.++++|++|+++|++.++| .... ..|+||+||+ ++++++|||||||||||||||++|
T Consensus 384 ~~~-----~Ivekil~~a~aR~aa~~ak~~~~~K-~~~~-~~ipKL~Dc~~aG~k~~~~ceL~lvEGDSAggsAk~Gl~v 456 (1388)
T PTZ00108 384 LKS-----PILENIVEWAQAKLAAELNKKMKAGK-KSRI-LGIPKLDDANDAGGKNSEECTLILTEGDSAKALALAGLSV 456 (1388)
T ss_pred hhh-----HHHHHHHHHHHHHHHHHHHHHHhhhh-hhcc-cCchhhhhcccccCCChhhcEEEEEecCcccchhhhcccc
Confidence 873 58999999999999999999988776 2233 3445999999 689999999999999999999999
Q ss_pred CCCCceEeeccCCccccccccCHHHHhhCcchHHHHHHhcCCccCCcCcccccccceEEEeecCCCCChhhHHHHHHHHH
Q 010553 306 RDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFY 385 (507)
Q Consensus 306 Rdr~~qailPLrGKiLNv~ka~~~ki~~N~Ei~~li~alG~~~~~~~~~~~~LRY~kiiImtDaD~DG~HI~~Llltff~ 385 (507)
|||+|||||||||||||||+|+.++|++|+||++|++|||||++.++||+++|||||||||||||+||||||||||||||
T Consensus 457 rdR~~qaVfPLRGKiLNV~kas~~ki~~N~EI~~li~aLGlg~g~~y~d~~~LRYgkIiIMTDADvDGsHIr~LLlnff~ 536 (1388)
T PTZ00108 457 VGRDYYGVFPLRGKLLNVRDASLKQLMNNKEIQNLFKILGLDIGKKYEDPKGLRYGSLMIMTDQDHDGSHIKGLLINMIH 536 (1388)
T ss_pred cCccceeeeccCCcccccccccHhhhhccHHHHHHHHHhCCCcCccccccccCCCCeEEEEeCCCCCccHHHHHHHHHHH
Confidence 79999999999999999999999999999999999999999996555899999999999999999999999999999999
Q ss_pred HHHHHHhh-cCcEEEecCCeEEEEe-CCEEEEEeCHHHHHHHHHhCCCCCCccceeeeccCCCChhhHHhhhcCcCcceE
Q 010553 386 RYQKTLFD-EGCIYVGVPPLYKVER-GKQVQYCYDDAELKKVKSSFPSNALYSIQRFKGLGEMMPVQLWETTLNPEQRML 463 (507)
Q Consensus 386 ~~~p~Li~-~G~v~~~~tPl~kv~~-gk~~~~~y~~~e~~~~~~~~~~~~~~~i~ryKGLGe~~~~~l~et~~~p~~r~l 463 (507)
||||+||+ +||||+|+||||||++ ||+++||||++||++|+++++ .++|+||||||||||+|+|+|||||||+ |++
T Consensus 537 ~~~p~Li~~~Gfl~~~~tPl~kv~k~gk~~~~fys~~E~e~~~~~~~-~~~~~IkyyKGLGe~~~~e~~eyf~~~~-r~~ 614 (1388)
T PTZ00108 537 HFWPSLLKNPGFLKEFITPIVKATKKGNQVISFFTIPDFEKWKQTVG-LKGWKIKYYKGLGTSTDKEGKEYFSNID-KHR 614 (1388)
T ss_pred HhhHHhcccCCEEEEecCCEEEEEECCceeEEecCHHHHHHHHHHcC-CCCCccccccchhhcCHHHHHHHhcccC-ceE
Confidence 99999999 9999999999999999 999999999999999999875 4579999999999999999999999999 778
Q ss_pred EeeccccHHHHHHHHHHhcCCC-chHHHHHHHhccccCCcc
Q 010553 464 KQLVIEDAAEANVVFSSLMGAR-VDTRKELIQNAANLVNLD 503 (507)
Q Consensus 464 ~~v~~~d~~~~~~~f~~lmg~~-~~~Rk~~i~~~~~~~~~~ 503 (507)
++|+++|+ .++++|+++||++ +++||+||.+|++..++|
T Consensus 615 i~~~~~~~-~~~~~idl~fgk~~a~~RK~wi~~~~~~~~~d 654 (1388)
T PTZ00108 615 IRFVYVDD-SDDDSIDLAFSKKRVEDRKEWITNYKGGTYVD 654 (1388)
T ss_pred EEEecCCc-cHHHHHHHHhCCCChHHHHHHHHhhCcccccc
Confidence 99998887 4788999999986 999999999999876654
No 12
>PLN03128 DNA topoisomerase 2; Provisional
Probab=100.00 E-value=3.3e-130 Score=1117.53 Aligned_cols=471 Identities=23% Similarity=0.346 Sum_probs=409.6
Q ss_pred CEEEEEecCCCCCCcceeeecCCCCCCCCCeEEEEEeCccccccccCCCHH---HHHHHHHHHh-ccCCCcEEEEeecCC
Q 010553 1 MEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHN---TIAGRIRELA-FLNPKLTIALRKEDS 76 (507)
Q Consensus 1 k~y~q~F~~G~~~~~l~~~~~~~~~~~~~GT~V~F~PD~~iF~~~~~fd~~---~l~~Rl~elA-~Ln~Gl~I~l~der~ 76 (507)
++|+|+|++||++.++++++ .++.+++||+|+|+||++||++ ..||++ +|.+|++|+| ||||||+|+|+|+|.
T Consensus 160 k~y~q~f~~G~~~~~~p~i~--~~~~~~~GT~ItF~PD~~iF~~-~~fd~d~~~~l~kRl~elAa~Ln~GlkI~Lnder~ 236 (1135)
T PLN03128 160 KKYKQVFTNNMSVKSEPKIT--SCKASENWTKITFKPDLAKFNM-TRLDEDVVALMSKRVYDIAGCLGKKLKVELNGKKL 236 (1135)
T ss_pred eEEEEEeCCCcccCCCceec--cCCCCCCceEEEEEECHHHcCC-CccChHHHHHHHHHHHHHHHhCCCCcEEEEecCCC
Confidence 47999999999998888772 1223469999999999999985 479987 5899999999 999999999999985
Q ss_pred CCCCCcceeEecCCCHHHHHHHHh-cCCCCCCceeEEEEeccceEEEEeeeecCCCCCceeeeeeCceecCCCCcchhhH
Q 010553 77 DPEKNQYNEYFFAGGLEEYVQWLN-TDKKPLHDVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGV 155 (507)
Q Consensus 77 ~~~~~~~~~f~~~~Gl~~yv~~l~-~~~~~~~~~i~~~~~~~~~~veval~~s~~~~~~~~~SFvN~I~T~~GGTHv~g~ 155 (507)
. .+||.+||+++. .++++...++++.++ +..||||++|++ + +++++||||||+|++|||||+||
T Consensus 237 ~-----------~~G~~dyv~~~~~~~~~~~~~~i~~~~~--~~~~eva~~~s~-~-~~~~~SFVN~I~T~~GGTHv~g~ 301 (1135)
T PLN03128 237 P-----------VKSFQDYVGLYLGPNSREDPLPRIYEKV--NDRWEVCVSLSD-G-SFQQVSFVNSIATIKGGTHVDYV 301 (1135)
T ss_pred C-----------CCCHHHHHHHHhcCCCCCCCCCeEEEec--CceEEEEEEEcC-C-CceEEEEECcEecCCCCchHHHH
Confidence 3 379999999654 443333345666654 346999999995 4 46699999999999999999999
Q ss_pred HHHHHHHHHHHHHhccCCCCcCCCCCHHhHhcccEEEEEEeecCCCCCCccccccCChhhHhhhhHhhHHHHHHHHhhCh
Q 010553 156 KASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHP 235 (507)
Q Consensus 156 ~~al~~~in~~~kk~~~~k~~~~~i~~~diregL~~vvsv~i~nP~FegQTK~kL~n~~v~~~v~~~v~~~l~~~l~~n~ 235 (507)
+++|++.+++++++++ | ++.+++++|||+||++||||+|+||+|+||||++|+|++++.+|++++.+.|..||+
T Consensus 302 ~~~i~~~i~~~~~kk~--K-~~~~l~~~diregL~~vIs~ki~nP~FesQTKekL~s~~~~~~v~~~v~e~~~~~l~--- 375 (1135)
T PLN03128 302 ADQIVKHIQEKVKKKN--K-NATHVKPFQIKNHLWVFVNCLIENPTFDSQTKETLTTRPSSFGSKCELSEEFLKKVE--- 375 (1135)
T ss_pred HHHHHHHHHHHHHHcc--C-CCCCCCHHHHHhCcEEEEEEecCCCcccCcccccccChhHHHHHHHHHHHHHHHHHh---
Confidence 9999999999997754 2 245799999999999999999999999999999999999999999999999999995
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccCCCCCCCCCCC---CCCCCCceEEEeecCCCCCccccc---CCCC
Q 010553 236 DVLDSILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLADCS---STTPEESEIFIVEGDSAGGSAKQG---RDRR 309 (507)
Q Consensus 236 ~~~~~I~~~~~~~~k~r~aakkar~~~~~k~~~~~~~lpgKL~Dc~---~~~~~~~eL~lvEGDSA~gsak~g---Rdr~ 309 (507)
+..|+++++.++++|++|+++|+..++|+.+ .. ++||+||+ +++|++|||||||||||||||++| |||+
T Consensus 376 --~~~Ivekil~~a~aR~aa~~~k~~~~kk~~~--~~-ipKL~Dc~~ag~k~~~~ceLflvEGDSAggsAk~Gl~~rdR~ 450 (1135)
T PLN03128 376 --KCGVVENILSWAQFKQQKELKKKDGAKRQRL--TG-IPKLDDANDAGGKKSKDCTLILTEGDSAKALAMSGLSVVGRD 450 (1135)
T ss_pred --hHHHHHHHHHHHHHHHHHHHHHHHhhccCCC--CC-CcccccccccCCCChhHcEEEEEecCCCCcchhhcccccCcc
Confidence 3478888889999999999888877776432 23 44999997 899999999999999999999999 9999
Q ss_pred ceEeeccCCccccccccCHHHHhhCcchHHHHHHhcCCccCCcC---cccccccceEEEeecCCCCChhhHHHHHHHHHH
Q 010553 310 FQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDF---KKEALRYHKIIILTDADVDGAHIRTLLLTFFYR 386 (507)
Q Consensus 310 ~qailPLrGKiLNv~ka~~~ki~~N~Ei~~li~alG~~~~~~~~---~~~~LRY~kiiImtDaD~DG~HI~~Llltff~~ 386 (507)
|||||||||||||||+|+.+||++|+||++|++|||||++ ++| |+++|||||||||||||+|||||||||||||||
T Consensus 451 ~qaIlPLRGKiLNV~ka~~~ki~~N~EI~~li~alG~~~g-~~~~~~d~~~LRYgkIiIMTDaDvDGsHIr~LLltff~~ 529 (1135)
T PLN03128 451 HYGVFPLRGKLLNVREASHKQIMKNAEITNIKQILGLQFG-KTYDEENTKSLRYGHLMIMTDQDHDGSHIKGLIINFFHS 529 (1135)
T ss_pred ceeeeccCCceeccccCCHHHHhcchHHHHHHHHhCCCcC-ccccccChhhcccCeEEEEeCCCCCcchhHHHHHHHHHH
Confidence 9999999999999999999999999999999999999995 566 999999999999999999999999999999999
Q ss_pred HHHHHhhc-CcEEEecCCeEEEEeCCEEEEEeCHHHHHHHHHhCCCC-CCccceeeeccCCCChhhHHhhhcCcCcceEE
Q 010553 387 YQKTLFDE-GCIYVGVPPLYKVERGKQVQYCYDDAELKKVKSSFPSN-ALYSIQRFKGLGEMMPVQLWETTLNPEQRMLK 464 (507)
Q Consensus 387 ~~p~Li~~-G~v~~~~tPl~kv~~gk~~~~~y~~~e~~~~~~~~~~~-~~~~i~ryKGLGe~~~~~l~et~~~p~~r~l~ 464 (507)
|||+||+. ||||+|+||||||++|+++.||||++||++|++++++. ++|+||||||||||+|+|+||||+|+..+...
T Consensus 530 ~~p~Li~~~G~l~~~~tPl~kv~~gk~~~~~~s~~e~~~~~~~~~~~~~~~~ikyyKGLGe~~~~e~~e~f~~~~~~~~~ 609 (1135)
T PLN03128 530 FWPSLLKIPGFLVEFITPIVKATKGGKSLSFYTMPEYEAWKESLEGETKGWTIKYYKGLGTSTSEEAKEYFSNLDIHKKE 609 (1135)
T ss_pred hCHHhhccCCeEEEccCCEEEEEcCCeeEecCCHHHHHHHHHhhcccCCCccceeecccccCCHHHHHHHHHhHHHhEEE
Confidence 99999996 99999999999999999999999999999999987543 47999999999999999999999999887543
Q ss_pred eeccccHHHHHHHHHHhcC-CCchHHHHHHHhccccCCcc
Q 010553 465 QLVIEDAAEANVVFSSLMG-ARVDTRKELIQNAANLVNLD 503 (507)
Q Consensus 465 ~v~~~d~~~~~~~f~~lmg-~~~~~Rk~~i~~~~~~~~~~ 503 (507)
+.+.+.. ..+++++.|+ +++++||+||.++.+...+|
T Consensus 610 -f~~~~~~-~~~~i~~aF~k~~~~~RK~Wl~~~~~~~~~d 647 (1135)
T PLN03128 610 -FLWQSDE-DGDLIDMAFSKKRVEDRKIWLNNYEPGTFLD 647 (1135)
T ss_pred -EEeCCCC-cHHHHHHhcCCCcHHHHHHHHHhCCCCcccc
Confidence 3332211 2346666665 67999999999998876554
No 13
>PLN03237 DNA topoisomerase 2; Provisional
Probab=100.00 E-value=6.7e-127 Score=1091.91 Aligned_cols=463 Identities=25% Similarity=0.397 Sum_probs=388.6
Q ss_pred CEEEEEecC--CCCCCcceeeecCCCCCCCCCeEEEEEeCccccccccCCCHHHH---HHHHHHHh-ccCCCcEEEEeec
Q 010553 1 MEYHQKYSR--GKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTI---AGRIRELA-FLNPKLTIALRKE 74 (507)
Q Consensus 1 k~y~q~F~~--G~~~~~l~~~~~~~~~~~~~GT~V~F~PD~~iF~~~~~fd~~~l---~~Rl~elA-~Ln~Gl~I~l~de 74 (507)
++|+|+|++ |.+..|+ +. .+.++++||+|+||||++||++ ..||+++| .+|++||| ||||||+|+|+|+
T Consensus 185 k~y~Q~f~~nmG~~~~p~--i~--~~~~~~~GT~VtF~PD~eiF~~-~~fd~D~l~~~~rRlrdLAa~LnkGlkI~Lnde 259 (1465)
T PLN03237 185 KKYKQVFSNNMGKKSEPV--IT--KCKKSENWTKVTFKPDLAKFNM-THLEDDVVALMKKRVVDIAGCLGKTVKVELNGK 259 (1465)
T ss_pred eEEEEEEeCCCCccCCce--ec--cCCCCCCceEEEEEECHHHhCC-ceEcHHHHHHHHHHHHHHHhccCCCcEEEEEec
Confidence 479999999 6665663 31 1333479999999999999985 47999987 58999999 9999999999999
Q ss_pred CCCCCCCcceeEecCCCHHHHHHHHhcC----CCCCCceeEEEEeccceEEEEeeeecCCCCCceeeeeeCceecCCCCc
Q 010553 75 DSDPEKNQYNEYFFAGGLEEYVQWLNTD----KKPLHDVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGT 150 (507)
Q Consensus 75 r~~~~~~~~~~f~~~~Gl~~yv~~l~~~----~~~~~~~i~~~~~~~~~~veval~~s~~~~~~~~~SFvN~I~T~~GGT 150 (507)
|.. .+||++||+++... +.+.++++ +++ .+.+|||||+|++ + +++++||||||+|++|||
T Consensus 260 R~~-----------~~G~kdYV~~yl~~~~k~k~~~~~~i-~e~--~~~~~EVAl~~sd-~-~~~~~SFVNnI~T~~GGT 323 (1465)
T PLN03237 260 RIP-----------VKSFSDYVDLYLESANKSRPENLPRI-YEK--VNDRWEVCVSLSE-G-QFQQVSFVNSIATIKGGT 323 (1465)
T ss_pred CCC-----------CCCHHHHHHHHhhcccccCCCCCCcc-Eec--CCCeEEEEEEEeC-C-CceEEEEECcccCCCCCc
Confidence 853 26999999975432 12223333 433 4567999999995 4 477999999999999999
Q ss_pred chhhHHHHHHHHHHHHHHhccCCCCcCCCCCHHhHhcccEEEEEEeecCCCCCCccccccCChhhHhhhhHhhHHHHH--
Q 010553 151 HIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLT-- 228 (507)
Q Consensus 151 Hv~g~~~al~~~in~~~kk~~~~k~~~~~i~~~diregL~~vvsv~i~nP~FegQTK~kL~n~~v~~~v~~~v~~~l~-- 228 (507)
||+||+++|++.|++|++++ +++.+++++|||+||++||||+|+||+|+||||++|+|+++. +.+.+.
T Consensus 324 Hv~g~~~aIt~~l~~~~~kK----~k~~~l~~~DIregL~a~IsvkI~nP~FesQTKekLtn~~~~------f~s~l~l~ 393 (1465)
T PLN03237 324 HVDYVTNQIANHVMEAVNKK----NKNANIKAHNVKNHLWVFVNALIDNPAFDSQTKETLTLRQSS------FGSKCELS 393 (1465)
T ss_pred HHHHHHHHHHHHHHHHHHhc----cCCCCCCHHHHHhCcEEEEEEeCCCCccCCcccCcccChHHH------HHHHhccC
Confidence 99999999999999998763 334689999999999999999999999999999999998864 455555
Q ss_pred -HHHhhChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccc--ccCCCCCCCCCCC---CCCCCCceEEEeecCCCCCcc
Q 010553 229 -EYLELHPDVLDSILSKSLSALKAALAAKRARDLVRQKSVL--RSSSLPGKLADCS---STTPEESEIFIVEGDSAGGSA 302 (507)
Q Consensus 229 -~~l~~n~~~~~~I~~~~~~~~k~r~aakkar~~~~~k~~~--~~~~lpgKL~Dc~---~~~~~~~eL~lvEGDSA~gsa 302 (507)
.|++ +..++.|+++++.++++ ++++++.|+++.. ....+| ||+||+ +++|++|||||||||||||||
T Consensus 394 ~~flk--~~~~~~Ivekil~~A~a----k~arel~k~k~~k~~~~~~ip-KL~Dc~~aG~kd~~~ceLfLvEGDSAgGsA 466 (1465)
T PLN03237 394 EDFLK--KVMKSGIVENLLSWADF----KQSKELKKTDGAKTTRVTGIP-KLEDANEAGGKNSEKCTLILTEGDSAKALA 466 (1465)
T ss_pred HHHHh--HHHHHHHHHHHHHHHHH----HHHHHHHhhhcccccccCCCc-ccccccccccCCccccEEEEEecCcCCchh
Confidence 6665 34677799999888765 4566666665442 233345 999998 789999999999999999999
Q ss_pred cccC---CCCceEeeccCCccccccccCHHHHhhCcchHHHHHHhcCCccCCcCcccccccceEEEeecCCCCChhhHHH
Q 010553 303 KQGR---DRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTL 379 (507)
Q Consensus 303 k~gR---dr~~qailPLrGKiLNv~ka~~~ki~~N~Ei~~li~alG~~~~~~~~~~~~LRY~kiiImtDaD~DG~HI~~L 379 (507)
++|| ||+|||||||||||||||+|+.+||++|+||++|++|||||++.++||+++|||||||||||||+||||||||
T Consensus 467 k~GR~vvdR~~qaIlPLRGKILNV~kAs~~kil~N~EI~~ii~aLGlgig~~y~d~~~LRYgkIiIMTDADvDGsHIrgL 546 (1465)
T PLN03237 467 VAGLSVVGRNYYGVFPLRGKLLNVREASHKQIMNNAEIENIKQILGLQHGKQYESVKSLRYGHLMIMTDQDHDGSHIKGL 546 (1465)
T ss_pred hhhhcccCccceeeeccCCceehhccCcHHhhhcchHHHHHHHHhCCCcCcccCcccccccCcEEEEeCCCCCccHHHHH
Confidence 9999 8999999999999999999999999999999999999999996555799999999999999999999999999
Q ss_pred HHHHHHHHHHHHhh-cCcEEEecCCeEEEEe-CCEEEEEeCHHHHHHHHHhCCC-CCCccceeeeccCCCChhhHHhhhc
Q 010553 380 LLTFFYRYQKTLFD-EGCIYVGVPPLYKVER-GKQVQYCYDDAELKKVKSSFPS-NALYSIQRFKGLGEMMPVQLWETTL 456 (507)
Q Consensus 380 lltff~~~~p~Li~-~G~v~~~~tPl~kv~~-gk~~~~~y~~~e~~~~~~~~~~-~~~~~i~ryKGLGe~~~~~l~et~~ 456 (507)
||||||||||+||+ .||||+|+||||||++ ||+++||||++||++|++++++ .++|+||||||||||+|+|+||||.
T Consensus 547 LLtFF~r~~P~Li~~~Gfl~~~~tPL~Kv~~~gk~~~~fys~~E~e~w~~~~~~~~~~~~IkyYKGLGe~~~~e~keyf~ 626 (1465)
T PLN03237 547 LINFIHSFWPSLLKVPSFLVEFITPIVKATRRGKKVLSFYSMPEYEEWKESLGGNATGWSIKYYKGLGTSTAKEGKEYFK 626 (1465)
T ss_pred HHHHHHHhhHHhcccCCEEEEecCCeEEEEECCCeeEeecCHHHHHHHHHHhcccCCceeeEeeccCCCCCHHHHHHHHH
Confidence 99999999999999 8999999999999999 9999999999999999998653 3579999999999999999999999
Q ss_pred CcCcceEEeeccccHHHHHHHHHHhcCC-CchHHHHHHHhccccCCcc
Q 010553 457 NPEQRMLKQLVIEDAAEANVVFSSLMGA-RVDTRKELIQNAANLVNLD 503 (507)
Q Consensus 457 ~p~~r~l~~v~~~d~~~~~~~f~~lmg~-~~~~Rk~~i~~~~~~~~~~ 503 (507)
|..++.+ .+.+.+.. .+.++++.|++ ++++||+||.++.+..++|
T Consensus 627 ~~~~h~~-~f~~~~~~-~~~~i~laF~k~~~d~RK~Wl~~~~~~~~ld 672 (1465)
T PLN03237 627 NLGKHKK-DFVWEDEQ-DGDAIELAFSKKKIEARKNWLRQYEPGTHLD 672 (1465)
T ss_pred hHHhceE-EEEECCCC-cHHHHHHHhCCccHHHHHHHHHhCCCCcccc
Confidence 9888755 34332211 23466666654 5999999999998876554
No 14
>KOG0355 consensus DNA topoisomerase type II [Chromatin structure and dynamics]
Probab=100.00 E-value=2.7e-93 Score=768.17 Aligned_cols=466 Identities=31% Similarity=0.417 Sum_probs=399.2
Q ss_pred EEEEEecCCCCCCcceeeecCCCCCCCCCeEEEEEeCccccccccCCCHHH---HHHHHHHHhccCCCcEEEEeecCCCC
Q 010553 2 EYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNT---IAGRIRELAFLNPKLTIALRKEDSDP 78 (507)
Q Consensus 2 ~y~q~F~~G~~~~~l~~~~~~~~~~~~~GT~V~F~PD~~iF~~~~~fd~~~---l~~Rl~elA~Ln~Gl~I~l~der~~~ 78 (507)
.|+|.|.+||+....+.+. ...++.||+|||+||.+.|.++ .+|.|+ +.+|++++|....++++.+|+++...
T Consensus 161 ~~kQ~w~~nm~~~~~~~i~---~~~~~~yTkitF~PDl~~F~m~-eLD~Div~l~~rr~~d~a~~~~~vkv~ln~~~~~~ 236 (842)
T KOG0355|consen 161 AFKQTWINNMTRDEEPKIV---PSTDEDYTKITFSPDLEKFKMK-ELDDDIVALMARRAYDLAGSVKSVKVELNGKNIPV 236 (842)
T ss_pred HHHHhhhcCCcccCCceee---cCCCCCcceEEeCcChHhcCch-hhcchHHHhHHhhhhhhcccccceeeeecCCCCcc
Confidence 4889999999998877763 2344569999999999999986 688875 57999999988899999999998653
Q ss_pred CCCcceeEecCCCHHHHHHHHhcCCCCCCceeEEEEeccceEEEEeeeecCCCCCceeeeeeCceecCCCCcchhhHHHH
Q 010553 79 EKNQYNEYFFAGGLEEYVQWLNTDKKPLHDVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKAS 158 (507)
Q Consensus 79 ~~~~~~~f~~~~Gl~~yv~~l~~~~~~~~~~i~~~~~~~~~~veval~~s~~~~~~~~~SFvN~I~T~~GGTHv~g~~~a 158 (507)
+|+.+||+.+.+ .....++.....+..+-+||||++-++.+|+ ++||||+|+|.+|||||++++++
T Consensus 237 -----------~~f~~yv~~~~~-~~~~~~~~~~ihe~~~~RwEv~~a~s~~~fq--qisfvNsI~T~kGGThVd~V~D~ 302 (842)
T KOG0355|consen 237 -----------KGFYDYVKMYLE-VLWLNDDLKPLHEVLNFRWEVALALSDVGFQ--QVSFVNSIATTKGGTHVDYVVDQ 302 (842)
T ss_pred -----------chHHHHHhhccc-cccccCcchhhhcccchHHHHhhhccccccc--eeeeecceeecCCCcccchhhhh
Confidence 689999999986 3333222222223445578999888866776 59999999999999999999999
Q ss_pred HHHHHHHHHHhccCCCCcCCCCCHHhHhcccEEEEEEeecCCCCCCccccccCChhhHhhhhHhhHHHHHHHHhhChHHH
Q 010553 159 LTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVL 238 (507)
Q Consensus 159 l~~~in~~~kk~~~~k~~~~~i~~~diregL~~vvsv~i~nP~FegQTK~kL~n~~v~~~v~~~v~~~l~~~l~~n~~~~ 238 (507)
+++.|+...++.+.. ++.++++..|+++|+++|+|.|+||.|+||||++|+++..+..+.+.+.+.+...+.+++ ++
T Consensus 303 iv~~l~~vvkKk~~~--~~~svk~f~vkn~L~vfVN~lIENPtFesQTke~lt~~~~~fgs~~elsek~~k~~~~~~-i~ 379 (842)
T KOG0355|consen 303 IVAKLIDVVKKKKVK--KDISVKPFQVKNHLWVFVNCLIENPTFESQTKERLTLRPKRFGSDCELSEKFTKAIELKG-VV 379 (842)
T ss_pred HHHHHHHHhcccccc--cccccchhhhhcceEEEEEEEecCccccccchhhcccccccccceEeehhHHHHHHHhCc-hH
Confidence 999999999876543 457899999999999999999999999999999999999999999999999999999998 99
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhccccccCCCCCCCCCCC---CCCCCCceEEEeecCCCCCccc---ccCCCCceE
Q 010553 239 DSILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLADCS---STTPEESEIFIVEGDSAGGSAK---QGRDRRFQA 312 (507)
Q Consensus 239 ~~I~~~~~~~~k~r~aakkar~~~~~k~~~~~~~lpgKL~Dc~---~~~~~~~eL~lvEGDSA~gsak---~gRdr~~qa 312 (507)
+.|++++..+.+...+.++.++..+.+ .+| ||.|++ .+.+..|+|+++|||||...|. ...+|++++
T Consensus 380 esils~s~~~~~~dL~kk~~~~~s~~e------~I~-KleDa~~ag~k~s~kctlIltEgdsaksLavsGl~vvgRd~~g 452 (842)
T KOG0355|consen 380 ESILSKSLNKYKDDLAKKRGKLTSRSK------GIP-KLEDANDAGTKTSEKCTLILTEGDSAKSLAVSGLSVVGRDYYG 452 (842)
T ss_pred HHHHHHHHHHHHHhhhhhhhhhhcccc------chh-HhhhcccccccccccceeEEeccccchhheecccccccceeEe
Confidence 999999988777666555555332222 233 898875 4578899999999999974444 445677999
Q ss_pred eeccCCccccccccCHHHHhhCcchHHHHHHhcCCccCCcCcccccccceEEEeecCCCCChhhHHHHHHHHHHHHHHHh
Q 010553 313 ILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLF 392 (507)
Q Consensus 313 ilPLrGKiLNv~ka~~~ki~~N~Ei~~li~alG~~~~~~~~~~~~LRY~kiiImtDaD~DG~HI~~Llltff~~~~p~Li 392 (507)
|||||||+|||++++.+++++|+||++|+.+||++....+|+.++||||++|||||||+|||||+||||||||+|||+|+
T Consensus 453 VfplrgklLNv~e~s~kqilkn~EI~aIikIlgl~~~~~y~~~eslryg~~mimtDQd~dgshikgllInf~~~~~psl~ 532 (842)
T KOG0355|consen 453 VFPLRGKLLNVREASHKQILKNAEINAIIKILGLQYKKKYFDVESLRYGKLMIMTDQDHDGSHIKGLLINFIHHFWPSLL 532 (842)
T ss_pred ecccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccccccchhheEeeeccccccchHHHHHHHHHHHhhHHhh
Confidence 99999999999999999999999999999999999988899999999999999999999999999999999999999999
Q ss_pred hcCcEEEecCCeEEEEeCCEEEEEeCHHHHHHHHHhCCCCCCccceeeeccCCCChhhHHhhhcCcCcceEEeecc--cc
Q 010553 393 DEGCIYVGVPPLYKVERGKQVQYCYDDAELKKVKSSFPSNALYSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVI--ED 470 (507)
Q Consensus 393 ~~G~v~~~~tPl~kv~~gk~~~~~y~~~e~~~~~~~~~~~~~~~i~ryKGLGe~~~~~l~et~~~p~~r~l~~v~~--~d 470 (507)
+.+||+.+.|||+|+++|++..+|||++||++|++..+..++|.||||||||||+++|+||||+|+++|++..... .|
T Consensus 533 ~~~fleefitpi~k~~~~~~~~~fys~pey~kw~~~~~~~~~~~ikyykglgts~~~e~keyf~~~~~h~~~F~~~~~~d 612 (842)
T KOG0355|consen 533 QIPFLEEFITPIVKATKGKQEVSFYSLPEYEKWKKNTDNWKSWKIKYYKGLGTSTSKEAKEYFSDLDRHRILFKYDGGID 612 (842)
T ss_pred cCCcceecCCcceEeccCCcceeeeccHHHHHHHhcCccccccceEEeecCCcccHHHHHHHhcCcchheEEEeccCcch
Confidence 9999999999999999999999999999999999998777889999999999999999999999999997765433 23
Q ss_pred HHHHHHHHHHhcCCCchHHHHHHHhccc
Q 010553 471 AAEANVVFSSLMGARVDTRKELIQNAAN 498 (507)
Q Consensus 471 ~~~~~~~f~~lmg~~~~~Rk~~i~~~~~ 498 (507)
.+.++..|. .+..++||+||.++.+
T Consensus 613 ~~~i~~af~---k~k~~~rk~wL~~~~~ 637 (842)
T KOG0355|consen 613 DEAIDMAFS---KKKIDARKEWLRKYMP 637 (842)
T ss_pred HHHHhhhcc---cccHHHHHHHHHHHhH
Confidence 333444454 5679999999999876
No 15
>cd03366 TOPRIM_TopoIIA_GyrB TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. DNA gyrase is more effective at relaxing supercoils than decatentating DNA. DNA gyrase in addition inserts negative supercoils in the presence of ATP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in strand joining and as a general acid in strand cleava
Probab=100.00 E-value=1e-60 Score=409.58 Aligned_cols=114 Identities=73% Similarity=1.166 Sum_probs=112.1
Q ss_pred ceEEEeecCCCCCcccccCCCCceEeeccCCccccccccCHHHHhhCcchHHHHHHhcCCccCCcCcccccccceEEEee
Q 010553 288 SEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILT 367 (507)
Q Consensus 288 ~eL~lvEGDSA~gsak~gRdr~~qailPLrGKiLNv~ka~~~ki~~N~Ei~~li~alG~~~~~~~~~~~~LRY~kiiImt 367 (507)
|||||||||||||||+|||||+|||||||||||||||+++.+|+++|+||++|++|||||+ +++||+++||||||||||
T Consensus 1 ~eL~lvEGDSAggsak~gRdr~~qailPLrGKiLNv~ka~~~ki~~n~Ei~~li~alG~g~-~~~~~~~~lrY~kiiimt 79 (114)
T cd03366 1 SELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGI-GEDFDLEKLRYHKIIIMT 79 (114)
T ss_pred CEEEEEeCCCCccccccccCcCceEEeccCCccchHhhccHHHHhcChHHHHHHHHhCCCC-CCCCChhhCCcCeEEEEe
Confidence 8999999999999999999999999999999999999999999999999999999999999 478999999999999999
Q ss_pred cCCCCChhhHHHHHHHHHHHHHHHhhcCcEEEecC
Q 010553 368 DADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVP 402 (507)
Q Consensus 368 DaD~DG~HI~~Llltff~~~~p~Li~~G~v~~~~t 402 (507)
|||+||+||++|||||||||||+||++||||+|+|
T Consensus 80 DaD~DG~hI~~Llltff~~~~p~Li~~G~vyia~p 114 (114)
T cd03366 80 DADVDGAHIRTLLLTFFFRYMRPLIENGHVYIAQP 114 (114)
T ss_pred CCCCCchHHHHHHHHHHHHHhHHHHhCCeEEEecC
Confidence 99999999999999999999999999999999997
No 16
>cd01030 TOPRIM_TopoIIA_like TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in strand joining and as a general acid in strand cleavage by topisomerases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=100.00 E-value=2e-59 Score=403.97 Aligned_cols=115 Identities=64% Similarity=1.060 Sum_probs=113.0
Q ss_pred ceEEEeecCCCCCcccccCCCCceEeeccCCccccccccCHHHHhhCcchHHHHHHhcCCccCCcCcccccccceEEEee
Q 010553 288 SEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILT 367 (507)
Q Consensus 288 ~eL~lvEGDSA~gsak~gRdr~~qailPLrGKiLNv~ka~~~ki~~N~Ei~~li~alG~~~~~~~~~~~~LRY~kiiImt 367 (507)
|||||||||||||||+|||||++||||||||||||||+++.+|+++|+||.+|++||||+++..++|+++||||||||||
T Consensus 1 ~eL~lvEGDSA~gsak~gR~~~~qailPLrGKiLNv~ka~~~k~~~n~Ei~~l~~alG~~~~~~~~~~~~lrY~kiiimt 80 (115)
T cd01030 1 CELILVEGDSAGGSAKQGRDRVFQAVFPLRGKILNVEKASLKKILKNEEIQNIIKALGLGIGKDDFDLDKLRYGKIIIMT 80 (115)
T ss_pred CEEEEEecCCcchhhhhhcCcccEEEeccCCeeccHhcCCHHHHhcChHHHHHHHHhCCCCCcccCChhhcCcCeEEEEe
Confidence 89999999999999999999999999999999999999999999999999999999999997678999999999999999
Q ss_pred cCCCCChhhHHHHHHHHHHHHHHHhhcCcEEEecC
Q 010553 368 DADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVP 402 (507)
Q Consensus 368 DaD~DG~HI~~Llltff~~~~p~Li~~G~v~~~~t 402 (507)
|||+||+||++|||||||||||+|+++||||+|+|
T Consensus 81 DaD~DG~hI~~Llltff~~~~p~Li~~G~v~~~~~ 115 (115)
T cd01030 81 DADVDGSHIRTLLLTFFYRFWPSLLENGFLYIAQT 115 (115)
T ss_pred CCCCCccHhHHHHHHHHHHHhhHhhhCCEEEEeeC
Confidence 99999999999999999999999999999999987
No 17
>cd03365 TOPRIM_TopoIIA TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in strand joining and as a general acid in strand cleavage by topisomerases. The DXD motif may co-ordinate Mg2+, a cofact
Probab=100.00 E-value=4.2e-56 Score=385.55 Aligned_cols=115 Identities=35% Similarity=0.597 Sum_probs=110.5
Q ss_pred ceEEEeecCCCCCcccccC---CCCceEeeccCCccccccccCHHHHhhCcchHHHHHHhcCCccC-CcCcccccccceE
Q 010553 288 SEIFIVEGDSAGGSAKQGR---DRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKG-EDFKKEALRYHKI 363 (507)
Q Consensus 288 ~eL~lvEGDSA~gsak~gR---dr~~qailPLrGKiLNv~ka~~~ki~~N~Ei~~li~alG~~~~~-~~~~~~~LRY~ki 363 (507)
||||||||||||||||||| ||++|||||||||||||++++.+|+++|+||.+|++|||||++. +++|+++|||+||
T Consensus 1 ~eLflvEGDSA~gsak~gr~~~dr~~qailPLrGKiLNv~ka~~~ki~~n~Ei~~li~alG~g~~~~~~~~~~~lrY~ki 80 (120)
T cd03365 1 CTLILTEGDSAKALAVAGLSVVGRDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKILGLQHGKSDYESTKSLRYGRL 80 (120)
T ss_pred CEEEEEeCCCchhhHHhhhccCCCceEEEeccCCccchhhcCCHHHHhcCHHHHHHHHHhCCCCCcccccccccCCcCeE
Confidence 8999999999999999999 89999999999999999999999999999999999999999964 3489999999999
Q ss_pred EEeecCCCCChhhHHHHHHHHHHHHHHHhhc-CcEEEecC
Q 010553 364 IILTDADVDGAHIRTLLLTFFYRYQKTLFDE-GCIYVGVP 402 (507)
Q Consensus 364 iImtDaD~DG~HI~~Llltff~~~~p~Li~~-G~v~~~~t 402 (507)
|||||||+||+||++|||||||||||+||++ |||+.+.|
T Consensus 81 iimtDaD~DG~hI~~Llltff~r~~p~Li~~~~fi~~~~t 120 (120)
T cd03365 81 MIMTDQDHDGSHIKGLLINFIHSFWPSLLKIPGFLVEFIT 120 (120)
T ss_pred EEEeCCCCCccHHHHHHHHHHHHHhHHHhcCCCHHHHhcC
Confidence 9999999999999999999999999999997 99998865
No 18
>cd00822 TopoII_Trans_DNA_gyrase TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIA family of DNA topoisomerases similar to the B subunits of E. coli DNA gyrase and E. coli Topoisomerase IV which are heterodimers composed of two subunits. The type IIA enzymes are the predominant form of topoisomerase and are found in some bacteriophages, viruses and archaea, and in all bacteria and eukaryotes. All type IIA topoisomerases are related to each other at amino acid sequence level, though their oligomeric organization sometimes differs. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. TopoIIA enzymes also catenate/ decatenate duplex rings. E.coli DNA gyrase is a
Probab=100.00 E-value=1.6e-43 Score=331.78 Aligned_cols=170 Identities=48% Similarity=0.851 Sum_probs=162.1
Q ss_pred CCHHHHHHHHhcCCCCCC-ceeEEEEeccceEEEEeeeecCCCCCceeeeeeCceecCCCCcchhhHHHHHHHHHHHHHH
Q 010553 90 GGLEEYVQWLNTDKKPLH-DVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGK 168 (507)
Q Consensus 90 ~Gl~~yv~~l~~~~~~~~-~~i~~~~~~~~~~veval~~s~~~~~~~~~SFvN~I~T~~GGTHv~g~~~al~~~in~~~k 168 (507)
+||.+||++++.++++++ +++++.++.+++.|||||+|+ ++|+++++||||+|+|++||||++||+++|+++|++|++
T Consensus 1 gGl~~fl~~l~~~~~~l~~~~i~~~~~~~~~~veva~~~~-~~~~~~~~sfvN~i~T~~GGTH~~g~~~~l~~~i~~~~~ 79 (172)
T cd00822 1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWT-DSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAK 79 (172)
T ss_pred CCHHHHHHHHhCCCCcCCCCCeEEEEEecceEEEEEEEEe-CCCCeEEEEeECcccCCCCCCHHHHHHHHHHHHHHHHHH
Confidence 599999999999988887 688898887789999999999 688899999999999999999999999999999999999
Q ss_pred hccCCCCcCCCCCHHhHhcccEEEEEEeecCCCCCCccccccCChhhHhhhhHhhHHHHHHHHhhChHHHHHHHHHHHHH
Q 010553 169 KSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSLSA 248 (507)
Q Consensus 169 k~~~~k~~~~~i~~~diregL~~vvsv~i~nP~FegQTK~kL~n~~v~~~v~~~v~~~l~~~l~~n~~~~~~I~~~~~~~ 248 (507)
+++++|+++.+++++||++||++||+|+++||+|+||||++|+|++++.+|++++.+.|..||++||..++.|+++++.+
T Consensus 80 ~~~~~k~~~~~~~~~di~~~l~~vvsv~~~~P~F~gQTK~kL~~~~v~~~v~~~v~~~l~~~l~~n~~~a~~i~~k~~~~ 159 (172)
T cd00822 80 KNNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAILA 159 (172)
T ss_pred HhCcccccCCCCCHHHHHhCcEEEEEEEcCCCccCCcccccccCHhHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHH
Confidence 99988876689999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHH
Q 010553 249 LKAALAAKRARD 260 (507)
Q Consensus 249 ~k~r~aakkar~ 260 (507)
+++|++++++|+
T Consensus 160 ~~aR~aa~~ar~ 171 (172)
T cd00822 160 AKAREAARKARE 171 (172)
T ss_pred HHHHHHHHHhhc
Confidence 999999999886
No 19
>PF00204 DNA_gyraseB: DNA gyrase B; InterPro: IPR013506 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 second domain found in subunit B (gyrB and parE) of bacterial gyrase and topoisomerase IV, and the equivalent N-terminal region in eukaryotic topoisomerase II composed of a single polypeptide. 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: 3LPS_A 3LNU_A 1KIJ_B 1EI1_B 1S16_B 1QZR_B 1PVG_A 3CWV_B 1ZXN_A 1ZXM_B ....
Probab=100.00 E-value=4.1e-42 Score=323.12 Aligned_cols=168 Identities=43% Similarity=0.817 Sum_probs=152.6
Q ss_pred CHHHHHHHHhcCCCCCC-ceeEEEEec--cc-eEEEEeeeecCCCCCceeeeeeCceecCCCCcchhhHHHHHHHHHHHH
Q 010553 91 GLEEYVQWLNTDKKPLH-DVVGFRKDV--DG-ITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSL 166 (507)
Q Consensus 91 Gl~~yv~~l~~~~~~~~-~~i~~~~~~--~~-~~veval~~s~~~~~~~~~SFvN~I~T~~GGTHv~g~~~al~~~in~~ 166 (507)
||.+|+++++.+..+++ +++++.++. ++ +.|+||++|+ +++.+.++||||+|+|++|||||+||+++|+++|++|
T Consensus 1 G~~dyv~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~va~~~~-~~~~~~~~SfvN~i~T~~GGtHv~g~~~~i~~~i~~~ 79 (173)
T PF00204_consen 1 GFKDYVKLLNKDKEPLHPEPIYFEGEDKENDRWEVEVAFQWT-SGYDEKIVSFVNNIPTPEGGTHVDGFKDAITKAINDY 79 (173)
T ss_dssp SHHHHHHHHCTTS-BSSSSEEEEEEEEE-TTTEEEEEEEEEB-SSSSCEEEEEETTEE-TTEBHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHhcCCCcCCCCCeEEEEEeccCCcEEEEEEEEec-CCCceeeeeeeccccccccccHHHHHHHHHHHHHHHh
Confidence 89999999999988887 578888776 54 9999999999 6677799999999999999999999999999999999
Q ss_pred HHhccCCCCcCCCCCHHhHhcccEEEEEEeecCCCCCCccccccCChhhHhhhhHhhHHHHHHHHhhChHHHHHHHHHHH
Q 010553 167 GKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSL 246 (507)
Q Consensus 167 ~kk~~~~k~~~~~i~~~diregL~~vvsv~i~nP~FegQTK~kL~n~~v~~~v~~~v~~~l~~~l~~n~~~~~~I~~~~~ 246 (507)
+++++++|++. +++++||++||++||+|+|+||+|+||||++|+|++++..|..++.+.|..||++||++++.|+++++
T Consensus 80 ~~k~~~~k~~~-~i~~~di~~~l~~vv~~~i~nP~F~gQTK~~L~~~~~~~~v~~~v~~~l~~~l~~n~~~~~~i~~~~~ 158 (173)
T PF00204_consen 80 AKKKNKLKKKD-KITPEDIREGLTAVVSVKIPNPQFEGQTKEKLTNPEVRSIVEKAVSEKLEKWLEKNPEIAKAIIEKAL 158 (173)
T ss_dssp HHHTTCCCTTT-GSSHHHHHTTEEEEEEEEESSG-BSSTTTTSB--HHHHHHHHHHHHHHHHHHHHC-HHHHHHHHHHHH
T ss_pred HhhhCcccccc-ccchhhcccccEEEEEEEEecccccccccceeeHHHhhhhhhhhhHHHHHHHHHHCHHHHHHHHHHHH
Confidence 99999887665 99999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHH
Q 010553 247 SALKAALAAKRARD 260 (507)
Q Consensus 247 ~~~k~r~aakkar~ 260 (507)
.++++|+++++|||
T Consensus 159 ~~~~~r~~ak~are 172 (173)
T PF00204_consen 159 QAAKAREAAKKARE 172 (173)
T ss_dssp HHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHhcC
Confidence 99999999999986
No 20
>cd03481 TopoIIA_Trans_ScTopoIIA TopoIIA_Trans_ScTopoIIA: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topo IIA. S. cerevisiae Topo IIA is a homodimer encoded by a single gene. The type IIA enzymes are the predominant form of topoisomerase and are found in some bacteriophages, viruses and archaea, and in all bacteria and eukaryotes. All type IIA topoisomerases are related to each other at amino acid sequence level, though their oligomeric organization sometimes differs. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. TopoIIA enzymes also catenate/ decatenate duplex rings. This transducer domain is homologous to t
Probab=100.00 E-value=2.1e-32 Score=250.92 Aligned_cols=145 Identities=22% Similarity=0.284 Sum_probs=117.3
Q ss_pred CHHHHHHHHhcCCCCC---CceeEEEEeccceEEEEeeeecCCCCCceeeeeeCceecCCCCcchhhHHHHHHHHHHHHH
Q 010553 91 GLEEYVQWLNTDKKPL---HDVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLG 167 (507)
Q Consensus 91 Gl~~yv~~l~~~~~~~---~~~i~~~~~~~~~~veval~~s~~~~~~~~~SFvN~I~T~~GGTHv~g~~~al~~~in~~~ 167 (507)
+|++|++++..+..+. .+++.++. -+-+|||||+|++ + +++++||||+|+|++|||||+||+++|+++|++|+
T Consensus 2 ~f~~Y~~ly~~~~~~~~~~~~~~~~~~--~~~~veva~~~s~-~-~~~~~SFvN~I~T~~GGTHv~g~~~~lt~~i~~~~ 77 (153)
T cd03481 2 SFKDYVKLYLKDANKEDGPPPPVVYEP--VNDRWEVAVALSD-G-QFQQVSFVNSIATTKGGTHVDYVADQIVKKLDEVV 77 (153)
T ss_pred CHHHHHHHHhcccccccCCCCCeEecc--CCCcEEEEEEEcC-C-CcEEEEEECCcCCCCCCchHHHHHHHHHHHHHHHH
Confidence 6899999986432110 12333332 2346999999994 4 68899999999999999999999999999999999
Q ss_pred HhccCCCCcCCCCCHHhHhcccEEEEEEeecCCCCCCccccccCChhhHhhhhHhhHHHHHHHHhhChHHHHHHHHHHHH
Q 010553 168 KKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSLS 247 (507)
Q Consensus 168 kk~~~~k~~~~~i~~~diregL~~vvsv~i~nP~FegQTK~kL~n~~v~~~v~~~v~~~l~~~l~~n~~~~~~I~~~~~~ 247 (507)
++++ | ++.+++++|||+||++||+|+++||+|+||||++|+|++........+.+.|.+|+.++ .|+++++.
T Consensus 78 ~kk~--k-~~~~i~~~dire~l~~vvs~~i~~P~FegQTK~kL~s~~~~~~~~~~~~~~~~~~~~k~-----~ii~~i~~ 149 (153)
T cd03481 78 KKKN--K-GGINVKPFQVKNHLWIFVNCLIENPSFDSQTKETLTTKPKSFGSKCELSEKFLKKAVKS-----GIVESVLS 149 (153)
T ss_pred HHcC--C-CCCCcCHHHHhcCeEEEEEEecCCCccCCcccccccCcccccccccccCHHHHHHHHHc-----hHHHHHHH
Confidence 8865 2 24689999999999999999999999999999999999866666668899999999876 45555543
No 21
>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=99.94 E-value=2.5e-27 Score=183.79 Aligned_cols=63 Identities=56% Similarity=0.893 Sum_probs=60.0
Q ss_pred CCCccceeeeccCCCChhhHHhhhcCcCcceEEeeccccHHHHHHHHHHhcCCCchHHHHHHH
Q 010553 432 NALYSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQ 494 (507)
Q Consensus 432 ~~~~~i~ryKGLGe~~~~~l~et~~~p~~r~l~~v~~~d~~~~~~~f~~lmg~~~~~Rk~~i~ 494 (507)
.++++||||||||||||+|||||||||++|+|.+|+++|+.+++++|+.|||++|++||+||+
T Consensus 3 ~~~~~I~RfKGLGEM~p~qL~eTTmdP~~R~L~~V~i~d~~~~~~~~~~LMG~~v~~Rr~fIe 65 (65)
T PF00986_consen 3 KKKVEIQRFKGLGEMNPDQLWETTMDPETRRLIRVTIEDAEEADELFEMLMGKNVEPRREFIE 65 (65)
T ss_dssp TTTTEEEESSSGGGS-HHHHHHHHTSTTTTEEEEEEHCCHHHHHHHHHHHHSSTHHHHHHHHH
T ss_pred CCCceeEEecccccCCHHHHHHHccCccceEEEEEEECCHHHHHHHHHHHcCCCcHHHHHHhC
Confidence 367999999999999999999999999999999999999999999999999999999999995
No 22
>PF01751 Toprim: Toprim domain; InterPro: IPR006171 This is a conserved region from DNA primase. This corresponds to the Toprim (topoisomerase-primase) domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR/M DNA repair proteins []. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase 2.7.7.6 from EC is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division []. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases []. Type II DNA topoisomerases catalyse the relaxation of DNA supercoiling by causing transient double strand breaks.; PDB: 2ZJT_A 3IG0_A 3M4I_A 3NUH_B 1GKU_B 1GL9_C 3PWT_A 1CY4_A 1ECL_A 1CY7_A ....
Probab=99.21 E-value=7.8e-12 Score=107.00 Aligned_cols=97 Identities=22% Similarity=0.327 Sum_probs=85.5
Q ss_pred eEEEeecCCCCCcccccCCCCceEeeccCCccccccccCHHH-HhhCcchHHHHHHhcCCccCCcCcccccccceEEEee
Q 010553 289 EIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAA-MYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILT 367 (507)
Q Consensus 289 eL~lvEGDSA~gsak~gRdr~~qailPLrGKiLNv~ka~~~k-i~~N~Ei~~li~alG~~~~~~~~~~~~LRY~kiiImt 367 (507)
||+||||+|+..+..++.+...+.|+|+.|.++|....+... ..+++.|+.|.+.+ .+|+.|||+|
T Consensus 1 ~liIvE~ps~a~~i~~~l~~~~~~v~~~~Ghl~~~~~~~~~~~~~~~~~i~~l~~~~-------------~~~~~iiiat 67 (100)
T PF01751_consen 1 ELIIVEKPSDAKAIAKALGGEEYIVIATSGHLLELAKPEDYDPKDKKKQIKNLKKLL-------------KKADEIIIAT 67 (100)
T ss_dssp EEEEESSHHHHHHHHHHSSTTTEEEEEESSSSEESTTSSHHHCHTTHHHHHHHHHHH-------------HSCSEEEEEC
T ss_pred CEEEEeCHHHHHHHHHHcCCCCEEEEEeCCcccccccccccccccccccchhhHHHh-------------hhccEeeecC
Confidence 699999999998888888777799999999999999987655 78888899998887 4689999999
Q ss_pred cCCCCChhhHHHHHHHHHHHHHHHhhcCcEEEe
Q 010553 368 DADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVG 400 (507)
Q Consensus 368 DaD~DG~HI~~Llltff~~~~p~Li~~G~v~~~ 400 (507)
|+|.+|.||...++.++...+|.+ .+++++-
T Consensus 68 D~D~EGe~Ia~~i~~~~~~~~~~~--~~R~~~~ 98 (100)
T PF01751_consen 68 DPDREGELIAWEIIELLGKNNPKL--IKRVWFS 98 (100)
T ss_dssp -SSHHHHHHHHHHHHHHHHHSHHH--TTEEEEE
T ss_pred CCChHHHHHHHHHHHHHhHhCCCc--CCEEEEe
Confidence 999999999999999999999999 7777653
No 23
>cd00329 TopoII_MutL_Trans MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of type II DNA topoisomerases (Topo II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. The GyrB dimerizes in response to ATP binding, and is homologous to the N-terminal half of eukaryotic Topo II and the ATPase fragment of MutL. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. Included in this group are proteins similar to human MLH1 and PMS2. MLH1 forms a heterodimer with PMS2 which functions in meiosis and in DNA mismatch
Probab=98.80 E-value=1.3e-08 Score=86.89 Aligned_cols=100 Identities=23% Similarity=0.437 Sum_probs=76.3
Q ss_pred HHHHHHHhcCCCCCCceeEEEEeccceEEEEeeeecCC--CCCceeeeeeCceecCCCCcchhhHHHHHHHHHHHHHHhc
Q 010553 93 EEYVQWLNTDKKPLHDVVGFRKDVDGITIDLALQWCSD--AYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKS 170 (507)
Q Consensus 93 ~~yv~~l~~~~~~~~~~i~~~~~~~~~~veval~~s~~--~~~~~~~SFvN~I~T~~GGTHv~g~~~al~~~in~~~kk~ 170 (507)
.+++..+.+.+. ....+.+.....++.+++++.+... .....+++|||+.++..||+|..++.+++.+.++
T Consensus 2 ~~~i~~~~g~~~-~~~~~~~~~~~~~~~v~g~l~~~~~~~~~~~~~~~fvN~r~v~~~~~~~~~i~~~~~~~~~------ 74 (107)
T cd00329 2 KDRLAEILGDKV-ADKLIYVEGESDGFRVEGAISYPDSGRSSKDRQFSFVNGRPVREGGTHVKAVREAYTRALN------ 74 (107)
T ss_pred HhHHHHHhCHHh-HhhcEEEeccCCCEEEEEEEeCCccCcccCCcEEEEEcCeEEcCCHHHHHHHHHHHHHHhc------
Confidence 345555554332 1234555555567889999988732 1456799999999998899999999999988775
Q ss_pred cCCCCcCCCCCHHhHhcccEEEEEEeecC--CCCC-Ccccccc
Q 010553 171 KTVKDKDISLSGEHVREGLTCIISVRVPN--PEFE-GQTKTRL 210 (507)
Q Consensus 171 ~~~k~~~~~i~~~diregL~~vvsv~i~n--P~Fe-gQTK~kL 210 (507)
++++.....++|++.++. |.|. +|||+.+
T Consensus 75 -----------~~~~~~~p~~vl~i~~~~~~~d~nv~p~K~~v 106 (107)
T cd00329 75 -----------GDDVRRYPVAVLSLKIPPSLVDVNVHPTKEEV 106 (107)
T ss_pred -----------ccCCCCCCEEEEEEEeChHHeeeCCCCCcccc
Confidence 345677889999999999 9999 9999876
No 24
>PRK00095 mutL DNA mismatch repair protein; Reviewed
Probab=98.47 E-value=4.2e-06 Score=93.71 Aligned_cols=193 Identities=13% Similarity=0.179 Sum_probs=118.9
Q ss_pred EEEEEecCCCCCCcceeeecCCCCCCCCCeEEEEE------eCccccccccCCCHHHHHHHHHHHhccCCCcEEEEeecC
Q 010553 2 EYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFW------PDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALRKED 75 (507)
Q Consensus 2 ~y~q~F~~G~~~~~l~~~~~~~~~~~~~GT~V~F~------PD~~iF~~~~~fd~~~l~~Rl~elA~Ln~Gl~I~l~der 75 (507)
.|++.|++|.++. .. .....+||+|+++ |+...|-.....+...|.++++.+|++|||+.+.|.+..
T Consensus 120 ~~~~~~~~G~~~~-~~------~~~~~~GT~V~v~~LF~n~P~Rrkflk~~~~e~~~i~~~v~~~Al~~p~i~f~l~~~~ 192 (617)
T PRK00095 120 GWQIVYEGGEIVE-VK------PAAHPVGTTIEVRDLFFNTPARRKFLKSEKTELGHIDDVVNRLALAHPDVAFTLTHNG 192 (617)
T ss_pred eEEEEecCCcCcc-ee------cccCCCCCEEEechhhccCcHHHHhccCcHHHHHHHHHHHHHHhhcCCCcEEEEEECC
Confidence 4788899886542 11 1124699999996 999999433345677899999999999999999999863
Q ss_pred CCCCCCcceeEecC--CCHHHHHHHHhcCCCCCCceeEEEEeccceEEE--Eee-eecCCCCCceeeeeeCceecCCCCc
Q 010553 76 SDPEKNQYNEYFFA--GGLEEYVQWLNTDKKPLHDVVGFRKDVDGITID--LAL-QWCSDAYSDTMLGYANSIRTIDGGT 150 (507)
Q Consensus 76 ~~~~~~~~~~f~~~--~Gl~~yv~~l~~~~~~~~~~i~~~~~~~~~~ve--val-~~s~~~~~~~~~SFvN~I~T~~GGT 150 (507)
...|++. +++.+++..+.+.. .....+.+..+.+++.++ ++. .|+ ......++.|||+.++..
T Consensus 193 -------~~~~~~~~~~~~~~~i~~i~g~~-~~~~l~~~~~~~~~~~i~g~is~p~~~-~~~~~~~~~fvN~R~v~~--- 260 (617)
T PRK00095 193 -------KLVLQTRGAGQLLQRLAAILGRE-FAENALPIDAEHGDLRLSGYVGLPTLS-RANRDYQYLFVNGRYVRD--- 260 (617)
T ss_pred -------EEEEEeCCCCCHHHHHHHHhCHH-hHhheEEEeccCCCEEEEEEEeCcccc-cCCCcceEEEECCcEecC---
Confidence 3457776 57888888775432 122344555555666676 444 343 344566899999999763
Q ss_pred chhhHHHHHHHHHHHHHHhccCCCCcCCCCCHHhHhcccEEEEEEeecCCCCC---CccccccCChhhHhhhhHhhHHHH
Q 010553 151 HIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFE---GQTKTRLGNPEVRKVVDQSVQEYL 227 (507)
Q Consensus 151 Hv~g~~~al~~~in~~~kk~~~~k~~~~~i~~~diregL~~vvsv~i~nP~Fe---gQTK~kL~n~~v~~~v~~~v~~~l 227 (507)
..|.++|++..+... .+. ..-.++|++.++.-.+| ..+|...--.. ...+...+.+.+
T Consensus 261 ------~~l~~ai~~~y~~~~-~~~-----------~~P~~~l~i~~~~~~~DvNvhP~K~ev~f~~-e~~i~~~i~~~i 321 (617)
T PRK00095 261 ------KLLNHAIRQAYHDLL-PRG-----------RYPAFVLFLELDPHQVDVNVHPAKHEVRFRD-ERLVHDLIVQAI 321 (617)
T ss_pred ------HHHHHHHHHHHHHhc-cCC-----------CCcEEEEEEEeChHhcccccCCCcCEEEeCC-HHHHHHHHHHHH
Confidence 234455544322211 011 11268888888755555 33444332221 223334445555
Q ss_pred HHHHh
Q 010553 228 TEYLE 232 (507)
Q Consensus 228 ~~~l~ 232 (507)
..+|.
T Consensus 322 ~~~l~ 326 (617)
T PRK00095 322 QEALA 326 (617)
T ss_pred HHHHh
Confidence 55554
No 25
>PRK14939 gyrB DNA gyrase subunit B; Provisional
Probab=97.79 E-value=1.7e-06 Score=97.76 Aligned_cols=48 Identities=13% Similarity=0.077 Sum_probs=45.3
Q ss_pred ceeeeccCCCChhhHH-hhhcCcCcceEEeeccccHHHHHHHHHHhcCCC
Q 010553 437 IQRFKGLGEMMPVQLW-ETTLNPEQRMLKQLVIEDAAEANVVFSSLMGAR 485 (507)
Q Consensus 437 i~ryKGLGe~~~~~l~-et~~~p~~r~l~~v~~~d~~~~~~~f~~lmg~~ 485 (507)
||| ||||||+|+|+| ||||||.+|++.++.++|..+++.+|+.+||+.
T Consensus 575 ~~~-~~l~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~ 623 (756)
T PRK14939 575 ISG-EALEKLVKEYRAVRKIIDRLERRYPRAVLEALIYAPALDLDDLADE 623 (756)
T ss_pred ccH-HHHHHHHHHHHHHHHHHhHHhccccHHHHHHHHhccccchhhhcch
Confidence 789 999999999999 999999999999999999988899999999954
No 26
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=96.18 E-value=0.79 Score=50.63 Aligned_cols=99 Identities=17% Similarity=0.384 Sum_probs=64.9
Q ss_pred eEEEEeeeecCCCC----CceeeeeeCceec-CCCCcchhhHHHHHHHHHHHHH-HhccCCCCcCCCCCHHhHhcccEEE
Q 010553 119 ITIDLALQWCSDAY----SDTMLGYANSIRT-IDGGTHIEGVKASLTRTLNSLG-KKSKTVKDKDISLSGEHVREGLTCI 192 (507)
Q Consensus 119 ~~veval~~s~~~~----~~~~~SFvN~I~T-~~GGTHv~g~~~al~~~in~~~-kk~~~~k~~~~~i~~~diregL~~v 192 (507)
..||+|+.|. +.. .-+++-|+|-||. .+.|. .++|+++...- +..++-.. =..-+.++
T Consensus 353 fiVE~~iayG-g~~~~~~~~~i~RfANrvPLl~~~g~------~~~t~~v~~i~w~~Y~~~~~---------~~~p~~v~ 416 (535)
T PRK04184 353 FIVEVGIAYG-GEIPPDDKPELLRFANRVPLLYDEGS------CVITKAVESIDWKRYGIEQP---------PQAPLVVL 416 (535)
T ss_pred eEEEEEeeec-CCCCCCCCceEEEEccCCceeecCCc------cHHHHHHHhCChhhcCcCCC---------CCCCEEEE
Confidence 5699999996 322 2368999999984 45554 45566664432 23333111 01236888
Q ss_pred EEEeecCCCCCCccccccCC-hhhHhhhhHhh---HHHHHHHHhh
Q 010553 193 ISVRVPNPEFEGQTKTRLGN-PEVRKVVDQSV---QEYLTEYLEL 233 (507)
Q Consensus 193 vsv~i~nP~FegQTK~kL~n-~~v~~~v~~~v---~~~l~~~l~~ 233 (507)
|++-.++--|.|-.|+...+ ||+...+...+ ...|..||..
T Consensus 417 vhi~St~vP~~s~~Ke~ia~~~ei~~ei~~al~~~~r~L~~~l~~ 461 (535)
T PRK04184 417 VHVASTKVPYTSEGKEAIADVPEIEKEIRLALQEVARKLKKYLSR 461 (535)
T ss_pred EEEeecCCCCCCcchhhhcCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999986 66666555443 4567777754
No 27
>TIGR00585 mutl DNA mismatch repair protein MutL. All proteins in this family for which the functions are known are involved in the process of generalized mismatch repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=94.56 E-value=0.83 Score=47.01 Aligned_cols=149 Identities=9% Similarity=0.128 Sum_probs=82.5
Q ss_pred CCCCCeEEEEE------eCccccccccCCCHHHHHHHHHHHhccCCCcEEEEeecCCCCCCCcceeEec----CCCHHHH
Q 010553 26 KDRQGTRIRFW------PDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFF----AGGLEEY 95 (507)
Q Consensus 26 ~~~~GT~V~F~------PD~~iF~~~~~fd~~~l~~Rl~elA~Ln~Gl~I~l~der~~~~~~~~~~f~~----~~Gl~~y 95 (507)
..++||+|++. |+...|-......++.+..++..+|.++|++++.+.+... ..+.. ...+.+.
T Consensus 138 ~~~~GTtV~v~~lf~n~p~r~~~~~~~~~~~~~i~~~l~~~al~~p~i~f~l~~~~~-------~~~~~~~~~~~~~~~~ 210 (312)
T TIGR00585 138 PRPVGTTVEVRDLFYNLPVRRKFLKSPKKEFRKILDLLNRYALIHPDVSFSLTHDGK-------KVLQLSTKPNQSLKER 210 (312)
T ss_pred cCCCccEEEEchhhccCchhhhhccCcHHHHHHHHHHHHHHhhcCCCeEEEEEECCE-------EEEEEcCCCCCCHHHH
Confidence 45799999999 9998874322334568999999999999999999998631 12222 2346663
Q ss_pred -HHHHhcCCCCCCceeEEE-EeccceEEEEeeeecC--CCCCce-eeeeeCceecCCCCcchhhHHHHHHHHHHHHHHhc
Q 010553 96 -VQWLNTDKKPLHDVVGFR-KDVDGITIDLALQWCS--DAYSDT-MLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKS 170 (507)
Q Consensus 96 -v~~l~~~~~~~~~~i~~~-~~~~~~~veval~~s~--~~~~~~-~~SFvN~I~T~~GGTHv~g~~~al~~~in~~~kk~ 170 (507)
+..+-+... ....+.+. .+.+++.++.-+.-.. ...... ++-|||+=+-.. ..|.++|++.-+..
T Consensus 211 ~i~~v~G~~~-~~~l~~~~~~~~~~~~v~G~is~p~~~~~~~~~~q~ifvNgR~v~~---------~~l~k~I~~~y~~~ 280 (312)
T TIGR00585 211 RIRSVFGTAV-LSKLFPLLEWEDGDLQLEGFISEPNVTRSRRSGWQFLFINGRPVEL---------KLLLKAIREVYHEY 280 (312)
T ss_pred HHHHHhChHh-HhhceeeecccCCCEEEEEEEcCcccccCCCCcceEEEECCcEecc---------hHHHHHHHHHHHHh
Confidence 443333211 11112222 2334555553221110 011123 799999855221 22556665544332
Q ss_pred cCCCCcCCCCCHHhHhcccEEEEEEeecCCCCC
Q 010553 171 KTVKDKDISLSGEHVREGLTCIISVRVPNPEFE 203 (507)
Q Consensus 171 ~~~k~~~~~i~~~diregL~~vvsv~i~nP~Fe 203 (507)
.. + ...-.+++++.+|.-.+|
T Consensus 281 ~~-~-----------~~~P~~vL~i~~p~~~iD 301 (312)
T TIGR00585 281 LP-K-----------GQYPVFVLNLEIDPELVD 301 (312)
T ss_pred cc-C-----------CCCcEEEEEEEEChHHcc
Confidence 21 0 012378899998866555
No 28
>cd00188 TOPRIM Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=92.94 E-value=0.12 Score=40.57 Aligned_cols=71 Identities=35% Similarity=0.419 Sum_probs=46.8
Q ss_pred eEEEeecCCCCCcccccCCCCceEeeccCCccccccccCHHHHhhCcchHHHHHHhcCCccCCcCcccccccceEEEeec
Q 010553 289 EIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTD 368 (507)
Q Consensus 289 eL~lvEGDSA~gsak~gRdr~~qailPLrGKiLNv~ka~~~ki~~N~Ei~~li~alG~~~~~~~~~~~~LRY~kiiImtD 368 (507)
.++||||.+-.-+..+.... ...++++.|...+ .....+...++. +.+|+|++|
T Consensus 2 ~viivEg~~d~~~l~~~~~~-~~~~~~~~G~~~~------------~~~~~~~~~~~~-------------~~~v~i~~D 55 (83)
T cd00188 2 KLIIVEGPSDALALAQAGGY-GGAVVALGGHALN------------KTRELLKRLLGE-------------AKEVIIATD 55 (83)
T ss_pred EEEEEecHHHHHHHHHHcCC-CEEEEEEccEEcH------------HHHHHHHHHhcC-------------CCEEEEEcC
Confidence 58999999987666555443 3588999998776 111111222111 578999999
Q ss_pred CCCCChhhHHHHHHHHH
Q 010553 369 ADVDGAHIRTLLLTFFY 385 (507)
Q Consensus 369 aD~DG~HI~~Llltff~ 385 (507)
.|..|..+...+.....
T Consensus 56 ~D~~g~~~~~~~~~~~~ 72 (83)
T cd00188 56 ADREGEAIALRLLELLK 72 (83)
T ss_pred CChhHHHHHHHHHHHHH
Confidence 99999966655544433
No 29
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=92.19 E-value=0.41 Score=52.23 Aligned_cols=98 Identities=18% Similarity=0.376 Sum_probs=62.5
Q ss_pred eEEEEeeeecCCCC---CceeeeeeCceec-CCCCcchhhHHHHHHHHHHHHH-HhccCCCCcCCCCCHHhHh-cccEEE
Q 010553 119 ITIDLALQWCSDAY---SDTMLGYANSIRT-IDGGTHIEGVKASLTRTLNSLG-KKSKTVKDKDISLSGEHVR-EGLTCI 192 (507)
Q Consensus 119 ~~veval~~s~~~~---~~~~~SFvN~I~T-~~GGTHv~g~~~al~~~in~~~-kk~~~~k~~~~~i~~~dir-egL~~v 192 (507)
..||+|+.|.-+.- .-+++-|+|-||. .+.|. .++|+++...- +..++ + ++- .-+.++
T Consensus 348 fiVE~~iayGg~~~~~~~~~i~RfaNrvPLl~~~g~------~~~t~~v~~i~w~~Y~~-~---------~~~~~p~~v~ 411 (488)
T TIGR01052 348 FIVEVGIAYGGNIGRRSEPEILRYANKVPLLYDAGS------CVLTKAVKSINWKRYGI-R---------DFPSAPLVVL 411 (488)
T ss_pred eEEEEeeecCCcCCCCCceeEEEecccCceeecccc------cHHHHHHHhCChhhcCC-C---------CCCCCCEEEE
Confidence 46899999962211 2458999999984 34554 45666665432 22232 1 122 136888
Q ss_pred EEEeecCCCCCCccccccC-ChhhHhhhhHhh---HHHHHHHHh
Q 010553 193 ISVRVPNPEFEGQTKTRLG-NPEVRKVVDQSV---QEYLTEYLE 232 (507)
Q Consensus 193 vsv~i~nP~FegQTK~kL~-n~~v~~~v~~~v---~~~l~~~l~ 232 (507)
|++-.++--|.|-.|+... .||+...+...+ ...|..||.
T Consensus 412 vhi~St~vPf~s~~Ke~ia~~~ei~~ei~~al~~~~r~L~~~l~ 455 (488)
T TIGR01052 412 VNLASTNVPYTSTGKQSVADIPEIYNEIRLALMEVARRLRLYLS 455 (488)
T ss_pred EEEeecCCCCCCcchhhhcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999996 466665555443 345666654
No 30
>cd00823 TopoIIB_Trans TopoIIB_Trans: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIB family of DNA topoisomerases similar to Sulfolobus shibatae topoisomerase VI (topoVI). The sole representative of the Type IIB family is topo VI. Topo VI enzymes are heterotetramers found in archaea and plants. S. shibatae topoVI relaxes both positive and negative supercoils, and in addition has a strong decatenase activity. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes.
Probab=89.29 E-value=4.1 Score=37.42 Aligned_cols=89 Identities=18% Similarity=0.402 Sum_probs=56.7
Q ss_pred eEEEEeeeecCCC---CCceeeeeeCceec-CCCCcchhhHHHHHHHHHHHHH-HhccCCCCcCCCCCHHhHhcccEEEE
Q 010553 119 ITIDLALQWCSDA---YSDTMLGYANSIRT-IDGGTHIEGVKASLTRTLNSLG-KKSKTVKDKDISLSGEHVREGLTCII 193 (507)
Q Consensus 119 ~~veval~~s~~~---~~~~~~SFvN~I~T-~~GGTHv~g~~~al~~~in~~~-kk~~~~k~~~~~i~~~diregL~~vv 193 (507)
..||+|+.|--+. -.-+++-|+|-||. .+.|. .++|+++...- +..++-.. + ..-+.++|
T Consensus 33 FiVEagiayGG~~~~~~~~~i~RfANRVPLlf~~g~------cvit~av~~i~W~~Ygi~~~------~---~~p~~v~V 97 (151)
T cd00823 33 FIVEVGIAYGGDIPADEKVELLRFANRVPLLYDAGA------CVITKAVESINWKRYGLEQP------G---QGPLVVLV 97 (151)
T ss_pred eEEEEeeeecCccCCCCCceEEEEcccCceeecccc------hHHHHHHHhCChhhcCcCCC------C---CCCEEEEE
Confidence 4589999986221 12568999999984 45554 34555554432 22232111 0 23468889
Q ss_pred EEeecCCCCCCccccccCC-hhhHhhhhHh
Q 010553 194 SVRVPNPEFEGQTKTRLGN-PEVRKVVDQS 222 (507)
Q Consensus 194 sv~i~nP~FegQTK~kL~n-~~v~~~v~~~ 222 (507)
|+-.++--|.|-.|+...+ ||+...+...
T Consensus 98 hi~St~VPfts~~KeaIadvpEI~~EIrlA 127 (151)
T cd00823 98 HVASTKVPFTSEGKEAIADIPEIEEEIKLA 127 (151)
T ss_pred EEeecCCCcCCcchhhhcCCHHHHHHHHHH
Confidence 9999999999999999987 5555444433
No 31
>PF09239 Topo-VIb_trans: Topoisomerase VI B subunit, transducer; InterPro: IPR015320 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 []. This entry represents subunit B of topoisomerase VI, an ATP-dependent type IIB enzyme. Members of this family adopt a structure consisting of a four-stranded beta-sheet backed by three alpha-helices, the last of which is over 50 amino acids long and extends from the body of the protein by several turns. This domain has been proposed to mediate intersubunit communication by structurally transducing signals from the ATP binding and hydrolysis domains to the DNA binding and cleavage domains of the gyrase holoenzyme []. 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, 0006265 DNA topological change, 0005694 chromosome; PDB: 2ZBK_F 2HKJ_A 1Z5B_A 1Z5C_B 1MX0_F 1Z5A_A 1MU5_A 1Z59_A 2Q2E_B.
Probab=87.77 E-value=4.7 Score=37.31 Aligned_cols=89 Identities=15% Similarity=0.296 Sum_probs=53.1
Q ss_pred eEEEEeeeecCCC---CCceeeeeeCceec-CCCCcchhhHHHHHHHHHHHHHH-hccCCCCcCCCCCHHhHhcccEEEE
Q 010553 119 ITIDLALQWCSDA---YSDTMLGYANSIRT-IDGGTHIEGVKASLTRTLNSLGK-KSKTVKDKDISLSGEHVREGLTCII 193 (507)
Q Consensus 119 ~~veval~~s~~~---~~~~~~SFvN~I~T-~~GGTHv~g~~~al~~~in~~~k-k~~~~k~~~~~i~~~diregL~~vv 193 (507)
..||+|+.|.-+. -.-.++-|+|-||. .+.|. .++|+++.+.-= ..++- ..+ ..-+.++|
T Consensus 42 FiVEagiayGG~~~~~~~~~ilRfANRVPLly~~g~------cvit~av~~i~W~~Y~l~--------~~~-~~p~~v~V 106 (160)
T PF09239_consen 42 FIVEAGIAYGGEIPPEGKIEILRFANRVPLLYDQGS------CVITKAVKSINWKRYGLD--------QPG-NGPLVVFV 106 (160)
T ss_dssp EEEEEEEEESTTS-SCSS-EEEEEETTEEE-STGCC------SHHHHHHHHS-GCCCT----------SSS--CSEEEEE
T ss_pred EEEEEehhhccCCCCCCCceEEEEccCCceeecCCc------hHHHHHHHhCCchhcCcC--------CCC-CCCEEEEE
Confidence 4589999996211 23468999999984 45554 456677765431 22221 111 34578999
Q ss_pred EEeecCCCCCCccccccCC-hhhHhhhhHh
Q 010553 194 SVRVPNPEFEGQTKTRLGN-PEVRKVVDQS 222 (507)
Q Consensus 194 sv~i~nP~FegQTK~kL~n-~~v~~~v~~~ 222 (507)
++-.++--|.|-.|+...+ +|+...+...
T Consensus 107 hi~ST~VPfts~~KeaIa~~pEI~~Ei~lA 136 (160)
T PF09239_consen 107 HIASTKVPFTSEGKEAIADVPEIEKEIRLA 136 (160)
T ss_dssp EEEESS--BSSTTSSSB---HHHHHHHHHH
T ss_pred EEeecccCccccchhhhcCcHHHHHHHHHH
Confidence 9999999999999999983 5555444433
No 32
>PRK04017 hypothetical protein; Provisional
Probab=80.73 E-value=0.51 Score=42.49 Aligned_cols=29 Identities=34% Similarity=0.540 Sum_probs=24.9
Q ss_pred ccceEEEeecCCCCChhhHHHHHHHHHHH
Q 010553 359 RYHKIIILTDADVDGAHIRTLLLTFFYRY 387 (507)
Q Consensus 359 RY~kiiImtDaD~DG~HI~~Llltff~~~ 387 (507)
.+..|||+||.|-=|..|+..|...|..+
T Consensus 64 ~~r~VIILTD~D~~GekIr~~l~~~l~~~ 92 (132)
T PRK04017 64 RGKEVIILTDFDRKGEELAKKLSEYLQGY 92 (132)
T ss_pred cCCeEEEEECCCcchHHHHHHHHHHHHhC
Confidence 46689999999999999999988777653
No 33
>PRK14867 DNA topoisomerase VI subunit B; Provisional
Probab=74.48 E-value=30 Score=39.40 Aligned_cols=99 Identities=13% Similarity=0.288 Sum_probs=64.8
Q ss_pred eEEEEeeeecCC---CC----CceeeeeeCceec-CCCCcchhhHHHHHHHHHHHHH-HhccCCCCcCCCCCHHhHhc-c
Q 010553 119 ITIDLALQWCSD---AY----SDTMLGYANSIRT-IDGGTHIEGVKASLTRTLNSLG-KKSKTVKDKDISLSGEHVRE-G 188 (507)
Q Consensus 119 ~~veval~~s~~---~~----~~~~~SFvN~I~T-~~GGTHv~g~~~al~~~in~~~-kk~~~~k~~~~~i~~~dire-g 188 (507)
..||+|+.|.-+ .- .-+++-|+|-||- .+.|. .++|+++...- +..|+-. .-. =
T Consensus 498 FiVE~giayGG~~~~~~~~~~~~~i~RfANrvPLly~~g~------c~~t~~v~~i~W~~Y~l~~----------~~~~p 561 (659)
T PRK14867 498 FAVEVGLAYGGNAGRQGDEGRKMEIMRFSNHVPLLFDTSG------CGLTNAVKSVNWRRYGLRS----------DEDAP 561 (659)
T ss_pred EEEEEeeecCCcCCCCCccCCcceEEEeeccCceeecCcc------cHHHHHHHhCChhhcCcCC----------CCCCC
Confidence 468999999622 11 2369999999984 34444 45666665442 2333211 111 2
Q ss_pred cEEEEEEeecCCCCCCccccccC-----ChhhHhhhhHhh---HHHHHHHHhh
Q 010553 189 LTCIISVRVPNPEFEGQTKTRLG-----NPEVRKVVDQSV---QEYLTEYLEL 233 (507)
Q Consensus 189 L~~vvsv~i~nP~FegQTK~kL~-----n~~v~~~v~~~v---~~~l~~~l~~ 233 (507)
++++|++-.++--|.|-.|+.+. .||+...+...+ ...|..||.+
T Consensus 562 ~~v~vhv~St~vPfts~~Keaia~~~~~~~eI~~Ei~lAl~~~~r~L~~~l~~ 614 (659)
T PRK14867 562 ITVFVNLISTHIPYTSAGKQAIACSEEENEEIFNEIRQALMICARELEKYISR 614 (659)
T ss_pred EEEEEEEeecCCCCCCccHHHhhccCCCChHHHHHHHHHHHHHHHHHHHHHHH
Confidence 68899999999999999999998 677776665554 3466666653
No 34
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=72.37 E-value=47 Score=36.55 Aligned_cols=45 Identities=24% Similarity=0.308 Sum_probs=36.8
Q ss_pred CCCeEEEEEeCccccccccCCCHHHHHHHHHHHhccCCCcEEEEeecCC
Q 010553 28 RQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDS 76 (507)
Q Consensus 28 ~~GT~V~F~PD~~iF~~~~~fd~~~l~~Rl~elA~Ln~Gl~I~l~der~ 76 (507)
.+||+|+++|+.... .+....+.++|+.+|.+||+++|.|.+...
T Consensus 162 ~~GT~V~v~f~~~~~----r~~k~~i~e~l~~~Al~nP~~~i~l~~~~~ 206 (488)
T TIGR01052 162 WRGTRIELEFKGVSY----RRSKQGVYEYLRRTAVANPHAKIVLVDPDG 206 (488)
T ss_pred CCceEEEEEECCcee----eccHHHHHHHHHHHHhhCCCeEEEEEeCCC
Confidence 479999999766542 234578999999999999999999998643
No 35
>PRK14868 DNA topoisomerase VI subunit B; Provisional
Probab=69.68 E-value=44 Score=38.63 Aligned_cols=103 Identities=17% Similarity=0.336 Sum_probs=65.0
Q ss_pred eEEEEeeeecCCCC----CceeeeeeCceec-CCCCcchhhHHHHHHHHHHHHH-HhccCCCCcCCCCCHHhHhc-ccEE
Q 010553 119 ITIDLALQWCSDAY----SDTMLGYANSIRT-IDGGTHIEGVKASLTRTLNSLG-KKSKTVKDKDISLSGEHVRE-GLTC 191 (507)
Q Consensus 119 ~~veval~~s~~~~----~~~~~SFvN~I~T-~~GGTHv~g~~~al~~~in~~~-kk~~~~k~~~~~i~~~dire-gL~~ 191 (507)
..||+|+.|. +.. .-.++-|+|-||. .+.|. .++|++|.... +..|+-..++ +.+-. -+++
T Consensus 542 FiVEagiAYG-G~~~~~g~~~i~RfANRVPLly~~ga------c~iT~~v~~i~Wr~Ygl~q~~g-----~g~p~~P~~v 609 (795)
T PRK14868 542 FIVEAGIAYG-GEIDSEGSVDVMRFANRVPLVYQRGA------CATTDVVKSIGWRNYGLDQPGG-----SGLPNGPAVI 609 (795)
T ss_pred eEEEEEeecC-CcCCCCCCceEEEecccCceeecccc------cHHHHHHHhCChhhcCcCCCCC-----CCCCCCCEEE
Confidence 5689999996 322 2358999999984 33444 45566665442 3334322211 11111 2688
Q ss_pred EEEEeecCCCCCCccccccCC-hhhHhhhhHhh---HHHHHHHHhh
Q 010553 192 IISVRVPNPEFEGQTKTRLGN-PEVRKVVDQSV---QEYLTEYLEL 233 (507)
Q Consensus 192 vvsv~i~nP~FegQTK~kL~n-~~v~~~v~~~v---~~~l~~~l~~ 233 (507)
+|++-.+|--|.|-.|+.+.+ |++...++..+ ...|..||.+
T Consensus 610 ~VhvaST~VPfts~sKeaIA~vpEI~~EI~lAl~~~aR~Lk~yl~k 655 (795)
T PRK14868 610 MVHVASTNVPFTSESKDAIANVPEIEDEIELAIREAARELKSYLNK 655 (795)
T ss_pred EEEEeecCCCCCCcchhhhcCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999965 66665555444 3466666653
No 36
>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]
Probab=66.82 E-value=73 Score=34.67 Aligned_cols=100 Identities=18% Similarity=0.362 Sum_probs=66.9
Q ss_pred eEEEEeeeecCC---CCCceeeeeeCceec-CCCCcchhhHHHHHHHHHHHHH-HhccCCCCcCCCCCHHhHhcccEEEE
Q 010553 119 ITIDLALQWCSD---AYSDTMLGYANSIRT-IDGGTHIEGVKASLTRTLNSLG-KKSKTVKDKDISLSGEHVREGLTCII 193 (507)
Q Consensus 119 ~~veval~~s~~---~~~~~~~SFvN~I~T-~~GGTHv~g~~~al~~~in~~~-kk~~~~k~~~~~i~~~diregL~~vv 193 (507)
..||+|+.|..+ +....+.-|+|-||. .+-|. .++++++.++- +..|+ ...+ --|.++|
T Consensus 357 FiVEvgiAYGG~i~~~e~~~llRyANrvPLlyd~g~------cv~tk~V~~i~WkrYgl--------~~~~--aplvvlV 420 (538)
T COG1389 357 FIVEVGIAYGGNIPGGEKPLLLRYANRVPLLYDAGS------CVITKVVESIDWKRYGL--------DQPD--APLVVLV 420 (538)
T ss_pred eEEEEEeeccCCCCCCcchhhhhhcccCceeeecCc------chhhHhhhhccceecCc--------CCCC--CcEEEEE
Confidence 569999999621 122348899999984 23333 35667776553 23332 1222 4678999
Q ss_pred EEeecCCCCCCccccccC-ChhhHhhhhHhh---HHHHHHHHhhC
Q 010553 194 SVRVPNPEFEGQTKTRLG-NPEVRKVVDQSV---QEYLTEYLELH 234 (507)
Q Consensus 194 sv~i~nP~FegQTK~kL~-n~~v~~~v~~~v---~~~l~~~l~~n 234 (507)
++-.+|--|.|--|+... .|++..-+...+ ..+|..||...
T Consensus 421 hv~St~VPyts~gKqsIa~vpeIe~Eir~Al~evaRkL~~yLsrk 465 (538)
T COG1389 421 HVASTNVPYTSAGKQSIADVPEIENEIRLALMEVARKLKLYLSRK 465 (538)
T ss_pred EecccCCCcCCccchhccccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999998 566655554443 56788888753
No 37
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=65.03 E-value=5.9 Score=35.51 Aligned_cols=25 Identities=48% Similarity=0.699 Sum_probs=21.8
Q ss_pred ccccceEEEeecCCCCChhhHHHHH
Q 010553 357 ALRYHKIIILTDADVDGAHIRTLLL 381 (507)
Q Consensus 357 ~LRY~kiiImtDaD~DG~HI~~Lll 381 (507)
.++|..|||+||.|.=|.-||--|.
T Consensus 52 ~~~~k~VIILTD~D~~Ge~Irk~l~ 76 (127)
T COG1658 52 AQKYKGVIILTDPDRKGERIRKKLK 76 (127)
T ss_pred hhccCCEEEEeCCCcchHHHHHHHH
Confidence 4578889999999999999998764
No 38
>PF10691 DUF2497: Protein of unknown function (DUF2497) ; InterPro: IPR019632 Members of this family belong to the Alphaproteobacteria. The function of the family is not known.
Probab=63.73 E-value=16 Score=29.51 Aligned_cols=33 Identities=15% Similarity=0.503 Sum_probs=26.9
Q ss_pred hhHhhhhHhhHHHHHHHHhhC-hHHHHHHHHHHH
Q 010553 214 EVRKVVDQSVQEYLTEYLELH-PDVLDSILSKSL 246 (507)
Q Consensus 214 ~v~~~v~~~v~~~l~~~l~~n-~~~~~~I~~~~~ 246 (507)
-+...|..++...|+.||.+| |.+++.++.+=+
T Consensus 34 TlE~lvremLRPmLkeWLD~nLP~lVErlVr~EI 67 (73)
T PF10691_consen 34 TLEDLVREMLRPMLKEWLDENLPGLVERLVREEI 67 (73)
T ss_pred cHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHH
Confidence 356678888899999999999 888888886544
No 39
>cd01027 TOPRIM_RNase_M5_like TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in Ribonuclease M5: (RNase M5) and other small primase-like proteins from bacteria and archaea. RNase M5 catalyzes the maturation of 5S rRNA in low G+C Gram-positive bacteria. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=61.56 E-value=1.1 Score=36.79 Aligned_cols=27 Identities=41% Similarity=0.655 Sum_probs=23.6
Q ss_pred cceEEEeecCCCCChhhHHHHHHHHHH
Q 010553 360 YHKIIILTDADVDGAHIRTLLLTFFYR 386 (507)
Q Consensus 360 Y~kiiImtDaD~DG~HI~~Llltff~~ 386 (507)
+..|||+||.|-=|..|+.-+...+-.
T Consensus 45 ~~~VIiltD~D~aG~~i~~~~~~~l~~ 71 (81)
T cd01027 45 YRGVIILTDPDRKGEKIRKKLSEYLSG 71 (81)
T ss_pred CCEEEEEECCCHHHHHHHHHHHHHhcc
Confidence 789999999999999999988776643
No 40
>cd01028 TOPRIM_TopoIA TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IA family of DNA topoisomerases (TopoIA). This subgroup contains proteins similar to the Type I DNA topoisomerases: E. coli topisomerases I and III, eukaryotic topoisomerase III and, ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA. These enzymes cleave one strand of the DNA duplex, covalently link to the 5' phosphoryl end of the DNA break and allow the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general b
Probab=55.80 E-value=9.4 Score=34.49 Aligned_cols=25 Identities=28% Similarity=0.423 Sum_probs=21.8
Q ss_pred cceEEEeecCCCCChhhHHHHHHHH
Q 010553 360 YHKIIILTDADVDGAHIRTLLLTFF 384 (507)
Q Consensus 360 Y~kiiImtDaD~DG~HI~~Llltff 384 (507)
...|||+||+|--|-+|.-.++.++
T Consensus 91 ~d~iiiAtD~DrEGE~I~~~i~~~~ 115 (142)
T cd01028 91 ADEIVLATDPDREGELIAWEILEVL 115 (142)
T ss_pred CCEEEEcCCCCcchHHHHHHHHHHh
Confidence 4689999999999999988777665
No 41
>PF13662 Toprim_4: Toprim domain; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=53.47 E-value=2.1 Score=34.65 Aligned_cols=18 Identities=28% Similarity=0.396 Sum_probs=14.3
Q ss_pred cceEEEeecCCCCChhhH
Q 010553 360 YHKIIILTDADVDGAHIR 377 (507)
Q Consensus 360 Y~kiiImtDaD~DG~HI~ 377 (507)
+.+|||++|.|..|--..
T Consensus 46 ~~~Vii~~D~D~~G~~~a 63 (81)
T PF13662_consen 46 VKEVIIAFDNDKAGEKAA 63 (81)
T ss_dssp -SEEEEEEESSHHHHHHH
T ss_pred CceEEEEeCcCHHHHHHH
Confidence 489999999999996433
No 42
>PRK04031 DNA primase; Provisional
Probab=45.11 E-value=18 Score=38.54 Aligned_cols=53 Identities=25% Similarity=0.316 Sum_probs=33.8
Q ss_pred ccceEEEeecCCCCChhhHHHHHHHHHHHHHHHhhcC-cEEEecCCeEEEEeCCEEEEEeCHHHHHHHHHh
Q 010553 359 RYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEG-CIYVGVPPLYKVERGKQVQYCYDDAELKKVKSS 428 (507)
Q Consensus 359 RY~kiiImtDaD~DG~HI~~Llltff~~~~p~Li~~G-~v~~~~tPl~kv~~gk~~~~~y~~~e~~~~~~~ 428 (507)
+-..|++++|.|.-|--|+--| ++.+ +.|++.-| .|+.. --++-++..+.+.+
T Consensus 209 k~~~Vil~~DgD~aGe~I~k~l-----------~~v~~~d~VaraP-----~G~dV-E~ls~eeI~kAL~~ 262 (408)
T PRK04031 209 KKKTVTAFLDGDRGGELILKEL-----------LQVADIDYVARAP-----PGKEV-EELTKKEIAKALRN 262 (408)
T ss_pred cCCCEEEEECCCHHHHHHHHHH-----------HhhcceeEEecCC-----CCCCh-hhCCHHHHHHHHHh
Confidence 3568999999999997664433 3323 67888888 55433 33455555555443
No 43
>cd03363 TOPRIM_TopoIA_TopoI TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=42.86 E-value=18 Score=32.06 Aligned_cols=24 Identities=29% Similarity=0.390 Sum_probs=19.8
Q ss_pred ceEEEeecCCCCChhhHHHHHHHH
Q 010553 361 HKIIILTDADVDGAHIRTLLLTFF 384 (507)
Q Consensus 361 ~kiiImtDaD~DG~HI~~Llltff 384 (507)
.-|||.||+|..|.+|.-.++..+
T Consensus 74 ~eiiiAtD~drEGe~i~~~i~~~~ 97 (123)
T cd03363 74 DEIYLATDPDREGEAIAWHLAEVL 97 (123)
T ss_pred CEEEEcCCCCcchHHHHHHHHHHc
Confidence 369999999999999987665544
No 44
>PF14484 FISNA: Fish-specific NACHT associated domain
Probab=40.48 E-value=16 Score=29.46 Aligned_cols=13 Identities=38% Similarity=0.680 Sum_probs=11.7
Q ss_pred CceEEEeecCCCC
Q 010553 287 ESEIFIVEGDSAG 299 (507)
Q Consensus 287 ~~eL~lvEGDSA~ 299 (507)
-++||||||+|.+
T Consensus 30 YTeLyIteg~~~~ 42 (73)
T PF14484_consen 30 YTELYITEGGSGE 42 (73)
T ss_pred ceeeeEeccCCCc
Confidence 5899999999986
No 45
>TIGR00334 5S_RNA_mat_M5 ribonuclease M5. This family of orthologous proteins shows a weak but significant similarity to the central region of the DnaG-type DNA primase. The region of similarity is termed the Toprim (topoisomerase-primase) domain and is also shared by RecR, OLD family nucleases, and type IA and II topoisomerases.
Probab=39.44 E-value=23 Score=33.46 Aligned_cols=23 Identities=39% Similarity=0.599 Sum_probs=19.9
Q ss_pred ccceEEEeecCCCCChhhHHHHH
Q 010553 359 RYHKIIILTDADVDGAHIRTLLL 381 (507)
Q Consensus 359 RY~kiiImtDaD~DG~HI~~Lll 381 (507)
...-|||+||+|.-|-.||.-|.
T Consensus 46 ~~rgVIIfTDpD~~GekIRk~i~ 68 (174)
T TIGR00334 46 KKQGVIILTDPDFPGEKIRKKIE 68 (174)
T ss_pred hcCCEEEEeCCCCchHHHHHHHH
Confidence 45679999999999999998764
No 46
>cd03362 TOPRIM_TopoIA_TopoIII TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=34.17 E-value=36 Score=31.01 Aligned_cols=25 Identities=36% Similarity=0.514 Sum_probs=20.9
Q ss_pred cceEEEeecCCCCChhhHHHHHHHH
Q 010553 360 YHKIIILTDADVDGAHIRTLLLTFF 384 (507)
Q Consensus 360 Y~kiiImtDaD~DG~HI~~Llltff 384 (507)
...|||+||+|--|.+|.-.++..+
T Consensus 99 ad~ii~atD~DrEGE~I~~~i~~~~ 123 (151)
T cd03362 99 ADEIVIATDADREGELIGREILEYA 123 (151)
T ss_pred CCeEEEccCCCccccHHHHHHHHHh
Confidence 3679999999999999987776654
No 47
>PRK14867 DNA topoisomerase VI subunit B; Provisional
Probab=27.66 E-value=84 Score=35.92 Aligned_cols=44 Identities=18% Similarity=0.175 Sum_probs=30.1
Q ss_pred CCCCeEEEEEeCccccccccCCCHHHHHHHHHHHhccCCCcEEEEeec
Q 010553 27 DRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALRKE 74 (507)
Q Consensus 27 ~~~GT~V~F~PD~~iF~~~~~fd~~~l~~Rl~elA~Ln~Gl~I~l~de 74 (507)
..+||+|+|.-. ..|- ... ...+.+.++.+|..||++.|.|.+.
T Consensus 167 ~~~GT~Ie~~V~-dLFy-nR~--E~~i~e~l~r~ALanP~i~f~l~~~ 210 (659)
T PRK14867 167 FWRGTRVEGEFK-EVTY-NRR--EQGPFEYLRRISLSTPHAKITLKDP 210 (659)
T ss_pred CCCCcEEEEEEe-ecee-chh--hHHHHHHHHHHHHhCCCcEEEEEeC
Confidence 368999996210 1221 110 1127899999999999999999875
No 48
>PF11169 DUF2956: Protein of unknown function (DUF2956); InterPro: IPR021339 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=26.21 E-value=1.4e+02 Score=25.77 Aligned_cols=24 Identities=33% Similarity=0.591 Sum_probs=12.7
Q ss_pred CCccccccCChhhHhhhhHhhHHHHHHHHh
Q 010553 203 EGQTKTRLGNPEVRKVVDQSVQEYLTEYLE 232 (507)
Q Consensus 203 egQTK~kL~n~~v~~~v~~~v~~~l~~~l~ 232 (507)
.|||||. .+.+.+-+.+.+..|-+
T Consensus 18 pGQTKEQ------TKLIAqGIeKGIa~YKK 41 (103)
T PF11169_consen 18 PGQTKEQ------TKLIAQGIEKGIAEYKK 41 (103)
T ss_pred CCCCHHH------HHHHHHHHHHHHHHHHH
Confidence 4788875 22333334455555544
No 49
>cd01026 TOPRIM_OLD TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as RNase activity, consists of an N-terminal ABC-type ATPase domain and a C-terminal Toprim domain; the nuclease activity of OLD is stimulated by ATP, though the ATPase activity is not DNA-dependent. Functional details on OLD are scant and further experimentation is required to define the relationship between the ATPase and Toprim nuclease domains. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general acid in strand cleavage by nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=26.03 E-value=25 Score=29.36 Aligned_cols=58 Identities=38% Similarity=0.540 Sum_probs=37.3
Q ss_pred EEEeecCCCCCc----cc-cc--CCCCceEeeccCCccccccccCHHHHhhCcchHHHHHHhcCCccCCcCcccccccce
Q 010553 290 IFIVEGDSAGGS----AK-QG--RDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHK 362 (507)
Q Consensus 290 L~lvEGDSA~gs----ak-~g--Rdr~~qailPLrGKiLNv~ka~~~ki~~N~Ei~~li~alG~~~~~~~~~~~~LRY~k 362 (507)
.+||||+|=-.. +. .+ ++...-.|.|..|| |+... ..++..+|. +
T Consensus 6 vIlVEG~tE~~~l~~~~~~~~~~~~~~~i~ii~~gG~--~~~~~-----------~~ll~~~~i---------------~ 57 (97)
T cd01026 6 VILVEGDSEEILLPALAKKLGLDLDEAGISIIPVGGK--NFKPF-----------IKLLNALGI---------------P 57 (97)
T ss_pred EEEEecHHHHHHHHHHHHHhCCCHHHCCEEEEEeCCc--chHHH-----------HHHHHHcCC---------------C
Confidence 689999997432 11 12 33345688888887 55432 234444443 5
Q ss_pred EEEeecCCCCChh
Q 010553 363 IIILTDADVDGAH 375 (507)
Q Consensus 363 iiImtDaD~DG~H 375 (507)
+.+++|.|..+.+
T Consensus 58 ~~vi~D~D~~~~~ 70 (97)
T cd01026 58 VAVLTDLDAKRNE 70 (97)
T ss_pred EEEEEeCCCCCCc
Confidence 7899999998876
No 50
>smart00493 TOPRIM topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins.
Probab=24.81 E-value=54 Score=25.54 Aligned_cols=20 Identities=35% Similarity=0.518 Sum_probs=16.6
Q ss_pred ceEEEeecCCCCChhhHHHH
Q 010553 361 HKIIILTDADVDGAHIRTLL 380 (507)
Q Consensus 361 ~kiiImtDaD~DG~HI~~Ll 380 (507)
.+|||++|.|..|..+.--+
T Consensus 48 ~~Iii~~D~D~~G~~~~~~i 67 (76)
T smart00493 48 KEVILATDPDREGEAIAWKL 67 (76)
T ss_pred CEEEEEcCCChhHHHHHHHH
Confidence 57999999999998776544
No 51
>cd03361 TOPRIM_TopoIA_RevGyr TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to the ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=24.08 E-value=57 Score=30.55 Aligned_cols=25 Identities=24% Similarity=0.367 Sum_probs=20.5
Q ss_pred cceEEEeecCCCCChhhHHHHHHHH
Q 010553 360 YHKIIILTDADVDGAHIRTLLLTFF 384 (507)
Q Consensus 360 Y~kiiImtDaD~DG~HI~~Llltff 384 (507)
-..|||.||+|-.|..|.-.++..+
T Consensus 119 ~~~iiiatD~drEGe~I~~~i~~~~ 143 (170)
T cd03361 119 VDEVLIATDPDTEGEKIAWDVYLAL 143 (170)
T ss_pred CCEEEEecCCCccHHHHHHHHHHHh
Confidence 3479999999999999887776554
No 52
>cd06404 PB1_aPKC PB1 domain is an essential modular domain of the atypical protein kinase C (aPKC) which in complex with Par6 and Par3 proteins is crucial for establishment of apical-basal polarity of animal cells. PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi,
Probab=23.18 E-value=3.4e+02 Score=22.58 Aligned_cols=67 Identities=13% Similarity=0.169 Sum_probs=44.5
Q ss_pred EEEEEeCccccccccCCCHHHHHHHHHHHhccCC--CcEEEEeecCCCCCCCcceeEecCCCHHHHHHHHhcCC
Q 010553 32 RIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNP--KLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDK 103 (507)
Q Consensus 32 ~V~F~PD~~iF~~~~~fd~~~l~~Rl~elA~Ln~--Gl~I~l~der~~~~~~~~~~f~~~~Gl~~yv~~l~~~~ 103 (507)
++.|.=|--++..+...+++.|.+.++++.-+.+ ..++.+.|+..+ .-++....=|.+-++.+..++
T Consensus 4 K~~y~gdi~it~~d~~~s~e~L~~~v~~~c~~~~~q~ft~kw~DEEGD-----p~tiSS~~EL~EA~rl~~~n~ 72 (83)
T cd06404 4 KAAYNGDIMITSIDPSISLEELCNEVRDMCRFHNDQPFTLKWIDEEGD-----PCTISSQMELEEAFRLYELNK 72 (83)
T ss_pred EEEecCcEEEEEcCCCcCHHHHHHHHHHHhCCCCCCcEEEEEECCCCC-----ceeecCHHHHHHHHHHHHhcC
Confidence 3455556555544445679999999999997765 689999998654 234545445666666655444
No 53
>cd00818 IleRS_core catalytic core domain of isoleucyl-tRNA synthetases. Isoleucine amino-acyl tRNA synthetases (IleRS) catalytic core domain . This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. IleRS has an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids.
Probab=22.75 E-value=2.8e+02 Score=28.76 Aligned_cols=97 Identities=20% Similarity=0.234 Sum_probs=60.1
Q ss_pred CcchHHHHHHhcCCccCCcCcccccccceEEEeecCCCCChhhHHHHHHHHHHHHHHHhhcCcEEEecCCeE-EEEeCCE
Q 010553 334 NEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLY-KVERGKQ 412 (507)
Q Consensus 334 N~Ei~~li~alG~~~~~~~~~~~~LRY~kiiImtDaD~DG~HI~~Llltff~~~~p~Li~~G~v~~~~tPl~-kv~~gk~ 412 (507)
.+++.+.+..||+...-+.+ +-| .|-.|+.. ...++-.|+++|+||....|.+ .+..-..
T Consensus 90 ~~~~~~~~~~lgi~~~~~~~-----------~~T---~~~~~~~~-----v~~~f~~L~~~G~iY~~~~~v~~~v~~~~~ 150 (338)
T cd00818 90 VDEQEEQFQRLGVWVDWENP-----------YKT---MDPEYMES-----VWWVFKQLHEKGLLYRGYKVVPWPLIYRAT 150 (338)
T ss_pred HHHHHHHHHHhCceecCCCC-----------eEC---CCHHHHHH-----HHHHHHHHHHCCCEeccCCeeeeEEEEEec
Confidence 36777888999985421111 123 23346554 4466788999999999888763 3333344
Q ss_pred EEEEeCHHHHHHHHHh----C---------------CCCCCccceeeeccCCCChh
Q 010553 413 VQYCYDDAELKKVKSS----F---------------PSNALYSIQRFKGLGEMMPV 449 (507)
Q Consensus 413 ~~~~y~~~e~~~~~~~----~---------------~~~~~~~i~ryKGLGe~~~~ 449 (507)
..||+...++.+.+.+ . .+...|.|.|=-++|.==|-
T Consensus 151 ~qwf~~l~~~~~~l~~~~~~~~~~P~~~~~~~~~~l~~l~dw~iSR~~~WGip~P~ 206 (338)
T cd00818 151 PQWFIRVTKIKDRLLEANDKVNWIPEWVKNRFGNWLENRRDWCISRQRYWGTPIPV 206 (338)
T ss_pred CeEEEEcHHHHHHHHHHHhcCcEECHHHHHHHHHHHhcchhcceeeecccCceeeE
Confidence 5688777666655433 1 12345778888888886663
No 54
>KOG4174 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.13 E-value=7.7e+02 Score=25.04 Aligned_cols=64 Identities=22% Similarity=0.282 Sum_probs=42.0
Q ss_pred CcchHHHHHHhcCCccC--------CcCcccccccceEEEeecCCCCChhhH------------HHHHHHHHHHHHHHh-
Q 010553 334 NEEIQNLIRALGLGVKG--------EDFKKEALRYHKIIILTDADVDGAHIR------------TLLLTFFYRYQKTLF- 392 (507)
Q Consensus 334 N~Ei~~li~alG~~~~~--------~~~~~~~LRY~kiiImtDaD~DG~HI~------------~Llltff~~~~p~Li- 392 (507)
+.+=-..+.+|||.+-- ..++...=||.+||.- ==+-|+||+ .|+..||..- .+|+
T Consensus 104 ~~~nv~~Lk~lG~~I~h~Vdv~sl~~~~~~~~~~~d~IiFN--FPH~G~g~~~e~d~~~i~~~qkL~rgFle~a-kemL~ 180 (282)
T KOG4174|consen 104 AKENVEALKRLGGTILHGVDVTSLKFHADLRLQRYDNIIFN--FPHSGKGIKFEQDRNIIPLHQKLFRGFLESA-KEMLK 180 (282)
T ss_pred hHHHHHHHHHcCCceEecccceeEEecccccccccceEEEc--CCCCCCCcccccchHHHHHHHHHHHHHHHHH-HHHHH
Confidence 34445668899997621 1235666778888775 667788775 6777888755 4454
Q ss_pred -hcCcEEEe
Q 010553 393 -DEGCIYVG 400 (507)
Q Consensus 393 -~~G~v~~~ 400 (507)
+.|-|.+.
T Consensus 181 ~edGeI~it 189 (282)
T KOG4174|consen 181 DEDGEIHIT 189 (282)
T ss_pred hcCCcEEEE
Confidence 46877764
Done!