Query 001100
Match_columns 1158
No_of_seqs 415 out of 2531
Neff 5.7
Searched_HMMs 46136
Date Thu Mar 28 15:50:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001100.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001100hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK08780 DNA topoisomerase I; 100.0 6E-163 1E-167 1504.5 74.8 758 348-1149 1-772 (780)
2 PRK07561 DNA topoisomerase I s 100.0 6E-156 1E-160 1458.7 75.5 737 350-1138 2-755 (859)
3 PRK06319 DNA topoisomerase I/S 100.0 5E-154 1E-158 1438.9 70.6 737 348-1144 1-763 (860)
4 PRK06599 DNA topoisomerase I; 100.0 2E-137 5E-142 1265.7 69.1 673 348-1072 1-673 (675)
5 COG0550 TopA Topoisomerase IA 100.0 2E-136 3E-141 1222.6 53.4 546 350-935 1-553 (570)
6 PRK05776 DNA topoisomerase I; 100.0 8E-136 2E-140 1245.4 59.6 596 349-1003 1-638 (670)
7 PRK07219 DNA topoisomerase I; 100.0 7E-135 2E-139 1265.3 65.7 695 350-1115 1-764 (822)
8 PRK05582 DNA topoisomerase I; 100.0 7E-133 1E-137 1222.7 65.0 635 348-1049 1-636 (650)
9 PRK07220 DNA topoisomerase I; 100.0 5E-132 1E-136 1225.8 60.9 624 350-1049 1-661 (740)
10 TIGR01056 topB DNA topoisomera 100.0 5E-132 1E-136 1211.8 59.5 585 350-1000 1-643 (660)
11 TIGR01051 topA_bact DNA topois 100.0 2E-131 4E-136 1200.8 62.7 608 352-1002 1-609 (610)
12 PRK14973 DNA topoisomerase I; 100.0 1E-131 3E-136 1233.8 61.8 625 350-1048 1-660 (936)
13 PRK08173 DNA topoisomerase III 100.0 5E-129 1E-133 1209.5 67.6 710 348-1138 1-781 (862)
14 PRK14724 DNA topoisomerase III 100.0 3E-128 7E-133 1213.5 66.3 723 350-1138 2-814 (987)
15 PRK07726 DNA topoisomerase III 100.0 2E-126 5E-131 1164.7 59.0 586 350-997 1-640 (658)
16 TIGR01057 topA_arch DNA topois 100.0 3E-123 7E-128 1131.8 59.8 577 354-996 1-618 (618)
17 PTZ00407 DNA topoisomerase IA; 100.0 6E-120 1E-124 1101.3 48.0 572 350-937 10-695 (805)
18 PRK09401 reverse gyrase; Revie 100.0 9E-111 2E-115 1071.5 54.3 511 348-932 600-1172(1176)
19 TIGR01054 rgy reverse gyrase. 100.0 9E-110 2E-114 1063.5 55.6 515 345-930 597-1169(1171)
20 KOG1956 DNA topoisomerase III 100.0 4E-101 1E-105 882.8 41.2 692 350-1148 2-745 (758)
21 PRK14701 reverse gyrase; Provi 100.0 3.9E-96 8E-101 953.1 52.1 517 345-931 576-1636(1638)
22 cd00186 TOP1Ac DNA Topoisomera 100.0 5.6E-90 1.2E-94 797.9 38.2 375 482-931 1-379 (381)
23 PF01131 Topoisom_bac: DNA top 100.0 8.7E-89 1.9E-93 793.7 32.9 398 479-923 1-403 (403)
24 COG1110 Reverse gyrase [DNA re 100.0 5.5E-87 1.2E-91 800.1 40.3 521 336-931 604-1185(1187)
25 smart00437 TOP1Ac Bacterial DN 100.0 1.4E-60 3.1E-65 525.4 24.6 255 604-884 2-259 (259)
26 KOG1957 DNA topoisomerase III 100.0 2.1E-53 4.6E-58 474.0 14.1 494 349-927 2-530 (555)
27 cd03363 TOPRIM_TopoIA_TopoI TO 100.0 1.5E-30 3.2E-35 257.2 13.9 122 350-477 1-123 (123)
28 cd01028 TOPRIM_TopoIA TOPRIM_T 100.0 8.4E-30 1.8E-34 257.9 14.7 123 350-477 1-142 (142)
29 cd03362 TOPRIM_TopoIA_TopoIII 100.0 3.4E-29 7.4E-34 256.0 14.2 124 350-477 1-151 (151)
30 smart00436 TOP1Bc Bacterial DN 100.0 9.1E-30 2E-34 237.5 8.6 88 457-544 1-89 (89)
31 cd03361 TOPRIM_TopoIA_RevGyr T 99.9 8E-27 1.7E-31 242.9 13.7 122 351-477 2-170 (170)
32 COG1754 Uncharacterized C-term 99.9 2.3E-26 5.1E-31 248.1 12.0 167 964-1138 23-192 (298)
33 COG1754 Uncharacterized C-term 99.9 1.3E-24 2.7E-29 234.8 12.8 170 962-1140 76-258 (298)
34 PF01751 Toprim: Toprim domain 99.8 4.7E-21 1E-25 182.7 6.2 99 351-465 1-100 (100)
35 PRK07561 DNA topoisomerase I s 99.7 9.1E-17 2E-21 203.8 14.7 155 962-1138 643-818 (859)
36 PRK08780 DNA topoisomerase I; 99.7 5.8E-17 1.2E-21 203.2 11.0 118 1022-1140 588-705 (780)
37 PF13368 Toprim_C_rpt: Topoiso 98.8 5.6E-09 1.2E-13 91.5 5.6 50 1089-1139 1-50 (61)
38 smart00493 TOPRIM topoisomeras 98.6 1.7E-07 3.8E-12 84.5 8.5 73 350-447 1-73 (76)
39 COG0551 TopA Zn-finger domain 98.5 2.9E-07 6.3E-12 93.6 9.6 100 962-1101 15-116 (140)
40 cd01025 TOPRIM_recR TOPRIM_rec 98.4 8.1E-07 1.8E-11 86.9 9.0 88 350-462 1-93 (112)
41 PF13368 Toprim_C_rpt: Topoiso 98.4 3.2E-07 7E-12 80.5 5.3 55 1028-1090 1-55 (61)
42 PRK06319 DNA topoisomerase I/S 98.3 4.5E-07 9.8E-12 116.2 6.3 119 520-645 384-509 (860)
43 PF01396 zf-C4_Topoisom: Topoi 98.3 9.2E-07 2E-11 70.8 4.3 36 965-1003 2-37 (39)
44 PRK07219 DNA topoisomerase I; 97.9 1.7E-05 3.7E-10 101.7 7.8 70 964-1049 688-757 (822)
45 COG0551 TopA Zn-finger domain 97.8 1.7E-05 3.7E-10 80.7 4.3 100 1023-1141 15-119 (140)
46 PRK14973 DNA topoisomerase I; 97.6 4.6E-05 9.9E-10 98.3 4.3 54 815-869 257-310 (936)
47 cd00188 TOPRIM Topoisomerase-p 97.5 0.00064 1.4E-08 60.3 9.9 82 350-461 1-82 (83)
48 PRK00076 recR recombination pr 97.2 0.001 2.2E-08 71.4 8.7 105 350-478 79-194 (196)
49 cd01027 TOPRIM_RNase_M5_like T 96.9 0.0048 1E-07 57.4 8.6 79 350-461 2-80 (81)
50 PRK06599 DNA topoisomerase I; 96.8 0.001 2.2E-08 84.0 4.7 55 814-869 240-303 (675)
51 PF01396 zf-C4_Topoisom: Topoi 96.6 0.002 4.4E-08 51.8 3.3 35 1026-1071 2-36 (39)
52 PRK07220 DNA topoisomerase I; 95.1 0.023 5E-07 72.7 5.2 66 814-880 257-324 (740)
53 COG4026 Uncharacterized protei 95.0 0.13 2.8E-06 55.6 9.4 95 351-476 9-114 (290)
54 PRK05582 DNA topoisomerase I; 94.8 0.044 9.4E-07 69.3 6.6 55 814-869 233-297 (650)
55 PF13662 Toprim_4: Toprim doma 94.8 0.07 1.5E-06 49.2 6.3 79 350-460 1-80 (81)
56 PRK13844 recombination protein 94.5 0.23 5E-06 53.8 10.0 107 350-479 83-199 (200)
57 TIGR00334 5S_RNA_mat_M5 ribonu 93.9 0.43 9.2E-06 50.7 10.4 104 349-479 2-110 (174)
58 TIGR00615 recR recombination p 93.9 0.2 4.4E-06 54.0 8.1 105 350-476 79-193 (195)
59 COG1658 Small primase-like pro 92.7 0.47 1E-05 48.0 8.2 102 350-478 10-120 (127)
60 PF09151 DUF1936: Domain of un 92.7 0.16 3.4E-06 38.6 3.5 32 966-998 3-34 (36)
61 COG0353 RecR Recombinational D 91.9 0.91 2E-05 48.9 9.5 88 350-461 80-171 (198)
62 PRK04031 DNA primase; Provisio 84.1 1.3 2.9E-05 52.5 5.0 65 414-482 204-268 (408)
63 TIGR01057 topA_arch DNA topois 80.7 4.9 0.00011 51.0 8.6 58 811-869 251-309 (618)
64 PRK05776 DNA topoisomerase I; 80.2 1.1 2.4E-05 57.0 2.8 54 815-869 258-312 (670)
65 smart00437 TOP1Ac Bacterial DN 76.7 6.8 0.00015 44.4 7.4 51 594-645 189-240 (259)
66 PF09664 DUF2399: Protein of u 74.9 8.6 0.00019 40.2 7.0 73 349-446 18-91 (152)
67 PF01131 Topoisom_bac: DNA top 70.3 7.7 0.00017 46.6 6.2 122 519-660 224-351 (403)
68 PRK04017 hypothetical protein; 66.3 6.3 0.00014 40.3 3.6 69 351-448 24-92 (132)
69 TIGR01056 topB DNA topoisomera 65.4 21 0.00045 45.8 8.9 55 814-869 263-319 (660)
70 COG0550 TopA Topoisomerase IA 64.8 22 0.00047 44.8 8.7 69 810-880 236-309 (570)
71 PRK03573 transcriptional regul 63.5 10 0.00022 38.5 4.7 51 835-889 47-104 (144)
72 TIGR01051 topA_bact DNA topois 61.5 27 0.00058 44.4 8.8 55 814-869 232-295 (610)
73 PF08259 Periviscerokin: Periv 60.0 3 6.6E-05 24.8 0.1 9 654-662 3-11 (11)
74 cd00186 TOP1Ac DNA Topoisomera 59.0 21 0.00046 42.6 6.9 55 594-658 262-317 (381)
75 PRK03902 manganese transport t 54.8 22 0.00047 36.3 5.3 56 846-911 31-87 (142)
76 cd00223 TOPRIM_TopoIIB_SPO TOP 54.5 60 0.0013 33.9 8.6 98 351-472 2-102 (160)
77 PRK10870 transcriptional repre 52.8 16 0.00036 38.8 4.2 54 832-889 69-129 (176)
78 smart00529 HTH_DTXR Helix-turn 52.7 13 0.00029 34.9 3.1 43 845-888 7-50 (96)
79 PRK11512 DNA-binding transcrip 52.5 13 0.00028 38.0 3.2 50 835-888 55-111 (144)
80 PRK08173 DNA topoisomerase III 52.2 43 0.00094 44.3 8.6 122 520-658 401-540 (862)
81 PF14947 HTH_45: Winged helix- 50.3 8.8 0.00019 35.3 1.5 38 853-890 34-71 (77)
82 COG1846 MarR Transcriptional r 49.3 19 0.00041 34.4 3.7 39 851-889 49-94 (126)
83 PRK13777 transcriptional regul 48.6 27 0.00059 37.7 5.1 51 835-889 60-117 (185)
84 TIGR02647 DNA conserved hypoth 48.6 14 0.00031 34.2 2.4 49 615-675 17-65 (77)
85 PF06969 HemN_C: HemN C-termin 47.7 14 0.00031 32.4 2.3 36 847-882 30-65 (66)
86 PF07848 PaaX: PaaX-like prote 47.5 8.2 0.00018 35.3 0.8 38 834-872 20-57 (70)
87 TIGR02337 HpaR homoprotocatech 47.3 40 0.00088 33.0 5.7 51 835-889 43-100 (118)
88 TIGR01889 Staph_reg_Sar staphy 46.9 19 0.00041 35.1 3.3 55 831-889 40-101 (109)
89 PF04216 FdhE: Protein involve 43.0 70 0.0015 36.8 7.6 32 964-999 172-206 (290)
90 PRK07726 DNA topoisomerase III 41.8 33 0.00071 44.1 5.1 56 813-869 259-316 (658)
91 PRK14165 winged helix-turn-hel 41.0 19 0.00041 39.9 2.5 51 832-886 19-73 (217)
92 TIGR00373 conserved hypothetic 40.3 24 0.00052 37.1 3.0 30 624-662 34-63 (158)
93 PRK14724 DNA topoisomerase III 39.0 60 0.0013 43.7 7.0 75 594-679 488-578 (987)
94 cd03364 TOPRIM_DnaG_primases T 37.8 39 0.00084 30.9 3.7 36 409-447 34-69 (79)
95 TIGR02698 CopY_TcrY copper tra 37.4 2E+02 0.0042 29.3 8.9 78 835-927 19-98 (130)
96 PF06839 zf-GRF: GRF zinc fing 36.7 42 0.00092 27.8 3.3 35 966-1002 2-42 (45)
97 COG1198 PriA Primosomal protei 36.6 83 0.0018 40.9 7.4 34 485-518 72-108 (730)
98 PF14354 Lar_restr_allev: Rest 36.4 43 0.00093 29.1 3.5 32 964-998 3-37 (61)
99 smart00347 HTH_MARR helix_turn 36.0 43 0.00094 30.9 3.8 50 835-888 25-81 (101)
100 KOG1956 DNA topoisomerase III 35.4 30 0.00065 43.4 3.1 56 332-387 51-106 (758)
101 cd01029 TOPRIM_primases TOPRIM 35.2 47 0.001 30.0 3.7 27 421-447 43-69 (79)
102 TIGR01054 rgy reverse gyrase. 34.7 42 0.0009 45.9 4.7 52 817-869 867-919 (1171)
103 PF03965 Penicillinase_R: Peni 34.1 75 0.0016 31.3 5.3 79 835-928 18-98 (115)
104 PF04606 Ogr_Delta: Ogr/Delta- 34.0 49 0.0011 27.8 3.3 32 966-999 1-36 (47)
105 KOG2907 RNA polymerase I trans 33.2 25 0.00055 34.9 1.7 33 964-999 74-111 (116)
106 COG2176 PolC DNA polymerase II 33.0 60 0.0013 43.7 5.4 41 430-472 309-349 (1444)
107 PRK09710 lar restriction allev 32.6 51 0.0011 29.8 3.3 33 963-1000 5-37 (64)
108 PRK06266 transcription initiat 32.3 41 0.0009 36.1 3.3 30 623-661 41-70 (178)
109 COG0068 HypF Hydrogenase matur 32.3 59 0.0013 41.6 5.0 31 961-992 98-128 (750)
110 PF13601 HTH_34: Winged helix 31.8 13 0.00028 34.7 -0.5 40 845-885 22-69 (80)
111 TIGR02679 conserved hypothetic 31.5 1.5E+02 0.0032 35.8 8.0 88 351-476 252-340 (385)
112 PRK05978 hypothetical protein; 31.2 33 0.00071 35.9 2.2 13 964-976 33-45 (148)
113 PRK14701 reverse gyrase; Provi 30.8 59 0.0013 46.0 5.2 65 816-882 838-903 (1638)
114 PF02002 TFIIE_alpha: TFIIE al 29.5 36 0.00077 33.0 2.1 32 622-662 31-62 (105)
115 PRK00420 hypothetical protein; 28.7 43 0.00093 33.5 2.5 10 964-973 23-32 (112)
116 COG1675 TFA1 Transcription ini 28.1 57 0.0012 35.1 3.5 31 623-662 37-67 (176)
117 TIGR03655 anti_R_Lar restricti 28.1 87 0.0019 26.9 3.9 34 965-1001 2-37 (53)
118 cd00092 HTH_CRP helix_turn_hel 26.5 79 0.0017 27.3 3.6 42 834-879 25-67 (67)
119 PF13362 Toprim_3: Toprim doma 26.0 2E+02 0.0043 27.1 6.4 65 351-447 1-69 (96)
120 PRK04023 DNA polymerase II lar 26.0 58 0.0013 43.2 3.5 53 959-1096 621-673 (1121)
121 PF13463 HTH_27: Winged helix 24.8 31 0.00067 30.1 0.6 30 852-881 32-68 (68)
122 COG1321 TroR Mn-dependent tran 24.7 1.4E+02 0.0031 31.3 5.7 51 621-680 27-77 (154)
123 PRK09401 reverse gyrase; Revie 24.5 69 0.0015 43.9 4.0 52 818-870 868-920 (1176)
124 KOG1589 Uncharacterized conser 24.3 32 0.00069 34.0 0.7 14 38-51 6-19 (118)
125 TIGR02277 PaaX_trns_reg phenyl 24.1 66 0.0014 37.0 3.3 52 834-886 17-72 (280)
126 COG3024 Uncharacterized protei 24.0 30 0.00066 31.1 0.4 29 964-998 7-35 (65)
127 PRK05978 hypothetical protein; 23.9 42 0.00092 35.1 1.5 22 1087-1108 53-75 (148)
128 TIGR03433 padR_acidobact trans 23.3 1.6E+02 0.0035 28.3 5.3 52 836-888 19-84 (100)
129 PRK03902 manganese transport t 23.0 1.7E+02 0.0036 29.9 5.7 48 622-678 26-73 (142)
130 PRK03564 formate dehydrogenase 22.8 2E+02 0.0042 33.8 6.7 33 964-999 187-221 (309)
131 COG1321 TroR Mn-dependent tran 22.7 58 0.0013 34.2 2.3 39 848-887 35-74 (154)
132 PRK09416 lstR lineage-specific 22.5 99 0.0022 32.0 3.8 51 836-886 57-116 (135)
133 PF05191 ADK_lid: Adenylate ki 20.6 70 0.0015 25.6 1.8 19 1081-1099 16-34 (36)
134 PF02037 SAP: SAP domain; Int 20.3 1.3E+02 0.0028 23.8 3.2 31 834-864 3-33 (35)
No 1
>PRK08780 DNA topoisomerase I; Provisional
Probab=100.00 E-value=5.9e-163 Score=1504.54 Aligned_cols=758 Identities=39% Similarity=0.632 Sum_probs=674.7
Q ss_pred CCCeEEEEecchHHHHHHhhcCCCEEEEeeccccccccccCCCCCCCCCCcceEecCcchHHHHHHHHHHhccCCeEEEc
Q 001100 348 SGKSVVVVESVTKAKVIQGYLGDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILA 427 (1158)
Q Consensus 348 ~~k~LIIvEkPskAk~Ia~~LG~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~~~k~lk~Ik~l~k~ad~IIlA 427 (1158)
|+++|||||||+||++|++|||.+|+|+||+|||+||++++.+++++++|.+.|.+.++++++++.|++++++||.||||
T Consensus 1 m~~~LiIvEsPskAk~I~~~Lg~~y~V~as~GHi~dL~~~~~~vd~~~~f~~~y~~~~~k~~~~~~lk~~~k~ad~vilA 80 (780)
T PRK08780 1 MSKHLVIVESPAKAKTINKYLGKDFTVLASYGHVRDLVPKEGAVDPENGFAMRYDLIDKNEKHVEAIAKAAKSADDLYLA 80 (780)
T ss_pred CCCeEEEEeCHHHHHHHHHHcCCCCEEEeccCCcccCCCcccCCChhhCCceEEEEcCchHHHHHHHHHHHHhCCEEEEC
Confidence 56899999999999999999999999999999999999988888888889999998888999999999999999999999
Q ss_pred cCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhcccccHhHHHHHHHHHHHhhhhhhcccHHHH
Q 001100 428 SDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAAREIDANLVQAYLARRALDYLIGFNISPLLW 507 (1158)
Q Consensus 428 TDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fs~lT~~aI~~A~~nlr~~d~~L~~A~~AR~~lD~LiG~nlSR~l~ 507 (1158)
||||||||+|||||+++|+..+. ...++|+|||||+||+++|++||+|++++|++|++||+|||++|||||||+||+||
T Consensus 81 tD~DREGE~Ia~~i~~~l~~~~~-~~~~~v~Ri~f~eiT~~aI~~A~~n~r~~d~~l~~A~~aRr~lD~lvG~~lSr~l~ 159 (780)
T PRK08780 81 TDPDREGEAISWHLAEILKERGL-LKDKPMQRVVFTEITPRAIKEAMAKPRDIASDLVDAQQARRALDYLVGFNLSPLLW 159 (780)
T ss_pred CCCCcccHHHHHHHHHHhccccc-CCCCceEEEEEccCCHHHHHHHHhCCCcCcHhHHHHHHHHHHHHHhcCeeecHHHH
Confidence 99999999999999999964221 12468999999999999999999999999999999999999999999999999999
Q ss_pred hhCCCcccCCcchhHHHHHHHHHHHHHHhcCCcceEEEEEEEecCcCCCCCCceeeeeccccccccccccCcCCHHHHHH
Q 001100 508 RKLPGCQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDTFSFPAHLTHFQSKRLNQLSIGSHTEAKD 587 (1158)
Q Consensus 508 ~k~~~~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~g~~f~a~l~~~~~~k~~~~~i~d~~~Ae~ 587 (1158)
+++++.+|+||||||||+|||+||+||++|+|++||.|.+.+... +..|.++|...++.++++++|.|+++|++
T Consensus 160 ~~~~~~lSaGRVQspaL~lIveRE~eI~~F~p~~yw~i~~~~~~~------~~~f~a~~~~~~~~~~~~~~~~~~~~a~~ 233 (780)
T PRK08780 160 RKIQRGLSAGRVQSPALRMIVEREEEIEAFIAREYWSIEADCAHP------SQPFNAKLIKLDGQKFEQFTITDGDTAEA 233 (780)
T ss_pred HhhCCCCcccccHHHHHHHHHHHHHHHHhCCCcceEEEEEEEecC------CceEEEEEEecCCccccccccCCHHHHHH
Confidence 999888999999999999999999999999999999999999631 34688888766666656678999999999
Q ss_pred HHHHHcc---CCeEEEEeeeeeeeecCCCCcchHHHHHHHHHhcCCCHHHHHHHHHHHhccccCCCCCeeEEEEEecCCC
Q 001100 588 IEQKINS---ANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRTDG 664 (1158)
Q Consensus 588 i~~~l~~---~~~~V~~v~~k~~~~~PP~Pf~tstLQ~~AskklG~Sa~~Tm~iAQ~LYE~~k~~~g~~~GlITYPRTDS 664 (1158)
+.+.|.. ..++|.+|+.++++++||+||+|++||++||++|||||++||++||+|||+++|++|++.||||||||||
T Consensus 234 i~~~~~~~~~~~~~V~~v~~k~~~~~pp~Pf~tstLQq~As~klg~s~~~Tm~iAQ~LYE~~~~~~~~~~glITYpRTDS 313 (780)
T PRK08780 234 ARLRIQQAAQGTLHVTDVESKERKRNPAPPFTTSTLQQEASRKLGFTTRRTMQVAQKLYEGVDLGDEGSVGLITYMRTDS 313 (780)
T ss_pred HHHHHhhccCCCeEEEEEEeeeeecCCCCCccHHHHHHHHHHHcCCCHHHHHHHHHHHHhhcccccCCceeEEEecccCC
Confidence 9999974 5799999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCHHHHHHHHHHHHHHhCCCCCCCCCCCccccccccccccCCCCCCCcccCChhhhhCCCCHHHHHHHHHHHHHHHHc
Q 001100 665 LHISDEAAKEIRSLIFERYGSHHAPEEGPRKYFKKVKNAQEAHEAIRPTDIRRLPAMLSGLLDEDCLKLYSLIWSRTMAC 744 (1158)
Q Consensus 665 ~~Ls~~~~~~i~~~i~~~~g~~~~~~~~~r~~~~k~k~~qeAH~AI~PT~~~~~P~~l~~~Ls~dE~kLY~LI~rRfLAs 744 (1158)
++||++++.+++++|...||..|.+ ..++.|.++.+++|+||||||||+....|+.+...|+++|++||+|||+||||+
T Consensus 314 ~~ls~~~~~~~~~~i~~~~g~~~~~-~~~~~~~~~~~~~q~aHeAI~PT~~~~~p~~~~~~L~~de~klY~LI~~R~lAs 392 (780)
T PRK08780 314 VNLSQDALAEIRDVIARDYGTASLP-DQPNTYKTKSKNAQEAHEAVRPTSALRTPAQVARFLSDDQRRLYELIWKRAVAC 392 (780)
T ss_pred ccCCHHHHHHHHHHHHHHhChhhhh-hcccccCCCCCCCcCCCCCCCCCCCCcChhhhhccCCHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999987775 446666666677899999999998765677655679999999999999999999
Q ss_pred cCCCcEEEEEEEEEEecCccEEEEEEeEEEEEcCceeeccccchhhhccccccchhhhhhHHhcCCCCCCCeeEeeeEEE
Q 001100 745 QMQPATVGQIQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLKTGDPLYLGEVEL 824 (1158)
Q Consensus 745 ~~~~a~~e~t~v~i~~~~~~~~F~asg~~i~~~Gw~~vy~~~~~~~~~~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i 824 (1158)
||+||+|++++|++.+++ .+.|+++|++++++||+++|.+...+ ++.+++ +....||.|++||.+.+.++.+
T Consensus 393 ~m~~a~~~~t~v~~~~~~-~~~F~a~G~~i~~~G~~~vy~~~~~~-----~~~~~~--~~~~~LP~l~~G~~~~~~~~~~ 464 (780)
T PRK08780 393 QMIPATLNTVSVDLAAGS-EHVFRATGSTVVVPGFLAVYEEGKDD-----KSAEDE--DEGRKLPPMKEGDNVPLERIRA 464 (780)
T ss_pred hCchhEEEEEEEEEEeCC-eeEEEEEEEEEeEcCeEEeecccccc-----cccccc--chhccCCCcCCCCEeeeeeeee
Confidence 999999999999998753 26899999999999999999753210 000000 0014699999999999999999
Q ss_pred eccccCCCCCCCHhHHHHHHHhcCCCCCcchHHHHHHhhccceEEEcCcccccccccchhhhhhhcccccccChhhhHHH
Q 001100 825 KQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKSRILYPEFRGRMVSAFLSHYFSEVTDYSFTADM 904 (1158)
Q Consensus 825 ~e~~TkPP~ryTEasLI~~MEk~GIGTpATrAsIIe~L~~R~YV~~k~k~L~PT~lG~~v~~~L~~~f~~l~~p~~TA~~ 904 (1158)
.+|+|+||+|||||+||++||+.|||||||||+||++|++|+||..+++.|+||++|+.|+++|..+|+.|+||+|||.|
T Consensus 465 ~~~~T~PP~ryTEasLik~mE~~GIGtpST~A~iI~~L~~R~Yv~~~~k~l~pT~~G~~v~~~L~~~f~~l~~~~~Ta~~ 544 (780)
T PRK08780 465 EQHFTEPPPRYTEASLVKALEEYGIGRPSTYASIISTLQFRKYVEMEGRRFRPTDVGRAVNKFLTGHFTRYVDYDFTARL 544 (780)
T ss_pred eeeecCCCCCCCHHHHHHHHHhCCCCchhhHHHHHHHHHhCCcEeccCCEEeecHHHHHHHHHHHHhchhcCCHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhhhhcCCchHHHHHHHHHHHhhhhhhhccchhHHHHHHHHHhhhcCcccCCCCCCCCCCCCCCCCeEEEEecccCc
Q 001100 905 ETELDNVSAGLTEWKGLLVDYWSRFSSYCTCAQSLHIHQVEKMLEKTFGDSLFASLPNKDRSCPVCGEGTLIFKVSRFGA 984 (1158)
Q Consensus 905 E~~Ld~Ia~Gk~~~~~~L~~F~~~f~~~i~~~~~~~i~~V~e~l~~~~g~~~~~~~~~~~g~CPkCGkG~l~~k~gr~G~ 984 (1158)
|++||+|++|+.+|++||++||+.|...+.... +.+... . . ......+.||.||+ .++++.||||+
T Consensus 545 E~~Ld~I~~G~~~~~~~l~~~~~~~~~~~~~~~--------~~i~~~-~---~-~~~r~lG~cP~CG~-~l~~r~gr~G~ 610 (780)
T PRK08780 545 EDDLDAVSRGEKEWIPLMEKFWGPFKELVEEKK--------DSVDRT-E---A-GQVRELGTDPKSGK-PVSVRIGRFGP 610 (780)
T ss_pred HHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHH--------hhhhhc-c---c-cccccCCCCCCCCC-EEEEEeCCCCC
Confidence 999999999999999999999999887654421 111100 0 0 01234689999996 78899999998
Q ss_pred eeEEec-----CCCCCCcccccCCCCCCchhhhhhhccCCCCCcccCCCCCccceeeeccCCCcceEEeCCCCCCCCCcc
Q 001100 985 GYFIGC-----NQHPRCNYIAKTLYGDDDEEDTLQRNTNVDEPKLIGHHPASKEKVLLKSGPYGFYVQLGEDRTGYLPKR 1059 (1158)
Q Consensus 985 ~~f~GC-----s~yP~C~~~~~~~~~e~~~~e~~~~~~~~~lPr~LG~cPkcG~~v~lk~GrfG~yv~c~~d~kg~kpK~ 1059 (1158)
|++| +++|.|..+.+....++++.+.+. .++++||.+|.+|+ |.+|+++.|||||||+++ +++
T Consensus 611 --fl~~g~~~~~~~p~~asl~~~~~~~~itle~A~--~ll~~pr~lG~~P~-g~~I~~~~GRfGpYv~~~-------~~~ 678 (780)
T PRK08780 611 --MVQIGTKDDEEKPRFASLRPGQSIDSITLEEAL--ELFKLPRALGETDE-GEDVSVGIGRFGPFVKRG-------SKY 678 (780)
T ss_pred --eeeccCcccccccccccCCCCCCcccCCHHHHH--HHhcCccccCcCCC-CCeeEEeeCCCCCeEeeC-------Ccc
Confidence 7889 468999999888888888877775 46788999999995 889999999999999986 378
Q ss_pred cccCCCCCccccCHHHHHHHhcC------CcccCCCCCCCcCeEEeeccCcceeecCCeeeecCCCCCCCCCCHHHHHHH
Q 001100 1060 ASVSHIKDVDSITLEDALELLRY------PVNLGNHPKDGQPIMLRLARAGFSVRHRRTIASVPKNMKPNDVTLEKALEF 1133 (1158)
Q Consensus 1060 ~slpk~~~~~sItle~Al~ll~~------pk~lG~cP~cG~~I~i~~GRyG~Yi~~~~~~~~lpk~~~~~~itle~A~~L 1133 (1158)
+++|+..++++||+++|++||+. ++.++.|| |+.|.+.+||||||+.+++.+++||++.++.++|+|+|++|
T Consensus 679 ~sl~k~~~~~~itle~A~~ll~~k~~~~~~~~l~~~~--~~~i~~~~Gr~Gpyv~~~k~~~~lpk~~~~~~~tle~a~~l 756 (780)
T PRK08780 679 ASLKKEDDPYTIDLARALFLIEEKEEIARNRVIKDFE--GSGIQVLNGRYGPYITDGKLNGKIPKDREPASLTLEEVQQL 756 (780)
T ss_pred cCCCCCCCcccCCHHHHHHHHHhhhhccCCccccccC--CCceEeecCCCCccccccccccccCCCCCcccccHHHHHHH
Confidence 89999999999999999999987 67888887 46899999999999999999999999999999999999999
Q ss_pred hhccccccCCCCCCCC
Q 001100 1134 LSGKDVRRCGRPKGKP 1149 (1158)
Q Consensus 1134 L~~k~~k~~gr~~~~~ 1149 (1158)
|+++.+|+++|++++-
T Consensus 757 i~~~~~~~~~~~~~~~ 772 (780)
T PRK08780 757 LADAPVRKGFRAKKAA 772 (780)
T ss_pred HhCcccccCCCccccc
Confidence 9999888877877643
No 2
>PRK07561 DNA topoisomerase I subunit omega; Validated
Probab=100.00 E-value=6.3e-156 Score=1458.74 Aligned_cols=737 Identities=42% Similarity=0.680 Sum_probs=651.5
Q ss_pred CeEEEEecchHHHHHHhhcCCCEEEEeeccccccccccCCC--------------CCCCCCCcceEecCcchHHHHHHHH
Q 001100 350 KSVVVVESVTKAKVIQGYLGDMYEVLPSYGHVRDLAARSGS--------------VRPDDDFSMVWEVPSAAWTHLKSIK 415 (1158)
Q Consensus 350 k~LIIvEkPskAk~Ia~~LG~~y~V~~s~GHl~dL~~~~~~--------------v~p~~~f~~~~~v~~~~~k~lk~Ik 415 (1158)
+.|||||||+||++|++|||.+|+|+||+|||++|+.+... ++|+++|.+.|.+.++++++++.|+
T Consensus 2 ~~LvIvEkP~kak~I~~~Lg~~~~V~~s~GHi~dL~~~~~~~~~~~k~~~w~~l~i~~~~~f~~~y~~~~~k~~~~~~lk 81 (859)
T PRK07561 2 KSLVIVESPAKAKTINKYLGSDYVVKASVGHIRDLPTSASSVPAKEKGALWARMGVDPDHDFEALYEVLPGKEKVVSELK 81 (859)
T ss_pred CEEEEEeCHHHHHHHHHHcCCCCEEEeccCChhhCCCccccChhhhhhchHhhcCcCcccCcceeEEECccHHHHHHHHH
Confidence 68999999999999999999999999999999999975433 7887789999999888999999999
Q ss_pred HHhccCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhcccccHhHHHHHHHHHHHh
Q 001100 416 VALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAAREIDANLVQAYLARRALD 495 (1158)
Q Consensus 416 ~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fs~lT~~aI~~A~~nlr~~d~~L~~A~~AR~~lD 495 (1158)
+++++||+||||||||||||+|||||+++|+. .+++|+|||||+||+++|++||+|++++|++|++||+|||++|
T Consensus 82 ~~~k~ad~iilAtD~DREGE~I~~~i~~~l~~-----~~~~v~Ri~f~~iT~~aI~~A~~n~~~~~~~l~~A~~aRr~lD 156 (859)
T PRK07561 82 KAAKDADELYLATDPDREGEAIAWHLLEVLGG-----DDVPVKRVVFNEITKNAIQEAFENPRELDINLVNAQQARRFLD 156 (859)
T ss_pred HHHhcCCEEEECCCCCccchHHHHHHHHHhCC-----CCCCeEEEEEccCCHHHHHHHHhCcccCCHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999962 3579999999999999999999999999999999999999999
Q ss_pred hhhhhcccHHHHhhCCCcccCCcchhHHHHHHHHHHHHHHhcCCcceEEEEEEEecCcCCCCCCceeeeecccccccccc
Q 001100 496 YLIGFNISPLLWRKLPGCQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDTFSFPAHLTHFQSKRLN 575 (1158)
Q Consensus 496 ~LiG~nlSR~l~~k~~~~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~g~~f~a~l~~~~~~k~~ 575 (1158)
||||||+||+||+++.+.+|+||||||||+|||+||+||++|+|++||.|.+.+... .|..|.+.|.+.++++++
T Consensus 157 ~lvG~~lS~~l~~~~~~~lSaGRVQsp~L~lIv~Re~eI~~F~p~~yw~i~~~~~~~-----~~~~f~a~~~~~~~~~~~ 231 (859)
T PRK07561 157 RLVGYMVSPLLWKKIARGLSAGRVQSVAVRLIVEREREIEAFVPEEYWDIHADLTTP-----RGDAFEARLTHLDGKKFA 231 (859)
T ss_pred HHhhhhcCHHHHHhhccCCCcccchhhhhHHHHHHHHHHHhcCCCccEEEEEEEEec-----CCCeEEEEEEeeCCceec
Confidence 999999999999999888999999999999999999999999999999999999631 244688888766666666
Q ss_pred ccCcCCHHHHHHHHHHHccCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHhcCCCHHHHHHHHHHHhccccCCCCCeeE
Q 001100 576 QLSIGSHTEAKDIEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKLAQKLYEGVQLPDGTAAG 655 (1158)
Q Consensus 576 ~~~i~d~~~Ae~i~~~l~~~~~~V~~v~~k~~~~~PP~Pf~tstLQ~~AskklG~Sa~~Tm~iAQ~LYE~~k~~~g~~~G 655 (1158)
.++|.|+++|+++++.+.+..++|.+|+.++++++||+||+|++||++||++|||||++||++||+|||+ |
T Consensus 232 ~~~~~~~~~a~~~~~~~~~~~~~V~~v~~k~~~~~pp~pf~ts~LQ~~As~klg~s~~~tm~~aQ~LYE~---------g 302 (859)
T PRK07561 232 PVDLLNEAQAEAAVAALEGARYSVASVEDKPTTRKPSAPFTTSTLQQEASRKLGFSVKKTMRIAQRLYEA---------G 302 (859)
T ss_pred ccccCCHHHHHHHHHHhcCCCeEEEEEEeceeEecCCCCccHHHHHHHHHHhcCCCHHHHHHHHHHHHhC---------C
Confidence 6789999999999999988889999999999999999999999999999999999999999999999995 9
Q ss_pred EEEEecCCCcCCCHHHHHHHHHHHHHHhCCCCCCCCCCCccccccccccccCCCCCCCcccCChhhhhCCCCHHHHHHHH
Q 001100 656 LITYMRTDGLHISDEAAKEIRSLIFERYGSHHAPEEGPRKYFKKVKNAQEAHEAIRPTDIRRLPAMLSGLLDEDCLKLYS 735 (1158)
Q Consensus 656 lITYPRTDS~~Ls~~~~~~i~~~i~~~~g~~~~~~~~~r~~~~k~k~~qeAH~AI~PT~~~~~P~~l~~~Ls~dE~kLY~ 735 (1158)
|||||||||++||++++++++++|...||..|.+ ..+|.|..+.+++|+||||||||+....|+.+ ..|+++|++||+
T Consensus 303 lITYpRTDs~~ls~~~~~~~~~~i~~~~g~~~~~-~~~r~~~~~~k~~q~aHeAI~Pt~~~~~~~~~-~~L~~~e~~lY~ 380 (859)
T PRK07561 303 YITYMRTDSTNLSQEAINAARGYIGDNYGKKYLP-EKPRQYSSKAKNAQEAHEAIRPSDVFRTPDQL-KGLEGDAQRLYE 380 (859)
T ss_pred eEEecCCCCCcCCHHHHHHHHHHHHHHhhhhhcc-cCCccCCCcCCCCCCCcCCcccCCCCcChhhh-ccCCHHHHHHHH
Confidence 9999999999999999999999999999988876 56777766557789999999999765567655 569999999999
Q ss_pred HHHHHHHHccCCCcEEEEEEEEEEecCccEEEEEEeEEEEEcCceeeccccchhhhccccccchhhhhhHHhcCCCCCCC
Q 001100 736 LIWSRTMACQMQPATVGQIQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLKTGD 815 (1158)
Q Consensus 736 LI~rRfLAs~~~~a~~e~t~v~i~~~~~~~~F~asg~~i~~~Gw~~vy~~~~~~~~~~~e~~e~~~~~~~~~LP~l~~Gd 815 (1158)
|||+||||+||+||+|++++|++.+++ +.|+++|++++++||++||.+... +++++ ....||.|++||
T Consensus 381 LI~~R~lAs~m~~a~~~~~~v~~~~~~--~~F~a~g~~i~~~G~~~vy~~~~~-----~~~~~-----~~~~LP~l~~g~ 448 (859)
T PRK07561 381 LIWKRFVASQMAPARYDSTTVTIAAGD--AELRATGRVLRFDGFLKVYVEGRD-----DALDD-----EDRRLPALKVGD 448 (859)
T ss_pred HHHHHHHHHhCchheEEEEEEEEEeCC--EEEEEEEEEEeeCCchheeccccc-----ccccc-----ccccCCCCCCCC
Confidence 999999999999999999999998753 689999999999999999975321 10011 114699999999
Q ss_pred eeEeeeEEEeccccCCCCCCCHhHHHHHHHhcCCCCCcchHHHHHHhhccceEEEcCcccccccccchhhhhhhcccccc
Q 001100 816 PLYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKSRILYPEFRGRMVSAFLSHYFSEV 895 (1158)
Q Consensus 816 ~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk~GIGTpATrAsIIe~L~~R~YV~~k~k~L~PT~lG~~v~~~L~~~f~~l 895 (1158)
.+.+.++.+.+++|+||+|||||+||++||+.|||||||||+||++|++||||.++++.|+||++|+.|+++|..+|+.|
T Consensus 449 ~~~~~~~~~~~~~T~PP~ryTeasLv~~me~~GIGtpsT~a~iI~~L~~R~Yv~~~~~~l~pT~~G~~v~~~l~~~f~~l 528 (859)
T PRK07561 449 ALTLEKLDPTQHFTKPPARYSEASLVKELEKLGIGRPSTYASIISTIQDRGYVRLENRRFYPEKMGRIVTDRLEEFFPRL 528 (859)
T ss_pred EeeeeeeEecccccCCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhhcCeEEeeCCEEeecHHHHHHHHHHHHhhhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cChhhhHHHHHHhhhhhcCCchHHHHHHHHHHHhhhhhhhccchhHHHHHHHHHhhhcCcccCCCCCCCCCCCCCCCCeE
Q 001100 896 TDYSFTADMETELDNVSAGLTEWKGLLVDYWSRFSSYCTCAQSLHIHQVEKMLEKTFGDSLFASLPNKDRSCPVCGEGTL 975 (1158)
Q Consensus 896 ~~p~~TA~~E~~Ld~Ia~Gk~~~~~~L~~F~~~f~~~i~~~~~~~i~~V~e~l~~~~g~~~~~~~~~~~g~CPkCGkG~l 975 (1158)
+||+|||+||+.||+|++|+.+|++||++||..|...+..+.. ... .+...........+.||.||++ +
T Consensus 529 ~~~~~Ta~~E~~Ld~I~~G~~~~~~~l~~~~~~~~~~~~~~~~--------~~~--~~~~~~~~~~~~~~~CP~Cg~~-l 597 (859)
T PRK07561 529 VDYDFTARMEEELDDIANGEADWKPVLDDFYKDFSQQLEKAEE--------LRE--EGGMRPNQMVITDRDCPTCGRG-M 597 (859)
T ss_pred cCHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHhh--------hcc--cccccccccccccccCcccCCc-c
Confidence 9999999999999999999999999999999998876544321 100 0000000011235799999975 7
Q ss_pred EEEecccCceeEEecCCC---CCCcccccCCCCCCchhhhhhhccCCCCCcccCCCCCccceeeeccCCCcceEEeCCCC
Q 001100 976 IFKVSRFGAGYFIGCNQH---PRCNYIAKTLYGDDDEEDTLQRNTNVDEPKLIGHHPASKEKVLLKSGPYGFYVQLGEDR 1052 (1158)
Q Consensus 976 ~~k~gr~G~~~f~GCs~y---P~C~~~~~~~~~e~~~~e~~~~~~~~~lPr~LG~cPkcG~~v~lk~GrfG~yv~c~~d~ 1052 (1158)
.++.|+||+ ||+|++| |.|.++.+....+.. .+... ...+.|+.+|.||+||..|+++.||||+||+.++
T Consensus 598 ~~r~gr~G~--Fl~Cs~y~~~p~C~~~~~l~~~~~~-~~~~~--~~~~~~~~lg~~P~cg~~i~~r~Gr~Gpyv~~~~-- 670 (859)
T PRK07561 598 GIRTGKTGV--FLGCSGYALKERCKTTRNLTPEEET-LNVLE--GEDAETRALGADPECGTAMVLRSGRFGPYVQEGE-- 670 (859)
T ss_pred eEEecCCCC--eeeccCCcCCCCCCCCCCCCccchh-hhhhh--ccccCccccCCCCCCCCeeEEecCCCCCeeeccc--
Confidence 889999997 9999999 999998766543222 22221 2456789999999999999999999999999643
Q ss_pred CCCCCcccccCCCCCccccCHHHHHHHhcCCcccCCCCCCCcCeEEeeccCcceeecCCeeeecCCCCCCCCCCHHHHHH
Q 001100 1053 TGYLPKRASVSHIKDVDSITLEDALELLRYPVNLGNHPKDGQPIMLRLARAGFSVRHRRTIASVPKNMKPNDVTLEKALE 1132 (1158)
Q Consensus 1053 kg~kpK~~slpk~~~~~sItle~Al~ll~~pk~lG~cP~cG~~I~i~~GRyG~Yi~~~~~~~~lpk~~~~~~itle~A~~ 1132 (1158)
+.++++++++++.+++.+++++|+.++..|+.+|.||+||++|+++.||||+|+.|++.+.+++...++.++++++|++
T Consensus 671 -~~~~~~~sic~~~~p~c~~~e~a~~ll~~pr~lg~cPecg~~i~~k~gr~G~yl~c~~~~~sc~~~~~~~~i~l~~a~~ 749 (859)
T PRK07561 671 -GDKPRRLSLPKGNNPECVGLEIALGLLSLPRPVGEHPECGSEIQAKIGRFGPYVKCGGTYASLKNTRKVLTIGLNRAVE 749 (859)
T ss_pred -CCCCceeccCCCCCCCcCCHHHHHhhhccccccCcCCCCCCeeEEecCCCCCeEEeCCCcCCCCCCCccccCCHHHHHH
Confidence 4468999999888889999999999999999999999999999999999999999988888888888889999999999
Q ss_pred Hhhccc
Q 001100 1133 FLSGKD 1138 (1158)
Q Consensus 1133 LL~~k~ 1138 (1158)
||..++
T Consensus 750 ll~~~~ 755 (859)
T PRK07561 750 LLAEPK 755 (859)
T ss_pred HHhccc
Confidence 998764
No 3
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=100.00 E-value=4.7e-154 Score=1438.89 Aligned_cols=737 Identities=34% Similarity=0.522 Sum_probs=625.4
Q ss_pred CCCeEEEEecchHHHHHHhhcCCCEEEEeeccccccccccCCCCCCCCCCcceEecCcchHHHHHHHHHHhccCCeEEEc
Q 001100 348 SGKSVVVVESVTKAKVIQGYLGDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILA 427 (1158)
Q Consensus 348 ~~k~LIIvEkPskAk~Ia~~LG~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~~~k~lk~Ik~l~k~ad~IIlA 427 (1158)
|+++|||||||+|||+|++|||++|+|+||+|||+||+.+..+|+++++|.|.|.+.++++++|+.|++++++||.||||
T Consensus 1 m~~~LvIvEsP~kak~I~~~Lg~~~~V~as~GHl~dLp~~~~~~~~~~~f~p~y~~~~~k~~~~~~ik~~~k~ad~iilA 80 (860)
T PRK06319 1 MKKSLIIVESPAKIKTLQKLLGEGFIFASSLGHIVDLPAKEFGIDIENDFEPDYQILPDKEEVINKICKLAKKCDVVYLS 80 (860)
T ss_pred CCCeEEEEeCHHHHHHHHHHhCCCCEEEecccCcccCCcccCCcCCCCCCCcceEECccHHHHHHHHHHHHHhCCEEEEC
Confidence 67899999999999999999999999999999999998888889988889999999888999999999999999999999
Q ss_pred cCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhcccccHhHHHHHHHHHHHhhhhhhcccHHHH
Q 001100 428 SDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAAREIDANLVQAYLARRALDYLIGFNISPLLW 507 (1158)
Q Consensus 428 TDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fs~lT~~aI~~A~~nlr~~d~~L~~A~~AR~~lD~LiG~nlSR~l~ 507 (1158)
||||||||+|+|||+++|+ .+++|+|||||+||+++|++||+|++++|++|++||+|||++|||||||+||+||
T Consensus 81 tDpDREGE~I~~~i~~~l~------~~~~v~Rv~f~~iT~~aI~~A~~~~~~~d~~l~~A~~aR~~lD~lvG~nlSr~l~ 154 (860)
T PRK06319 81 PDPDREGEAIAWHIANQLP------KNTKIQRISFNAITKGAVTEALKHPREIDMALVNAQQARRLLDRIVGYKISPILS 154 (860)
T ss_pred CCCCcchHHHHHHHHHHcC------CCCCeeEEEEccCCHHHHHHHHhCccccCHHHHHHHHHHHHHHHHhhhhcCHHHH
Confidence 9999999999999999984 3569999999999999999999999999999999999999999999999999999
Q ss_pred hhCCC--cccCCcchhHHHHHHHHHHHHHHhcCCcceEEEEEEEecCcCCCCCCceeeeeccccccccccc---------
Q 001100 508 RKLPG--CQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDTFSFPAHLTHFQSKRLNQ--------- 576 (1158)
Q Consensus 508 ~k~~~--~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~g~~f~a~l~~~~~~k~~~--------- 576 (1158)
++++. .+|+||||||||+|||+||+||++|+|++||+|.+.+.... .+..|.++|...+++++..
T Consensus 155 ~~~~~~~~lSaGRVQsp~L~lIveRe~eI~~F~p~~yw~i~~~~~~~~----~~~~f~a~~~~~~~~~~~~~~~~~~~~~ 230 (860)
T PRK06319 155 RKLQRRSGVSAGRVQSVALKLVVDREKAIEAFVPVEYWNIRVHLKDPK----TQKTFWAHLYSVDGKKWEKEIPEGKTED 230 (860)
T ss_pred HhhccCCCCcCCccchhhhHHHHHHHHHHHcCCCCceEEEEEEEecCC----CCcceEEEeecccCcccccccccccccc
Confidence 98864 79999999999999999999999999999999999986421 1346888887666554421
Q ss_pred --cCcCCHHHHHHHHHHHccCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHhcCCCHHHHHHHHHHHhccccCCCCCee
Q 001100 577 --LSIGSHTEAKDIEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKLAQKLYEGVQLPDGTAA 654 (1158)
Q Consensus 577 --~~i~d~~~Ae~i~~~l~~~~~~V~~v~~k~~~~~PP~Pf~tstLQ~~AskklG~Sa~~Tm~iAQ~LYE~~k~~~g~~~ 654 (1158)
++|.++++|+++++.+++..++|.+|+.++++++||+||+|++||++||++|||||++||++||+|||+++||++++.
T Consensus 231 ~~~~~~~~~~a~~i~~~l~~~~~~V~~v~~k~~~~~pp~pf~ts~LQ~~As~~~g~sa~~tm~iAQ~LYE~~~~~~~~~~ 310 (860)
T PRK06319 231 EVLLINSKEKADHIVELLESATYTVTRVESKEKRRNAYPPFITSTLQQEASRHFRFSSSRTMNIAQTLYEGVDLDSEGAT 310 (860)
T ss_pred cccccCCHHHHHHHHHHhcCCCeEEEEEEeeEeecCCCCCccHHHHHHHHHHHcCCCHHHHHHHHHHHHhccccccCCce
Confidence 457899999999999998899999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEecCCCcCCCHHHHHHHHHHHHHHhCCCCCCCCCCCccccccccccccCCCCCCCcccCChhhhhCCCCHHHHHHH
Q 001100 655 GLITYMRTDGLHISDEAAKEIRSLIFERYGSHHAPEEGPRKYFKKVKNAQEAHEAIRPTDIRRLPAMLSGLLDEDCLKLY 734 (1158)
Q Consensus 655 GlITYPRTDS~~Ls~~~~~~i~~~i~~~~g~~~~~~~~~r~~~~k~k~~qeAH~AI~PT~~~~~P~~l~~~Ls~dE~kLY 734 (1158)
||||||||||++||++++++++.+|...+|.+|.+ ..++.|..+ +++|+||||||||+....|+.+...|+++|++||
T Consensus 311 glITYpRTDs~~ls~~~~~~~~~~i~~~~g~~~~~-~~~~~~~~~-k~~q~aH~AI~PT~~~~~p~~~~~~L~~de~klY 388 (860)
T PRK06319 311 GLITYMRTDSVRTDPEALKQVRKYIEGTFGKEFLP-SSPNVYTTK-KMAQDAHEAIRPTDITLTPEKLRSKLTEDQYKLY 388 (860)
T ss_pred eEEeecCcCcccCCHHHHHHHHHHHHHhhhhhhcc-cCCcccCCC-CCCCCCcCCCccCCCCcChhHhhccCCHHHHHHH
Confidence 99999999999999999999999999889988876 445555443 6789999999999876678766667999999999
Q ss_pred HHHHHHHHHccCCCcEEEEEEEEEEecCccEEEEEEeEEEEEcCceeeccccchhhhccccccchhhhhhHHhcCCCCCC
Q 001100 735 SLIWSRTMACQMQPATVGQIQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLKTG 814 (1158)
Q Consensus 735 ~LI~rRfLAs~~~~a~~e~t~v~i~~~~~~~~F~asg~~i~~~Gw~~vy~~~~~~~~~~~e~~e~~~~~~~~~LP~l~~G 814 (1158)
+|||+||||+||+||+|++|+|++.++++ +.|+++|++++++||++||..... ++++++ ....||.|++|
T Consensus 389 ~LI~~RflAs~m~~a~~~~t~v~~~~~~~-~~F~a~G~~i~~~G~~~vy~~~~~----~~~~~~-----~~~~LP~l~~G 458 (860)
T PRK06319 389 SLIWKRFVASQMIPAIYDTLAIRITTNKG-IDLRATGSLLKFKGFLAVYEEKRD----DEGDEE-----ENIHLPKLHEQ 458 (860)
T ss_pred HHHHHHHHHHhCchhheEEEEEEEEeCCe-eEEEEEeEEEeeCCHHHHhCcccc----cccccc-----ccccCCCCCCC
Confidence 99999999999999999999999988643 689999999999999999964321 001001 11469999999
Q ss_pred CeeEeeeEEEeccccCCCCCCCHhHHHHHHHhcCCCCCcchHHHHHHhhccceEEEcCcccccccccchhhhhhhccccc
Q 001100 815 DPLYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKSRILYPEFRGRMVSAFLSHYFSE 894 (1158)
Q Consensus 815 d~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk~GIGTpATrAsIIe~L~~R~YV~~k~k~L~PT~lG~~v~~~L~~~f~~ 894 (1158)
|.+.+.++.+.+++|+||+|||||+||++||+.|||||||||+||++|++|+||..+++.|+||++|+.|+++|..+|+.
T Consensus 459 e~~~~~~~~~~~~~T~PP~ryTeasLvk~me~~GIGtpsT~A~iI~~L~~R~Yv~~~~k~l~pT~~G~~v~~~L~~~f~~ 538 (860)
T PRK06319 459 DVLTKEELSAEQAFTKPLPRFTEASLVKELEKSGIGRPSTYATIMNKIQSREYTLKENQRLRPTELGKIISQFLETNFPR 538 (860)
T ss_pred CEeeeeeeeecccccCCCCCCCHHHHHHHHHhcCCCchhhHHHHHHHHhhCCeEEccCCEEEECHHHHHHHHHHHHhchh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccChhhhHHHHHHhhhhhcCCchHHHHHHHHHHHhhhhhhhccchhHHHHHHHHHhhhcCcccCCCCCCCCCCCCCCCCe
Q 001100 895 VTDYSFTADMETELDNVSAGLTEWKGLLVDYWSRFSSYCTCAQSLHIHQVEKMLEKTFGDSLFASLPNKDRSCPVCGEGT 974 (1158)
Q Consensus 895 l~~p~~TA~~E~~Ld~Ia~Gk~~~~~~L~~F~~~f~~~i~~~~~~~i~~V~e~l~~~~g~~~~~~~~~~~g~CPkCGkG~ 974 (1158)
|+||+|||.||.+||+|++|+.+|++||++||..|...+..+.. ++. .+. ......||+||++.
T Consensus 539 i~~~~~Ta~~E~~Ld~I~~G~~~~~~~l~~f~~~~~~~~~~~~~-------~~~--------~~~-~~~~~~CP~Cg~~~ 602 (860)
T PRK06319 539 IMDIGFTALMEDELELIADNKKPWKLLLQEFWELFLPVVVTAEK-------EAF--------IPR-IVTEIDCPKCHKGK 602 (860)
T ss_pred hcChhHHHHHHHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHhh-------hhc--------ccc-cccCcccCCCCCcc
Confidence 99999999999999999999999999999999999876554321 100 010 12357899999889
Q ss_pred EEEEecccCceeEEecCCCCCCcccccCCCCCCchhhhhhhccCCCCCcccCCCCCccceeeeccCCCcceEEeCCCCCC
Q 001100 975 LIFKVSRFGAGYFIGCNQHPRCNYIAKTLYGDDDEEDTLQRNTNVDEPKLIGHHPASKEKVLLKSGPYGFYVQLGEDRTG 1054 (1158)
Q Consensus 975 l~~k~gr~G~~~f~GCs~yP~C~~~~~~~~~e~~~~e~~~~~~~~~lPr~LG~cPkcG~~v~lk~GrfG~yv~c~~d~kg 1054 (1158)
++++.|++|. ||||++||.|+++.+.........+.. ......+.||+||..|+++.||||+||.|+
T Consensus 603 L~~k~gr~G~--Fl~Cs~yP~C~~t~~~~~~~~~~~~~~------~~~~~~~~CP~Cg~~m~lK~gr~G~Fl~Cs----- 669 (860)
T PRK06319 603 LVKIWAKNRY--FYGCSEYPECDYKTSEEELTFNKEDYA------EDTPWDSPCPLCGGEMKVRHGRFGTFLGCE----- 669 (860)
T ss_pred eeEEecCCCc--eeeccCCccccccCCcccccccccccc------cccccCCcCccCCCeeEEecCCCCceeeCC-----
Confidence 9999999985 999999999999876543210000000 001224579999999999999999999997
Q ss_pred CCCcccccCCCCCccccCHHHHHHHhcCCcccC-CCCC--CCcCeEEeeccCcc-e--eecCCeeeecCCCCC--C----
Q 001100 1055 YLPKRASVSHIKDVDSITLEDALELLRYPVNLG-NHPK--DGQPIMLRLARAGF-S--VRHRRTIASVPKNMK--P---- 1122 (1158)
Q Consensus 1055 ~kpK~~slpk~~~~~sItle~Al~ll~~pk~lG-~cP~--cG~~I~i~~GRyG~-Y--i~~~~~~~~lpk~~~--~---- 1122 (1158)
++|+|....++.-+.... ....+| .||+ ||+++++++||||+ | |..++.|.++-++.+ .
T Consensus 670 ------~yP~Ck~~~~l~k~~~~~---~~~~~~~~CP~~~C~g~l~~r~gr~G~~f~~Cs~yp~C~~~~~~~~~~~~~~~ 740 (860)
T PRK06319 670 ------NYPECRGIINIHKKGEEG---IEPEETVPCPAIGCTGHIVKRRSRFNKMFYSCSEYPACSVIGNSIDAVITKYA 740 (860)
T ss_pred ------CCccccccccCCcccccc---cCcccCCCCCCcCCCCcEEEEecCCCCeeeccCCCCCCceeeccCCccccccC
Confidence 467777654443110000 001223 6995 88899999999997 4 777788876633332 2
Q ss_pred -CCCCHHHHHHHhhccccccCCC
Q 001100 1123 -NDVTLEKALEFLSGKDVRRCGR 1144 (1158)
Q Consensus 1123 -~~itle~A~~LL~~k~~k~~gr 1144 (1158)
..-||.|...++.++..+++|+
T Consensus 741 ~~~~~~~~~~~~~~~~~~~~~~~ 763 (860)
T PRK06319 741 GTPKTPYEKKTKAKKKSASTKGK 763 (860)
T ss_pred CCCCCcccchHHHHhhhccccCc
Confidence 4456667778887665544444
No 4
>PRK06599 DNA topoisomerase I; Validated
Probab=100.00 E-value=2.4e-137 Score=1265.69 Aligned_cols=673 Identities=45% Similarity=0.739 Sum_probs=569.6
Q ss_pred CCCeEEEEecchHHHHHHhhcCCCEEEEeeccccccccccCCCCCCCCCCcceEecCcchHHHHHHHHHHhccCCeEEEc
Q 001100 348 SGKSVVVVESVTKAKVIQGYLGDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILA 427 (1158)
Q Consensus 348 ~~k~LIIvEkPskAk~Ia~~LG~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~~~k~lk~Ik~l~k~ad~IIlA 427 (1158)
|++.|||||||++|++|+++||.+|.|+||+|||++|++++..|++++.|.+.|.+.+++++|++.|++++++||+||||
T Consensus 1 m~~~LiIaEKPs~ak~Ia~~lg~~~~V~~~~GHl~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ik~l~~~~d~iiiA 80 (675)
T PRK06599 1 MAKKLVIVESPAKAKTIKKYLGKDYKVLASFGHVRDLPKKKGGVDPDNDFAPKYEIIEGKEKVVDALKKAAKKADAVYLA 80 (675)
T ss_pred CCCeEEEEeCHHHHHHHHHHcCCCCEEEecccchhcCCccccCCCcccCCCceEEECCcHHHHHHHHHHHHhhCCEEEEC
Confidence 56889999999999999999999999999999999999887788887778888888888899999999999999999999
Q ss_pred cCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhcccccHhHHHHHHHHHHHhhhhhhcccHHHH
Q 001100 428 SDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAAREIDANLVQAYLARRALDYLIGFNISPLLW 507 (1158)
Q Consensus 428 TDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fs~lT~~aI~~A~~nlr~~d~~L~~A~~AR~~lD~LiG~nlSR~l~ 507 (1158)
||||||||+|||||++++++. .+.+++|+|||||+||+++|++||+|+++++.+|++||+||+++|||||||+||++|
T Consensus 81 tD~DrEGE~I~~~i~~~~~~~--~~~~~~v~Rl~~s~lt~~~I~~a~~n~~~~~~~l~~a~~aR~~~D~liG~n~tr~~t 158 (675)
T PRK06599 81 TDPDREGEAIAWHIAEVLKEA--KLKDKNVKRVVFNEITKKAVQEAIENPRDIDMDLVDAQQARRALDYLVGFKLSPLLW 158 (675)
T ss_pred CCCCcchHHHHHHHHHHHHhh--cCCCCCeeEEEEccCCHHHHHHHHhCcccCCHHHHHHHHHHHHHHHHhhhhhCHHHH
Confidence 999999999999999999531 124579999999999999999999999999999999999999999999999999999
Q ss_pred hhCCCcccCCcchhHHHHHHHHHHHHHHhcCCcceEEEEEEEecCcCCCCCCceeeeeccccccccccccCcCCHHHHHH
Q 001100 508 RKLPGCQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDTFSFPAHLTHFQSKRLNQLSIGSHTEAKD 587 (1158)
Q Consensus 508 ~k~~~~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~g~~f~a~l~~~~~~k~~~~~i~d~~~Ae~ 587 (1158)
..++..+|+||||||||+|||+||+||+||+|++||.|.+.+... +|..|.+.+...+++....++|.++++|++
T Consensus 159 ~~~~~~lS~GRVQtPtL~lvv~Re~eI~~F~p~~y~~i~~~~~~~-----~~~~~~~~~~~~~~~~~~~~r~~~~~~a~~ 233 (675)
T PRK06599 159 KKVRRGLSAGRVQSVALRLICEREDEIEAFIPQEYWTIEADLATS-----NGEPFTAKLVEVNGKKLEKFSITNEEQAKA 233 (675)
T ss_pred HhccCCCccceeHHHHhHHHHHhHHHHHhcCCCceEEEEEEEEcC-----CCCeeEEEEEeccCccccccCCCCHHHHHH
Confidence 988778999999999999999999999999999999999988631 234577765433332222346889999999
Q ss_pred HHHHHccCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHhcCCCHHHHHHHHHHHhccccCCCCCeeEEEEEecCCCcCC
Q 001100 588 IEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRTDGLHI 667 (1158)
Q Consensus 588 i~~~l~~~~~~V~~v~~k~~~~~PP~Pf~tstLQ~~AskklG~Sa~~Tm~iAQ~LYE~~k~~~g~~~GlITYPRTDS~~L 667 (1158)
+++.+.+..++|.+|+.+++++.||+||||++||++|+++|||||++||++||+|||+++++ |++.||||||||||+||
T Consensus 234 ~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~~aQ~LYe~~~~~-~~~~g~iSYPRTds~~l 312 (675)
T PRK06599 234 LVKALEGQAYTVDKIEKKERKRNPPPPFITSTLQQEASRKLGFSAKKTMRIAQKLYEGIDLG-EGTVGLITYMRTDSVRL 312 (675)
T ss_pred HHHHhcCCCeEEEEEEeeEEecCCCCCCcHHHHHHHHHHHcCCCHHHHHHHHHHHHhccccc-cccceeEEeccCCCccC
Confidence 99999888899999999999999999999999999999999999999999999999998887 66789999999999999
Q ss_pred CHHHHHHHHHHHHHHhCCCCCCCCCCCccccccccccccCCCCCCCcccCChhhhhCCCCHHHHHHHHHHHHHHHHccCC
Q 001100 668 SDEAAKEIRSLIFERYGSHHAPEEGPRKYFKKVKNAQEAHEAIRPTDIRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQ 747 (1158)
Q Consensus 668 s~~~~~~i~~~i~~~~g~~~~~~~~~r~~~~k~k~~qeAH~AI~PT~~~~~P~~l~~~Ls~dE~kLY~LI~rRfLAs~~~ 747 (1158)
|++.++++..++...++..|.. ...+.+..+.+..|+|||||+||.....|+.+.+.|+++|++||+||||||||+||+
T Consensus 313 ~~~~~~~~~~~l~~~~~~~~~~-~~~~~~~~~~~~~~~aH~aI~Pt~~~~~~~~~~~~l~~~e~~iY~lI~~rfla~~~~ 391 (675)
T PRK06599 313 SNEALDEARKYITKKYGKEYLP-AKPRVYKKKSKNAQEAHEAIRPTSINRTPESLKPYLTPDQFKLYELIWKRTVASQMA 391 (675)
T ss_pred CHHHHHHHHHHHHHHhchhhcc-ccCcccCCCCCCCCCCCCCCccCCCCCChhHhhccCCHHHHHHHHHHHHHHHHHhCc
Confidence 9999999999998888765653 234444333344578999999998644565444569999999999999999999999
Q ss_pred CcEEEEEEEEEEecCccEEEEEEeEEEEEcCceeeccccchhhhccccccchhhhhhHHhcCCCCCCCeeEeeeEEEecc
Q 001100 748 PATVGQIQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLKTGDPLYLGEVELKQH 827 (1158)
Q Consensus 748 ~a~~e~t~v~i~~~~~~~~F~asg~~i~~~Gw~~vy~~~~~~~~~~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~ 827 (1158)
||+|++++|.+.+.+++..|.++|++++++||+++|+..+. ++++++ ...||.+++||.+.+.++.+.++
T Consensus 392 ~~~~~~t~v~~~~~~~~~~F~a~g~~~~~~Gw~~~~~~~~~-----~~~~~~-----~~~lp~~~~g~~~~~~~~~~~~~ 461 (675)
T PRK06599 392 PAILDQTSVDIASENGKYVFRATGSVILFPGFLKVYGESKD-----DEEEDD-----EKLLPPLKEGEKLKLDELLPEQH 461 (675)
T ss_pred hheEEEEEEEEEEcCCCeEEEEEEEEEEecCeeeeeccccc-----cccccc-----cccCCCCCCCCEeeeeeeeeccc
Confidence 99999999999872234689999999999999999975321 010111 14599999999999999999999
Q ss_pred ccCCCCCCCHhHHHHHHHhcCCCCCcchHHHHHHhhccceEEEcCcccccccccchhhhhhhcccccccChhhhHHHHHH
Q 001100 828 HTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKSRILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETE 907 (1158)
Q Consensus 828 ~TkPP~ryTEasLI~~MEk~GIGTpATrAsIIe~L~~R~YV~~k~k~L~PT~lG~~v~~~L~~~f~~l~~p~~TA~~E~~ 907 (1158)
+|+||+||||++||++||+.|||||||||+||++|++||||.++++.|+||++|+.|++.|+..|+.|++|+|||.||..
T Consensus 462 ~T~PP~r~te~tLi~~Me~~GIGT~ATra~iIe~L~~r~Yi~~~~~~l~~T~~G~~l~~~l~~~~~~l~~p~lTa~~E~~ 541 (675)
T PRK06599 462 FTEPPPRYSEASLVKKLEEYGIGRPSTYASIISTLQDREYVELEKKRFIPTDLGRIVNDFLVEHFPKYVDYDFTAGLEDE 541 (675)
T ss_pred ccCCCCCCCHHHHHHHHhhCCCCccccHHHHHHHHhhCCeEEeeCCEEeecHHHHHHHHHHHHhchhhCCHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999888899999999999999
Q ss_pred hhhhhcCCchHHHHHHHHHHHhhhhhhhccchhHHHHHHHHHhhhcCcccCCCCCCCCCCCCCCCCeEEEEecccCceeE
Q 001100 908 LDNVSAGLTEWKGLLVDYWSRFSSYCTCAQSLHIHQVEKMLEKTFGDSLFASLPNKDRSCPVCGEGTLIFKVSRFGAGYF 987 (1158)
Q Consensus 908 Ld~Ia~Gk~~~~~~L~~F~~~f~~~i~~~~~~~i~~V~e~l~~~~g~~~~~~~~~~~g~CPkCGkG~l~~k~gr~G~~~f 987 (1158)
|++|++|+.++++||+.|++.+...+..+. ..... +. . ......+.||.||++.++.+.|++|+ |
T Consensus 542 L~~I~~G~~~~~~~l~~~~~~~~~~~~~~~--------~~~~~-~~--~--~~~~~~~~CP~C~~~~l~~k~~k~g~--F 606 (675)
T PRK06599 542 LDEIAEGKKDWKPVLREFWEPFISNLEKVE--------EDVRT-EK--V--TQEETDETCPKCGGGPLVLKLGKNGK--F 606 (675)
T ss_pred HHHHHcCCCCHHHHHHHHHHHHHHHHHHHH--------hhhhh-hc--c--cccccCccccccCCCcceEEecCCCc--e
Confidence 999999999999999999998877654432 11110 00 0 01123578999966677788888886 9
Q ss_pred EecCCCCCCcccccCCCCCCchhhhhhhccCCCCCcccCCCCCccceeeeccCCCcceEEeCCCCCCCCCcccccCCCCC
Q 001100 988 IGCNQHPRCNYIAKTLYGDDDEEDTLQRNTNVDEPKLIGHHPASKEKVLLKSGPYGFYVQLGEDRTGYLPKRASVSHIKD 1067 (1158)
Q Consensus 988 ~GCs~yP~C~~~~~~~~~e~~~~e~~~~~~~~~lPr~LG~cPkcG~~v~lk~GrfG~yv~c~~d~kg~kpK~~slpk~~~ 1067 (1158)
|+|++||.|.++.+....... +. ........|.||+|+..++++.|++|.|+.|+ ++|.|..
T Consensus 607 ~~Cs~~p~C~~~~~~~~~~~~----~~---~~~~~~~~~~Cp~C~~~~~~kkgk~g~f~~Cs-----------~yp~ck~ 668 (675)
T PRK06599 607 LGCSGYPECKYTKNITRDEDE----PI---EEEEIVEEEKCPKCGGPLVLKKGRYGKFLACS-----------GYPECKH 668 (675)
T ss_pred eeCCCCCccCCCCCCcccccc----cc---ccccccccCCCCCCCCeeEEEeCCCCceeeCC-----------CCCCCCc
Confidence 999999999987764421110 00 00011235689999998999999999999997 3466776
Q ss_pred ccccC
Q 001100 1068 VDSIT 1072 (1158)
Q Consensus 1068 ~~sIt 1072 (1158)
+.+++
T Consensus 669 ~~~~~ 673 (675)
T PRK06599 669 IKPLE 673 (675)
T ss_pred eeeCC
Confidence 66553
No 5
>COG0550 TopA Topoisomerase IA [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.5e-136 Score=1222.56 Aligned_cols=546 Identities=45% Similarity=0.682 Sum_probs=498.5
Q ss_pred CeEEEEecchHHHHHHhhcCCCEEEEeecccccccccc---CCCCCCCCC-CcceEecCcc-hHHHHHHHHHHhccCCeE
Q 001100 350 KSVVVVESVTKAKVIQGYLGDMYEVLPSYGHVRDLAAR---SGSVRPDDD-FSMVWEVPSA-AWTHLKSIKVALSGAENL 424 (1158)
Q Consensus 350 k~LIIvEkPskAk~Ia~~LG~~y~V~~s~GHl~dL~~~---~~~v~p~~~-f~~~~~v~~~-~~k~lk~Ik~l~k~ad~I 424 (1158)
+.|||||||+|||+|++|||.+|+|+||+|||+||+.+ ...++++.+ |.+.|.+.+. +.+.+..|+.++++||.|
T Consensus 1 ~~LiIvEsPskAk~Ia~~Lg~~~~V~as~GHi~dl~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~v~~lk~~ak~ad~v 80 (570)
T COG0550 1 KRLIIVESPSKAKTIAKYLGKGYVVTASVGHLRDLPFPEEYKGWVDVDLPIFEPKYIIKPGKKKKVVKKLKKLAKKADEV 80 (570)
T ss_pred CeEEEEeCHHHHHHHHHhcCCCcEEEEcccccccCCChhhccCCcCCcccccccceeccchhhHHHHHHHHHHhccCCEE
Confidence 57999999999999999999999999999999999985 344556655 8899988777 889999999999999999
Q ss_pred EEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhcccccHhHHHHHHHHHHHhhhhhhcccH
Q 001100 425 ILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAAREIDANLVQAYLARRALDYLIGFNISP 504 (1158)
Q Consensus 425 IlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fs~lT~~aI~~A~~nlr~~d~~L~~A~~AR~~lD~LiG~nlSR 504 (1158)
|||||||||||+|||||+++|+.. +. .+++|||||+||+++|++||+||+++|++||+||+||+++|||||||+||
T Consensus 81 ~lAtD~DREGE~I~~~i~~~l~~~---~~-~~~~R~~F~eiT~~aI~~A~~~p~~id~~lv~A~~aR~~lD~lvG~~lSr 156 (570)
T COG0550 81 YLATDPDREGEAIGWHILEVLKLK---NP-SKVKRVVFSEITKKAILSAFKNPREIDMNLVDAQLARRILDRLVGYNLSR 156 (570)
T ss_pred EECCCCCcchHHHHHHHHHHhCcc---CC-CceeEEEEecCCHHHHHHHHhCchhhchHHHHHHHHHHHHHHHhhhhhhH
Confidence 999999999999999999999752 11 47999999999999999999999999999999999999999999999999
Q ss_pred HHHhhCCCc-ccCCcchhHHHHHHHHHHHHHHhcCCcceEEEEEEEecCcCCCCCCceeeeeccccccccccccCcCCHH
Q 001100 505 LLWRKLPGC-QSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDTFSFPAHLTHFQSKRLNQLSIGSHT 583 (1158)
Q Consensus 505 ~l~~k~~~~-lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~g~~f~a~l~~~~~~k~~~~~i~d~~ 583 (1158)
+||+++++. ||+||||||||+|||+||+||++|+|++||+|.+.+..+ +..|.+.|...++++. .++.+.+
T Consensus 157 ~l~~~~~~~~LSaGRVQSpaL~lVveRE~EI~~F~p~~yw~i~a~~~~~------~~~f~a~~~~~~~~~~--~~~~~~~ 228 (570)
T COG0550 157 LLWKKLKRGVLSAGRVQSPALRLVVEREREIEAFVPEEYWEIKAIFEKG------GGEFSARLTEIEGKKE--GRLKDKD 228 (570)
T ss_pred HHHHhhccCCCCCccccchhhhhhHhhHHHHHhCCCCcceEEEEEEecC------CccEEEEEeccccccc--cccccHH
Confidence 999999875 999999999999999999999999999999999999753 2239999877665432 3567888
Q ss_pred HHHHHHHHHccCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHhcCCCHHHHHHHHHHHhccccCCCCCeeEEEEEecCC
Q 001100 584 EAKDIEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRTD 663 (1158)
Q Consensus 584 ~Ae~i~~~l~~~~~~V~~v~~k~~~~~PP~Pf~tstLQ~~AskklG~Sa~~Tm~iAQ~LYE~~k~~~g~~~GlITYPRTD 663 (1158)
.|..+.+.+++..+.|.+++.+++++.||+||+|++||++|+++|||||++||+|||+|||+| |||||||||
T Consensus 229 ~a~~~~~~l~~~~~~V~~ve~k~~~~~pp~Pf~tstLQq~As~~lgfs~kktm~iAQ~LYE~~--------glITYpRTD 300 (570)
T COG0550 229 EAEEIVNKLKGKPAKVVSVEKKPKKRSPPPPFTTSTLQQEASRKLGFSAKKTMDIAQKLYEGH--------GLITYPRTD 300 (570)
T ss_pred HHHHHHHHccCCceEEEEEeeeeeccCCCCCCcHHHHHHHHHHhCCCCHHHHHHHHHHHhcCC--------CcEEecCCC
Confidence 999999999989999999999999999999999999999999999999999999999999963 899999999
Q ss_pred CcCCCHHHHHHHHHHHHHH-hCCCCCCCCCCCccccccccccccCCCCCCCcccCChhhhhCCCCHHHHHHHHHHHHHHH
Q 001100 664 GLHISDEAAKEIRSLIFER-YGSHHAPEEGPRKYFKKVKNAQEAHEAIRPTDIRRLPAMLSGLLDEDCLKLYSLIWSRTM 742 (1158)
Q Consensus 664 S~~Ls~~~~~~i~~~i~~~-~g~~~~~~~~~r~~~~k~k~~qeAH~AI~PT~~~~~P~~l~~~Ls~dE~kLY~LI~rRfL 742 (1158)
|++||+++..+++.++... ||..|++ ..++.+..+.+++|+||||||||+ ..+|+.+. + .||++||+|||||||
T Consensus 301 s~~ls~~~~~~~~~~i~~~~yg~~~l~-~~~~~~~~~~~~~q~AHeAIrPT~-~~~p~~~~--~-~de~klY~LI~rrfl 375 (570)
T COG0550 301 STRLSEEALAEARLYILAIAYGKEYLP-LKPRRYPSKGKKAQEAHEAIRPTD-FETPESLK--A-YDELKLYDLIWRRFL 375 (570)
T ss_pred CCcCCHHHHHHHHHHHHhhccHHhhcc-cccccCCCCCCCCcCCCCCcCCCC-CCCccccc--c-hhHHHHHHHHHHHHH
Confidence 9999999999999999888 9999987 456666666778999999999998 45677653 2 899999999999999
Q ss_pred HccCCCcEEEEEEEEEEecCccEEEEEEeEEEEEcCceeeccccchhhhccccccchhhhhhHHhcCCCCCCCeeEeeeE
Q 001100 743 ACQMQPATVGQIQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLKTGDPLYLGEV 822 (1158)
Q Consensus 743 As~~~~a~~e~t~v~i~~~~~~~~F~asg~~i~~~Gw~~vy~~~~~~~~~~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~ 822 (1158)
||||+||+|+.++|++.++++ .|+++|++++++||++||++. . ++++ ...||.|++||.+.+.++
T Consensus 376 As~m~~A~~~~~~v~l~~~~~--~F~a~g~~~~~~Gw~~vy~~~-~-----~~~~-------~~~lP~l~~gd~l~~~~~ 440 (570)
T COG0550 376 ASQMPDAIYEKTTVTLEVAGE--KFKASGKVLKFDGWLKVYGED-K-----DEEE-------DKELPELKEGDELKVEKL 440 (570)
T ss_pred HHhCchhhheEEEEEEEecCc--EEEEeeeEEecCcHHHhhccc-c-----cccc-------cccCCCCCCCCeeEEeee
Confidence 999999999999999998665 799999999999999999764 1 1111 157999999999999999
Q ss_pred EEeccccCCCCCCCHhHHHHHHHhcCCCCCcchHHHHHHhhccceEEEcCcccccccccchhhhhhhcccccccChhhhH
Q 001100 823 ELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKSRILYPEFRGRMVSAFLSHYFSEVTDYSFTA 902 (1158)
Q Consensus 823 ~i~e~~TkPP~ryTEasLI~~MEk~GIGTpATrAsIIe~L~~R~YV~~k~k~L~PT~lG~~v~~~L~~~f~~l~~p~~TA 902 (1158)
.+.+|+|+||+|||||+||++||+.|||||||||+||++|++||||..+++.|+||++|+.|+++|+.+|+.+++|+|||
T Consensus 441 ~~~~~~T~PP~rytEasLvk~mE~~GIGrpSTyA~iI~~L~~RgYv~~~~~~~~pT~~G~~v~~~L~~~f~~l~~~~~Ta 520 (570)
T COG0550 441 EVEEHFTKPPPRYTEASLVKAMEKLGIGTPSTYASIIETLQKRGYVEKKGKRLVPTELGEAVIELLEEYFPELVDPDFTA 520 (570)
T ss_pred eecccccCCcCCCCHHHHHHHHHhCCCCCcccHHHHHHHHhcCCcEEecCCeeEEcHHHHHHHHHHHHhchhhcCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhhhcCCchHHHHHHHHHHHhhhhhhh
Q 001100 903 DMETELDNVSAGLTEWKGLLVDYWSRFSSYCTC 935 (1158)
Q Consensus 903 ~~E~~Ld~Ia~Gk~~~~~~L~~F~~~f~~~i~~ 935 (1158)
+||++||+|++|+.+|++||++|+..|.+.+..
T Consensus 521 ~mE~~Ld~I~~gk~~~~~~l~e~~~~~~~~~~~ 553 (570)
T COG0550 521 KMEEKLDEIAEGKLEWKDVLDEFKKKFSKLLEE 553 (570)
T ss_pred HHHHHHHHHHcCCccHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999988776543
No 6
>PRK05776 DNA topoisomerase I; Provisional
Probab=100.00 E-value=8.1e-136 Score=1245.45 Aligned_cols=596 Identities=26% Similarity=0.370 Sum_probs=513.5
Q ss_pred CCeEEEEecchHHHHHHhhcC--------------------CCEEEEeeccccccccccCCCCC-CCCCCcceEecCcc-
Q 001100 349 GKSVVVVESVTKAKVIQGYLG--------------------DMYEVLPSYGHVRDLAARSGSVR-PDDDFSMVWEVPSA- 406 (1158)
Q Consensus 349 ~k~LIIvEkPskAk~Ia~~LG--------------------~~y~V~~s~GHl~dL~~~~~~v~-p~~~f~~~~~v~~~- 406 (1158)
++.|||||||++|++|+++|| .+|+|+|++|||++|+.++..++ .+.+|.+.|.+...
T Consensus 1 ~~~LiIaEKPs~Ak~Ia~~Lg~~~~~~~~~g~~~~e~~~~g~~~~V~~~~GHl~~L~~~~~~~~~~~~~~~p~~~~~~~~ 80 (670)
T PRK05776 1 GYILVIAEKPKAARKIAEALSEKPIRCRIYGVPYWIVKRDGKKIVVAPAAGHLFGLHTKSKGFPVFDYEWKPLYEIDKGS 80 (670)
T ss_pred CCEEEEEcCHHHHHHHHHHhCCCccccccCCCceEEEecCCCCEEEEEecccCccCCCcccCCCCCCcCcccceEeccCc
Confidence 378999999999999999997 45899999999999998875543 33468888876543
Q ss_pred --hHHHHHHHHHHhccCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhcccccHhH
Q 001100 407 --AWTHLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAAREIDANL 484 (1158)
Q Consensus 407 --~~k~lk~Ik~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fs~lT~~aI~~A~~nlr~~d~~L 484 (1158)
++++++.|++++++||+||||||||||||+|||||+++|+ +.++|+|+|||+||+++|++||+||+++|++|
T Consensus 81 ~~~~~~~~~lk~l~k~ad~iiiAtD~DREGE~I~~~i~~~~~------~~~~v~R~~fs~iT~~~I~~A~~n~~~~d~~l 154 (670)
T PRK05776 81 KYTKKYYELLSSLSKYADEFINACDYDIEGSVIGYLIIKYLG------DPKKAKRMKFSALTKSDIRRAFRNLETLDYEM 154 (670)
T ss_pred ccHHHHHHHHHHHHhcCCEEEECCCCChhHHHHHHHHHHHhC------CCCCeeEEEEccCCHHHHHHHHhCccccchhH
Confidence 3589999999999999999999999999999999999985 24589999999999999999999999999999
Q ss_pred HHHHHHHHHHhhhhhhcccHHHHhhCC------CcccCCcchhHHHHHHHHHHHHHHhcCCcceEEEEEEEecCcCCCCC
Q 001100 485 VQAYLARRALDYLIGFNISPLLWRKLP------GCQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLD 558 (1158)
Q Consensus 485 ~~A~~AR~~lD~LiG~nlSR~l~~k~~------~~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~ 558 (1158)
++||+|||++||||||||||++|.++. +++|+||||||||+|||+||+||++|+|++||.|.+.+...
T Consensus 155 ~~A~~aR~~lD~lvG~nlSr~lt~~~~~~~g~~~~lS~GRVQsptL~lVveRe~eI~~Fvp~~yw~i~~~~~~~------ 228 (670)
T PRK05776 155 INAGIARHELDWLWGINVSRALMSSVRDASGKRVILSAGRVQSPTLKYVVEREIERNLFVPLPYFSVSIIIEKN------ 228 (670)
T ss_pred HHHHHHHHHHHHHHhHHHhHHHHHHhhhhcCCccceecceecCchhhHhHhhHHHHHcCCCCcceEEEEEEecC------
Confidence 999999999999999999999998654 26999999999999999999999999999999999998642
Q ss_pred CceeeeeccccccccccccCcCCHHHHHHHHHHHcc-CCeEEEEeeeeeeeecCCCCcchHHHHHHHHHhcCCCHHHHHH
Q 001100 559 TFSFPAHLTHFQSKRLNQLSIGSHTEAKDIEQKINS-ANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMK 637 (1158)
Q Consensus 559 g~~f~a~l~~~~~~k~~~~~i~d~~~Ae~i~~~l~~-~~~~V~~v~~k~~~~~PP~Pf~tstLQ~~AskklG~Sa~~Tm~ 637 (1158)
+..|.+.|.. .++.++++|+++++.+++ ..++|.+|+.++++++||+||+|++||++||++|||||++||+
T Consensus 229 ~~~f~~~~~~--------~~~~~~~~a~~i~~~~~~~~~~~V~~v~~k~~~~~pP~pf~ts~LQ~~As~~lg~sa~ktm~ 300 (670)
T PRK05776 229 GYEFTLKYEN--------KKFETKEEAKEILEEIKKTGYLKVTKVEVKIEILEPPPPFNLGDLQVEAARIYGFSPYKTQS 300 (670)
T ss_pred CceEEEEEcC--------CccCCHHHHHHHHHHhcCCCCEEEEEEEeeeEEcCCCCCCCHHHHHHHHHhhcCCCHHHHHH
Confidence 3468877631 257899999999999987 7899999999999999999999999999999999999999999
Q ss_pred HHHHHhccccCCCCCeeEEEEEecCCCcCCCHHH-HHHHHHHHHHH--hCC---CCCCCCCCCcc-ccccccccccCCCC
Q 001100 638 LAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEA-AKEIRSLIFER--YGS---HHAPEEGPRKY-FKKVKNAQEAHEAI 710 (1158)
Q Consensus 638 iAQ~LYE~~k~~~g~~~GlITYPRTDS~~Ls~~~-~~~i~~~i~~~--~g~---~~~~~~~~r~~-~~k~k~~qeAH~AI 710 (1158)
+||+|||+ ||||||||||++||+++ +.++.+.|... ||. .+.. ..++.+ ..+.++.++|||||
T Consensus 301 iAQ~LYe~---------glISYPRTDs~~ls~~~~~~~~~~~l~~~~~~~~~~~~~l~-~~~~~~~~~~~~k~~~aH~AI 370 (670)
T PRK05776 301 IAEDLYLD---------GLISYPRTNSQKLPPTLNIRNILKGLSRSPQYRPLVNLLLK-ETKGVLKPVQGPKDDPAHPAI 370 (670)
T ss_pred HHHHHHhc---------CceecCCCccCCCChhhCHHHHHHHHhcchhHHHHHHHhhc-ccCCccccCCCCCCCCCCCCC
Confidence 99999995 89999999999999986 56666666542 443 2222 111111 11222235699999
Q ss_pred CCCcccCChhhhhCCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEEEEEecCccEEEEEEeEEEEEcCceeeccccchhh
Q 001100 711 RPTDIRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGA 790 (1158)
Q Consensus 711 ~PT~~~~~P~~l~~~Ls~dE~kLY~LI~rRfLAs~~~~a~~e~t~v~i~~~~~~~~F~asg~~i~~~Gw~~vy~~~~~~~ 790 (1158)
|||+. .|+ .|+++|++||+||||||||+||+||+|++|+|++.++++.+.|+++|++++++||++||++.+
T Consensus 371 ~PT~~--~p~----~L~~de~klY~LI~rRflA~~~~~a~~~~t~v~~~~~~~~~~F~a~G~~i~~~Gw~~vy~~~~--- 441 (670)
T PRK05776 371 YPTGE--PPK----NLSKDEFKLYDLIVRRFLASFAAPAVLSNTIVTLRVPGFPLVFSASGQRIEERGWLKYYPFHK--- 441 (670)
T ss_pred CCCCC--Ccc----cCCHHHHHHHHHHHHHHHHHhChhheEEEEEEEEEECCeEEEEEEEEEEEEECCceeecccCc---
Confidence 99986 354 499999999999999999999999999999999998654448999999999999999996431
Q ss_pred hccccccchhhhhhHHhcCCCCCCCeeEeeeEEEeccccCCCCCCCHhHHHHHHHhcCCCCCcchHHHHHHhhccceEEE
Q 001100 791 IRYKENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTV 870 (1158)
Q Consensus 791 ~~~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk~GIGTpATrAsIIe~L~~R~YV~~ 870 (1158)
+ ++ ..||.|++||.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++|+||.+
T Consensus 442 ----~-~~-------~~LP~l~~G~~~~~~~~~~~~~~TkPP~ryTeasLi~~ME~~GIGtpATra~iI~~L~~R~Yv~~ 509 (670)
T PRK05776 442 ----F-DE-------EELPLLKKGERVKIVDVKVRKSYTKPPSRYSKASLLKWMESVGIGTEATRARIIETLFKRGYLTS 509 (670)
T ss_pred ----c-cc-------ccCCCcCCCCEeEeeeeeeeccccCCCCCCCHHHHHHHHhhCCCCCCccHHHHHHHHHhCCCEEe
Confidence 0 11 35999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCcccccccccchhhhhhhcccccccChhhhHHHHHHhhhhhcCCchHHHHHHHHHHHhhhhhhhccchhHHHHHHHHHh
Q 001100 871 KSRILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKGLLVDYWSRFSSYCTCAQSLHIHQVEKMLEK 950 (1158)
Q Consensus 871 k~k~L~PT~lG~~v~~~L~~~f~~l~~p~~TA~~E~~Ld~Ia~Gk~~~~~~L~~F~~~f~~~i~~~~~~~i~~V~e~l~~ 950 (1158)
+++.|+||++|+.|+++|..+||.|++|+|||+||.+||+|++|+.+|++||++|+..|...+..+.. ....+.+.+..
T Consensus 510 ~~k~l~pT~~G~~v~~~L~~~~~~l~~~~~Ta~~E~~Ld~I~~G~~~~~~vl~~~~~~~~~~~~~~~~-~~~~i~~~l~~ 588 (670)
T PRK05776 510 NGKYIEVTPLGFGVAEVLEKYFPDIVSVELTRDFEEKLEMIRTGKATREEVIEEAKETLNKLLEEFKK-NKDEIGEELAK 588 (670)
T ss_pred eCCEEeECHHHHHHHHHHHHhccccCCHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999887766532 23333333333
Q ss_pred hhcCcccCCCCCCCCCCCCCCCCeE----EEEecccCceeEEecCCCCCCcccccCC
Q 001100 951 TFGDSLFASLPNKDRSCPVCGEGTL----IFKVSRFGAGYFIGCNQHPRCNYIAKTL 1003 (1158)
Q Consensus 951 ~~g~~~~~~~~~~~g~CPkCGkG~l----~~k~gr~G~~~f~GCs~yP~C~~~~~~~ 1003 (1158)
.++. ....+.||+||+ .+ +.+.+++|.+.|+||++||+|+++.+..
T Consensus 589 ~~~~------~~~~~~Cp~Cg~-~l~~~~~~~~~~~~~~~f~~c~~~p~c~~~~~~~ 638 (670)
T PRK05776 589 ALGL------IKPVGKCKICGR-EAYKDGLCKYHYEAKKRLVKAYEEWKERTGYDHK 638 (670)
T ss_pred hccC------cCCCCcCCCCCC-ccccCceEEecccCCccceecCCCccccCCCCcc
Confidence 3221 233579999997 67 7888999887899999999999887654
No 7
>PRK07219 DNA topoisomerase I; Validated
Probab=100.00 E-value=7e-135 Score=1265.33 Aligned_cols=695 Identities=24% Similarity=0.370 Sum_probs=549.2
Q ss_pred CeEEEEecchHHHHHHhhc---------------------CCCEEEEeeccccccccccCC--CCC---CCCCCcceEec
Q 001100 350 KSVVVVESVTKAKVIQGYL---------------------GDMYEVLPSYGHVRDLAARSG--SVR---PDDDFSMVWEV 403 (1158)
Q Consensus 350 k~LIIvEkPskAk~Ia~~L---------------------G~~y~V~~s~GHl~dL~~~~~--~v~---p~~~f~~~~~v 403 (1158)
+.|||||||++|++|+++| |.+|+|+|+.|||++|+.|+. .|. |...+..-+..
T Consensus 1 ~~LiIaEKps~Ak~Ia~~L~~g~~~~~~~~g~~~~~~~~~g~~~~v~~~~GHl~~l~~p~~y~~w~~~~l~~l~~~~~~~ 80 (822)
T PRK07219 1 TELIIAEKNNAARRIADILSGGKAKKKRVNGVPYYEFERKGEKWIVIGLSGHIVTVDFPEEYGDWRDVDPAELIDADPVK 80 (822)
T ss_pred CEEEEEeCHHHHHHHHHHhcCCCcccccCCCcceEEecCCCCeEEEEEecCcccccCCchhcCCcCcCChhhccccceee
Confidence 4799999999999999999 345889999999999987642 232 21111111222
Q ss_pred CcchHHHHHHHHHHhccCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhcccccHh
Q 001100 404 PSAAWTHLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAAREIDAN 483 (1158)
Q Consensus 404 ~~~~~k~lk~Ik~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fs~lT~~aI~~A~~nlr~~d~~ 483 (1158)
.+.+++|++.|++|+++||.||||||||||||+|||||++++.. + .+++|+|||||+||+++|++||+||+++|++
T Consensus 81 ~~~~~~~~~~lk~l~~~ad~iiiAtD~DREGE~I~~ei~~i~~~---~-~~~~v~R~~fs~iT~~~I~~A~~n~~~~d~~ 156 (822)
T PRK07219 81 KITKQNYINALKKLAKDADEIIIATDYDREGELIGKEAYHILRE---V-CQVPVKRARFSSLTKKEIRKAFENPDEIDFN 156 (822)
T ss_pred cCCHHHHHHHHHHHHhcCCEEEEcCCCChhHHHHHHHHHHHHHh---c-CCCceeEEEEccCCHHHHHHHHhCcccCCHH
Confidence 34578999999999999999999999999999999777666643 2 3579999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhhhhhcccHHHHhhCC-----CcccCCcchhHHHHHHHHHHHHHHhcCCcceEEEEEEEecCcCCCCC
Q 001100 484 LVQAYLARRALDYLIGFNISPLLWRKLP-----GCQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLD 558 (1158)
Q Consensus 484 L~~A~~AR~~lD~LiG~nlSR~l~~k~~-----~~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~ 558 (1158)
|++||+|||++||||||||||+||..++ .++|+||||||||+|||+||+||+||+|++||.|.+.+...
T Consensus 157 l~~a~~aR~~~D~lvG~nlSr~lt~~~~~~g~~~~lS~GRVQtPtL~lIv~Re~eI~~F~p~~yw~i~~~~~~~------ 230 (822)
T PRK07219 157 LADAGEARQIIDLYWGAALTRFLSLSVRQLGRWDFLSVGRVQTPTLAFIVDREREIRAFDPEDYWKIEALLDKE------ 230 (822)
T ss_pred HHHHHHHHHHHHHHhhhhhCHHHHHHHHhccccCccccccccchhhHHHHHHHHHHHcCCCcccEEEEEEEEec------
Confidence 9999999999999999999999997653 36999999999999999999999999999999999988531
Q ss_pred CceeeeeccccccccccccCcCCHHHHHHHHHHHcc-CCeEEEEeeeeeeeecCCCCcchHHHHHHHHHhcCCCHHHHHH
Q 001100 559 TFSFPAHLTHFQSKRLNQLSIGSHTEAKDIEQKINS-ANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMK 637 (1158)
Q Consensus 559 g~~f~a~l~~~~~~k~~~~~i~d~~~Ae~i~~~l~~-~~~~V~~v~~k~~~~~PP~Pf~tstLQ~~AskklG~Sa~~Tm~ 637 (1158)
+..|.+.|.. . .+..+|+|+++|+++++.+++ ..++|.+|+.++++++||+||||++||++|+++|||||++||+
T Consensus 231 ~~~~~~~~~~--~--~~~~r~~d~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~t~~Lq~~a~~~~g~sa~~tm~ 306 (822)
T PRK07219 231 AQYFYRDLIG--G--HEAEKFWDEEEAEEIYEKLKGAKEATVSSVKKRERTISPPAPFNTTEFLREASKIFGISPKRAME 306 (822)
T ss_pred Ccceeeeccc--c--cccCccCCHHHHHHHHHHhcCCCCeEEEEEEEeeEEccCCCCccHHHHHHHHHHHcCCCHHHHHH
Confidence 2235554421 1 123478999999999999988 6899999999999999999999999999999999999999999
Q ss_pred HHHHHhccccCCCCCeeEEEEEecCCCcCCCHHHHHHHHHHHHH-----HhCCC---CCCCCCCCccccccccccccCCC
Q 001100 638 LAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFE-----RYGSH---HAPEEGPRKYFKKVKNAQEAHEA 709 (1158)
Q Consensus 638 iAQ~LYE~~k~~~g~~~GlITYPRTDS~~Ls~~~~~~i~~~i~~-----~~g~~---~~~~~~~r~~~~k~k~~qeAH~A 709 (1158)
+||+|||+ ||||||||||++||+++. +++++.. .|+.. +.. . .+......+.+++||||
T Consensus 307 iaQ~LYe~---------glITYpRTds~~l~~~~~--~~~~~~~l~~~~~~~~~~~~~l~-~-~~~~~~~~~~~~~aH~a 373 (822)
T PRK07219 307 IAEKLYTA---------GYISYPRTDNTVYPDDLD--PKELLKKLSKKKEYGPYAESILE-Q-ENIKPTEGKKETTDHPP 373 (822)
T ss_pred HHHHHHhC---------CceeccCcccccCCHHHH--HHHHHHHhhcccchhhHhhhhcc-c-CCcccCCCCCCCCCCCC
Confidence 99999995 899999999999999873 5555532 23321 211 1 11111223345799999
Q ss_pred CCCCcccCChhhhhCCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEEEEEecCccEEEEEEeEEEEEcCceeeccccchh
Q 001100 710 IRPTDIRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAG 789 (1158)
Q Consensus 710 I~PT~~~~~P~~l~~~Ls~dE~kLY~LI~rRfLAs~~~~a~~e~t~v~i~~~~~~~~F~asg~~i~~~Gw~~vy~~~~~~ 789 (1158)
||||+.. |. +.|+++|++||+||||||||+||+||+|++++|.+.+++ +.|+++|++++++||++||++..
T Consensus 374 I~PT~~~--~~---~~L~~~e~~lY~LI~rrfla~~~~~a~~~~t~v~~~~~~--~~F~a~g~~i~~~Gw~~vy~~~~-- 444 (822)
T PRK07219 374 IHPVDVP--KR---EELSDDEWKVYELIVRRFLATLADPAEWEYLKVELDVNG--EIFKASGSRLVEEGWHEVYPYEK-- 444 (822)
T ss_pred CCCcCCC--Cc---ccCCHHHHHHHHHHHHHHHHHhCccceeeEEEEEEEeCC--eEEEEEEEEEccCCcHhhcCccc--
Confidence 9999863 32 359999999999999999999999999999999999864 58999999999999999996531
Q ss_pred hhccccccchhhhhhHHhcCCCCCCCeeEeeeEEEeccccCCCCCCCHhHHHHHHHhcCCCCCcchHHHHHHhhccceEE
Q 001100 790 AIRYKENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVT 869 (1158)
Q Consensus 790 ~~~~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk~GIGTpATrAsIIe~L~~R~YV~ 869 (1158)
+ ++ ..||.|++||.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++||||
T Consensus 445 -----~-~~-------~~lP~l~~G~~~~~~~~~~~~~~T~PP~rytea~Li~~Me~~GIGT~ATra~iI~~L~~R~Yv- 510 (822)
T PRK07219 445 -----F-DE-------KELPDLEEGEKLKVNKIEIEAKETQPPKRYTQSSLIKEMEKRGLGTKATRHDIIEKLYKRGYV- 510 (822)
T ss_pred -----c-cc-------ccCCCCCCCCEeeeeeeEecccccCCCCCCCHHHHHHHHHhCCCCCCccHHHHHHHHHhcCcE-
Confidence 0 00 359999999999999999999999999999999999999999999999999999999999999
Q ss_pred EcCcccccccccchhhhhhhcccccccChhhhHHHHHHhhhhhcCCchHHHHHHHHHHHhhhhhhhccchhHHHHHHHHH
Q 001100 870 VKSRILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKGLLVDYWSRFSSYCTCAQSLHIHQVEKMLE 949 (1158)
Q Consensus 870 ~k~k~L~PT~lG~~v~~~L~~~f~~l~~p~~TA~~E~~Ld~Ia~Gk~~~~~~L~~F~~~f~~~i~~~~~~~i~~V~e~l~ 949 (1158)
++++.|+||++|+.|+++|+..||.|++|+|||.||..|++|++|+.+|++||+++++.+...+..+.. ....+.+.+.
T Consensus 511 ~~~~~l~pT~~G~~l~~~l~~~~~~l~~~~~Ta~~E~~L~~I~~G~~~~~~~l~~~~~~~~~~~~~~~~-~~~~~~~~~~ 589 (822)
T PRK07219 511 IEGDPPRPTDLGIAVIEALEKYAPEIVSEEMTAQLEADMQAIEDGKKKKEDVTEESREMLKEILSELKE-KRKEIGDHLA 589 (822)
T ss_pred ecCCEeeecHHHHHHHHHHHHhchhhcChhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHH
Confidence 889999999999999999999999999999999999999999999999999999988888776655421 1112221111
Q ss_pred hhhcCcccCCCCCCCCCCCCCCCCeEEEEecccCceeEEecCCCCCCcccccCCCCCC-----chhhhhhhcc--C----
Q 001100 950 KTFGDSLFASLPNKDRSCPVCGEGTLIFKVSRFGAGYFIGCNQHPRCNYIAKTLYGDD-----DEEDTLQRNT--N---- 1018 (1158)
Q Consensus 950 ~~~g~~~~~~~~~~~g~CPkCGkG~l~~k~gr~G~~~f~GCs~yP~C~~~~~~~~~e~-----~~~e~~~~~~--~---- 1018 (1158)
..+... .......+.||+||++ +.++.++.| +.||||++||.|+++.++..... ..+..|.... .
T Consensus 590 ~~~~~~--~~~~~~~~~CP~Cg~~-l~~r~~~~g-~~F~gCs~yp~C~~t~~lp~~~~~~~~~~~Cp~CG~~lvk~~~~r 665 (822)
T PRK07219 590 GSLKAE--NRSLKTIGKCPECGGD-LIIIRTDKG-SRFVGCSGYPDCRNTFPLPSTGRIKVLDEVCEKCGLPVIKILRGK 665 (822)
T ss_pred hhhccc--cccccccCcCCCCCCc-ceeeeccCC-ceeeecCCCcCCCCeeecCCCCccccccCCCCCCCcceEEEeccC
Confidence 111100 0011235789999974 555656666 25999999999999887654221 1111111000 0
Q ss_pred --------------CCC--CcccCCCCCccceeeeccCCCcceEEeCCCCCCCCCcccccCCCCCccccCHHHHHHHhcC
Q 001100 1019 --------------VDE--PKLIGHHPASKEKVLLKSGPYGFYVQLGEDRTGYLPKRASVSHIKDVDSITLEDALELLRY 1082 (1158)
Q Consensus 1019 --------------~~l--Pr~LG~cPkcG~~v~lk~GrfG~yv~c~~d~kg~kpK~~slpk~~~~~sItle~Al~ll~~ 1082 (1158)
... +...+.||+||..|+++.|++|.|+.|+ ++|.|.....+.-... .
T Consensus 666 ~~~~~~CP~C~~~~~~~~~~~~~~~CP~Cg~~l~~k~gr~G~F~~Cs-----------~yp~C~~~~~l~~~~~-----~ 729 (822)
T PRK07219 666 QTFVVGCPDCEAEKEEEDPDEVIGPCPKCGGELAIKQLKYGSFLGCT-----------NYPKCKYTLPLPRRGK-----I 729 (822)
T ss_pred ccccccCCCCCCCccccccccccccCCCCCCeeEEEcCCCCCeeeCC-----------CCCCCCceeecccccc-----c
Confidence 000 1235689999999999999999999997 4577765544321100 0
Q ss_pred CcccCCCCCCCcCeEEeeccCcce--eecCCeeee
Q 001100 1083 PVNLGNHPKDGQPIMLRLARAGFS--VRHRRTIAS 1115 (1158)
Q Consensus 1083 pk~lG~cP~cG~~I~i~~GRyG~Y--i~~~~~~~~ 1115 (1158)
......||+||.++++..+++|+| |..++.|..
T Consensus 730 ~~~~~~CpkCg~~l~~~k~~~g~~~~Cs~~p~C~~ 764 (822)
T PRK07219 730 TVTDEKCPECGLPLLRVKGGFGDELGCCNNPKCNY 764 (822)
T ss_pred ccccCCCCCCCCeEEEEecCCCceeeeCCCCCCCc
Confidence 012357999999999999999986 444455543
No 8
>PRK05582 DNA topoisomerase I; Validated
Probab=100.00 E-value=6.8e-133 Score=1222.73 Aligned_cols=635 Identities=41% Similarity=0.692 Sum_probs=545.3
Q ss_pred CCCeEEEEecchHHHHHHhhcCCCEEEEeeccccccccccCCCCCCCCCCcceEecCcchHHHHHHHHHHhccCCeEEEc
Q 001100 348 SGKSVVVVESVTKAKVIQGYLGDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILA 427 (1158)
Q Consensus 348 ~~k~LIIvEkPskAk~Ia~~LG~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~~~k~lk~Ik~l~k~ad~IIlA 427 (1158)
|++.|||||||++|++|+++||.+|+|+||+|||++|+++..+++|++.|.+.|.+.+++++|++.|++++++||+||||
T Consensus 1 mm~~LiIaEkps~a~~ia~~lg~~~~V~~~~GHl~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ik~l~~~~d~ii~A 80 (650)
T PRK05582 1 MMKKLVIVESPAKAKTIEKYLGKNYKVVASMGHIRDLPKSQLGIDIENNFEPKYITIRGKGPVIKELKKAAKKAKKVYLA 80 (650)
T ss_pred CCCeEEEEeCHHHHHHHHHHcCCCCEEEeccCchhcCCCccCCCCcccCCceeeEECCcHHHHHHHHHHHHhcCCEEEEC
Confidence 56789999999999999999999999999999999999875566675448888988888999999999999999999999
Q ss_pred cCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhcccccHhHHHHHHHHHHHhhhhhhcccHHHH
Q 001100 428 SDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAAREIDANLVQAYLARRALDYLIGFNISPLLW 507 (1158)
Q Consensus 428 TDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fs~lT~~aI~~A~~nlr~~d~~L~~A~~AR~~lD~LiG~nlSR~l~ 507 (1158)
||||||||+|||||+++++.. .++++|||||+||+++|++||+|+++++++|++||+||+++|||||||+||++|
T Consensus 81 tD~DrEGE~I~~~i~~~~~~~-----~~~~~R~~~s~lt~~~I~~a~~nl~~~~~~l~~a~~aR~~~D~liG~n~tr~~t 155 (650)
T PRK05582 81 TDPDREGEAIAWHLAHILGLD-----EKEKNRIVFNEITKDAIKNAFKNPRKIDMNLVDAQQARRILDRLVGYKLSPLLW 155 (650)
T ss_pred CCCCcchHHHHHHHHHHhCCC-----CCCceEEEEcccCHHHHHHHHhCcccccHHHHHHHHHHHHHHHHhhhhcCHHHH
Confidence 999999999999999998631 267899999999999999999999999999999999999999999999999999
Q ss_pred hhCCCcccCCcchhHHHHHHHHHHHHHHhcCCcceEEEEEEEecCcCCCCCCceeeeeccccccccccccCcCCHHHHHH
Q 001100 508 RKLPGCQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDTFSFPAHLTHFQSKRLNQLSIGSHTEAKD 587 (1158)
Q Consensus 508 ~k~~~~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~g~~f~a~l~~~~~~k~~~~~i~d~~~Ae~ 587 (1158)
.++++.+|+||||||||+|||+||+||+||+|++||.|.+.+... +..|.+.|....+ +..+|.|+++|++
T Consensus 156 ~~~~~~ls~GRVQtPtL~lvv~Re~eI~~F~p~~y~~i~~~~~~~------~~~~~~~~~~~~~---~~~~~~~~~~a~~ 226 (650)
T PRK05582 156 KKVKKGLSAGRVQSVALKLIIDREKEIRAFVPEEYWTIDAEFKKG------KKKFEASFYGYKG---KKIELKNEEDVKE 226 (650)
T ss_pred HhhcCCCccccchHhHHHHHHhHHHHHHhCCCCccEEEEEEEecC------CccEEEEEEecCC---CccccCCHHHHHH
Confidence 987778999999999999999999999999999999999988532 2257776633221 2357889999999
Q ss_pred HHHHHccCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHhcCCCHHHHHHHHHHHhccccCCCCCeeEEEEEecCCCcCC
Q 001100 588 IEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRTDGLHI 667 (1158)
Q Consensus 588 i~~~l~~~~~~V~~v~~k~~~~~PP~Pf~tstLQ~~AskklG~Sa~~Tm~iAQ~LYE~~k~~~g~~~GlITYPRTDS~~L 667 (1158)
+++.+.+..++|.+|+.++++..||+||||++||++|+++|||||++||++||+|||+++|++++..||||||||||+||
T Consensus 227 ~~~~~~~~~~~v~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~~aQ~LYe~~~~~~~~~~gliSYPRTds~~l 306 (650)
T PRK05582 227 ILAELKKKDFKVSKVKKKERKRNPPPPFTTSTLQQEAARKLNFSTKKTMMIAQQLYEGIDLGKQGTVGLITYMRTDSTRI 306 (650)
T ss_pred HHHHhcCCCeEEEEEeeeeeecCCCCCccHHHHHHHHHHHcCCCHHHHHHHHHHHhcccccCCCCceEEEEecCCCcccC
Confidence 99999888899999999999999999999999999999999999999999999999998888776679999999999999
Q ss_pred CHHHHHHHHHHHHHHhCCCCCCCCCCCccccccccccccCCCCCCCcccCChhhhhCCCCHHHHHHHHHHHHHHHHccCC
Q 001100 668 SDEAAKEIRSLIFERYGSHHAPEEGPRKYFKKVKNAQEAHEAIRPTDIRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQ 747 (1158)
Q Consensus 668 s~~~~~~i~~~i~~~~g~~~~~~~~~r~~~~k~k~~qeAH~AI~PT~~~~~P~~l~~~Ls~dE~kLY~LI~rRfLAs~~~ 747 (1158)
|+++++.+.+++...+|..+.. ...+.+..+ +..++|||||+||.....|+.+.+.|+++|++||+||+|||||+||+
T Consensus 307 ~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~-~k~~~~H~aI~PT~~~~~p~~~~~~L~~~e~~iY~lI~~rfla~~~~ 384 (650)
T PRK05582 307 SDTAQEEAREFIEEKYGKEYLP-KKPKVYKKK-SGAQDAHEAIRPTSVFLTPESAKKYLTKDQLKLYKLIWNRFVASQMA 384 (650)
T ss_pred CHHHHHHHHHHHHHHhHHHhhc-cCCcccCCC-cCCCCCCCCEeecCCCcChhHHhccCCHHHHHHHHHHHHHHHHHhCc
Confidence 9999999999888767755543 223333322 23457999999998643465433469999999999999999999999
Q ss_pred CcEEEEEEEEEEecCccEEEEEEeEEEEEcCceeeccccchhhhccccccchhhhhhHHhcCCCCCCCeeEeeeEEEecc
Q 001100 748 PATVGQIQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLKTGDPLYLGEVELKQH 827 (1158)
Q Consensus 748 ~a~~e~t~v~i~~~~~~~~F~asg~~i~~~Gw~~vy~~~~~~~~~~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~ 827 (1158)
||+|++|+|.+.+++ ..|+++|++++++||+.+|+..+ + + ...||.|++||.+.+.++.+.++
T Consensus 385 ~~~~~~t~v~~~~~~--~~F~a~g~~~~~~Gw~~~~~~~~-------~-~-------~~~lp~l~~g~~~~~~~~~~~~~ 447 (650)
T PRK05582 385 PAVFDTVSVDLENNG--VKFRASGSKVKFDGFMKVYVGDE-------E-K-------DKMLPELEEGEKVKLKKIEPEQH 447 (650)
T ss_pred hhheeEEEEEEEeCC--EEEEEEEEEEeeCChHhhcCCcc-------c-c-------cccCCCCCCCCEeEEEEeeeccc
Confidence 999999999998854 58999999999999999996311 0 0 03599999999999999999999
Q ss_pred ccCCCCCCCHhHHHHHHHhcCCCCCcchHHHHHHhhccceEEEcCcccccccccchhhhhhhcccccccChhhhHHHHHH
Q 001100 828 HTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKSRILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETE 907 (1158)
Q Consensus 828 ~TkPP~ryTEasLI~~MEk~GIGTpATrAsIIe~L~~R~YV~~k~k~L~PT~lG~~v~~~L~~~f~~l~~p~~TA~~E~~ 907 (1158)
+|+||+||||++||++||+.|||||||||+||++|++||||+.+++.|+||++|++|+++|+..++.|++|+|||.||.+
T Consensus 448 ~T~PP~~~Te~~Ll~~Me~~GIGT~ATra~iI~~L~~r~Yi~~~~k~l~pT~~G~~l~~~l~~~~~~l~~p~lTa~~E~~ 527 (650)
T PRK05582 448 FTQPPARYTEASLIKTLEELGIGRPSTYAPTISTIQKRGYVKLEKKRLVPTELGEIVNELLEEFFPDIVDVEFTAEMEEK 527 (650)
T ss_pred ccCCCCCCCHHHHHHHHHHcCCCCcccHHHHHHHHHhCCeEEeeCCEEeecHHHHHHHHHHHHhchhhcCHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999988899999999999999
Q ss_pred hhhhhcCCchHHHHHHHHHHHhhhhhhhccchhHHHHHHHHHhhhcCcccCCCCCCCCCCCCCCCCeEEEEecccCceeE
Q 001100 908 LDNVSAGLTEWKGLLVDYWSRFSSYCTCAQSLHIHQVEKMLEKTFGDSLFASLPNKDRSCPVCGEGTLIFKVSRFGAGYF 987 (1158)
Q Consensus 908 Ld~Ia~Gk~~~~~~L~~F~~~f~~~i~~~~~~~i~~V~e~l~~~~g~~~~~~~~~~~g~CPkCGkG~l~~k~gr~G~~~f 987 (1158)
|++|++|+.++++||+++++.+...+..+. +.... +. ... ......||+||+ .++.+.+++|. |
T Consensus 528 L~~I~~G~~~~~~~l~~~~~~~~~~~~~~~--------~~~~~-~~---~~~-~~~~~~CP~Cg~-~l~~~~~k~gk--f 591 (650)
T PRK05582 528 LDEIEEGKEDWKKVLDDFYKPFEKEIEKAE--------KEIEK-IK---IKD-EPAGEDCPKCGS-PMVIKMGRYGK--F 591 (650)
T ss_pred HHHHHcCCCCHHHHHHHHHHHHHHHHHHHH--------hhhhc-cc---ccc-cccCCCCCCCCC-EeEEEecCCCc--e
Confidence 999999999999999999988776654321 10000 00 000 112468999986 56666777774 9
Q ss_pred EecCCCCCCcccccCCCCCCchhhhhhhccCCCCCcccCCCCCccceeeeccCCCcc-eEEeC
Q 001100 988 IGCNQHPRCNYIAKTLYGDDDEEDTLQRNTNVDEPKLIGHHPASKEKVLLKSGPYGF-YVQLG 1049 (1158)
Q Consensus 988 ~GCs~yP~C~~~~~~~~~e~~~~e~~~~~~~~~lPr~LG~cPkcG~~v~lk~GrfG~-yv~c~ 1049 (1158)
|+|++||.|++..+... ...+.||+|+..++++.+++|. |+.|+
T Consensus 592 ~~Cs~~~~C~~~~~~~~------------------~~~~~CP~C~~~l~l~k~k~gk~f~~Cs 636 (650)
T PRK05582 592 IACSNFPDCRNTKPIVK------------------EIGVKCPKCGGQIVERKSKKGRKFYGCS 636 (650)
T ss_pred eecCCccccccCCCccc------------------ccCCCCCCCCCceEEEcCCCCceeeccC
Confidence 99999999998653221 0125699999888878888885 88886
No 9
>PRK07220 DNA topoisomerase I; Validated
Probab=100.00 E-value=5e-132 Score=1225.76 Aligned_cols=624 Identities=24% Similarity=0.361 Sum_probs=514.0
Q ss_pred CeEEEEecchHHHHHHhhcC---------------------CCEEEEeeccccccccccC-----CCCCCCCCCcceEec
Q 001100 350 KSVVVVESVTKAKVIQGYLG---------------------DMYEVLPSYGHVRDLAARS-----GSVRPDDDFSMVWEV 403 (1158)
Q Consensus 350 k~LIIvEkPskAk~Ia~~LG---------------------~~y~V~~s~GHl~dL~~~~-----~~v~p~~~f~~~~~v 403 (1158)
|.|||||||++|++|+++|| ++|+|+|++|||++|+.|+ ..|++++.|...|..
T Consensus 1 m~LiIaEKPs~Ak~Ia~~Lg~~~~~~~~~~g~~~y~~~~~g~~~~v~~~~GHl~~l~~P~~y~~w~~~~~~~l~~~~~~~ 80 (740)
T PRK07220 1 MHLIITEKNIAARRIAQILAPKKPKKTRVSGVDVYRYEDNGDDTVVVGLSGHIVNIDFPKEYNNWQKVDARDLIDAEIIT 80 (740)
T ss_pred CeEEEEeCHHHHHHHHHHhCCCCccccccCCcceeEEecCCCCEEEEEeCcccccCCCCccccccCCCChhHcCCcceEe
Confidence 46999999999999999997 2478999999999986653 246766666667776
Q ss_pred CcchHHHHHHHHHHhccCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhcccccHh
Q 001100 404 PSAAWTHLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAAREIDAN 483 (1158)
Q Consensus 404 ~~~~~k~lk~Ik~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fs~lT~~aI~~A~~nlr~~d~~ 483 (1158)
.+.+++|++.|++++++||.||||||||||||+|||||+++++. .+++++|+|+|||+||+++|++||+||+++|++
T Consensus 81 ~~~~~~~~~~lk~l~k~ad~viiAtD~DREGE~I~~~i~~~l~~---~~~~~~~~R~~fs~iT~~~I~~A~~n~~~~d~~ 157 (740)
T PRK07220 81 TPTQKKIVTALKKLGKEADRVTIATDYDREGELIGVEALNIIKK---VNPDIKFDRVRYSAITKKEIERAFSNPVEVDFN 157 (740)
T ss_pred cCCHHHHHHHHHHHHhcCCEEEECCCCCccHHHHHHHHHHHHHh---cCCCCceEEEEEccCCHHHHHHHHhCCCCCChh
Confidence 67788999999999999999999999999999999999999975 245679999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhhhhhcccHHHHhhCC----CcccCCcchhHHHHHHHHHHHHHHhcCCcceEEEEEEEecCcCCCCCC
Q 001100 484 LVQAYLARRALDYLIGFNISPLLWRKLP----GCQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDT 559 (1158)
Q Consensus 484 L~~A~~AR~~lD~LiG~nlSR~l~~k~~----~~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~g 559 (1158)
|++||+|||++||||||||||++|..++ +++|+||||||||+|||+||+||++|+|++||.|.+.+.. .+
T Consensus 158 l~~A~~aR~~~D~lvG~nlSr~~t~~~~~~~~~~lS~GRVQtptL~lIv~Re~eI~~F~p~~y~~i~~~~~~------~~ 231 (740)
T PRK07220 158 LADAGHSRQVIDLVWGAALTRYISLAAGRLGKMFLSVGRVQSPTLALIVDREKEREAFVPTPYWEIYATLEN------NG 231 (740)
T ss_pred HHHHHHHHHHHHHHhchhcCHHHHHHHHhhCCccccccccchhhhHHHHhhHHHHHhCCCCccEEEEEEEEc------CC
Confidence 9999999999999999999999998653 3699999999999999999999999999999999999864 23
Q ss_pred ceeeeeccccccccccccCcCCHHHHHHHHHHHccCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHhcCCCHHHHHHHH
Q 001100 560 FSFPAHLTHFQSKRLNQLSIGSHTEAKDIEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKLA 639 (1158)
Q Consensus 560 ~~f~a~l~~~~~~k~~~~~i~d~~~Ae~i~~~l~~~~~~V~~v~~k~~~~~PP~Pf~tstLQ~~AskklG~Sa~~Tm~iA 639 (1158)
..|.+.|. ..+|.++++|+++++.+ +..++|.+|+.+++++.||+||+|++||++|++ +||||++||++|
T Consensus 232 ~~~~~~~~--------~~r~~~~~~a~~~~~~~-~~~~~V~~v~~~~~~~~pP~pf~ts~Lq~~a~~-~g~s~~~tm~ia 301 (740)
T PRK07220 232 ETFVAQHS--------TRRFWEKEEADRVFEKL-GKTAEVTEVEKGTKTDKPPTPFNTTEFISAANS-IGFSAANAMRIA 301 (740)
T ss_pred ceEEEEec--------cCcCCCHHHHHHHHHhh-CCCeEEEEEeeeeEecCCCCCcCHHHHHHHHHH-cCCCHHHHHHHH
Confidence 46777662 13688999999999999 667999999999999999999999999999986 899999999999
Q ss_pred HHHhccccCCCCCeeEEEEEecCCCcCCCHHH--HHHHHHHHHHHhCC---CCCCCCCCCccccccccccccCCCCCCCc
Q 001100 640 QKLYEGVQLPDGTAAGLITYMRTDGLHISDEA--AKEIRSLIFERYGS---HHAPEEGPRKYFKKVKNAQEAHEAIRPTD 714 (1158)
Q Consensus 640 Q~LYE~~k~~~g~~~GlITYPRTDS~~Ls~~~--~~~i~~~i~~~~g~---~~~~~~~~r~~~~k~k~~qeAH~AI~PT~ 714 (1158)
|+|||+ ||||||||||++||+++ .+.+..++...||. .+.. .. +....+.+..++||||||||+
T Consensus 302 Q~LYe~---------g~ITYPRTDs~~l~~~~~~~~~i~~l~~~~~~~~~~~~l~-~~-~~~~~~~~~~~~~H~aI~PT~ 370 (740)
T PRK07220 302 ESLYTN---------GYISYPRTDNTVYPESLDLREQIEIFAEGPFGEYAQKLLE-KG-ELVPTRGKKETTDHPPIYPAS 370 (740)
T ss_pred HHHHhC---------CceeecccCCeecCchhhHHHHHHHHHHHHHHHHHHHhcc-cC-CccCCCCCCCCCCCCCCCccc
Confidence 999996 89999999999999965 45555554434543 2322 11 001111223346899999998
Q ss_pred ccCChhhhhCCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEEEEEecCccEEEEEEeEEEEEcCceeeccccchhhhccc
Q 001100 715 IRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYK 794 (1158)
Q Consensus 715 ~~~~P~~l~~~Ls~dE~kLY~LI~rRfLAs~~~~a~~e~t~v~i~~~~~~~~F~asg~~i~~~Gw~~vy~~~~~~~~~~~ 794 (1158)
.. +. +.|+++|++||+||||||||+||+||+|++++|.+.+++ +.|+++|++++++||++||++.+
T Consensus 371 ~~--~~---~~L~~de~~lY~LI~rRfla~~~~~a~~~~t~v~~~~~~--~~F~a~g~~~~~~Gw~~vy~~~~------- 436 (740)
T PRK07220 371 LA--KK---SELKEDEWKVYELVVRRFFATFAGPAEWETMKLRFDIGG--EEFRANGSRLTEPGWRWYYPYNA------- 436 (740)
T ss_pred CC--Cc---ccCCHHHHHHHHHHHHHHHHHhCchheEEEEEEEEEECC--eEEEEeeeEEeeCChHHHcCccc-------
Confidence 63 21 359999999999999999999999999999999998864 58999999999999999996531
Q ss_pred cccchhhhhhHHhcCCCCCCCeeEeeeEEEeccccCCCCCCCHhHHHHHHHhcCCCCCcchHHHHHHhhccceEEEcCcc
Q 001100 795 ENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKSRI 874 (1158)
Q Consensus 795 e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk~GIGTpATrAsIIe~L~~R~YV~~k~k~ 874 (1158)
+ ++ ..||.|++||.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++||||+ ++.
T Consensus 437 ~-~~-------~~LP~l~~Ge~~~~~~~~~~ek~TkPP~ryTea~Li~~Me~~GIGTpATra~iI~~L~~R~Yi~--~k~ 506 (740)
T PRK07220 437 P-ED-------RLLPELSEGEELKVKKKEMLDKETQPPGRYGQGRLIKLMEDLGLGTKATRHEIISKLYSRAYIH--GNP 506 (740)
T ss_pred c-cc-------ccCCCCCCCCEeeeeeeeecccccCCCCCCCHHHHHHHHHhCCCCCCCcHHHHHHHHHhcCCcc--CCc
Confidence 0 10 3599999999999999999999999999999999999999999999999999999999999996 778
Q ss_pred cccccccchhhhhhhcccccccChhhhHHHHHHhhhhhcCCchHHHHHHHHHHHhhhhhhhccchhHHHHHHHHHhhhcC
Q 001100 875 LYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKGLLVDYWSRFSSYCTCAQSLHIHQVEKMLEKTFGD 954 (1158)
Q Consensus 875 L~PT~lG~~v~~~L~~~f~~l~~p~~TA~~E~~Ld~Ia~Gk~~~~~~L~~F~~~f~~~i~~~~~~~i~~V~e~l~~~~g~ 954 (1158)
|+||++|+.|+++|+.+|+.|++|+|||+||..||+|++|+.+|++||++|++.+...+..+... ...+.+.+...+.
T Consensus 507 l~pT~~G~~v~~~l~~~~~~i~~~~~Ta~~E~~Ld~I~~G~~~~~~~l~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~- 584 (740)
T PRK07220 507 IQPTNTAFAVVDALEKYAPTITKPDMTSRLEEDMDKIAEGKIKEDAVLEESREMLEQVFDELDKN-REKIRESLREGLR- 584 (740)
T ss_pred ccccHHHHHHHHHHHHhchhhcChhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHH-HHHHHHhhhhhhc-
Confidence 99999999999999999999999999999999999999999999999999998777655443211 1111111111110
Q ss_pred cccCCCCCCCCCCCCCCCCeEEEEecccCceeEEecCCCCCCcccccCCCCCCchhhhhhhccCCCCCcccCCCCCccce
Q 001100 955 SLFASLPNKDRSCPVCGEGTLIFKVSRFGAGYFIGCNQHPRCNYIAKTLYGDDDEEDTLQRNTNVDEPKLIGHHPASKEK 1034 (1158)
Q Consensus 955 ~~~~~~~~~~g~CPkCGkG~l~~k~gr~G~~~f~GCs~yP~C~~~~~~~~~e~~~~e~~~~~~~~~lPr~LG~cPkcG~~ 1034 (1158)
.....+.||.||+ .+..+.+++|. .||||++||.|.++.+......+. ..-..||+||..
T Consensus 585 -----~~~~~~~CP~Cg~-~l~~r~~r~g~-~f~gCs~yp~C~~~~~l~~~g~~~-------------~~~~~Cp~Cg~~ 644 (740)
T PRK07220 585 -----EDKIIGKCPLCGS-DLMVRRSKRGS-RFIGCEGYPECTFSLPLPKSGQII-------------VTDKVCEAHGLN 644 (740)
T ss_pred -----ccccccccccCCC-eeeEEecCCCc-eEEEcCCCCCCCceeeCCCCCccc-------------cCCCCCCCCCCc
Confidence 1123568999996 67777787763 599999999999987765422210 112369999964
Q ss_pred eee-c-cCCCcceEEeC
Q 001100 1035 VLL-K-SGPYGFYVQLG 1049 (1158)
Q Consensus 1035 v~l-k-~GrfG~yv~c~ 1049 (1158)
++. . .|+.+.|+.|.
T Consensus 645 ~~k~~~~g~~~~~~~Cp 661 (740)
T PRK07220 645 HIRIINGGKRPWDLGCP 661 (740)
T ss_pred eEEEEecCCccceeeCC
Confidence 332 2 23323378883
No 10
>TIGR01056 topB DNA topoisomerase III, bacteria and conjugative plasmid. This model describes topoisomerase III from bacteria and its equivalents encoded on plasmids. The gene is designated topB if found in the bacterial chromosome, traE on conjugative plasmid RP4, etc. These enzymes are involved in the control of DNA topology. DNA topoisomerase III belongs to the type I topoisomerases, which are ATP-independent.
Probab=100.00 E-value=4.8e-132 Score=1211.80 Aligned_cols=585 Identities=25% Similarity=0.368 Sum_probs=499.8
Q ss_pred CeEEEEecchHHHHHHhhc------------CCCEEEEeeccccccccccCC------C-------CCCCCCCcceEecC
Q 001100 350 KSVVVVESVTKAKVIQGYL------------GDMYEVLPSYGHVRDLAARSG------S-------VRPDDDFSMVWEVP 404 (1158)
Q Consensus 350 k~LIIvEkPskAk~Ia~~L------------G~~y~V~~s~GHl~dL~~~~~------~-------v~p~~~f~~~~~v~ 404 (1158)
|.|||||||++|++|+++| |.+|+|+||+|||++|++|+. . ++|+ +| .|.+.
T Consensus 1 ~~LiIaEKPs~Ak~Ia~~L~~~~~~~gy~e~g~~~~V~~~~GHl~~L~~p~~~~~~~~~W~~~~lp~~p~-~f--~~~~~ 77 (660)
T TIGR01056 1 MTLVLCEKPSQARDLATVLAKKKKGNGYLEIGVGGFVTWAVGHLVELAEPEEYDEKYKNWRTYDLPLEPE-DW--QLVVS 77 (660)
T ss_pred CeEEEEeCHHHHHHHHHHhCCCcCCCCcEEECCcEEEEeCchhhhcCCChhhcccccCccccCCCCcccc-cc--eeeec
Confidence 5799999999999999999 899999999999999986631 2 2222 23 35666
Q ss_pred cchHHHHHHHHHHhc--cCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhcccc--
Q 001100 405 SAAWTHLKSIKVALS--GAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAAREI-- 480 (1158)
Q Consensus 405 ~~~~k~lk~Ik~l~k--~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fs~lT~~aI~~A~~nlr~~-- 480 (1158)
+.++++++.|+++++ +||.||||||||||||+|||||+++|+. +...+|+|+|||+||+++|++||+||+++
T Consensus 78 ~~~~~~~~~ik~l~k~~~ad~Ii~AtDpDREGE~I~~~i~~~l~~----~~~~~v~Ri~f~~iT~~~I~~A~~n~~~~~~ 153 (660)
T TIGR01056 78 DKTKKQFNVIKRILKENKVDEVVIATDPDREGELIAREILDYLKV----TDKVTIKRLWISSLVDSSIRKAFKNLRPKSE 153 (660)
T ss_pred cchHHHHHHHHHHhhhcCCCEEEECCCCCcchHHHHHHHHHHhCC----CCCCceEEEEeccCCHHHHHHHHHcCCCchh
Confidence 778999999999999 9999999999999999999999999963 12248999999999999999999999985
Q ss_pred cHhHHHHHHHHHHHhhhhhhcccHHHHhh-----CCCcccCCcchhHHHHHHHHHHHHHHhcCCcceEEEEEEEecCcCC
Q 001100 481 DANLVQAYLARRALDYLIGFNISPLLWRK-----LPGCQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESH 555 (1158)
Q Consensus 481 d~~L~~A~~AR~~lD~LiG~nlSR~l~~k-----~~~~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~ 555 (1158)
+++|++||+|||++||||||||||++|.+ +.+++|+||||||||+|||+||+||+||+|++||.|.+.+...
T Consensus 154 ~~~l~~a~~aR~~~D~lvG~nlSr~lt~~~~~~g~~~~lS~GRVQtptL~lIveRe~eI~~F~p~~y~~i~~~~~~~--- 230 (660)
T TIGR01056 154 TEGLYKSGVARARADWLVGINLTRAFTKLGREAGNDGVLSVGRVQTPTLAMVVKRENEIKNFVGKPFYEVSATINKD--- 230 (660)
T ss_pred hhhHHHHHHHHHHHHHHHHHhHhHHHHHhhhhcCCCCceecccchhhhhHHHHHHHHHHHcCCCCccEEEEEEEEcC---
Confidence 79999999999999999999999999987 5568999999999999999999999999999999999998642
Q ss_pred CCCCceeeeeccccccccccccCcCCHHHHHHHHHHHccCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHhcCCCHHHH
Q 001100 556 SLDTFSFPAHLTHFQSKRLNQLSIGSHTEAKDIEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYT 635 (1158)
Q Consensus 556 ~~~g~~f~a~l~~~~~~k~~~~~i~d~~~Ae~i~~~l~~~~~~V~~v~~k~~~~~PP~Pf~tstLQ~~AskklG~Sa~~T 635 (1158)
+..|.+.|....+ +..++.++++|+.+++.+.+..++|.+|+.+++++.||+||+|++||++|+++|||||++|
T Consensus 231 ---~~~~~~~~~~~~~---~~~~~~~~~~a~~i~~~~~~~~~~V~~v~~k~~~~~pP~pf~ts~LQ~~as~~~g~s~~~t 304 (660)
T TIGR01056 231 ---EQEFTTEWQPYKD---EEERELHEFLAENVVTDLTQKPALVTDIEKERKKTSAPLFYDLSALQEDANKRFGISAKRT 304 (660)
T ss_pred ---CceEEEEEeccCC---cccCcCCHHHHHHHHHHhhCCCeEEEEEEeeeeecCCCCCCCHHHHHHHHHHhcCCCHHHH
Confidence 3358888754322 2357899999999999998888999999999999999999999999999999999999999
Q ss_pred HHHHHHHhccccCCCCCeeEEEEEecCCCcCCCHHHHHHHHHHHHHHhCCCC--CCC-----CCCCccccccccccccCC
Q 001100 636 MKLAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFERYGSHH--APE-----EGPRKYFKKVKNAQEAHE 708 (1158)
Q Consensus 636 m~iAQ~LYE~~k~~~g~~~GlITYPRTDS~~Ls~~~~~~i~~~i~~~~g~~~--~~~-----~~~r~~~~k~k~~qeAH~ 708 (1158)
|++||+|||++ ||||||||||++||++++++++++|...++..+ ... ...++++++ ..|+|||
T Consensus 305 m~iAQ~LYE~~--------glITYpRTDS~~ls~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~aH~ 374 (660)
T TIGR01056 305 LDIAQKLYETH--------KLITYPRTDSRYLPEDEKEMLLEVLDALKVITPALLPIKKRDELTNNRLWND--KKIEDHH 374 (660)
T ss_pred HHHHHHHHHhC--------CEEEEecCCCccCCHHHHHHHHHHHHHhhccchhhhcccccccccccCcCCC--CccCCcC
Confidence 99999999952 799999999999999999999999877665332 110 001122222 3578999
Q ss_pred CCCCCcccCChhhhhCCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEEEEEecCccEEEEEEeEEEEEcCceeeccccch
Q 001100 709 AIRPTDIRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDA 788 (1158)
Q Consensus 709 AI~PT~~~~~P~~l~~~Ls~dE~kLY~LI~rRfLAs~~~~a~~e~t~v~i~~~~~~~~F~asg~~i~~~Gw~~vy~~~~~ 788 (1158)
|||||+....+ +.|+++|++||+|||+||||+||+||+|++|+|++.+++ ..|+++|++++++||++||...+.
T Consensus 375 AI~PT~~~~~~----~~L~~de~klY~LI~~Rflas~~~~a~~~~t~v~~~~~~--~~F~a~g~~i~~~Gw~~v~~~~~~ 448 (660)
T TIGR01056 375 AIIPTGNDFNL----SDLSEEERNVYKLIAQNYLMQFMPKEEYETTTIEIAIGK--LMFEAKGKILQDNGWKALLGKQEE 448 (660)
T ss_pred CccccCCcccc----ccCCHHHHHHHHHHHHHHHHHhCchhEEEEEEEEEEECC--EEEEEEEEEEcccCHHHHhccccc
Confidence 99999863221 359999999999999999999999999999999998853 589999999999999999965321
Q ss_pred hhhccccccchhhhhhHHhcCCCCCCCeeEeeeEEEeccccCCCCCCCHhHHHHHHH-----------------hcCCCC
Q 001100 789 GAIRYKENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSEGSLVKKLE-----------------ELGIGR 851 (1158)
Q Consensus 789 ~~~~~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~ME-----------------k~GIGT 851 (1158)
+++++ ...||.|++||.+.+.++.+.+++|+||+||||++||++|| +.||||
T Consensus 449 ------~~~~~-----~~~LP~l~~G~~~~~~~~~~~~~~TkPP~ryTeasLi~~Me~~~k~v~d~~l~~~l~e~~GIGt 517 (660)
T TIGR01056 449 ------DEETE-----DTTLPAFQKGDELDVETLELLEKQTKPPARYTEGTLLSAMTNPAAFVQDKGLKKTLKETKGLGT 517 (660)
T ss_pred ------ccccc-----cccCCCCCCCCEeeeeecccccCcCCCCCCcCHHHHHHHHHhhhhcccCHHHHHHhhhccCCCC
Confidence 11111 13599999999999999999999999999999999999999 789999
Q ss_pred CcchHHHHHHhhccceEEEcCcccccccccchhhhhhhcccccccChhhhHHHHHHhhhhhcCCchHHHHHHHHHHHhhh
Q 001100 852 PSTYASTLKVLQDRNYVTVKSRILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKGLLVDYWSRFSS 931 (1158)
Q Consensus 852 pATrAsIIe~L~~R~YV~~k~k~L~PT~lG~~v~~~L~~~f~~l~~p~~TA~~E~~Ld~Ia~Gk~~~~~~L~~F~~~f~~ 931 (1158)
|||||+||++|++|+||+.+++.|+||++|+.|+++|+. .|++|+|||.||++||+|++|+.+|++||+.|+..+..
T Consensus 518 pATrA~iI~~L~~R~Yv~~~~k~l~pT~~G~~v~~~L~~---~i~~~~~Ta~~E~~Ld~I~~G~~~~~~~~~~~~~~~~~ 594 (660)
T TIGR01056 518 EATRADIIENLFKRGFIQKKKNKIYITKNGKLLCLLLPE---LLTKPDLTAQWEQYLNGISAGEKDDDDFINTINEMIKQ 594 (660)
T ss_pred cccHHHHHHHHHhCCCEEeeCCEEEEcHHHHHHHHHhHH---hcCChhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999984 68999999999999999999999999999999998877
Q ss_pred hhhhccchhHHHHHHHHHhhhcCcccCCCCCCCCCCCCCCCCeEEEEecccCceeEEecCCCCCCcccc
Q 001100 932 YCTCAQSLHIHQVEKMLEKTFGDSLFASLPNKDRSCPVCGEGTLIFKVSRFGAGYFIGCNQHPRCNYIA 1000 (1158)
Q Consensus 932 ~i~~~~~~~i~~V~e~l~~~~g~~~~~~~~~~~g~CPkCGkG~l~~k~gr~G~~~f~GCs~yP~C~~~~ 1000 (1158)
.+..+. .... .+. ....+.|| ||+ .++.+.+++|. |+||++||+|++..
T Consensus 595 ~~~~~~--------~~~~-~~~-------~~~~~~cp-cg~-~l~~~~~~~g~--f~~c~~~p~C~~~~ 643 (660)
T TIGR01056 595 TINEEK--------KNPE-TIQ-------KVAKEPVS-CGG-IAKCPAKDNGR--LIDCKKFPECTEYG 643 (660)
T ss_pred HHHHHH--------hhhh-hhc-------CCCCccCC-CCC-ceeeeecCCCe--eecCCCCCCccCcC
Confidence 654431 1110 000 12467899 996 67778888886 99999999998743
No 11
>TIGR01051 topA_bact DNA topoisomerase I, bacterial. This model describes DNA topoisomerase I among the members of bacteria. DNA topoisomerase I transiently cleaves one DNA strand and thus relaxes negatively supercoiled DNA during replication, transcription and recombination events.
Probab=100.00 E-value=1.8e-131 Score=1200.79 Aligned_cols=608 Identities=44% Similarity=0.709 Sum_probs=522.0
Q ss_pred EEEEecchHHHHHHhhcCCCEEEEeeccccccccccCCCCCCCCCCcceEecCcchHHHHHHHHHHhccCCeEEEccCCC
Q 001100 352 VVVVESVTKAKVIQGYLGDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILASDPD 431 (1158)
Q Consensus 352 LIIvEkPskAk~Ia~~LG~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~~~k~lk~Ik~l~k~ad~IIlATDpD 431 (1158)
|||||||++|++|+++||++|+|+||+|||++|+++...++...+|.+.|.+.+++++|++.|++++++||+||||||||
T Consensus 1 LiIaEkps~a~~Ia~~lg~~~~Vt~~~GHl~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~~~~d~ii~AtD~D 80 (610)
T TIGR01051 1 LVIVESPAKAKTIKKYLGDEYEVEASMGHIRDLPKSRLGVDIEKDFEPEYVVSKGKKKVVKELKTLAKKADEVYLATDPD 80 (610)
T ss_pred CEEEeChHHHHHHHHHhCCCCEEEeccCeeccCCCcccCCChhhcCceeEEEcccHHHHHHHHHHHHhcCCEEEECCCCC
Confidence 79999999999999999999999999999999987633222223477778887888999999999999999999999999
Q ss_pred ccccHHHHHHHHHHhhcccccCCccE-EEEEEcccCHHHHHHHHHhcccccHhHHHHHHHHHHHhhhhhhcccHHHHhhC
Q 001100 432 REGEAIAWHIVEMLQQQDALHENITV-ARVVFHEITEASIKVALQAAREIDANLVQAYLARRALDYLIGFNISPLLWRKL 510 (1158)
Q Consensus 432 REGE~Ia~~Ile~l~~~~~~~~~k~v-kRl~fs~lT~~aI~~A~~nlr~~d~~L~~A~~AR~~lD~LiG~nlSR~l~~k~ 510 (1158)
||||+|+|||+++|+. ++++ +|+|||+||+++|++||+|+++++.+|++||.||+++|||||||+||++|..+
T Consensus 81 rEGE~I~~~i~~~~~~------~~~~~~Rl~~s~lt~~~I~~a~~~l~~~~~~l~~aa~aR~~~D~liG~n~Tr~~t~~~ 154 (610)
T TIGR01051 81 REGEAIAWHLAEVLKP------KDPVYKRIVFNEITKKAIRAALKNPREIDMNLVNAQQARRILDRLVGYTLSPLLWKKV 154 (610)
T ss_pred cchhHHHHHHHHHhCC------CCCCceEEEEccCCHHHHHHHHhCccccchhHHHHHHHHHHHHHHHhHhhhHHHHHhh
Confidence 9999999999999863 3456 99999999999999999999999999999999999999999999999999887
Q ss_pred CCcccCCcchhHHHHHHHHHHHHHHhcCCcceEEEEEEEecCcCCCCCCceeeeeccccccccccccCcCCHHHHHHHHH
Q 001100 511 PGCQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDTFSFPAHLTHFQSKRLNQLSIGSHTEAKDIEQ 590 (1158)
Q Consensus 511 ~~~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~g~~f~a~l~~~~~~k~~~~~i~d~~~Ae~i~~ 590 (1158)
+..+|+||||||||+|||+||+||+||+|++||.|.+.+... +..|.+.|....+.++...++.++++|+++.+
T Consensus 155 ~~~lSvGRVQtPtL~lvv~Re~eI~~F~p~~y~~i~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~ 228 (610)
T TIGR01051 155 AKGLSAGRVQSVALRLIVDREREIKRFVPEEYWTIDATFQKG------EETFEALLTEVNGKKLKAGSDLDEAEATALKE 228 (610)
T ss_pred cCCCCcceehHHHHHHHHHHHHHHHhcCCCceEEEEEEEecC------CcceEEEEEecCCccccccccCCHHHHHHHHH
Confidence 777999999999999999999999999999999999988642 34687776432222222347889999999999
Q ss_pred HHccCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHhcCCCHHHHHHHHHHHhccccCCCCCeeEEEEEecCCCcCCCHH
Q 001100 591 KINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRTDGLHISDE 670 (1158)
Q Consensus 591 ~l~~~~~~V~~v~~k~~~~~PP~Pf~tstLQ~~AskklG~Sa~~Tm~iAQ~LYE~~k~~~g~~~GlITYPRTDS~~Ls~~ 670 (1158)
.+++..++|.+|+.+++++.||+||||++||++|+++|||||++||++||+|||+++++ |++.||||||||||+|||++
T Consensus 229 ~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~S~~~tl~iaQ~LYe~~~~~-~~~~g~iSYPRTds~~l~~~ 307 (610)
T TIGR01051 229 QLKGEELVVEEIEKKPKKSRPPPPFTTSTLQQEASRKLGFSAKKTMMIAQRLYEGVSTG-DGTIGLITYMRTDSTRLSNQ 307 (610)
T ss_pred HhcCCCeEEEEEeeceeeeCCCCCcCHHHHHHHHHHhcCCCHHHHHHHHHHHHhccccc-CCceeEEeecCcCccccCHH
Confidence 99888899999999999999999999999999999999999999999999999987787 66679999999999999999
Q ss_pred HHHHHHHHHHHHhCCCCCCCCCCCccccccccccccCCCCCCCcccCChhhhhCCCCHHHHHHHHHHHHHHHHccCCCcE
Q 001100 671 AAKEIRSLIFERYGSHHAPEEGPRKYFKKVKNAQEAHEAIRPTDIRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPAT 750 (1158)
Q Consensus 671 ~~~~i~~~i~~~~g~~~~~~~~~r~~~~k~k~~qeAH~AI~PT~~~~~P~~l~~~Ls~dE~kLY~LI~rRfLAs~~~~a~ 750 (1158)
.++.+..++...++..+.. ...+.++++.++.|+|||||+||.....|+.+.+.|+++|++||+||+|||||+||+||+
T Consensus 308 ~~~~~~~~l~~~~~~~~~~-~~~~~~~~~~k~~~~~H~aI~Pt~~~~~~~~~~~~Ls~~e~~iY~lI~rr~la~~~~~~~ 386 (610)
T TIGR01051 308 AVNEARNLIDKNYGKEYLG-PKPKRYKSKEKNAQEAHEAIRPTSVFRTPEELKDYLKRDEFRLYELIWKRFVASQMADAR 386 (610)
T ss_pred HHHHHHHHHHHhhhHhhcc-ccCcccCCCCCCCCCCcCCCCCCCCCcChhhhhccCCHHHHHHHHHHHHHHHHHhCccce
Confidence 9999999998777754543 233344444444568999999998644466544569999999999999999999999999
Q ss_pred EEEEEEEEEecCccEEEEEEeEEEEEcCceeeccccchhhhccccccchhhhhhHHhcCCCCCCCeeEeeeEEEeccccC
Q 001100 751 VGQIQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQ 830 (1158)
Q Consensus 751 ~e~t~v~i~~~~~~~~F~asg~~i~~~Gw~~vy~~~~~~~~~~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~Tk 830 (1158)
|++|+|.+.+.++++.|.++|++++++||++||+.... +++++ ....||.+++||.+.+.++.+.+++|+
T Consensus 387 ~~~t~v~~~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~~-----~~~~~-----~~~~Lp~l~~g~~~~~~~~~~~~~~T~ 456 (610)
T TIGR01051 387 YDSTSVRLTNEDGEYVFKATGRKLIFDGYYKVYVEGSD-----DPLEE-----KDRILPPLKEGDAVKLVEVKPNQHFTQ 456 (610)
T ss_pred EEEEEEEEEEcCCCeEEEEEEEEEEeCCHHHhcccccc-----ccccc-----ccccCCCCCCCCEeEeeeeeecccccc
Confidence 99999999884445689999999999999999965321 00011 114599999999999999999999999
Q ss_pred CCCCCCHhHHHHHHHhcCCCCCcchHHHHHHhhccceEEEcCcccccccccchhhhhhhcccccccChhhhHHHHHHhhh
Q 001100 831 PPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKSRILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDN 910 (1158)
Q Consensus 831 PP~ryTEasLI~~MEk~GIGTpATrAsIIe~L~~R~YV~~k~k~L~PT~lG~~v~~~L~~~f~~l~~p~~TA~~E~~Ld~ 910 (1158)
||+||||++||++||+.|||||||||+||++|++||||.++++.|+||++|+.|++.|+..++.|++|+|||.||..|++
T Consensus 457 PP~~yTe~tLl~~Me~~GIGTpATra~iIe~L~~r~Yi~~~~~~l~pT~~G~~li~~l~~~~~~l~~p~lTa~~E~~L~~ 536 (610)
T TIGR01051 457 PPARYTEASLVKELEELGIGRPSTYASIISTIQDRGYVKKENKRLYPTELGFAVTDLLEKHFGDVVDYDFTAKMEKDLDE 536 (610)
T ss_pred CCCCCCHHHHHHHHhcCCCCccccHHHHHHHHhhCCeEEeeCCEEeECHHHHHHHHHHHHhhhhhcCHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999888899999999999999999
Q ss_pred hhcCCchHHHHHHHHHHHhhhhhhhccchhHHHHHHHHHhhhcCcccCCCCCCCCCCCCCCCCeEEEEecccCceeEEec
Q 001100 911 VSAGLTEWKGLLVDYWSRFSSYCTCAQSLHIHQVEKMLEKTFGDSLFASLPNKDRSCPVCGEGTLIFKVSRFGAGYFIGC 990 (1158)
Q Consensus 911 Ia~Gk~~~~~~L~~F~~~f~~~i~~~~~~~i~~V~e~l~~~~g~~~~~~~~~~~g~CPkCGkG~l~~k~gr~G~~~f~GC 990 (1158)
|++|+.++++||+.+++.+.+.+..+. .... .. .....+.||.||+ .+..+.+++|. ||||
T Consensus 537 I~~G~~~~~~~l~~~~~~~~~~v~~~~--------~~~~--~~------~~~~~~~CP~Cg~-~~~~~~~~~gk--f~gC 597 (610)
T TIGR01051 537 IAEGKAEWKPVLKNFYTGFSSKVKKLR--------NMRI--IV------DFKTSQDCPLCGR-PMVVKLGKYGP--FLAC 597 (610)
T ss_pred HHcCCCCHHHHHHHHHHHHHHHHHHhh--------hccc--cc------ccccCCCCCCCCC-eeEEEecCCCc--eeeC
Confidence 999999999999999887766544321 1000 00 0012478999996 56667778775 8999
Q ss_pred CCCCCCcccccC
Q 001100 991 NQHPRCNYIAKT 1002 (1158)
Q Consensus 991 s~yP~C~~~~~~ 1002 (1158)
++||.|+++.++
T Consensus 598 s~y~~C~~~~~l 609 (610)
T TIGR01051 598 SNFPECKYTKSI 609 (610)
T ss_pred CCCCCCCCCCCC
Confidence 999999987643
No 12
>PRK14973 DNA topoisomerase I; Provisional
Probab=100.00 E-value=1.3e-131 Score=1233.77 Aligned_cols=625 Identities=23% Similarity=0.339 Sum_probs=513.4
Q ss_pred CeEEEEecchHHHHHHhhcCCC------------------EEEEeeccccccccccC--CCCCCC-----CCCcceEecC
Q 001100 350 KSVVVVESVTKAKVIQGYLGDM------------------YEVLPSYGHVRDLAARS--GSVRPD-----DDFSMVWEVP 404 (1158)
Q Consensus 350 k~LIIvEkPskAk~Ia~~LG~~------------------y~V~~s~GHl~dL~~~~--~~v~p~-----~~f~~~~~v~ 404 (1158)
|.|||+|||++|+.|+.+||.. ++|+|++|||++|..+. ..|..+ +.|+..|.+.
T Consensus 1 m~LiIAEKPSvAk~IA~~L~~~~~~~~k~~g~~~~y~~~~~~vt~~~GHLl~l~y~~~yk~W~~~~LPP~~l~~~~~~~~ 80 (936)
T PRK14973 1 MHLIIAEKNIAANRIAQILAGKTKVQVKKDGGVSTYSFDDTVVVGLRGHVVEVDFEPGYTNWRSEEHTPRSLIDADTIKK 80 (936)
T ss_pred CEEEEEcCHHHHHHHHHHhCCCCccccccCCCcceEEeCCCEEEEEcccceecccCcccCCCccccCChhhccCcceeec
Confidence 3599999999999999999632 36999999999996532 345421 1122235555
Q ss_pred cchHHHHHHHHHHhccCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhcccccHhH
Q 001100 405 SAAWTHLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAAREIDANL 484 (1158)
Q Consensus 405 ~~~~k~lk~Ik~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fs~lT~~aI~~A~~nlr~~d~~L 484 (1158)
+.+++|++.|++++++||.||||||||||||+|||||+++|+. .+.+++|+|+|||+||+++|++||+|++++|++|
T Consensus 81 ~~~kk~~~~Ik~l~k~ad~IiiAtD~DREGE~I~~~i~e~~~~---~~~~~~v~R~~fs~iT~~~I~~A~~nl~~~d~~l 157 (936)
T PRK14973 81 PTEKKIVGLIQKLAKKADRVTIATDFDTEGELIGKEAYELVRA---VNPKVPIDRARFSAITKEEIVTAFAEPTDLDFAL 157 (936)
T ss_pred CchHHHHHHHHHHHHhCCEEEECCCCCcchHHHHHHHHHHhhh---ccCCCceEEEEEccCCHHHHHHHHhCCCCCcHHH
Confidence 6678999999999999999999999999999999999999964 2345799999999999999999999999999999
Q ss_pred HHHHHHHHHHhhhhhhcccHHHHhhCC----CcccCCcchhHHHHHHHHHHHHHHhcCCcceEEEEEEEecCcCCCCCCc
Q 001100 485 VQAYLARRALDYLIGFNISPLLWRKLP----GCQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDTF 560 (1158)
Q Consensus 485 ~~A~~AR~~lD~LiG~nlSR~l~~k~~----~~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~g~ 560 (1158)
++||+||+++||||||||||++|.++. +++|+||||||||+|||+||+||+||+|++||.|.+.+.. .+.
T Consensus 158 ~~A~~aR~~~D~lvG~nlSr~lt~~~~~g~~~~lS~GRVQTPtL~lIveRe~EI~~Fvp~~Yw~I~~~~~~------~~~ 231 (936)
T PRK14973 158 AAAGEARQIIDLIWGASLTRFISLAAHRGGDNILSVGRVQSPTLAMIVDREKEIEAFVPEKYWMLSLATEK------DGE 231 (936)
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCcceeeccccchHHHHHHhHHHHHHcCCCCceEEEEEEEec------CCc
Confidence 999999999999999999999998654 3599999999999999999999999999999999999863 244
Q ss_pred eeeeeccccccccccccCcCCHHHHHHHHHHHccCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHhcCCCHHHHHHHHH
Q 001100 561 SFPAHLTHFQSKRLNQLSIGSHTEAKDIEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKLAQ 640 (1158)
Q Consensus 561 ~f~a~l~~~~~~k~~~~~i~d~~~Ae~i~~~l~~~~~~V~~v~~k~~~~~PP~Pf~tstLQ~~AskklG~Sa~~Tm~iAQ 640 (1158)
.|.++|. ..+|.++++|+.+++.+. ..++|.+|+.++++++||+||||++||++|++ |||||++||++||
T Consensus 232 ~~~a~~~--------~~r~~d~~~A~~i~~~~~-~~~~V~~v~~k~~~~~pP~Pf~ts~LQ~~ask-lg~Sa~kTm~iAQ 301 (936)
T PRK14973 232 GIEARHT--------HGRFTDSAAAEAAYDATK-EPLVVTEVKEGHKVDRAPTPFDTTTFIVAASR-LGFSAANAMRIAE 301 (936)
T ss_pred eEEEEEc--------CCCCCCHHHHHHHHHHcC-CCeEEEEEEeeeEeccCCCCccHHHHHHHHHH-cCCCHHHHHHHHH
Confidence 6777763 236889999999998885 67999999999999999999999999999875 9999999999999
Q ss_pred HHhccccCCCCCeeEEEEEecCCCcCCCHHH-HHHHHHHH-HHHhCCC--CCCCCCCCccccccccccccCCCCCCCccc
Q 001100 641 KLYEGVQLPDGTAAGLITYMRTDGLHISDEA-AKEIRSLI-FERYGSH--HAPEEGPRKYFKKVKNAQEAHEAIRPTDIR 716 (1158)
Q Consensus 641 ~LYE~~k~~~g~~~GlITYPRTDS~~Ls~~~-~~~i~~~i-~~~~g~~--~~~~~~~r~~~~k~k~~qeAH~AI~PT~~~ 716 (1158)
+|||. ||||||||||++||+++ +..+...+ ...|+.. +.. ...+.+..+.+++++||||||||+..
T Consensus 302 ~LYE~---------glITYPRTDS~~l~~~~~~~~il~~l~~~~~~~~~~~l~-~~~~~~~~~~kk~~~aH~AI~PT~~~ 371 (936)
T PRK14973 302 DLYMN---------GYISYPRTDNTIYPKSLDLNGVLATLAKGAFSKDVAWVK-DNRRPVPTRGKKSSTDHPPIHPTGVA 371 (936)
T ss_pred HHHhC---------CeeeccCcccccCchhhhHHHHHHHHHHhhhHHHHHHHh-hcCCccCCCCCCCcCCcCCccCcCCc
Confidence 99995 89999999999999984 44444322 2233332 222 12233333334568899999999864
Q ss_pred CChhhhhCCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEEEEEecCccEEEEEEeEEEEEcCceeeccccchhhhccccc
Q 001100 717 RLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYKEN 796 (1158)
Q Consensus 717 ~~P~~l~~~Ls~dE~kLY~LI~rRfLAs~~~~a~~e~t~v~i~~~~~~~~F~asg~~i~~~Gw~~vy~~~~~~~~~~~e~ 796 (1158)
+. ..|+++|++||+||||||||+||+||+|++|+|.+.+++ ..|+++|++++++||++||++.+ +
T Consensus 372 --~~---~~Ls~de~klY~LI~rRfLA~~~~~a~~~~t~v~~~~~~--~~F~a~G~~i~~~Gw~~vy~~~~-------~- 436 (936)
T PRK14973 372 --TR---EELGDDRWKLYELVVRRFLATLSPDAEWATMKVNFDAGG--EPYTATGGRLLEAGWRTVYPYSE-------A- 436 (936)
T ss_pred --Ch---hhCCHHHHHHHHHHHHHHHHHhChhheEEEEEEEEEECC--EEEEEEEEEEeecCeeEeecccc-------c-
Confidence 21 359999999999999999999999999999999998864 47999999999999999996431 0
Q ss_pred cchhhhhhHHhcCCCCCCCeeEeeeEEEeccccCCCCCCCHhHHHHHHHhcCCCCCcchHHHHHHhhccceEEEcCcccc
Q 001100 797 EENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKSRILY 876 (1158)
Q Consensus 797 ~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk~GIGTpATrAsIIe~L~~R~YV~~k~k~L~ 876 (1158)
++ ..||.|++||.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++|+||+ ++.|+
T Consensus 437 ~~-------~~LP~l~~Ge~~~~~~~~~~e~~T~PP~ryTEatLik~ME~~GIGTpATrA~II~~L~~R~Yve--~k~l~ 507 (936)
T PRK14973 437 KE-------NILPAFALGEKLPILAVNLEEKETQPPARYSQSRLIQRMEELGLGTKSTRHEVIGKLVSRKYIE--GNPLR 507 (936)
T ss_pred cc-------ccCCCccCCCEEEeeeeEEeecCCCCCCCCCHHHHHHHhccCCCCCcccHHHHHHHHHHccCee--CCcee
Confidence 10 3599999999999999999999999999999999999999999999999999999999999994 77899
Q ss_pred cccccchhhhhhhcccccccChhhhHHHHHHhhhhhcCCchHHHHHHHHHHHhhhhhhhccchhHHHHHHHHHhhhcCcc
Q 001100 877 PEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKGLLVDYWSRFSSYCTCAQSLHIHQVEKMLEKTFGDSL 956 (1158)
Q Consensus 877 PT~lG~~v~~~L~~~f~~l~~p~~TA~~E~~Ld~Ia~Gk~~~~~~L~~F~~~f~~~i~~~~~~~i~~V~e~l~~~~g~~~ 956 (1158)
||++|+.|+++|+.+|++|++|+|||.||++|++|++|+.+|++||++|++.|...+..+... ...+.. .+....
T Consensus 508 pT~~G~~li~~L~~~~~~l~~p~lTA~~E~~Ld~I~~G~~~~~~~l~~~~~~~~~~~~~~~~~-~~~~~~----~~~~~~ 582 (936)
T PRK14973 508 PTLVGRAVTESLEEHAGTITEPDMTQTLEEHMQQIKERKRTRDDVVTESRKMLHRAFDELEAN-EAVIGR----DIMERT 582 (936)
T ss_pred EcHHHHHHHHHHHHhchhhcCHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHhhhh-HHhhhh----hhcccc
Confidence 999999999999999999999999999999999999999999999999999888766554210 011111 111000
Q ss_pred cCCCCCCCCCCCCCCCCeEEEEecccCceeEEecCCCCCCcccccCCCCCCchhhhhhhccCCCCCcccCCCCCccc--e
Q 001100 957 FASLPNKDRSCPVCGEGTLIFKVSRFGAGYFIGCNQHPRCNYIAKTLYGDDDEEDTLQRNTNVDEPKLIGHHPASKE--K 1034 (1158)
Q Consensus 957 ~~~~~~~~g~CPkCGkG~l~~k~gr~G~~~f~GCs~yP~C~~~~~~~~~e~~~~e~~~~~~~~~lPr~LG~cPkcG~--~ 1034 (1158)
......+.||.||+ .+.++.+++|. ||||++||.|+++.++...... .....-..||+||. .
T Consensus 583 --~~~~~~~~CP~CG~-~l~ik~~k~gk--FigCS~Yp~Ck~t~~L~~~~~g-----------~~~~~~~~Cp~CG~p~~ 646 (936)
T PRK14973 583 --AEELTIGPCPVCGK-DLRIKHIGSSQ--FIGCSGYPDCTFNIGLPGTTWG-----------WAIRTDEVCPIHHLNHV 646 (936)
T ss_pred --ccccccccCCcccc-cceeecccCce--eEECCCCCCCCccccCCccccc-----------cCCCCCCCCCCCCCCce
Confidence 00123578999996 56666666664 9999999999998766422110 00111136999997 6
Q ss_pred eeeccCCCcceEEe
Q 001100 1035 VLLKSGPYGFYVQL 1048 (1158)
Q Consensus 1035 v~lk~GrfG~yv~c 1048 (1158)
++++.||||.|++|
T Consensus 647 ~~~r~Gr~g~fl~C 660 (936)
T PRK14973 647 RLIRKGARPWDIGC 660 (936)
T ss_pred EEeecCCCcccccC
Confidence 77899999999999
No 13
>PRK08173 DNA topoisomerase III; Validated
Probab=100.00 E-value=5e-129 Score=1209.52 Aligned_cols=710 Identities=21% Similarity=0.295 Sum_probs=534.4
Q ss_pred CCCeEEEEecchHHHHHHhhcC-----------CCEEEEeeccccccccccCC------CCCCCC--CCcceEe--cCcc
Q 001100 348 SGKSVVVVESVTKAKVIQGYLG-----------DMYEVLPSYGHVRDLAARSG------SVRPDD--DFSMVWE--VPSA 406 (1158)
Q Consensus 348 ~~k~LIIvEkPskAk~Ia~~LG-----------~~y~V~~s~GHl~dL~~~~~------~v~p~~--~f~~~~~--v~~~ 406 (1158)
|+++||||||||+|++|+++|| ++|+|+|++|||++|+.|+. .|..++ .++..|. +...
T Consensus 1 Mm~~LiIAEKPs~Ak~Ia~~Lg~~~k~~gy~e~~~~~Vtwa~GHL~el~~Pe~Y~~~~~~W~~~~LPi~p~~f~~~~~~~ 80 (862)
T PRK08173 1 MSKALIIAEKPSVANDIARALGGFTKHDEYFESDEYVLSSAVGHLLEIAAPEEYEVKRGKWSFAHLPVIPPHFDLNPIAK 80 (862)
T ss_pred CCCEEEEEeCHHHHHHHHHHhCCCcCCCCeEeCCcEEEEeeccccccCCCchhcccccccccccccCCCCcccccccccc
Confidence 6788999999999999999997 57999999999999987642 343211 1222343 5566
Q ss_pred hHHHHHHHHHHhc--cCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhccccc--H
Q 001100 407 AWTHLKSIKVALS--GAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAAREID--A 482 (1158)
Q Consensus 407 ~~k~lk~Ik~l~k--~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fs~lT~~aI~~A~~nlr~~d--~ 482 (1158)
+++||++|++|++ ++|+||||||||||||+|+|+|+++++ +++||+|||||+||+++|++||+||++++ .
T Consensus 81 ~~~q~~~ik~l~k~~~~d~Ii~AtD~dREGElI~~~I~~~~~------~~kpv~Rlw~sslt~~aI~~a~~nl~~~~~~~ 154 (862)
T PRK08173 81 TESRLKVLTKLIKRKDVTRLINACDAGREGELIFRLIAQHAK------AKKPVKRLWLQSMTPQAIRDGFANLRSDEDMQ 154 (862)
T ss_pred HHHHHHHHHHHHhhCCCCEEEECCCCChhHHHHHHHHHHHhC------CCCCeEEEEEccCCHHHHHHHHhcCCCchhhH
Confidence 7899999999995 589999999999999999999999984 45799999999999999999999999997 6
Q ss_pred hHHHHHHHHHHHhhhhhhcccHHHHhhC---C--CcccCCcchhHHHHHHHHHHHHHHhcCCcceEEEEEEEecCcCCCC
Q 001100 483 NLVQAYLARRALDYLIGFNISPLLWRKL---P--GCQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSL 557 (1158)
Q Consensus 483 ~L~~A~~AR~~lD~LiG~nlSR~l~~k~---~--~~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~ 557 (1158)
+|++||+||+++|||||||+||++|... + +++|+||||||||+|||+||+||+||+|++||+|.+.+...
T Consensus 155 ~L~~aa~aR~~aDwlvG~N~TR~~T~~~~~~g~~~~lSvGRVQTPtL~lVv~Re~eI~~F~p~~y~~i~~~~~~~----- 229 (862)
T PRK08173 155 PLADAARCRSEADWLVGINGTRAMTAFNSKGGGFFLTTVGRVQTPTLSIVVEREEKIRRFVPRDYWEVRAEFVAA----- 229 (862)
T ss_pred HHHHHHHHHHHHHHHhhHHHhHHHHHhHhhcCCccccccccchhhHHHHHHHHHHHHHcCCCCccEEEEEEEecC-----
Confidence 9999999999999999999999998632 2 25899999999999999999999999999999999999642
Q ss_pred CCceeeeecccccc--ccc----cccCcCCHHHHHHHHHHHccCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHhcCCC
Q 001100 558 DTFSFPAHLTHFQS--KRL----NQLSIGSHTEAKDIEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFS 631 (1158)
Q Consensus 558 ~g~~f~a~l~~~~~--~k~----~~~~i~d~~~Ae~i~~~l~~~~~~V~~v~~k~~~~~PP~Pf~tstLQ~~AskklG~S 631 (1158)
+..|.++|..... ..+ +..+|.|+++|+++++.+.+..++|.+ +.+++++.||+||+|++||++||++||||
T Consensus 230 -~~~~~~~~~~~~~~~~~~~~~~~~~r~~d~~~A~~i~~~~~~~~~~V~~-~~k~~~~~pP~~f~Lt~LQ~~A~~~~g~s 307 (862)
T PRK08173 230 -AGFYEGRWFDPKFKKDEFDPEKRASRLWSEAAAEAIVAACRGKPGTVTE-ESKPSTQLSPLLFDLTSLQREANGRFGFS 307 (862)
T ss_pred -CccEEEEEeccccccccccccccccccCCHHHHHHHHHHhcCCCcEEEE-eeeEEecCCCCCCCHHHHHHHHHHhcCCC
Confidence 2357777742110 001 235789999999999999988899998 88999999999999999999999999999
Q ss_pred HHHHHHHHHHHhccccCCCCCeeEEEEEecCCCcCCCHHHHHHHHHHHHHHhC-CCCCC-------C---CCCCcccccc
Q 001100 632 ATYTMKLAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFERYG-SHHAP-------E---EGPRKYFKKV 700 (1158)
Q Consensus 632 a~~Tm~iAQ~LYE~~k~~~g~~~GlITYPRTDS~~Ls~~~~~~i~~~i~~~~g-~~~~~-------~---~~~r~~~~k~ 700 (1158)
|++||+|||+|||+| ||||||||||+|||++++++++.+|....+ ..|.. . ...++++++.
T Consensus 308 a~~tL~iaQ~LYE~~--------k~iTYPRTDs~~l~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~r~~~~~ 379 (862)
T PRK08173 308 AKNTLGLAQALYEKH--------KVLTYPRTDSRALPEDYLGTVKQTLEMLKESNNYLPHAKQILDKGWVKPNKRIFDNS 379 (862)
T ss_pred HHHHHHHHHHHHhcC--------CEEEecCCCCccCCHHHHHHHHHHHHHHhCCcccHHHHHHhhcccccCCCCCcCCCC
Confidence 999999999999964 699999999999999999999998876543 11210 0 0111222222
Q ss_pred ccccccCCCCCCCcccCChhhhhCCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEEEEEecCccEEEEEEeEEEEEcCce
Q 001100 701 KNAQEAHEAIRPTDIRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGNADESIVFRSSCSRVEFLGFQ 780 (1158)
Q Consensus 701 k~~qeAH~AI~PT~~~~~P~~l~~~Ls~dE~kLY~LI~rRfLAs~~~~a~~e~t~v~i~~~~~~~~F~asg~~i~~~Gw~ 780 (1158)
..+||||||||.. .|+ .|+++|++||+||||||||+||+||+|+.|+|.+.+++ +.|+++|++++++||+
T Consensus 380 --kv~dH~AIiPT~~--~~~----~Ls~~E~~iY~lI~rRfla~f~~~a~~~~t~v~~~v~~--~~F~a~G~~~~~~Gw~ 449 (862)
T PRK08173 380 --KISDHFAIIPTLQ--APK----SLSEPEQKLYDLVVKRFLAVFFPAAEFLVTTRITEVAG--HHFKTEGKVLVNPGWL 449 (862)
T ss_pred --CCCCCCCcCccCC--Ccc----cCCHHHHHHHHHHHHHHHHHhCchheEEEEEEEEEeCC--cEEEEEEEEEeeCChH
Confidence 1468999999985 243 49999999999999999999999999999999998864 4899999999999999
Q ss_pred eeccccchhhhccccccchhhhhhHHhcCCCCCCCeeEeeeEEEeccccCCCCCCCHhHHHHHHH---------------
Q 001100 781 AAYEDVDAGAIRYKENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSEGSLVKKLE--------------- 845 (1158)
Q Consensus 781 ~vy~~~~~~~~~~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~ME--------------- 845 (1158)
+||.... ++++ ..||.|++||.+.+.++.+.+++|+||+||||++||++||
T Consensus 450 ~vy~~~~-------~~~~-------~~LP~l~~Ge~~~~~~~~~~e~~TkPP~ryTEatLl~aMe~~gk~v~D~el~~~~ 515 (862)
T PRK08173 450 AVYGKEA-------QGAD-------ANLVPVQKGEKVKTDKIEAVALTTKPPARYNEATLLSAMEGAGKLVEDDELREAM 515 (862)
T ss_pred HHhCccc-------cccc-------ccCCCcCCCCEeeeeeeeecccccCCCCCcCHHHHHHHHHhhhhccccHHHHhhh
Confidence 9996421 0010 3599999999999999999999999999999999999999
Q ss_pred -hcCCCCCcchHHHHHHhhccceEEEcCcccccccccchhhhhhhc-ccccccChhhhHHHHHHhhhhhcCCchHHHHHH
Q 001100 846 -ELGIGRPSTYASTLKVLQDRNYVTVKSRILYPEFRGRMVSAFLSH-YFSEVTDYSFTADMETELDNVSAGLTEWKGLLV 923 (1158)
Q Consensus 846 -k~GIGTpATrAsIIe~L~~R~YV~~k~k~L~PT~lG~~v~~~L~~-~f~~l~~p~~TA~~E~~Ld~Ia~Gk~~~~~~L~ 923 (1158)
+.|||||||||+||++|++||||+++++.|+||++|+.|+++|+. .|+.|++|+|||.||..|++|++|+.++++||+
T Consensus 516 ~~~GIGTpATRA~IIe~L~~r~Yi~~~~k~l~pT~~G~~li~~l~~~~~~~l~~p~lTa~wE~~L~~I~~G~~~~~~f~~ 595 (862)
T PRK08173 516 AEKGLGTPATRAAIIEGLLGEKYLVREGRELIPTAKAFQLMTLLRGLGVEELTSPELTGEWEYKLSQIERGKLSRDAFMQ 595 (862)
T ss_pred hcCCCCchhhHHHHHHHHHhCCcEEecCCEechhHHHHHHHHHHhhcCcccccChhHHHHHHHHHHHHHcCCCCHHHHHH
Confidence 579999999999999999999999999999999999999999986 578899999999999999999999999999999
Q ss_pred HHHHHhhhhhhhccchhHHHHHHHHHhhhcCcccCCCCCCCCCCCCCCCCeEEEEecccCceeEEecCCCCCCcccccCC
Q 001100 924 DYWSRFSSYCTCAQSLHIHQVEKMLEKTFGDSLFASLPNKDRSCPVCGEGTLIFKVSRFGAGYFIGCNQHPRCNYIAKTL 1003 (1158)
Q Consensus 924 ~F~~~f~~~i~~~~~~~i~~V~e~l~~~~g~~~~~~~~~~~g~CPkCGkG~l~~k~gr~G~~~f~GCs~yP~C~~~~~~~ 1003 (1158)
+++..+...+..+. +.....+. .......+.||+||++ +. .. +.+|+|++ |.|..|..
T Consensus 596 ~i~~~~~~~v~~~~--------~~~~~~~~----~~~~~~~~~CP~Cg~~-~~-~~-----~~~~~Cs~---C~f~~~~~ 653 (862)
T PRK08173 596 EIAQMTQQIVKRAK--------EYDSDTIP----GDYATLQTPCPNCGGV-VK-EN-----YRRFACTK---CDFSISKI 653 (862)
T ss_pred HHHHHHHHHHHHHH--------hhhhcccc----cccccccccCCccccc-cc-cc-----CceeEcCC---CCcccchh
Confidence 98877665543321 10000000 0001124789999974 32 11 12589998 99877532
Q ss_pred C-CCCchhhhhhhc-cCCCCCcccCCCCCccceeeeccCCCcceEEeCCCCCCCCCcccccCCCCCccccCHHHHHHHhc
Q 001100 1004 Y-GDDDEEDTLQRN-TNVDEPKLIGHHPASKEKVLLKSGPYGFYVQLGEDRTGYLPKRASVSHIKDVDSITLEDALELLR 1081 (1158)
Q Consensus 1004 ~-~e~~~~e~~~~~-~~~~lPr~LG~cPkcG~~v~lk~GrfG~yv~c~~d~kg~kpK~~slpk~~~~~sItle~Al~ll~ 1081 (1158)
. +...+....... .......+.|+..+.|+ .|...+...++..+++-.+ .++...+... .+++.+.
T Consensus 654 ~~gk~~~~~~~~~Ll~~~~t~~~~gf~sk~g~-------~f~a~l~l~~~~~~~~~~f-~f~~~~~~~~---~~~~~~~- 721 (862)
T PRK08173 654 PGGRQFEIAEVEELLRKKEIGPLSGFRSKMGR-------PFSAILKLSDETKNYKLEF-DFGQDQGGED---GEPVDFS- 721 (862)
T ss_pred hccccCcHHHHHHHHhCCCcceeccccccCCC-------ccceEEEecccCCCceEEE-ecCCcccccc---ccccccc-
Confidence 2 222222111100 00111112233322221 2444444431101111111 1111000000 0111111
Q ss_pred CCcccCCCCCCCcCeEEeeccCcceeecC----C-eeeecCCCCCCCCCCHHHHHHHhhccc
Q 001100 1082 YPVNLGNHPKDGQPIMLRLARAGFSVRHR----R-TIASVPKNMKPNDVTLEKALEFLSGKD 1138 (1158)
Q Consensus 1082 ~pk~lG~cP~cG~~I~i~~GRyG~Yi~~~----~-~~~~lpk~~~~~~itle~A~~LL~~k~ 1138 (1158)
....+|.||.||+.|+. .++ +.+|..+ + |.+.+++......++.+++.+||..++
T Consensus 722 ~~~~~g~CPkCg~~v~e-~~k-~y~Cs~~~~~~~~C~f~i~k~i~gK~it~~~~kkLL~~Gk 781 (862)
T PRK08173 722 AQEPVGACPKCGGRVFE-HGM-SYVCEKSVGPPKTCDFRSGKVILQQEISREQMAKLLADGK 781 (862)
T ss_pred ccccccCCCCCCCeeEe-ece-EEEeCCCcCCCCCCCeeeCceecCccCCHHHHHHHHHcCC
Confidence 12246899999987764 333 3346653 3 445666655556789999999997554
No 14
>PRK14724 DNA topoisomerase III; Provisional
Probab=100.00 E-value=3.5e-128 Score=1213.48 Aligned_cols=723 Identities=22% Similarity=0.280 Sum_probs=534.1
Q ss_pred CeEEEEecchHHHHHHhhc---------------CCCEEEEeeccccccccccCC------CCCCCCCCc---ceE--ec
Q 001100 350 KSVVVVESVTKAKVIQGYL---------------GDMYEVLPSYGHVRDLAARSG------SVRPDDDFS---MVW--EV 403 (1158)
Q Consensus 350 k~LIIvEkPskAk~Ia~~L---------------G~~y~V~~s~GHl~dL~~~~~------~v~p~~~f~---~~~--~v 403 (1158)
+.||||||||+|++|+++| |++|+|+||+|||++|++|+. .|..+ +++ ..| .+
T Consensus 2 k~LiIAEKPSvAk~IA~aL~~~~g~~~k~~gy~eg~~~~Vtwa~GHL~eL~~Pe~y~~~~~~W~~~-~LPiiP~~f~~~~ 80 (987)
T PRK14724 2 KTLVIAEKPSVAQDIVRALTPVAGKFEKHDEHFESDSYVVTSAVGHLVEIQAPEEFDVKRGKWSFA-NLPVIPPYFDLKP 80 (987)
T ss_pred CEEEEEeCHHHHHHHHHHhhhccCCCcCCCceecCCCEEEEecccccccCCChhhcccccCCcccc-ccccCCccceeee
Confidence 6899999999999999999 457999999999999987643 23221 222 124 35
Q ss_pred CcchHHHHHHHHHHhc--cCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhccccc
Q 001100 404 PSAAWTHLKSIKVALS--GAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAAREID 481 (1158)
Q Consensus 404 ~~~~~k~lk~Ik~l~k--~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fs~lT~~aI~~A~~nlr~~d 481 (1158)
.+.+++||+.|++|++ ++|+||||||||||||+|+|||+++++... .+.++||+|||||+||+++|++||+||++++
T Consensus 81 ~~~~k~q~~~Ik~l~k~~~~~~II~AtD~DREGElI~~~I~~~~~~~~-~~~~kpv~Rlw~sslT~~aI~~af~nlr~~~ 159 (987)
T PRK14724 81 VDKTKTRLNAVVKLAKRKDVTELVNACDAGREGELIFRLIEQYAGGAK-GGLGKPVKRLWLQSMTPQAIRDGFDNLRSDA 159 (987)
T ss_pred ccchHHHHHHHHHHHhhCCCCeEEECCCCCcchhHHHHHHHHHhCccc-ccCCCceEEEEEccCCHHHHHHHHhCCCCch
Confidence 5677899999999995 567999999999999999999999985310 0124799999999999999999999999988
Q ss_pred --HhHHHHHHHHHHHhhhhhhcccHHHHhhC---CC--cccCCcchhHHHHHHHHHHHHHHhcCCcceEEEEEEEecCcC
Q 001100 482 --ANLVQAYLARRALDYLIGFNISPLLWRKL---PG--CQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKES 554 (1158)
Q Consensus 482 --~~L~~A~~AR~~lD~LiG~nlSR~l~~k~---~~--~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~ 554 (1158)
.+|++||+||+++|||||||+||++|... ++ ++|+||||||||+|||+||+||++|+|++||.|.+.+...
T Consensus 160 ~~~~L~~Aa~aR~~aDwLvG~N~SR~~T~~~~~~~~~~~lSvGRVQTPtL~lVv~Re~eI~~F~p~~Y~~i~a~~~~~-- 237 (987)
T PRK14724 160 QMQGLASAARSRSEADWLVGINGTRAMTAFNSRDGGFFLTTVGRVQTPTLSLVVEREEKIRKFVSRDYWEIHAGFHAE-- 237 (987)
T ss_pred hhhhHHHHHHHHHHHHHHhHHHHhHHHHHHHHhcCCcceeccccchhHHHHHHHHHHHHHHhCCCCccEEEEEEEecC--
Confidence 69999999999999999999999998632 22 4899999999999999999999999999999999999642
Q ss_pred CCCCCceeeeecccccccc------ccccCcCCHHHHHHHHHHHccCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHhc
Q 001100 555 HSLDTFSFPAHLTHFQSKR------LNQLSIGSHTEAKDIEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKL 628 (1158)
Q Consensus 555 ~~~~g~~f~a~l~~~~~~k------~~~~~i~d~~~Ae~i~~~l~~~~~~V~~v~~k~~~~~PP~Pf~tstLQ~~Askkl 628 (1158)
+..|.++|......+ ....+|.++++|+++++.+++..++|.+ +.+++++.||+||+|++||++||++|
T Consensus 238 ----~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~A~~i~~~~~~~~~~V~~-~~k~~~~~pP~pf~Lt~LQ~eA~~~~ 312 (987)
T PRK14724 238 ----AGEYLGKWFDPQWKKASDDPEARADRVWSEREARAIADAVRGKAATVTE-ESKPTTQASPLLFDLTSLQREANGKF 312 (987)
T ss_pred ----CCceeEEEeecccccccccccccccccCCHHHHHHHHHHhcCCCeEEEE-eeeeEecCCCCCCcHHHHHHHHHHHc
Confidence 235777663211111 1235789999999999999888899998 89999999999999999999999999
Q ss_pred CCCHHHHHHHHHHHhccccCCCCCeeEEEEEecCCCcCCCHHHHHHHHHHHHHHhC---------------CCCCCCCCC
Q 001100 629 NFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFERYG---------------SHHAPEEGP 693 (1158)
Q Consensus 629 G~Sa~~Tm~iAQ~LYE~~k~~~g~~~GlITYPRTDS~~Ls~~~~~~i~~~i~~~~g---------------~~~~~~~~~ 693 (1158)
||||++||+|||+|||+| ||||||||||+|||+++++.++.+|...-. ..+.. ...
T Consensus 313 g~Sa~~TL~iAQ~LYE~~--------klITYPRTDS~~l~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~~~~~~~-~~~ 383 (987)
T PRK14724 313 GFSAKTTLALAQSLYERH--------KALTYPRTDSRALPEDYLPVAKQTFEMLATSGMRHLAPFAQQALDGNYVR-PSK 383 (987)
T ss_pred CCCHHHHHHHHHHHHHcC--------CeEeecCcCCccCCHHHHHHHHHHHHHHhcccchhHHHHHHHHhcccccC-CCC
Confidence 999999999999999964 699999999999999998888887753211 11111 112
Q ss_pred CccccccccccccCCCCCCCcccCChhhhhCCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEEEEEecCccEEEEEEeEE
Q 001100 694 RKYFKKVKNAQEAHEAIRPTDIRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGNADESIVFRSSCSR 773 (1158)
Q Consensus 694 r~~~~k~k~~qeAH~AI~PT~~~~~P~~l~~~Ls~dE~kLY~LI~rRfLAs~~~~a~~e~t~v~i~~~~~~~~F~asg~~ 773 (1158)
+ +++..+ .+||||||||.. .| ..|+++|++||+||||||||+||+||+|+.|+|.+.+++ +.|+++|++
T Consensus 384 r-~~~~~K--v~~H~AIiPT~~--~p----~~Ls~~E~kiY~lI~rRfla~f~~~a~~~~t~v~~~~~~--~~F~a~G~~ 452 (987)
T PRK14724 384 R-IFDNSK--VSDHFAIIPTTQ--AP----SGLSEAEQKLYDLVVRRFMAVFFPSAEYQVTTRISQVVG--HSFKTEGKV 452 (987)
T ss_pred C-cCCCCC--CCCcCCcCCCCC--Cc----ccCCHHHHHHHHHHHHHHHHHhCchhEEEEEEEEEEecC--cEEEEEEEE
Confidence 2 222222 479999999985 34 359999999999999999999999999999999998864 489999999
Q ss_pred EEEcCceeeccccchhhhccccccchhhhhhHHhcCCCCCCCeeEeeeEEEeccccCCCCCCCHhHHHHHHH--------
Q 001100 774 VEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSEGSLVKKLE-------- 845 (1158)
Q Consensus 774 i~~~Gw~~vy~~~~~~~~~~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~ME-------- 845 (1158)
++++||++||...... +.++.+++ +....||.|++||.+.+.++.+.+++|+||+||||++||++||
T Consensus 453 i~~~GW~~vy~~~~~~---~~~~~~~~--~~~~~LP~l~~Ge~v~~~~~~~~e~~TkPP~ryTEatLl~aME~~gk~v~d 527 (987)
T PRK14724 453 LVKPGWLAIYGKEAAN---EVEDAKDG--DKGQPLVPVKPGEMVRTEFAEAKGLKTKPPARYSEATLLGAMESAGKQIDD 527 (987)
T ss_pred ECcCChHHHhCccccc---cccccccc--cccccCCCcCCCCEeeeeeccccccccCCCCCcCHHHHHHHHHhhhhcccc
Confidence 9999999999643110 00000000 0113599999999999999999999999999999999999999
Q ss_pred --------hcCCCCCcchHHHHHHhhccceEEEcCcccccccccchhhhhhhcc-cccccChhhhHHHHHHhhhhhcCCc
Q 001100 846 --------ELGIGRPSTYASTLKVLQDRNYVTVKSRILYPEFRGRMVSAFLSHY-FSEVTDYSFTADMETELDNVSAGLT 916 (1158)
Q Consensus 846 --------k~GIGTpATrAsIIe~L~~R~YV~~k~k~L~PT~lG~~v~~~L~~~-f~~l~~p~~TA~~E~~Ld~Ia~Gk~ 916 (1158)
+.|||||||||+||++|++|+||+++++.|+||++|+.|+++|+.. |+.|++|+|||+||..|++|++|+.
T Consensus 528 ~el~~~~~~~GIGTpATRA~IIe~L~~r~Yi~~~~k~l~pT~~G~~li~~L~~~~~~~l~~pelTa~wE~~L~~I~~G~~ 607 (987)
T PRK14724 528 DELREAMQEKGLGTPATRAAIIEGLLTEKYMLREGRELIPTAKAFQLMTLLRGLGVEELSRAELTGEWEYKLAQMEKGQL 607 (987)
T ss_pred hhhhhhhhcCCCCCcccHHHHHHHHHhCCcEEecCCEEeEcHHHHHHHHHHHhcCchhhcChhHHHHHHHHHHHHHhCCC
Confidence 5799999999999999999999999999999999999999999864 7789999999999999999999999
Q ss_pred hHHHHHHHHHHHhhhhhhhccchhHHHHHHHHHhhhcCcccCCCCCCCCCCCCCCCCeEEEEecccCceeEEecCCC---
Q 001100 917 EWKGLLVDYWSRFSSYCTCAQSLHIHQVEKMLEKTFGDSLFASLPNKDRSCPVCGEGTLIFKVSRFGAGYFIGCNQH--- 993 (1158)
Q Consensus 917 ~~~~~L~~F~~~f~~~i~~~~~~~i~~V~e~l~~~~g~~~~~~~~~~~g~CPkCGkG~l~~k~gr~G~~~f~GCs~y--- 993 (1158)
++++||+++++.+...+..+. +.....+. .......+.||+||++ +. . + +.+|+|+++
T Consensus 608 ~~~~fl~~i~~~~~~~v~~~~--------~~~~~~~~----~~~~~~~~~CP~Cg~~-~~-~--~---~~~~~Cs~~~~~ 668 (987)
T PRK14724 608 SREAFMQQIAAMTEKLVKKAK--------EYDRDTIP----GDYATLSTPCPNCGGV-VK-E--N---YRRYACTGANGA 668 (987)
T ss_pred CHHHHHHHHHHHHHHHHHHHH--------hccccccc----cccccccccCCccccc-cc-c--c---CceeecCCCcCC
Confidence 999999998887665544321 10000000 0001124789999974 32 1 1 126899994
Q ss_pred -CCCcccccCCC-CCCchhhhhhhc-cCCCCCcccCCCCCccceeeeccCCCcceEEeCCCC--CCCCCcccccCCCCCc
Q 001100 994 -PRCNYIAKTLY-GDDDEEDTLQRN-TNVDEPKLIGHHPASKEKVLLKSGPYGFYVQLGEDR--TGYLPKRASVSHIKDV 1068 (1158)
Q Consensus 994 -P~C~~~~~~~~-~e~~~~e~~~~~-~~~~lPr~LG~cPkcG~~v~lk~GrfG~yv~c~~d~--kg~kpK~~slpk~~~~ 1068 (1158)
+.|.|+.|... +...+....... .....+.+.|+..+.|+ .|-..+....|. .+++-.| .++..++-
T Consensus 669 ~~~C~f~~~k~~~gk~l~~~~~~~Ll~~g~t~~~~gf~sK~gk-------~f~A~l~l~~d~~~~~~k~~f-~f~~~~~~ 740 (987)
T PRK14724 669 GEGCGFSFTKSPAGRTFETAEAEQLLRDRRIGPLEGFRSKAGW-------PFTAEVVIKRDEEAKNYKLEF-DFGDDKNA 740 (987)
T ss_pred CCCCCcccchhhccccCcHHHHHHHHhCCCcceeccccccCCC-------ccCcEEEecccccccCceEEE-ecCCcccc
Confidence 47999875322 222222222100 00111112233222221 355555554221 1111111 11211000
Q ss_pred cccCHHHHHHHhcCCcccCCCCCCCcCeEEeeccCcceeecC---------CeeeecCCCCCCCCCCHHHHHHHhhccc
Q 001100 1069 DSITLEDALELLRYPVNLGNHPKDGQPIMLRLARAGFSVRHR---------RTIASVPKNMKPNDVTLEKALEFLSGKD 1138 (1158)
Q Consensus 1069 ~sItle~Al~ll~~pk~lG~cP~cG~~I~i~~GRyG~Yi~~~---------~~~~~lpk~~~~~~itle~A~~LL~~k~ 1138 (1158)
.. -.+++... ....+|.||.||+.|+. .|+ +..|..+ .|.+.+++.+....++.+++.+||...+
T Consensus 741 ~~--~~~~~~~~-~~~~~g~CPkCg~~v~e-~gk-~y~Cs~~~~~~~~~~~~C~f~i~k~i~gK~is~~~~~kLl~~Gk 814 (987)
T PRK14724 741 ED--TGEIVDFA-GQESLGPCPKCGAPVFE-HGS-NYVCEKSVPTLAQPTPSCTFKSGQVILQQPIEREQMQKLLATGK 814 (987)
T ss_pred cc--cccccccc-ccccccCCCCCCCceEe-ecc-eEEcCCCcccccCCCCCCCceecccccCcCCCHHHHHHHHhcCC
Confidence 00 00011111 12357899999988764 333 2235543 2345666665556689999999997654
No 15
>PRK07726 DNA topoisomerase III; Provisional
Probab=100.00 E-value=2.3e-126 Score=1164.68 Aligned_cols=586 Identities=27% Similarity=0.380 Sum_probs=488.6
Q ss_pred CeEEEEecchHHHHHHhhc-----------CCCEEEEeeccccccccccCC------CCCCCCCCc-----ceEecCcch
Q 001100 350 KSVVVVESVTKAKVIQGYL-----------GDMYEVLPSYGHVRDLAARSG------SVRPDDDFS-----MVWEVPSAA 407 (1158)
Q Consensus 350 k~LIIvEkPskAk~Ia~~L-----------G~~y~V~~s~GHl~dL~~~~~------~v~p~~~f~-----~~~~v~~~~ 407 (1158)
|+|||||||++|++|+++| |++|+|+||+|||++|++|+. .|..+ +++ +.|.+.+++
T Consensus 1 ~~LiIaEKPs~Ak~Ia~~L~~~~~~~g~~~g~~~~Vt~~~GHl~~L~~p~~y~~~~~~W~~~-~lpi~p~~~~~~~~~~~ 79 (658)
T PRK07726 1 MRLFIAEKPSVGRDIADVLKPHKKGDGYIEGNGYIVTWAIGHLLELAEPEAYDERYKRWRLE-DLPIIPEKWKLVVKKKT 79 (658)
T ss_pred CeEEEEeCHHHHHHHHHHhCCccCCCCeEeCCCEEEEechhhhccCCCchhcccccCccccc-cCCCCcccceeeeccch
Confidence 5899999999999999999 678999999999999987642 12211 111 135566678
Q ss_pred HHHHHHHHHHhccCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhcccc--cHhHH
Q 001100 408 WTHLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAAREI--DANLV 485 (1158)
Q Consensus 408 ~k~lk~Ik~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fs~lT~~aI~~A~~nlr~~--d~~L~ 485 (1158)
++|++.|++|+++||+||||||||||||+|||||+++++ ++++|+|+|||+||+++|++||+||+++ +++|+
T Consensus 80 ~~~~~~ik~l~~~~d~Ii~AtD~DREGE~I~~~i~~~~~------~~~~v~Rl~~sslt~~~I~~A~~nl~~~~~~~~l~ 153 (658)
T PRK07726 80 AKQFNVVKKLLKQATEIVIATDADREGELIAREILDYCG------VRKPIKRLWISSLTDKAIKRAFANLKPGKETIPLY 153 (658)
T ss_pred HHHHHHHHHHHhhCCeEEEcCCCCccccHHHHHHHHHhC------CCCCeEEEEEccCCHHHHHHHHHhcCCchhhHHHH
Confidence 899999999999999999999999999999999999985 3579999999999999999999999997 47999
Q ss_pred HHHHHHHHHhhhhhhcccHHHHhh-----CCCcccCCcchhHHHHHHHHHHHHHHhcCCcceEEEEEEEecCcCCCCCCc
Q 001100 486 QAYLARRALDYLIGFNISPLLWRK-----LPGCQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDTF 560 (1158)
Q Consensus 486 ~A~~AR~~lD~LiG~nlSR~l~~k-----~~~~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~g~ 560 (1158)
+||+||+++|||||||+||++|.. +++++|+||||||||+|||+||+||+||+|++||.|.+.+ .. +.
T Consensus 154 ~aa~aR~~~D~liG~nlSr~~t~~~~~~g~~~~lS~GRVQTPtL~lVv~Re~eI~~F~p~~y~~i~~~~-~~------~~ 226 (658)
T PRK07726 154 YSALARSRADWLVGINMTRAYTLLGRKAGYNGVLSVGRVQTPTLALVVRRDEEIENFVPKPYWEVEAHL-TP------GE 226 (658)
T ss_pred HHHHHHHHHHHHhhhhHhHHHHHHHhhcCCCcceeecccccchhHHHHHHHHHHHcCCCcccEEEEEEE-cC------CC
Confidence 999999999999999999999986 5568999999999999999999999999999999999988 31 33
Q ss_pred eeeeeccccccccccccCcCCHHHHHHHHHHHccCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHhcCCCHHHHHHHHH
Q 001100 561 SFPAHLTHFQSKRLNQLSIGSHTEAKDIEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKLAQ 640 (1158)
Q Consensus 561 ~f~a~l~~~~~~k~~~~~i~d~~~Ae~i~~~l~~~~~~V~~v~~k~~~~~PP~Pf~tstLQ~~AskklG~Sa~~Tm~iAQ 640 (1158)
.|.+.|........+..++.++++|+.+.+.+.+..++|.+|+.+++++.||+||+|++||++|+++|||||++||++||
T Consensus 227 ~~~~~~~~~~~~~~~~~r~~~~~~a~~~~~~~~~~~~~V~~v~~k~~~~~pP~pf~ls~Lq~~a~~~~g~s~~~tl~iaQ 306 (658)
T PRK07726 227 RFTAKWQPSEPYQDEEGRLLDRPLAEQVVARIQGQPAKVTEVETKRKKEYAPLLYDLSELQIDANKRFGLSAKETLDIAQ 306 (658)
T ss_pred eEEEEEeccccccccccccCCHHHHHHHHHHhcCCCeEEEEEEeeEEecCCCCCCCHHHHHHHHHHhcCCCHHHHHHHHH
Confidence 57777643211111235789999999999999888899999999999999999999999999999999999999999999
Q ss_pred HHhccccCCCCCeeEEEEEecCCCcCCCHHHHHHHHHHHHHHh-CCCCCCC-----C--CCCccccccccccccCCCCCC
Q 001100 641 KLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFERY-GSHHAPE-----E--GPRKYFKKVKNAQEAHEAIRP 712 (1158)
Q Consensus 641 ~LYE~~k~~~g~~~GlITYPRTDS~~Ls~~~~~~i~~~i~~~~-g~~~~~~-----~--~~r~~~~k~k~~qeAH~AI~P 712 (1158)
+|||++ ||||||||||+|||++++++++.+|.... +..|... . ..+++++. ..++|||||||
T Consensus 307 ~LYE~~--------glITYPRTds~~ls~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~aH~AI~P 376 (658)
T PRK07726 307 SLYETH--------KLITYPRTDSRYLPEDMVATLPEVLNAISKVDPYLLLAPPVLDPSIRSRAWND--KKVTAHHAIIP 376 (658)
T ss_pred HHHHhc--------CEEEecCCCCccCCHHHHHHHHHHHHHHhccCcchhhhhhhhccccccCcCCC--CcCCCCCCcCc
Confidence 999952 79999999999999999999999997654 2334320 0 00111111 13689999999
Q ss_pred CcccCChhhhhCCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEEEEEecCccEEEEEEeEEEEEcCceeeccccchhhhc
Q 001100 713 TDIRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIR 792 (1158)
Q Consensus 713 T~~~~~P~~l~~~Ls~dE~kLY~LI~rRfLAs~~~~a~~e~t~v~i~~~~~~~~F~asg~~i~~~Gw~~vy~~~~~~~~~ 792 (1158)
|+.. |. + +.|+++|++||+||||||||+||+||+|++++|.+.+++ ..|.++|++++++||+.+|+..+.
T Consensus 377 T~~~--~~-~-~~L~~~e~~iY~lI~~r~la~~~~~~~~~~t~v~~~~~~--~~F~~~g~~i~~~Gw~~v~~~~~~---- 446 (658)
T PRK07726 377 TEQP--PN-L-SKLSEDERKVYDLIARRYLAQFLPPAEYDKTTIELEIAG--GTFIAKGKQVVEAGWKALLGKKEE---- 446 (658)
T ss_pred cCCC--CC-c-ccCCHHHHHHHHHHHHHHHHHhCchhEEEEEEEEEEECC--EEEEEEEEEEccCCHHHHcccccc----
Confidence 9864 22 1 359999999999999999999999999999999998864 479999999999999999964311
Q ss_pred cccccchhhhhhHHhcCCCCCCCeeEeeeEEEeccccCCCCCCCHhHHHHHHHhc-----------------CCCCCcch
Q 001100 793 YKENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSEGSLVKKLEEL-----------------GIGRPSTY 855 (1158)
Q Consensus 793 ~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk~-----------------GIGTpATr 855 (1158)
+ +++ ...||.|++||.+.+.++.+.+++|+||+||||++||++||+. ||||||||
T Consensus 447 --~-~~~-----~~~lp~l~~g~~~~~~~~~~~e~~TkPP~~yTe~tLi~~Me~~~k~v~d~~~~~~l~e~~GIGTpATr 518 (658)
T PRK07726 447 --D-EEK-----EQPLPVLAKGDELKVEKGEVKEGQTQPPKRFTEGTLLSAMENIARFVQDKELKKTLKETDGLGTEATR 518 (658)
T ss_pred --c-ccc-----cccCCCcCCCCEeeecccccccccCCCCCCcCHHHHHHHHHhhhhhccCHHHHHhhcccCCCCccccH
Confidence 1 110 1359999999999999999999999999999999999999875 99999999
Q ss_pred HHHHHHhhccceEEEcCcccccccccchhhhhhhcccccccChhhhHHHHHHhhhhhcCCchHHHHHHHHHHHhhhhhhh
Q 001100 856 ASTLKVLQDRNYVTVKSRILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKGLLVDYWSRFSSYCTC 935 (1158)
Q Consensus 856 AsIIe~L~~R~YV~~k~k~L~PT~lG~~v~~~L~~~f~~l~~p~~TA~~E~~Ld~Ia~Gk~~~~~~L~~F~~~f~~~i~~ 935 (1158)
|+||++|++||||.++++.|+||++|+.|+++|+. .|++|+|||.||.+|++|++|+.++++||+.+++.+...+..
T Consensus 519 a~iIe~L~~R~Yi~~~~k~l~pT~~G~~li~~l~~---~l~~p~~Ta~~E~~L~~I~~G~~~~~~fl~~~~~~~~~~v~~ 595 (658)
T PRK07726 519 AGIIEKLFKRGYLEKKGKYIHATDKGKQLIDALPE---ELTSPDMTAKWEQALDQISEGQLSYQDFMQPLKQWLKQLVEQ 595 (658)
T ss_pred HHHHHHHHhCCCEEecCCEEEECHHHHHHHHHHHH---HcCChhhHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999986 389999999999999999999999999999999877665443
Q ss_pred ccchhHHHHHHHHHhhhcCcccCCCCCCCCCCCCCCCCeEEEEecccCceeEEecCCCCCCc
Q 001100 936 AQSLHIHQVEKMLEKTFGDSLFASLPNKDRSCPVCGEGTLIFKVSRFGAGYFIGCNQHPRCN 997 (1158)
Q Consensus 936 ~~~~~i~~V~e~l~~~~g~~~~~~~~~~~g~CPkCGkG~l~~k~gr~G~~~f~GCs~yP~C~ 997 (1158)
+. ..... .. . .....+.||.||++ ++.+.+++|. ||||++++.|.
T Consensus 596 ~~--------~~~~~-~~---~--~~~~~~~CP~C~~~-~~~~~~~~~~--f~~Cs~~~~~~ 640 (658)
T PRK07726 596 AK--------QSSEK-YK---F--DNLTGPKCPDCGKP-MLKVKGKNGK--MLVCQDRECGK 640 (658)
T ss_pred HH--------hcccc-cc---c--ccCCcccccccCcc-ceeecccCCe--eEecCCCcccc
Confidence 21 10000 00 0 01135789999975 4444556654 99999976443
No 16
>TIGR01057 topA_arch DNA topoisomerase I, archaeal. This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent.
Probab=100.00 E-value=3.2e-123 Score=1131.83 Aligned_cols=577 Identities=29% Similarity=0.420 Sum_probs=473.8
Q ss_pred EEecchHHHHHHhhcCC---------------------CEEEEeeccccccccccCC-CCCCCC-CCcceEecC---cch
Q 001100 354 VVESVTKAKVIQGYLGD---------------------MYEVLPSYGHVRDLAARSG-SVRPDD-DFSMVWEVP---SAA 407 (1158)
Q Consensus 354 IvEkPskAk~Ia~~LG~---------------------~y~V~~s~GHl~dL~~~~~-~v~p~~-~f~~~~~v~---~~~ 407 (1158)
||||||+|++|+++||. +|+|+|++|||++|++|+. .+...+ ++-|.+... ..+
T Consensus 1 iAEKPs~A~~ia~~l~~~~~~~~~~~g~~y~~~~~~g~~~~Vt~~~GHl~~l~~p~~~~~~~w~~~~lP~~~~~~~~~~~ 80 (618)
T TIGR01057 1 IAEKPKVAAKIAGALSDGRVLKKSEYGVPYWEVRRDGKKIIVASAVGHLFGLHPKSRGGYPVFDIEWVPIFEFDKGKGYV 80 (618)
T ss_pred CCCChHHHHHHHHHhCCCCcccccCCCceEEEEecCCCeEEEEEeccccccCCCccccCCCCCCcccCceeeecCCcccH
Confidence 79999999999999843 2579999999999987653 221110 122222221 123
Q ss_pred HHHHHHHHHHhccCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhcccccHhHHHH
Q 001100 408 WTHLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAAREIDANLVQA 487 (1158)
Q Consensus 408 ~k~lk~Ik~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fs~lT~~aI~~A~~nlr~~d~~L~~A 487 (1158)
++|++.|++++++||+||||||||||||+|||||+++++. .++|+|+|||+||+++|++||+|+++.+++|++|
T Consensus 81 ~~~~~~ik~l~~~~d~ii~AtD~DREGE~I~~~i~~~~~~------~~~v~Rl~~~~lt~~~I~~a~~nl~~~~~~l~~a 154 (618)
T TIGR01057 81 SKYIKALSKLAKGADEYINACDYDIEGEVIGFKALKYFCG------VERAKRMKFSTLTKQDIRRAYANPEEIDYGMVDA 154 (618)
T ss_pred HHHHHHHHHHHhcCCEEEECCCCCccHHHHHHHHHHHhcc------CCCceEEEEccCCHHHHHHHHhCcccCCHhHHHH
Confidence 6899999999999999999999999999999999999853 2589999999999999999999999999999999
Q ss_pred HHHHHHHhhhhhhcccHHHHhhCC------CcccCCcchhHHHHHHHHHHHHHHhcCCcceEEEEEEEecCcCCCCCCce
Q 001100 488 YLARRALDYLIGFNISPLLWRKLP------GCQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDTFS 561 (1158)
Q Consensus 488 ~~AR~~lD~LiG~nlSR~l~~k~~------~~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~g~~ 561 (1158)
|+||+++|||||||+||++|..++ +++|+||||||||+|||+||+||++|+|++||.|.+.+..+ +..
T Consensus 155 ~~aR~~~D~liG~n~Sr~~t~~~~~~~~~~~~lS~GRVQtPtL~lvv~Re~eI~~F~p~~y~~i~~~~~~~------~~~ 228 (618)
T TIGR01057 155 GMARHILDWYWGINLSRALMEAIRAAAGRWVILSAGRVQGPTLAFLVEREREINLFVPKPYWVIKATLEKG------GGV 228 (618)
T ss_pred HHHHHHHHHHHhhhhhHHHHHHhhccCCCcccccccccchhHHHHHHHhHHHHHcCcCCccEEEEEEEecC------Cce
Confidence 999999999999999999997543 25999999999999999999999999999999999998642 346
Q ss_pred eeeeccccccccccccCcCCHHHHHHHHHHHccC-CeEEEEeeeeeeeecCCCCcchHHHHHHHHHhcCCCHHHHHHHHH
Q 001100 562 FPAHLTHFQSKRLNQLSIGSHTEAKDIEQKINSA-NFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKLAQ 640 (1158)
Q Consensus 562 f~a~l~~~~~~k~~~~~i~d~~~Ae~i~~~l~~~-~~~V~~v~~k~~~~~PP~Pf~tstLQ~~AskklG~Sa~~Tm~iAQ 640 (1158)
|.+.|. ..+++++++|+.+.+.+++. .++|++|++++++..||+||+|++||++|+++|||||++||++||
T Consensus 229 ~~~~~~--------~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~iaQ 300 (618)
T TIGR01057 229 FDARPE--------KWKIWSEEEAKSIKEELKKSPWAAVEEVRSERSILKPPPPFDLGTLQREAYRIFGFSPKKTQSIAQ 300 (618)
T ss_pred EEEEEc--------cCCcCCHHHHHHHHHHHhCCCCeEEEEEEeeeeeccCCCCccHHHHHHHHHHhcCCCHHHHHHHHH
Confidence 777652 23688999999999999876 899999999999999999999999999999999999999999999
Q ss_pred HHhccccCCCCCeeEEEEEecCCCcCCCHHHHHHHHHHHHHH-----hCCCCCCC---CCCCccccccccccccCCCCCC
Q 001100 641 KLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFER-----YGSHHAPE---EGPRKYFKKVKNAQEAHEAIRP 712 (1158)
Q Consensus 641 ~LYE~~k~~~g~~~GlITYPRTDS~~Ls~~~~~~i~~~i~~~-----~g~~~~~~---~~~r~~~~k~k~~qeAH~AI~P 712 (1158)
+|||+ ||||||||||+|||+++. +..++... |+. +... ....+..+ .+..++|||||||
T Consensus 301 ~LYe~---------g~ISYPRTds~~l~~~~~--~~~~l~~l~~~~~~~~-~~~~~~~~~~~~~~~-~~~~~~aH~aI~P 367 (618)
T TIGR01057 301 ELYEE---------ALISYPRTSSQKLPPSIN--YRAILDNLAKGPLYRE-AAERLLETGVLKPVE-GKKEDPAHPAIHP 367 (618)
T ss_pred HHHhc---------CceeecCcccCccCHHHh--HHHHHHHHhcccchHH-HHHHhhcccccccCC-CCCCCCCCCCcCc
Confidence 99995 899999999999999862 33333221 111 1000 01111111 1223569999999
Q ss_pred CcccCChhhhhCCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEEEEEecCccEEEEEEeEEEEEcCceeeccccchhhhc
Q 001100 713 TDIRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIR 792 (1158)
Q Consensus 713 T~~~~~P~~l~~~Ls~dE~kLY~LI~rRfLAs~~~~a~~e~t~v~i~~~~~~~~F~asg~~i~~~Gw~~vy~~~~~~~~~ 792 (1158)
|... |+. .|+++|++||+|||+||||+||+||+|++|+|.+.+++ ..|.++|++++++||++||+..+
T Consensus 368 T~~~--~~~---~L~~~e~~iY~lI~~r~la~~~~~a~~~~t~v~~~~~~--~~F~~~g~~~~~~Gw~~v~~~~~----- 435 (618)
T TIGR01057 368 TGEI--PSQ---ELSKDEKKVYDLIVRRFLAAFSEEAIREKSKVLLRIGQ--EKFRLSGLRVVKLGWLEYYHYSK----- 435 (618)
T ss_pred cCCC--ccc---cCCHHHHHHHHHHHHHHHHHhChhhheeEEEEEEEECC--eEEEEEEEEEEeCCcceeccCcc-----
Confidence 9753 331 49999999999999999999999999999999998854 58999999999999999996421
Q ss_pred cccccchhhhhhHHhcCCCCCCCeeEeeeEEEeccccCCCCCCCHhHHHHHHHhcCCCCCcchHHHHHHhhccceEEEcC
Q 001100 793 YKENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKS 872 (1158)
Q Consensus 793 ~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk~GIGTpATrAsIIe~L~~R~YV~~k~ 872 (1158)
+ ++ ..||.+++||.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++|+||+.+
T Consensus 436 --~-~~-------~~lp~~~~gd~~~~~~~~~~e~~TkPP~~~Te~tLi~~Me~~GIGTpATra~iIe~L~~r~Yi~~~- 504 (618)
T TIGR01057 436 --F-EE-------KELPPLDRGDKIKVVRVDVRVKETQPPARYDKASLIREMESRGLGTKATRARIIETLYKRGYIEGK- 504 (618)
T ss_pred --c-cc-------ccCCCCCCCCEeeeeeeeecccccCCCCCCCHHHHHHHHHhCCCCCCCcHHHHHHHHHhCCcEeEC-
Confidence 0 10 359999999999999999999999999999999999999999999999999999999999999865
Q ss_pred cccccccccchhhhhhhcccccccChhhhHHHHHHhhhhhcCCchHHHHHHHHHHHhhhhhhhccchhHHHHHHHHHhhh
Q 001100 873 RILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKGLLVDYWSRFSSYCTCAQSLHIHQVEKMLEKTF 952 (1158)
Q Consensus 873 k~L~PT~lG~~v~~~L~~~f~~l~~p~~TA~~E~~Ld~Ia~Gk~~~~~~L~~F~~~f~~~i~~~~~~~i~~V~e~l~~~~ 952 (1158)
++|+||++|+.|+++|+..++.|++|+|||.||.+|++|++|+.++++||+++++.+...+..+... ...+...+...+
T Consensus 505 ~~l~pT~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L~~I~~G~~~~~~fl~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~ 583 (618)
T TIGR01057 505 KSIKVTPLGEAVIETLQRYCPEIISEELTRRFESKLEDIMSGRITKDEVIDEAKKRLRKILEEFKKR-LDDIGIELGKSL 583 (618)
T ss_pred CEEeeehHHHHHHHHHHHhchhhcChhhHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHH-HHHHhhhhhhhc
Confidence 5699999999999999998889999999999999999999999999999999999887766554221 111111111101
Q ss_pred cCcccCCCCCCCCCCCCCCCCeEEEEecccCceeEEecCCCCCC
Q 001100 953 GDSLFASLPNKDRSCPVCGEGTLIFKVSRFGAGYFIGCNQHPRC 996 (1158)
Q Consensus 953 g~~~~~~~~~~~g~CPkCGkG~l~~k~gr~G~~~f~GCs~yP~C 996 (1158)
. .....+.||+||++ ++.+.+++| .||||++||+|
T Consensus 584 ~------~~~~~~~CPkCg~~-l~~~~~k~g--~f~gCs~yp~C 618 (618)
T TIGR01057 584 G------SVEVVGKCPKCGGK-LVSKYAKKG--RFVGCSNYPEC 618 (618)
T ss_pred c------cccccCCCCcCCCe-eeeeecCCc--cEEECCCCCCC
Confidence 0 01234789999974 554545555 49999999998
No 17
>PTZ00407 DNA topoisomerase IA; Provisional
Probab=100.00 E-value=5.6e-120 Score=1101.30 Aligned_cols=572 Identities=28% Similarity=0.403 Sum_probs=469.2
Q ss_pred CeEEEEecchHHHHHHhhcCCC----------------------EEEEeeccccccccccCCC---------C-CCCC--
Q 001100 350 KSVVVVESVTKAKVIQGYLGDM----------------------YEVLPSYGHVRDLAARSGS---------V-RPDD-- 395 (1158)
Q Consensus 350 k~LIIvEkPskAk~Ia~~LG~~----------------------y~V~~s~GHl~dL~~~~~~---------v-~p~~-- 395 (1158)
..|||||||+|.-++.+.|.+. .+-.++-||++.|.+-.+. + .+++
T Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 89 (805)
T PTZ00407 10 EKLVIVESPNKVIKVEGLLSDPKVIPDWSFKQSHLRRIGTGAEKAVAMATTGHFMALKEITWSPQASSPASVVGAGDEPF 89 (805)
T ss_pred hheeEEecCCceEEEeecccCCCcCCCcccccccceeeccchHHHHHHhhcccceeehheecccCCCCCcccCCCCCCCC
Confidence 4699999999999999888641 2346788999998752110 0 0111
Q ss_pred -------CCcceEecCcchH--HHHH-HHHHHhccCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEccc
Q 001100 396 -------DFSMVWEVPSAAW--THLK-SIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEI 465 (1158)
Q Consensus 396 -------~f~~~~~v~~~~~--k~lk-~Ik~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fs~l 465 (1158)
.|.|.|++.++++ +++. .|++++++||+||||||||||||+|+|||+++|+... ...+++|+|+|||+|
T Consensus 90 ~~~~~~~~f~~~y~~~~~~~~~~~i~~~i~~~ak~ad~IIlATDpDREGE~Ia~hIle~l~~~~-~~~~k~v~Rv~FseI 168 (805)
T PTZ00407 90 PSNGTLAEYTLEWELLPGRRIQETLERYIEEKADNVTEIILATDPDREGELIAVHALQTIKRLY-PKLKVPFSRAYMHSI 168 (805)
T ss_pred CCCCceEEEEEEEEEcCCCchhHHHHHHHHHHHhcCCEEEECCCCCcchHHHHHHHHHHhchhc-cccCCcceEEEEccC
Confidence 3567899887765 6777 6999999999999999999999999999999997532 124578999999999
Q ss_pred CHHHHHHHHHh--cccccHhHHHHHHHHHHHhhhhhhcccHHHHhhCCCcccCCcchhHHHHHHHHHHHHHHhcCCc--c
Q 001100 466 TEASIKVALQA--AREIDANLVQAYLARRALDYLIGFNISPLLWRKLPGCQSAGRVQSAALSLICDREMEIDEFKPQ--E 541 (1158)
Q Consensus 466 T~~aI~~A~~n--lr~~d~~L~~A~~AR~~lD~LiG~nlSR~l~~k~~~~lS~GRVQTPtL~LVveRe~EI~~Fkp~--~ 541 (1158)
|+++|++||+| ++++|++|++||+|||++|||||||+||++|++.++.+|+||||||||+|||+||+||++|+|+ +
T Consensus 169 Tk~aI~~A~~nlkp~~~d~~L~~Aa~ARr~lD~LVG~nlS~~l~~~~~~~lSaGRVQTPtL~LIVeRE~EIe~Fkpee~~ 248 (805)
T PTZ00407 169 TEDGIRKAMRERHVEACDYDLANAAETRHAMDRIFGFLGSSVVRAANSQMRSIGRVQTPALILINEREDKIKAFLESNKS 248 (805)
T ss_pred CHHHHHHHHhCCCCCcccHhHHHHHHHHHHHHHHhhhhhhHHHHhhccCceeecccchHHHHHHHHHHHHHHhcCCccCc
Confidence 99999999999 5789999999999999999999999999999988888999999999999999999999999999 5
Q ss_pred eEEEEEEEecCcCCCCCCceeeeeccccccccccccCcCCHHHHHHHHHHHc--c-CCeEEE-EeeeeeeeecCCCCcch
Q 001100 542 YWTVEAVLDKKESHSLDTFSFPAHLTHFQSKRLNQLSIGSHTEAKDIEQKIN--S-ANFQVI-KNSKRSMVRKNPTPYIT 617 (1158)
Q Consensus 542 Yw~I~a~~~~~~~~~~~g~~f~a~l~~~~~~k~~~~~i~d~~~Ae~i~~~l~--~-~~~~V~-~v~~k~~~~~PP~Pf~t 617 (1158)
||.|.+.+... ...|..|.+.|....+.+.++.++.++++|+++++.++ + ..+.|. .++.++++++||+||+|
T Consensus 249 Yw~I~a~~~~~---~~~g~~F~a~~~~~~~~~~~~~~~~~~~eA~~~~~~~~~~~~~~~~V~~~v~~k~kk~~PP~PF~t 325 (805)
T PTZ00407 249 TFEVQAMCQFP---SPHGTTFSQVVTITPDRKGGASHWATEAEARRCLEQWKLNNCTGFSVPLEPKPQPSVVPPPQPFTM 325 (805)
T ss_pred eEEEEEEEeec---CCCCcceeEEeeccccccccccccCCHHHHHHHHHHhhhccCCcEEEEEEEEEEEEEcCCCCCccH
Confidence 99999887531 11245687776533332233456889999999988764 2 346664 45678999999999999
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHhccccCCCCCeeEEEEEecCCCcCCCHHHHHHHHHHHHHHhCCCCC---------
Q 001100 618 STLQQDAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFERYGSHHA--------- 688 (1158)
Q Consensus 618 stLQ~~AskklG~Sa~~Tm~iAQ~LYE~~k~~~g~~~GlITYPRTDS~~Ls~~~~~~i~~~i~~~~g~~~~--------- 688 (1158)
++||++||++|||||++||++||+|||+ ||||||||||++||++++.++++.|...||.+|.
T Consensus 326 stLQqeAsrkLG~Sa~kTM~iAQ~LYE~---------GlITYPRTDS~~l~~e~~~~i~~~I~~~~g~~~l~~~~~~~~~ 396 (805)
T PTZ00407 326 ATAIAKANRQLKYSSEMVSGCLQDLFQL---------GHITYPRTDSTRIDESALPDIYAAVKKEFGKEFLYRLEDRTVS 396 (805)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHcC---------CceeccCCCCCcCCHHHHHHHHHHHHHhhhhhhhhhhcccccc
Confidence 9999999999999999999999999995 8999999999999999999999999887887655
Q ss_pred -CCCCCCccc--------cc------cccccccCCCCCCCcccCChhhhhCCCCHHHHHHHHHHHHHHHHccCCCcEEEE
Q 001100 689 -PEEGPRKYF--------KK------VKNAQEAHEAIRPTDIRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQ 753 (1158)
Q Consensus 689 -~~~~~r~~~--------~k------~k~~qeAH~AI~PT~~~~~P~~l~~~Ls~dE~kLY~LI~rRfLAs~~~~a~~e~ 753 (1158)
+ ..++.+. .+ .++.|+||||||||+....|+.+ .|+++|++||+||||||||+||+||+|++
T Consensus 397 ~~-~~~~~~k~~k~~~~~~k~~~d~~~~kvqeAHeAIrPT~~~~~~~~~--~Ls~de~kLYdLI~rRfLAs~m~~a~~e~ 473 (805)
T PTZ00407 397 AQ-EGKGSKKTGKKRSTKQKKGADTPVGNVEDAHEAIRPTNIDTTGESL--SLSPPTRAVYDLVRRNTLAVFMIPMKTEK 473 (805)
T ss_pred cc-cccccccccccccccccccccccccCCCCCcCCCCccCCCCChhhc--cCCHHHHHHHHHHHHHHHHHhCchhEEEE
Confidence 2 1222111 01 12567899999999976555433 49999999999999999999999999999
Q ss_pred EEEEEEec---CccEEEEEEeEEEEEcCceeeccccchhhhc--cccccchh-hhhhHHhcCCCCCCC------------
Q 001100 754 IQVDIGNA---DESIVFRSSCSRVEFLGFQAAYEDVDAGAIR--YKENEEND-RHEAFAILNSLKTGD------------ 815 (1158)
Q Consensus 754 t~v~i~~~---~~~~~F~asg~~i~~~Gw~~vy~~~~~~~~~--~~e~~e~~-~~~~~~~LP~l~~Gd------------ 815 (1158)
++|++.+. ++...|+++|++++++||++||.+....... .+++++.. .++....||.|++||
T Consensus 474 t~v~i~~~~~~g~~~~F~asGk~v~~~Gw~~vy~~~~~~~~~~~~e~~e~~~~~~e~~~~LP~l~~Gd~~~~~~~~~~~g 553 (805)
T PTZ00407 474 IVATVKFTSGSGEKLEFELQGKRVVEPGWTRAFHKGDKGTTGPAEETDEDITAVEEGAPVVPSLSQEEFKAIMNLRSQLG 553 (805)
T ss_pred EEEEEEEeccCCCceEEEEEEEEEeeCCHHHHhcccccccccccccccccccccccccccCCcccCCccccccccccccc
Confidence 99888763 2346899999999999999999742110000 00000000 011113599999998
Q ss_pred ------eeEeeeEEEeccccCCCCCCCHhHHHHHHHhcCCCCCcchHHHHHHhhccceEEEc-Ccccccccccchhhhhh
Q 001100 816 ------PLYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVK-SRILYPEFRGRMVSAFL 888 (1158)
Q Consensus 816 ------~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk~GIGTpATrAsIIe~L~~R~YV~~k-~k~L~PT~lG~~v~~~L 888 (1158)
.+.+.++.+.+++|+||+|||||+||++||+.|||||||||+||++|++|+||.++ +++|+||++|+.|+++|
T Consensus 554 ~~~~q~~~~i~~~~l~ek~TkPPpryTEAtLIk~ME~~GIGTPATrAsIIetL~~R~YV~~~~kkrl~PT~lG~~Li~~L 633 (805)
T PTZ00407 554 SGVQKGFFELRSPQVRENRPVPPLPHSEGTLIEELKNNGVGRPSTYPMIVKTLLARGYIAVNPKGRCETTPVGRMLVETA 633 (805)
T ss_pred cccccceeecceeeeecccCCCCCCCCHHHHHHHHHhCCCCCcccHHHHHHHHHhcCCEEeccCceeeecHHHHHHHHHH
Confidence 35567889999999999999999999999999999999999999999999999998 88999999999999999
Q ss_pred hcccccccChhhhHHHHHHhhhhhcCCchHH-------------HHHHHHHHHhhhhhhhcc
Q 001100 889 SHYFSEVTDYSFTADMETELDNVSAGLTEWK-------------GLLVDYWSRFSSYCTCAQ 937 (1158)
Q Consensus 889 ~~~f~~l~~p~~TA~~E~~Ld~Ia~Gk~~~~-------------~~L~~F~~~f~~~i~~~~ 937 (1158)
+.+|++|++|+|||.||.+||+|++|+.+|+ .+|+.||..|..++.++.
T Consensus 634 ~~~fp~lv~p~~TA~~E~~Ld~Ia~G~~~~~~~~~~~~~~~~~~~vl~~F~~~F~~~v~~a~ 695 (805)
T PTZ00407 634 KSTFPSIVDIGFTAAFEKKLDRIAKPGPAKRPALLRPTNVSQADYVLSMFLSTFLNYVTEAT 695 (805)
T ss_pred HHhhhhhcChHHHHHHHHHHHHHHcCCcchhhhccccccchhHHHHHHHHHHHHHHHHhhhh
Confidence 9999999999999999999999999988887 689999999999887754
No 18
>PRK09401 reverse gyrase; Reviewed
Probab=100.00 E-value=8.6e-111 Score=1071.52 Aligned_cols=511 Identities=32% Similarity=0.444 Sum_probs=443.5
Q ss_pred CCCeEEEEecchHHHHHHhhcCCC----------E---------EEEeeccccccccccC--CCCCCCCC-CcceEecC-
Q 001100 348 SGKSVVVVESVTKAKVIQGYLGDM----------Y---------EVLPSYGHVRDLAARS--GSVRPDDD-FSMVWEVP- 404 (1158)
Q Consensus 348 ~~k~LIIvEkPskAk~Ia~~LG~~----------y---------~V~~s~GHl~dL~~~~--~~v~p~~~-f~~~~~v~- 404 (1158)
+.+.|||||||+|||+|+++||.. | +|+||.|||++|+.++ .+|..++. |.|.|.+.
T Consensus 600 ~k~~LiIaEkPskAk~IA~~lg~~~~r~~g~~~~ye~~~~~~~~~Vt~s~GHl~dL~~~~~y~g~~~~~~p~~P~y~~~k 679 (1176)
T PRK09401 600 IKTTLLIVESPTKARTIANFFGRPSRRRIGGLVVYETVTGDRILTITASKGHVYDLTTEIGYYGVLVKDGGFVPVYDTIK 679 (1176)
T ss_pred CCCEEEEEcCHHHHHHHHHHhCCCccccCCCceeEEEecCCcEEEEEEeccccccCCCccccCcccccCCcccceeeeec
Confidence 447999999999999999999753 3 6999999999999764 24544322 55555432
Q ss_pred ------------------------cchHHHHHHHHHHhccCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEE
Q 001100 405 ------------------------SAAWTHLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARV 460 (1158)
Q Consensus 405 ------------------------~~~~k~lk~Ik~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl 460 (1158)
++++++++.|++++++||+||||||||||||+|||||+++|+. .+++|+|+
T Consensus 680 ~c~~~g~~f~~~~~~~~~c~~~~~~~k~~~~~~Lr~l~~~~d~IiiAtDpDrEGE~Ia~~i~~~l~~-----~~~~i~R~ 754 (1176)
T PRK09401 680 RCRDCGYQFTDESDKCPRCGSTNIEDKEEIIEALRELALEVDEVLIATDPDTEGEKIAWDLYLLLSP-----YNSNIKRI 754 (1176)
T ss_pred cccccccccccccccccccccccCCCHHHHHHHHHHHHhcCCEEEEccCcChhHHHHHHHHHHHhcc-----cCCCEEEE
Confidence 5578999999999999999999999999999999999999863 34689999
Q ss_pred EEcccCHHHHHHHHHhcccccHhHHHHHHHHHHHhhhhhhcccHHHHhhCC-CcccCCcchhHHHHHHHHHHHHHHhcCC
Q 001100 461 VFHEITEASIKVALQAAREIDANLVQAYLARRALDYLIGFNISPLLWRKLP-GCQSAGRVQSAALSLICDREMEIDEFKP 539 (1158)
Q Consensus 461 ~fs~lT~~aI~~A~~nlr~~d~~L~~A~~AR~~lD~LiG~nlSR~l~~k~~-~~lS~GRVQTPtL~LVveRe~EI~~Fkp 539 (1158)
|||++|+++|++||+|++++|.||++||+|||++||+||||+||+||.+++ ..+|+||||||||+|||+||+||++|++
T Consensus 755 ~f~eiT~~aI~~A~~n~r~~~~~l~~A~~aRr~~D~~iG~~lSr~l~~~~~~~~lSaGRVQTPtL~~IVeRe~ei~~f~~ 834 (1176)
T PRK09401 755 EFHEVTRKAILEALRNPRDVNENLVKAQIVRRIEDRWIGFELSQKLQKKFGKRNLSAGRVQTPVLGWIVERYKEYKKSKG 834 (1176)
T ss_pred EeecCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccccccccchhhhhhhhHHHhcccCC
Confidence 999999999999999999999999999999999999999999999998875 4699999999999999999999999975
Q ss_pred cceEEEEEEEecCcCCCCCCceeeeeccccccccccccCcCCHHHHHHHHHHHccCCeEEEEeeeeeeeecCCCCcchHH
Q 001100 540 QEYWTVEAVLDKKESHSLDTFSFPAHLTHFQSKRLNQLSIGSHTEAKDIEQKINSANFQVIKNSKRSMVRKNPTPYITST 619 (1158)
Q Consensus 540 ~~Yw~I~a~~~~~~~~~~~g~~f~a~l~~~~~~k~~~~~i~d~~~Ae~i~~~l~~~~~~V~~v~~k~~~~~PP~Pf~tst 619 (1158)
||.+ .... ++..|.+.+ ++.++++|+++.+.++ +|.+++.++++++||+||+|++
T Consensus 835 --~~~~-~~~~-------~~~~~~~~~-----------~~~~~~~a~~~~~~l~----~V~~v~~k~~~~~pP~Pf~t~~ 889 (1176)
T PRK09401 835 --YVLV-IKLE-------NGGGLELEG-----------EFSEKEEAEKFYNNLI----EVEKVEEKEEELNPLPPYTTDT 889 (1176)
T ss_pred --EEEE-EEec-------CCceEEEEE-----------eeCCHHHHHHHHHhCC----eeeEEEeeEEEecCCCCCccHH
Confidence 5544 3332 123454332 4568889999888875 8899999999999999999999
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHHhccccCCCCCeeEEEEEecCCCcCCCHHHHHHHHHHHHHHhCCCCCCCCCCCccccc
Q 001100 620 LQQDAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFERYGSHHAPEEGPRKYFKK 699 (1158)
Q Consensus 620 LQ~~AskklG~Sa~~Tm~iAQ~LYE~~k~~~g~~~GlITYPRTDS~~Ls~~~~~~i~~~i~~~~g~~~~~~~~~r~~~~k 699 (1158)
||++||++|||||++||++||+|||. ||||||||||+|||++.+..++.++...++..+. .+|.|
T Consensus 890 Lq~~As~~lg~Sa~~tm~iAQ~LYE~---------glITYpRTDS~~ls~~~~~~a~~~l~~~~~~~~~---~~r~~--- 954 (1176)
T PRK09401 890 LLSDASRKLRLSAQETMRIAQDLFEL---------GLITYHRTDSTRVSDVGISVAKEYLEKRGGEEYF---VPRSW--- 954 (1176)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHhC---------CceeecCCCCCcCCHHHHHHHHHHHHHhhCcccc---CCCCC---
Confidence 99999999999999999999999995 9999999999999999999999999887775542 35555
Q ss_pred cccccccCCCCCCCcccCChhhh-----------hCCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEEEEEecCccEEEE
Q 001100 700 VKNAQEAHEAIRPTDIRRLPAML-----------SGLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGNADESIVFR 768 (1158)
Q Consensus 700 ~k~~qeAH~AI~PT~~~~~P~~l-----------~~~Ls~dE~kLY~LI~rRfLAs~~~~a~~e~t~v~i~~~~~~~~F~ 768 (1158)
++++||||||||.... ++++ ...|+++|++||+||||||||+||+||++++++|.+.+++ ..|.
T Consensus 955 --~~~~aH~AI~PT~~~~-~~~l~~~~~~g~~~~~~~Lt~~e~~lY~LI~rRflAs~~~~a~~~~t~v~~~~~~--~~f~ 1029 (1176)
T PRK09401 955 --GEGGAHEAIRPTRPLD-AEELRQMIEEGILKLSEGLTKNHLRLYDLIFRRFMASQMKPAKVRYQKVLIKADG--KELE 1029 (1176)
T ss_pred --CCCCCcCCcCccCCCC-chhhhhhhccccccccccCCHHHHHHHHHHHHHHHHHhCchhEEEEEEEEEEECC--EEEE
Confidence 2368999999998542 2222 2468999999999999999999999999999999998864 4799
Q ss_pred EE-eEEEEEcCceeeccccchhhhccccccchhhhhhHHhcCCCCCCCeeEeeeEEEeccccCCCCCCCHhHHHHHHHhc
Q 001100 769 SS-CSRVEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSEGSLVKKLEEL 847 (1158)
Q Consensus 769 as-g~~i~~~Gw~~vy~~~~~~~~~~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk~ 847 (1158)
++ |++++++||+++|+.. .+|.++.|+.+.+ +..++|.||+|||||+||++||+.
T Consensus 1030 ~~~g~~i~~~Gw~~v~~~~--------------------~~p~~~~g~~~~~----~~~~~~~pp~~yTea~Li~~Me~~ 1085 (1176)
T PRK09401 1030 LELVVEILEDGFNKVLPLK--------------------LYPLLEGKVKVKE----KKTYKKSKVPLYTQGDLISEMKER 1085 (1176)
T ss_pred EeeeeEEeeCChheeeccc--------------------cCCCCCCCCEeee----eccccCCCcCCCCHHHHHHHHHhC
Confidence 99 9999999999999541 3788999998874 556666679999999999999999
Q ss_pred CCCCCcchHHHHHHhhccceEEEcC--cccccccccchhhhhhhcccccccChhhhHHHHHHhhhhhcCCchHHHHHHHH
Q 001100 848 GIGRPSTYASTLKVLQDRNYVTVKS--RILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKGLLVDY 925 (1158)
Q Consensus 848 GIGTpATrAsIIe~L~~R~YV~~k~--k~L~PT~lG~~v~~~L~~~f~~l~~p~~TA~~E~~Ld~Ia~Gk~~~~~~L~~F 925 (1158)
|||||||||+||++|++||||..++ +.|+||++|+.|+++|...|+.|++|+|||+||+.||+|++|+.++++||+++
T Consensus 1086 GIGtpAT~A~IIe~L~~R~YV~~~~~~k~l~pT~~G~~l~~~L~~~~~~l~s~e~Ta~~E~~ld~Ie~G~~~~~~~l~~~ 1165 (1176)
T PRK09401 1086 GIGRPSTYAKIVETLLRRGYVIESKGKKRLIPTKLGIKVYEYLSEKYKDLVSEERTRKLEEKMDKVEEGKEDYQEVLKEL 1165 (1176)
T ss_pred CCCCcCcHHHHHHHHhccCcEEEcCCcceEeECHHHHHHHHHHHHhhhhcCCHHHHHHHHHHHHHHHCCCCCHHHHHHHH
Confidence 9999999999999999999998644 48999999999999999989999999999999999999999999999999999
Q ss_pred HHHhhhh
Q 001100 926 WSRFSSY 932 (1158)
Q Consensus 926 ~~~f~~~ 932 (1158)
+..+...
T Consensus 1166 ~~~i~~~ 1172 (1176)
T PRK09401 1166 YEEIKEL 1172 (1176)
T ss_pred HHHHHHH
Confidence 9876554
No 19
>TIGR01054 rgy reverse gyrase. Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.
Probab=100.00 E-value=8.5e-110 Score=1063.51 Aligned_cols=515 Identities=31% Similarity=0.468 Sum_probs=445.6
Q ss_pred CCCCCCeEEEEecchHHHHHHhhcCCC----------E---------EEEeeccccccccccC--CCCCCCCC-CcceEe
Q 001100 345 YPPSGKSVVVVESVTKAKVIQGYLGDM----------Y---------EVLPSYGHVRDLAARS--GSVRPDDD-FSMVWE 402 (1158)
Q Consensus 345 ~~~~~k~LIIvEkPskAk~Ia~~LG~~----------y---------~V~~s~GHl~dL~~~~--~~v~p~~~-f~~~~~ 402 (1158)
...+...|||||||+|||+|+++||.. | +|+||.|||+||+.+. .+|+.++. |.|.|.
T Consensus 597 ~~~~k~~LiIvEsP~kAk~Ia~~lg~~~~r~~~g~~~yE~~~g~~~~~Vtas~GHl~dL~~~~~~~g~~~~~~~f~P~y~ 676 (1171)
T TIGR01054 597 KDLVKTALLVVESPNKARTIARFFGKPSVRKIGGSVVYEVPVGDLILMITASGGHVFDLVTDKGFHGVLVENGRYVPVYT 676 (1171)
T ss_pred ccccCceEEEEcChHHHHHHHHHhCCCcccccCCcceEEEecCCeeEEEEEeCceeeeCCCccccCcccccCCccccccc
Confidence 455568999999999999999999863 4 6999999999998764 34544332 555432
Q ss_pred cC-------------------------cchHHHHHHHHHHhccCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccE
Q 001100 403 VP-------------------------SAAWTHLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITV 457 (1158)
Q Consensus 403 v~-------------------------~~~~k~lk~Ik~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~v 457 (1158)
.. ++++++++.|++++++||+||||||||||||+|||||+++|+. ++++|
T Consensus 677 ~~k~~~~~~~~f~~~~~~~p~~~~~~~~~k~~~~~~lr~l~~~~d~ViiATDpDrEGE~Ia~~i~~~l~~-----~~~~i 751 (1171)
T TIGR01054 677 SIKRCRDCGYQFTEDRESCPKCGSENIEDSKSIIEILRELAHEVDEVFIGTDPDTEGEKIGWDLALLLSP-----YNPNV 751 (1171)
T ss_pred ccccCCchhhhccccccccccccccccccHHHHHHHHHHHHhcCCEEEECCCCCccHHHHHHHHHHHhcc-----cCCCe
Confidence 11 4578999999999999999999999999999999999999853 35689
Q ss_pred EEEEEcccCHHHHHHHHHhcccccHhHHHHHHHHHHHhhhhhhcccHHHHhhCCC-cccCCcchhHHHHHHHHHHHHHHh
Q 001100 458 ARVVFHEITEASIKVALQAAREIDANLVQAYLARRALDYLIGFNISPLLWRKLPG-CQSAGRVQSAALSLICDREMEIDE 536 (1158)
Q Consensus 458 kRl~fs~lT~~aI~~A~~nlr~~d~~L~~A~~AR~~lD~LiG~nlSR~l~~k~~~-~lS~GRVQTPtL~LVveRe~EI~~ 536 (1158)
+|+|||++|+++|++||+|++++|++|++||+|||++|||||||+||++|.++++ .+|+||||||||+|||+||+||++
T Consensus 752 ~R~~f~eiT~~aI~~A~~n~r~~~~~L~~A~~aRr~~D~liG~~lSr~lt~~~~~~~lSaGRVQTPtL~lIVeRe~ei~~ 831 (1171)
T TIGR01054 752 KRAEFHEVTRRAILEALESPRSVDENLVKAQVVRRIEDRWIGFTLSQKLWEAFNKRWLSAGRVQTPVLGWIIDRYRESRE 831 (1171)
T ss_pred EEEEEccCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhhhhCHHHHHhhcCCCcccceecchhhHHHHHHHHHHhC
Confidence 9999999999999999999999999999999999999999999999999998764 599999999999999999999999
Q ss_pred cCCcceEEEEEEEecCcCCCCCCceeeeeccccccccccccCcCCHHHHHHHHHHHccCCeEEEEeeeeeeeecCCCCcc
Q 001100 537 FKPQEYWTVEAVLDKKESHSLDTFSFPAHLTHFQSKRLNQLSIGSHTEAKDIEQKINSANFQVIKNSKRSMVRKNPTPYI 616 (1158)
Q Consensus 537 Fkp~~Yw~I~a~~~~~~~~~~~g~~f~a~l~~~~~~k~~~~~i~d~~~Ae~i~~~l~~~~~~V~~v~~k~~~~~PP~Pf~ 616 (1158)
|+ +||.|.+... +..+.. .+.++++|+++.+.+. .+.|.+|+.++++++||+||+
T Consensus 832 ~~--~~~~i~~~~~--------~~~~~~-------------~~~~~~~a~~~~~~~~--~~~V~~v~~k~~~~~pP~Pf~ 886 (1171)
T TIGR01054 832 KR--GYLLIFALES--------DFRLGL-------------EHDNRLEAKEFEKDLT--WLDVEDIAEREEERNPLPPYT 886 (1171)
T ss_pred CC--ceEEEEEecC--------CeEEEE-------------EeCCHHHHHHHHHhCC--CcEEEEEEeeEEeccCCCCCC
Confidence 65 5998865331 112221 2346778888888773 588999999999999999999
Q ss_pred hHHHHHHHHHhcCCCHHHHHHHHHHHhccccCCCCCeeEEEEEecCCCcCCCHHHHHHHHHHHHHHhCCCCCCCCCCCcc
Q 001100 617 TSTLQQDAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFERYGSHHAPEEGPRKY 696 (1158)
Q Consensus 617 tstLQ~~AskklG~Sa~~Tm~iAQ~LYE~~k~~~g~~~GlITYPRTDS~~Ls~~~~~~i~~~i~~~~g~~~~~~~~~r~~ 696 (1158)
|++||++||++|||||++||++||+|||+ ||||||||||++||++.+..++++|...+|..|. .+|.|
T Consensus 887 t~~Lq~~As~~lg~sa~~tm~iAQ~LYE~---------GlITYpRTDS~~ls~~~~~~~~~~l~~~~~~~~~---~~r~~ 954 (1171)
T TIGR01054 887 TDTMLEDANRKLGLSVKETMQIAQELFEN---------GLITYHRTDSTRVSDVGMRVAKEYLASRLGGEYF---YPREW 954 (1171)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHhC---------CEEEecCCCCCcCCHHHHHHHHHHHHHHhccccc---CCCCC
Confidence 99999999999999999999999999995 9999999999999999999999999887876653 24544
Q ss_pred ccccccccccCCCCCCCcccCChhhhh----------CCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEEEEEecCccEE
Q 001100 697 FKKVKNAQEAHEAIRPTDIRRLPAMLS----------GLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGNADESIV 766 (1158)
Q Consensus 697 ~~k~k~~qeAH~AI~PT~~~~~P~~l~----------~~Ls~dE~kLY~LI~rRfLAs~~~~a~~e~t~v~i~~~~~~~~ 766 (1158)
++++||||||||... .|+.+. ..|+.+|++||+||||||||+||+||+|++++|.+.+++ ...
T Consensus 955 -----~~~~aHeAI~PT~~~-~~~~l~~~~~~g~~~~~~Ls~~e~~lY~LI~rRflAs~~~~a~~~~t~v~~~~~~-~~~ 1027 (1171)
T TIGR01054 955 -----GEGGAHECIRPTRPL-DVDDLQRLILEGVIELEGLTREHLRLYDLIFRRFMASQMRPAKVDTKEITLKADG-KEA 1027 (1171)
T ss_pred -----CCCCCcCCcCCcCCC-ChhhhhhhhcccccccccCCHHHHHHHHHHHHHHHHHhCchheEEEEEEEEEeCC-eeE
Confidence 236899999999863 343221 358999999999999999999999999999999998854 358
Q ss_pred EEEEeEEEEEcCceeeccccchhhhccccccchhhhhhHHhcCCCCCCCeeEeeeEEEeccccCCCCCCCHhHHHHHHHh
Q 001100 767 FRSSCSRVEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSEGSLVKKLEE 846 (1158)
Q Consensus 767 F~asg~~i~~~Gw~~vy~~~~~~~~~~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk 846 (1158)
|.++|++++++||+++|+... ++.+.+||.+.+.++.+.++. ||+||||++||++||+
T Consensus 1028 f~~~g~~i~~~Gw~~v~~~~~--------------------~~~~~~G~~~~~~~~~~~~~~--~~p~yTe~~Li~~Me~ 1085 (1171)
T TIGR01054 1028 EEEGIVEIVERGFELVYPLWR--------------------KNELEKGSTFIVKDKELRSVP--KVYPYTQGEIVQEMKE 1085 (1171)
T ss_pred EEEEEEEEeeCCHHHHcCccc--------------------cccccCCCEeeeecceeeecC--CCCCCCHHHHHHHHHh
Confidence 999999999999999996421 234678999988877777765 4559999999999999
Q ss_pred cCCCCCcchHHHHHHhhccceEEEcCcccccccccchhhhhhhcccccccChhhhHHHHHHhhhhhcCCchHHHHHHHHH
Q 001100 847 LGIGRPSTYASTLKVLQDRNYVTVKSRILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKGLLVDYW 926 (1158)
Q Consensus 847 ~GIGTpATrAsIIe~L~~R~YV~~k~k~L~PT~lG~~v~~~L~~~f~~l~~p~~TA~~E~~Ld~Ia~Gk~~~~~~L~~F~ 926 (1158)
.|||||||||+||++|++|+||..+++.|+||++|+.|+++|+..|+.|++|+|||.||+.||+|++|+.++++||++++
T Consensus 1086 ~GIGtpsT~A~II~~L~~R~YV~~~~k~l~pT~lG~~v~~~L~~~~~~l~~~~~Ta~~E~~Ld~Ie~G~~~~~~~l~~~~ 1165 (1171)
T TIGR01054 1086 RGIGRPSTYATIVEKLLRRGYVVESKGFLIPTKLGIEVYNYLTNRYPKLVSEDRTRELEEAMDKIERGELDYLEVLESVY 1165 (1171)
T ss_pred CCCCCcccHHHHHHHhhccCcEEeeCCEEeECHHHHHHHHHHHhhhhhcCCHhHHHHHHHHHHHHHcCCCCHHHHHHHHH
Confidence 99999999999999999999999888999999999999999999999999999999999999999999999999999998
Q ss_pred HHhh
Q 001100 927 SRFS 930 (1158)
Q Consensus 927 ~~f~ 930 (1158)
+.+.
T Consensus 1166 ~~i~ 1169 (1171)
T TIGR01054 1166 REIK 1169 (1171)
T ss_pred HHHh
Confidence 7653
No 20
>KOG1956 consensus DNA topoisomerase III alpha [Replication, recombination and repair]
Probab=100.00 E-value=4.4e-101 Score=882.79 Aligned_cols=692 Identities=31% Similarity=0.426 Sum_probs=548.6
Q ss_pred CeEEEEecchHHHHHHhhcCC---------------------------CEEEEeeccccccccccCC-----CCCCCCCC
Q 001100 350 KSVVVVESVTKAKVIQGYLGD---------------------------MYEVLPSYGHVRDLAARSG-----SVRPDDDF 397 (1158)
Q Consensus 350 k~LIIvEkPskAk~Ia~~LG~---------------------------~y~V~~s~GHl~dL~~~~~-----~v~p~~~f 397 (1158)
+.|.++||++.||.++.+|++ +.++++..||+..+..+.+ ...+.+.|
T Consensus 2 ~vl~vAekn~~ak~va~il~~g~~~~re~rSk~~kiy~f~~~~~g~~~~~~mtsvsghl~~~~f~~~~s~w~s~~~~~lf 81 (758)
T KOG1956|consen 2 RVLCVAEKNSIAKSVASILSGGTVRRREGRSKYNKIYDFDFNLFGQNCDVTMTSVSGHLTEADFPSEYSKWQSCPPDELF 81 (758)
T ss_pred CcccccccchhhhhhhhhcCCCCcCCccchhhhhhhhhhhhhhcCCcceeEEeeccccccccCCcccccceeecCHHHHh
Confidence 578999999999999999964 1367899999999977542 22333333
Q ss_pred cc-eE-ecCcchHHHHHHHHHHhccCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHH
Q 001100 398 SM-VW-EVPSAAWTHLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQ 475 (1158)
Q Consensus 398 ~~-~~-~v~~~~~k~lk~Ik~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fs~lT~~aI~~A~~ 475 (1158)
.. .+ .++...+.+.+.|++++++||.+|||||||||||+|||||.++|+.. +....|.|++||+||+.+|+.|++
T Consensus 82 ~a~~~~~~~~~~~~i~~~ir~eAr~ad~LviwtDcDREGE~Ig~eI~~v~~~~---~~~~~V~RA~Fs~it~~~I~sA~~ 158 (758)
T KOG1956|consen 82 DAPVIKSVPENAKDIAKTIREEARRADYLVIWTDCDREGENIGWEIIDVCRAV---KRLLQVRRARFSEITRSAIKSAAR 158 (758)
T ss_pred hhhhhhcCchhhhHHHHHHHHHHhhcceEEEeccCCccchhhhHHHHHHHHhh---CccceeehhhhhcccHHHHHHHHh
Confidence 32 11 24566788999999999999999999999999999999999999874 556679999999999999999999
Q ss_pred hcccccHhHHHHHHHHHHHhhhhhhcccHH----HHhhCC----CcccCCcchhHHHHHHHHHHHHHHhcCCcceEEEEE
Q 001100 476 AAREIDANLVQAYLARRALDYLIGFNISPL----LWRKLP----GCQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEA 547 (1158)
Q Consensus 476 nlr~~d~~L~~A~~AR~~lD~LiG~nlSR~----l~~k~~----~~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a 547 (1158)
||+++|+.+++|+.||+++|++||..|||+ ||++++ +++|+|+||.|||+|||||+.||++|+|+.||+|.+
T Consensus 159 nlreid~~~v~AvdaR~ELDlrIGa~FTRlqT~~L~r~f~~~~~~viSyG~cQfpTLgfVvdR~~eIe~FvPEefWtl~~ 238 (758)
T KOG1956|consen 159 NLREIDEKLVHAVDARIELDLRIGAAFTRLQTLLLRRKFPILGEQVISYGPCQFPTLGFVVDRYKEIENFVPEEFWTLKF 238 (758)
T ss_pred CccccchHHHHHHHHHHHHHHHhhhhHHHHHhHHHHhhhhhhhccccccccccCcceeeeeehHHHHhccCCcceEEEEE
Confidence 999999999999999999999999888876 467776 899999999999999999999999999999999998
Q ss_pred EEecCcCCCCCCceeeeeccccccccccccCcCCHHHHHHHHHHHc-cCCeEEEEeeeeeeeecCCCCcchHHHHHHHHH
Q 001100 548 VLDKKESHSLDTFSFPAHLTHFQSKRLNQLSIGSHTEAKDIEQKIN-SANFQVIKNSKRSMVRKNPTPYITSTLQQDAAN 626 (1158)
Q Consensus 548 ~~~~~~~~~~~g~~f~a~l~~~~~~k~~~~~i~d~~~Ae~i~~~l~-~~~~~V~~v~~k~~~~~PP~Pf~tstLQ~~Ask 626 (1158)
...... ...+| ++++ ..+.|..-+--+.+.|. ...+.|+++.+++++++||+||+|.+||+.|++
T Consensus 239 ~~~~~~----~~~~f-------nw~R---~~lfdr~s~~~~~e~c~e~k~a~Vv~~~kkpktKyrP~pl~TvELqK~~s~ 304 (758)
T KOG1956|consen 239 KHTHKG----GLTEF-------NWKR---GHLFDRLSVVILYEICVEEKEATVVKVTKKPKTKYRPLPLDTVELQKLASR 304 (758)
T ss_pred EEeccC----ceeEE-------eecc---cccccHHHHHHHHHHHhcccceeEEecccCCccCCCCCcchHHHHHhhhhh
Confidence 775321 11233 3322 23445554444555543 467899999999999999999999999999999
Q ss_pred hcCCCHHHHHHHHHHHhccccCCCCCeeEEEEEecCCCcCCCHHHHHHHHHHHHH-----HhCCCCCCC-CCCC-ccccc
Q 001100 627 KLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFE-----RYGSHHAPE-EGPR-KYFKK 699 (1158)
Q Consensus 627 klG~Sa~~Tm~iAQ~LYE~~k~~~g~~~GlITYPRTDS~~Ls~~~~~~i~~~i~~-----~~g~~~~~~-~~~r-~~~~k 699 (1158)
+|.||+++||+||++||.+ |+||||||+...++.++ .++.++.. .||. |+.. ..++ +..++
T Consensus 305 ~lrlSak~TM~iAE~ly~~---------gfisyprtetd~F~s~~--~lk~lv~~qt~~~~wg~-yA~~ll~~~~r~Prn 372 (758)
T KOG1956|consen 305 KLRLSAKHTMKIAEKLYQK---------GFISYPRTETDNFPSDM--DLKALVEKQTQDPAWGS-YAQRLLQPENRNPRN 372 (758)
T ss_pred heeccHHHHHHHHHHHHhc---------cceeccccccccCCCcC--chHHHHHhhccCchhHH-HHHHhhccCCCCCCC
Confidence 9999999999999999985 99999999999998864 33344432 2332 2210 1122 34556
Q ss_pred cccccccCCCCCCCcccCChhhhhCCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEEEEEecCccEEEEEEeEEEEEcCc
Q 001100 700 VKNAQEAHEAIRPTDIRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGNADESIVFRSSCSRVEFLGF 779 (1158)
Q Consensus 700 ~k~~qeAH~AI~PT~~~~~P~~l~~~Ls~dE~kLY~LI~rRfLAs~~~~a~~e~t~v~i~~~~~~~~F~asg~~i~~~Gw 779 (1158)
+++.+.||++|+||... .++ ..|+.|+++||++|+||||||.+.+|.-..|+|+++.+.+ .|.++|-.+++.+|
T Consensus 373 g~~~d~Ahppihp~k~~-s~~---~~~s~d~~~vye~v~rhflAc~S~dakg~et~vel~~~~E--~F~asgl~vl~~Ny 446 (758)
T KOG1956|consen 373 GKHNDKAHPPIHPTKFT-SRE---ANLSGDHRKVYELVVRHFLACCSQDAKGAETTVELDIAQE--RFSASGLRVLERNY 446 (758)
T ss_pred CccccccCCCccceeec-ccc---ccCCcchHHHHHHHHHHHHHhhcccccccceEEEEeehhh--hccccccchhhccc
Confidence 67778999999999753 222 3589999999999999999999999999999999998654 79999999999999
Q ss_pred eeeccccchhhhccccccchhhhhhHHhcCCCCCCCeeEeeeEEEeccccCCCCCCCHhHHHHHHHhcCCCCCcchHHHH
Q 001100 780 QAAYEDVDAGAIRYKENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTL 859 (1158)
Q Consensus 780 ~~vy~~~~~~~~~~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk~GIGTpATrAsII 859 (1158)
+.||+++.. + +..||.++.|+.+.+..+++.++.|+||++|||++||..|+++|||||||+|+||
T Consensus 447 ldVy~yekw--------------e-~k~Lp~y~~ge~fq~~~lem~~g~T~~P~~ltEaeLI~lMdk~GIGtdAT~aehi 511 (758)
T KOG1956|consen 447 LDVYPYEKW--------------E-DKQLPVYEDGELFQPGELEMKDGETSPPKYLTEAELISLMDKNGIGTDATIAEHI 511 (758)
T ss_pred ccccccccc--------------c-cccCcccccccccccceEEeccCccCCCCccCHHHHHHHHHHcCCCCchhHHHHH
Confidence 999988643 1 2579999999999999999999999999999999999999999999999999999
Q ss_pred HHhhccceEEEcCc--ccccccccchhhhhhhcccccccChhhhHHHHHHhhhhhcCCchHHHHHHHHHHHhhhhhhhcc
Q 001100 860 KVLQDRNYVTVKSR--ILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKGLLVDYWSRFSSYCTCAQ 937 (1158)
Q Consensus 860 e~L~~R~YV~~k~k--~L~PT~lG~~v~~~L~~~f~~l~~p~~TA~~E~~Ld~Ia~Gk~~~~~~L~~F~~~f~~~i~~~~ 937 (1158)
++|++|+||.++++ +|+||.+|.+|++.+.+++-++.+|+++|+||.+|++|+.|..+|.++|.+.+..|..++...+
T Consensus 512 ~kiq~R~Yv~~~~~~~~~~P~~lg~aLv~gyd~~g~e~sKp~lra~mE~~Lk~Is~G~~~k~~vl~~~v~kyra~f~~~~ 591 (758)
T KOG1956|consen 512 EKIQERGYVTKKNKVGRFVPTFLGVALVEGYDDMGLEMSKPFLRAEMEVDLKNISDGRKDKKEVLRDIVTKYRAYFHETE 591 (758)
T ss_pred HHHHhhcceeeeccccccCchHHHHHHHHhHHhhhhhcCChHHHHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHHHHH
Confidence 99999999998544 5779999999999999998899999999999999999999999999999999999998765543
Q ss_pred chhHHHHHHHHHhhhcCcccCCCCCCCCCCCCCCCCeEEEEecccCceeEEecCCCCCCcccccCCCCCCchhhhhhhcc
Q 001100 938 SLHIHQVEKMLEKTFGDSLFASLPNKDRSCPVCGEGTLIFKVSRFGAGYFIGCNQHPRCNYIAKTLYGDDDEEDTLQRNT 1017 (1158)
Q Consensus 938 ~~~i~~V~e~l~~~~g~~~~~~~~~~~g~CPkCGkG~l~~k~gr~G~~~f~GCs~yP~C~~~~~~~~~e~~~~e~~~~~~ 1017 (1158)
.. .....+.+...+... . ..... | -+ |.
T Consensus 592 ~~-~~~l~~~l~~y~~~~-a----~~~~~-~-------------~~----------p~---------------------- 619 (758)
T KOG1956|consen 592 RK-IGCLGESLQRYLEFI-A----STLTG-P-------------DD----------PE---------------------- 619 (758)
T ss_pred HH-HHHHHHHHHHHHhhc-c----ccccC-C-------------CC----------CC----------------------
Confidence 21 222222222111100 0 00000 0 00 00
Q ss_pred CCCCCcccCCCCCccceeeeccCCCcceEEeCCCCCCCCCcccccCCCCCccccCHHHHHHHhcCCcccCCCCCCCcCeE
Q 001100 1018 NVDEPKLIGHHPASKEKVLLKSGPYGFYVQLGEDRTGYLPKRASVSHIKDVDSITLEDALELLRYPVNLGNHPKDGQPIM 1097 (1158)
Q Consensus 1018 ~~~lPr~LG~cPkcG~~v~lk~GrfG~yv~c~~d~kg~kpK~~slpk~~~~~sItle~Al~ll~~pk~lG~cP~cG~~I~ 1097 (1158)
..|..+|-.+.++.++-.+-|.++.|.+.+.+.+|..|+.++-....+...+++..++.++..+...+ ||+-|.++.
T Consensus 620 --~~Pp~~~l~~s~~~~v~p~cgp~p~y~~~~~~~rg~ipp~~~~g~~~~~~~~t~~~~~~~l~~~~tn~-~p~~~~~~~ 696 (758)
T KOG1956|consen 620 --GEPPLLGLEGSTSEKVGPKCGPKPVYRQLGKFKRGGIPPAANAGHPKDANSITGRSALNLLRGSMTNG-HPKPGQPVV 696 (758)
T ss_pred --CCCCCCCCCCCCCCccCCCCCCCCcceeccccCCCCCCCCCCCCCccccccccchhhHHHhhcccccC-CCCCCcccc
Confidence 11222233333444444445678888888876666556666544556677799999999999999888 999998899
Q ss_pred EeeccCcceeecCCeeeecCCCCCCCCCCHHHHHHHhhccccccCCCCCCC
Q 001100 1098 LRLARAGFSVRHRRTIASVPKNMKPNDVTLEKALEFLSGKDVRRCGRPKGK 1148 (1158)
Q Consensus 1098 i~~GRyG~Yi~~~~~~~~lpk~~~~~~itle~A~~LL~~k~~k~~gr~~~~ 1148 (1158)
..-.+-|..+++.++....+++.... |...|..|+..+...++||++.+
T Consensus 697 ~~psk~~a~~~~~p~~a~~~~~~~c~--c~~ra~~l~v~k~~~nrGR~f~s 745 (758)
T KOG1956|consen 697 LKPSKSGATIKSRPTAATEEEEVTCG--CGTRAVKLLVAKTEPNRGRKFYS 745 (758)
T ss_pred CCcccccccccCCccccCCCcccccC--CcchhhhhhhhccCccCCCCCcc
Confidence 88899999999988888777775544 44489999988887777887764
No 21
>PRK14701 reverse gyrase; Provisional
Probab=100.00 E-value=3.9e-96 Score=953.08 Aligned_cols=517 Identities=30% Similarity=0.431 Sum_probs=434.6
Q ss_pred CCCCCCeEEEEecchHHHHHHhhcCCC-------------------EEEEeeccccccccccCC--CCCCCC-CCcceE-
Q 001100 345 YPPSGKSVVVVESVTKAKVIQGYLGDM-------------------YEVLPSYGHVRDLAARSG--SVRPDD-DFSMVW- 401 (1158)
Q Consensus 345 ~~~~~k~LIIvEkPskAk~Ia~~LG~~-------------------y~V~~s~GHl~dL~~~~~--~v~p~~-~f~~~~- 401 (1158)
-..+.+.|||||||+|||+|+++||.. |+|+||.|||++|+.+++ +|...+ .|.|.|
T Consensus 576 ~~~~~~~LiIaEkPs~Ak~IA~~lg~~~~r~~g~~~~ye~~~g~~~~~Vtas~GHl~dL~~~~~~~g~~~~~~~f~P~y~ 655 (1638)
T PRK14701 576 KDLVKSALMIVESPNKARTIANFFGQPSVRKIGDLVAYEVSIGDHMLIITASGGHVFDLVTNEGFHGVLINNNLFIPIYD 655 (1638)
T ss_pred hhhcCCeEEEEeChHHHHHHHHHhCCCccccCCCcceEEEecCCcEEEEEEecceeccCCCccccCccccccCccCCccc
Confidence 344568999999999999999999742 579999999999986543 232221 133322
Q ss_pred --ec------------------------CcchHHHHHHHHHHhccCCeEEEccCCCccccHHHHHHHHHHhhcccccCCc
Q 001100 402 --EV------------------------PSAAWTHLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENI 455 (1158)
Q Consensus 402 --~v------------------------~~~~~k~lk~Ik~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k 455 (1158)
+. ..+++++++.|++++++||+||||||||||||+|||+|+++|.. +++
T Consensus 656 ~~k~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~lr~l~~~ad~viiatD~DrEGE~I~~~i~~~~~~-----~~~ 730 (1638)
T PRK14701 656 SIKRCRDCGHQFTDWEDKGVCPRCGSKNVDDAKENIKAMRELAHEVDEILIGTDPDTEGEKIAWDIRNVLAP-----YGP 730 (1638)
T ss_pred ccccCCCchhhccccccccccccccccccccHHHHHHHHHHHHHhCCeEEECCCCChhhHHHHHHHHHHhcc-----CCC
Confidence 11 12367899999999999999999999999999999999999842 457
Q ss_pred cEEEEEEcccCHHHHHHHHHhcccccHhHHHHHHHHHHHhhhhhhcccHHHHhhCCC-cccCCcchhHHHHHHHHHHHHH
Q 001100 456 TVARVVFHEITEASIKVALQAAREIDANLVQAYLARRALDYLIGFNISPLLWRKLPG-CQSAGRVQSAALSLICDREMEI 534 (1158)
Q Consensus 456 ~vkRl~fs~lT~~aI~~A~~nlr~~d~~L~~A~~AR~~lD~LiG~nlSR~l~~k~~~-~lS~GRVQTPtL~LVveRe~EI 534 (1158)
+++|+|||++|+++|++||+|++++|++|++||+|||++||+||||+||++|..++. .+|+||||||||+|||+||+||
T Consensus 731 ~i~R~~fs~lT~~aI~~A~~nlr~~d~~l~~A~~aRr~~D~~iG~nlSr~l~~~~~~~~lS~GRVQTPtL~~Iv~Re~ei 810 (1638)
T PRK14701 731 NIKRIEFHEVTRRAILKAIKEARDIDENRVKAQIVRRIEDRWIGFELSQKLWEVFEDRNLSAGRVQTPVLGWIIQRYKEF 810 (1638)
T ss_pred CeeEEEEccCCHHHHHHHHhCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHhccCCceeecccccchhhhhHhhHHHH
Confidence 899999999999999999999999999999999999999999999999999988764 6999999999999999999999
Q ss_pred HhcCCcceEEEEEEEecCcCCCCCCceeeeeccccccccccccCcCCHHHHHHHHHHHccCCeEEEEeeeeeeeecCCCC
Q 001100 535 DEFKPQEYWTVEAVLDKKESHSLDTFSFPAHLTHFQSKRLNQLSIGSHTEAKDIEQKINSANFQVIKNSKRSMVRKNPTP 614 (1158)
Q Consensus 535 ~~Fkp~~Yw~I~a~~~~~~~~~~~g~~f~a~l~~~~~~k~~~~~i~d~~~Ae~i~~~l~~~~~~V~~v~~k~~~~~PP~P 614 (1158)
++ +|++||.|.+.. +..+ .+. . ++++ ..+.|.+|+.++++.+||+|
T Consensus 811 ~~-~~~~~~~i~~~~---------~~~~--~~~---~---------~~~~----------~~~~V~~v~~k~~~~~pP~p 856 (1638)
T PRK14701 811 TE-SKVPFLGIILEN---------DLTV--TIE---D---------SKDE----------VEVEVELVEEEEKERNPLPP 856 (1638)
T ss_pred hc-CCCceEEEEEcC---------ceEE--Eec---c---------cccC----------CeEEEEEEEeeEEEccCCCC
Confidence 99 599999975432 1112 110 0 1010 24789999999999999999
Q ss_pred cchHHHHHHHHHhcCCCHHHHHHHHHHHhcccc-----------------------------------------------
Q 001100 615 YITSTLQQDAANKLNFSATYTMKLAQKLYEGVQ----------------------------------------------- 647 (1158)
Q Consensus 615 f~tstLQ~~AskklG~Sa~~Tm~iAQ~LYE~~k----------------------------------------------- 647 (1158)
|||++||++||++|||||++||++||+|||+..
T Consensus 857 f~t~~Lq~~As~~~g~s~~~tm~iAQ~LYE~g~~~~p~t~V~l~dG~~~~I~el~e~~~~~vl~~~~~~~~~~~~~~~~~ 936 (1638)
T PRK14701 857 YTTDTMLRDASAFLKLSAKETMKLAQDLFEAGLCVTPDTYVSLHDGRIKEIDEIVEGSERNVLGLNGLKPKEAKALKFWE 936 (1638)
T ss_pred cCHHHHHHHHHHhcCCCHHHHHHHHHHHHhCceeeCCCceeecCchHHHHHHHHHhhccceeecccCceecccceeEEEE
Confidence 999999999999999999999999999999711
Q ss_pred ----------------------------C---------------------------C-----------------C-----
Q 001100 648 ----------------------------L---------------------------P-----------------D----- 650 (1158)
Q Consensus 648 ----------------------------~---------------------------~-----------------~----- 650 (1158)
+ . +
T Consensus 937 ~~~~~~~~~i~~~~G~~i~~T~dH~~lv~~~g~~~~~~a~~lk~gD~vav~~~~~~~~~~~i~~~~ll~~~~~~~~~~~~ 1016 (1638)
T PRK14701 937 IDYNGPIKVITLKNNYEIKATPDHGLLVMRDGKLGWVSAKNIREGDYVAFAFNTGVEGRKDYSLLKLLKELGITDVCVEF 1016 (1638)
T ss_pred eccCCcEEEEEECCCCEEEeCCCceEEeecCCceeeEEHHHCCcCCEEEecccCCCCccccccHHHHhhhccccceeeee
Confidence 0 0 0
Q ss_pred ---------------------------C----------------------------------------------------
Q 001100 651 ---------------------------G---------------------------------------------------- 651 (1158)
Q Consensus 651 ---------------------------g---------------------------------------------------- 651 (1158)
+
T Consensus 1017 ~~~~~~~~~~~~~i~~i~~~~~~~~lr~~~~pl~~l~e~g~~~~~~~~~~~~~~~~~~~~~~i~~~k~de~~~yLlG~~l 1096 (1638)
T PRK14701 1017 DENSKLFEKLAEKIRGIATSTKYKYLRNRVIPLKYLIEWNVNLDEVEREAKAIYRQRAGSKKIPIFKLDERFWYLFGLVL 1096 (1638)
T ss_pred ccchhHHHHHHHHHHhhccchhhhhccCCcccHHHHHHhcccccccchhhhhhhhcccCcccccccccChhHHhHhheeE
Confidence 0
Q ss_pred -------------------------------------C--------e---------------------------------
Q 001100 652 -------------------------------------T--------A--------------------------------- 653 (1158)
Q Consensus 652 -------------------------------------~--------~--------------------------------- 653 (1158)
. .
T Consensus 1097 gdG~~~~~~~~i~~~~~~~v~~i~~~~~~~~~~~~~~~~v~i~~~~l~~l~~~lG~~~~~ip~~vf~~p~e~~~~fL~G~ 1176 (1638)
T PRK14701 1097 GDGTLRDSKVAIAQTPLKDVKSILEDILPFLRTWESGNQVGFSNSIIAEILRRLGVRNGKLNGLVFSLPEEYINAMIAGY 1176 (1638)
T ss_pred ecceeccCeEEEecccHHHHHHHHHHHhhhhhccCCCceEEEccHHHHHHHHHhCCccCCCCHHHHcCCHHHHHHHHhhe
Confidence 0 0
Q ss_pred --------------------------------------------------------------------------------
Q 001100 654 -------------------------------------------------------------------------------- 653 (1158)
Q Consensus 654 -------------------------------------------------------------------------------- 653 (1158)
T Consensus 1177 fd~DG~v~~~~~~~~~~~~~~i~~~s~s~~ll~~v~~lLlrlGI~s~l~~~~~~~~~~l~I~g~~l~~F~e~Ig~~~~~k 1256 (1638)
T PRK14701 1177 FDTDGCFSLLFDKKTGKHNLRIVLTSKRRDVLEKLGVYLYSIGILNTLHRDERNGVWTLIISNRSLETFKEKIYKYLRIK 1256 (1638)
T ss_pred EeCCCceEecccccCCccceEEEEecCCHHHHHHHHHHHHHCCceeEEEEcccCccEEEEEccHHHHHHHHHhCcccHHH
Confidence
Q ss_pred ------------------------e---------------------E---------------------------------
Q 001100 654 ------------------------A---------------------G--------------------------------- 655 (1158)
Q Consensus 654 ------------------------~---------------------G--------------------------------- 655 (1158)
. |
T Consensus 1257 ~~~l~~~~~~~~~~~~~~~~D~iP~~~~~~~v~~~~g~~~~~~~~~g~~~~~~~~~~~isR~~l~~~~~~~~~~~~~~~L 1336 (1638)
T PRK14701 1257 KEQFDRAYSVYKNEHKQFEGDLLPVAKVFKKLKFKRGIKNRILKEFGIDVWNWNKCVEIPREKLRKVLEYAEDSPEKEFL 1336 (1638)
T ss_pred HHHHHHHHHHHhccccCCCcCccchHHHHHHHHHhcCCchHHHHhhccccccccccCCcCHHHHHHHHHHHhhhhHHHHH
Confidence 0 1
Q ss_pred --------------------E-----------------------EEEecCCCcCCCHHHHHHHHHHHHHHhCCCCCCCCC
Q 001100 656 --------------------L-----------------------ITYMRTDGLHISDEAAKEIRSLIFERYGSHHAPEEG 692 (1158)
Q Consensus 656 --------------------l-----------------------ITYPRTDS~~Ls~~~~~~i~~~i~~~~g~~~~~~~~ 692 (1158)
+ +|||||||++||+++++.++++|...||.+|..
T Consensus 1337 ~~la~~dv~~~~i~~ie~~~~~g~vyd~~v~~~nf~angiv~HN~TY~RTDS~~lS~~~~~~~~~~i~~~~g~~y~~--- 1413 (1638)
T PRK14701 1337 LSLVNANVTWVKVKKVEERYYTGYVYDFTTTTENFISNGMVSHNCTYHRTDSTRVSNTGIRVAREYLTQENGEDYFK--- 1413 (1638)
T ss_pred HHHhhCCeEEEEEEEEEEeccCCeEEEeEecccceeEccEeecCcccccCCCCccCHHHHHHHHHHHHHhhChhhcC---
Confidence 1 289999999999999999999999999998863
Q ss_pred CCccccccccccccCCCCCCCcccCChhhhh---------CCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEEEEEecCc
Q 001100 693 PRKYFKKVKNAQEAHEAIRPTDIRRLPAMLS---------GLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGNADE 763 (1158)
Q Consensus 693 ~r~~~~k~k~~qeAH~AI~PT~~~~~P~~l~---------~~Ls~dE~kLY~LI~rRfLAs~~~~a~~e~t~v~i~~~~~ 763 (1158)
++.+ ++|+||||||||+....|+.+. ..|+++|++||+|||+|||||||+||+|+.++|.+.+++
T Consensus 1414 ~r~~-----~~q~AHeAIrPT~~~~~~~~~~~~~~~~~~~~~Ls~de~klY~LI~rRflAs~m~~a~~~~t~v~~~~~~- 1487 (1638)
T PRK14701 1414 PRDW-----FMEGAHECIRPTRPIDTDRLIQLIREGIIQVPGLTRNHLRLYDLIFRRFMASQMKPAKVLYEKALIRYDG- 1487 (1638)
T ss_pred cccC-----CCcCCcCCCCCCCCCcChhhhhcccccccccccCCHHHHHHHHHHHHHHHHHhCchheEEEEEEEEEECC-
Confidence 5544 3689999999998766665321 258999999999999999999999999999999998864
Q ss_pred cEEEEEEeEE-EEEcCceeeccccchhhhccccccchhhhhhHHhcCCCCCCCeeEeeeEEEeccccCCCCCCCHhHHHH
Q 001100 764 SIVFRSSCSR-VEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSEGSLVK 842 (1158)
Q Consensus 764 ~~~F~asg~~-i~~~Gw~~vy~~~~~~~~~~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~ 842 (1158)
..|+++|++ ++++||+++|+..+ ..||.|++| .+.+.+ +.+++|.||+|||||+||+
T Consensus 1488 -~~F~a~G~~~i~~~Gw~~vy~~~~------------------~~LP~l~~G-~l~~~~--~~~t~~ppP~ryTEasLI~ 1545 (1638)
T PRK14701 1488 -KDVEVEGYVEIEGDGWSRLYSLPL------------------RVLPKLEKG-KLKVLE--AKIRKAPKVPLYTQGDIVA 1545 (1638)
T ss_pred -EEEEEEeEEEEEEcCchhcccccc------------------ccCCccccC-ceEEec--cceeECCCCCCCCHHHHHH
Confidence 589999995 79999999985310 249999999 888755 4567777789999999999
Q ss_pred HHHhcCCCCCcchHHHHHHhhccceEEEcCc--ccccccccchhhhhhhcccccccChhhhHHHHHHhhhhhcCCchHHH
Q 001100 843 KLEELGIGRPSTYASTLKVLQDRNYVTVKSR--ILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKG 920 (1158)
Q Consensus 843 ~MEk~GIGTpATrAsIIe~L~~R~YV~~k~k--~L~PT~lG~~v~~~L~~~f~~l~~p~~TA~~E~~Ld~Ia~Gk~~~~~ 920 (1158)
+||+.|||||||||+||++|++||||..+++ .|+||++|+.|+++|.++|+.|++|+|||+||.+||+|++|+.+|++
T Consensus 1546 ~Me~~GIGTpATrA~IIe~L~~R~YV~~~~~k~~l~pT~lG~~li~~L~~~~~~l~~p~~TA~~E~~Ld~Ia~G~~~~~~ 1625 (1638)
T PRK14701 1546 LMKERGIGRPSTYAKIVDTLLMRGYVIETKGRKKLIPTKKGIKVYNYLISNYGDLVSEERTRELEEIMDAVEEGELDYIK 1625 (1638)
T ss_pred HHhhCCCCCcccHHHHHHHHHhCCCEEEeCCCceEEECHHHHHHHHHHHhhchhhcChhhHHHHHHHHHHHHcCCCCHHH
Confidence 9999999999999999999999999997654 59999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhh
Q 001100 921 LLVDYWSRFSS 931 (1158)
Q Consensus 921 ~L~~F~~~f~~ 931 (1158)
||++|++.+.+
T Consensus 1626 ~l~~~~~~i~~ 1636 (1638)
T PRK14701 1626 VLQELYEEIRR 1636 (1638)
T ss_pred HHHHHHHHHHh
Confidence 99999986643
No 22
>cd00186 TOP1Ac DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand.
Probab=100.00 E-value=5.6e-90 Score=797.87 Aligned_cols=375 Identities=44% Similarity=0.658 Sum_probs=330.8
Q ss_pred HhHHHHHHHHHHHhhhhhhcccHHHHhhCC--CcccCCcchhHHHHHHHHHHHHHHhcCCcceEEEEEEEecCcCCCCCC
Q 001100 482 ANLVQAYLARRALDYLIGFNISPLLWRKLP--GCQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDT 559 (1158)
Q Consensus 482 ~~L~~A~~AR~~lD~LiG~nlSR~l~~k~~--~~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~g 559 (1158)
.+|++||+||+++|||||||+||++|..++ +++|+||||||||+|||+||+||+||+|++||.|
T Consensus 1 ~~l~~a~~aR~~~D~liG~n~sr~~t~~~~~~~~lS~GRVQtPtL~liv~Re~ei~~F~p~~y~~i-------------- 66 (381)
T cd00186 1 ENLVNAQLARRILDRLVGFNLSRLLTKKLRRKGVLSAGRVQSPTLGLIVEREREIKAFVPEDYWEI-------------- 66 (381)
T ss_pred CcHHHHHHHHHHHHHHhhhhhhHHHHHHhCCCCCCccccchhhHhHHHHHHHHHHHhCCCcceEEe--------------
Confidence 379999999999999999999999998776 6899999999999999999999999999999987
Q ss_pred ceeeeeccccccccccccCcCCHHHHHHHHHHHccCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHhcCCCHHHHHHHH
Q 001100 560 FSFPAHLTHFQSKRLNQLSIGSHTEAKDIEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKLA 639 (1158)
Q Consensus 560 ~~f~a~l~~~~~~k~~~~~i~d~~~Ae~i~~~l~~~~~~V~~v~~k~~~~~PP~Pf~tstLQ~~AskklG~Sa~~Tm~iA 639 (1158)
..++|++++.++++..||+||||++||++|+++|||||++||++|
T Consensus 67 -----------------------------------~~~~v~~~~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~ia 111 (381)
T cd00186 67 -----------------------------------KEAVVVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIA 111 (381)
T ss_pred -----------------------------------eeEEEEEEEeeeeecCCCCCcCHHHHHHHHHHhcCCCHHHHHHHH
Confidence 125688999999999999999999999999999999999999999
Q ss_pred HHHhccccCCCCCeeEEEEEecCCCcCCCHHHHHHHHHHHHHHhCCCCCCCC-C-CCccccccccccccCCCCCCCcccC
Q 001100 640 QKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFERYGSHHAPEE-G-PRKYFKKVKNAQEAHEAIRPTDIRR 717 (1158)
Q Consensus 640 Q~LYE~~k~~~g~~~GlITYPRTDS~~Ls~~~~~~i~~~i~~~~g~~~~~~~-~-~r~~~~k~k~~qeAH~AI~PT~~~~ 717 (1158)
|+|||+ ||||||||||++||+++...+..++...++..+.... . .+......++.++||||||||+...
T Consensus 112 Q~LYe~---------glISYPRTds~~ls~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aH~AI~PT~~~~ 182 (381)
T cd00186 112 QKLYEA---------GLITYPRTDSTRLSEEAILEAREYIQAIYGKEYLYPAPLLGRRNPKRGKKEQGAHEAIRPTKVAP 182 (381)
T ss_pred HHHHcC---------CeeeecCCCCccCCHHHHHHHHHHHHHhcCccccchhhccccccccCCCCCcCCCCCCCcCCCCc
Confidence 999995 8999999999999999999999888776654332211 0 0001111234578999999998753
Q ss_pred ChhhhhCCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEEEEEecCccEEEEEEeEEEEEcCceeeccccchhhhcccccc
Q 001100 718 LPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYKENE 797 (1158)
Q Consensus 718 ~P~~l~~~Ls~dE~kLY~LI~rRfLAs~~~~a~~e~t~v~i~~~~~~~~F~asg~~i~~~Gw~~vy~~~~~~~~~~~e~~ 797 (1158)
.| .+...|+++|++||+||||||||+||++|+|++++|.+.+++ ..|.++|++++++||++||+.... + +
T Consensus 183 ~~-~~~~~l~~~e~~iY~LI~rrfla~~~~~~~~~~t~v~~~~~~--~~F~a~g~~i~~~Gw~~v~~~~~~------~-~ 252 (381)
T cd00186 183 TP-ELEANLSEDEFKLYELIWRRFLASQMADAKYEETTVTLEIGG--EKFKASGKVLLEDGWLEVYPEEKD------D-E 252 (381)
T ss_pred Cc-hhhccCCHHHHHHHHHHHHHHHHHhCchhhEEEEEEEEEECC--eEEEEEEEEEeeCCHHHHhCcccc------c-c
Confidence 32 112469999999999999999999999999999999998864 579999999999999999965321 1 1
Q ss_pred chhhhhhHHhcCCCCCCCeeEeeeEEEeccccCCCCCCCHhHHHHHHHhcCCCCCcchHHHHHHhhccceEEEcCccccc
Q 001100 798 ENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKSRILYP 877 (1158)
Q Consensus 798 e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk~GIGTpATrAsIIe~L~~R~YV~~k~k~L~P 877 (1158)
+ ..+|.|++||.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++||||..+++.|+|
T Consensus 253 ~-------~~~p~l~~g~~~~~~~~~~~~~~T~PP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~k~l~p 325 (381)
T cd00186 253 E-------EEPPPLKEGDELKLEEVELEEKETQPPPRYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEKEKKKLIP 325 (381)
T ss_pred c-------ccCCCCCCCCEEeeeeeeeeecccCCCCCCCHHHHHHHHHhCCCCccccHHHHHHHHHhCCcEEeeCCEEeE
Confidence 0 247999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccchhhhhhhcccccccChhhhHHHHHHhhhhhcCCchHHHHHHHHHHHhhh
Q 001100 878 EFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKGLLVDYWSRFSS 931 (1158)
Q Consensus 878 T~lG~~v~~~L~~~f~~l~~p~~TA~~E~~Ld~Ia~Gk~~~~~~L~~F~~~f~~ 931 (1158)
|++|+.|+++|++.|+.|++|+|||+||.+|++|++|+.++++||+++++.+.+
T Consensus 326 T~~G~~li~~l~~~~~~l~~p~lTa~~E~~L~~I~~G~~~~~~~l~~~~~~~~~ 379 (381)
T cd00186 326 TELGFAVIELLEKHFPELVDPEFTAKLEEKLDEIAEGKKDYQEVLEEFYEEFKK 379 (381)
T ss_pred CHHHHHHHHHHHHhchhccCHhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHh
Confidence 999999999999988999999999999999999999999999999998876543
No 23
>PF01131 Topoisom_bac: DNA topoisomerase; InterPro: IPR013497 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 I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. Type IA topoisomerases are comprised of four domains that together form a toroidal structure with a central hole large enough to accommodate single- and double-stranded DNA: an N-terminal alpha/beta Toprim domain, domain 2 and the C-terminal domain 4 are winged-helix domains, and domain 3 is a beta-barrel. Domains 1 (Toprim) and 3 form the active site of the enzyme, while the winged helix domains 2 and 4 form a single-strand DNA-binding groove [, ]. This entry represents the central portion of the enzyme, which covers domains 2 and 3 in topoisomerase type IA enzymes. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome; PDB: 1CYY_A 3PWT_A 1CY4_A 1CY9_A 1ECL_A 1CY7_A 1CY8_A 1CY6_A 1MW8_X 1CY0_A ....
Probab=100.00 E-value=8.7e-89 Score=793.70 Aligned_cols=398 Identities=36% Similarity=0.531 Sum_probs=312.4
Q ss_pred cccHhHHHHHHHHHHHhhhhhhcccHHHHhhCCCcccCCcchhHHHHHHHHHHHHHHhcCCcceEEEEEEEecCcCCCCC
Q 001100 479 EIDANLVQAYLARRALDYLIGFNISPLLWRKLPGCQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLD 558 (1158)
Q Consensus 479 ~~d~~L~~A~~AR~~lD~LiG~nlSR~l~~k~~~~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~ 558 (1158)
+++++|++||+||+++|||||||+||+++ + ++++|+||||||||+|||+||+||+||+|++||.|.+.+....
T Consensus 1 ~~~~~l~~a~~aR~~~D~liG~n~Sr~~t-~-~~~ls~GRVQtp~L~li~~Re~ei~~f~~~~y~~i~~~~~~~~----- 73 (403)
T PF01131_consen 1 EEDKNLYNAAEARQEADWLIGMNLSRALT-G-NGVLSVGRVQTPTLGLIVEREREIENFKPEPYYEIKAQFKKGG----- 73 (403)
T ss_dssp --GHHHHHHHHHHHHHHHHHHHHHHHHHH-H-STT-TTHTTHHHHHHHHHHHHHHHHCEEEEEEEEEEEEEETCC-----
T ss_pred CCCHhHHHHHHHHHHHHHhcChhcCHhhc-C-CCccccCcccchHHHHHHHHHhhhhccCCCceEEEEEEecccc-----
Confidence 35789999999999999999999999998 4 7899999999999999999999999999999999999986421
Q ss_pred CceeeeeccccccccccccCcCCHHHHHHHHHHHccCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHhcCCCHHHHHHH
Q 001100 559 TFSFPAHLTHFQSKRLNQLSIGSHTEAKDIEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKL 638 (1158)
Q Consensus 559 g~~f~a~l~~~~~~k~~~~~i~d~~~Ae~i~~~l~~~~~~V~~v~~k~~~~~PP~Pf~tstLQ~~AskklG~Sa~~Tm~i 638 (1158)
+ .+. .....+|.++++|+.+++.+... .|.+++.++++.+||.||+|++||++|+++|||||++||++
T Consensus 74 ~-~~~---------~~~~~~~~~~~~a~~~~~~~~~~--~v~~~~~~~~~~~pP~p~~l~~Lq~~a~k~~g~s~~~tl~i 141 (403)
T PF01131_consen 74 F-EFK---------NDDKKRFDDKEEAEQILEKLKNS--KVTEVEEKEKKKPPPLPFNLSTLQKEASKKLGFSAKETLDI 141 (403)
T ss_dssp S--EE---------TTEES-CTSHHHHHHHHHHHHHC--EEEEEEEEEEEE----SB-HHHHHHHHHHHH---HHHHHHH
T ss_pred c-ccc---------cccccccccHHHHHHHhhcccCc--eEEEEEEEEeeecCCChHHHHHHHHHHHHHhhhhHHHHHHH
Confidence 1 110 11235788999999999999875 99999999999999999999999999999999999999999
Q ss_pred HHHHhccccCCCCCeeEEEEEecCCCcCCCHHH-HHHHHHHHHHHhCCCCCCCCCCCccc-cc-ccccc-ccCCCCCCCc
Q 001100 639 AQKLYEGVQLPDGTAAGLITYMRTDGLHISDEA-AKEIRSLIFERYGSHHAPEEGPRKYF-KK-VKNAQ-EAHEAIRPTD 714 (1158)
Q Consensus 639 AQ~LYE~~k~~~g~~~GlITYPRTDS~~Ls~~~-~~~i~~~i~~~~g~~~~~~~~~r~~~-~k-~k~~q-eAH~AI~PT~ 714 (1158)
||+|||+| ||||||||||++||++. +..+...|...++..|... .++... .+ ..+++ +||||||||.
T Consensus 142 aQ~LYE~~--------g~ISYPRTds~~l~~~~~~~~i~~~l~~~~~~~~~~~-~~~~~~~~~~~~~~kv~aH~AI~PT~ 212 (403)
T PF01131_consen 142 AQKLYEKH--------GLISYPRTDSRYLPEDEDLKEILKYLKKHYGEDYFPE-APNLLKSPKSKNDSKVTAHHAIIPTG 212 (403)
T ss_dssp HHHHHHTT--------TSBS-SS-S---B-HHHGHHHHHHHHHHHTTGGGS-S-S--TTSSSTTC-CCC-SSSS-B-BSS
T ss_pred HHHHHhhh--------heeeeeccchhhhcchhhHHHHHHHHHHhcccccccc-chhhhhcccccCCccccCCCCccccc
Confidence 99999964 79999999999999997 7778888877777554431 111110 00 02334 8999999997
Q ss_pred ccCChhhhhCCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEEEEEecCccEEEEEEeEEEEEcCceeeccccchhhhccc
Q 001100 715 IRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYK 794 (1158)
Q Consensus 715 ~~~~P~~l~~~Ls~dE~kLY~LI~rRfLAs~~~~a~~e~t~v~i~~~~~~~~F~asg~~i~~~Gw~~vy~~~~~~~~~~~ 794 (1158)
.. |.++ ..|+++|++||+||||||||+||+||+|+.++|.+.++ ++.|+++|++++++||+++|+.... +
T Consensus 213 ~~--~~~~-~~Ls~~e~~vY~LI~rr~la~~~~~~~~~~t~v~~~~~--~~~F~~~g~~~~~~Gw~~~~~~~~~-----~ 282 (403)
T PF01131_consen 213 KI--PPDL-SNLSEDERKVYDLIARRFLAAFMPDAKYEKTTVTFEVG--GEEFKASGKVIIDPGWKKVYPYEEE-----E 282 (403)
T ss_dssp ST--THCG-HHCHHHHHHHHHHHHHHHHHHTS--EEEEEEEEEEEET--TEEEEEEEEEEEEHGGGGCS-HCHC-----C
T ss_pred cC--ccch-hhcCHHHHHHHHHHHHHHHHHHHHHHheeeEEEEEEec--CcEEEEEEeEEEECceeEEEEcccc-----c
Confidence 64 3222 24899999999999999999999999999999999884 4689999999999999999964321 0
Q ss_pred cccchhhhhhHHhcCCCCCCCeeEeeeEEEeccccCCCCCCCHhHHHHHHHhcCCCCCcchHHHHHHhhccceEEE-cCc
Q 001100 795 ENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTV-KSR 873 (1158)
Q Consensus 795 e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk~GIGTpATrAsIIe~L~~R~YV~~-k~k 873 (1158)
+ .+ ..||.|++||.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++|+||++ +++
T Consensus 283 ~-~~-------~~lp~l~~g~~~~~~~~~~~e~~TkPP~~~Te~~Ll~~Me~~GIGTpATra~iI~~L~~r~Yi~~~k~~ 354 (403)
T PF01131_consen 283 D-EE-------EDLPSLKEGDEIPIEDVEIKEKKTKPPKRYTEASLLKAMEKAGIGTPATRASIIEKLIKRGYIERSKGK 354 (403)
T ss_dssp T-TS-------BB-----TTEEEEEEEEEEEEEEEESS--EBHHHHHHHHHHTTSS-TTTHHHHHHHHHHTTSEEE-ETT
T ss_pred c-cc-------cccccccCCcEEeecccchhhhccCCCCCCCHHHHHhhhhhcCCCccccHHHHHHHhhccceeecccCc
Confidence 0 00 25999999999999999999999999999999999999999999999999999999999999999 468
Q ss_pred ccccccccchhhhhhhcccccccChhhhHHHHHHhhhhhcCCchHHHHHH
Q 001100 874 ILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKGLLV 923 (1158)
Q Consensus 874 ~L~PT~lG~~v~~~L~~~f~~l~~p~~TA~~E~~Ld~Ia~Gk~~~~~~L~ 923 (1158)
.|+||++|+.|+++|+ .|+.|++|+|||.||+.|++|++|+.++++||+
T Consensus 355 ~l~~T~~G~~li~~l~-~~~~l~~p~~Ta~~E~~L~~I~~G~~~~~~fl~ 403 (403)
T PF01131_consen 355 KLIPTPKGRALIEALP-NFPELISPEMTAQWEEKLDKIAEGKASKEEFLK 403 (403)
T ss_dssp EEEEBHHHHHHHHHHH-HCCCCCSHHHHHHHHHHHHHHHTTSS-HHHHHH
T ss_pred eeeeehHHHHHHHHHH-hhHHhcCHHHHHHHHHHHHHHHcCCCCHHHHhC
Confidence 9999999999999995 458999999999999999999999999999884
No 24
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=100.00 E-value=5.5e-87 Score=800.11 Aligned_cols=521 Identities=31% Similarity=0.500 Sum_probs=426.8
Q ss_pred CCCCCCCCCCCCCCCeEEEEecchHHHHHHhhcCCC-------------------EEEEeeccccccccccCC--CCCCC
Q 001100 336 RGQNTQNPLYPPSGKSVVVVESVTKAKVIQGYLGDM-------------------YEVLPSYGHVRDLAARSG--SVRPD 394 (1158)
Q Consensus 336 ~~~~~~~~~~~~~~k~LIIvEkPskAk~Ia~~LG~~-------------------y~V~~s~GHl~dL~~~~~--~v~p~ 394 (1158)
+.|..-..-.....-.|+|||||+|||+||.|+|.. -.|+||.||++||....+ ++..+
T Consensus 604 ~~g~~~~~~~dlvkt~L~IVESPnKARTIA~FFgrPS~R~~~~~~vYEv~~gD~vL~ItAS~GHv~DLvt~~g~hGvl~~ 683 (1187)
T COG1110 604 LEGKLKEETKDLVKTALMIVESPNKARTIASFFGRPSVRRLGGGVVYEVAIGDLVLTITASGGHVFDLVTEPGVHGVLVK 683 (1187)
T ss_pred HhccchhhhhhhhhceEEEEeCChHHHHHHHHhCCcceeeeCCeeEEEEecCCeEEEEEecCCeeEEeecccccceeecc
Confidence 344443444455557999999999999999999841 358999999999987543 22111
Q ss_pred -CCCcceEe------------------cC-------cchHHHHHHHHHHhccCCeEEEccCCCccccHHHHHHHHHHhhc
Q 001100 395 -DDFSMVWE------------------VP-------SAAWTHLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQ 448 (1158)
Q Consensus 395 -~~f~~~~~------------------v~-------~~~~k~lk~Ik~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~ 448 (1158)
..|.|.|. .| .++...++.|++++-.+|+|+||||||.|||-|||+|..++.+
T Consensus 684 ~~~~vPvY~tIKrC~dcg~q~~~~~~~cP~Cgs~~v~d~~~~ve~lRelA~EvDeVlIgTDPDtEGEKIawDv~~~l~P- 762 (1187)
T COG1110 684 DGKYVPVYDTIKRCRDCGEQFVDSEDKCPRCGSRNVEDKTETVEALRELALEVDEILIGTDPDTEGEKIAWDVFNYLRP- 762 (1187)
T ss_pred CCceEehHHHHHHHhhcCceeccccccCCCCCCccccccHHHHHHHHHHHhhcCEEEEcCCCCCccchhHHHHHHhhCc-
Confidence 12433331 11 2456789999999999999999999999999999999999865
Q ss_pred ccccCCccEEEEEEcccCHHHHHHHHHhcccccHhHHHHHHHHHHHhhhhhhcccHHHHhhCC-CcccCCcchhHHHHHH
Q 001100 449 DALHENITVARVVFHEITEASIKVALQAAREIDANLVQAYLARRALDYLIGFNISPLLWRKLP-GCQSAGRVQSAALSLI 527 (1158)
Q Consensus 449 ~~~~~~k~vkRl~fs~lT~~aI~~A~~nlr~~d~~L~~A~~AR~~lD~LiG~nlSR~l~~k~~-~~lS~GRVQTPtL~LV 527 (1158)
.+..|+|+.||++|+.||.+|++|++++|.||+.||..||+.|++|||.||+.||..++ ..||+||||||+|++|
T Consensus 763 ----y~~nikR~eFHEVTrrAIleAl~n~r~vd~nlVkAQiVRRIeDRWIGF~LS~~Lw~~F~~~nLsAGRVQTPVLGWI 838 (1187)
T COG1110 763 ----YNPNVKRIEFHEVTRRAILEALKNPRDVDENLVKAQIVRRIEDRWIGFELSQKLWDVFNNKNLSAGRVQTPVLGWI 838 (1187)
T ss_pred ----CCCceeEEEeeeecHHHHHHHHhCccccchhhhHHHhhhhhhhcccceeecHHHHHHhCccCccccccccccceee
Confidence 46689999999999999999999999999999999999999999999999999999886 5799999999999999
Q ss_pred HHHHHHHHhcCCcceEEEEEEEecCcCCCCCCceeeeeccccccccccccCcCCHHHHHHHHHHHccCCeEEEEeeeeee
Q 001100 528 CDREMEIDEFKPQEYWTVEAVLDKKESHSLDTFSFPAHLTHFQSKRLNQLSIGSHTEAKDIEQKINSANFQVIKNSKRSM 607 (1158)
Q Consensus 528 veRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~g~~f~a~l~~~~~~k~~~~~i~d~~~Ae~i~~~l~~~~~~V~~v~~k~~ 607 (1158)
|+|+.|-+.-+. |..+...+ .+ .+.+...++.+...+....+.|.++..++.
T Consensus 839 V~Ry~e~~~~~~--~~~~~~~~-----------~~---------------~~~~~~~~~~~~~~~~~~~v~v~~~~e~ee 890 (1187)
T COG1110 839 VNRYEEYKEKRG--YLVIQLDL-----------DL---------------PSGNREEVENVKRKLKLIVVEVVDVVEREE 890 (1187)
T ss_pred hhhHHHHhhccc--eeEeeccc-----------ee---------------eccchhhhhhhhhhcccceEEEeehhhhhh
Confidence 999999776444 44441111 11 122334455555555555567777767777
Q ss_pred eecCCCCcchHHHHHHHHHhcCCCHHHHHHHHHHHhccccCCCCCeeEEEEEecCCCcCCCHHHHHHHHHHHHHHhCCCC
Q 001100 608 VRKNPTPYITSTLQQDAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFERYGSHH 687 (1158)
Q Consensus 608 ~~~PP~Pf~tstLQ~~AskklG~Sa~~Tm~iAQ~LYE~~k~~~g~~~GlITYPRTDS~~Ls~~~~~~i~~~i~~~~g~~~ 687 (1158)
..+|||||+|++|+++||++||+|+++||+|||.|+|. |||||+||||+++|+..+..++.+|...++..|
T Consensus 891 ~~~PlPPyTTDt~L~dAs~~L~lsa~~~M~iaQdLFE~---------GlITYHRTDSTrVS~~Gi~vAreyl~~~~~e~~ 961 (1187)
T COG1110 891 EKNPLPPYTTDTMLRDASRRLRLSADETMQIAQDLFEG---------GLITYHRTDSTRVSDVGIRVAREYLRKEFGEEY 961 (1187)
T ss_pred ccCCCCCcCcchHHHHHHHHhCCChhHHHHHHHHHHhc---------cceEEeecCCcccchhhHHHHHHHHHHhhcccc
Confidence 78999999999999999999999999999999999996 999999999999999999999999998888776
Q ss_pred CCCCCCCccccccccccccCCCCCCCcccCChhh-----------hhCCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEE
Q 001100 688 APEEGPRKYFKKVKNAQEAHEAIRPTDIRRLPAM-----------LSGLLDEDCLKLYSLIWSRTMACQMQPATVGQIQV 756 (1158)
Q Consensus 688 ~~~~~~r~~~~k~k~~qeAH~AI~PT~~~~~P~~-----------l~~~Ls~dE~kLY~LI~rRfLAs~~~~a~~e~t~v 756 (1158)
. .||.|.. ..||+|||||.+.+. .. +...|+..+.+||+||.|||||+||.|+++....+
T Consensus 962 f---~pR~Wge-----~GAHEaIRPtrPid~-~eL~~~i~~G~i~~~~~Lt~~HlrvYdLIFrRFmASQm~pa~v~~~~~ 1032 (1187)
T COG1110 962 F---RPRSWGE-----EGAHEAIRPTRPIDV-EELITLIEEGVIQLPIRLTKNHLRVYDLIFRRFMASQMRPAKVLKEKA 1032 (1187)
T ss_pred c---cCCcccc-----CCcccccCCCCCCCH-HHHHHHHHcCCeeccchhhHHHHHHHHHHHHHHHHhhCCceeEEEEEE
Confidence 4 3788753 469999999986532 22 12348999999999999999999999999988888
Q ss_pred EEEecCccEEEEEEeEEEEEcCceeeccccchhhhccccccchhhhhhHHhcCCCCCCCeeEeeeEEEeccccCCCCCCC
Q 001100 757 DIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYS 836 (1158)
Q Consensus 757 ~i~~~~~~~~F~asg~~i~~~Gw~~vy~~~~~~~~~~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryT 836 (1158)
.+..++.+. ..-....+...||..+|+. ..+|.|..|+ +.+....+...-. -..||
T Consensus 1033 ~i~~~~~~~-~~e~~ve~~~~G~~~vy~~--------------------~~~p~l~~g~-l~v~~~~~~~~~k--v~lyt 1088 (1187)
T COG1110 1033 EVKADGKDV-ELEALVEILEDGFALVYPT--------------------RVLPELEKGT-LKVTEVEIRKVSK--VYLYT 1088 (1187)
T ss_pred EEecCccee-eeeehhhhhccchhhhccc--------------------cccCccCCCc-eeeeeeEEEEccc--ccccc
Confidence 887754332 2222344677999999863 2478899998 7776666665433 34799
Q ss_pred HhHHHHHHHhcCCCCCcchHHHHHHhhccceEEEcCcc--cccccccchhhhhhhcccccccChhhhHHHHHHhhhhhcC
Q 001100 837 EGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKSRI--LYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAG 914 (1158)
Q Consensus 837 EasLI~~MEk~GIGTpATrAsIIe~L~~R~YV~~k~k~--L~PT~lG~~v~~~L~~~f~~l~~p~~TA~~E~~Ld~Ia~G 914 (1158)
|+++|+.|++.|||||||||.||++|.+||||...++. ++||.+|+.|+++|...|+.+++.+.|.++|+.||+|+.|
T Consensus 1089 qg~vi~~MKerGIGRPSTYAkive~L~~RgYvie~kg~~~lipTk~Gi~Vy~yL~~~~~~lVSEerTR~LEe~MD~vE~g 1168 (1187)
T COG1110 1089 QGEVVEEMKERGIGRPSTYAKIVETLLRRGYVIESKGRKKLIPTKLGIEVYEYLSEKYKKLVSEERTRRLEEIMDKVEEG 1168 (1187)
T ss_pred cchHHHHHHhcCCCCCcHHHHHHHHHhcCCeEEEecCceEeccccccHHHHHHHHHhcccccchhHHHHHHHHHHHHHhc
Confidence 99999999999999999999999999999999765443 9999999999999999999999999999999999999999
Q ss_pred CchHHHHHHHHHHHhhh
Q 001100 915 LTEWKGLLVDYWSRFSS 931 (1158)
Q Consensus 915 k~~~~~~L~~F~~~f~~ 931 (1158)
+.++.++|...|+.+..
T Consensus 1169 k~dy~~vL~ely~ei~~ 1185 (1187)
T COG1110 1169 KADYQEVLKELYEEIKS 1185 (1187)
T ss_pred ccCHHHHHHHHHHHHHh
Confidence 99999999998877654
No 25
>smart00437 TOP1Ac Bacterial DNA topoisomerase I DNA-binding domain. Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit
Probab=100.00 E-value=1.4e-60 Score=525.41 Aligned_cols=255 Identities=43% Similarity=0.601 Sum_probs=216.3
Q ss_pred eeeeeecCCCCcchHHHHHHHHHhcCCCHHHHHHHHHHHhccccCCCCCeeEEEEEecCCCcCCCHHHHHHHHHHHHHHh
Q 001100 604 KRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFERY 683 (1158)
Q Consensus 604 ~k~~~~~PP~Pf~tstLQ~~AskklG~Sa~~Tm~iAQ~LYE~~k~~~g~~~GlITYPRTDS~~Ls~~~~~~i~~~i~~~~ 683 (1158)
+++++..||+||||++||++||++|||||++||++||+|||+ ||||||||||+|||+++..++..++....
T Consensus 2 ~~~~~~~pP~pf~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYe~---------g~iTYPRTds~~l~~~~~~~~~~~l~~~~ 72 (259)
T smart00437 2 EKEKKKNPPPPFTTSTLQQEASRKLGFSAKKTMQIAQKLYEK---------GLITYPRTDSTRLSEEAVLEARNYISKHY 72 (259)
T ss_pred CCcccCCCCCCccHHHHHHHHHHhcCCCHHHHHHHHHHHHhC---------CeeEecCCCCCcCCHHHHHHHHHHHHHhh
Confidence 456788999999999999999999999999999999999995 89999999999999999999888887665
Q ss_pred CCCCCCC--C-CCCccccccccccccCCCCCCCcccCChhhhhCCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEEEEEe
Q 001100 684 GSHHAPE--E-GPRKYFKKVKNAQEAHEAIRPTDIRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGN 760 (1158)
Q Consensus 684 g~~~~~~--~-~~r~~~~k~k~~qeAH~AI~PT~~~~~P~~l~~~Ls~dE~kLY~LI~rRfLAs~~~~a~~e~t~v~i~~ 760 (1158)
+..|... . ..++........++||||||||+....++.+ ..|+++|++||+||+|||||+||++|+|++++|.+.+
T Consensus 73 ~~~~~~~~~~~~~~~~~~~~~~k~~~H~aI~PT~~~~~~~~~-~~L~~~e~~iY~lI~rr~la~~~~~~~~~~t~v~~~~ 151 (259)
T smart00437 73 GKEYLPLAVSLLKPRKPRWGKKEQGAHEAIRPTKPIPTPELE-KELSEDEKKLYELIWRRFLASQMPDAKYEETKVIIKI 151 (259)
T ss_pred chhhhhhhhhhccCccccCCCCCCCCCCCCCccCCCCCchhh-hhCCHHHHHHHHHHHHHHHHHhChhheEEEEEEEEEE
Confidence 5333321 0 1111111112246899999999864332222 3599999999999999999999999999999999988
Q ss_pred cCccEEEEEEeEEEEEcCceeeccccchhhhccccccchhhhhhHHhcCCCCCCCeeEeeeEEEeccccCCCCCCCHhHH
Q 001100 761 ADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSEGSL 840 (1158)
Q Consensus 761 ~~~~~~F~asg~~i~~~Gw~~vy~~~~~~~~~~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasL 840 (1158)
++ +.|.++|++++++||+.||++.+. ++ ...||.|++||.+.+.++.+.+++|+||+||||++|
T Consensus 152 ~~--~~F~a~g~~i~~~Gw~~v~~~~~~-------~~-------~~~lp~~~~g~~~~~~~~~~~e~~TkPP~~~Te~tL 215 (259)
T smart00437 152 GG--EKFKAKGKTLLFDGWLKVYPEEKK-------EE-------EIELPTLKKGDELKVEEVEVEEKKTKPPARYTEASL 215 (259)
T ss_pred CC--eEEEEEEEEEeECCHHHhhccccc-------Cc-------cccCCCcCCCCEeeeeeeEEEecccCCCCCCCHHHH
Confidence 64 589999999999999999965311 00 135999999999999999999999999999999999
Q ss_pred HHHHHhcCCCCCcchHHHHHHhhccceEEEcCcccccccccchh
Q 001100 841 VKKLEELGIGRPSTYASTLKVLQDRNYVTVKSRILYPEFRGRMV 884 (1158)
Q Consensus 841 I~~MEk~GIGTpATrAsIIe~L~~R~YV~~k~k~L~PT~lG~~v 884 (1158)
|++||+.|||||||||+||++|++||||.++++.|+||++|+.|
T Consensus 216 l~~Me~~GIGTpATra~iIe~L~~r~Yi~~~~k~l~~T~~G~~l 259 (259)
T smart00437 216 IKLMEKRGIGRPSTYAEIIETLLDRGYVTKEKKKLIPTELGIAV 259 (259)
T ss_pred HHHHHHCCCCchhhHHHHHHHHHhCCcEEeeCCEEeEccceecC
Confidence 99999999999999999999999999999999999999999864
No 26
>KOG1957 consensus DNA topoisomerase III beta [Replication, recombination and repair]
Probab=100.00 E-value=2.1e-53 Score=474.03 Aligned_cols=494 Identities=21% Similarity=0.237 Sum_probs=385.6
Q ss_pred CCeEEEEecchHHHHHHhhcCC------------------------CEEEEeecccccccccc-----CCCCCCCCCCcc
Q 001100 349 GKSVVVVESVTKAKVIQGYLGD------------------------MYEVLPSYGHVRDLAAR-----SGSVRPDDDFSM 399 (1158)
Q Consensus 349 ~k~LIIvEkPskAk~Ia~~LG~------------------------~y~V~~s~GHl~dL~~~-----~~~v~p~~~f~~ 399 (1158)
.-.|.|+|||+.|..||++|.+ .|.||+..||++.|..+ |..|||.+.|..
T Consensus 2 ~tvlmvaekpsla~sia~ils~g~~s~~kg~csvhe~~g~f~g~~~~fk~tsvcghvmsldf~~kyn~w~~vdp~elf~a 81 (555)
T KOG1957|consen 2 KTVLMVAEKPSLADSIANILSNGQASKRKGWCSVHEYDGQFRGRAARFKVTSVCGHVMSLDFPPKYNNWDKVDPAELFSA 81 (555)
T ss_pred CceeEeecCchHHHHHHHHhhCCccccccCceeeeeccccccCceeeEEEeeeeceeEeccCchhcCCccccCHHHHhCC
Confidence 4579999999999999999942 38999999999999765 445677666652
Q ss_pred eE-e-cCcchHHHHHHHHHHhccCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhc
Q 001100 400 VW-E-VPSAAWTHLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAA 477 (1158)
Q Consensus 400 ~~-~-v~~~~~k~lk~Ik~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fs~lT~~aI~~A~~nl 477 (1158)
-- + -...+....+.|...+++||.+|||.|+|+|||+|.+||++..+.... .....++|++||+||+++|.+||+||
T Consensus 82 pt~kkeanpk~~m~kfl~~eargcdy~vlwldcdkegenicfevidav~~~m~-~~~~~tyra~fsaitekdi~~am~~l 160 (555)
T KOG1957|consen 82 PTEKKEANPKMNMNKFLASEARGCDYLVLWLDCDKEGENICFEVIDAVKCVMN-RSDFKTYRAHFSAITEKDIKKAMRNL 160 (555)
T ss_pred cchhcccCchhhHHHHHhhhccCCcEEEEEeecCCCcCeeehhhhhhhhhhhc-cCcceEEeeeeccccHHHHHHHHHhc
Confidence 10 1 112255678889999999999999999999999999999998876432 33457899999999999999999999
Q ss_pred ccccHhHHHHHHHHHHHhhhhhhcccHHHHhhCCCcccCCcchhHHHHHHHHHHHHHHhcCCcceEEEEEEEecCcCCCC
Q 001100 478 REIDANLVQAYLARRALDYLIGFNISPLLWRKLPGCQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSL 557 (1158)
Q Consensus 478 r~~d~~L~~A~~AR~~lD~LiG~nlSR~l~~k~~~~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~ 557 (1158)
.++|.|.+.+..|||++|+.| .....+|+|+||||||++.|+|...|+.|+|+.||.+.+.+...
T Consensus 161 g~p~~nea~svdarqeldlri----------lds~~isygpcqtptlgfcv~rhd~i~tfkpe~~w~l~~~~~~~----- 225 (555)
T KOG1957|consen 161 GEPDQNEALSVDARQELDLRI----------LDSSLISYGPCQTPTLGFCVTRHDQIQTFKPEQYWVLQTNFTTD----- 225 (555)
T ss_pred CCCCcchhcccchhhhhhhhh----------hhhcceeecCCCCCcceeeeeehhhhhccCccceEEEeeecCCC-----
Confidence 999999999999999999987 12346899999999999999999999999999999999888542
Q ss_pred CCceeeeeccccccccccccCcCCHHHHHHHHHHHcc-CCeEEEEeeeeeeeecCCCCcchHHHHHHHHHhcCCCHHHHH
Q 001100 558 DTFSFPAHLTHFQSKRLNQLSIGSHTEAKDIEQKINS-ANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTM 636 (1158)
Q Consensus 558 ~g~~f~a~l~~~~~~k~~~~~i~d~~~Ae~i~~~l~~-~~~~V~~v~~k~~~~~PP~Pf~tstLQ~~AskklG~Sa~~Tm 636 (1158)
.+...| +..|+.|.+.|..+++.++. +.+.|.+|.+|+..+..|..+||.+|.+.|
T Consensus 226 ---~~~lew--------~r~rvfd~eia~~f~~~vk~~~~a~v~~vs~ke~~k~rp~alntvel~rv~------------ 282 (555)
T KOG1957|consen 226 ---DLSLEW--------QRGRVFDAEIARVFLNRVKECKTALVEDVSKKEARKERPCALNTVELMRVA------------ 282 (555)
T ss_pred ---Cccchh--------hhcchhhHHHHHHHHHHHHhhhhheehhhhhhHHhhcCCcccchhheeeee------------
Confidence 133333 24578899999999998864 689999999999999999999999998776
Q ss_pred HHHHHHhccccCCCCCeeEEEEEecCCCcCCCHHHHHHHHHHHHHHhCCCCCCCCCCCccccccccccccCCCCCCCccc
Q 001100 637 KLAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFERYGSHHAPEEGPRKYFKKVKNAQEAHEAIRPTDIR 716 (1158)
Q Consensus 637 ~iAQ~LYE~~k~~~g~~~GlITYPRTDS~~Ls~~~~~~i~~~i~~~~g~~~~~~~~~r~~~~k~k~~qeAH~AI~PT~~~ 716 (1158)
+|+.+.+|..+-..+ + .+..+.. + +... ..++|+||.|-..-
T Consensus 283 ------------------------itett~y~~nfd~si---~---~~D~L~~---~----s~gt-dAgdgpPitpmr~~ 324 (555)
T KOG1957|consen 283 ------------------------ITETTAYPANFDTSI---I---LGDTLFE---A----SFGT-DAGDGPPITPMRKC 324 (555)
T ss_pred ------------------------EeecccCcccccccc---c---ccccccc---c----cccC-cCCCCCCcCccccc
Confidence 155555555431100 0 0110100 0 1111 12579999998742
Q ss_pred CChhhhhCCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEEEEEecCccEEEE--EEeEEEEEcCceeeccccchhhhccc
Q 001100 717 RLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGNADESIVFR--SSCSRVEFLGFQAAYEDVDAGAIRYK 794 (1158)
Q Consensus 717 ~~P~~l~~~Ls~dE~kLY~LI~rRfLAs~~~~a~~e~t~v~i~~~~~~~~F~--asg~~i~~~Gw~~vy~~~~~~~~~~~ 794 (1158)
.. ...+.+-++||..++++|++.-+...+|..+++...++++ .|. .+|+++.+.||..+......-.-...
T Consensus 325 ---~R--~m~~~dtkRLY~~vCqhf~~tp~~~~~k~it~~k~slgde--qf~lw~~Gk~~~~~gft~fm~n~p~m~wgag 397 (555)
T KOG1957|consen 325 ---NR--YMKSGDTKRLYCYVCQHFYATPQFKCKKVITTVKCSLGDE--QFILWCTGKRLREFGFTPFMPNNPKMPWGAG 397 (555)
T ss_pred ---cc--ccccccceeecchhhhhheeccCcCceEEEeeeeeccCCe--eEEeccCcceeccCCccccccCCCccccccC
Confidence 11 2356678899999999999999999999999998888654 677 99999999999998652100000000
Q ss_pred cccchhhhhhHHhcCCCCCCCeeEeeeEEEeccccCCCCCCCHhHHHHHHHhcCCCCCcchHHHHHHhhccceEEEc-Cc
Q 001100 795 ENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVK-SR 873 (1158)
Q Consensus 795 e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk~GIGTpATrAsIIe~L~~R~YV~~k-~k 873 (1158)
.++.. ...-...|.-+--|+.+.+.++.+...+|.||-++|+..|+..||++||||.+..+-+|..+-+|+||..+ +|
T Consensus 398 cdECt-hPScq~slSmlgiG~~vEc~~v~Lv~~qTsPkwylTcnkcisvme~hgigtdasI~VhinsiceRnYv~Ve~gr 476 (555)
T KOG1957|consen 398 CDECT-HPSCQQSLSMLGIGQCVECESVELVLDQTSPKWYLTCNKCISVMEKHGIGTDASIPVHINSICERNYVTVESGR 476 (555)
T ss_pred CCccC-CchHHhhhhcccceeEEEeccEEEEecCCCCCceeehhhhHHHHHhhcccceeeEEEeecchhhhheEeeecCc
Confidence 11100 00001223334459999999999999999999999999999999999999999999999999999999987 78
Q ss_pred ccccccccchhhhhhhcccccccChhhhHHHHHHhhhhhcCCchHHHHHHHHHH
Q 001100 874 ILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKGLLVDYWS 927 (1158)
Q Consensus 874 ~L~PT~lG~~v~~~L~~~f~~l~~p~~TA~~E~~Ld~Ia~Gk~~~~~~L~~F~~ 927 (1158)
.++||++|+.+......--|++.-|.+.++.|.++-.++.|..+..++++.+..
T Consensus 477 ~~~Pt~Lg~~l~~Gy~~~DP~l~lpt~r~~~es~~~lvA~G~A~~q~v~R~r~r 530 (555)
T KOG1957|consen 477 ALVPTPLGETLVRGYVKCDPELVLPTMRKEAESQLPLVAGGPADFQDVWRNRGR 530 (555)
T ss_pred ccCCCccchhhhcCceeeCcceechhHHHHHHhhchhhhCCccchhhhhhccee
Confidence 899999999877655444578889999999999999999999998887766443
No 27
>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=99.97 E-value=1.5e-30 Score=257.23 Aligned_cols=122 Identities=48% Similarity=0.708 Sum_probs=109.8
Q ss_pred CeEEEEecchHHHHHHhhcCCCEEEEeeccccccccccCCCCCCCCC-CcceEecCcchHHHHHHHHHHhccCCeEEEcc
Q 001100 350 KSVVVVESVTKAKVIQGYLGDMYEVLPSYGHVRDLAARSGSVRPDDD-FSMVWEVPSAAWTHLKSIKVALSGAENLILAS 428 (1158)
Q Consensus 350 k~LIIvEkPskAk~Ia~~LG~~y~V~~s~GHl~dL~~~~~~v~p~~~-f~~~~~v~~~~~k~lk~Ik~l~k~ad~IIlAT 428 (1158)
|+|||+|||++|++|+++||.+|+|+||.|||++|++|+...++.+. |.+.|.+.+.++++++.|+++++++|+|||||
T Consensus 1 ~~LiIaEKp~~a~~ia~~Lg~~~~v~~~~GHl~~l~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~ik~l~~~~~eiiiAt 80 (123)
T cd03363 1 KKLVIVESPAKAKTIKKYLGKEYEVLASVGHIRDLPKKGLGVDGEDDGFEPKYVVIPGKKKVVKELKKLAKKADEIYLAT 80 (123)
T ss_pred CEEEEEeCHHHHHHHHHHhCCCcEEEeccCccccCCCcccCCChhccCcCceEEECccHHHHHHHHHHHHhcCCEEEEcC
Confidence 68999999999999999999999999999999999987665433322 56678887788999999999999999999999
Q ss_pred CCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhc
Q 001100 429 DPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAA 477 (1158)
Q Consensus 429 DpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fs~lT~~aI~~A~~nl 477 (1158)
|||||||+|+|+|+++++. +.+|+|+|||++|+++|++||+||
T Consensus 81 D~drEGe~i~~~i~~~~~~------~~~v~Rl~~sslt~~~I~~A~~n~ 123 (123)
T cd03363 81 DPDREGEAIAWHLAEVLKL------KKNVKRVVFNEITKEAIKEALKNP 123 (123)
T ss_pred CCCcchHHHHHHHHHHcCC------CCCeEEEEEccCCHHHHHHHHhCc
Confidence 9999999999999999852 578999999999999999999986
No 28
>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=99.96 E-value=8.4e-30 Score=257.87 Aligned_cols=123 Identities=37% Similarity=0.531 Sum_probs=105.8
Q ss_pred CeEEEEecchHHHHHHhhcCC------------CEEEEeeccccccccccCCCCCCCC-------CCcceEecCcchHHH
Q 001100 350 KSVVVVESVTKAKVIQGYLGD------------MYEVLPSYGHVRDLAARSGSVRPDD-------DFSMVWEVPSAAWTH 410 (1158)
Q Consensus 350 k~LIIvEkPskAk~Ia~~LG~------------~y~V~~s~GHl~dL~~~~~~v~p~~-------~f~~~~~v~~~~~k~ 410 (1158)
+.|||||||++|++|+++||. +|+|+|+.|||++|+++........ .+.+.|.+...+.++
T Consensus 1 ~~LiIaEKPs~a~~ia~~L~~~~~~~~~~~~~~~~~v~~~~GHl~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (142)
T cd01028 1 KVLIIAEKPSKAKTIAKILGKGSKKKGFYGEGGGYVVTASVGHLLELPFPEEYVDWDKDWPLELFPFEPKYVVIPDKKKQ 80 (142)
T ss_pred CEEEEEeCHHHHHHHHHHhCCCcccCCceecCCCEEEEEEccccccCCCcccccccccCCchhhCCCCceEEeCCcHHHH
Confidence 579999999999999999975 6899999999999998764321111 123456666778999
Q ss_pred HHHHHHHhccCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhc
Q 001100 411 LKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAA 477 (1158)
Q Consensus 411 lk~Ik~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fs~lT~~aI~~A~~nl 477 (1158)
++.|++++++||+||||||||||||+|||||+++++. .+++++|+|||+||+++|++||+||
T Consensus 81 ~~~ik~l~~~~d~iiiAtD~DrEGE~I~~~i~~~~~~-----~~~~v~R~~fsslT~~~I~~A~~nl 142 (142)
T cd01028 81 LKALKKLAKKADEIVLATDPDREGELIAWEILEVLKC-----DNKPVKRAWFSEITPKAIREAFKNL 142 (142)
T ss_pred HHHHHHHHhcCCEEEEcCCCCcchHHHHHHHHHHhCC-----CCCCeEEEEEccCCHHHHHHHHhCc
Confidence 9999999999999999999999999999999999863 2579999999999999999999986
No 29
>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=99.96 E-value=3.4e-29 Score=255.97 Aligned_cols=124 Identities=27% Similarity=0.332 Sum_probs=105.5
Q ss_pred CeEEEEecchHHHHHHhhcC------------------CCEEEEeeccccccccccCCC-----CCCC----CCCcceEe
Q 001100 350 KSVVVVESVTKAKVIQGYLG------------------DMYEVLPSYGHVRDLAARSGS-----VRPD----DDFSMVWE 402 (1158)
Q Consensus 350 k~LIIvEkPskAk~Ia~~LG------------------~~y~V~~s~GHl~dL~~~~~~-----v~p~----~~f~~~~~ 402 (1158)
|.|||||||++|++|+++|| .+|+|+|+.|||++|+.|+.. ..+. ..+.+.|+
T Consensus 1 ~~LiIAEKPs~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~~~~vt~~~GHl~~l~~p~~y~~~~~~~~~~~p~~~~~~~~~ 80 (151)
T cd03362 1 MVLIIAEKPSVAKAIAKILGGGSKKKGKGRYYEFYGEGGGYVVTWASGHLLELDFPEEYDPWDKVWPLEDPLFPAPFKLK 80 (151)
T ss_pred CEEEEecCHHHHHHHHHHhCCCCccCCcccccceecCCCCEEEEEEhhHhhcccChHHhccCCCCCccccCCcCCceEEE
Confidence 57999999999999999994 368999999999999876421 1111 22344567
Q ss_pred cCcchHHHHHHHHHHhccCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhc
Q 001100 403 VPSAAWTHLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAA 477 (1158)
Q Consensus 403 v~~~~~k~lk~Ik~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fs~lT~~aI~~A~~nl 477 (1158)
+...++++++.|++++++||.||||||||||||+|||+|+++++.. .+++|+|||||+||+++|++||+||
T Consensus 81 ~~~~~~~~~~~ik~l~~~ad~ii~atD~DrEGE~I~~~i~~~~~~~----~~~~v~R~~fsslT~~~I~~A~~nl 151 (151)
T cd03362 81 VDKGKKKQFKVLKKLAKRADEIVIATDADREGELIGREILEYAKCV----KRKPVKRAWFSSLTPKAIRRAFKNL 151 (151)
T ss_pred ECccHHHHHHHHHHHHhCCCeEEEccCCCccccHHHHHHHHHhCCC----CCCcEEEEEEccCCHHHHHHHHhcC
Confidence 7778899999999999999999999999999999999999998641 3679999999999999999999986
No 30
>smart00436 TOP1Bc Bacterial DNA topoisomeraes I ATP-binding domain. Extension of TOPRIM in Bacterial DNA topoisomeraes I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase beta subunit
Probab=99.96 E-value=9.1e-30 Score=237.47 Aligned_cols=88 Identities=56% Similarity=0.844 Sum_probs=84.7
Q ss_pred EEEEEEcccCHHHHHHHHHhcccccHhHHHHHHHHHHHhhhhhhcccHHHHhhCCC-cccCCcchhHHHHHHHHHHHHHH
Q 001100 457 VARVVFHEITEASIKVALQAAREIDANLVQAYLARRALDYLIGFNISPLLWRKLPG-CQSAGRVQSAALSLICDREMEID 535 (1158)
Q Consensus 457 vkRl~fs~lT~~aI~~A~~nlr~~d~~L~~A~~AR~~lD~LiG~nlSR~l~~k~~~-~lS~GRVQTPtL~LVveRe~EI~ 535 (1158)
|+|+|||++|+++|++||+|+++.+.+|++|++||+++|||+|||+||++|.++.. .+|+||||||||+|||+||+||+
T Consensus 1 v~R~~fs~lt~~~I~~a~~~l~~~~~~l~~a~~aR~~~D~l~G~n~Sr~~t~~~~~~~ls~GRVQtptL~lIv~R~~ei~ 80 (89)
T smart00436 1 IKRIEFSEITKKAIREALKNPREIDENLVNAQLARRILDRLIGFNLSRLLTKKLRKGVLSAGRVQTPTLGLIVEREREIK 80 (89)
T ss_pred CEEEEEecCCHHHHHHHHHCcccccHHHHHHHHHHHHHHHHHhHhhhHHHHHHhCCCCcceecchHHHHHHHHHHHHHHH
Confidence 58999999999999999999999999999999999999999999999999988764 79999999999999999999999
Q ss_pred hcCCcceEE
Q 001100 536 EFKPQEYWT 544 (1158)
Q Consensus 536 ~Fkp~~Yw~ 544 (1158)
+|+|++||.
T Consensus 81 ~F~~~~y~~ 89 (89)
T smart00436 81 NFVPKPYWE 89 (89)
T ss_pred cCCCCCCCC
Confidence 999999994
No 31
>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=99.94 E-value=8e-27 Score=242.85 Aligned_cols=122 Identities=30% Similarity=0.516 Sum_probs=101.1
Q ss_pred eEEEEecchHHHHHHhhcCCC-------------------EEEEeeccccccccccCCCC--CCC-CCCcceEec-----
Q 001100 351 SVVVVESVTKAKVIQGYLGDM-------------------YEVLPSYGHVRDLAARSGSV--RPD-DDFSMVWEV----- 403 (1158)
Q Consensus 351 ~LIIvEkPskAk~Ia~~LG~~-------------------y~V~~s~GHl~dL~~~~~~v--~p~-~~f~~~~~v----- 403 (1158)
.|||||||++||+|+++||.. |+|+|+.|||++|+.++... ... ..|.+.|..
T Consensus 2 ~LiIaEKPs~Ak~Ia~~L~~~~~~~~~~~~~~e~~~~~~~~~Vt~~~GHl~~l~~~~~~~~~~~~~~~~~p~~~~~~~c~ 81 (170)
T cd03361 2 ALMIVESPNKARTIANFFGRPSVRRLGGLVVYEVSTGDGVLMITASGGHVYDLVTKEGGHGVVEDDGRYVPVYDSIKRCR 81 (170)
T ss_pred eEEEEeChHHHHHHHHHhCCCcccccCCceeEEEecCCeEEEEEeCCCeeecCCCccCccCccccCCcceeeeeEeeccC
Confidence 699999999999999999753 36999999999998765422 111 125443321
Q ss_pred --------------------CcchHHHHHHHHHHhccCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEc
Q 001100 404 --------------------PSAAWTHLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFH 463 (1158)
Q Consensus 404 --------------------~~~~~k~lk~Ik~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fs 463 (1158)
.++++++++.|++++++||+||||||||||||+|+|||+++++. .+.+++|+|||
T Consensus 82 pc~~lF~~~~~~cp~c~~~~~~~~~~~~~~l~~l~~~~~~iiiatD~drEGe~I~~~i~~~~~~-----~~~~v~R~~fs 156 (170)
T cd03361 82 DCGYQFTEDSDKCPRCGSENIDDKLETLEALRELALEVDEVLIATDPDTEGEKIAWDVYLALRP-----YNKNIKRAEFH 156 (170)
T ss_pred CcccccccccccCCcCCCcCCcchHHHHHHHHHHHhhCCEEEEecCCCccHHHHHHHHHHHhcc-----CCCCeEEEEEe
Confidence 14578999999999999999999999999999999999999863 24689999999
Q ss_pred ccCHHHHHHHHHhc
Q 001100 464 EITEASIKVALQAA 477 (1158)
Q Consensus 464 ~lT~~aI~~A~~nl 477 (1158)
+||+++|++||+||
T Consensus 157 ~it~~~I~~a~~n~ 170 (170)
T cd03361 157 EVTRRAILEALRNP 170 (170)
T ss_pred cCCHHHHHHHHhCc
Confidence 99999999999986
No 32
>COG1754 Uncharacterized C-terminal domain of topoisomerase IA [General function prediction only]
Probab=99.93 E-value=2.3e-26 Score=248.06 Aligned_cols=167 Identities=33% Similarity=0.606 Sum_probs=143.7
Q ss_pred CCCCCCCCCCeEEEEecccCceeEEecCCCCCCcccccCCCCCCchhhhhhhccCCCCCcccCCCCCccceeeeccCCCc
Q 001100 964 DRSCPVCGEGTLIFKVSRFGAGYFIGCNQHPRCNYIAKTLYGDDDEEDTLQRNTNVDEPKLIGHHPASKEKVLLKSGPYG 1043 (1158)
Q Consensus 964 ~g~CPkCGkG~l~~k~gr~G~~~f~GCs~yP~C~~~~~~~~~e~~~~e~~~~~~~~~lPr~LG~cPkcG~~v~lk~GrfG 1043 (1158)
..+||.|+.+.+.++.|+||+ |++|+|||.|.+...+.....+..+. .....|++||.+|.+|.+|+++.||||
T Consensus 23 ~rt~~~~~~~~~slk~GKyGp--yl~~an~Pe~~~~~eL~~e~~~~l~~----~~~~~~r~LG~DP~tG~eI~~k~GryG 96 (298)
T COG1754 23 PRTCPLCGTGELSLKLGKYGP--YLECANYPECTTPKELTLEVAENLEA----TPQGGPRVLGIDPETGEEIYLKNGRYG 96 (298)
T ss_pred CcccccccccceeEEeccccc--cceeccCccccChhhhcchhcccccc----ccCCCCcccccCCCCCceeEEeccCCC
Confidence 578999999999999999999 88999999999876443322221111 123456999999999999999999999
Q ss_pred ceEEe--CCCCCCCCCcccccCCCCCccccCHHHHHHHhcCCcccCCCCCCCcCeEEeeccCccee-ecCCeeeecCCCC
Q 001100 1044 FYVQL--GEDRTGYLPKRASVSHIKDVDSITLEDALELLRYPVNLGNHPKDGQPIMLRLARAGFSV-RHRRTIASVPKNM 1120 (1158)
Q Consensus 1044 ~yv~c--~~d~kg~kpK~~slpk~~~~~sItle~Al~ll~~pk~lG~cP~cG~~I~i~~GRyG~Yi-~~~~~~~~lpk~~ 1120 (1158)
|||+. ++ .+.+|++.|||+..++++||||+||.||++|+.+|+||+.|+.|.+..||||||+ ..|...++|....
T Consensus 97 PYVq~~lg~--~~~kpkraSLpkg~~~e~ItLE~AL~LLsLPR~iG~hp~sge~I~ag~GRfGPyv~k~Gsd~~sL~~~d 174 (298)
T COG1754 97 PYVQEQLGD--PKPKPKRASLPKGWKPETITLEKALKLLSLPRVIGKHPDSGEEISAGLGRFGPYVKKRGSDYRSLKSED 174 (298)
T ss_pred ceeeeecCC--CCCCcccccCCCCCChhhCcHHHHHHHHcCchhhCCCCCCCcEEEecccccCcceeecCcccccccccc
Confidence 99985 43 2478999999999999999999999999999999999999999999999999998 4455599999999
Q ss_pred CCCCCCHHHHHHHhhccc
Q 001100 1121 KPNDVTLEKALEFLSGKD 1138 (1158)
Q Consensus 1121 ~~~~itle~A~~LL~~k~ 1138 (1158)
++.+|||++|+.||++++
T Consensus 175 d~ftItL~rA~~liaEk~ 192 (298)
T COG1754 175 DVFTITLDRALKLIAEKR 192 (298)
T ss_pred ceeeecHHHHHHHHHhhh
Confidence 999999999999999955
No 33
>COG1754 Uncharacterized C-terminal domain of topoisomerase IA [General function prediction only]
Probab=99.91 E-value=1.3e-24 Score=234.77 Aligned_cols=170 Identities=30% Similarity=0.451 Sum_probs=150.8
Q ss_pred CCCCCCCCCCCCeEEEEecccCceeE--EecC-CCCCCcccccCCCCCCchhhhhhhccCCCCCcccCCCCCccceeeec
Q 001100 962 NKDRSCPVCGEGTLIFKVSRFGAGYF--IGCN-QHPRCNYIAKTLYGDDDEEDTLQRNTNVDEPKLIGHHPASKEKVLLK 1038 (1158)
Q Consensus 962 ~~~g~CPkCGkG~l~~k~gr~G~~~f--~GCs-~yP~C~~~~~~~~~e~~~~e~~~~~~~~~lPr~LG~cPkcG~~v~lk 1038 (1158)
..+|..|..|. .+..|.||||+|++ +|.. ..|+....++.+..++++.|.+. .++++||.||.||.+|+.|.+.
T Consensus 76 r~LG~DP~tG~-eI~~k~GryGPYVq~~lg~~~~kpkraSLpkg~~~e~ItLE~AL--~LLsLPR~iG~hp~sge~I~ag 152 (298)
T COG1754 76 RVLGIDPETGE-EIYLKNGRYGPYVQEQLGDPKPKPKRASLPKGWKPETITLEKAL--KLLSLPRVIGKHPDSGEEISAG 152 (298)
T ss_pred cccccCCCCCc-eeEEeccCCCceeeeecCCCCCCcccccCCCCCChhhCcHHHHH--HHHcCchhhCCCCCCCcEEEec
Confidence 46899999997 89999999999987 4776 45777777888888888888876 5889999999999999999999
Q ss_pred cCCCcceEEeCCCCCCCCCcccccCCCCCccccCHHHHHHHhcCCc----------ccCCCCCCCcCeEEeeccCcceee
Q 001100 1039 SGPYGFYVQLGEDRTGYLPKRASVSHIKDVDSITLEDALELLRYPV----------NLGNHPKDGQPIMLRLARAGFSVR 1108 (1158)
Q Consensus 1039 ~GrfG~yv~c~~d~kg~kpK~~slpk~~~~~sItle~Al~ll~~pk----------~lG~cP~cG~~I~i~~GRyG~Yi~ 1108 (1158)
.|||||||.+.. ..++||...+++++|+|++|+.||+.++ +||.||+.|++|.|+.||||||++
T Consensus 153 ~GRfGPyv~k~G------sd~~sL~~~dd~ftItL~rA~~liaEk~~~G~s~~alk~lg~~p~~g~pI~v~dGrfGpYv~ 226 (298)
T COG1754 153 LGRFGPYVKKRG------SDYRSLKSEDDVFTITLDRALKLIAEKRSRGRSAAALKELGTHPEGGKPITVKDGRFGPYVK 226 (298)
T ss_pred ccccCcceeecC------ccccccccccceeeecHHHHHHHHHhhhccCcchhhHHHhccCccCCcceEEecCCcCcccc
Confidence 999999996531 1378999999999999999999998765 578999999999999999999999
Q ss_pred cCCeeeecCCCCCCCCCCHHHHHHHhhccccc
Q 001100 1109 HRRTIASVPKNMKPNDVTLEKALEFLSGKDVR 1140 (1158)
Q Consensus 1109 ~~~~~~~lpk~~~~~~itle~A~~LL~~k~~k 1140 (1158)
+++.|++||++.++.+||+|+|++||+++.++
T Consensus 227 ~Gk~Na~Lpkg~d~~sit~e~A~~LLaer~a~ 258 (298)
T COG1754 227 DGKTNATLPKGKDPASITLEEALELLAERRAK 258 (298)
T ss_pred cccccccCCCCCCccccCHHHHHHHHHHhccc
Confidence 99999999999999999999999999986644
No 34
>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=99.83 E-value=4.7e-21 Score=182.72 Aligned_cols=99 Identities=36% Similarity=0.630 Sum_probs=84.0
Q ss_pred eEEEEecchHHHHHHhhcC-CCEEEEeeccccccccccCCCCCCCCCCcceEecCcchHHHHHHHHHHhccCCeEEEccC
Q 001100 351 SVVVVESVTKAKVIQGYLG-DMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILASD 429 (1158)
Q Consensus 351 ~LIIvEkPskAk~Ia~~LG-~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~~~k~lk~Ik~l~k~ad~IIlATD 429 (1158)
.|||||+|++|++|+++|+ ..|.|+|+.||++++..++.... ..+.++++.|+++++++|.||||||
T Consensus 1 ~liIvE~ps~a~~i~~~l~~~~~~v~~~~Ghl~~~~~~~~~~~------------~~~~~~i~~l~~~~~~~~~iiiatD 68 (100)
T PF01751_consen 1 ELIIVEKPSDAKAIAKALGGEEYIVIATSGHLLELAKPEDYDP------------KDKKKQIKNLKKLLKKADEIIIATD 68 (100)
T ss_dssp EEEEESSHHHHHHHHHHSSTTTEEEEEESSSSEESTTSSHHHC------------HTTHHHHHHHHHHHHSCSEEEEEC-
T ss_pred CEEEEeCHHHHHHHHHHcCCCCEEEEEeCCccccccccccccc------------ccccccchhhHHHhhhccEeeecCC
Confidence 5999999999999999998 45999999999999977432111 4678999999999999999999999
Q ss_pred CCccccHHHHHHHHHHhhcccccCCccEEEEEEccc
Q 001100 430 PDREGEAIAWHIVEMLQQQDALHENITVARVVFHEI 465 (1158)
Q Consensus 430 pDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fs~l 465 (1158)
||||||+|+|+|+++++... +.. ++|+|||+|
T Consensus 69 ~D~EGe~Ia~~i~~~~~~~~---~~~-~~R~~~~~i 100 (100)
T PF01751_consen 69 PDREGELIAWEIIELLGKNN---PKL-IKRVWFSSI 100 (100)
T ss_dssp SSHHHHHHHHHHHHHHHHHS---HHH-TTEEEEESS
T ss_pred CChHHHHHHHHHHHHHhHhC---CCc-CCEEEEecC
Confidence 99999999999999997632 111 699999986
No 35
>PRK07561 DNA topoisomerase I subunit omega; Validated
Probab=99.69 E-value=9.1e-17 Score=203.76 Aligned_cols=155 Identities=33% Similarity=0.532 Sum_probs=124.7
Q ss_pred CCCCCCCCCCCCeEEEEecccCceeEEe----------c-CCCCCCcccccCCCCCCchhhhhhhccCCCCCcccCCCCC
Q 001100 962 NKDRSCPVCGEGTLIFKVSRFGAGYFIG----------C-NQHPRCNYIAKTLYGDDDEEDTLQRNTNVDEPKLIGHHPA 1030 (1158)
Q Consensus 962 ~~~g~CPkCGkG~l~~k~gr~G~~~f~G----------C-s~yP~C~~~~~~~~~e~~~~e~~~~~~~~~lPr~LG~cPk 1030 (1158)
..++.||.||. .++++.||||++++.+ | +.+|.|.. .+.+. .++++|+.+|.||+
T Consensus 643 ~~lg~~P~cg~-~i~~r~Gr~Gpyv~~~~~~~~~~~sic~~~~p~c~~-----------~e~a~--~ll~~pr~lg~cPe 708 (859)
T PRK07561 643 RALGADPECGT-AMVLRSGRFGPYVQEGEGDKPRRLSLPKGNNPECVG-----------LEIAL--GLLSLPRPVGEHPE 708 (859)
T ss_pred cccCCCCCCCC-eeEEecCCCCCeeecccCCCCceeccCCCCCCCcCC-----------HHHHH--hhhccccccCcCCC
Confidence 34678999997 6777999999854322 5 34555532 22222 34567899999999
Q ss_pred ccceeeeccCCCcceEEeCCCCCCCCCcccccCCCCCccccCHHHHHHHhcCC----------cccCCCCCCCcCeEEee
Q 001100 1031 SKEKVLLKSGPYGFYVQLGEDRTGYLPKRASVSHIKDVDSITLEDALELLRYP----------VNLGNHPKDGQPIMLRL 1100 (1158)
Q Consensus 1031 cG~~v~lk~GrfG~yv~c~~d~kg~kpK~~slpk~~~~~sItle~Al~ll~~p----------k~lG~cP~cG~~I~i~~ 1100 (1158)
||..|+++.||||+||+|+. .+.+++...++.++++++|+.+|..| +.+| ||.||++|.+.+
T Consensus 709 cg~~i~~k~gr~G~yl~c~~-------~~~sc~~~~~~~~i~l~~a~~ll~~~~~~~~~~~~~k~~g-~p~~g~~i~~~~ 780 (859)
T PRK07561 709 CGSEIQAKIGRFGPYVKCGG-------TYASLKNTRKVLTIGLNRAVELLAEPKRPKEDPVPLPELG-CPKSGAPFVLRD 780 (859)
T ss_pred CCCeeEEecCCCCCeEEeCC-------CcCCCCCCCccccCCHHHHHHHHhcccccccccccccccC-CCCCCCeEEEec
Confidence 99999999999999999963 33455555678889999999999888 3343 699999999999
Q ss_pred ccCcceeecCCeeeecCCCCCCCCCCHHHHHHHhhccc
Q 001100 1101 ARAGFSVRHRRTIASVPKNMKPNDVTLEKALEFLSGKD 1138 (1158)
Q Consensus 1101 GRyG~Yi~~~~~~~~lpk~~~~~~itle~A~~LL~~k~ 1138 (1158)
||||+|+.|++.|+++|++.++.++|+++|++||+++.
T Consensus 781 Gr~Gpyi~~~~~~~slpk~~~~~~itle~a~~li~~~~ 818 (859)
T PRK07561 781 GRYGPYVKHGKANATLPKGRETRAPTVEEALELLAEKP 818 (859)
T ss_pred CCCCccccccchhccCCCCCCcccCCHHHHHHHHhhcc
Confidence 99999999999999999999999999999999998763
No 36
>PRK08780 DNA topoisomerase I; Provisional
Probab=99.68 E-value=5.8e-17 Score=203.20 Aligned_cols=118 Identities=31% Similarity=0.477 Sum_probs=108.4
Q ss_pred CcccCCCCCccceeeeccCCCcceEEeCCCCCCCCCcccccCCCCCccccCHHHHHHHhcCCcccCCCCCCCcCeEEeec
Q 001100 1022 PKLIGHHPASKEKVLLKSGPYGFYVQLGEDRTGYLPKRASVSHIKDVDSITLEDALELLRYPVNLGNHPKDGQPIMLRLA 1101 (1158)
Q Consensus 1022 Pr~LG~cPkcG~~v~lk~GrfG~yv~c~~d~kg~kpK~~slpk~~~~~sItle~Al~ll~~pk~lG~cP~cG~~I~i~~G 1101 (1158)
++.+|.||+||..|+++.||||+||+|++...+..|+++|||+..++++||+++|++||++|+.+|.||+ |++|+++.|
T Consensus 588 ~r~lG~cP~CG~~l~~r~gr~G~fl~~g~~~~~~~p~~asl~~~~~~~~itle~A~~ll~~pr~lG~~P~-g~~I~~~~G 666 (780)
T PRK08780 588 VRELGTDPKSGKPVSVRIGRFGPMVQIGTKDDEEKPRFASLRPGQSIDSITLEEALELFKLPRALGETDE-GEDVSVGIG 666 (780)
T ss_pred cccCCCCCCCCCEEEEEeCCCCCeeeccCcccccccccccCCCCCCcccCCHHHHHHHhcCccccCcCCC-CCeeEEeeC
Confidence 4678999999999999999999999997533334689999999999999999999999999999999996 779999999
Q ss_pred cCcceeecCCeeeecCCCCCCCCCCHHHHHHHhhccccc
Q 001100 1102 RAGFSVRHRRTIASVPKNMKPNDVTLEKALEFLSGKDVR 1140 (1158)
Q Consensus 1102 RyG~Yi~~~~~~~~lpk~~~~~~itle~A~~LL~~k~~k 1140 (1158)
|||||+++++++.+||+..++.++|+++|++||++++.+
T Consensus 667 RfGpYv~~~~~~~sl~k~~~~~~itle~A~~ll~~k~~~ 705 (780)
T PRK08780 667 RFGPFVKRGSKYASLKKEDDPYTIDLARALFLIEEKEEI 705 (780)
T ss_pred CCCCeEeeCCcccCCCCCCCcccCCHHHHHHHHHhhhhc
Confidence 999999999999999999999999999999999886543
No 37
>PF13368 Toprim_C_rpt: Topoisomerase C-terminal repeat
Probab=98.81 E-value=5.6e-09 Score=91.52 Aligned_cols=50 Identities=42% Similarity=0.740 Sum_probs=46.3
Q ss_pred CCCCCcCeEEeeccCcceeecCCeeeecCCCCCCCCCCHHHHHHHhhcccc
Q 001100 1089 HPKDGQPIMLRLARAGFSVRHRRTIASVPKNMKPNDVTLEKALEFLSGKDV 1139 (1158)
Q Consensus 1089 cP~cG~~I~i~~GRyG~Yi~~~~~~~~lpk~~~~~~itle~A~~LL~~k~~ 1139 (1158)
||+.|..| |+.|||||||+++..+++||++.++.++|+++|++||++++.
T Consensus 1 ~Pe~g~~i-v~~GRfGPYv~~g~~~~slpk~~~~~~itle~a~~ll~~~~~ 50 (61)
T PF13368_consen 1 HPESGKPI-VKNGRFGPYVKHGKKNASLPKDEDPEEITLEEAVELLAEKKK 50 (61)
T ss_pred CCCCCCEE-EeECCCCceEEECCcccccCCCCCcccCCHHHHHHHHhchhh
Confidence 78888777 799999999999999999999999999999999999987754
No 38
>smart00493 TOPRIM topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins.
Probab=98.59 E-value=1.7e-07 Score=84.49 Aligned_cols=73 Identities=36% Similarity=0.499 Sum_probs=63.1
Q ss_pred CeEEEEecchHHHHHHhhcCCCEEEEeeccccccccccCCCCCCCCCCcceEecCcchHHHHHHHHHHhccCCeEEEccC
Q 001100 350 KSVVVVESVTKAKVIQGYLGDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILASD 429 (1158)
Q Consensus 350 k~LIIvEkPskAk~Ia~~LG~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~~~k~lk~Ik~l~k~ad~IIlATD 429 (1158)
+.|+|||.|.-|.++..+++.++.+.++.||+. ..++++.|++...+ +.||||+|
T Consensus 1 ~~l~ivEg~~da~~~~~~~~~~~~~~~~~G~~~------------------------~~~~~~~l~~~~~~-~~Iii~~D 55 (76)
T smart00493 1 KVLIIVEGPADAIALEKAGGFGGNVVALGGHLL------------------------KKEIIKLLKRLAKK-KEVILATD 55 (76)
T ss_pred CEEEEEcCHHHHHHHHHhcCCCEEEEEEeeeec------------------------HHHHHHHHHHHhcC-CEEEEEcC
Confidence 469999999999999999998888999999972 23577778887766 89999999
Q ss_pred CCccccHHHHHHHHHHhh
Q 001100 430 PDREGEAIAWHIVEMLQQ 447 (1158)
Q Consensus 430 pDREGE~Ia~~Ile~l~~ 447 (1158)
+|+||+.++++|.+++..
T Consensus 56 ~D~~G~~~~~~i~~~l~~ 73 (76)
T smart00493 56 PDREGEAIAWKLAELLKP 73 (76)
T ss_pred CChhHHHHHHHHHHHhhh
Confidence 999999999999998753
No 39
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=98.54 E-value=2.9e-07 Score=93.56 Aligned_cols=100 Identities=21% Similarity=0.477 Sum_probs=69.9
Q ss_pred CCCCCCCCCCCCeEEEEecccCceeEEecCCCCCCcccccCCCCCCchhhhhhhccCCCCCcccCCCCCcc-ceeeeccC
Q 001100 962 NKDRSCPVCGEGTLIFKVSRFGAGYFIGCNQHPRCNYIAKTLYGDDDEEDTLQRNTNVDEPKLIGHHPASK-EKVLLKSG 1040 (1158)
Q Consensus 962 ~~~g~CPkCGkG~l~~k~gr~G~~~f~GCs~yP~C~~~~~~~~~e~~~~e~~~~~~~~~lPr~LG~cPkcG-~~v~lk~G 1040 (1158)
.+.+.||+||+ .|+++.+++| .|+||++||.|.+.. .. ... ....-+.||+|| ..++++.|
T Consensus 15 ~~~~~Cp~Cg~-~m~~~~~~~g--~f~gCs~yP~C~~~~-~~--~~~------------~~~~~~~Cp~C~~~~~~~k~~ 76 (140)
T COG0551 15 KTGQICPKCGK-NMVKKFGKYG--IFLGCSNYPKCDYYE-PE--KAI------------AEKTGVKCPKCGKGLLVLKKG 76 (140)
T ss_pred ccCccCCcCCC-eeEEEEccCC--eEEEeCCCCCCCCCc-cc--ccc------------cccCceeCCCCCCCceEEEec
Confidence 34679999996 7888899999 699999999999711 10 000 112235699999 68999999
Q ss_pred CCc-ceEEeCCCCCCCCCcccccCCCCCccccCHHHHHHHhcCCcccCCCCCCCcCeEEeec
Q 001100 1041 PYG-FYVQLGEDRTGYLPKRASVSHIKDVDSITLEDALELLRYPVNLGNHPKDGQPIMLRLA 1101 (1158)
Q Consensus 1041 rfG-~yv~c~~d~kg~kpK~~slpk~~~~~sItle~Al~ll~~pk~lG~cP~cG~~I~i~~G 1101 (1158)
+|| .|+.|. .+|+|..+.... .....||+||.+.++.++
T Consensus 77 ~~~~~f~~~~-----------~~Pkc~~~~~~~-----------~~~~~cp~c~~~~~~~k~ 116 (140)
T COG0551 77 RFGKNFLGCS-----------NYPKCRFTEKPK-----------PKEKKCPKCGSRKLVEKK 116 (140)
T ss_pred cCCceEEeec-----------CCCcCceeecCC-----------cccccCCcCCCceeEEEe
Confidence 998 688886 568887655432 112239999975554333
No 40
>cd01025 TOPRIM_recR TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in Escherichia coli RecR. RecR participates in the RecFOR pathway of homologous recombinational repair in prokaryotes. This pathway provides a single-stranded DNA molecule coated with RecA to allow invasion of a homologous molecule. The RecFOR system directs the loading of RecA onto gapped DNA coated with SSB protein. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). In RecR sequences this glutamate in the first turn of the TOPRIM domain is semiconserved, the DXD motif is not conserved.
Probab=98.43 E-value=8.1e-07 Score=86.91 Aligned_cols=88 Identities=31% Similarity=0.493 Sum_probs=66.5
Q ss_pred CeEEEEecchHHHHHHh---hcCCCEEEEeeccccccccccCCCCCCCCCCcceEecCcchHHHHHHHHHHhcc--CCeE
Q 001100 350 KSVVVVESVTKAKVIQG---YLGDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSG--AENL 424 (1158)
Q Consensus 350 k~LIIvEkPskAk~Ia~---~LG~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~~~k~lk~Ik~l~k~--ad~I 424 (1158)
+.|.|||.|....+|.+ |.|. |.|. .||+-.+. ++.|+ + -.++.|.+.+++ .++|
T Consensus 1 ~~lcVVE~~~Dv~~iE~~~~y~G~-Y~VL--~G~ispl~----gi~p~-~------------l~i~~L~~ri~~~~i~EV 60 (112)
T cd01025 1 NKLCVVEEPRDVLAIEESGEYRGL-YHVL--GGLISPLD----GIGPD-D------------LNIDKLLERIAKGQVKEV 60 (112)
T ss_pred CEEEEECCHHHHHHHHhhCccceE-EEEe--CCCcCCCC----CCCcc-c------------cCHHHHHHHHhcCCCcEE
Confidence 36899999999999998 6666 8888 67887664 23343 1 223445555543 5899
Q ss_pred EEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEE
Q 001100 425 ILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVF 462 (1158)
Q Consensus 425 IlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~f 462 (1158)
|+|||||+|||+++|+|.+.++. ...+|.|+-+
T Consensus 61 IlA~~pt~EGe~Ta~yi~~~l~~-----~~~kvsRlA~ 93 (112)
T cd01025 61 ILATNPTVEGEATALYIAKLLKD-----FGVKVTRLAQ 93 (112)
T ss_pred EEecCCCchHHHHHHHHHHHHhH-----cCCCeEEEEE
Confidence 99999999999999999999975 3467888865
No 41
>PF13368 Toprim_C_rpt: Topoisomerase C-terminal repeat
Probab=98.42 E-value=3.2e-07 Score=80.50 Aligned_cols=55 Identities=40% Similarity=0.620 Sum_probs=48.2
Q ss_pred CCCccceeeeccCCCcceEEeCCCCCCCCCcccccCCCCCccccCHHHHHHHhcCCcccCCCC
Q 001100 1028 HPASKEKVLLKSGPYGFYVQLGEDRTGYLPKRASVSHIKDVDSITLEDALELLRYPVNLGNHP 1090 (1158)
Q Consensus 1028 cPkcG~~v~lk~GrfG~yv~c~~d~kg~kpK~~slpk~~~~~sItle~Al~ll~~pk~lG~cP 1090 (1158)
+|++|..| ++.|||||||+++. .+++||+..++++||+++|++||+.|+..+...
T Consensus 1 ~Pe~g~~i-v~~GRfGPYv~~g~-------~~~slpk~~~~~~itle~a~~ll~~~~~~~~~k 55 (61)
T PF13368_consen 1 HPESGKPI-VKNGRFGPYVKHGK-------KNASLPKDEDPEEITLEEAVELLAEKKKKGKAK 55 (61)
T ss_pred CCCCCCEE-EeECCCCceEEECC-------cccccCCCCCcccCCHHHHHHHHhchhhcCCCC
Confidence 58888888 79999999999984 568999999999999999999999888766554
No 42
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=98.34 E-value=4.5e-07 Score=116.17 Aligned_cols=119 Identities=13% Similarity=0.099 Sum_probs=69.2
Q ss_pred hhHHHHHHHHHHHHHHhcCCcceEEEEEEEecCcCCCCCCceeeeecccc--ccc-cccccCcCCHH--HHHHHHHHH-c
Q 001100 520 QSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDTFSFPAHLTHF--QSK-RLNQLSIGSHT--EAKDIEQKI-N 593 (1158)
Q Consensus 520 QTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~g~~f~a~l~~~--~~~-k~~~~~i~d~~--~Ae~i~~~l-~ 593 (1158)
|--+-.||++|...-. ..|..|-...+.+..+. +..|.+.-... .|- .+-...-.+.+ +.+..+-.+ .
T Consensus 384 e~klY~LI~~RflAs~-m~~a~~~~t~v~~~~~~-----~~~F~a~G~~i~~~G~~~vy~~~~~~~~~~~~~~~LP~l~~ 457 (860)
T PRK06319 384 QYKLYSLIWKRFVASQ-MIPAIYDTLAIRITTNK-----GIDLRATGSLLKFKGFLAVYEEKRDDEGDEEENIHLPKLHE 457 (860)
T ss_pred HHHHHHHHHHHHHHHh-CchhheEEEEEEEEeCC-----eeEEEEEeEEEeeCCHHHHhCccccccccccccccCCCCCC
Confidence 3345578888887754 35666777777776421 12465542111 110 00000000000 111111112 3
Q ss_pred cCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHhcCCCHHHHHH-HHHHHhcc
Q 001100 594 SANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMK-LAQKLYEG 645 (1158)
Q Consensus 594 ~~~~~V~~v~~k~~~~~PP~Pf~tstLQ~~AskklG~Sa~~Tm~-iAQ~LYE~ 645 (1158)
+..+.+.+++..+....||+.|+-++|.+++-+ +|+.-.-|.. |.+.|.+.
T Consensus 458 Ge~~~~~~~~~~~~~T~PP~ryTeasLvk~me~-~GIGtpsT~A~iI~~L~~R 509 (860)
T PRK06319 458 QDVLTKEELSAEQAFTKPLPRFTEASLVKELEK-SGIGRPSTYATIMNKIQSR 509 (860)
T ss_pred CCEeeeeeeeecccccCCCCCCCHHHHHHHHHh-cCCCchhhHHHHHHHHhhC
Confidence 456778888888888999999999999999865 6887666665 78888885
No 43
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 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 I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=98.27 E-value=9.2e-07 Score=70.82 Aligned_cols=36 Identities=36% Similarity=0.993 Sum_probs=31.9
Q ss_pred CCCCCCCCCeEEEEecccCceeEEecCCCCCCcccccCC
Q 001100 965 RSCPVCGEGTLIFKVSRFGAGYFIGCNQHPRCNYIAKTL 1003 (1158)
Q Consensus 965 g~CPkCGkG~l~~k~gr~G~~~f~GCs~yP~C~~~~~~~ 1003 (1158)
..||.|| +.|++|.+++| .||||++||.|+++.++.
T Consensus 2 ~~CP~Cg-~~lv~r~~k~g--~F~~Cs~yP~C~~~~~~~ 37 (39)
T PF01396_consen 2 EKCPKCG-GPLVLRRGKKG--KFLGCSNYPECKYTEPLP 37 (39)
T ss_pred cCCCCCC-ceeEEEECCCC--CEEECCCCCCcCCeEeCC
Confidence 4799999 58999999999 499999999999988764
No 44
>PRK07219 DNA topoisomerase I; Validated
Probab=97.90 E-value=1.7e-05 Score=101.66 Aligned_cols=70 Identities=24% Similarity=0.470 Sum_probs=54.6
Q ss_pred CCCCCCCCCCeEEEEecccCceeEEecCCCCCCcccccCCCCCCchhhhhhhccCCCCCcccCCCCCccceeeeccCCCc
Q 001100 964 DRSCPVCGEGTLIFKVSRFGAGYFIGCNQHPRCNYIAKTLYGDDDEEDTLQRNTNVDEPKLIGHHPASKEKVLLKSGPYG 1043 (1158)
Q Consensus 964 ~g~CPkCGkG~l~~k~gr~G~~~f~GCs~yP~C~~~~~~~~~e~~~~e~~~~~~~~~lPr~LG~cPkcG~~v~lk~GrfG 1043 (1158)
...||+||+ .+..+.|++|. ||+|++||.|+++.++...... ...-..||+||..++.+.+++|
T Consensus 688 ~~~CP~Cg~-~l~~k~gr~G~--F~~Cs~yp~C~~~~~l~~~~~~-------------~~~~~~CpkCg~~l~~~k~~~g 751 (822)
T PRK07219 688 IGPCPKCGG-ELAIKQLKYGS--FLGCTNYPKCKYTLPLPRRGKI-------------TVTDEKCPECGLPLLRVKGGFG 751 (822)
T ss_pred cccCCCCCC-eeEEEcCCCCC--eeeCCCCCCCCceeeccccccc-------------ccccCCCCCCCCeEEEEecCCC
Confidence 468999985 67788899987 9999999999987654422111 0123469999999999999999
Q ss_pred ceEEeC
Q 001100 1044 FYVQLG 1049 (1158)
Q Consensus 1044 ~yv~c~ 1049 (1158)
.|+.|.
T Consensus 752 ~~~~Cs 757 (822)
T PRK07219 752 DELGCC 757 (822)
T ss_pred ceeeeC
Confidence 999986
No 45
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=97.80 E-value=1.7e-05 Score=80.71 Aligned_cols=100 Identities=17% Similarity=0.135 Sum_probs=72.6
Q ss_pred cccCCCCCccceeeeccCCCcceEEeCCCCCCCCCcccccCCCCC-ccccCHHHHHHHhcCCcccCCCCCCC-cCeEEee
Q 001100 1023 KLIGHHPASKEKVLLKSGPYGFYVQLGEDRTGYLPKRASVSHIKD-VDSITLEDALELLRYPVNLGNHPKDG-QPIMLRL 1100 (1158)
Q Consensus 1023 r~LG~cPkcG~~v~lk~GrfG~yv~c~~d~kg~kpK~~slpk~~~-~~sItle~Al~ll~~pk~lG~cP~cG-~~I~i~~ 1100 (1158)
+..+.||+||..|+++.++||.|++|+ .+|+|+. +.. .+ ........||+|| ..++++.
T Consensus 15 ~~~~~Cp~Cg~~m~~~~~~~g~f~gCs-----------~yP~C~~~~~~----~~----~~~~~~~~Cp~C~~~~~~~k~ 75 (140)
T COG0551 15 KTGQICPKCGKNMVKKFGKYGIFLGCS-----------NYPKCDYYEPE----KA----IAEKTGVKCPKCGKGLLVLKK 75 (140)
T ss_pred ccCccCCcCCCeeEEEEccCCeEEEeC-----------CCCCCCCCccc----cc----ccccCceeCCCCCCCceEEEe
Confidence 456789999999999999999999998 4677774 111 00 0112235699999 6889999
Q ss_pred ccCc--ce-eecCCeeeecCCCCCCCCCCHHHHHHHhhcccccc
Q 001100 1101 ARAG--FS-VRHRRTIASVPKNMKPNDVTLEKALEFLSGKDVRR 1141 (1158)
Q Consensus 1101 GRyG--~Y-i~~~~~~~~lpk~~~~~~itle~A~~LL~~k~~k~ 1141 (1158)
|||| +| +..+++|..+.+.......|+.|....+..++.++
T Consensus 76 ~~~~~~f~~~~~~Pkc~~~~~~~~~~~~cp~c~~~~~~~k~~~~ 119 (140)
T COG0551 76 GRFGKNFLGCSNYPKCRFTEKPKPKEKKCPKCGSRKLVEKKEKK 119 (140)
T ss_pred ccCCceEEeecCCCcCceeecCCcccccCCcCCCceeEEEeeec
Confidence 9999 45 77888888887777666679998864444444343
No 46
>PRK14973 DNA topoisomerase I; Provisional
Probab=97.58 E-value=4.6e-05 Score=98.29 Aligned_cols=54 Identities=17% Similarity=0.354 Sum_probs=45.5
Q ss_pred CeeEeeeEEEeccccCCCCCCCHhHHHHHHHhcCCCCCcchHHHHHHhhccceEE
Q 001100 815 DPLYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVT 869 (1158)
Q Consensus 815 d~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk~GIGTpATrAsIIe~L~~R~YV~ 869 (1158)
..+.|.++..++.++.||.+|+-.+|.++.-+.|+...-|. .|.+.|++.|||.
T Consensus 257 ~~~~V~~v~~k~~~~~pP~Pf~ts~LQ~~asklg~Sa~kTm-~iAQ~LYE~glIT 310 (936)
T PRK14973 257 EPLVVTEVKEGHKVDRAPTPFDTTTFIVAASRLGFSAANAM-RIAEDLYMNGYIS 310 (936)
T ss_pred CCeEEEEEEeeeEeccCCCCccHHHHHHHHHHcCCCHHHHH-HHHHHHHhCCeee
Confidence 45778899999999999999999999988777676665555 4889999999996
No 47
>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=97.54 E-value=0.00064 Score=60.29 Aligned_cols=82 Identities=32% Similarity=0.425 Sum_probs=63.0
Q ss_pred CeEEEEecchHHHHHHhhcCCCEEEEeeccccccccccCCCCCCCCCCcceEecCcchHHHHHHHHHHhccCCeEEEccC
Q 001100 350 KSVVVVESVTKAKVIQGYLGDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILASD 429 (1158)
Q Consensus 350 k~LIIvEkPskAk~Ia~~LG~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~~~k~lk~Ik~l~k~ad~IIlATD 429 (1158)
+.|||||.++-+..+..+...++.|+++.||... .....+..+++....|++++|
T Consensus 1 ~~viivEg~~d~~~l~~~~~~~~~~~~~~G~~~~-------------------------~~~~~~~~~~~~~~~v~i~~D 55 (83)
T cd00188 1 KKLIIVEGPSDALALAQAGGYGGAVVALGGHALN-------------------------KTRELLKRLLGEAKEVIIATD 55 (83)
T ss_pred CEEEEEecHHHHHHHHHHcCCCEEEEEEccEEcH-------------------------HHHHHHHHHhcCCCEEEEEcC
Confidence 3689999999999999998777788888887553 223345555555789999999
Q ss_pred CCccccHHHHHHHHHHhhcccccCCccEEEEE
Q 001100 430 PDREGEAIAWHIVEMLQQQDALHENITVARVV 461 (1158)
Q Consensus 430 pDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~ 461 (1158)
+|.+|+.+++++.+.+... ...+.|++
T Consensus 56 ~D~~g~~~~~~~~~~~~~~-----~~~~~~~~ 82 (83)
T cd00188 56 ADREGEAIALRLLELLKSL-----GKKVRRLL 82 (83)
T ss_pred CChhHHHHHHHHHHHHHhc-----CCceEEee
Confidence 9999999999999987531 34566654
No 48
>PRK00076 recR recombination protein RecR; Reviewed
Probab=97.23 E-value=0.001 Score=71.35 Aligned_cols=105 Identities=30% Similarity=0.468 Sum_probs=74.4
Q ss_pred CeEEEEecchHHHHHHh---hcCCCEEEEeeccccccccccCCCCCCCCCCcceEecCcchHHHHHHHHHHhccCCeEEE
Q 001100 350 KSVVVVESVTKAKVIQG---YLGDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLIL 426 (1158)
Q Consensus 350 k~LIIvEkPskAk~Ia~---~LG~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~~~k~lk~Ik~l~k~ad~IIl 426 (1158)
..|.|||.|.-..+|++ |-|. |.|.. ||+--|. ++.|+ ++.+ .+.++.| -.+..+||+
T Consensus 79 ~~icVVE~~~Dv~aiE~s~~y~G~-YhVL~--G~ispl~----gi~p~-~l~i--------~~L~~ri---~~~v~EVIl 139 (196)
T PRK00076 79 SLICVVESPADVLAIERTGEYRGL-YHVLG--GLLSPLD----GIGPE-DLNI--------DELLERL---DGEVKEVIL 139 (196)
T ss_pred CEEEEECCHHHHHHHHhhCcCceE-EEEec--CCcCCCC----CCCcc-ccCH--------HHHHHHH---hCCCCEEEE
Confidence 56999999999999987 4444 88876 7776554 35553 3331 2444444 246889999
Q ss_pred ccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEc--------ccCHHHHHHHHHhcc
Q 001100 427 ASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFH--------EITEASIKVALQAAR 478 (1158)
Q Consensus 427 ATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fs--------~lT~~aI~~A~~nlr 478 (1158)
||+|+.|||+.+++|.+.++. ...+|.|+-.- =++.-.+.+||++-+
T Consensus 140 A~~pt~EGe~Ta~yi~~~lk~-----~~ikvtRiA~GiP~G~~ley~D~~TL~~Al~~R~ 194 (196)
T PRK00076 140 ATNPTVEGEATAHYIARLLKP-----LGVKVTRLAHGVPVGGELEYVDEGTLSRALEGRR 194 (196)
T ss_pred eCCCCchHHHHHHHHHHHHHH-----cCCCeeeeeeCCCCCcceeeCCHHHHHHHHHhCc
Confidence 999999999999999999875 24578887542 345555666666543
No 49
>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=96.89 E-value=0.0048 Score=57.41 Aligned_cols=79 Identities=24% Similarity=0.356 Sum_probs=56.9
Q ss_pred CeEEEEecchHHHHHHhhcCCCEEEEeeccccccccccCCCCCCCCCCcceEecCcchHHHHHHHHHHhccCCeEEEccC
Q 001100 350 KSVVVVESVTKAKVIQGYLGDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILASD 429 (1158)
Q Consensus 350 k~LIIvEkPskAk~Ia~~LG~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~~~k~lk~Ik~l~k~ad~IIlATD 429 (1158)
+.+||||-..-+.++.++..+ ..+.++.|..+ ...+++.|+++ .+.||++||
T Consensus 2 ~~vIiVEG~~D~~~l~~~g~~-~~~i~t~Gt~~------------------------~~~~~~~l~~~---~~~VIiltD 53 (81)
T cd01027 2 GEVIIVEGKNDTESLKKLGIE-AEIIETNGSII------------------------NKETIELIKKA---YRGVIILTD 53 (81)
T ss_pred CeEEEEEchHHHHHHHHhCCC-ccEEEECCCcC------------------------CHHHHHHHHHh---CCEEEEEEC
Confidence 468999999988889887542 34556666332 12455566655 689999999
Q ss_pred CCccccHHHHHHHHHHhhcccccCCccEEEEE
Q 001100 430 PDREGEAIAWHIVEMLQQQDALHENITVARVV 461 (1158)
Q Consensus 430 pDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~ 461 (1158)
+|+.||.|.+.+.++|+. +...++|+.
T Consensus 54 ~D~aG~~i~~~~~~~l~~-----~~~~~~~~~ 80 (81)
T cd01027 54 PDRKGEKIRKKLSEYLSG-----PVPEIKRAF 80 (81)
T ss_pred CCHHHHHHHHHHHHHhcc-----cCCCeeecc
Confidence 999999999999999853 233466653
No 50
>PRK06599 DNA topoisomerase I; Validated
Probab=96.81 E-value=0.001 Score=84.01 Aligned_cols=55 Identities=20% Similarity=0.403 Sum_probs=43.2
Q ss_pred CCeeEeeeEEEeccccCCCCCCCHhHHHHHHH-hcCCCCCcchHHHHHHhhcc--------ceEE
Q 001100 814 GDPLYLGEVELKQHHTQPPARYSEGSLVKKLE-ELGIGRPSTYASTLKVLQDR--------NYVT 869 (1158)
Q Consensus 814 Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~ME-k~GIGTpATrAsIIe~L~~R--------~YV~ 869 (1158)
+....|.++..++.+..||.+|+-++|.+.+- +.|+.-.-|. .|++.|++. |||.
T Consensus 240 ~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl-~~aQ~LYe~~~~~~~~~g~iS 303 (675)
T PRK06599 240 GQAYTVDKIEKKERKRNPPPPFITSTLQQEASRKLGFSAKKTM-RIAQKLYEGIDLGEGTVGLIT 303 (675)
T ss_pred CCCeEEEEEEeeEEecCCCCCCcHHHHHHHHHHHcCCCHHHHH-HHHHHHHhccccccccceeEE
Confidence 34466778889999999999999999999885 4577655554 588999985 8885
No 51
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 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 I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=96.59 E-value=0.002 Score=51.77 Aligned_cols=35 Identities=14% Similarity=0.299 Sum_probs=30.5
Q ss_pred CCCCCccceeeeccCCCcceEEeCCCCCCCCCcccccCCCCCcccc
Q 001100 1026 GHHPASKEKVLLKSGPYGFYVQLGEDRTGYLPKRASVSHIKDVDSI 1071 (1158)
Q Consensus 1026 G~cPkcG~~v~lk~GrfG~yv~c~~d~kg~kpK~~slpk~~~~~sI 1071 (1158)
..||+||..|+++.+++|.|++|+ ++|+|+.+..+
T Consensus 2 ~~CP~Cg~~lv~r~~k~g~F~~Cs-----------~yP~C~~~~~~ 36 (39)
T PF01396_consen 2 EKCPKCGGPLVLRRGKKGKFLGCS-----------NYPECKYTEPL 36 (39)
T ss_pred cCCCCCCceeEEEECCCCCEEECC-----------CCCCcCCeEeC
Confidence 469999999999999999999998 56888876655
No 52
>PRK07220 DNA topoisomerase I; Validated
Probab=95.08 E-value=0.023 Score=72.70 Aligned_cols=66 Identities=18% Similarity=0.382 Sum_probs=51.3
Q ss_pred CCeeEeeeEEEeccccCCCCCCCHhHHHHHHHhcCCCCCcchHHHHHHhhccceEE--EcCcccccccc
Q 001100 814 GDPLYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVT--VKSRILYPEFR 880 (1158)
Q Consensus 814 Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk~GIGTpATrAsIIe~L~~R~YV~--~k~k~L~PT~l 880 (1158)
+..+.|.++..+++...||.+|+-.+|.+++-+.|+. |..--.|.+.|++.|||. +.....+|.+.
T Consensus 257 ~~~~~V~~v~~~~~~~~pP~pf~ts~Lq~~a~~~g~s-~~~tm~iaQ~LYe~g~ITYPRTDs~~l~~~~ 324 (740)
T PRK07220 257 GKTAEVTEVEKGTKTDKPPTPFNTTEFISAANSIGFS-AANAMRIAESLYTNGYISYPRTDNTVYPESL 324 (740)
T ss_pred CCCeEEEEEeeeeEecCCCCCcCHHHHHHHHHHcCCC-HHHHHHHHHHHHhCCceeecccCCeecCchh
Confidence 4467788999999999999999999999999887773 444456999999999996 33444455533
No 53
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=94.95 E-value=0.13 Score=55.61 Aligned_cols=95 Identities=27% Similarity=0.391 Sum_probs=68.2
Q ss_pred eEEEEecchHHHHHHhhc-----CCCEEEEeeccccccccccCCCCCCCCCCcceEecCcchHHHHHHHHHHhccCCeEE
Q 001100 351 SVVVVESVTKAKVIQGYL-----GDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLI 425 (1158)
Q Consensus 351 ~LIIvEkPskAk~Ia~~L-----G~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~~~k~lk~Ik~l~k~ad~II 425 (1158)
.=||||-.+-+.+|.++| |..|.||-| ++.|. ..+..-+..+.+||.|+
T Consensus 9 VRIiVEGAsDvE~iSkalQr~aLG~eYnITis------------SIiPT--------------T~~eIA~raaeGADlvl 62 (290)
T COG4026 9 VRIIVEGASDVEVISKALQRLALGSEYNITIS------------SIIPT--------------TNVEIAKRAAEGADLVL 62 (290)
T ss_pred EEEEeeccchHHHHHHHHHHhhhcccceeEEE------------eeccC--------------chHHHHHHhhccCCEEE
Confidence 458999999999998865 788877654 12232 12334567889999999
Q ss_pred EccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEc------ccCHHHHHHHHHh
Q 001100 426 LASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFH------EITEASIKVALQA 476 (1158)
Q Consensus 426 lATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fs------~lT~~aI~~A~~n 476 (1158)
||||+||-|--+|....+.|.. --..|-||.+. -++.+-|++-++|
T Consensus 63 IATDaD~~GReLA~kf~eeLrg-----~VGhiERmK~PiGHDvEhiD~elvrkEl~n 114 (290)
T COG4026 63 IATDADRVGRELAEKFFEELRG-----MVGHIERMKIPIGHDVEHIDVELVRKELKN 114 (290)
T ss_pred EeecCcchhHHHHHHHHHHHHH-----hhhhhheeccCCCCCccccCHHHHHHHHHH
Confidence 9999999999999999888753 22467888764 2455555555544
No 54
>PRK05582 DNA topoisomerase I; Validated
Probab=94.80 E-value=0.044 Score=69.34 Aligned_cols=55 Identities=16% Similarity=0.320 Sum_probs=47.6
Q ss_pred CCeeEeeeEEEeccccCCCCCCCHhHHHHHHH-hcCCCCCcchHHHHHHhhc---------cceEE
Q 001100 814 GDPLYLGEVELKQHHTQPPARYSEGSLVKKLE-ELGIGRPSTYASTLKVLQD---------RNYVT 869 (1158)
Q Consensus 814 Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~ME-k~GIGTpATrAsIIe~L~~---------R~YV~ 869 (1158)
|..+.+.++..+++++.||.+|+-++|.+.|- +.|+...-|. .|++.|++ .|||.
T Consensus 233 ~~~~~v~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl-~~aQ~LYe~~~~~~~~~~gliS 297 (650)
T PRK05582 233 KKDFKVSKVKKKERKRNPPPPFTTSTLQQEAARKLNFSTKKTM-MIAQQLYEGIDLGKQGTVGLIT 297 (650)
T ss_pred CCCeEEEEEeeeeeecCCCCCccHHHHHHHHHHHcCCCHHHHH-HHHHHHhcccccCCCCceEEEE
Confidence 35577788999999999999999999998885 5699888888 69999999 68986
No 55
>PF13662 Toprim_4: Toprim domain; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=94.80 E-value=0.07 Score=49.20 Aligned_cols=79 Identities=29% Similarity=0.330 Sum_probs=44.3
Q ss_pred CeEEEEecchHHHHHHhhcCCCEEEEeeccccc-cccccCCCCCCCCCCcceEecCcchHHHHHHHHHHhccCCeEEEcc
Q 001100 350 KSVVVVESVTKAKVIQGYLGDMYEVLPSYGHVR-DLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILAS 428 (1158)
Q Consensus 350 k~LIIvEkPskAk~Ia~~LG~~y~V~~s~GHl~-dL~~~~~~v~p~~~f~~~~~v~~~~~k~lk~Ik~l~k~ad~IIlAT 428 (1158)
|.|||||-+.=+.++.+. |-...| ++.|+.+ .+ +++...+.. ....+||+|+
T Consensus 1 k~viIvEG~~D~~~l~~~-g~~~~v-~~~g~~~~~~------------------------~~~~~~~~~-~~~~~Vii~~ 53 (81)
T PF13662_consen 1 KEVIIVEGEFDAIALEQA-GYKNVV-AVLGGNLSPL------------------------DQILREKLE-KKVKEVIIAF 53 (81)
T ss_dssp --EEEESSHHHHHHHHHT-T-TTEE-EESSSS---H------------------------HHHHHHHHH----SEEEEEE
T ss_pred CEEEEECCHHHHHHHHHh-CCCeEE-EECCCCCChH------------------------HHhChHhhh-ccCceEEEEe
Confidence 479999999999999998 554433 3344332 11 111100100 0157899999
Q ss_pred CCCccccHHHHHHHHHHhhcccccCCccEEEE
Q 001100 429 DPDREGEAIAWHIVEMLQQQDALHENITVARV 460 (1158)
Q Consensus 429 DpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl 460 (1158)
|+|.+|+..+.+|.+.|.. ...+|+|+
T Consensus 54 D~D~~G~~~a~~i~~~l~~-----~gi~v~~v 80 (81)
T PF13662_consen 54 DNDKAGEKAAQKIAKKLLP-----LGIRVTRV 80 (81)
T ss_dssp ESSHHHHHHHHHHHHHHG--------------
T ss_pred CcCHHHHHHHHHHHHHHHh-----hccccccC
Confidence 9999999999999997753 23456654
No 56
>PRK13844 recombination protein RecR; Provisional
Probab=94.45 E-value=0.23 Score=53.78 Aligned_cols=107 Identities=23% Similarity=0.375 Sum_probs=69.8
Q ss_pred CeEEEEecchHHHHHHhh--cCCCEEEEeeccccccccccCCCCCCCCCCcceEecCcchHHHHHHHHHHhccCCeEEEc
Q 001100 350 KSVVVVESVTKAKVIQGY--LGDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILA 427 (1158)
Q Consensus 350 k~LIIvEkPskAk~Ia~~--LG~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~~~k~lk~Ik~l~k~ad~IIlA 427 (1158)
..|.|||.|.-...|.+. +.+-|.|.. ||+=-| .++.|+ ++. -.+.++.|++ .+..+||+|
T Consensus 83 ~~iCVVE~~~Dv~aiE~t~~y~G~YhVL~--G~ispl----~gi~p~-~l~--------i~~L~~Ri~~--~~v~EVIlA 145 (200)
T PRK13844 83 TKLCIIESMLDMIAIEEAGIYRGKYFVLN--GRISPL----DGIGPS-ELK--------LDILQQIIAD--RKIDEVILA 145 (200)
T ss_pred CEEEEECCHHHHHHHHhhCccceEEEEcc--CccCcc----CCCChh-hcC--------HHHHHHHHhc--CCCcEEEEe
Confidence 568999999999999863 445676653 333222 133343 222 1133334432 257899999
Q ss_pred cCCCccccHHHHHHHHHHhhcccccCCccEEEEEE--------cccCHHHHHHHHHhccc
Q 001100 428 SDPDREGEAIAWHIVEMLQQQDALHENITVARVVF--------HEITEASIKVALQAARE 479 (1158)
Q Consensus 428 TDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~f--------s~lT~~aI~~A~~nlr~ 479 (1158)
|.|+-|||+-+.+|.+.++. ..+|.|+=. .=++...+.+||++-+.
T Consensus 146 t~~t~EGe~Ta~yi~~~lk~------~vkvtRlA~GiP~G~~ley~D~~TL~~Al~~R~~ 199 (200)
T PRK13844 146 ISPTVEGETTAHFISQMIAK------DIKISRIGFGVPFGGELEYLDQQTLLHAFNARTN 199 (200)
T ss_pred CCCCccHHHHHHHHHHHhcC------CCcEEeeeecCcCCcceeecCHHHHHHHHHhCcC
Confidence 99999999999999999863 457888753 23456667777766543
No 57
>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=93.89 E-value=0.43 Score=50.68 Aligned_cols=104 Identities=23% Similarity=0.308 Sum_probs=68.8
Q ss_pred CCeEEEEecchHHHHHHhhcCCCEEEEeeccccccccccCCCCCCCCCCcceEecCcchHHHHHHHHHHhccCCeEEEcc
Q 001100 349 GKSVVVVESVTKAKVIQGYLGDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILAS 428 (1158)
Q Consensus 349 ~k~LIIvEkPskAk~Ia~~LG~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~~~k~lk~Ik~l~k~ad~IIlAT 428 (1158)
-+.+||||=-+-...|..++. ..+..|.|..+ ..+.++.|+.+.+. .-||+-|
T Consensus 2 IkevIVVEGK~D~~~lk~~~d--~~~I~T~Gs~i------------------------~~~~i~~i~~~~~~-rgVIIfT 54 (174)
T TIGR00334 2 IKEIIVVEGKDDQARIKQAFD--VDVIETNGSAL------------------------KDETINLIKKAQKK-QGVIILT 54 (174)
T ss_pred CCeEEEEecchHHHHHHHhcC--ceEEEECCCcc------------------------CHHHHHHHHHHhhc-CCEEEEe
Confidence 367899997776677777764 34556655221 23556677777654 5689999
Q ss_pred CCCccccHHHHHHHHHHhhccc--ccCCccE---EEEEEcccCHHHHHHHHHhccc
Q 001100 429 DPDREGEAIAWHIVEMLQQQDA--LHENITV---ARVVFHEITEASIKVALQAARE 479 (1158)
Q Consensus 429 DpDREGE~Ia~~Ile~l~~~~~--~~~~k~v---kRl~fs~lT~~aI~~A~~nlr~ 479 (1158)
|||.-||.|=..|.+++..... +.....+ .-+=+-..++++|++||++...
T Consensus 55 DpD~~GekIRk~i~~~vp~~khafi~~~~a~~~~~~iGVE~As~e~I~~AL~~~~~ 110 (174)
T TIGR00334 55 DPDFPGEKIRKKIEQHLPGYENCFIPKHLAKPNKKKIGVEEASVEAIIAALENVHE 110 (174)
T ss_pred CCCCchHHHHHHHHHHCCCCeEEeeeHHhcCcCCCCcccCCCCHHHHHHHHHHhcc
Confidence 9999999999999998642100 0000000 1144556789999999999875
No 58
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=93.87 E-value=0.2 Score=54.03 Aligned_cols=105 Identities=29% Similarity=0.447 Sum_probs=67.4
Q ss_pred CeEEEEecchHHHHHHhh--cCCCEEEEeeccccccccccCCCCCCCCCCcceEecCcchHHHHHHHHHHhccCCeEEEc
Q 001100 350 KSVVVVESVTKAKVIQGY--LGDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILA 427 (1158)
Q Consensus 350 k~LIIvEkPskAk~Ia~~--LG~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~~~k~lk~Ik~l~k~ad~IIlA 427 (1158)
..|.|||.|.-.-.|++. +.+-|.|.. |||=-| .++.|+ ++. -.+.++.|++ .+..+||+|
T Consensus 79 ~~iCVVE~~~Dv~aiE~~~~y~G~YhVL~--G~iSPl----dgigp~-~l~--------i~~L~~Ri~~--~~v~EVIlA 141 (195)
T TIGR00615 79 SVICVVEDPKDVFALEKTKEFRGRYHVLG--GHISPL----DGIGPE-DLT--------IAALLKRLQE--ESVKEVILA 141 (195)
T ss_pred CEEEEECCHHHHHHHHhhCccceEEEEcc--CccCcc----CCCChh-hcC--------HHHHHHHHhc--CCCcEEEEe
Confidence 568999999999999863 455676653 443322 133443 222 1133333332 257899999
Q ss_pred cCCCccccHHHHHHHHHHhhcccccCCccEEEEEE--------cccCHHHHHHHHHh
Q 001100 428 SDPDREGEAIAWHIVEMLQQQDALHENITVARVVF--------HEITEASIKVALQA 476 (1158)
Q Consensus 428 TDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~f--------s~lT~~aI~~A~~n 476 (1158)
|+|+-|||+-+.+|.+.++. ...+|.|+=. .=++...+.+||++
T Consensus 142 t~~tvEGe~Ta~yi~~~lk~-----~~ikvtRlA~GiP~G~~ley~D~~TL~~Al~~ 193 (195)
T TIGR00615 142 TNPTVEGEATALYIARLLQP-----FGVKVTRIASGLPVGGDLEYADEVTLARALEG 193 (195)
T ss_pred CCCCchHHHHHHHHHHHhhh-----cCCcEEeeeecCCCCcceeecCHHHHHHHHHc
Confidence 99999999999999999874 2457888743 22344555556554
No 59
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=92.72 E-value=0.47 Score=48.02 Aligned_cols=102 Identities=21% Similarity=0.245 Sum_probs=67.1
Q ss_pred CeEEEEecchHHHHHHhhcCCCEEEEeeccccccccccCCCCCCCCCCcceEecCcchHHHHHHHHHHhccCCeEEEccC
Q 001100 350 KSVVVVESVTKAKVIQGYLGDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILASD 429 (1158)
Q Consensus 350 k~LIIvEkPskAk~Ia~~LG~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~~~k~lk~Ik~l~k~ad~IIlATD 429 (1158)
+.+||||=.+-...|+++.-.+-+++.+.|+.. ...++.|+++.+. ..|||-||
T Consensus 10 ~~vIVVEGK~D~~~l~~~~~~~~i~~~g~~i~~-------------------------~~~ie~i~~~~~~-k~VIILTD 63 (127)
T COG1658 10 KEVIVVEGKDDTASLKRLGDAGVIITNGSAINS-------------------------LETIELIKKAQKY-KGVIILTD 63 (127)
T ss_pred CceEEEeCCcHHHHHHHhcCCceEEEcCCccch-------------------------HHHHHHHHHhhcc-CCEEEEeC
Confidence 578999999988889888766644554433221 1233455554443 46899999
Q ss_pred CCccccHHHHHHHHHHhh-cccccCC----cc---EEE-EEEcccCHHHHHHHHHhcc
Q 001100 430 PDREGEAIAWHIVEMLQQ-QDALHEN----IT---VAR-VVFHEITEASIKVALQAAR 478 (1158)
Q Consensus 430 pDREGE~Ia~~Ile~l~~-~~~~~~~----k~---vkR-l~fs~lT~~aI~~A~~nlr 478 (1158)
||+.||-|...+.+++.. .+ ...+ .+ ..| +-+-++...+++.||.+..
T Consensus 64 ~D~~Ge~Irk~l~~~l~~~~~-~~id~~~~~~~~~~~~i~gVE~~~~~~~~~~l~~~~ 120 (127)
T COG1658 64 PDRKGERIRKKLKEYLPGAKG-AFIDREIRNKLKINGKIIGVEEASSEALRKALKEVP 120 (127)
T ss_pred CCcchHHHHHHHHHHhccccc-ccccHHHhhhcccccccccceecChHHHHHHHHhCC
Confidence 999999999999999975 21 1111 11 222 2344677888888887765
No 60
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=92.66 E-value=0.16 Score=38.60 Aligned_cols=32 Identities=34% Similarity=0.766 Sum_probs=19.3
Q ss_pred CCCCCCCCeEEEEecccCceeEEecCCCCCCcc
Q 001100 966 SCPVCGEGTLIFKVSRFGAGYFIGCNQHPRCNY 998 (1158)
Q Consensus 966 ~CPkCGkG~l~~k~gr~G~~~f~GCs~yP~C~~ 998 (1158)
.||+||-|.++--....|.-..+.|+| |.|++
T Consensus 3 lcpkcgvgvl~pvy~~kgeikvfrcsn-pacdy 34 (36)
T PF09151_consen 3 LCPKCGVGVLEPVYNQKGEIKVFRCSN-PACDY 34 (36)
T ss_dssp B-TTTSSSBEEEEE-TTS-EEEEEES--TT---
T ss_pred cCCccCceEEEEeecCCCcEEEEEcCC-Ccccc
Confidence 599999888776666666655678998 88876
No 61
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=91.86 E-value=0.91 Score=48.90 Aligned_cols=88 Identities=27% Similarity=0.507 Sum_probs=60.6
Q ss_pred CeEEEEecchHHHHHHhh--cCCCEEEEeeccccccccccCCCCCCCCCCcceEecCcchHHHHHH-HHHHhccC-CeEE
Q 001100 350 KSVVVVESVTKAKVIQGY--LGDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKS-IKVALSGA-ENLI 425 (1158)
Q Consensus 350 k~LIIvEkPskAk~Ia~~--LG~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~~~k~lk~-Ik~l~k~a-d~II 425 (1158)
..|.|||.|.-.-+|++. +.+-|.|.- |||--|. ++.|+ +.. ++. ++.+.... ++||
T Consensus 80 ~~icVVe~p~Dv~a~E~~~~f~G~YhVL~--G~lspl~----gigpe-~l~------------i~~L~~Rl~~~~~~EvI 140 (198)
T COG0353 80 SQLCVVEEPKDVLALEKTGEFRGLYHVLG--GLLSPLD----GIGPE-DLN------------IDELLQRLAEGSIKEVI 140 (198)
T ss_pred ceEEEEcchHHHHHHHHhcccCeeEEEec--CccCccc----CCCcc-ccc------------HHHHHHHHhcCCCceEE
Confidence 579999999999999864 345677763 5554332 34443 111 122 23344443 3999
Q ss_pred EccCCCccccHHHHHHHHHHhhcccccCCccEEEEE
Q 001100 426 LASDPDREGEAIAWHIVEMLQQQDALHENITVARVV 461 (1158)
Q Consensus 426 lATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~ 461 (1158)
+||+|--|||+-|..|.++|+.. ..+|.|+-
T Consensus 141 lAtnpTvEGeaTA~YI~~~l~~~-----~ikvtRlA 171 (198)
T COG0353 141 LATNPTVEGEATALYIARLLKPL-----GLKVTRLA 171 (198)
T ss_pred EecCCCccchHHHHHHHHHHhhc-----CCeEEEEe
Confidence 99999999999999999999753 45788875
No 62
>PRK04031 DNA primase; Provisional
Probab=84.09 E-value=1.3 Score=52.53 Aligned_cols=65 Identities=18% Similarity=0.198 Sum_probs=46.3
Q ss_pred HHHHhccCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhcccccH
Q 001100 414 IKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAAREIDA 482 (1158)
Q Consensus 414 Ik~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fs~lT~~aI~~A~~nlr~~d~ 482 (1158)
++.+++ .+.|++++|+|+-||.|.+++++.++.. .+ ...| .-.-.-++++++|.+||.+..++.+
T Consensus 204 i~~l~k-~~~Vil~~DgD~aGe~I~k~l~~v~~~d-~V-araP-~G~dVE~ls~eeI~kAL~~~~p~~~ 268 (408)
T PRK04031 204 IIELSK-KKTVTAFLDGDRGGELILKELLQVADID-YV-ARAP-PGKEVEELTKKEIAKALRNKVPVEQ 268 (408)
T ss_pred HHHHhc-CCCEEEEECCCHHHHHHHHHHHhhccee-EE-ecCC-CCCChhhCCHHHHHHHHHhcCCHHH
Confidence 556666 7899999999999999999999854211 00 0111 1123557899999999998877653
No 63
>TIGR01057 topA_arch DNA topoisomerase I, archaeal. This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent.
Probab=80.69 E-value=4.9 Score=50.98 Aligned_cols=58 Identities=21% Similarity=0.288 Sum_probs=50.1
Q ss_pred CCCCCeeEeeeEEEeccccCCCCCCCHhHHHHHHH-hcCCCCCcchHHHHHHhhccceEE
Q 001100 811 LKTGDPLYLGEVELKQHHTQPPARYSEGSLVKKLE-ELGIGRPSTYASTLKVLQDRNYVT 869 (1158)
Q Consensus 811 l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~ME-k~GIGTpATrAsIIe~L~~R~YV~ 869 (1158)
++..+...+.++.-+++.+.||.+|+-++|.+.|- +.|++..-|. .|.+.|++.|||.
T Consensus 251 ~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl-~iaQ~LYe~g~IS 309 (618)
T TIGR01057 251 LKKSPWAAVEEVRSERSILKPPPPFDLGTLQREAYRIFGFSPKKTQ-SIAQELYEEALIS 309 (618)
T ss_pred HhCCCCeEEEEEEeeeeeccCCCCccHHHHHHHHHHhcCCCHHHHH-HHHHHHHhcCcee
Confidence 33333677888999999999999999999999886 5699999888 7999999999996
No 64
>PRK05776 DNA topoisomerase I; Provisional
Probab=80.25 E-value=1.1 Score=57.04 Aligned_cols=54 Identities=20% Similarity=0.236 Sum_probs=47.7
Q ss_pred CeeEeeeEEEeccccCCCCCCCHhHHHHHHH-hcCCCCCcchHHHHHHhhccceEE
Q 001100 815 DPLYLGEVELKQHHTQPPARYSEGSLVKKLE-ELGIGRPSTYASTLKVLQDRNYVT 869 (1158)
Q Consensus 815 d~v~~~~~~i~e~~TkPP~ryTEasLI~~ME-k~GIGTpATrAsIIe~L~~R~YV~ 869 (1158)
..+.|.++..+++...||++|+-++|.+.+- ..|++..-|.. |.+.|++.|||.
T Consensus 258 ~~~~V~~v~~k~~~~~pP~pf~ts~LQ~~As~~lg~sa~ktm~-iAQ~LYe~glIS 312 (670)
T PRK05776 258 GYLKVTKVEVKIEILEPPPPFNLGDLQVEAARIYGFSPYKTQS-IAEDLYLDGLIS 312 (670)
T ss_pred CCEEEEEEEeeeEEcCCCCCCCHHHHHHHHHhhcCCCHHHHHH-HHHHHHhcCcee
Confidence 4578889999999999999999999999986 45998877776 999999999996
No 65
>smart00437 TOP1Ac Bacterial DNA topoisomerase I DNA-binding domain. Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit
Probab=76.71 E-value=6.8 Score=44.36 Aligned_cols=51 Identities=14% Similarity=0.182 Sum_probs=43.0
Q ss_pred cCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHhcCCCHHHHHH-HHHHHhcc
Q 001100 594 SANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMK-LAQKLYEG 645 (1158)
Q Consensus 594 ~~~~~V~~v~~k~~~~~PP~Pf~tstLQ~~AskklG~Sa~~Tm~-iAQ~LYE~ 645 (1158)
+..+.|.+++..+.+..||++|+-++|..+|-+ .|+.-.-|.. |.+.|.+.
T Consensus 189 g~~~~~~~~~~~e~~TkPP~~~Te~tLl~~Me~-~GIGTpATra~iIe~L~~r 240 (259)
T smart00437 189 GDELKVEEVEVEEKKTKPPARYTEASLIKLMEK-RGIGRPSTYAEIIETLLDR 240 (259)
T ss_pred CCEeeeeeeEEEecccCCCCCCCHHHHHHHHHH-CCCCchhhHHHHHHHHHhC
Confidence 556788888888999999999999999999876 6887766665 78999985
No 66
>PF09664 DUF2399: Protein of unknown function C-terminus (DUF2399); InterPro: IPR024465 This domain is found in archaeal, bacterial and eukaryotic proteins. Its function is unknown.
Probab=74.87 E-value=8.6 Score=40.21 Aligned_cols=73 Identities=19% Similarity=0.188 Sum_probs=50.9
Q ss_pred CCeEEEEecchHHHHHHhhcCCC-EEEEeeccccccccccCCCCCCCCCCcceEecCcchHHHHHHHHHHhccCCeEEEc
Q 001100 349 GKSVVVVESVTKAKVIQGYLGDM-YEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILA 427 (1158)
Q Consensus 349 ~k~LIIvEkPskAk~Ia~~LG~~-y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~~~k~lk~Ik~l~k~ad~IIlA 427 (1158)
...++|||.|++-..++..+|.. .-++++.||. ....+.-|..+...--.++.+
T Consensus 18 ~~~V~VvENp~Vf~~~~~~~~~~~~pLVCt~G~p-------------------------~~A~~~LL~~L~~~g~~l~y~ 72 (152)
T PF09664_consen 18 SGRVYVVENPAVFSALADELGASCPPLVCTSGQP-------------------------SAAARRLLDRLAAAGARLYYS 72 (152)
T ss_pred CCEEEEEecHHHHHHHHHhcCCCCCeEEEcCCcH-------------------------HHHHHHHHHHHHhCCCEEEEe
Confidence 34499999999999999987652 2334444431 122333444454433479999
Q ss_pred cCCCccccHHHHHHHHHHh
Q 001100 428 SDPDREGEAIAWHIVEMLQ 446 (1158)
Q Consensus 428 TDpDREGE~Ia~~Ile~l~ 446 (1158)
+|.|-||=.|+..+++..+
T Consensus 73 GDfDp~Gl~IA~~l~~r~~ 91 (152)
T PF09664_consen 73 GDFDPEGLRIANRLIQRYG 91 (152)
T ss_pred cCCCHHHHHHHHHHHHHhC
Confidence 9999999999999988754
No 67
>PF01131 Topoisom_bac: DNA topoisomerase; InterPro: IPR013497 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 I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. Type IA topoisomerases are comprised of four domains that together form a toroidal structure with a central hole large enough to accommodate single- and double-stranded DNA: an N-terminal alpha/beta Toprim domain, domain 2 and the C-terminal domain 4 are winged-helix domains, and domain 3 is a beta-barrel. Domains 1 (Toprim) and 3 form the active site of the enzyme, while the winged helix domains 2 and 4 form a single-strand DNA-binding groove [, ]. This entry represents the central portion of the enzyme, which covers domains 2 and 3 in topoisomerase type IA enzymes. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome; PDB: 1CYY_A 3PWT_A 1CY4_A 1CY9_A 1ECL_A 1CY7_A 1CY8_A 1CY6_A 1MW8_X 1CY0_A ....
Probab=70.26 E-value=7.7 Score=46.58 Aligned_cols=122 Identities=15% Similarity=0.171 Sum_probs=69.5
Q ss_pred chhHHHHHHHHHHHHHHhcC-CcceEEEEEEEecCcCCCCCCceeeeeccccccccccccCcCCHHHHH----HHHHHHc
Q 001100 519 VQSAALSLICDREMEIDEFK-PQEYWTVEAVLDKKESHSLDTFSFPAHLTHFQSKRLNQLSIGSHTEAK----DIEQKIN 593 (1158)
Q Consensus 519 VQTPtL~LVveRe~EI~~Fk-p~~Yw~I~a~~~~~~~~~~~g~~f~a~l~~~~~~k~~~~~i~d~~~Ae----~i~~~l~ 593 (1158)
.+--+-.||+.|..+. |- |..|-...+.+.. ++..|.+.....-...+. .+......+ .+-..-.
T Consensus 224 ~e~~vY~LI~rr~la~--~~~~~~~~~t~v~~~~------~~~~F~~~g~~~~~~Gw~--~~~~~~~~~~~~~~lp~l~~ 293 (403)
T PF01131_consen 224 DERKVYDLIARRFLAA--FMPDAKYEKTTVTFEV------GGEEFKASGKVIIDPGWK--KVYPYEEEEDEEEDLPSLKE 293 (403)
T ss_dssp HHHHHHHHHHHHHHHH--TS--EEEEEEEEEEEE------TTEEEEEEEEEEEEHGGG--GCS-HCHCCTTSBB-----T
T ss_pred HHHHHHHHHHHHHHHH--HHHHHheeeEEEEEEe------cCcEEEEEEeEEEECcee--EEEEcccccccccccccccC
Confidence 3345678888887764 54 4445555666654 245676543221111010 011100000 1222223
Q ss_pred cCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHhcCCCHHHHHH-HHHHHhccccCCCCCeeEEEEEe
Q 001100 594 SANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMK-LAQKLYEGVQLPDGTAAGLITYM 660 (1158)
Q Consensus 594 ~~~~~V~~v~~k~~~~~PP~Pf~tstLQ~~AskklG~Sa~~Tm~-iAQ~LYE~~k~~~g~~~GlITYP 660 (1158)
+..+.+.++..++....||++|+-++|...+-+ .|+.-.-|.. |.+.|.+. |||.--
T Consensus 294 g~~~~~~~~~~~e~~TkPP~~~Te~~Ll~~Me~-~GIGTpATra~iI~~L~~r---------~Yi~~~ 351 (403)
T PF01131_consen 294 GDEIPIEDVEIKEKKTKPPKRYTEASLLKAMEK-AGIGTPATRASIIEKLIKR---------GYIERS 351 (403)
T ss_dssp TEEEEEEEEEEEEEEEESS--EBHHHHHHHHHH-TTSS-TTTHHHHHHHHHHT---------TSEEE-
T ss_pred CcEEeecccchhhhccCCCCCCCHHHHHhhhhh-cCCCccccHHHHHHHhhcc---------ceeecc
Confidence 445778888899999999999999999999855 6888766665 78999985 678764
No 68
>PRK04017 hypothetical protein; Provisional
Probab=66.27 E-value=6.3 Score=40.34 Aligned_cols=69 Identities=28% Similarity=0.365 Sum_probs=46.3
Q ss_pred eEEEEecchHHHHHHhhcCCCEEEEeeccccccccccCCCCCCCCCCcceEecCcchHHHHHHHHHHhccCCeEEEccCC
Q 001100 351 SVVVVESVTKAKVIQGYLGDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILASDP 430 (1158)
Q Consensus 351 ~LIIvEkPskAk~Ia~~LG~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~~~k~lk~Ik~l~k~ad~IIlATDp 430 (1158)
.+||||=..-..++.++ |-++.++.+-|. .+. + .. +.| +.+...||+.|||
T Consensus 24 ~vIVVEGk~D~~~L~~l-Gv~~~iI~t~g~--~~~----------~---------~~----e~i---a~~~r~VIILTD~ 74 (132)
T PRK04017 24 APIIVEGKRDVESLRKL-GVEGEIIKVSRT--PLA----------E---------IA----ELI---ASRGKEVIILTDF 74 (132)
T ss_pred CEEEEeCccHHHHHHHc-CCCccEEEECCe--ecc----------h---------HH----HHH---HhcCCeEEEEECC
Confidence 67899988888888875 322233333332 110 0 01 112 4567789999999
Q ss_pred CccccHHHHHHHHHHhhc
Q 001100 431 DREGEAIAWHIVEMLQQQ 448 (1158)
Q Consensus 431 DREGE~Ia~~Ile~l~~~ 448 (1158)
|.-||-|...|.+++...
T Consensus 75 D~~GekIr~~l~~~l~~~ 92 (132)
T PRK04017 75 DRKGEELAKKLSEYLQGY 92 (132)
T ss_pred CcchHHHHHHHHHHHHhC
Confidence 999999999999998754
No 69
>TIGR01056 topB DNA topoisomerase III, bacteria and conjugative plasmid. This model describes topoisomerase III from bacteria and its equivalents encoded on plasmids. The gene is designated topB if found in the bacterial chromosome, traE on conjugative plasmid RP4, etc. These enzymes are involved in the control of DNA topology. DNA topoisomerase III belongs to the type I topoisomerases, which are ATP-independent.
Probab=65.37 E-value=21 Score=45.80 Aligned_cols=55 Identities=20% Similarity=0.364 Sum_probs=47.1
Q ss_pred CCeeEeeeEEEeccccCCCCCCCHhHHHHHHHh-cCCCCCcchHHHHHHhhcc-ceEE
Q 001100 814 GDPLYLGEVELKQHHTQPPARYSEGSLVKKLEE-LGIGRPSTYASTLKVLQDR-NYVT 869 (1158)
Q Consensus 814 Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk-~GIGTpATrAsIIe~L~~R-~YV~ 869 (1158)
|..+.|.++..+++.+.||++|+-++|.+.+-+ .|+...-|. .|.+.|++. |||.
T Consensus 263 ~~~~~V~~v~~k~~~~~pP~pf~ts~LQ~~as~~~g~s~~~tm-~iAQ~LYE~~glIT 319 (660)
T TIGR01056 263 QKPALVTDIEKERKKTSAPLFYDLSALQEDANKRFGISAKRTL-DIAQKLYETHKLIT 319 (660)
T ss_pred CCCeEEEEEEeeeeecCCCCCCCHHHHHHHHHHhcCCCHHHHH-HHHHHHHHhCCEEE
Confidence 345778899999999999999999999999864 598766666 799999998 9996
No 70
>COG0550 TopA Topoisomerase IA [DNA replication, recombination, and repair]
Probab=64.81 E-value=22 Score=44.81 Aligned_cols=69 Identities=26% Similarity=0.366 Sum_probs=53.8
Q ss_pred CCCCCCeeEeeeEEEeccccCCCCCCCHhHHHHHHHh-cCCCCCcchHHHHHHhhcc-ceEEE---cCcccccccc
Q 001100 810 SLKTGDPLYLGEVELKQHHTQPPARYSEGSLVKKLEE-LGIGRPSTYASTLKVLQDR-NYVTV---KSRILYPEFR 880 (1158)
Q Consensus 810 ~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk-~GIGTpATrAsIIe~L~~R-~YV~~---k~k~L~PT~l 880 (1158)
.++ |+...|.++.-+.+...||++|+-++|.+..-+ .|++..-|. .|-++|++. |||.- +...|-++-.
T Consensus 236 ~l~-~~~~~V~~ve~k~~~~~pp~Pf~tstLQq~As~~lgfs~kktm-~iAQ~LYE~~glITYpRTDs~~ls~~~~ 309 (570)
T COG0550 236 KLK-GKPAKVVSVEKKPKKRSPPPPFTTSTLQQEASRKLGFSAKKTM-DIAQKLYEGHGLITYPRTDSTRLSEEAL 309 (570)
T ss_pred Hcc-CCceEEEEEeeeeeccCCCCCCcHHHHHHHHHHhCCCCHHHHH-HHHHHHhcCCCcEEecCCCCCcCCHHHH
Confidence 344 888999999999999999999999999998865 488877665 588999998 89863 4444444333
No 71
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=63.52 E-value=10 Score=38.45 Aligned_cols=51 Identities=16% Similarity=0.247 Sum_probs=39.1
Q ss_pred CCHhHHHHHHHhcCCCCCcchHHHHHHhhccceEEEc-------Ccccccccccchhhhhhh
Q 001100 835 YSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVK-------SRILYPEFRGRMVSAFLS 889 (1158)
Q Consensus 835 yTEasLI~~MEk~GIGTpATrAsIIe~L~~R~YV~~k-------~k~L~PT~lG~~v~~~L~ 889 (1158)
.|..+|.+.| |+ +++|-..+|+.|.++|||++. ...|.+|+.|+.+.+.+.
T Consensus 47 ~t~~eLa~~l---~~-~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~~~ 104 (144)
T PRK03573 47 QSQIQLAKAI---GI-EQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLISEVE 104 (144)
T ss_pred CCHHHHHHHh---CC-ChhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHHHHHHHHH
Confidence 3556666655 45 456899999999999999874 136999999998877654
No 72
>TIGR01051 topA_bact DNA topoisomerase I, bacterial. This model describes DNA topoisomerase I among the members of bacteria. DNA topoisomerase I transiently cleaves one DNA strand and thus relaxes negatively supercoiled DNA during replication, transcription and recombination events.
Probab=61.52 E-value=27 Score=44.40 Aligned_cols=55 Identities=24% Similarity=0.466 Sum_probs=47.3
Q ss_pred CCeeEeeeEEEeccccCCCCCCCHhHHHHHHH-hcCCCCCcchHHHHHHhhcc--------ceEE
Q 001100 814 GDPLYLGEVELKQHHTQPPARYSEGSLVKKLE-ELGIGRPSTYASTLKVLQDR--------NYVT 869 (1158)
Q Consensus 814 Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~ME-k~GIGTpATrAsIIe~L~~R--------~YV~ 869 (1158)
|....+.++..+++++.||.+|+-.+|.+.+- +.|+...-|.. |++.|++. |||.
T Consensus 232 ~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~S~~~tl~-iaQ~LYe~~~~~~~~~g~iS 295 (610)
T TIGR01051 232 GEELVVEEIEKKPKKSRPPPPFTTSTLQQEASRKLGFSAKKTMM-IAQRLYEGVSTGDGTIGLIT 295 (610)
T ss_pred CCCeEEEEEeeceeeeCCCCCcCHHHHHHHHHHhcCCCHHHHHH-HHHHHHhcccccCCceeEEe
Confidence 55677889999999999999999999998885 56888776665 99999999 8996
No 73
>PF08259 Periviscerokin: Periviscerokinin family; InterPro: IPR013231 Perviscerokinin neuropeptides are found in the abdominal perisympathetic organs of insects. They mediate visceral muscle contractile activity (myotropic activity). CAPA, which are in the periviscerokinin and pyrokinin peptide families, has potential medical importance. This is due to its myotropic effects on, for example, heart muscles and due to its occurrence in the Ixodoidea (ticks), which are important vectors in the transmission of many animal diseases []. These peptides also have a strong diuretic or anti-diuretic effect, suggesting they have significant medical implications [].
Probab=59.98 E-value=3 Score=24.77 Aligned_cols=9 Identities=44% Similarity=0.859 Sum_probs=8.0
Q ss_pred eEEEEEecC
Q 001100 654 AGLITYMRT 662 (1158)
Q Consensus 654 ~GlITYPRT 662 (1158)
.|||++|||
T Consensus 3 sGlI~fpR~ 11 (11)
T PF08259_consen 3 SGLIPFPRV 11 (11)
T ss_pred ccccccCCC
Confidence 489999997
No 74
>cd00186 TOP1Ac DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand.
Probab=58.95 E-value=21 Score=42.59 Aligned_cols=55 Identities=11% Similarity=0.201 Sum_probs=46.6
Q ss_pred cCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHhcCCCHHHHHH-HHHHHhccccCCCCCeeEEEE
Q 001100 594 SANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMK-LAQKLYEGVQLPDGTAAGLIT 658 (1158)
Q Consensus 594 ~~~~~V~~v~~k~~~~~PP~Pf~tstLQ~~AskklG~Sa~~Tm~-iAQ~LYE~~k~~~g~~~GlIT 658 (1158)
+..+.+.+++..+....||++|+-++|..++-+ .|+.-.-|+. |.+.|.+. |||.
T Consensus 262 g~~~~~~~~~~~~~~T~PP~~~Te~~Li~~Me~-~GIGTpATra~iI~~L~~r---------~Yi~ 317 (381)
T cd00186 262 GDELKLEEVELEEKETQPPPRYTEASLIKLMEK-RGIGRPSTYASIIETLLDR---------GYVE 317 (381)
T ss_pred CCEEeeeeeeeeecccCCCCCCCHHHHHHHHHh-CCCCccccHHHHHHHHHhC---------CcEE
Confidence 455778888888999999999999999999866 5998777776 89999985 7887
No 75
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=54.81 E-value=22 Score=36.33 Aligned_cols=56 Identities=21% Similarity=0.256 Sum_probs=41.2
Q ss_pred hcCCCCCcchHHHHHHhhccceEEE-cCcccccccccchhhhhhhcccccccChhhhHHHHHHhhhh
Q 001100 846 ELGIGRPSTYASTLKVLQDRNYVTV-KSRILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNV 911 (1158)
Q Consensus 846 k~GIGTpATrAsIIe~L~~R~YV~~-k~k~L~PT~lG~~v~~~L~~~f~~l~~p~~TA~~E~~Ld~I 911 (1158)
..|+ +++|-..+|..|.++|||.. ..+.+.+|+.|+.+...+. .--..||.-|+.+
T Consensus 31 ~l~v-s~~svs~~l~~L~~~Gli~~~~~~~i~LT~~G~~~a~~~~---------~~h~~~e~~l~~l 87 (142)
T PRK03902 31 ALSV-HPSSVTKMVQKLDKDEYLIYEKYRGLVLTPKGKKIGKRLV---------YRHELLEQFLRII 87 (142)
T ss_pred HhCC-ChhHHHHHHHHHHHCCCEEEecCceEEECHHHHHHHHHHH---------HHHHHHHHHHHHh
Confidence 3478 58888899999999999985 4578999999997655442 1235666666544
No 76
>cd00223 TOPRIM_TopoIIB_SPO TOPRIM_TopoIIB_SPO: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IIB family of DNA topoisomerases and Spo11. This subgroup contains proteins similar to Sulfolobus shibatae topoisomerase VI (TopoVI) and Saccharomyces cerevisiae meiotic recombination factor: Spo11. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. TopoVI enzymes are heterotetramers found in archaea and plants. Spo11 plays a role in generating the double strand breaks that initiate homologous recombination during meiosis. S. shibatae TopoVI relaxes both positive and negative supercoils, and in addition has a strong decatenase activity. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspart
Probab=54.46 E-value=60 Score=33.93 Aligned_cols=98 Identities=14% Similarity=0.092 Sum_probs=60.3
Q ss_pred eEEEEecchHHHHHHhhc---CCCEEEEeeccccccccccCCCCCCCCCCcceEecCcchHHHHHHHHHHhccCCeEEEc
Q 001100 351 SVVVVESVTKAKVIQGYL---GDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILA 427 (1158)
Q Consensus 351 ~LIIvEkPskAk~Ia~~L---G~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~~~k~lk~Ik~l~k~ad~IIlA 427 (1158)
.++||||+++...+-..- ..+.+++++.| |+ ....+..++.|.+.. + =.+++.
T Consensus 2 ~ilvVEk~avf~~L~~~~~~~~~~~ilit~kG-----------------~P-----~~~tr~~l~~L~~~~-~-~~~~~l 57 (160)
T cd00223 2 FVLVVEKEAVFQRLIEEGFHERNNCILITGKG-----------------YP-----DRATRRFLRRLHEEL-D-LPVYIL 57 (160)
T ss_pred EEEEEecHHHHHHHHHcCccccCCEEEEEcCC-----------------cC-----CHHHHHHHHHHHHhh-C-CCEEEE
Confidence 589999999999887642 23445555433 11 113456666665554 2 359999
Q ss_pred cCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHH
Q 001100 428 SDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKV 472 (1158)
Q Consensus 428 TDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fs~lT~~aI~~ 472 (1158)
+|.|-.|=.|+..+..-............+.++.+-.+.++++.+
T Consensus 58 ~D~DP~Gi~I~~~y~~gs~~~~~~~~~~~~~~l~~~G~~~~d~~~ 102 (160)
T cd00223 58 VDGDPYGISILLTYKYGSIKLAYESESLATPDLRWLGLRPSDIIR 102 (160)
T ss_pred ECCCcchhhhhHHHHhCccccccccccccCCCcEEccCCHHHHhh
Confidence 999999999988876521110000111224578887888888755
No 77
>PRK10870 transcriptional repressor MprA; Provisional
Probab=52.83 E-value=16 Score=38.81 Aligned_cols=54 Identities=13% Similarity=0.089 Sum_probs=40.1
Q ss_pred CCCCCHhHHHHHHHhcCCCCCcchHHHHHHhhccceEEEc-------Ccccccccccchhhhhhh
Q 001100 832 PARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVK-------SRILYPEFRGRMVSAFLS 889 (1158)
Q Consensus 832 P~ryTEasLI~~MEk~GIGTpATrAsIIe~L~~R~YV~~k-------~k~L~PT~lG~~v~~~L~ 889 (1158)
+...|..+|-+.| |+ +++|-..+|+.|.++|||++. ...+.+|+.|+.+++-+.
T Consensus 69 ~~~it~~eLa~~l---~l-~~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~~~~i~ 129 (176)
T PRK10870 69 NHSIQPSELSCAL---GS-SRTNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFLREVL 129 (176)
T ss_pred CCCcCHHHHHHHH---CC-CHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHHH
Confidence 3445666777666 34 347889999999999999973 236899999998776553
No 78
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=52.71 E-value=13 Score=34.86 Aligned_cols=43 Identities=28% Similarity=0.363 Sum_probs=36.0
Q ss_pred HhcCCCCCcchHHHHHHhhccceEEEcC-cccccccccchhhhhh
Q 001100 845 EELGIGRPSTYASTLKVLQDRNYVTVKS-RILYPEFRGRMVSAFL 888 (1158)
Q Consensus 845 Ek~GIGTpATrAsIIe~L~~R~YV~~k~-k~L~PT~lG~~v~~~L 888 (1158)
+..|| .++|-..+|..|.+.|||.+.. +.+.+|+.|..+...+
T Consensus 7 ~~l~i-s~stvs~~l~~L~~~glI~r~~~~~~~lT~~g~~~~~~~ 50 (96)
T smart00529 7 ERLNV-SPPTVTQMLKKLEKDGLVEYEPYRGITLTEKGRRLARRL 50 (96)
T ss_pred HHhCC-ChHHHHHHHHHHHHCCCEEEcCCCceEechhHHHHHHHH
Confidence 44577 7889999999999999999876 5899999999876544
No 79
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=52.51 E-value=13 Score=37.97 Aligned_cols=50 Identities=14% Similarity=0.105 Sum_probs=38.0
Q ss_pred CCHhHHHHHHHhcCCCCCcchHHHHHHhhccceEEEc-------Ccccccccccchhhhhh
Q 001100 835 YSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVK-------SRILYPEFRGRMVSAFL 888 (1158)
Q Consensus 835 yTEasLI~~MEk~GIGTpATrAsIIe~L~~R~YV~~k-------~k~L~PT~lG~~v~~~L 888 (1158)
.|..+|-..| || +++|-..+|+.|.++|||++. ...|.+|+.|+.+.+.+
T Consensus 55 ~t~~eLa~~l---~i-~~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~~~~ 111 (144)
T PRK11512 55 ITPVELKKVL---SV-DLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICEQC 111 (144)
T ss_pred CCHHHHHHHH---CC-CHHHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHHHHHH
Confidence 4556666554 44 578999999999999999874 23689999999876544
No 80
>PRK08173 DNA topoisomerase III; Validated
Probab=52.16 E-value=43 Score=44.32 Aligned_cols=122 Identities=11% Similarity=0.129 Sum_probs=71.1
Q ss_pred hhHHHHHHHHHHHHHHhcCCcceEE-EEEEEecCcCCCCCCceeeeecccccccccccc-CcCCHHHHHHHHHHHccCCe
Q 001100 520 QSAALSLICDREMEIDEFKPQEYWT-VEAVLDKKESHSLDTFSFPAHLTHFQSKRLNQL-SIGSHTEAKDIEQKINSANF 597 (1158)
Q Consensus 520 QTPtL~LVveRe~EI~~Fkp~~Yw~-I~a~~~~~~~~~~~g~~f~a~l~~~~~~k~~~~-~i~d~~~Ae~i~~~l~~~~~ 597 (1158)
+--+-.||++|... .|-|.--|. ..+.+.. .+..|.+.-...-...+-.+ .-.+.++...|-..-.+..+
T Consensus 401 E~~iY~lI~rRfla--~f~~~a~~~~t~v~~~v------~~~~F~a~G~~~~~~Gw~~vy~~~~~~~~~~LP~l~~Ge~~ 472 (862)
T PRK08173 401 EQKLYDLVVKRFLA--VFFPAAEFLVTTRITEV------AGHHFKTEGKVLVNPGWLAVYGKEAQGADANLVPVQKGEKV 472 (862)
T ss_pred HHHHHHHHHHHHHH--HhCchheEEEEEEEEEe------CCcEEEEEEEEEeeCChHHHhCcccccccccCCCcCCCCEe
Confidence 34456788888876 565544343 3444443 24467654322111110000 00000000112112234567
Q ss_pred EEEEeeeeeeeecCCCCcchHHHHHHHHH---------------hcCCCHHHHHH-HHHHHhccccCCCCCeeEEEE
Q 001100 598 QVIKNSKRSMVRKNPTPYITSTLQQDAAN---------------KLNFSATYTMK-LAQKLYEGVQLPDGTAAGLIT 658 (1158)
Q Consensus 598 ~V~~v~~k~~~~~PP~Pf~tstLQ~~Ask---------------klG~Sa~~Tm~-iAQ~LYE~~k~~~g~~~GlIT 658 (1158)
.+.+++..++...||++|+=++|..+|-+ ..|+.-.-|.. |.+.|++. |||.
T Consensus 473 ~~~~~~~~e~~TkPP~ryTEatLl~aMe~~gk~v~D~el~~~~~~~GIGTpATRA~IIe~L~~r---------~Yi~ 540 (862)
T PRK08173 473 KTDKIEAVALTTKPPARYNEATLLSAMEGAGKLVEDDELREAMAEKGLGTPATRAAIIEGLLGE---------KYLV 540 (862)
T ss_pred eeeeeeecccccCCCCCcCHHHHHHHHHhhhhccccHHHHhhhhcCCCCchhhHHHHHHHHHhC---------CcEE
Confidence 78888888999999999999999998863 45776666655 88999995 8887
No 81
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=50.34 E-value=8.8 Score=35.34 Aligned_cols=38 Identities=21% Similarity=0.195 Sum_probs=31.2
Q ss_pred cchHHHHHHhhccceEEEcCcccccccccchhhhhhhc
Q 001100 853 STYASTLKVLQDRNYVTVKSRILYPEFRGRMVSAFLSH 890 (1158)
Q Consensus 853 ATrAsIIe~L~~R~YV~~k~k~L~PT~lG~~v~~~L~~ 890 (1158)
.+-..+|+.|.++|+|...++.+..|++|..+.+.+.+
T Consensus 34 ~~~~~yL~~L~~~gLI~~~~~~Y~lTekG~~~l~~l~~ 71 (77)
T PF14947_consen 34 STLKKYLKELEEKGLIKKKDGKYRLTEKGKEFLEELEE 71 (77)
T ss_dssp HHHHHHHHHHHHTTSEEEETTEEEE-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHCcCeeCCCCEEEECccHHHHHHHHHH
Confidence 34567899999999998888999999999988877653
No 82
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=49.34 E-value=19 Score=34.38 Aligned_cols=39 Identities=23% Similarity=0.221 Sum_probs=32.2
Q ss_pred CCcchHHHHHHhhccceEEEc-------Ccccccccccchhhhhhh
Q 001100 851 RPSTYASTLKVLQDRNYVTVK-------SRILYPEFRGRMVSAFLS 889 (1158)
Q Consensus 851 TpATrAsIIe~L~~R~YV~~k-------~k~L~PT~lG~~v~~~L~ 889 (1158)
+++|-..+|+.|.++|||.+. ...+..|+.|+.+...+.
T Consensus 49 ~~~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~~~~~~ 94 (126)
T COG1846 49 DRSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGRELLEQLL 94 (126)
T ss_pred CHHHHHHHHHHHHHCCCeeecCCccccceeeEEECccHHHHHHHhc
Confidence 678889999999999999874 236899999998776554
No 83
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=48.63 E-value=27 Score=37.73 Aligned_cols=51 Identities=20% Similarity=0.079 Sum_probs=38.2
Q ss_pred CCHhHHHHHHHhcCCCCCcchHHHHHHhhccceEEEc-------Ccccccccccchhhhhhh
Q 001100 835 YSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVK-------SRILYPEFRGRMVSAFLS 889 (1158)
Q Consensus 835 yTEasLI~~MEk~GIGTpATrAsIIe~L~~R~YV~~k-------~k~L~PT~lG~~v~~~L~ 889 (1158)
.|..+|-+.| ++ +++|-..+|+.|.++|||.+. .+.+.+|+.|+.+.+-+.
T Consensus 60 itq~eLa~~l---~l-~~sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG~~l~~~l~ 117 (185)
T PRK13777 60 ASISEIAKFG---VM-HVSTAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKGEELLLETM 117 (185)
T ss_pred cCHHHHHHHH---CC-CHhhHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHHH
Confidence 4555655533 33 568999999999999999974 236999999998776553
No 84
>TIGR02647 DNA conserved hypothetical protein TIGR02647. Members of this family are found, so far, only in the Gammaproteobacteria. The function is unknown. The location on the chromosome usually is not far from housekeeping genes rather than in what is clearly, say, a prophage region. Some members have been annotated in public databases as DNA-binding protein inhibitor Id-2-related protein, putative transcriptional regulator, or hypothetical DNA binding protein.
Probab=48.56 E-value=14 Score=34.21 Aligned_cols=49 Identities=20% Similarity=0.193 Sum_probs=33.6
Q ss_pred cchHHHHHHHHHhcCCCHHHHHHHHHHHhccccCCCCCeeEEEEEecCCCcCCCHHHHHHH
Q 001100 615 YITSTLQQDAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEI 675 (1158)
Q Consensus 615 f~tstLQ~~AskklG~Sa~~Tm~iAQ~LYE~~k~~~g~~~GlITYPRTDS~~Ls~~~~~~i 675 (1158)
|++++.|. --|...=-+.....++++|||+ ||||=| |..||+++.++.+
T Consensus 17 F~~~S~~~-GIKvH~dA~p~~i~a~~RLheK---------GLI~~p--dGgyLT~~G~~~a 65 (77)
T TIGR02647 17 FNLSSTQE-GIKVHSTASPAAVAAAARLHEK---------GLTTQP--DGGYLTSLGLEAA 65 (77)
T ss_pred CCchhhhc-CccccccCCHHHHHHHHHHHHc---------CCccCC--CCCEecHHHHHHH
Confidence 66666664 2233333345677899999997 999987 4559999875543
No 85
>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.
Probab=47.73 E-value=14 Score=32.42 Aligned_cols=36 Identities=22% Similarity=0.370 Sum_probs=26.7
Q ss_pred cCCCCCcchHHHHHHhhccceEEEcCcccccccccc
Q 001100 847 LGIGRPSTYASTLKVLQDRNYVTVKSRILYPEFRGR 882 (1158)
Q Consensus 847 ~GIGTpATrAsIIe~L~~R~YV~~k~k~L~PT~lG~ 882 (1158)
.|+--...+...|+.+++.|+|+.+++.|.+|+.|+
T Consensus 30 ~g~~~~~~~~~~l~~l~~~Gll~~~~~~l~lT~~G~ 65 (66)
T PF06969_consen 30 FGIDFAEEFQKELEELQEDGLLEIDGGRLRLTEKGR 65 (66)
T ss_dssp TT--THHH-HHHHHHHHHTTSEEE-SSEEEE-TTTG
T ss_pred HCcCHHHHHHHHHHHHHHCCCEEEeCCEEEECcccC
Confidence 355444556788999999999999999999999997
No 86
>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT). PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.
Probab=47.53 E-value=8.2 Score=35.26 Aligned_cols=38 Identities=16% Similarity=0.271 Sum_probs=29.6
Q ss_pred CCCHhHHHHHHHhcCCCCCcchHHHHHHhhccceEEEcC
Q 001100 834 RYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKS 872 (1158)
Q Consensus 834 ryTEasLI~~MEk~GIGTpATrAsIIe~L~~R~YV~~k~ 872 (1158)
...-++||..|+..||..+|+|..+ ..|.++|.++..+
T Consensus 20 ~i~~~~Li~ll~~~Gv~e~avR~al-sRl~~~G~L~~~r 57 (70)
T PF07848_consen 20 WIWVASLIRLLAAFGVSESAVRTAL-SRLVRRGWLESER 57 (70)
T ss_dssp -EEHHHHHHHHCCTT--HHHHHHHH-HHHHHTTSEEEEC
T ss_pred ceeHHHHHHHHHHcCCChHHHHHHH-HHHHHcCceeeee
Confidence 3445899999999999999999875 5888999998653
No 87
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=47.28 E-value=40 Score=33.04 Aligned_cols=51 Identities=24% Similarity=0.192 Sum_probs=37.6
Q ss_pred CCHhHHHHHHHhcCCCCCcchHHHHHHhhccceEEEc-----C--cccccccccchhhhhhh
Q 001100 835 YSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVK-----S--RILYPEFRGRMVSAFLS 889 (1158)
Q Consensus 835 yTEasLI~~MEk~GIGTpATrAsIIe~L~~R~YV~~k-----~--k~L~PT~lG~~v~~~L~ 889 (1158)
.|..+|-+.| ||-++ |-..+|+.|.++|||++. + +.+.+|+.|+.+.+.+.
T Consensus 43 ~t~~ela~~~---~~~~~-tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~~~~~ 100 (118)
T TIGR02337 43 MEFTQLANQA---CILRP-SLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALYASLS 100 (118)
T ss_pred cCHHHHHHHh---CCCch-hHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHHhh
Confidence 3444444443 66665 889999999999999873 2 36999999998776654
No 88
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=46.90 E-value=19 Score=35.11 Aligned_cols=55 Identities=16% Similarity=0.201 Sum_probs=41.7
Q ss_pred CCCCCCHhHHHHHHHhcCCCCCcchHHHHHHhhccceEEEc-----C--cccccccccchhhhhhh
Q 001100 831 PPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVK-----S--RILYPEFRGRMVSAFLS 889 (1158)
Q Consensus 831 PP~ryTEasLI~~MEk~GIGTpATrAsIIe~L~~R~YV~~k-----~--k~L~PT~lG~~v~~~L~ 889 (1158)
++...|..+|-..| ++- ++|-..+|+.|.++|||.+. + ..+.+|+.|+.+++.+.
T Consensus 40 ~~~~~t~~eL~~~l---~~~-~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT~~G~~~~~~~~ 101 (109)
T TIGR01889 40 NEGKLTLKEIIKEI---LIK-QSALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQRSKIESLI 101 (109)
T ss_pred cCCcCcHHHHHHHH---CCC-HHHHHHHHHHHHHCCCEeccCCcccCCeEEEEECHHHHHHHHHHH
Confidence 44556677777665 554 78999999999999999863 2 25889999998776554
No 89
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=42.97 E-value=70 Score=36.76 Aligned_cols=32 Identities=25% Similarity=0.632 Sum_probs=13.7
Q ss_pred CCCCCCCCCCeEEEEeccc---CceeEEecCCCCCCccc
Q 001100 964 DRSCPVCGEGTLIFKVSRF---GAGYFIGCNQHPRCNYI 999 (1158)
Q Consensus 964 ~g~CPkCGkG~l~~k~gr~---G~~~f~GCs~yP~C~~~ 999 (1158)
.+.||.||.....-.+... |. .|+-|+- |.+.
T Consensus 172 ~g~CPvCGs~P~~s~l~~~~~~G~-R~L~Cs~---C~t~ 206 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRGGEREGK-RYLHCSL---CGTE 206 (290)
T ss_dssp -SS-TTT---EEEEEEE------E-EEEEETT---T--E
T ss_pred CCcCCCCCCcCceEEEecCCCCcc-EEEEcCC---CCCe
Confidence 4799999986543332222 33 5788874 6654
No 90
>PRK07726 DNA topoisomerase III; Provisional
Probab=41.82 E-value=33 Score=44.08 Aligned_cols=56 Identities=23% Similarity=0.366 Sum_probs=47.8
Q ss_pred CCCeeEeeeEEEeccccCCCCCCCHhHHHHHHHh-cCCCCCcchHHHHHHhhcc-ceEE
Q 001100 813 TGDPLYLGEVELKQHHTQPPARYSEGSLVKKLEE-LGIGRPSTYASTLKVLQDR-NYVT 869 (1158)
Q Consensus 813 ~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk-~GIGTpATrAsIIe~L~~R-~YV~ 869 (1158)
.|....|.++.-+++.+.||.+|+-.+|.+.+-+ .|+...-|.. |.+.|++. |||.
T Consensus 259 ~~~~~~V~~v~~k~~~~~pP~pf~ls~Lq~~a~~~~g~s~~~tl~-iaQ~LYE~~glIT 316 (658)
T PRK07726 259 QGQPAKVTEVETKRKKEYAPLLYDLSELQIDANKRFGLSAKETLD-IAQSLYETHKLIT 316 (658)
T ss_pred cCCCeEEEEEEeeEEecCCCCCCCHHHHHHHHHHhcCCCHHHHHH-HHHHHHHhcCEEE
Confidence 3456778899999999999999999999999965 5988777665 79999997 9996
No 91
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=40.95 E-value=19 Score=39.92 Aligned_cols=51 Identities=24% Similarity=0.303 Sum_probs=41.4
Q ss_pred CCCCCHhHHHHHHHhcCCCCCcchHHHHHHhhccceEEEc----Ccccccccccchhhh
Q 001100 832 PARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVK----SRILYPEFRGRMVSA 886 (1158)
Q Consensus 832 P~ryTEasLI~~MEk~GIGTpATrAsIIe~L~~R~YV~~k----~k~L~PT~lG~~v~~ 886 (1158)
|...|..+|-+.| |+ +++|-+.+|..|.+.|||++. +..+.+|+.|+.+.+
T Consensus 19 ~~~IS~~eLA~~L---~i-S~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LTekG~~ll~ 73 (217)
T PRK14165 19 TVKISSSEFANHT---GT-SSKTAARILKQLEDEGYITRTIVPRGQLITITEKGLDVLY 73 (217)
T ss_pred CCCcCHHHHHHHH---Cc-CHHHHHHHHHHHHHCCCEEEEEcCCceEEEECHHHHHHHH
Confidence 4466777887777 66 789999999999999999874 567999999997653
No 92
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=40.35 E-value=24 Score=37.14 Aligned_cols=30 Identities=27% Similarity=0.371 Sum_probs=26.1
Q ss_pred HHHhcCCCHHHHHHHHHHHhccccCCCCCeeEEEEEecC
Q 001100 624 AANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRT 662 (1158)
Q Consensus 624 AskklG~Sa~~Tm~iAQ~LYE~~k~~~g~~~GlITYPRT 662 (1158)
.+..+|++...+-+++++|||. |||+|-|+
T Consensus 34 La~~Lgi~~~~VRk~L~~L~e~---------~Lv~~~r~ 63 (158)
T TIGR00373 34 ISLELGIKLNEVRKALYALYDA---------GLADYKRR 63 (158)
T ss_pred HHHHHCCCHHHHHHHHHHHHHC---------CCceeeee
Confidence 3455799999999999999995 89999984
No 93
>PRK14724 DNA topoisomerase III; Provisional
Probab=38.97 E-value=60 Score=43.66 Aligned_cols=75 Identities=15% Similarity=0.169 Sum_probs=50.8
Q ss_pred cCCeEEEEeeeeeeeecCCCCcchHHHHHHHHH---------------hcCCCHHHHHH-HHHHHhccccCCCCCeeEEE
Q 001100 594 SANFQVIKNSKRSMVRKNPTPYITSTLQQDAAN---------------KLNFSATYTMK-LAQKLYEGVQLPDGTAAGLI 657 (1158)
Q Consensus 594 ~~~~~V~~v~~k~~~~~PP~Pf~tstLQ~~Ask---------------klG~Sa~~Tm~-iAQ~LYE~~k~~~g~~~GlI 657 (1158)
+..+.+.+++..+....||++|+=++|..+|-+ ..|+.-.-|.. |.+.|.+. |||
T Consensus 488 Ge~v~~~~~~~~e~~TkPP~ryTEatLl~aME~~gk~v~d~el~~~~~~~GIGTpATRA~IIe~L~~r---------~Yi 558 (987)
T PRK14724 488 GEMVRTEFAEAKGLKTKPPARYSEATLLGAMESAGKQIDDDELREAMQEKGLGTPATRAAIIEGLLTE---------KYM 558 (987)
T ss_pred CCEeeeeeccccccccCCCCCcCHHHHHHHHHhhhhcccchhhhhhhhcCCCCCcccHHHHHHHHHhC---------CcE
Confidence 455777788888899999999999999998862 34665544544 78999985 788
Q ss_pred EEecCCCcCCCHHHHHHHHHHH
Q 001100 658 TYMRTDGLHISDEAAKEIRSLI 679 (1158)
Q Consensus 658 TYPRTDS~~Ls~~~~~~i~~~i 679 (1158)
. |-....+|.+.-..+.++|
T Consensus 559 ~--~~~k~l~pT~~G~~li~~L 578 (987)
T PRK14724 559 L--REGRELIPTAKAFQLMTLL 578 (987)
T ss_pred E--ecCCEEeEcHHHHHHHHHH
Confidence 6 4333344444323333434
No 94
>cd03364 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. E. coli DnaG is a single subunit enzyme.
Probab=37.79 E-value=39 Score=30.88 Aligned_cols=36 Identities=31% Similarity=0.414 Sum_probs=28.3
Q ss_pred HHHHHHHHHhccCCeEEEccCCCccccHHHHHHHHHHhh
Q 001100 409 THLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQ 447 (1158)
Q Consensus 409 k~lk~Ik~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~ 447 (1158)
.++..|+.. ...||+|+|.|..|..-+..+.+.+..
T Consensus 34 ~~~~~L~~~---~~~vii~~D~D~aG~~a~~~~~~~l~~ 69 (79)
T cd03364 34 EQAELLKRL---AKEVILAFDGDEAGQKAALRALELLLK 69 (79)
T ss_pred HHHHHHHhc---CCeEEEEECCCHHHHHHHHHHHHHHHH
Confidence 445555543 578999999999999999888888764
No 95
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=37.39 E-value=2e+02 Score=29.31 Aligned_cols=78 Identities=17% Similarity=0.227 Sum_probs=50.2
Q ss_pred CCHhHHHHHHHh-cCCCCCcchHHHHHHhhccceEEEcCcccccccccchhhhhhhcccccccChhh-hHHHHHHhhhhh
Q 001100 835 YSEGSLVKKLEE-LGIGRPSTYASTLKVLQDRNYVTVKSRILYPEFRGRMVSAFLSHYFSEVTDYSF-TADMETELDNVS 912 (1158)
Q Consensus 835 yTEasLI~~MEk-~GIGTpATrAsIIe~L~~R~YV~~k~k~L~PT~lG~~v~~~L~~~f~~l~~p~~-TA~~E~~Ld~Ia 912 (1158)
.|-.++++.|.+ .|+. .+|-.++|..|.++|||.+++ .|+.. .|.|-+..-++ ...+...++.+-
T Consensus 19 ~t~~eI~~~l~~~~~~~-~tTv~T~L~rL~~KG~v~~~k-------~gr~~-----~Y~p~vs~ee~~~~~~~~~~~~~f 85 (130)
T TIGR02698 19 TTSRDIIRILAEKKDWS-DSTIKTLLGRLVDKGCLTTEK-------EGRKF-----IYTALVSEDEAVENAAQELFSRIC 85 (130)
T ss_pred CCHHHHHHHHhhccCCc-HHHHHHHHHHHHHCCceeeec-------CCCcE-----EEEecCCHHHHHHHHHHHHHHHHH
Confidence 366788888854 3444 578899999999999998652 24431 12344444455 345566666676
Q ss_pred cCCchHHHHHHHHHH
Q 001100 913 AGLTEWKGLLVDYWS 927 (1158)
Q Consensus 913 ~Gk~~~~~~L~~F~~ 927 (1158)
.|.. ..++..|.+
T Consensus 86 ~gs~--~~ll~~l~~ 98 (130)
T TIGR02698 86 SRKV--GAVIADLIE 98 (130)
T ss_pred CCCH--HHHHHHHHh
Confidence 6754 457777655
No 96
>PF06839 zf-GRF: GRF zinc finger; InterPro: IPR010666 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This presumed zinc-binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to IPR000380 from INTERPRO. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=36.75 E-value=42 Score=27.80 Aligned_cols=35 Identities=31% Similarity=0.757 Sum_probs=22.8
Q ss_pred CCCCCCCCeEEEEecc-cCc---eeEEecCCCC--CCcccccC
Q 001100 966 SCPVCGEGTLIFKVSR-FGA---GYFIGCNQHP--RCNYIAKT 1002 (1158)
Q Consensus 966 ~CPkCGkG~l~~k~gr-~G~---~~f~GCs~yP--~C~~~~~~ 1002 (1158)
.|+ ||. ..+++..+ -|. ..||.|..+. .|.|..|.
T Consensus 2 ~C~-Cg~-~~~~~~s~k~~~N~GR~Fy~C~~~~~~~C~fF~W~ 42 (45)
T PF06839_consen 2 KCP-CGE-PAVRRTSKKTGPNPGRRFYKCPNYKDKGCNFFQWE 42 (45)
T ss_pred CCC-CCC-EeEEEEEeCCCCCCCCcceECCCCCCCCcCCEEec
Confidence 488 985 44444443 232 2699999876 49987664
No 97
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=36.64 E-value=83 Score=40.91 Aligned_cols=34 Identities=24% Similarity=0.217 Sum_probs=20.5
Q ss_pred HHHHHHHHHHhhhhhhcccHHHH---hhCCCcccCCc
Q 001100 485 VQAYLARRALDYLIGFNISPLLW---RKLPGCQSAGR 518 (1158)
Q Consensus 485 ~~A~~AR~~lD~LiG~nlSR~l~---~k~~~~lS~GR 518 (1158)
+.....++.+||+..+-++++-+ ..++..+..|+
T Consensus 72 ~l~~~~~~L~~w~s~yy~~~~g~vl~~~lP~~l~~~~ 108 (730)
T COG1198 72 VLTPELLRLIEWAADYYLSPLGDVLRLALPVLLRQGY 108 (730)
T ss_pred CCCHHHHHHHHHHHHhhcCcHHHHHHHhCchhhcccc
Confidence 34456778888888888887532 23444444444
No 98
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=36.37 E-value=43 Score=29.15 Aligned_cols=32 Identities=22% Similarity=0.743 Sum_probs=19.3
Q ss_pred CCCCCCCCCCeEEEEeccc-Cc--eeEEecCCCCCCcc
Q 001100 964 DRSCPVCGEGTLIFKVSRF-GA--GYFIGCNQHPRCNY 998 (1158)
Q Consensus 964 ~g~CPkCGkG~l~~k~gr~-G~--~~f~GCs~yP~C~~ 998 (1158)
+.+||.||...+..+.... +. ++++-|.+ |..
T Consensus 3 LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~---Cga 37 (61)
T PF14354_consen 3 LKPCPFCGSADVLIRQDEGFDYGMYYYVECTD---CGA 37 (61)
T ss_pred CcCCCCCCCcceEeecccCCCCCCEEEEEcCC---CCC
Confidence 4689999876665553221 11 16777875 654
No 99
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=35.95 E-value=43 Score=30.88 Aligned_cols=50 Identities=26% Similarity=0.343 Sum_probs=35.4
Q ss_pred CCHhHHHHHHHhcCCCCCcchHHHHHHhhccceEEEcC-------cccccccccchhhhhh
Q 001100 835 YSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKS-------RILYPEFRGRMVSAFL 888 (1158)
Q Consensus 835 yTEasLI~~MEk~GIGTpATrAsIIe~L~~R~YV~~k~-------k~L~PT~lG~~v~~~L 888 (1158)
.|-..|...| +| .++|-..+|..|.++|||+... ..+.+|+.|..+...+
T Consensus 25 ~~~~~la~~~---~~-s~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~~g~~~~~~~ 81 (101)
T smart00347 25 LSVSELAKRL---GV-SPSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEEGRELIEEL 81 (101)
T ss_pred cCHHHHHHHH---CC-CchhHHHHHHHHHHCCCeEecCCCCCCCeEEEEECHhHHHHHHHH
Confidence 4455565554 66 3566779999999999998642 2578899998766543
No 100
>KOG1956 consensus DNA topoisomerase III alpha [Replication, recombination and repair]
Probab=35.35 E-value=30 Score=43.44 Aligned_cols=56 Identities=13% Similarity=-0.140 Sum_probs=48.5
Q ss_pred EeecCCCCCCCCCCCCCCCeEEEEecchHHHHHHhhcCCCEEEEeecccccccccc
Q 001100 332 VIVPRGQNTQNPLYPPSGKSVVVVESVTKAKVIQGYLGDMYEVLPSYGHVRDLAAR 387 (1158)
Q Consensus 332 ~~~~~~~~~~~~~~~~~~k~LIIvEkPskAk~Ia~~LG~~y~V~~s~GHl~dL~~~ 387 (1158)
+++---..-|.++++++++..|..++|.++..+.-+++..+.+.-..|||++++..
T Consensus 51 ~~mtsvsghl~~~~f~~~~s~w~s~~~~~lf~a~~~~~~~~~~~~i~~~ir~eAr~ 106 (758)
T KOG1956|consen 51 VTMTSVSGHLTEADFPSEYSKWQSCPPDELFDAPVIKSVPENAKDIAKTIREEARR 106 (758)
T ss_pred eEEeeccccccccCCcccccceeecCHHHHhhhhhhhcCchhhhHHHHHHHHHHhh
Confidence 34444556688899999999999999999999999999999999999999999863
No 101
>cd01029 TOPRIM_primases TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. The prototypical bacterial primase. Escherichia coli DnaG is a single subunit enzyme.
Probab=35.21 E-value=47 Score=29.98 Aligned_cols=27 Identities=37% Similarity=0.460 Sum_probs=23.3
Q ss_pred CCeEEEccCCCccccHHHHHHHHHHhh
Q 001100 421 AENLILASDPDREGEAIAWHIVEMLQQ 447 (1158)
Q Consensus 421 ad~IIlATDpDREGE~Ia~~Ile~l~~ 447 (1158)
...||+|.|.|..|+..+..+.+.+..
T Consensus 43 ~~~vii~~D~D~~G~~~~~~~~~~~~~ 69 (79)
T cd01029 43 ARTVILAFDNDEAGKKAAARALELLLA 69 (79)
T ss_pred CCEEEEEECCCHHHHHHHHHHHHHHHH
Confidence 478999999999999888888887753
No 102
>TIGR01054 rgy reverse gyrase. Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.
Probab=34.73 E-value=42 Score=45.94 Aligned_cols=52 Identities=15% Similarity=0.356 Sum_probs=45.2
Q ss_pred eEeeeEEEeccccCCCCCCCHhHHHHHHH-hcCCCCCcchHHHHHHhhccceEE
Q 001100 817 LYLGEVELKQHHTQPPARYSEGSLVKKLE-ELGIGRPSTYASTLKVLQDRNYVT 869 (1158)
Q Consensus 817 v~~~~~~i~e~~TkPP~ryTEasLI~~ME-k~GIGTpATrAsIIe~L~~R~YV~ 869 (1158)
+.+.++..++.+..||++||-.+|++.+- +.|++..-|.. |.+.|++.|||.
T Consensus 867 ~~V~~v~~k~~~~~pP~Pf~t~~Lq~~As~~lg~sa~~tm~-iAQ~LYE~GlIT 919 (1171)
T TIGR01054 867 LDVEDIAEREEERNPLPPYTTDTMLEDANRKLGLSVKETMQ-IAQELFENGLIT 919 (1171)
T ss_pred cEEEEEEeeEEeccCCCCCCHHHHHHHHHHhcCCCHHHHHH-HHHHHHhCCEEE
Confidence 56778888999999999999999999986 46998877764 899999999997
No 103
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=34.12 E-value=75 Score=31.26 Aligned_cols=79 Identities=18% Similarity=0.217 Sum_probs=51.9
Q ss_pred CCHhHHHHHHHhc-CCCCCcchHHHHHHhhccceEEEcCcccccccccchhhhhhhcccccccChhhh-HHHHHHhhhhh
Q 001100 835 YSEGSLVKKLEEL-GIGRPSTYASTLKVLQDRNYVTVKSRILYPEFRGRMVSAFLSHYFSEVTDYSFT-ADMETELDNVS 912 (1158)
Q Consensus 835 yTEasLI~~MEk~-GIGTpATrAsIIe~L~~R~YV~~k~k~L~PT~lG~~v~~~L~~~f~~l~~p~~T-A~~E~~Ld~Ia 912 (1158)
.|-.++++.|.+. ++ .++|-.+.+..|.++|||..+. .|+..+ |.|.+..-++. ..+.+.++.+.
T Consensus 18 ~t~~eI~~~l~~~~~~-~~sTv~t~L~rL~~Kg~l~~~~-------~gr~~~-----Y~p~is~~e~~~~~~~~~l~~~~ 84 (115)
T PF03965_consen 18 ATVREIHEALPEERSW-AYSTVQTLLNRLVEKGFLTREK-------IGRAYV-----YSPLISREEYLAQELRQFLDRLF 84 (115)
T ss_dssp EEHHHHHHHHCTTSS---HHHHHHHHHHHHHTTSEEEEE-------ETTCEE-----EEESSSHHHHHHHHHHHHHHHHS
T ss_pred CCHHHHHHHHHhcccc-chhHHHHHHHHHHhCCceeEee-------cCCceE-----EEeCCcHHHHHHHHHHHHHHHHh
Confidence 4567788888665 66 7899999999999999998753 244211 22333334443 46777788888
Q ss_pred cCCchHHHHHHHHHHH
Q 001100 913 AGLTEWKGLLVDYWSR 928 (1158)
Q Consensus 913 ~Gk~~~~~~L~~F~~~ 928 (1158)
.| +...++..|.+.
T Consensus 85 ~g--s~~~l~~~l~~~ 98 (115)
T PF03965_consen 85 DG--SIPQLVAALVES 98 (115)
T ss_dssp TT--HHHHHHHHHHHC
T ss_pred CC--CHHHHHHHHHhc
Confidence 77 455677777653
No 104
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=33.99 E-value=49 Score=27.75 Aligned_cols=32 Identities=28% Similarity=0.729 Sum_probs=20.1
Q ss_pred CCCCCCCCeEEEEeccc----CceeEEecCCCCCCccc
Q 001100 966 SCPVCGEGTLIFKVSRF----GAGYFIGCNQHPRCNYI 999 (1158)
Q Consensus 966 ~CPkCGkG~l~~k~gr~----G~~~f~GCs~yP~C~~~ 999 (1158)
.||.||. ...++.++. ....++.|.| +.|..+
T Consensus 1 ~CP~Cg~-~a~ir~S~~~s~~~~~~Y~qC~N-~~Cg~t 36 (47)
T PF04606_consen 1 RCPHCGS-KARIRTSRQLSPLTRELYCQCTN-PECGHT 36 (47)
T ss_pred CcCCCCC-eeEEEEchhhCcceEEEEEEECC-CcCCCE
Confidence 4999997 445544432 2234778988 578764
No 105
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=33.22 E-value=25 Score=34.93 Aligned_cols=33 Identities=30% Similarity=0.804 Sum_probs=22.8
Q ss_pred CCCCCCCCCCe-----EEEEecccCceeEEecCCCCCCccc
Q 001100 964 DRSCPVCGEGT-----LIFKVSRFGAGYFIGCNQHPRCNYI 999 (1158)
Q Consensus 964 ~g~CPkCGkG~-----l~~k~gr~G~~~f~GCs~yP~C~~~ 999 (1158)
...||+||... +.+|..-=|.-+||-|. +|++.
T Consensus 74 ~~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~---kC~~k 111 (116)
T KOG2907|consen 74 KHKCPKCGHEEMSYHTLQLRSADEGQTVFYTCP---KCKYK 111 (116)
T ss_pred hccCcccCCchhhhhhhhcccccCCceEEEEcC---cccee
Confidence 46899999754 34565555666899984 47764
No 106
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=33.03 E-value=60 Score=43.69 Aligned_cols=41 Identities=22% Similarity=0.080 Sum_probs=28.9
Q ss_pred CCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHH
Q 001100 430 PDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKV 472 (1158)
Q Consensus 430 pDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fs~lT~~aI~~ 472 (1158)
.-|+..+|+..|.+...... ....+.+|+-||.=|+=+=..
T Consensus 309 f~~~l~m~i~~I~ei~~~~r--~D~~~eKRVELh~HTkMS~mD 349 (1444)
T COG2176 309 FTRDLTMIINDINEIENAKR--KDLAKEKRVELHFHTKMSQMD 349 (1444)
T ss_pred cccceEEEhhhhhhhhcccc--cccCccceEEEEeccchhhhc
Confidence 35889999999988765432 234579999999777544333
No 107
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=32.62 E-value=51 Score=29.80 Aligned_cols=33 Identities=27% Similarity=0.613 Sum_probs=21.0
Q ss_pred CCCCCCCCCCCeEEEEecccCceeEEecCCCCCCcccc
Q 001100 963 KDRSCPVCGEGTLIFKVSRFGAGYFIGCNQHPRCNYIA 1000 (1158)
Q Consensus 963 ~~g~CPkCGkG~l~~k~gr~G~~~f~GCs~yP~C~~~~ 1000 (1158)
.+.+||.||...+.++.. +.++++-|. +|....
T Consensus 5 ~lKPCPFCG~~~~~v~~~--~g~~~v~C~---~CgA~~ 37 (64)
T PRK09710 5 NVKPCPFCGCPSVTVKAI--SGYYRAKCN---GCESRT 37 (64)
T ss_pred cccCCCCCCCceeEEEec--CceEEEEcC---CCCcCc
Confidence 356899999876666643 444556664 465543
No 108
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=32.34 E-value=41 Score=36.13 Aligned_cols=30 Identities=27% Similarity=0.414 Sum_probs=26.4
Q ss_pred HHHHhcCCCHHHHHHHHHHHhccccCCCCCeeEEEEEec
Q 001100 623 DAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMR 661 (1158)
Q Consensus 623 ~AskklG~Sa~~Tm~iAQ~LYE~~k~~~g~~~GlITYPR 661 (1158)
+++..+|++...+-+++++|||. |||+|-|
T Consensus 41 eLA~~Lgi~~~~VRk~L~~L~e~---------gLv~~~r 70 (178)
T PRK06266 41 EIAEQTGIKLNTVRKILYKLYDA---------RLADYKR 70 (178)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHC---------CCeEEee
Confidence 34566899999999999999995 8999987
No 109
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=32.28 E-value=59 Score=41.61 Aligned_cols=31 Identities=29% Similarity=0.415 Sum_probs=19.5
Q ss_pred CCCCCCCCCCCCCeEEEEecccCceeEEecCC
Q 001100 961 PNKDRSCPVCGEGTLIFKVSRFGAGYFIGCNQ 992 (1158)
Q Consensus 961 ~~~~g~CPkCGkG~l~~k~gr~G~~~f~GCs~ 992 (1158)
+.+..+|+.|-. .+.-...|+=.|-|+.|++
T Consensus 98 ~pD~a~C~~Cl~-Ei~dp~~rrY~YPF~~CT~ 128 (750)
T COG0068 98 PPDAATCEDCLE-EIFDPNSRRYLYPFINCTN 128 (750)
T ss_pred CCchhhhHHHHH-HhcCCCCcceeccccccCC
Confidence 445789999975 3333333333445999986
No 110
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=31.76 E-value=13 Score=34.66 Aligned_cols=40 Identities=33% Similarity=0.454 Sum_probs=29.2
Q ss_pred HhcCCCCCcchHHHHHHhhccceEEEcC----c----ccccccccchhh
Q 001100 845 EELGIGRPSTYASTLKVLQDRNYVTVKS----R----ILYPEFRGRMVS 885 (1158)
Q Consensus 845 Ek~GIGTpATrAsIIe~L~~R~YV~~k~----k----~L~PT~lG~~v~ 885 (1158)
+..|| |+++-..|+++|.+.|||..++ + .+..|+.|+...
T Consensus 22 ~~l~l-t~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~ 69 (80)
T PF13601_consen 22 EELGL-TDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAF 69 (80)
T ss_dssp HHTT---HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHH
T ss_pred HHhCc-CHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHH
Confidence 45688 8899999999999999998742 2 377889998543
No 111
>TIGR02679 conserved hypothetical protein TIGR02679. Members of this protein belong to a conserved gene four-gene neighborhood found sporadically in a phylogenetically broad range of bacteria: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria).
Probab=31.46 E-value=1.5e+02 Score=35.85 Aligned_cols=88 Identities=20% Similarity=0.220 Sum_probs=56.4
Q ss_pred eEEEEecchHHHHHHhhcCCCE-EEEeeccccccccccCCCCCCCCCCcceEecCcchHHHHHHHHHHhccCCeEEEccC
Q 001100 351 SVVVVESVTKAKVIQGYLGDMY-EVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILASD 429 (1158)
Q Consensus 351 ~LIIvEkPskAk~Ia~~LG~~y-~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~~~k~lk~Ik~l~k~ad~IIlATD 429 (1158)
.++|||-|++-..+...++... -++++.|. . ......-|.++...-..|+-.+|
T Consensus 252 ~V~vvENp~vf~~~~~~~~~~~~~lIct~G~-----------------p--------~~a~~~LL~~L~~~g~~l~YhGD 306 (385)
T TIGR02679 252 RVYVVENPNVLAIALDRLGPRCAPLVCTDGQ-----------------P--------NAAQIKLLDLLAAAGARLYYHGD 306 (385)
T ss_pred eEEEEecHHHHHHHHHhcCCCCceEEECCCc-----------------c--------hHHHHHHHHHHHhcCCeEEEecC
Confidence 4999999999999988776553 34444441 1 22344455556543333455599
Q ss_pred CCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHh
Q 001100 430 PDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQA 476 (1158)
Q Consensus 430 pDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fs~lT~~aI~~A~~n 476 (1158)
.|-||=.|+.++....+ -+.| -++.++-++|+.+
T Consensus 307 fD~~Gi~Ia~~L~~r~~-----------~~pw--rmd~~dY~~a~~~ 340 (385)
T TIGR02679 307 FDWPGLRIANGLIRRYG-----------ARPW--RFSAADYRAAVVG 340 (385)
T ss_pred CChhHHHHHHHHHHHhC-----------Cccc--cCCHHHHHHHhcc
Confidence 99999999999987532 1223 3556666666654
No 112
>PRK05978 hypothetical protein; Provisional
Probab=31.18 E-value=33 Score=35.92 Aligned_cols=13 Identities=54% Similarity=1.308 Sum_probs=9.9
Q ss_pred CCCCCCCCCCeEE
Q 001100 964 DRSCPVCGEGTLI 976 (1158)
Q Consensus 964 ~g~CPkCGkG~l~ 976 (1158)
.+.||.||+|.+.
T Consensus 33 ~grCP~CG~G~LF 45 (148)
T PRK05978 33 RGRCPACGEGKLF 45 (148)
T ss_pred cCcCCCCCCCccc
Confidence 4689999987543
No 113
>PRK14701 reverse gyrase; Provisional
Probab=30.85 E-value=59 Score=46.00 Aligned_cols=65 Identities=14% Similarity=0.218 Sum_probs=54.5
Q ss_pred eeEeeeEEEeccccCCCCCCCHhHHHHHHHh-cCCCCCcchHHHHHHhhccceEEEcCcccccccccc
Q 001100 816 PLYLGEVELKQHHTQPPARYSEGSLVKKLEE-LGIGRPSTYASTLKVLQDRNYVTVKSRILYPEFRGR 882 (1158)
Q Consensus 816 ~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk-~GIGTpATrAsIIe~L~~R~YV~~k~k~L~PT~lG~ 882 (1158)
.+.+.++..+++...||++||-.+|.+.+-+ .|++..-|. .|.+.|++.||+. -.+..+.|+.|.
T Consensus 838 ~~~V~~v~~k~~~~~pP~pf~t~~Lq~~As~~~g~s~~~tm-~iAQ~LYE~g~~~-~p~t~V~l~dG~ 903 (1638)
T PRK14701 838 EVEVELVEEEEKERNPLPPYTTDTMLRDASAFLKLSAKETM-KLAQDLFEAGLCV-TPDTYVSLHDGR 903 (1638)
T ss_pred eEEEEEEEeeEEEccCCCCcCHHHHHHHHHHhcCCCHHHHH-HHHHHHHhCceee-CCCceeecCchH
Confidence 3567788889999999999999999999975 599877776 4899999999986 456677888886
No 114
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=29.51 E-value=36 Score=32.98 Aligned_cols=32 Identities=41% Similarity=0.643 Sum_probs=25.4
Q ss_pred HHHHHhcCCCHHHHHHHHHHHhccccCCCCCeeEEEEEecC
Q 001100 622 QDAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRT 662 (1158)
Q Consensus 622 ~~AskklG~Sa~~Tm~iAQ~LYE~~k~~~g~~~GlITYPRT 662 (1158)
.+.++.+|+++.++-++++.||+. |||+|-|.
T Consensus 31 e~la~~~~l~~~~vRkiL~~L~~~---------~lv~~~~~ 62 (105)
T PF02002_consen 31 EDLAKKLGLKPKEVRKILYKLYED---------GLVSYRRR 62 (105)
T ss_dssp HHHHHTT-S-HHHHHHHHHHHHHH---------SS-EEEEE
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHC---------CCeEEEEE
Confidence 567788999999999999999995 89999874
No 115
>PRK00420 hypothetical protein; Validated
Probab=28.68 E-value=43 Score=33.50 Aligned_cols=10 Identities=50% Similarity=1.305 Sum_probs=7.8
Q ss_pred CCCCCCCCCC
Q 001100 964 DRSCPVCGEG 973 (1158)
Q Consensus 964 ~g~CPkCGkG 973 (1158)
...||.||.+
T Consensus 23 ~~~CP~Cg~p 32 (112)
T PRK00420 23 SKHCPVCGLP 32 (112)
T ss_pred cCCCCCCCCc
Confidence 3689999964
No 116
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=28.14 E-value=57 Score=35.12 Aligned_cols=31 Identities=29% Similarity=0.502 Sum_probs=27.1
Q ss_pred HHHHhcCCCHHHHHHHHHHHhccccCCCCCeeEEEEEecC
Q 001100 623 DAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRT 662 (1158)
Q Consensus 623 ~AskklG~Sa~~Tm~iAQ~LYE~~k~~~g~~~GlITYPRT 662 (1158)
+.+..+|+....+.++.+.|||. |+|+|.|.
T Consensus 37 ela~~l~i~~~~vrriL~~L~e~---------~li~~~k~ 67 (176)
T COG1675 37 ELAELLGIKKNEVRRILYALYED---------GLISYRKK 67 (176)
T ss_pred HHHHHhCccHHHHHHHHHHHHhC---------CceEEEee
Confidence 55677999999999999999995 89998774
No 117
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=28.07 E-value=87 Score=26.88 Aligned_cols=34 Identities=18% Similarity=0.666 Sum_probs=18.2
Q ss_pred CCCCCCCCCeEEEEe--cccCceeEEecCCCCCCccccc
Q 001100 965 RSCPVCGEGTLIFKV--SRFGAGYFIGCNQHPRCNYIAK 1001 (1158)
Q Consensus 965 g~CPkCGkG~l~~k~--gr~G~~~f~GCs~yP~C~~~~~ 1001 (1158)
.+||.||+....++. ...+...++.|. .|....+
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~---~Cga~~~ 37 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECS---TCGASGP 37 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECC---CCCCCcc
Confidence 479999975553442 212222233675 3766543
No 118
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=26.45 E-value=79 Score=27.27 Aligned_cols=42 Identities=17% Similarity=0.235 Sum_probs=30.6
Q ss_pred CCCHhHHHHHHHhcCCCCCcchHHHHHHhhccceEEEcC-ccccccc
Q 001100 834 RYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKS-RILYPEF 879 (1158)
Q Consensus 834 ryTEasLI~~MEk~GIGTpATrAsIIe~L~~R~YV~~k~-k~L~PT~ 879 (1158)
.+|..+|-+.+ |+ +++|-..+|..|.+.|||...+ +.+.+++
T Consensus 25 ~~s~~ela~~~---g~-s~~tv~r~l~~L~~~g~i~~~~~~~~~l~~ 67 (67)
T cd00092 25 PLTRQEIADYL---GL-TRETVSRTLKELEEEGLISRRGRGKYRVNP 67 (67)
T ss_pred CcCHHHHHHHH---CC-CHHHHHHHHHHHHHCCCEEecCCCeEEeCC
Confidence 35666665544 67 5677888999999999999866 5666553
No 119
>PF13362 Toprim_3: Toprim domain
Probab=25.99 E-value=2e+02 Score=27.12 Aligned_cols=65 Identities=23% Similarity=0.433 Sum_probs=42.9
Q ss_pred eEEEEecchHHHHHHhhcCCCEEEEeecc--ccccccccCCCCCCCCCCcceEecCcchHHHHHHHHHHhccCCeEEEcc
Q 001100 351 SVVVVESVTKAKVIQGYLGDMYEVLPSYG--HVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILAS 428 (1158)
Q Consensus 351 ~LIIvEkPskAk~Ia~~LG~~y~V~~s~G--Hl~dL~~~~~~v~p~~~f~~~~~v~~~~~k~lk~Ik~l~k~ad~IIlAT 428 (1158)
+|+|+|-..-|=++ .+...++.|.++.| +|.... ++ .....||||.
T Consensus 1 tl~i~EG~etals~-~~~~~~~~~~a~~~~~nl~~~~-----------------~~--------------~~~~~vii~~ 48 (96)
T PF13362_consen 1 TLIIAEGIETALSI-AQQATGVPVVAALGAGNLKNVA-----------------IP--------------EPGRRVIIAA 48 (96)
T ss_pred CEEEEEhHHHHHHH-HHhcCCCeEEEEEChhhhhhhc-----------------CC--------------CCCCeEEEEE
Confidence 58999988888888 23344444444433 333211 00 2346789999
Q ss_pred CCCcc--ccHHHHHHHHHHhh
Q 001100 429 DPDRE--GEAIAWHIVEMLQQ 447 (1158)
Q Consensus 429 DpDRE--GE~Ia~~Ile~l~~ 447 (1158)
|.|.. |+.=+..+.+.+..
T Consensus 49 D~D~~~~G~~~a~~~~~~~~~ 69 (96)
T PF13362_consen 49 DNDKANEGQKAAEKAAERLEA 69 (96)
T ss_pred CCCCchhhHHHHHHHHHHHHh
Confidence 99999 99988888887754
No 120
>PRK04023 DNA polymerase II large subunit; Validated
Probab=25.97 E-value=58 Score=43.18 Aligned_cols=53 Identities=19% Similarity=0.254 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCCCCCeEEEEecccCceeEEecCCCCCCcccccCCCCCCchhhhhhhccCCCCCcccCCCCCccceeeec
Q 001100 959 SLPNKDRSCPVCGEGTLIFKVSRFGAGYFIGCNQHPRCNYIAKTLYGDDDEEDTLQRNTNVDEPKLIGHHPASKEKVLLK 1038 (1158)
Q Consensus 959 ~~~~~~g~CPkCGkG~l~~k~gr~G~~~f~GCs~yP~C~~~~~~~~~e~~~~e~~~~~~~~~lPr~LG~cPkcG~~v~lk 1038 (1158)
.++.....||.||......+ ||+||..
T Consensus 621 eVEVg~RfCpsCG~~t~~fr-------------------------------------------------CP~CG~~---- 647 (1121)
T PRK04023 621 EVEIGRRKCPSCGKETFYRR-------------------------------------------------CPFCGTH---- 647 (1121)
T ss_pred eecccCccCCCCCCcCCccc-------------------------------------------------CCCCCCC----
Q ss_pred cCCCcceEEeCCCCCCCCCcccccCCCCCccccCHHHHHHHhcCCcccCCCCCCCcCe
Q 001100 1039 SGPYGFYVQLGEDRTGYLPKRASVSHIKDVDSITLEDALELLRYPVNLGNHPKDGQPI 1096 (1158)
Q Consensus 1039 ~GrfG~yv~c~~d~kg~kpK~~slpk~~~~~sItle~Al~ll~~pk~lG~cP~cG~~I 1096 (1158)
..+...| |+|. .+..-..||+||.++
T Consensus 648 ---Te~i~fC--------------P~CG---------------~~~~~y~CPKCG~El 673 (1121)
T PRK04023 648 ---TEPVYRC--------------PRCG---------------IEVEEDECEKCGREP 673 (1121)
T ss_pred ---CCcceeC--------------cccc---------------CcCCCCcCCCCCCCC
No 121
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=24.79 E-value=31 Score=30.10 Aligned_cols=30 Identities=20% Similarity=0.227 Sum_probs=22.2
Q ss_pred CcchHHHHHHhhccceEEEc-----C--ccccccccc
Q 001100 852 PSTYASTLKVLQDRNYVTVK-----S--RILYPEFRG 881 (1158)
Q Consensus 852 pATrAsIIe~L~~R~YV~~k-----~--k~L~PT~lG 881 (1158)
.+|-..+|+.|.++|||++. + +.+.+|+.|
T Consensus 32 ~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~~G 68 (68)
T PF13463_consen 32 KSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTPAG 68 (68)
T ss_dssp HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-HHH
T ss_pred HHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCCCC
Confidence 35667999999999999763 2 357788876
No 122
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=24.71 E-value=1.4e+02 Score=31.30 Aligned_cols=51 Identities=20% Similarity=0.404 Sum_probs=41.3
Q ss_pred HHHHHHhcCCCHHHHHHHHHHHhccccCCCCCeeEEEEEecCCCcCCCHHHHHHHHHHHH
Q 001100 621 QQDAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIF 680 (1158)
Q Consensus 621 Q~~AskklG~Sa~~Tm~iAQ~LYE~~k~~~g~~~GlITYPRTDS~~Ls~~~~~~i~~~i~ 680 (1158)
+.+.++.|+.+|.-+.+.+++|.+. |||.|-+=....|++.....+..++.
T Consensus 27 ~~diA~~L~Vsp~sVt~ml~rL~~~---------GlV~~~~y~gi~LT~~G~~~a~~~~r 77 (154)
T COG1321 27 TKDIAERLKVSPPSVTEMLKRLERL---------GLVEYEPYGGVTLTEKGREKAKELLR 77 (154)
T ss_pred HHHHHHHhCCCcHHHHHHHHHHHHC---------CCeEEecCCCeEEChhhHHHHHHHHH
Confidence 4577888999999999999999995 99999777777888766555555543
No 123
>PRK09401 reverse gyrase; Reviewed
Probab=24.46 E-value=69 Score=43.95 Aligned_cols=52 Identities=19% Similarity=0.265 Sum_probs=45.0
Q ss_pred EeeeEEEeccccCCCCCCCHhHHHHHHHh-cCCCCCcchHHHHHHhhccceEEE
Q 001100 818 YLGEVELKQHHTQPPARYSEGSLVKKLEE-LGIGRPSTYASTLKVLQDRNYVTV 870 (1158)
Q Consensus 818 ~~~~~~i~e~~TkPP~ryTEasLI~~MEk-~GIGTpATrAsIIe~L~~R~YV~~ 870 (1158)
.+..+..++.+..||++||-.+|.+.+-+ .|++..-|.. |.+.|++.|||.-
T Consensus 868 ~V~~v~~k~~~~~pP~Pf~t~~Lq~~As~~lg~Sa~~tm~-iAQ~LYE~glITY 920 (1176)
T PRK09401 868 EVEKVEEKEEELNPLPPYTTDTLLSDASRKLRLSAQETMR-IAQDLFELGLITY 920 (1176)
T ss_pred eeeEEEeeEEEecCCCCCccHHHHHHHHHHcCCCHHHHHH-HHHHHHhCCceee
Confidence 56678889999999999999999999864 6998887775 8999999999963
No 124
>KOG1589 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.25 E-value=32 Score=34.01 Aligned_cols=14 Identities=43% Similarity=0.857 Sum_probs=9.4
Q ss_pred hhhhhhhhccCCCC
Q 001100 38 FMATHRAFWNHQGI 51 (1158)
Q Consensus 38 ~~~~~~~~~~~~~~ 51 (1158)
||++.|.|||||+-
T Consensus 6 ~~~k~r~~WnhpaG 19 (118)
T KOG1589|consen 6 FVAKLRPLWNHPAG 19 (118)
T ss_pred HHHHHHHHhcCCCC
Confidence 55677777777763
No 125
>TIGR02277 PaaX_trns_reg phenylacetic acid degradation operon negative regulatory protein PaaX. This transcriptional regulator is always found in association with operons believed to be involved in the degradation of phenylacetic acid. The gene product has been shown to bind to the promoter sites and repress their transcription.
Probab=24.08 E-value=66 Score=37.00 Aligned_cols=52 Identities=21% Similarity=0.215 Sum_probs=42.0
Q ss_pred CCCHhHHHHHHHhcCCCCCcchHHHHHHhhccceEEEcC----cccccccccchhhh
Q 001100 834 RYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKS----RILYPEFRGRMVSA 886 (1158)
Q Consensus 834 ryTEasLI~~MEk~GIGTpATrAsIIe~L~~R~YV~~k~----k~L~PT~lG~~v~~ 886 (1158)
...-++||+.|+..||...+.|. ++..|.++|+|+... +....|+.|+...+
T Consensus 17 ~i~~~~Li~l~~~~gi~~~~vr~-al~RL~~~G~l~~~~~grr~~Y~LT~~g~~~l~ 72 (280)
T TIGR02277 17 AIWLGSLIEFLAGLGINERLVRT-AVSRLVAQGWLQSERKGRRSFYSLTDKGRRRFA 72 (280)
T ss_pred ceeHHHHHHHHHhcCCCcchHHH-HHHHHHHCCCEEeeecCCCCEEEECHHHHHHHH
Confidence 34568999999999999888885 677999999998753 46788999986544
No 126
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.98 E-value=30 Score=31.13 Aligned_cols=29 Identities=34% Similarity=0.835 Sum_probs=16.6
Q ss_pred CCCCCCCCCCeEEEEecccCceeEEecCCCCCCcc
Q 001100 964 DRSCPVCGEGTLIFKVSRFGAGYFIGCNQHPRCNY 998 (1158)
Q Consensus 964 ~g~CPkCGkG~l~~k~gr~G~~~f~GCs~yP~C~~ 998 (1158)
..+||.||+.....-.+.|-+ | |+ ..|+.
T Consensus 7 ~v~CP~Cgkpv~w~~~s~frP--F--CS--kRCkl 35 (65)
T COG3024 7 TVPCPTCGKPVVWGEESPFRP--F--CS--KRCKL 35 (65)
T ss_pred cccCCCCCCcccccccCCcCc--c--hh--Hhhhh
Confidence 468999998543333344444 4 55 35654
No 127
>PRK05978 hypothetical protein; Provisional
Probab=23.89 E-value=42 Score=35.12 Aligned_cols=22 Identities=9% Similarity=-0.108 Sum_probs=15.9
Q ss_pred CCCCCCCcCeEEeeccCcc-eee
Q 001100 1087 GNHPKDGQPIMLRLARAGF-SVR 1108 (1158)
Q Consensus 1087 G~cP~cG~~I~i~~GRyG~-Yi~ 1108 (1158)
..||.||.+.....+-+|+ |+.
T Consensus 53 ~~C~~CG~~~~~~~a~DgpAy~~ 75 (148)
T PRK05978 53 DHCAACGEDFTHHRADDLPAYLV 75 (148)
T ss_pred CCccccCCccccCCccccCcchh
Confidence 3599999888877676665 643
No 128
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=23.25 E-value=1.6e+02 Score=28.35 Aligned_cols=52 Identities=12% Similarity=0.245 Sum_probs=38.5
Q ss_pred CHhHHHHHHHhcC-----CCCCcchHHHHHHhhccceEEEc---------Ccccccccccchhhhhh
Q 001100 836 SEGSLVKKLEELG-----IGRPSTYASTLKVLQDRNYVTVK---------SRILYPEFRGRMVSAFL 888 (1158)
Q Consensus 836 TEasLI~~MEk~G-----IGTpATrAsIIe~L~~R~YV~~k---------~k~L~PT~lG~~v~~~L 888 (1158)
+=-+|.+.|++.. |+ ++|--.++..|.+.|||+.. .+.+..|+.|+.+.+.+
T Consensus 19 ~GYei~~~l~~~~~~~~~i~-~gtlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT~~Gr~~l~~~ 84 (100)
T TIGR03433 19 HGYGIAQRIQQISEDVLQVE-EGSLYPALHRLERRGWIAAEWGESENNRRAKFYRLTAAGRKQLAAE 84 (100)
T ss_pred CHHHHHHHHHHHcCCccccC-CCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHHHHHHHHHH
Confidence 4457888887652 33 47888999999999999862 24688999999765443
No 129
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=23.05 E-value=1.7e+02 Score=29.87 Aligned_cols=48 Identities=25% Similarity=0.344 Sum_probs=39.5
Q ss_pred HHHHHhcCCCHHHHHHHHHHHhccccCCCCCeeEEEEEecCCCcCCCHHHHHHHHHH
Q 001100 622 QDAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSL 678 (1158)
Q Consensus 622 ~~AskklG~Sa~~Tm~iAQ~LYE~~k~~~g~~~GlITYPRTDS~~Ls~~~~~~i~~~ 678 (1158)
.+.+..+++|+.-+....++|-+. |||.|-|...-.|++.....+..+
T Consensus 26 ~ela~~l~vs~~svs~~l~~L~~~---------Gli~~~~~~~i~LT~~G~~~a~~~ 73 (142)
T PRK03902 26 SDIAEALSVHPSSVTKMVQKLDKD---------EYLIYEKYRGLVLTPKGKKIGKRL 73 (142)
T ss_pred HHHHHHhCCChhHHHHHHHHHHHC---------CCEEEecCceEEECHHHHHHHHHH
Confidence 577888999999999999999985 999998877788888765544443
No 130
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=22.81 E-value=2e+02 Score=33.83 Aligned_cols=33 Identities=24% Similarity=0.654 Sum_probs=19.0
Q ss_pred CCCCCCCCCCeE--EEEecccCceeEEecCCCCCCccc
Q 001100 964 DRSCPVCGEGTL--IFKVSRFGAGYFIGCNQHPRCNYI 999 (1158)
Q Consensus 964 ~g~CPkCGkG~l--~~k~gr~G~~~f~GCs~yP~C~~~ 999 (1158)
.+.||.||...+ +++.+..+...|+-|+- |.+-
T Consensus 187 ~~~CPvCGs~P~~s~v~~~~~~G~RyL~Csl---C~te 221 (309)
T PRK03564 187 RQFCPVCGSMPVSSVVQIGTTQGLRYLHCNL---CESE 221 (309)
T ss_pred CCCCCCCCCcchhheeeccCCCCceEEEcCC---CCCc
Confidence 578999998543 12332222235778864 6543
No 131
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=22.74 E-value=58 Score=34.21 Aligned_cols=39 Identities=18% Similarity=0.123 Sum_probs=31.9
Q ss_pred CCCCCcchHHHHHHhhccceEEE-cCcccccccccchhhhh
Q 001100 848 GIGRPSTYASTLKVLQDRNYVTV-KSRILYPEFRGRMVSAF 887 (1158)
Q Consensus 848 GIGTpATrAsIIe~L~~R~YV~~-k~k~L~PT~lG~~v~~~ 887 (1158)
++ .|+|-..++++|.+.|||.. +.+.+..|+.|..+...
T Consensus 35 ~V-sp~sVt~ml~rL~~~GlV~~~~y~gi~LT~~G~~~a~~ 74 (154)
T COG1321 35 KV-SPPSVTEMLKRLERLGLVEYEPYGGVTLTEKGREKAKE 74 (154)
T ss_pred CC-CcHHHHHHHHHHHHCCCeEEecCCCeEEChhhHHHHHH
Confidence 45 47788999999999999987 56789999999965443
No 132
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=22.49 E-value=99 Score=31.98 Aligned_cols=51 Identities=14% Similarity=0.199 Sum_probs=40.6
Q ss_pred CHhHHHHHHHhcCCCC----CcchHHHHHHhhccceEEEc-----Ccccccccccchhhh
Q 001100 836 SEGSLVKKLEELGIGR----PSTYASTLKVLQDRNYVTVK-----SRILYPEFRGRMVSA 886 (1158)
Q Consensus 836 TEasLI~~MEk~GIGT----pATrAsIIe~L~~R~YV~~k-----~k~L~PT~lG~~v~~ 886 (1158)
.=-.|++.|++.|+|. ++|-=.++..|.+.|||... .+.+.+|+.|+....
T Consensus 57 yGYeI~k~I~e~~~g~~~~s~GtIYp~L~RLE~~GlI~s~~~~~~RK~Y~ITe~Gre~L~ 116 (135)
T PRK09416 57 TGYELLQLLRQRGILTFEGNEGSLYTLLHRLEQNRFIQSSWDHEGAKYYQLTDKGNKMLR 116 (135)
T ss_pred CHHHHHHHHHHhcCCcccCCCccHHHHHHHHHHCCCeEEeecCCCceEEEECHHHHHHHH
Confidence 3457888898888775 78999999999999999752 457889999986443
No 133
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=20.59 E-value=70 Score=25.61 Aligned_cols=19 Identities=21% Similarity=0.190 Sum_probs=14.0
Q ss_pred cCCcccCCCCCCCcCeEEe
Q 001100 1081 RYPVNLGNHPKDGQPIMLR 1099 (1158)
Q Consensus 1081 ~~pk~lG~cP~cG~~I~i~ 1099 (1158)
..|+.-|+|..||++++.+
T Consensus 16 ~pP~~~~~Cd~cg~~L~qR 34 (36)
T PF05191_consen 16 NPPKVEGVCDNCGGELVQR 34 (36)
T ss_dssp B--SSTTBCTTTTEBEBEE
T ss_pred CCCCCCCccCCCCCeeEeC
Confidence 4567779999999988765
No 134
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=20.27 E-value=1.3e+02 Score=23.76 Aligned_cols=31 Identities=19% Similarity=0.369 Sum_probs=26.8
Q ss_pred CCCHhHHHHHHHhcCCCCCcchHHHHHHhhc
Q 001100 834 RYSEGSLVKKLEELGIGRPSTYASTLKVLQD 864 (1158)
Q Consensus 834 ryTEasLI~~MEk~GIGTpATrAsIIe~L~~ 864 (1158)
.+|-++|-+.+.+.||-+.-|.+.+|+.|.+
T Consensus 3 ~l~v~eLk~~l~~~gL~~~G~K~~Li~Rl~~ 33 (35)
T PF02037_consen 3 KLTVAELKEELKERGLSTSGKKAELIERLKE 33 (35)
T ss_dssp TSHHHHHHHHHHHTTS-STSSHHHHHHHHHH
T ss_pred cCcHHHHHHHHHHCCCCCCCCHHHHHHHHHH
Confidence 4677899999999999999999999999864
Done!