Query 001106
Match_columns 1157
No_of_seqs 358 out of 2545
Neff 5.7
Searched_HMMs 46136
Date Thu Mar 28 15:59:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001106.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001106hhsearch_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 5E-161 1E-165 1487.2 74.9 757 347-1147 1-771 (780)
2 PRK07561 DNA topoisomerase I s 100.0 9E-155 2E-159 1448.2 75.9 736 349-1137 2-755 (859)
3 PRK06319 DNA topoisomerase I/S 100.0 2E-152 4E-157 1424.5 71.1 741 347-1146 1-766 (860)
4 PRK06599 DNA topoisomerase I; 100.0 2E-137 4E-142 1266.9 69.6 661 347-1048 1-661 (675)
5 PRK05776 DNA topoisomerase I; 100.0 9E-136 2E-140 1245.1 60.2 596 348-1002 1-638 (670)
6 PRK07219 DNA topoisomerase I; 100.0 5E-135 1E-139 1266.9 66.8 689 349-1108 1-756 (822)
7 COG0550 TopA Topoisomerase IA 100.0 1E-135 3E-140 1214.4 54.1 546 349-934 1-553 (570)
8 PRK05582 DNA topoisomerase I; 100.0 3E-133 7E-138 1225.6 65.5 635 347-1048 1-636 (650)
9 TIGR01051 topA_bact DNA topois 100.0 5E-132 1E-136 1205.4 62.8 608 351-1001 1-609 (610)
10 PRK07220 DNA topoisomerase I; 100.0 3E-132 7E-137 1227.6 61.1 624 349-1048 1-661 (740)
11 TIGR01056 topB DNA topoisomera 100.0 7E-132 1E-136 1210.4 60.3 585 349-999 1-643 (660)
12 PRK14973 DNA topoisomerase I; 100.0 1E-131 3E-136 1234.2 61.9 626 349-1048 1-661 (936)
13 PRK08173 DNA topoisomerase III 100.0 7E-130 2E-134 1217.0 67.7 712 347-1139 1-783 (862)
14 PRK14724 DNA topoisomerase III 100.0 4E-129 8E-134 1222.1 66.6 726 349-1139 2-816 (987)
15 PRK07726 DNA topoisomerase III 100.0 1E-126 2E-131 1167.7 59.6 586 349-996 1-640 (658)
16 TIGR01057 topA_arch DNA topois 100.0 1E-123 3E-128 1135.7 60.1 577 353-995 1-618 (618)
17 PTZ00407 DNA topoisomerase IA; 100.0 2E-119 5E-124 1095.6 48.5 572 349-936 10-695 (805)
18 PRK09401 reverse gyrase; Revie 100.0 2E-110 3E-115 1069.0 55.0 511 347-931 600-1172(1176)
19 TIGR01054 rgy reverse gyrase. 100.0 2E-109 4E-114 1060.9 56.5 515 344-929 597-1169(1171)
20 KOG1956 DNA topoisomerase III 100.0 8E-102 2E-106 888.8 40.8 692 349-1147 2-745 (758)
21 PRK14701 reverse gyrase; Provi 100.0 1.1E-95 2E-100 948.9 52.7 516 345-930 577-1636(1638)
22 cd00186 TOP1Ac DNA Topoisomera 100.0 5.3E-90 1.1E-94 798.1 38.7 375 481-930 1-379 (381)
23 PF01131 Topoisom_bac: DNA top 100.0 6.1E-89 1.3E-93 794.9 33.6 398 478-922 1-403 (403)
24 COG1110 Reverse gyrase [DNA re 100.0 2E-86 4.3E-91 795.3 40.4 520 336-930 605-1185(1187)
25 smart00437 TOP1Ac Bacterial DN 100.0 1.4E-60 2.9E-65 525.6 24.5 255 603-883 2-259 (259)
26 KOG1957 DNA topoisomerase III 100.0 7.1E-54 1.5E-58 477.8 14.1 493 348-925 2-529 (555)
27 cd03363 TOPRIM_TopoIA_TopoI TO 100.0 1.5E-30 3.2E-35 257.2 14.0 122 349-476 1-123 (123)
28 cd01028 TOPRIM_TopoIA TOPRIM_T 100.0 9E-30 2E-34 257.6 14.8 123 349-476 1-142 (142)
29 cd03362 TOPRIM_TopoIA_TopoIII 100.0 3.3E-29 7.2E-34 256.0 14.1 124 349-476 1-151 (151)
30 smart00436 TOP1Bc Bacterial DN 100.0 8.6E-30 1.9E-34 237.6 8.9 88 456-543 1-89 (89)
31 cd03361 TOPRIM_TopoIA_RevGyr T 99.9 8.9E-27 1.9E-31 242.5 13.8 122 350-476 2-170 (170)
32 COG1754 Uncharacterized C-term 99.9 4.2E-26 9.1E-31 246.1 11.9 169 963-1137 23-192 (298)
33 COG1754 Uncharacterized C-term 99.9 2.5E-22 5.3E-27 217.1 12.3 171 961-1140 76-259 (298)
34 PF01751 Toprim: Toprim domain 99.8 5.4E-21 1.2E-25 182.3 6.3 99 350-464 1-100 (100)
35 PRK08780 DNA topoisomerase I; 99.7 1.9E-16 4.1E-21 198.6 10.8 119 1021-1140 588-706 (780)
36 PRK07561 DNA topoisomerase I s 99.7 4.3E-16 9.4E-21 197.6 13.5 156 962-1139 644-820 (859)
37 PF13368 Toprim_C_rpt: Topoiso 98.7 2.2E-08 4.8E-13 87.8 5.6 50 1088-1138 1-50 (61)
38 COG0551 TopA Zn-finger domain 98.6 1.1E-07 2.4E-12 96.6 9.8 100 961-1100 15-116 (140)
39 smart00493 TOPRIM topoisomeras 98.6 2.1E-07 4.5E-12 84.0 8.6 73 349-446 1-73 (76)
40 PRK06319 DNA topoisomerase I/S 98.4 3.3E-07 7.1E-12 117.4 7.0 119 519-644 384-509 (860)
41 PF01396 zf-C4_Topoisom: Topoi 98.4 3.6E-07 7.7E-12 73.2 4.3 36 964-1002 2-37 (39)
42 cd01025 TOPRIM_recR TOPRIM_rec 98.4 1.4E-06 3.1E-11 85.2 9.1 88 349-461 1-93 (112)
43 PF13368 Toprim_C_rpt: Topoiso 98.3 5.8E-07 1.3E-11 78.9 5.3 55 1027-1089 1-55 (61)
44 PRK07219 DNA topoisomerase I; 98.0 1.2E-05 2.5E-10 103.2 7.7 70 963-1048 688-757 (822)
45 cd00188 TOPRIM Topoisomerase-p 97.5 0.00077 1.7E-08 59.8 10.0 82 349-460 1-82 (83)
46 COG0551 TopA Zn-finger domain 97.4 0.00017 3.6E-09 73.5 4.5 103 1022-1142 15-121 (140)
47 PRK00076 recR recombination pr 97.3 0.0012 2.6E-08 70.8 10.7 106 349-477 79-194 (196)
48 PRK14973 DNA topoisomerase I; 97.3 0.00027 5.7E-09 91.4 6.2 54 814-868 257-310 (936)
49 cd01027 TOPRIM_RNase_M5_like T 96.9 0.0057 1.2E-07 56.9 8.8 79 349-460 2-80 (81)
50 PRK06599 DNA topoisomerase I; 96.7 0.0016 3.4E-08 82.4 5.7 54 814-868 241-303 (675)
51 PF01396 zf-C4_Topoisom: Topoi 96.5 0.0027 5.8E-08 51.1 3.2 35 1025-1070 2-36 (39)
52 COG4026 Uncharacterized protei 95.2 0.11 2.4E-06 56.2 9.6 95 350-475 9-114 (290)
53 PF13662 Toprim_4: Toprim doma 94.6 0.085 1.8E-06 48.6 6.3 79 349-459 1-80 (81)
54 PF09151 DUF1936: Domain of un 94.5 0.046 1E-06 41.4 3.5 32 965-997 3-34 (36)
55 PRK07220 DNA topoisomerase I; 94.3 0.063 1.4E-06 68.8 6.5 66 813-879 257-324 (740)
56 PRK13844 recombination protein 94.3 0.27 5.8E-06 53.3 10.1 106 349-477 83-198 (200)
57 TIGR00334 5S_RNA_mat_M5 ribonu 93.9 0.42 9.2E-06 50.7 10.4 104 348-478 2-110 (174)
58 TIGR00615 recR recombination p 93.6 0.25 5.4E-06 53.3 8.3 105 349-475 79-193 (195)
59 PRK05582 DNA topoisomerase I; 92.8 0.15 3.3E-06 64.5 6.0 54 814-868 234-297 (650)
60 COG1658 Small primase-like pro 92.7 0.48 1E-05 47.9 8.2 102 349-477 10-120 (127)
61 COG0353 RecR Recombinational D 91.3 1.1 2.5E-05 48.1 9.5 88 349-460 80-171 (198)
62 PRK04031 DNA primase; Provisio 82.4 1.7 3.8E-05 51.5 5.1 65 413-481 204-268 (408)
63 TIGR01057 topA_arch DNA topois 81.3 3.9 8.5E-05 51.8 8.1 58 810-868 251-309 (618)
64 smart00437 TOP1Ac Bacterial DN 78.3 6.3 0.00014 44.6 7.7 51 593-644 189-240 (259)
65 PF09664 DUF2399: Protein of u 75.3 8.8 0.00019 40.1 7.2 73 348-445 18-91 (152)
66 PF01131 Topoisom_bac: DNA top 73.0 6.9 0.00015 47.0 6.6 121 519-659 225-351 (403)
67 PRK04017 hypothetical protein; 67.5 5.8 0.00013 40.6 3.7 69 350-447 24-92 (132)
68 COG0550 TopA Topoisomerase IA 67.5 16 0.00035 45.9 8.3 71 809-881 236-311 (570)
69 TIGR01056 topB DNA topoisomera 66.5 17 0.00036 46.7 8.3 55 813-868 263-319 (660)
70 PRK05776 DNA topoisomerase I; 65.1 17 0.00037 46.6 8.1 142 516-678 381-527 (670)
71 PF08259 Periviscerokin: Periv 64.2 2.2 4.9E-05 25.3 0.0 9 653-661 3-11 (11)
72 TIGR01051 topA_bact DNA topois 63.2 22 0.00047 45.2 8.4 55 813-868 232-295 (610)
73 PRK14724 DNA topoisomerase III 62.2 5.9 0.00013 52.8 3.3 54 813-868 279-334 (987)
74 cd00186 TOP1Ac DNA Topoisomera 61.9 19 0.00042 43.0 7.2 55 593-657 262-317 (381)
75 PRK03573 transcriptional regul 59.8 7.4 0.00016 39.5 2.9 51 834-888 47-104 (144)
76 PRK08173 DNA topoisomerase III 55.2 40 0.00086 44.7 9.0 121 520-657 402-540 (862)
77 PRK11512 DNA-binding transcrip 54.0 11 0.00025 38.3 3.1 50 834-887 55-111 (144)
78 PRK10870 transcriptional repre 53.4 14 0.00031 39.2 3.9 54 831-888 69-129 (176)
79 PF14947 HTH_45: Winged helix- 52.9 8 0.00017 35.6 1.6 38 852-889 34-71 (77)
80 smart00529 HTH_DTXR Helix-turn 52.5 12 0.00027 35.0 2.9 43 844-887 7-50 (96)
81 cd00223 TOPRIM_TopoIIB_SPO TOP 52.4 66 0.0014 33.6 8.5 98 350-471 2-102 (160)
82 PRK13777 transcriptional regul 51.5 23 0.0005 38.2 5.1 51 834-888 60-117 (185)
83 COG1846 MarR Transcriptional r 50.0 17 0.00037 34.7 3.5 39 850-888 49-94 (126)
84 PF06839 zf-GRF: GRF zinc fing 49.7 22 0.00048 29.5 3.6 35 965-1001 2-42 (45)
85 TIGR02337 HpaR homoprotocatech 49.2 34 0.00074 33.5 5.5 51 834-888 43-100 (118)
86 PRK03902 manganese transport t 49.1 20 0.00043 36.6 4.0 55 846-910 32-87 (142)
87 TIGR01889 Staph_reg_Sar staphy 48.7 17 0.00036 35.5 3.2 55 830-888 40-101 (109)
88 KOG2907 RNA polymerase I trans 47.9 11 0.00023 37.5 1.7 33 963-998 74-111 (116)
89 PF07848 PaaX: PaaX-like prote 46.2 7.8 0.00017 35.4 0.4 47 833-880 20-70 (70)
90 PF06969 HemN_C: HemN C-termin 45.9 15 0.00032 32.3 2.1 36 846-881 30-65 (66)
91 TIGR02647 DNA conserved hypoth 45.8 17 0.00037 33.8 2.5 49 614-674 17-65 (77)
92 COG1198 PriA Primosomal protei 45.2 50 0.0011 42.8 7.4 22 484-505 72-93 (730)
93 PRK07726 DNA topoisomerase III 42.1 28 0.0006 44.7 4.6 56 812-868 259-316 (658)
94 TIGR00373 conserved hypothetic 41.6 23 0.00051 37.2 3.2 30 623-661 34-63 (158)
95 PF04606 Ogr_Delta: Ogr/Delta- 41.2 32 0.00069 28.9 3.3 33 965-999 1-37 (47)
96 PRK14165 winged helix-turn-hel 40.7 19 0.00042 39.8 2.5 51 831-885 19-73 (217)
97 PF14354 Lar_restr_allev: Rest 40.4 33 0.00073 29.8 3.5 32 963-997 3-37 (61)
98 PF04216 FdhE: Protein involve 39.0 94 0.002 35.7 7.8 32 963-998 172-206 (290)
99 cd03364 TOPRIM_DnaG_primases T 37.7 41 0.00089 30.7 3.8 36 408-446 34-69 (79)
100 smart00347 HTH_MARR helix_turn 36.8 38 0.00082 31.3 3.5 50 834-887 25-81 (101)
101 PRK09710 lar restriction allev 36.5 40 0.00087 30.4 3.3 32 963-999 6-37 (64)
102 TIGR01054 rgy reverse gyrase. 35.6 35 0.00076 46.6 4.2 52 816-868 867-919 (1171)
103 TIGR03655 anti_R_Lar restricti 35.4 54 0.0012 28.1 3.9 35 964-1001 2-38 (53)
104 TIGR02698 CopY_TcrY copper tra 34.8 1.9E+02 0.0041 29.4 8.4 96 834-949 19-116 (130)
105 cd01029 TOPRIM_primases TOPRIM 34.4 51 0.0011 29.7 3.9 27 420-446 43-69 (79)
106 PRK06266 transcription initiat 34.2 39 0.00084 36.3 3.5 30 622-660 41-70 (178)
107 COG3024 Uncharacterized protei 32.3 17 0.00038 32.6 0.4 30 963-998 7-36 (65)
108 PF02002 TFIIE_alpha: TFIIE al 32.2 35 0.00077 33.0 2.6 32 621-661 31-62 (105)
109 PF14354 Lar_restr_allev: Rest 31.9 74 0.0016 27.6 4.3 30 1084-1113 2-37 (61)
110 PRK14701 reverse gyrase; Provi 31.8 53 0.0011 46.4 5.0 65 815-881 838-903 (1638)
111 TIGR02679 conserved hypothetic 31.6 1.5E+02 0.0033 35.8 8.1 88 350-475 252-340 (385)
112 KOG1956 DNA topoisomerase III 29.3 40 0.00087 42.4 2.9 56 331-386 51-106 (758)
113 COG1675 TFA1 Transcription ini 29.3 56 0.0012 35.2 3.6 31 622-661 37-67 (176)
114 PF13601 HTH_34: Winged helix 28.6 14 0.0003 34.4 -0.9 41 844-885 22-70 (80)
115 PF02150 RNA_POL_M_15KD: RNA p 28.4 56 0.0012 25.9 2.6 29 965-1000 3-31 (35)
116 COG2176 PolC DNA polymerase II 28.0 76 0.0016 42.8 5.1 42 429-472 309-350 (1444)
117 PRK00420 hypothetical protein; 27.6 46 0.00099 33.3 2.4 11 963-973 23-33 (112)
118 PF03965 Penicillinase_R: Peni 27.4 94 0.002 30.6 4.6 79 834-927 18-98 (115)
119 PHA00626 hypothetical protein 26.9 59 0.0013 28.7 2.6 11 965-975 2-12 (59)
120 TIGR03433 padR_acidobact trans 26.2 1.3E+02 0.0029 28.9 5.4 52 835-887 19-84 (100)
121 PF13362 Toprim_3: Toprim doma 25.2 2.1E+02 0.0046 26.9 6.5 65 350-446 1-69 (96)
122 cd00092 HTH_CRP helix_turn_hel 24.9 77 0.0017 27.4 3.2 42 833-878 25-67 (67)
123 PRK09401 reverse gyrase; Revie 24.9 59 0.0013 44.6 3.5 51 817-868 868-919 (1176)
124 COG1321 TroR Mn-dependent tran 24.8 1.5E+02 0.0032 31.2 5.7 51 620-679 27-77 (154)
125 KOG1589 Uncharacterized conser 24.4 32 0.00069 34.0 0.7 14 38-51 6-19 (118)
126 smart00661 RPOL9 RNA polymeras 24.2 59 0.0013 27.2 2.2 29 965-999 2-30 (52)
127 TIGR02277 PaaX_trns_reg phenyl 23.9 65 0.0014 37.0 3.2 52 833-885 17-72 (280)
128 PF13463 HTH_27: Winged helix 23.6 30 0.00065 30.1 0.4 30 851-880 32-68 (68)
129 COG1321 TroR Mn-dependent tran 22.7 55 0.0012 34.4 2.1 40 847-887 35-75 (154)
130 PRK03902 manganese transport t 22.6 1.8E+02 0.0039 29.6 5.8 48 621-677 26-73 (142)
131 PLN03122 Poly [ADP-ribose] pol 22.4 1.9E+02 0.0041 38.2 7.1 33 963-1002 111-147 (815)
132 PF05191 ADK_lid: Adenylate ki 22.2 60 0.0013 26.0 1.7 20 1079-1098 15-34 (36)
133 PF13408 Zn_ribbon_recom: Reco 22.2 90 0.002 26.4 3.0 27 964-992 6-32 (58)
134 PRK09416 lstR lineage-specific 22.2 99 0.0021 32.0 3.7 51 835-885 57-116 (135)
135 PHA02998 RNA polymerase subuni 21.7 1.2E+02 0.0026 32.7 4.3 35 962-999 142-181 (195)
136 PRK09678 DNA-binding transcrip 21.7 84 0.0018 29.1 2.8 33 965-999 3-39 (72)
137 PF08063 PADR1: PADR1 (NUC008) 21.6 40 0.00088 29.4 0.7 31 963-999 14-48 (55)
138 PTZ00407 DNA topoisomerase IA; 20.8 1.7E+02 0.0037 38.5 6.3 72 596-679 561-634 (805)
No 1
>PRK08780 DNA topoisomerase I; Provisional
Probab=100.00 E-value=5.1e-161 Score=1487.24 Aligned_cols=757 Identities=39% Similarity=0.632 Sum_probs=672.2
Q ss_pred CCCeEEEEecchHHHHHHhhcCCCEEEEEeccccccccccCCCCCCCCCCcceEecccchHHHHHHHHHHhccCCeEEEc
Q 001106 347 SGKSVVVVESVTKAKVIQGYLGDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILA 426 (1157)
Q Consensus 347 ~~k~LiIaEkPskAk~Ia~~LG~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~kk~~lk~Lk~l~k~ad~IIlA 426 (1157)
|+++|||||||+||++|++|||.+|+|+||+|||++|+.++.+++++.+|.+.|.+.++++++++.|++++++||.||||
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 56899999999999999999999999999999999999988888888789999998888999999999999999999999
Q ss_pred cCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhcccccHhHHHHHHHHHHHhHhhhhhccHHHH
Q 001106 427 SDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAAREIDANLVQAYLARRALDYLIGFNISPLLW 506 (1157)
Q Consensus 427 TDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fsslT~~aI~~A~~nlr~~d~~L~~A~~AR~~lD~LiG~nlSR~lt 506 (1157)
||||||||+|||||+++|+..+. ...++|+|+|||+||+++|++||+|++++|++|++||+|||++|||||||+||+||
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 99999999999999999964211 12468999999999999999999999999999999999999999999999999999
Q ss_pred hhCCCccccCcchhHHHHHHHhHHHHHHhcCCcceEEEEEEEecCcCCCCCCceeeeeecccccccccccccCCHHHHHH
Q 001106 507 RKLPGCQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDTFSFPAHLTHFQSKRLNQLSIGSHTEAKD 586 (1157)
Q Consensus 507 ~k~~~~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~g~~f~a~l~~~~~~~~~~~~i~d~e~Ae~ 586 (1157)
+++++.+|+||||||||+|||+||+||++|+|++||.|.+.+... +..|.++|...++.++++++|.|+++|++
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 999888999999999999999999999999999999999999632 34688888766665555678999999999
Q ss_pred HHHHHcc---CCeEEEEeeeeeeeecCCCCcchHHHHHHHHHHcCCCHHHHHHHHHHHhhcccCCCCCceEEEEEEccCC
Q 001106 587 IEQKINS---ANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRTDG 663 (1157)
Q Consensus 587 i~~~l~~---~~~~V~~v~~k~~~~~PP~Pf~ts~LQ~~AskklG~Sa~~Tm~iAQ~LYE~~k~~~~~~~GlITYPRTDS 663 (1157)
+++.|+. ..++|.+|+.++++++||+||+|++||++||++|||||++||++||+|||+++|++|++.||||||||||
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 5789999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCHHHHHHHHHHHHHHhCCCCCCCCCCCccccccccccccCCCCCCCcccCChhhhhCCCCHHHHHHHHHHHHHHHHc
Q 001106 664 LHISDEAAKEIRSLIFERYGSHHAPEEGPRKYFKKVKNAQEAHEAIRPTDIRRLPAMLSGLLDEDCLKLYSLIWSRTMAC 743 (1157)
Q Consensus 664 ~~Ls~~~~~~i~~~i~~~~g~~~~~~~~~r~~~~k~k~~q~AH~AI~PT~~~~~p~~l~~~Ls~dE~klY~LI~rRfLAs 743 (1157)
++||++++.+++++|...||..|.+ ..++.+..+.+++|+||||||||+....|+.+...|+++|++||+|||+||||+
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 9999999999999999999987765 445666666677899999999998655676555579999999999999999999
Q ss_pred cCCCcEEEEEEEEEEecCccEEEEEEEEEEEEcCceecccccchhhhccccccchhhhhHHHhccCCCCCCeEEeeeEEe
Q 001106 744 QMQPATVGQIQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLKTGDPLYLGEVEL 823 (1157)
Q Consensus 744 ~~~~a~~e~t~v~i~~~~~~~~F~asg~~i~~~Gw~~vy~~~~~~~~~~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i 823 (1157)
||+||+|++++|++.+++ .+.|+++|++++++||+++|.+...+ ++.+++ +....||.|++||.+.+.++.+
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 26899999999999999999653210 000000 0114699999999999999999
Q ss_pred eecccCCCCCCCHHHHHHHHHhcCCCCCCchHHHHHhccccceEEEcCceeecccchhhhhhhhhcccccccChhhhHHH
Q 001106 824 KQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKSRILYPEFRGRMVSAFLSHYFSEVTDYSFTADM 903 (1157)
Q Consensus 824 ~e~~TkPP~ryTEasLI~~MEk~GIGTpATrA~IIe~L~~R~YV~~k~k~L~PT~lG~~vi~~L~~~f~~l~~p~~TA~~ 903 (1157)
.+++|+||+|||||+||++||+.|||||||||+||++|++|+||..+++.|+||++|+.|+++|..+|+.|+||+|||.|
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 HHHhhhHhhcCccHHHHHHHHHHHhhhhhhhccchhHHHHHHHHHhhhCCCccCCCCCCCCCCCCCCCceEEEEecccCc
Q 001106 904 ETELDNVSAGLTEWKGLLVDYWSRFSSYCTCAQSLHIHQVEKMLEKTFGDSLFASLPNKDRSCPVCGEGTLIFKVSRFGA 983 (1157)
Q Consensus 904 E~~Ld~Ia~G~~~~~~~l~~F~~~f~~~v~~~~~~~i~~V~k~l~~~~g~~~~~~~~~~~g~CPkCGkg~lv~K~gr~G~ 983 (1157)
|.+||+|++|+.+|++||++||+.|...+..+.. .+... . . ......+.||.||+ .++++.||||+
T Consensus 545 E~~Ld~I~~G~~~~~~~l~~~~~~~~~~~~~~~~----~i~~~-----~---~-~~~r~lG~cP~CG~-~l~~r~gr~G~ 610 (780)
T PRK08780 545 EDDLDAVSRGEKEWIPLMEKFWGPFKELVEEKKD----SVDRT-----E---A-GQVRELGTDPKSGK-PVSVRIGRFGP 610 (780)
T ss_pred HHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHh----hhhhc-----c---c-cccccCCCCCCCCC-EEEEEeCCCCC
Confidence 9999999999999999999999998876543211 11100 0 0 01133679999996 78889999998
Q ss_pred eeEEec-----CCCCCCcccccCCCCCCchhhhhhhccCCCCCcccCCCCCccceeeeccCCCcceEEeCCCCCCCCCcc
Q 001106 984 GYFIGC-----NQHPRCNYIAKTLYGDDDEEDTLQRNTNVDEPKLIGHHPASKEKVLLKSGPYGFYVQLGEDRTGYLPKR 1058 (1157)
Q Consensus 984 ~~F~GC-----snyP~Ck~t~~~~~~~~~~~e~~~~~~~~~~Pr~LG~cPkcGk~V~lK~GrfG~yv~c~~d~kg~~~k~ 1058 (1157)
||+| +++|.|..........+++.+.+. .++.+||.+|.+|+ |++|+++.||||+||+++ +++
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 8899 468999988777777777776665 35677999999995 889999999999999986 378
Q ss_pred ccCCCCCCccccCHHHHHHHhcC------CcccCCCCCCCcCeEEeeccCcceeecCCeeeecCCCCCCCCCCHHHHHHH
Q 001106 1059 ASVSHIKDVDSITLEDALELLRY------PVNLGNHPKDGQPIMLRLARAGFSVRHRRTIASVPKNMKPNDVTLEKALEF 1132 (1157)
Q Consensus 1059 ~slpk~~~~~sItLe~Al~ll~~------pk~lG~cP~cG~~v~v~~GryG~yi~~~~~~~~ipk~~~~~~itle~A~~L 1132 (1157)
+++|+..++++|||++|+.||.. ++.++.|| |+.|.+..||||||+.+++.+++||++.++.++|+++|++|
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 67788887 57899999999999999999999999999999999999999
Q ss_pred hcccccccCCCCCCC
Q 001106 1133 LSGKDVRRCGRPKGK 1147 (1157)
Q Consensus 1133 L~~k~~k~~gr~~~~ 1147 (1157)
|+++.+|+++||+++
T Consensus 757 i~~~~~~~~~~~~~~ 771 (780)
T PRK08780 757 LADAPVRKGFRAKKA 771 (780)
T ss_pred HhCcccccCCCcccc
Confidence 999998998998876
No 2
>PRK07561 DNA topoisomerase I subunit omega; Validated
Probab=100.00 E-value=9.1e-155 Score=1448.22 Aligned_cols=736 Identities=42% Similarity=0.679 Sum_probs=650.0
Q ss_pred CeEEEEecchHHHHHHhhcCCCEEEEEeccccccccccCCC--------------CCCCCCCcceEecccchHHHHHHHH
Q 001106 349 KSVVVVESVTKAKVIQGYLGDMYEVLPSYGHVRDLAARSGS--------------VRPDDDFSMVWEVPSAAWTHLKSIK 414 (1157)
Q Consensus 349 k~LiIaEkPskAk~Ia~~LG~~y~V~~s~GHl~dL~~~~~~--------------v~p~~~f~~~~~v~~~kk~~lk~Lk 414 (1157)
+.|||||||+||++|++|||.+|+|+||+|||++|+.+... ++|+++|.+.|.+.++++++++.|+
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 6787789999999888999999999
Q ss_pred HHhccCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhcccccHhHHHHHHHHHHHh
Q 001106 415 VALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAAREIDANLVQAYLARRALD 494 (1157)
Q Consensus 415 ~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fsslT~~aI~~A~~nlr~~d~~L~~A~~AR~~lD 494 (1157)
+++++||+||||||||||||+|||||+++|+. .+++|+|||||+||+++|++||+|++++|++|++||+|||++|
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 HhhhhhccHHHHhhCCCccccCcchhHHHHHHHhHHHHHHhcCCcceEEEEEEEecCcCCCCCCceeeeeeccccccccc
Q 001106 495 YLIGFNISPLLWRKLPGCQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDTFSFPAHLTHFQSKRLN 574 (1157)
Q Consensus 495 ~LiG~nlSR~lt~k~~~~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~g~~f~a~l~~~~~~~~~ 574 (1157)
||||||+||+||+++.+.+|+||||||||+|||+||+||++|+|++||.|.+.+... .|..|.+.|.+.++++++
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 999999999999999888999999999999999999999999999999999999641 244688888766666666
Q ss_pred ccccCCHHHHHHHHHHHccCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHHcCCCHHHHHHHHHHHhhcccCCCCCceE
Q 001106 575 QLSIGSHTEAKDIEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKLAQKLYEGVQLPDGTAAG 654 (1157)
Q Consensus 575 ~~~i~d~e~Ae~i~~~l~~~~~~V~~v~~k~~~~~PP~Pf~ts~LQ~~AskklG~Sa~~Tm~iAQ~LYE~~k~~~~~~~G 654 (1157)
.++|.|+++|+++++.|.+..++|.+|+.++++++||+||+|++||++|+++|||||++||++||+|||+ |
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 6779999999999999988889999999999999999999999999999999999999999999999995 9
Q ss_pred EEEEEccCCcCCCHHHHHHHHHHHHHHhCCCCCCCCCCCccccccccccccCCCCCCCcccCChhhhhCCCCHHHHHHHH
Q 001106 655 LITYMRTDGLHISDEAAKEIRSLIFERYGSHHAPEEGPRKYFKKVKNAQEAHEAIRPTDIRRLPAMLSGLLDEDCLKLYS 734 (1157)
Q Consensus 655 lITYPRTDS~~Ls~~~~~~i~~~i~~~~g~~~~~~~~~r~~~~k~k~~q~AH~AI~PT~~~~~p~~l~~~Ls~dE~klY~ 734 (1157)
|||||||||++||++++++++++|...||..|.+ ..+|.|..+.+++|+||||||||+....|+.+ ..|+++|++||+
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 9999999999999999999999999899988876 55676665557789999999999765557655 569999999999
Q ss_pred HHHHHHHHccCCCcEEEEEEEEEEecCccEEEEEEEEEEEEcCceecccccchhhhccccccchhhhhHHHhccCCCCCC
Q 001106 735 LIWSRTMACQMQPATVGQIQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLKTGD 814 (1157)
Q Consensus 735 LI~rRfLAs~~~~a~~e~t~v~i~~~~~~~~F~asg~~i~~~Gw~~vy~~~~~~~~~~~e~~e~~~~~~~~~LP~l~~Gd 814 (1157)
|||+||||+||+||+|++++|++.++ ++.|+++|++++++||+++|..... +++++ ....||.|++||
T Consensus 381 LI~~R~lAs~m~~a~~~~~~v~~~~~--~~~F~a~g~~i~~~G~~~vy~~~~~-----~~~~~-----~~~~LP~l~~g~ 448 (859)
T PRK07561 381 LIWKRFVASQMAPARYDSTTVTIAAG--DAELRATGRVLRFDGFLKVYVEGRD-----DALDD-----EDRRLPALKVGD 448 (859)
T ss_pred HHHHHHHHHhCchheEEEEEEEEEeC--CEEEEEEEEEEeeCCchheeccccc-----ccccc-----ccccCCCCCCCC
Confidence 99999999999999999999999875 3689999999999999999975321 00011 114699999999
Q ss_pred eEEeeeEEeeecccCCCCCCCHHHHHHHHHhcCCCCCCchHHHHHhccccceEEEcCceeecccchhhhhhhhhcccccc
Q 001106 815 PLYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKSRILYPEFRGRMVSAFLSHYFSEV 894 (1157)
Q Consensus 815 ~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk~GIGTpATrA~IIe~L~~R~YV~~k~k~L~PT~lG~~vi~~L~~~f~~l 894 (1157)
.+.+.++.+.+++|+||+|||||+||++||+.|||||||||+||++|++||||..+++.|+||++|+.|+++|..+|+.|
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 cChhhhHHHHHHhhhHhhcCccHHHHHHHHHHHhhhhhhhccchhHHHHHHHH-HhhhCCCccCCCCCCCCCCCCCCCce
Q 001106 895 TDYSFTADMETELDNVSAGLTEWKGLLVDYWSRFSSYCTCAQSLHIHQVEKML-EKTFGDSLFASLPNKDRSCPVCGEGT 973 (1157)
Q Consensus 895 ~~p~~TA~~E~~Ld~Ia~G~~~~~~~l~~F~~~f~~~v~~~~~~~i~~V~k~l-~~~~g~~~~~~~~~~~g~CPkCGkg~ 973 (1157)
+||+|||.||..||+|++|+.+|++||++||..|...++.+.. .. ...+. ........+.||.||++
T Consensus 529 ~~~~~Ta~~E~~Ld~I~~G~~~~~~~l~~~~~~~~~~~~~~~~--------~~~~~~~~---~~~~~~~~~~CP~Cg~~- 596 (859)
T PRK07561 529 VDYDFTARMEEELDDIANGEADWKPVLDDFYKDFSQQLEKAEE--------LREEGGMR---PNQMVITDRDCPTCGRG- 596 (859)
T ss_pred cCHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHhh--------hccccccc---ccccccccccCcccCCc-
Confidence 9999999999999999999999999999999998876544311 10 00000 00011235799999975
Q ss_pred EEEEecccCceeEEecCCC---CCCcccccCCCCCCchhhhhhhccCCCCCcccCCCCCccceeeeccCCCcceEEeCCC
Q 001106 974 LIFKVSRFGAGYFIGCNQH---PRCNYIAKTLYGDDDEEDTLQRNTNVDEPKLIGHHPASKEKVLLKSGPYGFYVQLGED 1050 (1157)
Q Consensus 974 lv~K~gr~G~~~F~GCsny---P~Ck~t~~~~~~~~~~~e~~~~~~~~~~Pr~LG~cPkcGk~V~lK~GrfG~yv~c~~d 1050 (1157)
+.+|.|++|+ ||+|++| |.|+++.+....+.. .+... ...+.|+.+|.||+||..|+++.||||+||+.++
T Consensus 597 l~~r~gr~G~--Fl~Cs~y~~~p~C~~~~~l~~~~~~-~~~~~--~~~~~~~~lg~~P~cg~~i~~r~Gr~Gpyv~~~~- 670 (859)
T PRK07561 597 MGIRTGKTGV--FLGCSGYALKERCKTTRNLTPEEET-LNVLE--GEDAETRALGADPECGTAMVLRSGRFGPYVQEGE- 670 (859)
T ss_pred ceEEecCCCC--eeeccCCcCCCCCCCCCCCCccchh-hhhhh--ccccCccccCCCCCCCCeeEEecCCCCCeeeccc-
Confidence 7889999996 9999999 999998766543221 11111 2446789999999999999999999999999642
Q ss_pred CCCCCCccccCCCCCCccccCHHHHHHHhcCCcccCCCCCCCcCeEEeeccCcceeecCCeeeecCCCCCCCCCCHHHHH
Q 001106 1051 RTGYLPKRASVSHIKDVDSITLEDALELLRYPVNLGNHPKDGQPIMLRLARAGFSVRHRRTIASVPKNMKPNDVTLEKAL 1130 (1157)
Q Consensus 1051 ~kg~~~k~~slpk~~~~~sItLe~Al~ll~~pk~lG~cP~cG~~v~v~~GryG~yi~~~~~~~~ipk~~~~~~itle~A~ 1130 (1157)
+.++++++|+++.+++.+++++|+.++..|+.+|.||+||++|++++||||+|+.|++.+.+++...++.+++++.|+
T Consensus 671 --~~~~~~~sic~~~~p~c~~~e~a~~ll~~pr~lg~cPecg~~i~~k~gr~G~yl~c~~~~~sc~~~~~~~~i~l~~a~ 748 (859)
T PRK07561 671 --GDKPRRLSLPKGNNPECVGLEIALGLLSLPRPVGEHPECGSEIQAKIGRFGPYVKCGGTYASLKNTRKVLTIGLNRAV 748 (859)
T ss_pred --CCCCceeccCCCCCCCcCCHHHHHhhhccccccCcCCCCCCeeEEecCCCCCeEEeCCCcCCCCCCCccccCCHHHHH
Confidence 456899999988888899999999999999999999999999999999999999998888888888888999999999
Q ss_pred HHhcccc
Q 001106 1131 EFLSGKD 1137 (1157)
Q Consensus 1131 ~LL~~k~ 1137 (1157)
+||..++
T Consensus 749 ~ll~~~~ 755 (859)
T PRK07561 749 ELLAEPK 755 (859)
T ss_pred HHHhccc
Confidence 9998874
No 3
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=100.00 E-value=1.8e-152 Score=1424.54 Aligned_cols=741 Identities=34% Similarity=0.523 Sum_probs=621.2
Q ss_pred CCCeEEEEecchHHHHHHhhcCCCEEEEEeccccccccccCCCCCCCCCCcceEecccchHHHHHHHHHHhccCCeEEEc
Q 001106 347 SGKSVVVVESVTKAKVIQGYLGDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILA 426 (1157)
Q Consensus 347 ~~k~LiIaEkPskAk~Ia~~LG~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~kk~~lk~Lk~l~k~ad~IIlA 426 (1157)
|+++|||||||+|||+|++|||++|+|+||+|||++|+....+|+++++|.|.|.+.++++++|+.|++++++||.||||
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 67899999999999999999999999999999999998877789888889999999888999999999999999999999
Q ss_pred cCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhcccccHhHHHHHHHHHHHhHhhhhhccHHHH
Q 001106 427 SDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAAREIDANLVQAYLARRALDYLIGFNISPLLW 506 (1157)
Q Consensus 427 TDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fsslT~~aI~~A~~nlr~~d~~L~~A~~AR~~lD~LiG~nlSR~lt 506 (1157)
||||||||+|+|||+++|+ .+++|+|||||+||+++|++||+|++++|++|++||+|||++|||||||+||+||
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--ccccCcchhHHHHHHHhHHHHHHhcCCcceEEEEEEEecCcCCCCCCceeeeeecccccccccc---------
Q 001106 507 RKLPG--CQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDTFSFPAHLTHFQSKRLNQ--------- 575 (1157)
Q Consensus 507 ~k~~~--~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~g~~f~a~l~~~~~~~~~~--------- 575 (1157)
++++. .+|+||||||||+|||+||+||++|+|++||+|.+.+.... .+..|.++|...+++++..
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 98764 79999999999999999999999999999999999986421 1346888887665554421
Q ss_pred --cccCCHHHHHHHHHHHccCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHHcCCCHHHHHHHHHHHhhcccCCCCCce
Q 001106 576 --LSIGSHTEAKDIEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKLAQKLYEGVQLPDGTAA 653 (1157)
Q Consensus 576 --~~i~d~e~Ae~i~~~l~~~~~~V~~v~~k~~~~~PP~Pf~ts~LQ~~AskklG~Sa~~Tm~iAQ~LYE~~k~~~~~~~ 653 (1157)
++|.++++|+++++.+++..++|.+|+.++++++||+||+|++||++||++|||||++||++||+|||+++|+++++.
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 001106 654 GLITYMRTDGLHISDEAAKEIRSLIFERYGSHHAPEEGPRKYFKKVKNAQEAHEAIRPTDIRRLPAMLSGLLDEDCLKLY 733 (1157)
Q Consensus 654 GlITYPRTDS~~Ls~~~~~~i~~~i~~~~g~~~~~~~~~r~~~~k~k~~q~AH~AI~PT~~~~~p~~l~~~Ls~dE~klY 733 (1157)
||||||||||++||++++++++.+|...+|.+|.+ ..++.|..+ +++|+||||||||+....|+.+...|+++|++||
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 99999999999999999999999999888887765 445555443 6789999999999876568766667999999999
Q ss_pred HHHHHHHHHccCCCcEEEEEEEEEEecCccEEEEEEEEEEEEcCceecccccchhhhccccccchhhhhHHHhccCCCCC
Q 001106 734 SLIWSRTMACQMQPATVGQIQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLKTG 813 (1157)
Q Consensus 734 ~LI~rRfLAs~~~~a~~e~t~v~i~~~~~~~~F~asg~~i~~~Gw~~vy~~~~~~~~~~~e~~e~~~~~~~~~LP~l~~G 813 (1157)
+|||+||||+||+||+|++|+|++.++++ +.|+++|++++++||++||..... +++++ +....||.|++|
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-----DEGDE----EENIHLPKLHEQ 458 (860)
T ss_pred HHHHHHHHHHhCchhheEEEEEEEEeCCe-eEEEEEeEEEeeCCHHHHhCcccc-----ccccc----cccccCCCCCCC
Confidence 99999999999999999999999988543 689999999999999999964311 00000 011469999999
Q ss_pred CeEEeeeEEeeecccCCCCCCCHHHHHHHHHhcCCCCCCchHHHHHhccccceEEEcCceeecccchhhhhhhhhccccc
Q 001106 814 DPLYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKSRILYPEFRGRMVSAFLSHYFSE 893 (1157)
Q Consensus 814 d~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk~GIGTpATrA~IIe~L~~R~YV~~k~k~L~PT~lG~~vi~~L~~~f~~ 893 (1157)
|.+.+.++.+.+++|+||+|||||+||++||+.|||||||||+||++|++|+||..+++.|+||++|+.|+++|..+||.
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 ccChhhhHHHHHHhhhHhhcCccHHHHHHHHHHHhhhhhhhccchhHHHHHHHHHhhhCCCccCCCCCCCCCCCCCCCce
Q 001106 894 VTDYSFTADMETELDNVSAGLTEWKGLLVDYWSRFSSYCTCAQSLHIHQVEKMLEKTFGDSLFASLPNKDRSCPVCGEGT 973 (1157)
Q Consensus 894 l~~p~~TA~~E~~Ld~Ia~G~~~~~~~l~~F~~~f~~~v~~~~~~~i~~V~k~l~~~~g~~~~~~~~~~~g~CPkCGkg~ 973 (1157)
|+||+|||.||.+||+|++|+.+|++||++||+.|...+..+.. .+. + + .......||+||++.
T Consensus 539 i~~~~~Ta~~E~~Ld~I~~G~~~~~~~l~~f~~~~~~~~~~~~~-------~~~---~-----~-~~~~~~~CP~Cg~~~ 602 (860)
T PRK06319 539 IMDIGFTALMEDELELIADNKKPWKLLLQEFWELFLPVVVTAEK-------EAF---I-----P-RIVTEIDCPKCHKGK 602 (860)
T ss_pred hcChhHHHHHHHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHhh-------hhc---c-----c-ccccCcccCCCCCcc
Confidence 99999999999999999999999999999999999876554321 000 0 0 112357899999889
Q ss_pred EEEEecccCceeEEecCCCCCCcccccCCCCCCchhhhhhhccCCCCCcccCCCCCccceeeeccCCCcceEEeCCCCCC
Q 001106 974 LIFKVSRFGAGYFIGCNQHPRCNYIAKTLYGDDDEEDTLQRNTNVDEPKLIGHHPASKEKVLLKSGPYGFYVQLGEDRTG 1053 (1157)
Q Consensus 974 lv~K~gr~G~~~F~GCsnyP~Ck~t~~~~~~~~~~~e~~~~~~~~~~Pr~LG~cPkcGk~V~lK~GrfG~yv~c~~d~kg 1053 (1157)
++++.|++|. ||||++||+|+++.+.........+ ........+.||+||..|+++.|+||+||.|+
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--FYGCSEYPECDYKTSEEELTFNKED------YAEDTPWDSPCPLCGGEMKVRHGRFGTFLGCE----- 669 (860)
T ss_pred eeEEecCCCc--eeeccCCccccccCCcccccccccc------cccccccCCcCccCCCeeEEecCCCCceeeCC-----
Confidence 9999999985 9999999999998766532100000 00011234579999999999999999999997
Q ss_pred CCCccccCCCCCCccccCHHHHHHHhcCCcccCCCCC--CCcCeEEeeccCcc-eeecC--CeeeecCCCC-------CC
Q 001106 1054 YLPKRASVSHIKDVDSITLEDALELLRYPVNLGNHPK--DGQPIMLRLARAGF-SVRHR--RTIASVPKNM-------KP 1121 (1157)
Q Consensus 1054 ~~~k~~slpk~~~~~sItLe~Al~ll~~pk~lG~cP~--cG~~v~v~~GryG~-yi~~~--~~~~~ipk~~-------~~ 1121 (1157)
++|+|....++.-+.... ..+.....||+ ||+.+++++||||+ |..|. +.|-.+-++. .|
T Consensus 670 ------~yP~Ck~~~~l~k~~~~~--~~~~~~~~CP~~~C~g~l~~r~gr~G~~f~~Cs~yp~C~~~~~~~~~~~~~~~~ 741 (860)
T PRK06319 670 ------NYPECRGIINIHKKGEEG--IEPEETVPCPAIGCTGHIVKRRSRFNKMFYSCSEYPACSVIGNSIDAVITKYAG 741 (860)
T ss_pred ------CCccccccccCCcccccc--cCcccCCCCCCcCCCCcEEEEecCCCCeeeccCCCCCCceeeccCCccccccCC
Confidence 457776544332110000 00111236995 88899999999997 44443 3343331121 12
Q ss_pred CCCCHHHHHHHhcccccccCCCCCC
Q 001106 1122 NDVTLEKALEFLSGKDVRRCGRPKG 1146 (1157)
Q Consensus 1122 ~~itle~A~~LL~~k~~k~~gr~~~ 1146 (1157)
..-|+.|...++.++..++.|+..+
T Consensus 742 ~~~~~~~~~~~~~~~~~~~~~~~~~ 766 (860)
T PRK06319 742 TPKTPYEKKTKAKKKSASTKGKAAK 766 (860)
T ss_pred CCCCcccchHHHHhhhccccCcccc
Confidence 4556667778887766555455433
No 4
>PRK06599 DNA topoisomerase I; Validated
Probab=100.00 E-value=1.7e-137 Score=1266.86 Aligned_cols=661 Identities=45% Similarity=0.746 Sum_probs=562.0
Q ss_pred CCCeEEEEecchHHHHHHhhcCCCEEEEEeccccccccccCCCCCCCCCCcceEecccchHHHHHHHHHHhccCCeEEEc
Q 001106 347 SGKSVVVVESVTKAKVIQGYLGDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILA 426 (1157)
Q Consensus 347 ~~k~LiIaEkPskAk~Ia~~LG~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~kk~~lk~Lk~l~k~ad~IIlA 426 (1157)
|++.|||||||++|++|+++||.+|+|+||+|||++|++++..|++++.|.+.|++.+++++|++.|++++++||+||||
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 56889999999999999999999999999999999999887788887778888888888999999999999999999999
Q ss_pred cCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhcccccHhHHHHHHHHHHHhHhhhhhccHHHH
Q 001106 427 SDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAAREIDANLVQAYLARRALDYLIGFNISPLLW 506 (1157)
Q Consensus 427 TDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fsslT~~aI~~A~~nlr~~d~~L~~A~~AR~~lD~LiG~nlSR~lt 506 (1157)
||||||||+|||||++++++. .+.+++|+|||||+||+++|++||+|+++++.+|++||+||+++|||||||+||++|
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 999999999999999999521 124579999999999999999999999999999999999999999999999999999
Q ss_pred hhCCCccccCcchhHHHHHHHhHHHHHHhcCCcceEEEEEEEecCcCCCCCCceeeeeecccccccccccccCCHHHHHH
Q 001106 507 RKLPGCQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDTFSFPAHLTHFQSKRLNQLSIGSHTEAKD 586 (1157)
Q Consensus 507 ~k~~~~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~g~~f~a~l~~~~~~~~~~~~i~d~e~Ae~ 586 (1157)
..++..+|+||||||||+|||+||+||+||+|++||.|.+.+... +|..|.+.+...+++....++|.++++|++
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 988778999999999999999999999999999999999998641 234577766433332222346889999999
Q ss_pred HHHHHccCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHHcCCCHHHHHHHHHHHhhcccCCCCCceEEEEEEccCCcCC
Q 001106 587 IEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRTDGLHI 666 (1157)
Q Consensus 587 i~~~l~~~~~~V~~v~~k~~~~~PP~Pf~ts~LQ~~AskklG~Sa~~Tm~iAQ~LYE~~k~~~~~~~GlITYPRTDS~~L 666 (1157)
+++.+++..++|.+|+.+++++.||+||||++||++|+++|||||++||++||+|||+++++ |++.||||||||||+||
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 99999887899999999999999999999999999999999999999999999999998887 66789999999999999
Q ss_pred CHHHHHHHHHHHHHHhCCCCCCCCCCCccccccccccccCCCCCCCcccCChhhhhCCCCHHHHHHHHHHHHHHHHccCC
Q 001106 667 SDEAAKEIRSLIFERYGSHHAPEEGPRKYFKKVKNAQEAHEAIRPTDIRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQ 746 (1157)
Q Consensus 667 s~~~~~~i~~~i~~~~g~~~~~~~~~r~~~~k~k~~q~AH~AI~PT~~~~~p~~l~~~Ls~dE~klY~LI~rRfLAs~~~ 746 (1157)
|+++++++..+|...++..|.. ...+.+..+.+..|+||||||||.....|+.+.+.|+++|++||+||+|||||+||+
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 9999999999998888765543 233444333344568999999998644565444569999999999999999999999
Q ss_pred CcEEEEEEEEEEecCccEEEEEEEEEEEEcCceecccccchhhhccccccchhhhhHHHhccCCCCCCeEEeeeEEeeec
Q 001106 747 PATVGQIQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLKTGDPLYLGEVELKQH 826 (1157)
Q Consensus 747 ~a~~e~t~v~i~~~~~~~~F~asg~~i~~~Gw~~vy~~~~~~~~~~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~ 826 (1157)
||+|++++|.+.+.++++.|.++|++++++||+++|+..+. +++++ ....||.+++||.+.+.++.+.++
T Consensus 392 ~~~~~~t~v~~~~~~~~~~F~a~g~~~~~~Gw~~~~~~~~~-----~~~~~-----~~~~lp~~~~g~~~~~~~~~~~~~ 461 (675)
T PRK06599 392 PAILDQTSVDIASENGKYVFRATGSVILFPGFLKVYGESKD-----DEEED-----DEKLLPPLKEGEKLKLDELLPEQH 461 (675)
T ss_pred hheEEEEEEEEEEcCCCeEEEEEEEEEEecCeeeeeccccc-----ccccc-----ccccCCCCCCCCEeeeeeeeeccc
Confidence 99999999999873234689999999999999999975321 00011 114599999999999999999999
Q ss_pred ccCCCCCCCHHHHHHHHHhcCCCCCCchHHHHHhccccceEEEcCceeecccchhhhhhhhhcccccccChhhhHHHHHH
Q 001106 827 HTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKSRILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETE 906 (1157)
Q Consensus 827 ~TkPP~ryTEasLI~~MEk~GIGTpATrA~IIe~L~~R~YV~~k~k~L~PT~lG~~vi~~L~~~f~~l~~p~~TA~~E~~ 906 (1157)
+|+||+||||++||++||+.|||||||||+||++|++||||+++++.|+||++|+.|+++|+..|+.|++|+|||.||..
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 hhhHhhcCccHHHHHHHHHHHhhhhhhhccchhHHHHHHHHHhhhCCCccCCCCCCCCCCCCCCCceEEEEecccCceeE
Q 001106 907 LDNVSAGLTEWKGLLVDYWSRFSSYCTCAQSLHIHQVEKMLEKTFGDSLFASLPNKDRSCPVCGEGTLIFKVSRFGAGYF 986 (1157)
Q Consensus 907 Ld~Ia~G~~~~~~~l~~F~~~f~~~v~~~~~~~i~~V~k~l~~~~g~~~~~~~~~~~g~CPkCGkg~lv~K~gr~G~~~F 986 (1157)
|++|++|+.++++||++|++.+...+.++. ..... +. . ......+.||.||++.++.+.+++|+ |
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 999999999999999999998877654431 11110 00 0 01123578999966677778888886 9
Q ss_pred EecCCCCCCcccccCCCCCCchhhhhhhccCCCCCcccCCCCCccceeeeccCCCcceEEeC
Q 001106 987 IGCNQHPRCNYIAKTLYGDDDEEDTLQRNTNVDEPKLIGHHPASKEKVLLKSGPYGFYVQLG 1048 (1157)
Q Consensus 987 ~GCsnyP~Ck~t~~~~~~~~~~~e~~~~~~~~~~Pr~LG~cPkcGk~V~lK~GrfG~yv~c~ 1048 (1157)
|+|++||.|.++.+....... +. ........|.||+|+..++++.|++|.|+.|+
T Consensus 607 ~~Cs~~p~C~~~~~~~~~~~~----~~---~~~~~~~~~~Cp~C~~~~~~kkgk~g~f~~Cs 661 (675)
T PRK06599 607 LGCSGYPECKYTKNITRDEDE----PI---EEEEIVEEEKCPKCGGPLVLKKGRYGKFLACS 661 (675)
T ss_pred eeCCCCCccCCCCCCcccccc----cc---ccccccccCCCCCCCCeeEEEeCCCCceeeCC
Confidence 999999999988765421100 00 00011245689999998999999999999997
No 5
>PRK05776 DNA topoisomerase I; Provisional
Probab=100.00 E-value=8.7e-136 Score=1245.13 Aligned_cols=596 Identities=26% Similarity=0.375 Sum_probs=513.5
Q ss_pred CCeEEEEecchHHHHHHhhcC--------------------CCEEEEEeccccccccccCCCCC-CCCCCcceEecccc-
Q 001106 348 GKSVVVVESVTKAKVIQGYLG--------------------DMYEVLPSYGHVRDLAARSGSVR-PDDDFSMVWEVPSA- 405 (1157)
Q Consensus 348 ~k~LiIaEkPskAk~Ia~~LG--------------------~~y~V~~s~GHl~dL~~~~~~v~-p~~~f~~~~~v~~~- 405 (1157)
++.|||||||++|++|+++|| .+|+|+|++|||++|+.++..++ .+.+|.+.|.+...
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 23468888876543
Q ss_pred --hHHHHHHHHHHhccCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhcccccHhH
Q 001106 406 --AWTHLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAAREIDANL 483 (1157)
Q Consensus 406 --kk~~lk~Lk~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fsslT~~aI~~A~~nlr~~d~~L 483 (1157)
++++++.|++++++||+||||||||||||+|||||+++|+ ..++|+|+|||+||+++|++||+||+++|++|
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 24689999999999999999999999999999
Q ss_pred HHHHHHHHHHhHhhhhhccHHHHhhCC------CccccCcchhHHHHHHHhHHHHHHhcCCcceEEEEEEEecCcCCCCC
Q 001106 484 VQAYLARRALDYLIGFNISPLLWRKLP------GCQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLD 557 (1157)
Q Consensus 484 ~~A~~AR~~lD~LiG~nlSR~lt~k~~------~~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~ 557 (1157)
++||+|||++||||||||||++|.++. +++|+||||||||+|||+||+||++|+|++||.|.+.+...
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 CceeeeeecccccccccccccCCHHHHHHHHHHHcc-CCeEEEEeeeeeeeecCCCCcchHHHHHHHHHHcCCCHHHHHH
Q 001106 558 TFSFPAHLTHFQSKRLNQLSIGSHTEAKDIEQKINS-ANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMK 636 (1157)
Q Consensus 558 g~~f~a~l~~~~~~~~~~~~i~d~e~Ae~i~~~l~~-~~~~V~~v~~k~~~~~PP~Pf~ts~LQ~~AskklG~Sa~~Tm~ 636 (1157)
+..|.+.|.. .++.++++|+++++.+++ ..++|.+|+.++++++||+||+|++||++||++|||||++||+
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 HHHHHhhcccCCCCCceEEEEEEccCCcCCCHHH-HHHHHHHHHHH--hCC---CCCCCCCCCcc-ccccccccccCCCC
Q 001106 637 LAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEA-AKEIRSLIFER--YGS---HHAPEEGPRKY-FKKVKNAQEAHEAI 709 (1157)
Q Consensus 637 iAQ~LYE~~k~~~~~~~GlITYPRTDS~~Ls~~~-~~~i~~~i~~~--~g~---~~~~~~~~r~~-~~k~k~~q~AH~AI 709 (1157)
+||+|||+ ||||||||||++||+++ +.++.+.|... ||. .+.. ..++.+ ..+.++.++|||||
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 89999999999999996 56666666532 443 2222 111111 11222235699999
Q ss_pred CCCcccCChhhhhCCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEEEEEecCccEEEEEEEEEEEEcCceecccccchhh
Q 001106 710 RPTDIRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGA 789 (1157)
Q Consensus 710 ~PT~~~~~p~~l~~~Ls~dE~klY~LI~rRfLAs~~~~a~~e~t~v~i~~~~~~~~F~asg~~i~~~Gw~~vy~~~~~~~ 789 (1157)
|||+. .|+ .|+++|++||+||||||||+||+||+|++|+|++.++++++.|+++|++++++||++||++.+
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 499999999999999999999999999999999988654448999999999999999996431
Q ss_pred hccccccchhhhhHHHhccCCCCCCeEEeeeEEeeecccCCCCCCCHHHHHHHHHhcCCCCCCchHHHHHhccccceEEE
Q 001106 790 IRYKENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTV 869 (1157)
Q Consensus 790 ~~~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk~GIGTpATrA~IIe~L~~R~YV~~ 869 (1157)
+ ++ ..||.|++||.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++|+||++
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 10 35999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCceeecccchhhhhhhhhcccccccChhhhHHHHHHhhhHhhcCccHHHHHHHHHHHhhhhhhhccchhHHHHHHHHHh
Q 001106 870 KSRILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKGLLVDYWSRFSSYCTCAQSLHIHQVEKMLEK 949 (1157)
Q Consensus 870 k~k~L~PT~lG~~vi~~L~~~f~~l~~p~~TA~~E~~Ld~Ia~G~~~~~~~l~~F~~~f~~~v~~~~~~~i~~V~k~l~~ 949 (1157)
+++.|+||++|+.|+++|..+||+|++|+|||.||.+||+|++|+++|++||++|++.|...+..+.. ....+.+.+..
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 23334333333
Q ss_pred hhCCCccCCCCCCCCCCCCCCCceE----EEEecccCceeEEecCCCCCCcccccCC
Q 001106 950 TFGDSLFASLPNKDRSCPVCGEGTL----IFKVSRFGAGYFIGCNQHPRCNYIAKTL 1002 (1157)
Q Consensus 950 ~~g~~~~~~~~~~~g~CPkCGkg~l----v~K~gr~G~~~F~GCsnyP~Ck~t~~~~ 1002 (1157)
.++ .....++||+||+ .+ +.+.+++|.+.|+||++||+|+++.+..
T Consensus 589 ~~~------~~~~~~~Cp~Cg~-~l~~~~~~~~~~~~~~~f~~c~~~p~c~~~~~~~ 638 (670)
T PRK05776 589 ALG------LIKPVGKCKICGR-EAYKDGLCKYHYEAKKRLVKAYEEWKERTGYDHK 638 (670)
T ss_pred hcc------CcCCCCcCCCCCC-ccccCceEEecccCCccceecCCCccccCCCCcc
Confidence 322 1223579999997 67 7888999887899999999999987654
No 6
>PRK07219 DNA topoisomerase I; Validated
Probab=100.00 E-value=4.7e-135 Score=1266.86 Aligned_cols=689 Identities=25% Similarity=0.374 Sum_probs=546.3
Q ss_pred CeEEEEecchHHHHHHhhc---------------------CCCEEEEEeccccccccccCC--CCC---CCCCCcceEec
Q 001106 349 KSVVVVESVTKAKVIQGYL---------------------GDMYEVLPSYGHVRDLAARSG--SVR---PDDDFSMVWEV 402 (1157)
Q Consensus 349 k~LiIaEkPskAk~Ia~~L---------------------G~~y~V~~s~GHl~dL~~~~~--~v~---p~~~f~~~~~v 402 (1157)
+.|||||||++|++|+++| |.+|+|+|+.|||++|+.|+. .|. |...+...+..
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 345889999999999987643 232 21111111222
Q ss_pred ccchHHHHHHHHHHhccCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhcccccHh
Q 001106 403 PSAAWTHLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAAREIDAN 482 (1157)
Q Consensus 403 ~~~kk~~lk~Lk~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fsslT~~aI~~A~~nlr~~d~~ 482 (1157)
...+++|++.|++|+++||.||||||||||||+|||+|++++.. + .+++|+|||||+||+++|++||+||+++|++
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 44578999999999999999999999999999999777666543 2 3579999999999999999999999999999
Q ss_pred HHHHHHHHHHHhHhhhhhccHHHHhhCC-----CccccCcchhHHHHHHHhHHHHHHhcCCcceEEEEEEEecCcCCCCC
Q 001106 483 LVQAYLARRALDYLIGFNISPLLWRKLP-----GCQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLD 557 (1157)
Q Consensus 483 L~~A~~AR~~lD~LiG~nlSR~lt~k~~-----~~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~ 557 (1157)
|++||+|||++||||||||||+||..++ .++|+||||||||+|||+||+||+||+|++||.|.+.+...
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 9999999999999999999999997643 36999999999999999999999999999999999998631
Q ss_pred CceeeeeecccccccccccccCCHHHHHHHHHHHcc-CCeEEEEeeeeeeeecCCCCcchHHHHHHHHHHcCCCHHHHHH
Q 001106 558 TFSFPAHLTHFQSKRLNQLSIGSHTEAKDIEQKINS-ANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMK 636 (1157)
Q Consensus 558 g~~f~a~l~~~~~~~~~~~~i~d~e~Ae~i~~~l~~-~~~~V~~v~~k~~~~~PP~Pf~ts~LQ~~AskklG~Sa~~Tm~ 636 (1157)
+..|.+.|.. . .+..+++|+++|+++++.+++ ..++|.+|+.++++++||+||||++||++|+++|||||++||+
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 HHHHHhhcccCCCCCceEEEEEEccCCcCCCHHHHHHHHHHHHH-----HhCCC---CCCCCCCCccccccccccccCCC
Q 001106 637 LAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFE-----RYGSH---HAPEEGPRKYFKKVKNAQEAHEA 708 (1157)
Q Consensus 637 iAQ~LYE~~k~~~~~~~GlITYPRTDS~~Ls~~~~~~i~~~i~~-----~~g~~---~~~~~~~r~~~~k~k~~q~AH~A 708 (1157)
+||+|||+ ||||||||||++||+++. ++++|.. .|+.. +.. . .+......+++++||||
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 5555432 23321 111 1 11111223345799999
Q ss_pred CCCCcccCChhhhhCCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEEEEEecCccEEEEEEEEEEEEcCceecccccchh
Q 001106 709 IRPTDIRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAG 788 (1157)
Q Consensus 709 I~PT~~~~~p~~l~~~Ls~dE~klY~LI~rRfLAs~~~~a~~e~t~v~i~~~~~~~~F~asg~~i~~~Gw~~vy~~~~~~ 788 (1157)
||||+.. |. +.|+++|++||+||||||||+||+||+|++++|.+.+++ +.|+++|++++++||++||++..
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 359999999999999999999999999999999998864 58999999999999999996531
Q ss_pred hhccccccchhhhhHHHhccCCCCCCeEEeeeEEeeecccCCCCCCCHHHHHHHHHhcCCCCCCchHHHHHhccccceEE
Q 001106 789 AIRYKENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVT 868 (1157)
Q Consensus 789 ~~~~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk~GIGTpATrA~IIe~L~~R~YV~ 868 (1157)
+ + ...||.|++||.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++||||
T Consensus 445 -----~-~-------~~~lP~l~~G~~~~~~~~~~~~~~T~PP~rytea~Li~~Me~~GIGT~ATra~iI~~L~~R~Yv- 510 (822)
T PRK07219 445 -----F-D-------EKELPDLEEGEKLKVNKIEIEAKETQPPKRYTQSSLIKEMEKRGLGTKATRHDIIEKLYKRGYV- 510 (822)
T ss_pred -----c-c-------cccCCCCCCCCEeeeeeeEecccccCCCCCCCHHHHHHHHHhCCCCCCccHHHHHHHHHhcCcE-
Confidence 0 0 0359999999999999999999999999999999999999999999999999999999999999
Q ss_pred EcCceeecccchhhhhhhhhcccccccChhhhHHHHHHhhhHhhcCccHHHHHHHHHHHhhhhhhhccchhHHHHHHHHH
Q 001106 869 VKSRILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKGLLVDYWSRFSSYCTCAQSLHIHQVEKMLE 948 (1157)
Q Consensus 869 ~k~k~L~PT~lG~~vi~~L~~~f~~l~~p~~TA~~E~~Ld~Ia~G~~~~~~~l~~F~~~f~~~v~~~~~~~i~~V~k~l~ 948 (1157)
++++.|+||++|+.|+++|+..||.|++|+|||.||..|++|++|+.+|++||+++++.+...+..+.. ....+.+.+.
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 1112222111
Q ss_pred hhhCCCccCCCCCCCCCCCCCCCceEEEEecccCceeEEecCCCCCCcccccCCCCCC-----chhhhhhhcc-------
Q 001106 949 KTFGDSLFASLPNKDRSCPVCGEGTLIFKVSRFGAGYFIGCNQHPRCNYIAKTLYGDD-----DEEDTLQRNT------- 1016 (1157)
Q Consensus 949 ~~~g~~~~~~~~~~~g~CPkCGkg~lv~K~gr~G~~~F~GCsnyP~Ck~t~~~~~~~~-----~~~e~~~~~~------- 1016 (1157)
..+... .......+.||.||++ +.++.++.| +.||||++||.|+++.+++.... ..+..|....
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 555555555 25999999999999987664321 1111111000
Q ss_pred -----------CC--CC--CcccCCCCCccceeeeccCCCcceEEeCCCCCCCCCccccCCCCCCccccCHHHHHHHhcC
Q 001106 1017 -----------NV--DE--PKLIGHHPASKEKVLLKSGPYGFYVQLGEDRTGYLPKRASVSHIKDVDSITLEDALELLRY 1081 (1157)
Q Consensus 1017 -----------~~--~~--Pr~LG~cPkcGk~V~lK~GrfG~yv~c~~d~kg~~~k~~slpk~~~~~sItLe~Al~ll~~ 1081 (1157)
.. .. ....+.||+||..|+++.|++|.|++|+ ++|+|.....+.-.. ..
T Consensus 666 ~~~~~~CP~C~~~~~~~~~~~~~~~CP~Cg~~l~~k~gr~G~F~~Cs-----------~yp~C~~~~~l~~~~-----~~ 729 (822)
T PRK07219 666 QTFVVGCPDCEAEKEEEDPDEVIGPCPKCGGELAIKQLKYGSFLGCT-----------NYPKCKYTLPLPRRG-----KI 729 (822)
T ss_pred ccccccCCCCCCCccccccccccccCCCCCCeeEEEcCCCCCeeeCC-----------CCCCCCceeeccccc-----cc
Confidence 00 00 1235689999999999999999999997 346676544332100 00
Q ss_pred CcccCCCCCCCcCeEEeeccCcceeec
Q 001106 1082 PVNLGNHPKDGQPIMLRLARAGFSVRH 1108 (1157)
Q Consensus 1082 pk~lG~cP~cG~~v~v~~GryG~yi~~ 1108 (1157)
......||+||.++++..+++|.|..|
T Consensus 730 ~~~~~~CpkCg~~l~~~k~~~g~~~~C 756 (822)
T PRK07219 730 TVTDEKCPECGLPLLRVKGGFGDELGC 756 (822)
T ss_pred ccccCCCCCCCCeEEEEecCCCceeee
Confidence 112357999999999999999987554
No 7
>COG0550 TopA Topoisomerase IA [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.4e-135 Score=1214.36 Aligned_cols=546 Identities=45% Similarity=0.685 Sum_probs=497.7
Q ss_pred CeEEEEecchHHHHHHhhcCCCEEEEEecccccccccc---CCCCCCCCC-CcceEecccc-hHHHHHHHHHHhccCCeE
Q 001106 349 KSVVVVESVTKAKVIQGYLGDMYEVLPSYGHVRDLAAR---SGSVRPDDD-FSMVWEVPSA-AWTHLKSIKVALSGAENL 423 (1157)
Q Consensus 349 k~LiIaEkPskAk~Ia~~LG~~y~V~~s~GHl~dL~~~---~~~v~p~~~-f~~~~~v~~~-kk~~lk~Lk~l~k~ad~I 423 (1157)
+.|||||||++||+|++|||.+|+|+||+|||+||+.+ ...++++.+ |.+.|.+.+. +++.+..|+.++++||.|
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 344555555 8899988777 889999999999999999
Q ss_pred EEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhcccccHhHHHHHHHHHHHhHhhhhhccH
Q 001106 424 ILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAAREIDANLVQAYLARRALDYLIGFNISP 503 (1157)
Q Consensus 424 IlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fsslT~~aI~~A~~nlr~~d~~L~~A~~AR~~lD~LiG~nlSR 503 (1157)
|||||||||||+|||||+++|+.. +. .+++|||||+||+++|++||+||+++|++||+||+||+++|||||||+||
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-cccCcchhHHHHHHHhHHHHHHhcCCcceEEEEEEEecCcCCCCCCceeeeeecccccccccccccCCHH
Q 001106 504 LLWRKLPGC-QSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDTFSFPAHLTHFQSKRLNQLSIGSHT 582 (1157)
Q Consensus 504 ~lt~k~~~~-lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~g~~f~a~l~~~~~~~~~~~~i~d~e 582 (1157)
+||+++++. ||+||||||||+|||+||+||++|+|++||+|.+.+..+ +..|.+.|...++++ ..++.+.+
T Consensus 157 ~l~~~~~~~~LSaGRVQSpaL~lVveRE~EI~~F~p~~yw~i~a~~~~~------~~~f~a~~~~~~~~~--~~~~~~~~ 228 (570)
T COG0550 157 LLWKKLKRGVLSAGRVQSPALRLVVEREREIEAFVPEEYWEIKAIFEKG------GGEFSARLTEIEGKK--EGRLKDKD 228 (570)
T ss_pred HHHHhhccCCCCCccccchhhhhhHhhHHHHHhCCCCcceEEEEEEecC------CccEEEEEecccccc--ccccccHH
Confidence 999999875 999999999999999999999999999999999999753 223999987666543 24567888
Q ss_pred HHHHHHHHHccCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHHcCCCHHHHHHHHHHHhhcccCCCCCceEEEEEEccC
Q 001106 583 EAKDIEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRTD 662 (1157)
Q Consensus 583 ~Ae~i~~~l~~~~~~V~~v~~k~~~~~PP~Pf~ts~LQ~~AskklG~Sa~~Tm~iAQ~LYE~~k~~~~~~~GlITYPRTD 662 (1157)
.|..+++.|++..+.|.+++.+++++.||+||+|++||++|+++|||||++||+|||+|||+| |||||||||
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 999999999988999999999999999999999999999999999999999999999999963 899999999
Q ss_pred CcCCCHHHHHHHHHHHHHH-hCCCCCCCCCCCccccccccccccCCCCCCCcccCChhhhhCCCCHHHHHHHHHHHHHHH
Q 001106 663 GLHISDEAAKEIRSLIFER-YGSHHAPEEGPRKYFKKVKNAQEAHEAIRPTDIRRLPAMLSGLLDEDCLKLYSLIWSRTM 741 (1157)
Q Consensus 663 S~~Ls~~~~~~i~~~i~~~-~g~~~~~~~~~r~~~~k~k~~q~AH~AI~PT~~~~~p~~l~~~Ls~dE~klY~LI~rRfL 741 (1157)
|++||+++...++.++... ||..|.+ ..++.+..+.+++|+||||||||+ ...|+.+. + .||++||+|||||||
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 9999886 355666666678899999999998 45676653 2 899999999999999
Q ss_pred HccCCCcEEEEEEEEEEecCccEEEEEEEEEEEEcCceecccccchhhhccccccchhhhhHHHhccCCCCCCeEEeeeE
Q 001106 742 ACQMQPATVGQIQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLKTGDPLYLGEV 821 (1157)
Q Consensus 742 As~~~~a~~e~t~v~i~~~~~~~~F~asg~~i~~~Gw~~vy~~~~~~~~~~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~ 821 (1157)
||||+||+|+.++|++.++++ .|.++|++++++||++||++. . ++++ ...||.|++||.+.+.++
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 EeeecccCCCCCCCHHHHHHHHHhcCCCCCCchHHHHHhccccceEEEcCceeecccchhhhhhhhhcccccccChhhhH
Q 001106 822 ELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKSRILYPEFRGRMVSAFLSHYFSEVTDYSFTA 901 (1157)
Q Consensus 822 ~i~e~~TkPP~ryTEasLI~~MEk~GIGTpATrA~IIe~L~~R~YV~~k~k~L~PT~lG~~vi~~L~~~f~~l~~p~~TA 901 (1157)
.+.+++|+||+|||||+||++||+.|||||||||+||++|++||||..+++.|+||++|+.|+++|+.+||.+++|+|||
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 HHHHHhhhHhhcCccHHHHHHHHHHHhhhhhhh
Q 001106 902 DMETELDNVSAGLTEWKGLLVDYWSRFSSYCTC 934 (1157)
Q Consensus 902 ~~E~~Ld~Ia~G~~~~~~~l~~F~~~f~~~v~~ 934 (1157)
.||+.||+|++|+.+|++||++|+..|.+.+..
T Consensus 521 ~mE~~Ld~I~~gk~~~~~~l~e~~~~~~~~~~~ 553 (570)
T COG0550 521 KMEEKLDEIAEGKLEWKDVLDEFKKKFSKLLEE 553 (570)
T ss_pred HHHHHHHHHHcCCccHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999988775543
No 8
>PRK05582 DNA topoisomerase I; Validated
Probab=100.00 E-value=3.2e-133 Score=1225.65 Aligned_cols=635 Identities=41% Similarity=0.692 Sum_probs=545.0
Q ss_pred CCCeEEEEecchHHHHHHhhcCCCEEEEEeccccccccccCCCCCCCCCCcceEecccchHHHHHHHHHHhccCCeEEEc
Q 001106 347 SGKSVVVVESVTKAKVIQGYLGDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILA 426 (1157)
Q Consensus 347 ~~k~LiIaEkPskAk~Ia~~LG~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~kk~~lk~Lk~l~k~ad~IIlA 426 (1157)
|++.|||||||++|++|+++||.+|+|+||+|||++|+.+...++|++.|.+.|.+.+++++|++.|++++++||.||||
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 56789999999999999999999999999999999999765566675448888988888999999999999999999999
Q ss_pred cCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhcccccHhHHHHHHHHHHHhHhhhhhccHHHH
Q 001106 427 SDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAAREIDANLVQAYLARRALDYLIGFNISPLLW 506 (1157)
Q Consensus 427 TDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fsslT~~aI~~A~~nlr~~d~~L~~A~~AR~~lD~LiG~nlSR~lt 506 (1157)
||||||||+|||||+++++. ..++++|||||+||+++|++||+|+++++++|++||+||+++|||||||+||++|
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 TDPDREGEAIAWHLAHILGL-----DEKEKNRIVFNEITKDAIKNAFKNPRKIDMNLVDAQQARRILDRLVGYKLSPLLW 155 (650)
T ss_pred CCCCcchHHHHHHHHHHhCC-----CCCCceEEEEcccCHHHHHHHHhCcccccHHHHHHHHHHHHHHHHhhhhcCHHHH
Confidence 99999999999999999853 1267899999999999999999999999999999999999999999999999999
Q ss_pred hhCCCccccCcchhHHHHHHHhHHHHHHhcCCcceEEEEEEEecCcCCCCCCceeeeeecccccccccccccCCHHHHHH
Q 001106 507 RKLPGCQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDTFSFPAHLTHFQSKRLNQLSIGSHTEAKD 586 (1157)
Q Consensus 507 ~k~~~~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~g~~f~a~l~~~~~~~~~~~~i~d~e~Ae~ 586 (1157)
.++++.+|+||||||||+|||+||+||+||+|++||.|.+.+... +..|.+.|....+ +..+|.|+++|++
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 987778999999999999999999999999999999999998642 2257776643221 2357899999999
Q ss_pred HHHHHccCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHHcCCCHHHHHHHHHHHhhcccCCCCCceEEEEEEccCCcCC
Q 001106 587 IEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRTDGLHI 666 (1157)
Q Consensus 587 i~~~l~~~~~~V~~v~~k~~~~~PP~Pf~ts~LQ~~AskklG~Sa~~Tm~iAQ~LYE~~k~~~~~~~GlITYPRTDS~~L 666 (1157)
+++.+.+..++|.+|+.++++..||+||||++||++|+++|||||++||++||+|||+++|++++..||||||||||+||
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 99999888899999999999999999999999999999999999999999999999998888777679999999999999
Q ss_pred CHHHHHHHHHHHHHHhCCCCCCCCCCCccccccccccccCCCCCCCcccCChhhhhCCCCHHHHHHHHHHHHHHHHccCC
Q 001106 667 SDEAAKEIRSLIFERYGSHHAPEEGPRKYFKKVKNAQEAHEAIRPTDIRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQ 746 (1157)
Q Consensus 667 s~~~~~~i~~~i~~~~g~~~~~~~~~r~~~~k~k~~q~AH~AI~PT~~~~~p~~l~~~Ls~dE~klY~LI~rRfLAs~~~ 746 (1157)
|+++++.+.+++...+|..+.. ...+.+..+ ++.++|||||+||.....|+.+.+.|+++|++||+||+|||||+||+
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 9999999999887767655543 223333322 23457999999998643465433469999999999999999999999
Q ss_pred CcEEEEEEEEEEecCccEEEEEEEEEEEEcCceecccccchhhhccccccchhhhhHHHhccCCCCCCeEEeeeEEeeec
Q 001106 747 PATVGQIQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLKTGDPLYLGEVELKQH 826 (1157)
Q Consensus 747 ~a~~e~t~v~i~~~~~~~~F~asg~~i~~~Gw~~vy~~~~~~~~~~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~ 826 (1157)
||+|++|+|.+.+++ ..|+++|++++++||+.+|+..+ + + ...||.+++||.+.+.++.+.++
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 999999999998853 58999999999999999996311 0 0 13599999999999999999999
Q ss_pred ccCCCCCCCHHHHHHHHHhcCCCCCCchHHHHHhccccceEEEcCceeecccchhhhhhhhhcccccccChhhhHHHHHH
Q 001106 827 HTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKSRILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETE 906 (1157)
Q Consensus 827 ~TkPP~ryTEasLI~~MEk~GIGTpATrA~IIe~L~~R~YV~~k~k~L~PT~lG~~vi~~L~~~f~~l~~p~~TA~~E~~ 906 (1157)
+|+||+||||++||++||+.|||||||||+||++|++||||+.+++.|+||++|++|+++|+..++.|++|+|||.||.+
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 hhhHhhcCccHHHHHHHHHHHhhhhhhhccchhHHHHHHHHHhhhCCCccCCCCCCCCCCCCCCCceEEEEecccCceeE
Q 001106 907 LDNVSAGLTEWKGLLVDYWSRFSSYCTCAQSLHIHQVEKMLEKTFGDSLFASLPNKDRSCPVCGEGTLIFKVSRFGAGYF 986 (1157)
Q Consensus 907 Ld~Ia~G~~~~~~~l~~F~~~f~~~v~~~~~~~i~~V~k~l~~~~g~~~~~~~~~~~g~CPkCGkg~lv~K~gr~G~~~F 986 (1157)
|++|++|+.++++||+++++.+...+..+. ..... +. ... ......||+||+ .++.+.+++|. |
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 999999999999999999988776554321 10000 00 000 112468999986 45666666664 9
Q ss_pred EecCCCCCCcccccCCCCCCchhhhhhhccCCCCCcccCCCCCccceeeeccCCCcc-eEEeC
Q 001106 987 IGCNQHPRCNYIAKTLYGDDDEEDTLQRNTNVDEPKLIGHHPASKEKVLLKSGPYGF-YVQLG 1048 (1157)
Q Consensus 987 ~GCsnyP~Ck~t~~~~~~~~~~~e~~~~~~~~~~Pr~LG~cPkcGk~V~lK~GrfG~-yv~c~ 1048 (1157)
|+|++||.|++..+... ...+.||+|+..++++.+++|. |+.|+
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 99999999998754321 1125699999888888888885 88886
No 9
>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=5.5e-132 Score=1205.36 Aligned_cols=608 Identities=44% Similarity=0.709 Sum_probs=521.6
Q ss_pred EEEEecchHHHHHHhhcCCCEEEEEeccccccccccCCCCCCCCCCcceEecccchHHHHHHHHHHhccCCeEEEccCCC
Q 001106 351 VVVVESVTKAKVIQGYLGDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILASDPD 430 (1157)
Q Consensus 351 LiIaEkPskAk~Ia~~LG~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~kk~~lk~Lk~l~k~ad~IIlATDpD 430 (1157)
|||||||++|++|+++||++|+|+||+|||++|+++...++...+|.+.|.+.+++++|++.|++++++||+||||||||
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 79999999999999999999999999999999987633222222477778887889999999999999999999999999
Q ss_pred ccccHHHHHHHHHHhhcccccCCccE-EEEEEcccCHHHHHHHHHhcccccHhHHHHHHHHHHHhHhhhhhccHHHHhhC
Q 001106 431 REGEAIAWHIVEMLQQQDALHENITV-ARVVFHEITEASIKVALQAAREIDANLVQAYLARRALDYLIGFNISPLLWRKL 509 (1157)
Q Consensus 431 REGE~Ia~~Ile~l~~~~~~~~~k~v-kRl~fsslT~~aI~~A~~nlr~~d~~L~~A~~AR~~lD~LiG~nlSR~lt~k~ 509 (1157)
||||+|+|||+++|+. .+|+ +|+|||+||+++|++||+|+++++.+|++||.||+++|||||||+||++|..+
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 9999999999999853 3466 99999999999999999999999999999999999999999999999999887
Q ss_pred CCccccCcchhHHHHHHHhHHHHHHhcCCcceEEEEEEEecCcCCCCCCceeeeeecccccccccccccCCHHHHHHHHH
Q 001106 510 PGCQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDTFSFPAHLTHFQSKRLNQLSIGSHTEAKDIEQ 589 (1157)
Q Consensus 510 ~~~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~g~~f~a~l~~~~~~~~~~~~i~d~e~Ae~i~~ 589 (1157)
+..+|+||||||||+|||+||+||+||+|++||.|.+.+... +..|.+.|....+.++...++.++++|+++++
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 34688776432222222347889999999999
Q ss_pred HHccCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHHcCCCHHHHHHHHHHHhhcccCCCCCceEEEEEEccCCcCCCHH
Q 001106 590 KINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRTDGLHISDE 669 (1157)
Q Consensus 590 ~l~~~~~~V~~v~~k~~~~~PP~Pf~ts~LQ~~AskklG~Sa~~Tm~iAQ~LYE~~k~~~~~~~GlITYPRTDS~~Ls~~ 669 (1157)
.+++..++|.+|+.+++++.||+||||++||++|+++|||||++||++||+|||+++++ |++.||||||||||+|||++
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 99888899999999999999999999999999999999999999999999999987777 56679999999999999999
Q ss_pred HHHHHHHHHHHHhCCCCCCCCCCCccccccccccccCCCCCCCcccCChhhhhCCCCHHHHHHHHHHHHHHHHccCCCcE
Q 001106 670 AAKEIRSLIFERYGSHHAPEEGPRKYFKKVKNAQEAHEAIRPTDIRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPAT 749 (1157)
Q Consensus 670 ~~~~i~~~i~~~~g~~~~~~~~~r~~~~k~k~~q~AH~AI~PT~~~~~p~~l~~~Ls~dE~klY~LI~rRfLAs~~~~a~ 749 (1157)
+++.+..++...++..+.. ...++++++.++.|+||||||||.....|+.+.+.|+++|++||+||+|||||+||+||+
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 EEEEEEEEEecCccEEEEEEEEEEEEcCceecccccchhhhccccccchhhhhHHHhccCCCCCCeEEeeeEEeeecccC
Q 001106 750 VGQIQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQ 829 (1157)
Q Consensus 750 ~e~t~v~i~~~~~~~~F~asg~~i~~~Gw~~vy~~~~~~~~~~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~Tk 829 (1157)
|++|+|.+.+.++++.|.++|++++++||++||+.... +++++ ....||.+++||.+.+.++.+.+++|+
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 CCCCCCHHHHHHHHHhcCCCCCCchHHHHHhccccceEEEcCceeecccchhhhhhhhhcccccccChhhhHHHHHHhhh
Q 001106 830 PPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKSRILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDN 909 (1157)
Q Consensus 830 PP~ryTEasLI~~MEk~GIGTpATrA~IIe~L~~R~YV~~k~k~L~PT~lG~~vi~~L~~~f~~l~~p~~TA~~E~~Ld~ 909 (1157)
||+||||++||++||+.|||||||||+||++|++||||+++++.|+||++|+.|++.|+..++.|++|+|||.||..|++
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 HhhcCccHHHHHHHHHHHhhhhhhhccchhHHHHHHHHHhhhCCCccCCCCCCCCCCCCCCCceEEEEecccCceeEEec
Q 001106 910 VSAGLTEWKGLLVDYWSRFSSYCTCAQSLHIHQVEKMLEKTFGDSLFASLPNKDRSCPVCGEGTLIFKVSRFGAGYFIGC 989 (1157)
Q Consensus 910 Ia~G~~~~~~~l~~F~~~f~~~v~~~~~~~i~~V~k~l~~~~g~~~~~~~~~~~g~CPkCGkg~lv~K~gr~G~~~F~GC 989 (1157)
|++|+.++++||+++++.+.+.+..+. .... .. .....+.||.||+ .+..+.+++|+ ||||
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 0012478999997 56666777775 9999
Q ss_pred CCCCCCcccccC
Q 001106 990 NQHPRCNYIAKT 1001 (1157)
Q Consensus 990 snyP~Ck~t~~~ 1001 (1157)
++||.|+++.++
T Consensus 598 s~y~~C~~~~~l 609 (610)
T TIGR01051 598 SNFPECKYTKSI 609 (610)
T ss_pred CCCCCCCCCCCC
Confidence 999999987653
No 10
>PRK07220 DNA topoisomerase I; Validated
Probab=100.00 E-value=3.1e-132 Score=1227.58 Aligned_cols=624 Identities=24% Similarity=0.366 Sum_probs=514.2
Q ss_pred CeEEEEecchHHHHHHhhcC---------------------CCEEEEEeccccccccccC-----CCCCCCCCCcceEec
Q 001106 349 KSVVVVESVTKAKVIQGYLG---------------------DMYEVLPSYGHVRDLAARS-----GSVRPDDDFSMVWEV 402 (1157)
Q Consensus 349 k~LiIaEkPskAk~Ia~~LG---------------------~~y~V~~s~GHl~dL~~~~-----~~v~p~~~f~~~~~v 402 (1157)
|.|||||||++|++|+.+|| ++|+|+|++|||++|+.|+ ..|++++.|.+.|..
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 346766666667776
Q ss_pred ccchHHHHHHHHHHhccCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhcccccHh
Q 001106 403 PSAAWTHLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAAREIDAN 482 (1157)
Q Consensus 403 ~~~kk~~lk~Lk~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fsslT~~aI~~A~~nlr~~d~~ 482 (1157)
.+.+++|++.|++++++||.||||||||||||+|||||+++++. .+++++|+|+|||+||+++|++||+||+++|++
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 HHHHHHHHHHHhHhhhhhccHHHHhhCC----CccccCcchhHHHHHHHhHHHHHHhcCCcceEEEEEEEecCcCCCCCC
Q 001106 483 LVQAYLARRALDYLIGFNISPLLWRKLP----GCQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDT 558 (1157)
Q Consensus 483 L~~A~~AR~~lD~LiG~nlSR~lt~k~~----~~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~g 558 (1157)
|++||+|||++||||||||||++|..++ +++|+||||||||+|||+||+||++|+|++||.|.+.+.. .+
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 ceeeeeecccccccccccccCCHHHHHHHHHHHccCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHHcCCCHHHHHHHH
Q 001106 559 FSFPAHLTHFQSKRLNQLSIGSHTEAKDIEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKLA 638 (1157)
Q Consensus 559 ~~f~a~l~~~~~~~~~~~~i~d~e~Ae~i~~~l~~~~~~V~~v~~k~~~~~PP~Pf~ts~LQ~~AskklG~Sa~~Tm~iA 638 (1157)
..|.+.|. ..+|.++++|+++++.+ +..++|.+|+.+++++.||+||+|++||++|++ +||||++||++|
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 46777762 23688999999999999 567999999999999999999999999999985 899999999999
Q ss_pred HHHhhcccCCCCCceEEEEEEccCCcCCCHHH--HHHHHHHHHHHhCC---CCCCCCCCCccccccccccccCCCCCCCc
Q 001106 639 QKLYEGVQLPDGTAAGLITYMRTDGLHISDEA--AKEIRSLIFERYGS---HHAPEEGPRKYFKKVKNAQEAHEAIRPTD 713 (1157)
Q Consensus 639 Q~LYE~~k~~~~~~~GlITYPRTDS~~Ls~~~--~~~i~~~i~~~~g~---~~~~~~~~r~~~~k~k~~q~AH~AI~PT~ 713 (1157)
|+|||+ ||||||||||++||+++ .+.+..++...||. .+.. .. +....+.+..++||||||||+
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 99999999999999965 45555554434543 2322 11 001111223356899999998
Q ss_pred ccCChhhhhCCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEEEEEecCccEEEEEEEEEEEEcCceecccccchhhhccc
Q 001106 714 IRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYK 793 (1157)
Q Consensus 714 ~~~~p~~l~~~Ls~dE~klY~LI~rRfLAs~~~~a~~e~t~v~i~~~~~~~~F~asg~~i~~~Gw~~vy~~~~~~~~~~~ 793 (1157)
.. +. +.|+++|++||+||||||||+||+||+|++++|.+.+++ +.|+++|++++++||++||++..
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 cccchhhhhHHHhccCCCCCCeEEeeeEEeeecccCCCCCCCHHHHHHHHHhcCCCCCCchHHHHHhccccceEEEcCce
Q 001106 794 ENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKSRI 873 (1157)
Q Consensus 794 e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk~GIGTpATrA~IIe~L~~R~YV~~k~k~ 873 (1157)
+ ++ ..||.|++||.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++||||+ ++.
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 eecccchhhhhhhhhcccccccChhhhHHHHHHhhhHhhcCccHHHHHHHHHHHhhhhhhhccchhHHHHHHHHHhhhCC
Q 001106 874 LYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKGLLVDYWSRFSSYCTCAQSLHIHQVEKMLEKTFGD 953 (1157)
Q Consensus 874 L~PT~lG~~vi~~L~~~f~~l~~p~~TA~~E~~Ld~Ia~G~~~~~~~l~~F~~~f~~~v~~~~~~~i~~V~k~l~~~~g~ 953 (1157)
|+||++|+.|+++|+.+|+.|++|+|||.||..||+|++|+.+|++||+++++.+...+..+.. ....+...+...+.
T Consensus 507 l~pT~~G~~v~~~l~~~~~~i~~~~~Ta~~E~~Ld~I~~G~~~~~~~l~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~- 584 (740)
T PRK07220 507 IQPTNTAFAVVDALEKYAPTITKPDMTSRLEEDMDKIAEGKIKEDAVLEESREMLEQVFDELDK-NREKIRESLREGLR- 584 (740)
T ss_pred ccccHHHHHHHHHHHHhchhhcChhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHH-HHHHHHHhhhhhhc-
Confidence 9999999999999999999999999999999999999999999999999999877765544321 11112111111110
Q ss_pred CccCCCCCCCCCCCCCCCceEEEEecccCceeEEecCCCCCCcccccCCCCCCchhhhhhhccCCCCCcccCCCCCccce
Q 001106 954 SLFASLPNKDRSCPVCGEGTLIFKVSRFGAGYFIGCNQHPRCNYIAKTLYGDDDEEDTLQRNTNVDEPKLIGHHPASKEK 1033 (1157)
Q Consensus 954 ~~~~~~~~~~g~CPkCGkg~lv~K~gr~G~~~F~GCsnyP~Ck~t~~~~~~~~~~~e~~~~~~~~~~Pr~LG~cPkcGk~ 1033 (1157)
.....+.||.||+ .++.+.+++|. .||||++||+|+++.++.....+ ..+-..||+||..
T Consensus 585 -----~~~~~~~CP~Cg~-~l~~r~~r~g~-~f~gCs~yp~C~~~~~l~~~g~~-------------~~~~~~Cp~Cg~~ 644 (740)
T PRK07220 585 -----EDKIIGKCPLCGS-DLMVRRSKRGS-RFIGCEGYPECTFSLPLPKSGQI-------------IVTDKVCEAHGLN 644 (740)
T ss_pred -----ccccccccccCCC-eeeEEecCCCc-eEEEcCCCCCCCceeeCCCCCcc-------------ccCCCCCCCCCCc
Confidence 1123468999996 56777777763 59999999999998776542211 0112369999864
Q ss_pred ee-ec-cCCCcceEEeC
Q 001106 1034 VL-LK-SGPYGFYVQLG 1048 (1157)
Q Consensus 1034 V~-lK-~GrfG~yv~c~ 1048 (1157)
++ .+ .|+.+.|+.|.
T Consensus 645 ~~k~~~~g~~~~~~~Cp 661 (740)
T PRK07220 645 HIRIINGGKRPWDLGCP 661 (740)
T ss_pred eEEEEecCCccceeeCC
Confidence 33 22 23333378884
No 11
>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=6.9e-132 Score=1210.40 Aligned_cols=585 Identities=25% Similarity=0.365 Sum_probs=499.3
Q ss_pred CeEEEEecchHHHHHHhhc------------CCCEEEEEeccccccccccCC------CC-------CCCCCCcceEecc
Q 001106 349 KSVVVVESVTKAKVIQGYL------------GDMYEVLPSYGHVRDLAARSG------SV-------RPDDDFSMVWEVP 403 (1157)
Q Consensus 349 k~LiIaEkPskAk~Ia~~L------------G~~y~V~~s~GHl~dL~~~~~------~v-------~p~~~f~~~~~v~ 403 (1157)
|.|||||||++|++|+++| |++|+|+||+|||++|+.|+. .| +|+ +| .|.+.
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 22 222 23 35666
Q ss_pred cchHHHHHHHHHHhc--cCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhcccc--
Q 001106 404 SAAWTHLKSIKVALS--GAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAAREI-- 479 (1157)
Q Consensus 404 ~~kk~~lk~Lk~l~k--~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fsslT~~aI~~A~~nlr~~-- 479 (1157)
+.++++++.|+++++ +||.||||||||||||+|||||+++|+. +...+|+|+|||+||+++|++||+||+++
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 cHhHHHHHHHHHHHhHhhhhhccHHHHhh-----CCCccccCcchhHHHHHHHhHHHHHHhcCCcceEEEEEEEecCcCC
Q 001106 480 DANLVQAYLARRALDYLIGFNISPLLWRK-----LPGCQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESH 554 (1157)
Q Consensus 480 d~~L~~A~~AR~~lD~LiG~nlSR~lt~k-----~~~~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~ 554 (1157)
+++|++||+||+++||||||||||++|.+ +.+++|+||||||||+|||+||+||+||+|++||.|.+.+...
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 78999999999999999999999999987 5568999999999999999999999999999999999998642
Q ss_pred CCCCceeeeeecccccccccccccCCHHHHHHHHHHHccCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHHcCCCHHHH
Q 001106 555 SLDTFSFPAHLTHFQSKRLNQLSIGSHTEAKDIEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYT 634 (1157)
Q Consensus 555 ~~~g~~f~a~l~~~~~~~~~~~~i~d~e~Ae~i~~~l~~~~~~V~~v~~k~~~~~PP~Pf~ts~LQ~~AskklG~Sa~~T 634 (1157)
+..|.+.|....+ +..++.++++|+.+++.+.+.+++|.+|+.+++++.||+||+|++||++|+++|||||++|
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 3458888754222 2357899999999999998888999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhcccCCCCCceEEEEEEccCCcCCCHHHHHHHHHHHHHHhCCCC--CCC-----CCCCccccccccccccCC
Q 001106 635 MKLAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFERYGSHH--APE-----EGPRKYFKKVKNAQEAHE 707 (1157)
Q Consensus 635 m~iAQ~LYE~~k~~~~~~~GlITYPRTDS~~Ls~~~~~~i~~~i~~~~g~~~--~~~-----~~~r~~~~k~k~~q~AH~ 707 (1157)
|++||+|||+| ||||||||||++||++++++++++|...++..+ ... ...++++++ .+|+|||
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 899999999999999999999999877655322 110 001122222 3578999
Q ss_pred CCCCCcccCChhhhhCCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEEEEEecCccEEEEEEEEEEEEcCceecccccch
Q 001106 708 AIRPTDIRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDA 787 (1157)
Q Consensus 708 AI~PT~~~~~p~~l~~~Ls~dE~klY~LI~rRfLAs~~~~a~~e~t~v~i~~~~~~~~F~asg~~i~~~Gw~~vy~~~~~ 787 (1157)
|||||+....+ +.|+++|++||+|||+||||+||+||+|++|+|.+.+++ +.|+++|++++++||++||...+.
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 hhhccccccchhhhhHHHhccCCCCCCeEEeeeEEeeecccCCCCCCCHHHHHHHHH-----------------hcCCCC
Q 001106 788 GAIRYKENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSEGSLVKKLE-----------------ELGIGR 850 (1157)
Q Consensus 788 ~~~~~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~ME-----------------k~GIGT 850 (1157)
+++++ ...||.|++||.+.+.++.+.+++|+||+|||||+||++|| +.||||
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 11110 13599999999999999999999999999999999999999 789999
Q ss_pred CCchHHHHHhccccceEEEcCceeecccchhhhhhhhhcccccccChhhhHHHHHHhhhHhhcCccHHHHHHHHHHHhhh
Q 001106 851 PSTYASTLKVLQDRNYVTVKSRILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKGLLVDYWSRFSS 930 (1157)
Q Consensus 851 pATrA~IIe~L~~R~YV~~k~k~L~PT~lG~~vi~~L~~~f~~l~~p~~TA~~E~~Ld~Ia~G~~~~~~~l~~F~~~f~~ 930 (1157)
|||||+||++|++||||+.+++.|+||++|+.|+++|+. .|++|+|||.||.+||+|++|+.+|++||+.|+..+..
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 68999999999999999999999999999999998876
Q ss_pred hhhhccchhHHHHHHHHHhhhCCCccCCCCCCCCCCCCCCCceEEEEecccCceeEEecCCCCCCcccc
Q 001106 931 YCTCAQSLHIHQVEKMLEKTFGDSLFASLPNKDRSCPVCGEGTLIFKVSRFGAGYFIGCNQHPRCNYIA 999 (1157)
Q Consensus 931 ~v~~~~~~~i~~V~k~l~~~~g~~~~~~~~~~~g~CPkCGkg~lv~K~gr~G~~~F~GCsnyP~Ck~t~ 999 (1157)
.+..+. .... .+. ....+.|| ||+ .++.+.+++|. |+||++||+|++..
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 654321 1110 010 12467899 996 67778888775 99999999999753
No 12
>PRK14973 DNA topoisomerase I; Provisional
Probab=100.00 E-value=1.2e-131 Score=1234.18 Aligned_cols=626 Identities=23% Similarity=0.334 Sum_probs=513.6
Q ss_pred CeEEEEecchHHHHHHhhcCCC------------------EEEEEeccccccccccC--CCCCCC-----CCCcceEecc
Q 001106 349 KSVVVVESVTKAKVIQGYLGDM------------------YEVLPSYGHVRDLAARS--GSVRPD-----DDFSMVWEVP 403 (1157)
Q Consensus 349 k~LiIaEkPskAk~Ia~~LG~~------------------y~V~~s~GHl~dL~~~~--~~v~p~-----~~f~~~~~v~ 403 (1157)
|.||||||||+|+.||.+||.. ++|+|++|||++|..+. ..|... +.|+..|.+.
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 36999999999996542 345421 1222235555
Q ss_pred cchHHHHHHHHHHhccCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhcccccHhH
Q 001106 404 SAAWTHLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAAREIDANL 483 (1157)
Q Consensus 404 ~~kk~~lk~Lk~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fsslT~~aI~~A~~nlr~~d~~L 483 (1157)
+.+++|++.|++++++||.||||||||||||+|||||+++|+. .+.+++|+|+|||+||+++|++||+|++++|++|
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 6688999999999999999999999999999999999999964 2345799999999999999999999999999999
Q ss_pred HHHHHHHHHHhHhhhhhccHHHHhhCC----CccccCcchhHHHHHHHhHHHHHHhcCCcceEEEEEEEecCcCCCCCCc
Q 001106 484 VQAYLARRALDYLIGFNISPLLWRKLP----GCQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDTF 559 (1157)
Q Consensus 484 ~~A~~AR~~lD~LiG~nlSR~lt~k~~----~~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~g~ 559 (1157)
++||+||+++|||||||+||++|.++. +++|+||||||||+|||+||+||+||+|++||.|.+.+.. .+.
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 3599999999999999999999999999999999999864 244
Q ss_pred eeeeeecccccccccccccCCHHHHHHHHHHHccCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHHcCCCHHHHHHHHH
Q 001106 560 SFPAHLTHFQSKRLNQLSIGSHTEAKDIEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKLAQ 639 (1157)
Q Consensus 560 ~f~a~l~~~~~~~~~~~~i~d~e~Ae~i~~~l~~~~~~V~~v~~k~~~~~PP~Pf~ts~LQ~~AskklG~Sa~~Tm~iAQ 639 (1157)
.|.++|. +.+|.|+++|+.+++.+. ..++|.+|+.++++++||+||||++||++|++ |||||++||+|||
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 236889999999999885 67999999999999999999999999999875 9999999999999
Q ss_pred HHhhcccCCCCCceEEEEEEccCCcCCCHHH-HHHHHHHH-HHHhCCC--CCCCCCCCccccccccccccCCCCCCCccc
Q 001106 640 KLYEGVQLPDGTAAGLITYMRTDGLHISDEA-AKEIRSLI-FERYGSH--HAPEEGPRKYFKKVKNAQEAHEAIRPTDIR 715 (1157)
Q Consensus 640 ~LYE~~k~~~~~~~GlITYPRTDS~~Ls~~~-~~~i~~~i-~~~~g~~--~~~~~~~r~~~~k~k~~q~AH~AI~PT~~~ 715 (1157)
+|||. ||||||||||+|||+++ +..+...+ ...|+.. +.. ...+.+..+.+++++||||||||+..
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 99999999999999984 44443322 2233332 222 12232333334568899999999864
Q ss_pred CChhhhhCCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEEEEEecCccEEEEEEEEEEEEcCceecccccchhhhccccc
Q 001106 716 RLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYKEN 795 (1157)
Q Consensus 716 ~~p~~l~~~Ls~dE~klY~LI~rRfLAs~~~~a~~e~t~v~i~~~~~~~~F~asg~~i~~~Gw~~vy~~~~~~~~~~~e~ 795 (1157)
+. ..|+++|++||+||||||||+||+||+|++|+|.+.+++ ..|+++|++++++||++||++.+ +
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 cchhhhhHHHhccCCCCCCeEEeeeEEeeecccCCCCCCCHHHHHHHHHhcCCCCCCchHHHHHhccccceEEEcCceee
Q 001106 796 EENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKSRILY 875 (1157)
Q Consensus 796 ~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk~GIGTpATrA~IIe~L~~R~YV~~k~k~L~ 875 (1157)
+ ...||.|++||.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++|+||+ ++.|+
T Consensus 437 ~-------~~~LP~l~~Ge~~~~~~~~~~e~~T~PP~ryTEatLik~ME~~GIGTpATrA~II~~L~~R~Yve--~k~l~ 507 (936)
T PRK14973 437 K-------ENILPAFALGEKLPILAVNLEEKETQPPARYSQSRLIQRMEELGLGTKSTRHEVIGKLVSRKYIE--GNPLR 507 (936)
T ss_pred c-------cccCCCccCCCEEEeeeeEEeecCCCCCCCCCHHHHHHHhccCCCCCcccHHHHHHHHHHccCee--CCcee
Confidence 1 03599999999999999999999999999999999999999999999999999999999999994 77899
Q ss_pred cccchhhhhhhhhcccccccChhhhHHHHHHhhhHhhcCccHHHHHHHHHHHhhhhhhhccchhHHHHHHHHHhhhCCCc
Q 001106 876 PEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKGLLVDYWSRFSSYCTCAQSLHIHQVEKMLEKTFGDSL 955 (1157)
Q Consensus 876 PT~lG~~vi~~L~~~f~~l~~p~~TA~~E~~Ld~Ia~G~~~~~~~l~~F~~~f~~~v~~~~~~~i~~V~k~l~~~~g~~~ 955 (1157)
||++|+.|+++|+.+|++|++|+|||.||..|++|++|+.+|++||++|++.|...+..+... ...+.. .+....
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 999999999999999999999999999999999999999999999999999887766554210 011111 111000
Q ss_pred cCCCCCCCCCCCCCCCceEEEEecccCceeEEecCCCCCCcccccCCCCCCchhhhhhhccCCCCCcccCCCCCccc--e
Q 001106 956 FASLPNKDRSCPVCGEGTLIFKVSRFGAGYFIGCNQHPRCNYIAKTLYGDDDEEDTLQRNTNVDEPKLIGHHPASKE--K 1033 (1157)
Q Consensus 956 ~~~~~~~~g~CPkCGkg~lv~K~gr~G~~~F~GCsnyP~Ck~t~~~~~~~~~~~e~~~~~~~~~~Pr~LG~cPkcGk--~ 1033 (1157)
......+.||.||+ .+.++.+++|. ||||++||+|+++.++...... .....-..||+||. .
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 00123578999997 56656566654 9999999999998776522110 00111236999997 6
Q ss_pred eeeccCCCcceEEeC
Q 001106 1034 VLLKSGPYGFYVQLG 1048 (1157)
Q Consensus 1034 V~lK~GrfG~yv~c~ 1048 (1157)
++++.||||.|++|.
T Consensus 647 ~~~r~Gr~g~fl~CP 661 (936)
T PRK14973 647 RLIRKGARPWDIGCP 661 (936)
T ss_pred EEeecCCCcccccCc
Confidence 777999999999994
No 13
>PRK08173 DNA topoisomerase III; Validated
Probab=100.00 E-value=7.2e-130 Score=1217.02 Aligned_cols=712 Identities=21% Similarity=0.287 Sum_probs=537.5
Q ss_pred CCCeEEEEecchHHHHHHhhcC-----------CCEEEEEeccccccccccCC------CCCCCC--CCcceEe--cccc
Q 001106 347 SGKSVVVVESVTKAKVIQGYLG-----------DMYEVLPSYGHVRDLAARSG------SVRPDD--DFSMVWE--VPSA 405 (1157)
Q Consensus 347 ~~k~LiIaEkPskAk~Ia~~LG-----------~~y~V~~s~GHl~dL~~~~~------~v~p~~--~f~~~~~--v~~~ 405 (1157)
|+++||||||||+|++|+++|| ++|+|+||+|||++|+.|+. .|..++ .+.+.|. +...
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 343210 1222343 4566
Q ss_pred hHHHHHHHHHHhc--cCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhccccc--H
Q 001106 406 AWTHLKSIKVALS--GAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAAREID--A 481 (1157)
Q Consensus 406 kk~~lk~Lk~l~k--~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fsslT~~aI~~A~~nlr~~d--~ 481 (1157)
+++||++|++|++ ++|+||||||||||||+|+|+|+++++ +++||+|||||+||+++|++||+||++++ .
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 hHHHHHHHHHHHhHhhhhhccHHHHhhC---C--CccccCcchhHHHHHHHhHHHHHHhcCCcceEEEEEEEecCcCCCC
Q 001106 482 NLVQAYLARRALDYLIGFNISPLLWRKL---P--GCQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSL 556 (1157)
Q Consensus 482 ~L~~A~~AR~~lD~LiG~nlSR~lt~k~---~--~~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~ 556 (1157)
+|++||+||+++|||||||+||++|... + +++|+||||||||+|||+||+||+||+|++||+|.+.+...
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 CCceeeeeeccccc--cc----ccccccCCHHHHHHHHHHHccCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHHcCCC
Q 001106 557 DTFSFPAHLTHFQS--KR----LNQLSIGSHTEAKDIEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFS 630 (1157)
Q Consensus 557 ~g~~f~a~l~~~~~--~~----~~~~~i~d~e~Ae~i~~~l~~~~~~V~~v~~k~~~~~PP~Pf~ts~LQ~~AskklG~S 630 (1157)
+..|.++|..... .. .+..+++|+++|+++++.+.+..++|.+ +.+++++.||+||+|++||++||++||||
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 3357777742110 00 1235789999999999999988899998 88999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhcccCCCCCceEEEEEEccCCcCCCHHHHHHHHHHHHHHhC-CCCCC-------C---CCCCcccccc
Q 001106 631 ATYTMKLAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFERYG-SHHAP-------E---EGPRKYFKKV 699 (1157)
Q Consensus 631 a~~Tm~iAQ~LYE~~k~~~~~~~GlITYPRTDS~~Ls~~~~~~i~~~i~~~~g-~~~~~-------~---~~~r~~~~k~ 699 (1157)
|++||+|||+|||+| ||||||||||+|||++++++++.+|....+ ..|.. . ...++++++.
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 001106 700 KNAQEAHEAIRPTDIRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGNADESIVFRSSCSRVEFLGFQ 779 (1157)
Q Consensus 700 k~~q~AH~AI~PT~~~~~p~~l~~~Ls~dE~klY~LI~rRfLAs~~~~a~~e~t~v~i~~~~~~~~F~asg~~i~~~Gw~ 779 (1157)
..+||||||||.. .|+ .|+++|++||+||||||||+||+||+|+.|+|.+.+++ +.|+++|++++++||+
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 2468999999985 243 49999999999999999999999999999999998864 4899999999999999
Q ss_pred ecccccchhhhccccccchhhhhHHHhccCCCCCCeEEeeeEEeeecccCCCCCCCHHHHHHHHH---------------
Q 001106 780 AAYEDVDAGAIRYKENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSEGSLVKKLE--------------- 844 (1157)
Q Consensus 780 ~vy~~~~~~~~~~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~ME--------------- 844 (1157)
+||.... +++ ...||.|++||.+.+.++.+.+++|+||+||||++||++||
T Consensus 450 ~vy~~~~-------~~~-------~~~LP~l~~Ge~~~~~~~~~~e~~TkPP~ryTEatLl~aMe~~gk~v~D~el~~~~ 515 (862)
T PRK08173 450 AVYGKEA-------QGA-------DANLVPVQKGEKVKTDKIEAVALTTKPPARYNEATLLSAMEGAGKLVEDDELREAM 515 (862)
T ss_pred HHhCccc-------ccc-------cccCCCcCCCCEeeeeeeeecccccCCCCCcCHHHHHHHHHhhhhccccHHHHhhh
Confidence 9996421 001 03599999999999999999999999999999999999999
Q ss_pred -hcCCCCCCchHHHHHhccccceEEEcCceeecccchhhhhhhhhc-ccccccChhhhHHHHHHhhhHhhcCccHHHHHH
Q 001106 845 -ELGIGRPSTYASTLKVLQDRNYVTVKSRILYPEFRGRMVSAFLSH-YFSEVTDYSFTADMETELDNVSAGLTEWKGLLV 922 (1157)
Q Consensus 845 -k~GIGTpATrA~IIe~L~~R~YV~~k~k~L~PT~lG~~vi~~L~~-~f~~l~~p~~TA~~E~~Ld~Ia~G~~~~~~~l~ 922 (1157)
+.|||||||||+||++|++||||+++++.|+||++|+.|+++|+. .|+.|++|+|||.||..|++|++|+.++++||+
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 579999999999999999999999999999999999999999987 478899999999999999999999999999999
Q ss_pred HHHHHhhhhhhhccchhHHHHHHHHHhhhCCCccCCCCCCCCCCCCCCCceEEEEecccCceeEEecCCCCCCcccccCC
Q 001106 923 DYWSRFSSYCTCAQSLHIHQVEKMLEKTFGDSLFASLPNKDRSCPVCGEGTLIFKVSRFGAGYFIGCNQHPRCNYIAKTL 1002 (1157)
Q Consensus 923 ~F~~~f~~~v~~~~~~~i~~V~k~l~~~~g~~~~~~~~~~~g~CPkCGkg~lv~K~gr~G~~~F~GCsnyP~Ck~t~~~~ 1002 (1157)
++++.+...++.+. +.....+. .......+.||+||++ +..+ +.+|+|++ |+|..|..
T Consensus 596 ~i~~~~~~~v~~~~--------~~~~~~~~----~~~~~~~~~CP~Cg~~-~~~~------~~~~~Cs~---C~f~~~~~ 653 (862)
T PRK08173 596 EIAQMTQQIVKRAK--------EYDSDTIP----GDYATLQTPCPNCGGV-VKEN------YRRFACTK---CDFSISKI 653 (862)
T ss_pred HHHHHHHHHHHHHH--------hhhhcccc----cccccccccCCccccc-cccc------CceeEcCC---CCcccchh
Confidence 88877665443321 10000000 0001124789999974 3211 12699998 99987532
Q ss_pred C-CCCchhhhhhhc-cCCCCCcccCCCCCccceeeeccCCCcceEEeCCCCCCCCCccccCCCCCCccccCHHHHHHHhc
Q 001106 1003 Y-GDDDEEDTLQRN-TNVDEPKLIGHHPASKEKVLLKSGPYGFYVQLGEDRTGYLPKRASVSHIKDVDSITLEDALELLR 1080 (1157)
Q Consensus 1003 ~-~~~~~~e~~~~~-~~~~~Pr~LG~cPkcGk~V~lK~GrfG~yv~c~~d~kg~~~k~~slpk~~~~~sItLe~Al~ll~ 1080 (1157)
. +...+....... .......+.|+..+.| ..|...+....+..+++..+ ..+...+-.. .++....
T Consensus 654 ~~gk~~~~~~~~~Ll~~~~t~~~~gf~sk~g-------~~f~a~l~l~~~~~~~~~~f-~f~~~~~~~~---~~~~~~~- 721 (862)
T PRK08173 654 PGGRQFEIAEVEELLRKKEIGPLSGFRSKMG-------RPFSAILKLSDETKNYKLEF-DFGQDQGGED---GEPVDFS- 721 (862)
T ss_pred hccccCcHHHHHHHHhCCCcceeccccccCC-------CccceEEEecccCCCceEEE-ecCCcccccc---ccccccc-
Confidence 2 222222111110 0111111223332222 13555555441101111111 1111000000 0011111
Q ss_pred CCcccCCCCCCCcCeEEeeccCcceeec-----CCeeeecCCCCCCCCCCHHHHHHHhcccccc
Q 001106 1081 YPVNLGNHPKDGQPIMLRLARAGFSVRH-----RRTIASVPKNMKPNDVTLEKALEFLSGKDVR 1139 (1157)
Q Consensus 1081 ~pk~lG~cP~cG~~v~v~~GryG~yi~~-----~~~~~~ipk~~~~~~itle~A~~LL~~k~~k 1139 (1157)
....+|.||.||+.|+. .++ +++|.. ..|.+.+++.+....++.+++.+||..++..
T Consensus 722 ~~~~~g~CPkCg~~v~e-~~k-~y~Cs~~~~~~~~C~f~i~k~i~gK~it~~~~kkLL~~Gkt~ 783 (862)
T PRK08173 722 AQEPVGACPKCGGRVFE-HGM-SYVCEKSVGPPKTCDFRSGKVILQQEISREQMAKLLADGKTD 783 (862)
T ss_pred ccccccCCCCCCCeeEe-ece-EEEeCCCcCCCCCCCeeeCceecCccCCHHHHHHHHHcCCcc
Confidence 11246899999998764 333 233443 3466778776666779999999999765543
No 14
>PRK14724 DNA topoisomerase III; Provisional
Probab=100.00 E-value=3.8e-129 Score=1222.15 Aligned_cols=726 Identities=22% Similarity=0.269 Sum_probs=538.7
Q ss_pred CeEEEEecchHHHHHHhhc---------------CCCEEEEEeccccccccccCC------CCCCCCCCc---ceE--ec
Q 001106 349 KSVVVVESVTKAKVIQGYL---------------GDMYEVLPSYGHVRDLAARSG------SVRPDDDFS---MVW--EV 402 (1157)
Q Consensus 349 k~LiIaEkPskAk~Ia~~L---------------G~~y~V~~s~GHl~dL~~~~~------~v~p~~~f~---~~~--~v 402 (1157)
+.||||||||+|++|+++| |++|+|+||+|||++|+.|+. .|..+ +++ ..| .+
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 221 124 35
Q ss_pred ccchHHHHHHHHHHhc--cCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhccccc
Q 001106 403 PSAAWTHLKSIKVALS--GAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAAREID 480 (1157)
Q Consensus 403 ~~~kk~~lk~Lk~l~k--~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fsslT~~aI~~A~~nlr~~d 480 (1157)
.+.+++||+.|++|++ ++|+||||||||||||+|+|+|+++++... .+.++||+|||||+||+++|++||+||++++
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 5668899999999995 567999999999999999999999985310 0124799999999999999999999999988
Q ss_pred --HhHHHHHHHHHHHhHhhhhhccHHHHhhC---CC--ccccCcchhHHHHHHHhHHHHHHhcCCcceEEEEEEEecCcC
Q 001106 481 --ANLVQAYLARRALDYLIGFNISPLLWRKL---PG--CQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKES 553 (1157)
Q Consensus 481 --~~L~~A~~AR~~lD~LiG~nlSR~lt~k~---~~--~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~ 553 (1157)
.+|++||+||+++|||||||+||++|... ++ ++|+||||||||+|||+||+||++|+|++||.|.+.|...
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 CCCCCceeeeeeccccccc------ccccccCCHHHHHHHHHHHccCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHHc
Q 001106 554 HSLDTFSFPAHLTHFQSKR------LNQLSIGSHTEAKDIEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKL 627 (1157)
Q Consensus 554 ~~~~g~~f~a~l~~~~~~~------~~~~~i~d~e~Ae~i~~~l~~~~~~V~~v~~k~~~~~PP~Pf~ts~LQ~~Askkl 627 (1157)
+..|.++|.....++ ....+++++++|+++++.+++..++|.+ +.+++++.||+||+|++||++||++|
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 235777664211111 1235789999999999999888899998 89999999999999999999999999
Q ss_pred CCCHHHHHHHHHHHhhcccCCCCCceEEEEEEccCCcCCCHHHHHHHHHHHHHHhC---------------CCCCCCCCC
Q 001106 628 NFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFERYG---------------SHHAPEEGP 692 (1157)
Q Consensus 628 G~Sa~~Tm~iAQ~LYE~~k~~~~~~~GlITYPRTDS~~Ls~~~~~~i~~~i~~~~g---------------~~~~~~~~~ 692 (1157)
||||++||+|||+|||+| ||||||||||+|||+++++.++++|...-. ..+.. ...
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 699999999999999998888887754211 11111 111
Q ss_pred CccccccccccccCCCCCCCcccCChhhhhCCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEEEEEecCccEEEEEEEEE
Q 001106 693 RKYFKKVKNAQEAHEAIRPTDIRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGNADESIVFRSSCSR 772 (1157)
Q Consensus 693 r~~~~k~k~~q~AH~AI~PT~~~~~p~~l~~~Ls~dE~klY~LI~rRfLAs~~~~a~~e~t~v~i~~~~~~~~F~asg~~ 772 (1157)
+ +++..+ .+||||||||.. .| ..|+++|++||+||||||||+||+||+|+.|+|.+.+++ +.|+++|++
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 222221 479999999985 34 359999999999999999999999999999999998864 489999999
Q ss_pred EEEcCceecccccchhhhccccccchhhhhHHHhccCCCCCCeEEeeeEEeeecccCCCCCCCHHHHHHHHH--------
Q 001106 773 VEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSEGSLVKKLE-------- 844 (1157)
Q Consensus 773 i~~~Gw~~vy~~~~~~~~~~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~ME-------- 844 (1157)
++++||++||...... +.++.+++ +....||.|++||.+.+.++.+.+++|+||+||||++||++||
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 --------hcCCCCCCchHHHHHhccccceEEEcCceeecccchhhhhhhhhcc-cccccChhhhHHHHHHhhhHhhcCc
Q 001106 845 --------ELGIGRPSTYASTLKVLQDRNYVTVKSRILYPEFRGRMVSAFLSHY-FSEVTDYSFTADMETELDNVSAGLT 915 (1157)
Q Consensus 845 --------k~GIGTpATrA~IIe~L~~R~YV~~k~k~L~PT~lG~~vi~~L~~~-f~~l~~p~~TA~~E~~Ld~Ia~G~~ 915 (1157)
+.|||||||||+||++|++|+||+++++.|+||++|+.|+++|+.. |++|++|+|||.||..|++|++|++
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 cHHHHHHHHHHHhhhhhhhccchhHHHHHHHHHhhhCCCccCCCCCCCCCCCCCCCceEEEEecccCceeEEecCCC---
Q 001106 916 EWKGLLVDYWSRFSSYCTCAQSLHIHQVEKMLEKTFGDSLFASLPNKDRSCPVCGEGTLIFKVSRFGAGYFIGCNQH--- 992 (1157)
Q Consensus 916 ~~~~~l~~F~~~f~~~v~~~~~~~i~~V~k~l~~~~g~~~~~~~~~~~g~CPkCGkg~lv~K~gr~G~~~F~GCsny--- 992 (1157)
++++||+++++.+...+..+. +.....+. .......+.||+||++ +..+ +.+|+|+++
T Consensus 608 ~~~~fl~~i~~~~~~~v~~~~--------~~~~~~~~----~~~~~~~~~CP~Cg~~-~~~~------~~~~~Cs~~~~~ 668 (987)
T PRK14724 608 SREAFMQQIAAMTEKLVKKAK--------EYDRDTIP----GDYATLSTPCPNCGGV-VKEN------YRRYACTGANGA 668 (987)
T ss_pred CHHHHHHHHHHHHHHHHHHHH--------hccccccc----cccccccccCCccccc-cccc------CceeecCCCcCC
Confidence 999999998887665544321 10000000 0001124789999974 3211 126999995
Q ss_pred -CCCcccccCCC-CCCchhhhhhhc-cCCCCCcccCCCCCccceeeeccCCCcceEEeCCCC--CCCCCccccCCCCCCc
Q 001106 993 -PRCNYIAKTLY-GDDDEEDTLQRN-TNVDEPKLIGHHPASKEKVLLKSGPYGFYVQLGEDR--TGYLPKRASVSHIKDV 1067 (1157)
Q Consensus 993 -P~Ck~t~~~~~-~~~~~~e~~~~~-~~~~~Pr~LG~cPkcGk~V~lK~GrfG~yv~c~~d~--kg~~~k~~slpk~~~~ 1067 (1157)
+.|+|+.|... +...+....... .....+.+.|+..+.| ..|-..+....|. .+++..+ ..+....-
T Consensus 669 ~~~C~f~~~k~~~gk~l~~~~~~~Ll~~g~t~~~~gf~sK~g-------k~f~A~l~l~~d~~~~~~k~~f-~f~~~~~~ 740 (987)
T PRK14724 669 GEGCGFSFTKSPAGRTFETAEAEQLLRDRRIGPLEGFRSKAG-------WPFTAEVVIKRDEEAKNYKLEF-DFGDDKNA 740 (987)
T ss_pred CCCCCcccchhhccccCcHHHHHHHHhCCCcceeccccccCC-------CccCcEEEecccccccCceEEE-ecCCcccc
Confidence 47999875322 222222222110 0111112223322222 1355566654321 1111111 11111000
Q ss_pred cccCHHHHHHHhcCCcccCCCCCCCcCeEEeecc-CcceeecC-------CeeeecCCCCCCCCCCHHHHHHHhcccccc
Q 001106 1068 DSITLEDALELLRYPVNLGNHPKDGQPIMLRLAR-AGFSVRHR-------RTIASVPKNMKPNDVTLEKALEFLSGKDVR 1139 (1157)
Q Consensus 1068 ~sItLe~Al~ll~~pk~lG~cP~cG~~v~v~~Gr-yG~yi~~~-------~~~~~ipk~~~~~~itle~A~~LL~~k~~k 1139 (1157)
.. -.++.... ....+|.||.||+.|+. .|+ |||--+.. .|.+.+++.+....++.+++.+||..+++.
T Consensus 741 ~~--~~~~~~~~-~~~~~g~CPkCg~~v~e-~gk~y~Cs~~~~~~~~~~~~C~f~i~k~i~gK~is~~~~~kLl~~GkT~ 816 (987)
T PRK14724 741 ED--TGEIVDFA-GQESLGPCPKCGAPVFE-HGSNYVCEKSVPTLAQPTPSCTFKSGQVILQQPIEREQMQKLLATGKTD 816 (987)
T ss_pred cc--cccccccc-ccccccCCCCCCCceEe-ecceEEcCCCcccccCCCCCCCceecccccCcCCCHHHHHHHHhcCCcc
Confidence 00 00011111 12357899999988764 444 55532211 455777877766779999999999766543
No 15
>PRK07726 DNA topoisomerase III; Provisional
Probab=100.00 E-value=1.1e-126 Score=1167.68 Aligned_cols=586 Identities=27% Similarity=0.379 Sum_probs=488.5
Q ss_pred CeEEEEecchHHHHHHhhc-----------CCCEEEEEeccccccccccCC------CCCCCCCCc--c---eEecccch
Q 001106 349 KSVVVVESVTKAKVIQGYL-----------GDMYEVLPSYGHVRDLAARSG------SVRPDDDFS--M---VWEVPSAA 406 (1157)
Q Consensus 349 k~LiIaEkPskAk~Ia~~L-----------G~~y~V~~s~GHl~dL~~~~~------~v~p~~~f~--~---~~~v~~~k 406 (1157)
|.|||||||++|++|+++| |++|+|+||+|||++|++|+. .|..+ +++ + .|.+.+++
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 12111 111 1 35566678
Q ss_pred HHHHHHHHHHhccCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhcccc--cHhHH
Q 001106 407 WTHLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAAREI--DANLV 484 (1157)
Q Consensus 407 k~~lk~Lk~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fsslT~~aI~~A~~nlr~~--d~~L~ 484 (1157)
++|++.|++|+++||+||||||||||||+|||||+++++ ++++|+|+|||+||+++|++||+||+++ +++|+
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 HHHHHHHHHhHhhhhhccHHHHhh-----CCCccccCcchhHHHHHHHhHHHHHHhcCCcceEEEEEEEecCcCCCCCCc
Q 001106 485 QAYLARRALDYLIGFNISPLLWRK-----LPGCQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDTF 559 (1157)
Q Consensus 485 ~A~~AR~~lD~LiG~nlSR~lt~k-----~~~~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~g~ 559 (1157)
+||+||+++|||||||+||++|.. +++++|+||||||||+|||+||+||+||+|++||.|.+.+ .. +.
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 34
Q ss_pred eeeeeecccccccccccccCCHHHHHHHHHHHccCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHHcCCCHHHHHHHHH
Q 001106 560 SFPAHLTHFQSKRLNQLSIGSHTEAKDIEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKLAQ 639 (1157)
Q Consensus 560 ~f~a~l~~~~~~~~~~~~i~d~e~Ae~i~~~l~~~~~~V~~v~~k~~~~~PP~Pf~ts~LQ~~AskklG~Sa~~Tm~iAQ 639 (1157)
.|.+.|........+..++.++++|+.+.+.+++..++|.+|+.+++++.||+||+|++||++|+++|||||++||++||
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 57777743211111235789999999999999888899999999999999999999999999999999999999999999
Q ss_pred HHhhcccCCCCCceEEEEEEccCCcCCCHHHHHHHHHHHHHHh-CCCCCCC-----C--CCCccccccccccccCCCCCC
Q 001106 640 KLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFERY-GSHHAPE-----E--GPRKYFKKVKNAQEAHEAIRP 711 (1157)
Q Consensus 640 ~LYE~~k~~~~~~~GlITYPRTDS~~Ls~~~~~~i~~~i~~~~-g~~~~~~-----~--~~r~~~~k~k~~q~AH~AI~P 711 (1157)
+|||++ ||||||||||+|||++++++++.+|.... +..|... . ..+++++. ..++|||||||
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 2333320 0 01111111 13689999999
Q ss_pred CcccCChhhhhCCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEEEEEecCccEEEEEEEEEEEEcCceecccccchhhhc
Q 001106 712 TDIRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIR 791 (1157)
Q Consensus 712 T~~~~~p~~l~~~Ls~dE~klY~LI~rRfLAs~~~~a~~e~t~v~i~~~~~~~~F~asg~~i~~~Gw~~vy~~~~~~~~~ 791 (1157)
|+.. |. + +.|+++|++||+||||||||+||+||+|++++|.+.+++ ..|.++|++++++||+.+|+..+.
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 9863 22 1 359999999999999999999999999999999998864 479999999999999999964211
Q ss_pred cccccchhhhhHHHhccCCCCCCeEEeeeEEeeecccCCCCCCCHHHHHHHHHhc-----------------CCCCCCch
Q 001106 792 YKENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSEGSLVKKLEEL-----------------GIGRPSTY 854 (1157)
Q Consensus 792 ~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk~-----------------GIGTpATr 854 (1157)
+ +++ ...||.|++||.+.+.++.+.+++|+||+||||++||++||+. ||||||||
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 HHHHHhccccceEEEcCceeecccchhhhhhhhhcccccccChhhhHHHHHHhhhHhhcCccHHHHHHHHHHHhhhhhhh
Q 001106 855 ASTLKVLQDRNYVTVKSRILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKGLLVDYWSRFSSYCTC 934 (1157)
Q Consensus 855 A~IIe~L~~R~YV~~k~k~L~PT~lG~~vi~~L~~~f~~l~~p~~TA~~E~~Ld~Ia~G~~~~~~~l~~F~~~f~~~v~~ 934 (1157)
|+||++|++||||+++++.|+||++|++|+++|+. .|++|+|||.||..|++|++|+.++++||+++++.+...+..
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 389999999999999999999999999999999877665433
Q ss_pred ccchhHHHHHHHHHhhhCCCccCCCCCCCCCCCCCCCceEEEEecccCceeEEecCCCCCCc
Q 001106 935 AQSLHIHQVEKMLEKTFGDSLFASLPNKDRSCPVCGEGTLIFKVSRFGAGYFIGCNQHPRCN 996 (1157)
Q Consensus 935 ~~~~~i~~V~k~l~~~~g~~~~~~~~~~~g~CPkCGkg~lv~K~gr~G~~~F~GCsnyP~Ck 996 (1157)
+. ..... .. . .....+.||.||++ ++.+.+++| .||||+|++.|.
T Consensus 596 ~~--------~~~~~-~~---~--~~~~~~~CP~C~~~-~~~~~~~~~--~f~~Cs~~~~~~ 640 (658)
T PRK07726 596 AK--------QSSEK-YK---F--DNLTGPKCPDCGKP-MLKVKGKNG--KMLVCQDRECGK 640 (658)
T ss_pred HH--------hcccc-cc---c--ccCCcccccccCcc-ceeecccCC--eeEecCCCcccc
Confidence 21 10000 00 0 11135789999975 444445555 499999976444
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=1.2e-123 Score=1135.69 Aligned_cols=577 Identities=29% Similarity=0.420 Sum_probs=473.8
Q ss_pred EEecchHHHHHHhhcCC---------------------CEEEEEeccccccccccCC-CCCCCC-CCcceEecc---cch
Q 001106 353 VVESVTKAKVIQGYLGD---------------------MYEVLPSYGHVRDLAARSG-SVRPDD-DFSMVWEVP---SAA 406 (1157)
Q Consensus 353 IaEkPskAk~Ia~~LG~---------------------~y~V~~s~GHl~dL~~~~~-~v~p~~-~f~~~~~v~---~~k 406 (1157)
||||||+|++||++||. +|+|+||+|||++|++|+. .+...+ ++-|.+... ..+
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 79999999999999943 2579999999999987653 221110 122222221 123
Q ss_pred HHHHHHHHHHhccCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhcccccHhHHHH
Q 001106 407 WTHLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAAREIDANLVQA 486 (1157)
Q Consensus 407 k~~lk~Lk~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fsslT~~aI~~A~~nlr~~d~~L~~A 486 (1157)
++|++.|++++++||+||||||||||||+|||||+++++. .++|+|+|||+||+++|++||+|+++.+++|++|
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 HHHHHHHhHhhhhhccHHHHhhCC------CccccCcchhHHHHHHHhHHHHHHhcCCcceEEEEEEEecCcCCCCCCce
Q 001106 487 YLARRALDYLIGFNISPLLWRKLP------GCQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDTFS 560 (1157)
Q Consensus 487 ~~AR~~lD~LiG~nlSR~lt~k~~------~~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~g~~ 560 (1157)
|+||+++|||||||+||++|..++ +++|+||||||||+|||+||+||++|+|++||.|.+.+... +..
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 26999999999999999999999999999999999998642 346
Q ss_pred eeeeecccccccccccccCCHHHHHHHHHHHccC-CeEEEEeeeeeeeecCCCCcchHHHHHHHHHHcCCCHHHHHHHHH
Q 001106 561 FPAHLTHFQSKRLNQLSIGSHTEAKDIEQKINSA-NFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKLAQ 639 (1157)
Q Consensus 561 f~a~l~~~~~~~~~~~~i~d~e~Ae~i~~~l~~~-~~~V~~v~~k~~~~~PP~Pf~ts~LQ~~AskklG~Sa~~Tm~iAQ 639 (1157)
|.+.|. ..+++++++|+.+++.+++. .++|++|++++++..||+||||++||++|+++|||||++||++||
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 777662 23688999999999999876 799999999999999999999999999999999999999999999
Q ss_pred HHhhcccCCCCCceEEEEEEccCCcCCCHHHHHHHHHHHHHH-----hCCCCCCC---CCCCccccccccccccCCCCCC
Q 001106 640 KLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFER-----YGSHHAPE---EGPRKYFKKVKNAQEAHEAIRP 711 (1157)
Q Consensus 640 ~LYE~~k~~~~~~~GlITYPRTDS~~Ls~~~~~~i~~~i~~~-----~g~~~~~~---~~~r~~~~k~k~~q~AH~AI~P 711 (1157)
+|||+ ||||||||||+|||+++. +..++... |+. +... ....+.++ .+..++|||||||
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 1233569999999
Q ss_pred CcccCChhhhhCCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEEEEEecCccEEEEEEEEEEEEcCceecccccchhhhc
Q 001106 712 TDIRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIR 791 (1157)
Q Consensus 712 T~~~~~p~~l~~~Ls~dE~klY~LI~rRfLAs~~~~a~~e~t~v~i~~~~~~~~F~asg~~i~~~Gw~~vy~~~~~~~~~ 791 (1157)
|... |+. .|+++|++||+||+|||||+||+||+|++|+|.+.+++ ..|.++|++++++||+++|...+
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 9752 331 49999999999999999999999999999999998754 58999999999999999996421
Q ss_pred cccccchhhhhHHHhccCCCCCCeEEeeeEEeeecccCCCCCCCHHHHHHHHHhcCCCCCCchHHHHHhccccceEEEcC
Q 001106 792 YKENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKS 871 (1157)
Q Consensus 792 ~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk~GIGTpATrA~IIe~L~~R~YV~~k~ 871 (1157)
+ ++ ..||.+++||.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++||||+.+
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 ceeecccchhhhhhhhhcccccccChhhhHHHHHHhhhHhhcCccHHHHHHHHHHHhhhhhhhccchhHHHHHHHHHhhh
Q 001106 872 RILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKGLLVDYWSRFSSYCTCAQSLHIHQVEKMLEKTF 951 (1157)
Q Consensus 872 k~L~PT~lG~~vi~~L~~~f~~l~~p~~TA~~E~~Ld~Ia~G~~~~~~~l~~F~~~f~~~v~~~~~~~i~~V~k~l~~~~ 951 (1157)
++|+||++|+.|+++|+..++.|++|+|||.||..|++|++|+.++++||+++++.+...+..+... ...+...+...+
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 6699999999999999998889999999999999999999999999999999999887766554221 111111111101
Q ss_pred CCCccCCCCCCCCCCCCCCCceEEEEecccCceeEEecCCCCCC
Q 001106 952 GDSLFASLPNKDRSCPVCGEGTLIFKVSRFGAGYFIGCNQHPRC 995 (1157)
Q Consensus 952 g~~~~~~~~~~~g~CPkCGkg~lv~K~gr~G~~~F~GCsnyP~C 995 (1157)
. .....+.||+||++ ++.+.+++| .||||++||+|
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=2.5e-119 Score=1095.57 Aligned_cols=572 Identities=28% Similarity=0.398 Sum_probs=468.9
Q ss_pred CeEEEEecchHHHHHHhhcCCC----------------------EEEEEecccccccccc-CC--CC-------CCC---
Q 001106 349 KSVVVVESVTKAKVIQGYLGDM----------------------YEVLPSYGHVRDLAAR-SG--SV-------RPD--- 393 (1157)
Q Consensus 349 k~LiIaEkPskAk~Ia~~LG~~----------------------y~V~~s~GHl~dL~~~-~~--~v-------~p~--- 393 (1157)
..|||||||+|.-++.+.|.+. .+-.++-||++.|.+- |. .. .++
T Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 89 (805)
T PTZ00407 10 EKLVIVESPNKVIKVEGLLSDPKVIPDWSFKQSHLRRIGTGAEKAVAMATTGHFMALKEITWSPQASSPASVVGAGDEPF 89 (805)
T ss_pred hheeEEecCCceEEEeecccCCCcCCCcccccccceeeccchHHHHHHhhcccceeehheecccCCCCCcccCCCCCCCC
Confidence 5699999999999999888641 2346788999998762 10 00 011
Q ss_pred ------CCCcceEecccchH--HHHH-HHHHHhccCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEccc
Q 001106 394 ------DDFSMVWEVPSAAW--THLK-SIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEI 464 (1157)
Q Consensus 394 ------~~f~~~~~v~~~kk--~~lk-~Lk~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fssl 464 (1157)
-.|.|.|++.+.++ +++. .|++++++||+||||||||||||+|+|||+++|+... ...+++|+|+|||+|
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 13567899887776 6777 6999999999999999999999999999999997531 124579999999999
Q ss_pred CHHHHHHHHHh--cccccHhHHHHHHHHHHHhHhhhhhccHHHHhhCCCccccCcchhHHHHHHHhHHHHHHhcCCc--c
Q 001106 465 TEASIKVALQA--AREIDANLVQAYLARRALDYLIGFNISPLLWRKLPGCQSAGRVQSAALSLICDREMEIDEFKPQ--E 540 (1157)
Q Consensus 465 T~~aI~~A~~n--lr~~d~~L~~A~~AR~~lD~LiG~nlSR~lt~k~~~~lS~GRVQTPtL~LVveRe~EI~~Fkp~--~ 540 (1157)
|+++|++||+| ++++|++|++||+|||++|||||||+||++|++.++.+|+||||||||+|||+||+||++|+|+ +
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 5788999999999999999999999999999988788999999999999999999999999999 5
Q ss_pred eEEEEEEEecCcCCCCCCceeeeeecccccccccccccCCHHHHHHHHHHHc--c-CCeEEE-EeeeeeeeecCCCCcch
Q 001106 541 YWTVEAVLDKKESHSLDTFSFPAHLTHFQSKRLNQLSIGSHTEAKDIEQKIN--S-ANFQVI-KNSKRSMVRKNPTPYIT 616 (1157)
Q Consensus 541 Yw~I~a~~~~~~~~~~~g~~f~a~l~~~~~~~~~~~~i~d~e~Ae~i~~~l~--~-~~~~V~-~v~~k~~~~~PP~Pf~t 616 (1157)
||.|.+.+... ...|..|.+.|....+.+.++.++.++++|+++++.++ + ..+.|. .++.++++++||+||+|
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 11245687776533332233456789999999988764 2 346664 45678999999999999
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHhhcccCCCCCceEEEEEEccCCcCCCHHHHHHHHHHHHHHhCCCCC---------
Q 001106 617 STLQQDAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFERYGSHHA--------- 687 (1157)
Q Consensus 617 s~LQ~~AskklG~Sa~~Tm~iAQ~LYE~~k~~~~~~~GlITYPRTDS~~Ls~~~~~~i~~~i~~~~g~~~~--------- 687 (1157)
++||++||++|||||++||++||+|||+ ||||||||||++||++++.++++.|...||.+|.
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 9999999999999999999999999887887655
Q ss_pred -CCCCCCccc-------cc-------cccccccCCCCCCCcccCChhhhhCCCCHHHHHHHHHHHHHHHHccCCCcEEEE
Q 001106 688 -PEEGPRKYF-------KK-------VKNAQEAHEAIRPTDIRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQ 752 (1157)
Q Consensus 688 -~~~~~r~~~-------~k-------~k~~q~AH~AI~PT~~~~~p~~l~~~Ls~dE~klY~LI~rRfLAs~~~~a~~e~ 752 (1157)
+ ..++.+. +. .++.|+||||||||+....|+.+ .|+++|++||+||||||||+||+||+|++
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 1221111 01 12557799999999875545422 49999999999999999999999999999
Q ss_pred EEEEEEec---CccEEEEEEEEEEEEcCceecccccchhhhc--cccccchh-hhhHHHhccCCCCCC------------
Q 001106 753 IQVDIGNA---DESIVFRSSCSRVEFLGFQAAYEDVDAGAIR--YKENEEND-RHEAFAILNSLKTGD------------ 814 (1157)
Q Consensus 753 t~v~i~~~---~~~~~F~asg~~i~~~Gw~~vy~~~~~~~~~--~~e~~e~~-~~~~~~~LP~l~~Gd------------ 814 (1157)
++|++.+. ++.+.|+++|++++++||++||.+....... .+++++.. .++....||.|++||
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 ------eEEeeeEEeeecccCCCCCCCHHHHHHHHHhcCCCCCCchHHHHHhccccceEEEc-Cceeecccchhhhhhhh
Q 001106 815 ------PLYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVK-SRILYPEFRGRMVSAFL 887 (1157)
Q Consensus 815 ------~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk~GIGTpATrA~IIe~L~~R~YV~~k-~k~L~PT~lG~~vi~~L 887 (1157)
.+.+.++.+.+++|+||+|||||+||++||++|||||||||+||++|++||||.++ ++.|+||++|+.|+++|
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 hcccccccChhhhHHHHHHhhhHhhcCccHH-------------HHHHHHHHHhhhhhhhcc
Q 001106 888 SHYFSEVTDYSFTADMETELDNVSAGLTEWK-------------GLLVDYWSRFSSYCTCAQ 936 (1157)
Q Consensus 888 ~~~f~~l~~p~~TA~~E~~Ld~Ia~G~~~~~-------------~~l~~F~~~f~~~v~~~~ 936 (1157)
+.+|++|++|+|||.||.+||+|++|+.+|+ .+|+.||..|..++.++.
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 689999999999887654
No 18
>PRK09401 reverse gyrase; Reviewed
Probab=100.00 E-value=1.6e-110 Score=1069.00 Aligned_cols=511 Identities=32% Similarity=0.451 Sum_probs=443.1
Q ss_pred CCCeEEEEecchHHHHHHhhcCCC----------E---------EEEEeccccccccccCC--CCCCCCC-CcceEecc-
Q 001106 347 SGKSVVVVESVTKAKVIQGYLGDM----------Y---------EVLPSYGHVRDLAARSG--SVRPDDD-FSMVWEVP- 403 (1157)
Q Consensus 347 ~~k~LiIaEkPskAk~Ia~~LG~~----------y---------~V~~s~GHl~dL~~~~~--~v~p~~~-f~~~~~v~- 403 (1157)
+.+.|||||||+|||+||++||.. | +|+||.|||++|+.+++ +|..++. |.|.|.+.
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 347999999999999999999753 3 69999999999997653 4544322 55544422
Q ss_pred ------------------------cchHHHHHHHHHHhccCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEE
Q 001106 404 ------------------------SAAWTHLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARV 459 (1157)
Q Consensus 404 ------------------------~~kk~~lk~Lk~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl 459 (1157)
++++++++.|++++++||+||||||||||||+|||+|+++++. .+++|+|+
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 5678999999999999999999999999999999999999863 34689999
Q ss_pred EEcccCHHHHHHHHHhcccccHhHHHHHHHHHHHhHhhhhhccHHHHhhCC-CccccCcchhHHHHHHHhHHHHHHhcCC
Q 001106 460 VFHEITEASIKVALQAAREIDANLVQAYLARRALDYLIGFNISPLLWRKLP-GCQSAGRVQSAALSLICDREMEIDEFKP 538 (1157)
Q Consensus 460 ~fsslT~~aI~~A~~nlr~~d~~L~~A~~AR~~lD~LiG~nlSR~lt~k~~-~~lS~GRVQTPtL~LVveRe~EI~~Fkp 538 (1157)
|||++|+++|++||+|++++|.||++||+|||++||+||||+||+||.+++ ..+|+||||||||+|||+||+||++|++
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 cceEEEEEEEecCcCCCCCCceeeeeecccccccccccccCCHHHHHHHHHHHccCCeEEEEeeeeeeeecCCCCcchHH
Q 001106 539 QEYWTVEAVLDKKESHSLDTFSFPAHLTHFQSKRLNQLSIGSHTEAKDIEQKINSANFQVIKNSKRSMVRKNPTPYITST 618 (1157)
Q Consensus 539 ~~Yw~I~a~~~~~~~~~~~g~~f~a~l~~~~~~~~~~~~i~d~e~Ae~i~~~l~~~~~~V~~v~~k~~~~~PP~Pf~ts~ 618 (1157)
||.+ .... ++..|.+.+ ++.++++|+.+.+.++ +|.+|+.++++++||+||+|++
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 123454432 4568889999888875 8899999999999999999999
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHHhhcccCCCCCceEEEEEEccCCcCCCHHHHHHHHHHHHHHhCCCCCCCCCCCccccc
Q 001106 619 LQQDAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFERYGSHHAPEEGPRKYFKK 698 (1157)
Q Consensus 619 LQ~~AskklG~Sa~~Tm~iAQ~LYE~~k~~~~~~~GlITYPRTDS~~Ls~~~~~~i~~~i~~~~g~~~~~~~~~r~~~~k 698 (1157)
||++||++|||||++||++||+|||+ ||||||||||+|||++.+..++.++...++..+. .+|.|
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 9999999999999999999999999887775442 35555
Q ss_pred cccccccCCCCCCCcccCChhhh-----------hCCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEEEEEecCccEEEE
Q 001106 699 VKNAQEAHEAIRPTDIRRLPAML-----------SGLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGNADESIVFR 767 (1157)
Q Consensus 699 ~k~~q~AH~AI~PT~~~~~p~~l-----------~~~Ls~dE~klY~LI~rRfLAs~~~~a~~e~t~v~i~~~~~~~~F~ 767 (1157)
++++||||||||.... ++.+ ...|+.+|++||+||+|||||+||+||+|++++|.+.+++ ..|.
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 5799
Q ss_pred EE-EEEEEEcCceecccccchhhhccccccchhhhhHHHhccCCCCCCeEEeeeEEeeecccCCCCCCCHHHHHHHHHhc
Q 001106 768 SS-CSRVEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSEGSLVKKLEEL 846 (1157)
Q Consensus 768 as-g~~i~~~Gw~~vy~~~~~~~~~~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk~ 846 (1157)
++ |++++++||+++|+.. .+|.++.|+.+.+ +..+.|.||+|||||+||++||+.
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 9999999999999531 3788999998874 555556669999999999999999
Q ss_pred CCCCCCchHHHHHhccccceEEEcC--ceeecccchhhhhhhhhcccccccChhhhHHHHHHhhhHhhcCccHHHHHHHH
Q 001106 847 GIGRPSTYASTLKVLQDRNYVTVKS--RILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKGLLVDY 924 (1157)
Q Consensus 847 GIGTpATrA~IIe~L~~R~YV~~k~--k~L~PT~lG~~vi~~L~~~f~~l~~p~~TA~~E~~Ld~Ia~G~~~~~~~l~~F 924 (1157)
|||||||||+||++|++||||..++ +.|+||++|+.|+++|...|+.|++|+|||.||+.||+|++|+.++++||+++
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 001106 925 WSRFSSY 931 (1157)
Q Consensus 925 ~~~f~~~ 931 (1157)
++.+...
T Consensus 1166 ~~~i~~~ 1172 (1176)
T PRK09401 1166 YEEIKEL 1172 (1176)
T ss_pred HHHHHHH
Confidence 9877654
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=1.6e-109 Score=1060.91 Aligned_cols=515 Identities=31% Similarity=0.468 Sum_probs=445.1
Q ss_pred CCCCCCeEEEEecchHHHHHHhhcCCC----------E---------EEEEeccccccccccC--CCCCCCCC-CcceEe
Q 001106 344 YPPSGKSVVVVESVTKAKVIQGYLGDM----------Y---------EVLPSYGHVRDLAARS--GSVRPDDD-FSMVWE 401 (1157)
Q Consensus 344 ~~~~~k~LiIaEkPskAk~Ia~~LG~~----------y---------~V~~s~GHl~dL~~~~--~~v~p~~~-f~~~~~ 401 (1157)
...+...|||||||+|||+||++||.. | +|+||.|||+||+.++ .+|+.++. |.|.|.
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 444568999999999999999999863 4 6999999999998764 24544322 555432
Q ss_pred c-------------------------ccchHHHHHHHHHHhccCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccE
Q 001106 402 V-------------------------PSAAWTHLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITV 456 (1157)
Q Consensus 402 v-------------------------~~~kk~~lk~Lk~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~v 456 (1157)
. .++++++++.|++++++||+||||||||||||+|||||+++++. ++++|
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 1 14578999999999999999999999999999999999999853 45689
Q ss_pred EEEEEcccCHHHHHHHHHhcccccHhHHHHHHHHHHHhHhhhhhccHHHHhhCCC-ccccCcchhHHHHHHHhHHHHHHh
Q 001106 457 ARVVFHEITEASIKVALQAAREIDANLVQAYLARRALDYLIGFNISPLLWRKLPG-CQSAGRVQSAALSLICDREMEIDE 535 (1157)
Q Consensus 457 kRl~fsslT~~aI~~A~~nlr~~d~~L~~A~~AR~~lD~LiG~nlSR~lt~k~~~-~lS~GRVQTPtL~LVveRe~EI~~ 535 (1157)
+|+|||++|+++|++||+|++++|++|++||+|||++|||||||+||++|+++++ .+|+||||||||+|||+||+||++
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 699999999999999999999999
Q ss_pred cCCcceEEEEEEEecCcCCCCCCceeeeeecccccccccccccCCHHHHHHHHHHHccCCeEEEEeeeeeeeecCCCCcc
Q 001106 536 FKPQEYWTVEAVLDKKESHSLDTFSFPAHLTHFQSKRLNQLSIGSHTEAKDIEQKINSANFQVIKNSKRSMVRKNPTPYI 615 (1157)
Q Consensus 536 Fkp~~Yw~I~a~~~~~~~~~~~g~~f~a~l~~~~~~~~~~~~i~d~e~Ae~i~~~l~~~~~~V~~v~~k~~~~~PP~Pf~ 615 (1157)
|+ +||.|.+... +..+.. .+.++++|+++.+.+. .+.|.+|+.++++++||+||+
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 hHHHHHHHHHHcCCCHHHHHHHHHHHhhcccCCCCCceEEEEEEccCCcCCCHHHHHHHHHHHHHHhCCCCCCCCCCCcc
Q 001106 616 TSTLQQDAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFERYGSHHAPEEGPRKY 695 (1157)
Q Consensus 616 ts~LQ~~AskklG~Sa~~Tm~iAQ~LYE~~k~~~~~~~GlITYPRTDS~~Ls~~~~~~i~~~i~~~~g~~~~~~~~~r~~ 695 (1157)
|++||++||++|||||++||++||+|||+ ||||||||||++||++.+..++++|...+|..|. .+|.|
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 9999999999999999999999999887776553 24544
Q ss_pred ccccccccccCCCCCCCcccCChhhhh----------CCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEEEEEecCccEE
Q 001106 696 FKKVKNAQEAHEAIRPTDIRRLPAMLS----------GLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGNADESIV 765 (1157)
Q Consensus 696 ~~k~k~~q~AH~AI~PT~~~~~p~~l~----------~~Ls~dE~klY~LI~rRfLAs~~~~a~~e~t~v~i~~~~~~~~ 765 (1157)
++++||||||||... .|+.+. ..|+.+|++||+||||||||+||+||+|++++|.+.+++ ...
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 236899999999853 343221 248999999999999999999999999999999998854 358
Q ss_pred EEEEEEEEEEcCceecccccchhhhccccccchhhhhHHHhccCCCCCCeEEeeeEEeeecccCCCCCCCHHHHHHHHHh
Q 001106 766 FRSSCSRVEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSEGSLVKKLEE 845 (1157)
Q Consensus 766 F~asg~~i~~~Gw~~vy~~~~~~~~~~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk 845 (1157)
|.++|++++++||+++|+... ++.+.+||.+.+.++.+.++. ||+||||++||++||+
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 234678999988777777765 4459999999999999
Q ss_pred cCCCCCCchHHHHHhccccceEEEcCceeecccchhhhhhhhhcccccccChhhhHHHHHHhhhHhhcCccHHHHHHHHH
Q 001106 846 LGIGRPSTYASTLKVLQDRNYVTVKSRILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKGLLVDYW 925 (1157)
Q Consensus 846 ~GIGTpATrA~IIe~L~~R~YV~~k~k~L~PT~lG~~vi~~L~~~f~~l~~p~~TA~~E~~Ld~Ia~G~~~~~~~l~~F~ 925 (1157)
.|||||||||+||++|++|+||..+++.|+||++|+.|+++|+..|+.|++|+|||.||+.||+|++|+.++++||++++
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 99999999999999999999999888999999999999999999999999999999999999999999999999999988
Q ss_pred HHhh
Q 001106 926 SRFS 929 (1157)
Q Consensus 926 ~~f~ 929 (1157)
+.+.
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=8.1e-102 Score=888.79 Aligned_cols=692 Identities=31% Similarity=0.423 Sum_probs=554.9
Q ss_pred CeEEEEecchHHHHHHhhcCC---------------------------CEEEEEeccccccccccCC-----CCCCCCCC
Q 001106 349 KSVVVVESVTKAKVIQGYLGD---------------------------MYEVLPSYGHVRDLAARSG-----SVRPDDDF 396 (1157)
Q Consensus 349 k~LiIaEkPskAk~Ia~~LG~---------------------------~y~V~~s~GHl~dL~~~~~-----~v~p~~~f 396 (1157)
+.|.++||++.||.++.+|+. +.++++..||+..+..+.+ ...+.+.|
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 1367999999999987543 22333334
Q ss_pred cc-eE-ecccchHHHHHHHHHHhccCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHH
Q 001106 397 SM-VW-EVPSAAWTHLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQ 474 (1157)
Q Consensus 397 ~~-~~-~v~~~kk~~lk~Lk~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fsslT~~aI~~A~~ 474 (1157)
.. .+ .++...+.+.+.|++++++||.+|||||||||||+|||||.++|+.. +....|.|++||+||+.+|+.|++
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 hcccccHhHHHHHHHHHHHhHhhhhhccHH----HHhhCC----CccccCcchhHHHHHHHhHHHHHHhcCCcceEEEEE
Q 001106 475 AAREIDANLVQAYLARRALDYLIGFNISPL----LWRKLP----GCQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEA 546 (1157)
Q Consensus 475 nlr~~d~~L~~A~~AR~~lD~LiG~nlSR~----lt~k~~----~~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a 546 (1157)
||+++|+.+++|+.||+++|++||..|||+ ||++++ +++|+|+||.|||+|||||+.||++|+|+.||+|.+
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 466676 799999999999999999999999999999999998
Q ss_pred EEecCcCCCCCCceeeeeecccccccccccccCCHHHHHHHHHHHc-cCCeEEEEeeeeeeeecCCCCcchHHHHHHHHH
Q 001106 547 VLDKKESHSLDTFSFPAHLTHFQSKRLNQLSIGSHTEAKDIEQKIN-SANFQVIKNSKRSMVRKNPTPYITSTLQQDAAN 625 (1157)
Q Consensus 547 ~~~~~~~~~~~g~~f~a~l~~~~~~~~~~~~i~d~e~Ae~i~~~l~-~~~~~V~~v~~k~~~~~PP~Pf~ts~LQ~~Ask 625 (1157)
...... ...+|. +++ ..+.|..-+--+.+.|. ...+.|+++.+++++++||+||+|.+||+.|++
T Consensus 239 ~~~~~~----~~~~fn-------w~R---~~lfdr~s~~~~~e~c~e~k~a~Vv~~~kkpktKyrP~pl~TvELqK~~s~ 304 (758)
T KOG1956|consen 239 KHTHKG----GLTEFN-------WKR---GHLFDRLSVVILYEICVEEKEATVVKVTKKPKTKYRPLPLDTVELQKLASR 304 (758)
T ss_pred EEeccC----ceeEEe-------ecc---cccccHHHHHHHHHHHhcccceeEEecccCCccCCCCCcchHHHHHhhhhh
Confidence 775321 112333 222 34456555555555554 357899999999999999999999999999999
Q ss_pred HcCCCHHHHHHHHHHHhhcccCCCCCceEEEEEEccCCcCCCHHHHHHHHHHHHH-----HhCCCCCCC-CCCC-ccccc
Q 001106 626 KLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFE-----RYGSHHAPE-EGPR-KYFKK 698 (1157)
Q Consensus 626 klG~Sa~~Tm~iAQ~LYE~~k~~~~~~~GlITYPRTDS~~Ls~~~~~~i~~~i~~-----~~g~~~~~~-~~~r-~~~~k 698 (1157)
+|.||+++||+||++||.+ |+||||||+...++.++ +++.++.. .||. |+.. ..+. +.+++
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 99999999999998875 34444432 2332 2211 1122 34556
Q ss_pred cccccccCCCCCCCcccCChhhhhCCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEEEEEecCccEEEEEEEEEEEEcCc
Q 001106 699 VKNAQEAHEAIRPTDIRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGNADESIVFRSSCSRVEFLGF 778 (1157)
Q Consensus 699 ~k~~q~AH~AI~PT~~~~~p~~l~~~Ls~dE~klY~LI~rRfLAs~~~~a~~e~t~v~i~~~~~~~~F~asg~~i~~~Gw 778 (1157)
+++.+.||++|+||... .++ ..|+.|+++||++|+||||||.+.+|.-..|+|+++.+.+ .|.++|-.+++.+|
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 eecccccchhhhccccccchhhhhHHHhccCCCCCCeEEeeeEEeeecccCCCCCCCHHHHHHHHHhcCCCCCCchHHHH
Q 001106 779 QAAYEDVDAGAIRYKENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTL 858 (1157)
Q Consensus 779 ~~vy~~~~~~~~~~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk~GIGTpATrA~II 858 (1157)
+.||+++.. + +..||.++.|+.+.+..+++.++.|+||++|||++||..|+++||||+||+|+||
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 999987532 1 2579999999999999999999999999999999999999999999999999999
Q ss_pred HhccccceEEEcCc--eeecccchhhhhhhhhcccccccChhhhHHHHHHhhhHhhcCccHHHHHHHHHHHhhhhhhhcc
Q 001106 859 KVLQDRNYVTVKSR--ILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKGLLVDYWSRFSSYCTCAQ 936 (1157)
Q Consensus 859 e~L~~R~YV~~k~k--~L~PT~lG~~vi~~L~~~f~~l~~p~~TA~~E~~Ld~Ia~G~~~~~~~l~~F~~~f~~~v~~~~ 936 (1157)
++|++|+||.++++ +|+||.+|.+|++.+.+++-++.+|++||+||.+|++|+.|+.+|.++|.+.+..|..++-..+
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 99999999988543 5779999999999999998899999999999999999999999999999999999998765432
Q ss_pred chhHHHHHHHHHhhhCCCccCCCCCCCCCCCCCCCceEEEEecccCceeEEecCCCCCCcccccCCCCCCchhhhhhhcc
Q 001106 937 SLHIHQVEKMLEKTFGDSLFASLPNKDRSCPVCGEGTLIFKVSRFGAGYFIGCNQHPRCNYIAKTLYGDDDEEDTLQRNT 1016 (1157)
Q Consensus 937 ~~~i~~V~k~l~~~~g~~~~~~~~~~~g~CPkCGkg~lv~K~gr~G~~~F~GCsnyP~Ck~t~~~~~~~~~~~e~~~~~~ 1016 (1157)
.. .....+.+...+... .... .|..+ |.
T Consensus 592 ~~-~~~l~~~l~~y~~~~-----a~~~--------------~~~~~----------p~---------------------- 619 (758)
T KOG1956|consen 592 RK-IGCLGESLQRYLEFI-----ASTL--------------TGPDD----------PE---------------------- 619 (758)
T ss_pred HH-HHHHHHHHHHHHhhc-----cccc--------------cCCCC----------CC----------------------
Confidence 11 122222222111100 0000 00000 00
Q ss_pred CCCCCcccCCCCCccceeeeccCCCcceEEeCCCCCCCCCccccCCCCCCccccCHHHHHHHhcCCcccCCCCCCCcCeE
Q 001106 1017 NVDEPKLIGHHPASKEKVLLKSGPYGFYVQLGEDRTGYLPKRASVSHIKDVDSITLEDALELLRYPVNLGNHPKDGQPIM 1096 (1157)
Q Consensus 1017 ~~~~Pr~LG~cPkcGk~V~lK~GrfG~yv~c~~d~kg~~~k~~slpk~~~~~sItLe~Al~ll~~pk~lG~cP~cG~~v~ 1096 (1157)
..|..+|-.+.++.+|-.+-|+++.|...+.+.+|..|+.++-....+...+++..++.++..+...+ ||+-|.++.
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 12233344445555565666788999998877677666766655566777899999999999999988 999998899
Q ss_pred EeeccCcceeecCCeeeecCCCCCCCCCCHHHHHHHhcccccccCCCCCCC
Q 001106 1097 LRLARAGFSVRHRRTIASVPKNMKPNDVTLEKALEFLSGKDVRRCGRPKGK 1147 (1157)
Q Consensus 1097 v~~GryG~yi~~~~~~~~ipk~~~~~~itle~A~~LL~~k~~k~~gr~~~~ 1147 (1157)
....+-|.++++.+....-+++......+ +|..|+.++...+.||++-+
T Consensus 697 ~~psk~~a~~~~~p~~a~~~~~~~c~c~~--ra~~l~v~k~~~nrGR~f~s 745 (758)
T KOG1956|consen 697 LKPSKSGATIKSRPTAATEEEEVTCGCGT--RAVKLLVAKTEPNRGRKFYS 745 (758)
T ss_pred CCcccccccccCCccccCCCcccccCCcc--hhhhhhhhccCccCCCCCcc
Confidence 89999999999999888877776555555 89999999888888997764
No 21
>PRK14701 reverse gyrase; Provisional
Probab=100.00 E-value=1.1e-95 Score=948.89 Aligned_cols=516 Identities=30% Similarity=0.431 Sum_probs=433.5
Q ss_pred CCCCCeEEEEecchHHHHHHhhcCCC-------------------EEEEEeccccccccccCC--CCCCCC-CCcceE--
Q 001106 345 PPSGKSVVVVESVTKAKVIQGYLGDM-------------------YEVLPSYGHVRDLAARSG--SVRPDD-DFSMVW-- 400 (1157)
Q Consensus 345 ~~~~k~LiIaEkPskAk~Ia~~LG~~-------------------y~V~~s~GHl~dL~~~~~--~v~p~~-~f~~~~-- 400 (1157)
..+.+.|||||||++||+|+++||.. |+|+||.|||++|+.+++ +|...+ .|.|.|
T Consensus 577 ~~~~~~LiIaEkPs~Ak~IA~~lg~~~~r~~g~~~~ye~~~g~~~~~Vtas~GHl~dL~~~~~~~g~~~~~~~f~P~y~~ 656 (1638)
T PRK14701 577 DLVKSALMIVESPNKARTIANFFGQPSVRKIGDLVAYEVSIGDHMLIITASGGHVFDLVTNEGFHGVLINNNLFIPIYDS 656 (1638)
T ss_pred hhcCCeEEEEeChHHHHHHHHHhCCCccccCCCcceEEEecCCcEEEEEEecceeccCCCccccCccccccCccCCcccc
Confidence 33458999999999999999999742 579999999999986543 232221 133322
Q ss_pred -ec------------------------ccchHHHHHHHHHHhccCCeEEEccCCCccccHHHHHHHHHHhhcccccCCcc
Q 001106 401 -EV------------------------PSAAWTHLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENIT 455 (1157)
Q Consensus 401 -~v------------------------~~~kk~~lk~Lk~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~ 455 (1157)
+. ..+++++++.|++++++||+||||||||||||+|||+|++++. +++++
T Consensus 657 ~k~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~lr~l~~~ad~viiatD~DrEGE~I~~~i~~~~~-----~~~~~ 731 (1638)
T PRK14701 657 IKRCRDCGHQFTDWEDKGVCPRCGSKNVDDAKENIKAMRELAHEVDEILIGTDPDTEGEKIAWDIRNVLA-----PYGPN 731 (1638)
T ss_pred cccCCCchhhccccccccccccccccccccHHHHHHHHHHHHHhCCeEEECCCCChhhHHHHHHHHHHhc-----cCCCC
Confidence 10 1236789999999999999999999999999999999999984 24578
Q ss_pred EEEEEEcccCHHHHHHHHHhcccccHhHHHHHHHHHHHhHhhhhhccHHHHhhCCC-ccccCcchhHHHHHHHhHHHHHH
Q 001106 456 VARVVFHEITEASIKVALQAAREIDANLVQAYLARRALDYLIGFNISPLLWRKLPG-CQSAGRVQSAALSLICDREMEID 534 (1157)
Q Consensus 456 vkRl~fsslT~~aI~~A~~nlr~~d~~L~~A~~AR~~lD~LiG~nlSR~lt~k~~~-~lS~GRVQTPtL~LVveRe~EI~ 534 (1157)
++|+|||++|+++|++||+|++++|++|++||+|||++||+||||+||++|..++. .+|+||||||||+|||+||+||+
T Consensus 732 i~R~~fs~lT~~aI~~A~~nlr~~d~~l~~A~~aRr~~D~~iG~nlSr~l~~~~~~~~lS~GRVQTPtL~~Iv~Re~ei~ 811 (1638)
T PRK14701 732 IKRIEFHEVTRRAILKAIKEARDIDENRVKAQIVRRIEDRWIGFELSQKLWEVFEDRNLSAGRVQTPVLGWIIQRYKEFT 811 (1638)
T ss_pred eeEEEEccCCHHHHHHHHhCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHhccCCceeecccccchhhhhHhhHHHHh
Confidence 99999999999999999999999999999999999999999999999999988764 69999999999999999999999
Q ss_pred hcCCcceEEEEEEEecCcCCCCCCceeeeeecccccccccccccCCHHHHHHHHHHHccCCeEEEEeeeeeeeecCCCCc
Q 001106 535 EFKPQEYWTVEAVLDKKESHSLDTFSFPAHLTHFQSKRLNQLSIGSHTEAKDIEQKINSANFQVIKNSKRSMVRKNPTPY 614 (1157)
Q Consensus 535 ~Fkp~~Yw~I~a~~~~~~~~~~~g~~f~a~l~~~~~~~~~~~~i~d~e~Ae~i~~~l~~~~~~V~~v~~k~~~~~PP~Pf 614 (1157)
+ +|++||.|.+.. + +...+. . ++++ ..+.|.+|+.++++.+||+||
T Consensus 812 ~-~~~~~~~i~~~~---------~--~~~~~~---~---------~~~~----------~~~~V~~v~~k~~~~~pP~pf 857 (1638)
T PRK14701 812 E-SKVPFLGIILEN---------D--LTVTIE---D---------SKDE----------VEVEVELVEEEEKERNPLPPY 857 (1638)
T ss_pred c-CCCceEEEEEcC---------c--eEEEec---c---------cccC----------CeEEEEEEEeeEEEccCCCCc
Confidence 9 599999975432 1 111111 0 1010 247899999999999999999
Q ss_pred chHHHHHHHHHHcCCCHHHHHHHHHHHhhccc------------------------------------------------
Q 001106 615 ITSTLQQDAANKLNFSATYTMKLAQKLYEGVQ------------------------------------------------ 646 (1157)
Q Consensus 615 ~ts~LQ~~AskklG~Sa~~Tm~iAQ~LYE~~k------------------------------------------------ 646 (1157)
||++||++||++|||||++||++||+|||+..
T Consensus 858 ~t~~Lq~~As~~~g~s~~~tm~iAQ~LYE~g~~~~p~t~V~l~dG~~~~I~el~e~~~~~vl~~~~~~~~~~~~~~~~~~ 937 (1638)
T PRK14701 858 TTDTMLRDASAFLKLSAKETMKLAQDLFEAGLCVTPDTYVSLHDGRIKEIDEIVEGSERNVLGLNGLKPKEAKALKFWEI 937 (1638)
T ss_pred CHHHHHHHHHHhcCCCHHHHHHHHHHHHhCceeeCCCceeecCchHHHHHHHHHhhccceeecccCceecccceeEEEEe
Confidence 99999999999999999999999999999711
Q ss_pred ---------------------------C---------------------------C-----------------C------
Q 001106 647 ---------------------------L---------------------------P-----------------D------ 649 (1157)
Q Consensus 647 ---------------------------~---------------------------~-----------------~------ 649 (1157)
+ . +
T Consensus 938 ~~~~~~~~i~~~~G~~i~~T~dH~~lv~~~g~~~~~~a~~lk~gD~vav~~~~~~~~~~~i~~~~ll~~~~~~~~~~~~~ 1017 (1638)
T PRK14701 938 DYNGPIKVITLKNNYEIKATPDHGLLVMRDGKLGWVSAKNIREGDYVAFAFNTGVEGRKDYSLLKLLKELGITDVCVEFD 1017 (1638)
T ss_pred ccCCcEEEEEECCCCEEEeCCCceEEeecCCceeeEEHHHCCcCCEEEecccCCCCccccccHHHHhhhccccceeeeec
Confidence 0 0 0
Q ss_pred --------------------------C-----------------------------------------------------
Q 001106 650 --------------------------G----------------------------------------------------- 650 (1157)
Q Consensus 650 --------------------------~----------------------------------------------------- 650 (1157)
+
T Consensus 1018 ~~~~~~~~~~~~i~~i~~~~~~~~lr~~~~pl~~l~e~g~~~~~~~~~~~~~~~~~~~~~~i~~~k~de~~~yLlG~~lg 1097 (1638)
T PRK14701 1018 ENSKLFEKLAEKIRGIATSTKYKYLRNRVIPLKYLIEWNVNLDEVEREAKAIYRQRAGSKKIPIFKLDERFWYLFGLVLG 1097 (1638)
T ss_pred cchhHHHHHHHHHHhhccchhhhhccCCcccHHHHHHhcccccccchhhhhhhhcccCcccccccccChhHHhHhheeEe
Confidence 0
Q ss_pred ------------------------------------C--------c----------------------------------
Q 001106 651 ------------------------------------T--------A---------------------------------- 652 (1157)
Q Consensus 651 ------------------------------------~--------~---------------------------------- 652 (1157)
. .
T Consensus 1098 dG~~~~~~~~i~~~~~~~v~~i~~~~~~~~~~~~~~~~v~i~~~~l~~l~~~lG~~~~~ip~~vf~~p~e~~~~fL~G~f 1177 (1638)
T PRK14701 1098 DGTLRDSKVAIAQTPLKDVKSILEDILPFLRTWESGNQVGFSNSIIAEILRRLGVRNGKLNGLVFSLPEEYINAMIAGYF 1177 (1638)
T ss_pred cceeccCeEEEecccHHHHHHHHHHHhhhhhccCCCceEEEccHHHHHHHHHhCCccCCCCHHHHcCCHHHHHHHHhheE
Confidence 0 0
Q ss_pred --------------------------------------------------------------------------------
Q 001106 653 -------------------------------------------------------------------------------- 652 (1157)
Q Consensus 653 -------------------------------------------------------------------------------- 652 (1157)
T Consensus 1178 d~DG~v~~~~~~~~~~~~~~i~~~s~s~~ll~~v~~lLlrlGI~s~l~~~~~~~~~~l~I~g~~l~~F~e~Ig~~~~~k~ 1257 (1638)
T PRK14701 1178 DTDGCFSLLFDKKTGKHNLRIVLTSKRRDVLEKLGVYLYSIGILNTLHRDERNGVWTLIISNRSLETFKEKIYKYLRIKK 1257 (1638)
T ss_pred eCCCceEecccccCCccceEEEEecCCHHHHHHHHHHHHHCCceeEEEEcccCccEEEEEccHHHHHHHHHhCcccHHHH
Confidence
Q ss_pred -----------------------e---------------------E----------------------------------
Q 001106 653 -----------------------A---------------------G---------------------------------- 654 (1157)
Q Consensus 653 -----------------------~---------------------G---------------------------------- 654 (1157)
. |
T Consensus 1258 ~~l~~~~~~~~~~~~~~~~D~iP~~~~~~~v~~~~g~~~~~~~~~g~~~~~~~~~~~isR~~l~~~~~~~~~~~~~~~L~ 1337 (1638)
T PRK14701 1258 EQFDRAYSVYKNEHKQFEGDLLPVAKVFKKLKFKRGIKNRILKEFGIDVWNWNKCVEIPREKLRKVLEYAEDSPEKEFLL 1337 (1638)
T ss_pred HHHHHHHHHHhccccCCCcCccchHHHHHHHHHhcCCchHHHHhhccccccccccCCcCHHHHHHHHHHHhhhhHHHHHH
Confidence 0 1
Q ss_pred -------------------E-----------------------EEEEccCCcCCCHHHHHHHHHHHHHHhCCCCCCCCCC
Q 001106 655 -------------------L-----------------------ITYMRTDGLHISDEAAKEIRSLIFERYGSHHAPEEGP 692 (1157)
Q Consensus 655 -------------------l-----------------------ITYPRTDS~~Ls~~~~~~i~~~i~~~~g~~~~~~~~~ 692 (1157)
+ +|||||||++||+++++.++++|...||.+|.. +
T Consensus 1338 ~la~~dv~~~~i~~ie~~~~~g~vyd~~v~~~nf~angiv~HN~TY~RTDS~~lS~~~~~~~~~~i~~~~g~~y~~---~ 1414 (1638)
T PRK14701 1338 SLVNANVTWVKVKKVEERYYTGYVYDFTTTTENFISNGMVSHNCTYHRTDSTRVSNTGIRVAREYLTQENGEDYFK---P 1414 (1638)
T ss_pred HHhhCCeEEEEEEEEEEeccCCeEEEeEecccceeEccEeecCcccccCCCCccCHHHHHHHHHHHHHhhChhhcC---c
Confidence 1 289999999999999999999999999988863 4
Q ss_pred CccccccccccccCCCCCCCcccCChhhhh---------CCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEEEEEecCcc
Q 001106 693 RKYFKKVKNAQEAHEAIRPTDIRRLPAMLS---------GLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGNADES 763 (1157)
Q Consensus 693 r~~~~k~k~~q~AH~AI~PT~~~~~p~~l~---------~~Ls~dE~klY~LI~rRfLAs~~~~a~~e~t~v~i~~~~~~ 763 (1157)
+.+ ++|+||||||||+....|+.+. ..|+++|++||+|||+|||||||+||+|+.++|.+.+++
T Consensus 1415 r~~-----~~q~AHeAIrPT~~~~~~~~~~~~~~~~~~~~~Ls~de~klY~LI~rRflAs~m~~a~~~~t~v~~~~~~-- 1487 (1638)
T PRK14701 1415 RDW-----FMEGAHECIRPTRPIDTDRLIQLIREGIIQVPGLTRNHLRLYDLIFRRFMASQMKPAKVLYEKALIRYDG-- 1487 (1638)
T ss_pred ccC-----CCcCCcCCCCCCCCCcChhhhhcccccccccccCCHHHHHHHHHHHHHHHHHhCchheEEEEEEEEEECC--
Confidence 544 3689999999998765665321 258999999999999999999999999999999998864
Q ss_pred EEEEEEEEE-EEEcCceecccccchhhhccccccchhhhhHHHhccCCCCCCeEEeeeEEeeecccCCCCCCCHHHHHHH
Q 001106 764 IVFRSSCSR-VEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSEGSLVKK 842 (1157)
Q Consensus 764 ~~F~asg~~-i~~~Gw~~vy~~~~~~~~~~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~ 842 (1157)
..|+++|++ ++++||+++|+..+ ..||.|++| .+.+.+ +.+++|.||+|||||+||++
T Consensus 1488 ~~F~a~G~~~i~~~Gw~~vy~~~~------------------~~LP~l~~G-~l~~~~--~~~t~~ppP~ryTEasLI~~ 1546 (1638)
T PRK14701 1488 KDVEVEGYVEIEGDGWSRLYSLPL------------------RVLPKLEKG-KLKVLE--AKIRKAPKVPLYTQGDIVAL 1546 (1638)
T ss_pred EEEEEEeEEEEEEcCchhcccccc------------------ccCCccccC-ceEEec--cceeECCCCCCCCHHHHHHH
Confidence 589999995 79999999985310 249999999 888755 45667777799999999999
Q ss_pred HHhcCCCCCCchHHHHHhccccceEEEcCc--eeecccchhhhhhhhhcccccccChhhhHHHHHHhhhHhhcCccHHHH
Q 001106 843 LEELGIGRPSTYASTLKVLQDRNYVTVKSR--ILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKGL 920 (1157)
Q Consensus 843 MEk~GIGTpATrA~IIe~L~~R~YV~~k~k--~L~PT~lG~~vi~~L~~~f~~l~~p~~TA~~E~~Ld~Ia~G~~~~~~~ 920 (1157)
||+.|||||||||+||++|++||||..+++ .|+||++|+.|+++|.++|+.|++|+|||.||.+||+|++|+.+|++|
T Consensus 1547 Me~~GIGTpATrA~IIe~L~~R~YV~~~~~k~~l~pT~lG~~li~~L~~~~~~l~~p~~TA~~E~~Ld~Ia~G~~~~~~~ 1626 (1638)
T PRK14701 1547 MKERGIGRPSTYAKIVDTLLMRGYVIETKGRKKLIPTKKGIKVYNYLISNYGDLVSEERTRELEEIMDAVEEGELDYIKV 1626 (1638)
T ss_pred HhhCCCCCcccHHHHHHHHHhCCCEEEeCCCceEEECHHHHHHHHHHHhhchhhcChhhHHHHHHHHHHHHcCCCCHHHH
Confidence 999999999999999999999999997654 699999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhh
Q 001106 921 LVDYWSRFSS 930 (1157)
Q Consensus 921 l~~F~~~f~~ 930 (1157)
|++|++.+..
T Consensus 1627 l~~~~~~i~~ 1636 (1638)
T PRK14701 1627 LQELYEEIRR 1636 (1638)
T ss_pred HHHHHHHHHh
Confidence 9999987653
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=5.3e-90 Score=798.06 Aligned_cols=375 Identities=44% Similarity=0.658 Sum_probs=330.5
Q ss_pred HhHHHHHHHHHHHhHhhhhhccHHHHhhCC--CccccCcchhHHHHHHHhHHHHHHhcCCcceEEEEEEEecCcCCCCCC
Q 001106 481 ANLVQAYLARRALDYLIGFNISPLLWRKLP--GCQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDT 558 (1157)
Q Consensus 481 ~~L~~A~~AR~~lD~LiG~nlSR~lt~k~~--~~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~g 558 (1157)
.+|++||+||+++|||||||+||++|..++ +++|+||||||||+|||+||+||+||+|++||.|
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 6899999999999999999999999999999997
Q ss_pred ceeeeeecccccccccccccCCHHHHHHHHHHHccCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHHcCCCHHHHHHHH
Q 001106 559 FSFPAHLTHFQSKRLNQLSIGSHTEAKDIEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKLA 638 (1157)
Q Consensus 559 ~~f~a~l~~~~~~~~~~~~i~d~e~Ae~i~~~l~~~~~~V~~v~~k~~~~~PP~Pf~ts~LQ~~AskklG~Sa~~Tm~iA 638 (1157)
..++|++++.++++..||+||||++||++|+++|||||++||++|
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 HHHhhcccCCCCCceEEEEEEccCCcCCCHHHHHHHHHHHHHHhCCCCCCCC-C-CCccccccccccccCCCCCCCcccC
Q 001106 639 QKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFERYGSHHAPEE-G-PRKYFKKVKNAQEAHEAIRPTDIRR 716 (1157)
Q Consensus 639 Q~LYE~~k~~~~~~~GlITYPRTDS~~Ls~~~~~~i~~~i~~~~g~~~~~~~-~-~r~~~~k~k~~q~AH~AI~PT~~~~ 716 (1157)
|+|||+ ||||||||||++||+++...+..++...++..+.... . ........++.++||||||||+...
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 8999999999999999999998888766654332111 0 0001111234578999999998653
Q ss_pred ChhhhhCCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEEEEEecCccEEEEEEEEEEEEcCceecccccchhhhcccccc
Q 001106 717 LPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYKENE 796 (1157)
Q Consensus 717 ~p~~l~~~Ls~dE~klY~LI~rRfLAs~~~~a~~e~t~v~i~~~~~~~~F~asg~~i~~~Gw~~vy~~~~~~~~~~~e~~ 796 (1157)
.| .+...|+++|++||+||||||||+||++++|++++|.+.+++ ..|.++|++++++||+++|+.... + +
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 112459999999999999999999999999999999998864 579999999999999999975321 1 1
Q ss_pred chhhhhHHHhccCCCCCCeEEeeeEEeeecccCCCCCCCHHHHHHHHHhcCCCCCCchHHHHHhccccceEEEcCceeec
Q 001106 797 ENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKSRILYP 876 (1157)
Q Consensus 797 e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk~GIGTpATrA~IIe~L~~R~YV~~k~k~L~P 876 (1157)
+ ..+|.|++||.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++||||..+++.|+|
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 ccchhhhhhhhhcccccccChhhhHHHHHHhhhHhhcCccHHHHHHHHHHHhhh
Q 001106 877 EFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKGLLVDYWSRFSS 930 (1157)
Q Consensus 877 T~lG~~vi~~L~~~f~~l~~p~~TA~~E~~Ld~Ia~G~~~~~~~l~~F~~~f~~ 930 (1157)
|++|+.|+++|++.|+.|++|+|||.||.+|++|++|+.++++||+++++.+.+
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=6.1e-89 Score=794.94 Aligned_cols=398 Identities=36% Similarity=0.531 Sum_probs=312.4
Q ss_pred cccHhHHHHHHHHHHHhHhhhhhccHHHHhhCCCccccCcchhHHHHHHHhHHHHHHhcCCcceEEEEEEEecCcCCCCC
Q 001106 478 EIDANLVQAYLARRALDYLIGFNISPLLWRKLPGCQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLD 557 (1157)
Q Consensus 478 ~~d~~L~~A~~AR~~lD~LiG~nlSR~lt~k~~~~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~ 557 (1157)
+++++|++||+||+++|||||||+||+++ + ++++|+||||||||+|||+||+||+||+|++||.|.+.+....
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 7899999999999999999999999999999999999986431
Q ss_pred CceeeeeecccccccccccccCCHHHHHHHHHHHccCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHHcCCCHHHHHHH
Q 001106 558 TFSFPAHLTHFQSKRLNQLSIGSHTEAKDIEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKL 637 (1157)
Q Consensus 558 g~~f~a~l~~~~~~~~~~~~i~d~e~Ae~i~~~l~~~~~~V~~v~~k~~~~~PP~Pf~ts~LQ~~AskklG~Sa~~Tm~i 637 (1157)
+ .+. .....++.++++|+.+++.+... .|.+++.++++.+||+||+|++||++|+++|||||++||++
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 1 111 11235789999999999999875 99999999999999999999999999999999999999999
Q ss_pred HHHHhhcccCCCCCceEEEEEEccCCcCCCHHH-HHHHHHHHHHHhCCCCCCCCCCCccc-cc-ccccc-ccCCCCCCCc
Q 001106 638 AQKLYEGVQLPDGTAAGLITYMRTDGLHISDEA-AKEIRSLIFERYGSHHAPEEGPRKYF-KK-VKNAQ-EAHEAIRPTD 713 (1157)
Q Consensus 638 AQ~LYE~~k~~~~~~~GlITYPRTDS~~Ls~~~-~~~i~~~i~~~~g~~~~~~~~~r~~~-~k-~k~~q-~AH~AI~PT~ 713 (1157)
||+|||+| ||||||||||+|||++. +..+...|...++..|... .+.... .+ ..+++ +||||||||.
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 7778888877777544331 111110 00 02233 8999999997
Q ss_pred ccCChhhhhCCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEEEEEecCccEEEEEEEEEEEEcCceecccccchhhhccc
Q 001106 714 IRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYK 793 (1157)
Q Consensus 714 ~~~~p~~l~~~Ls~dE~klY~LI~rRfLAs~~~~a~~e~t~v~i~~~~~~~~F~asg~~i~~~Gw~~vy~~~~~~~~~~~ 793 (1157)
.. |.++ ..|+++|++||+||||||||+||+||+|+.++|.+.++ ++.|.++|++++++||+++|+.... +
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 54 3222 24899999999999999999999999999999999884 4689999999999999999964321 0
Q ss_pred cccchhhhhHHHhccCCCCCCeEEeeeEEeeecccCCCCCCCHHHHHHHHHhcCCCCCCchHHHHHhccccceEEE-cCc
Q 001106 794 ENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTV-KSR 872 (1157)
Q Consensus 794 e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk~GIGTpATrA~IIe~L~~R~YV~~-k~k 872 (1157)
+ .+ ..||.+++||.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++|+||++ +++
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 469
Q ss_pred eeecccchhhhhhhhhcccccccChhhhHHHHHHhhhHhhcCccHHHHHH
Q 001106 873 ILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKGLLV 922 (1157)
Q Consensus 873 ~L~PT~lG~~vi~~L~~~f~~l~~p~~TA~~E~~Ld~Ia~G~~~~~~~l~ 922 (1157)
.|+||++|+.|+++|+ .|+.|++|+|||.||+.|++|++|+.++++||+
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 458999999999999999999999999999874
No 24
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=100.00 E-value=2e-86 Score=795.32 Aligned_cols=520 Identities=31% Similarity=0.507 Sum_probs=425.5
Q ss_pred CCCCCCCCCCCCCCeEEEEecchHHHHHHhhcCCC-------------------EEEEEeccccccccccCC--CCCCC-
Q 001106 336 GQNTQNPLYPPSGKSVVVVESVTKAKVIQGYLGDM-------------------YEVLPSYGHVRDLAARSG--SVRPD- 393 (1157)
Q Consensus 336 ~~~~~~~~~~~~~k~LiIaEkPskAk~Ia~~LG~~-------------------y~V~~s~GHl~dL~~~~~--~v~p~- 393 (1157)
.|..-..-.....-.|+|||||+|||+||.|+|.. -.|++|.||++||....+ ++.-+
T Consensus 605 ~g~~~~~~~dlvkt~L~IVESPnKARTIA~FFgrPS~R~~~~~~vYEv~~gD~vL~ItAS~GHv~DLvt~~g~hGvl~~~ 684 (1187)
T COG1110 605 EGKLKEETKDLVKTALMIVESPNKARTIASFFGRPSVRRLGGGVVYEVAIGDLVLTITASGGHVFDLVTEPGVHGVLVKD 684 (1187)
T ss_pred hccchhhhhhhhhceEEEEeCChHHHHHHHHhCCcceeeeCCeeEEEEecCCeEEEEEecCCeeEEeecccccceeeccC
Confidence 34333334444557999999999999999999841 358999999999987543 22111
Q ss_pred CCCcceEe------------------cc-------cchHHHHHHHHHHhccCCeEEEccCCCccccHHHHHHHHHHhhcc
Q 001106 394 DDFSMVWE------------------VP-------SAAWTHLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQD 448 (1157)
Q Consensus 394 ~~f~~~~~------------------v~-------~~kk~~lk~Lk~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~ 448 (1157)
..|.|.|. .| .++...++.|++++-.+|+|+||||||.|||-|||+|..++..
T Consensus 685 ~~~vPvY~tIKrC~dcg~q~~~~~~~cP~Cgs~~v~d~~~~ve~lRelA~EvDeVlIgTDPDtEGEKIawDv~~~l~P-- 762 (1187)
T COG1110 685 GKYVPVYDTIKRCRDCGEQFVDSEDKCPRCGSRNVEDKTETVEALRELALEVDEILIGTDPDTEGEKIAWDVFNYLRP-- 762 (1187)
T ss_pred CceEehHHHHHHHhhcCceeccccccCCCCCCccccccHHHHHHHHHHHhhcCEEEEcCCCCCccchhHHHHHHhhCc--
Confidence 12433331 11 2466789999999999999999999999999999999999865
Q ss_pred cccCCccEEEEEEcccCHHHHHHHHHhcccccHhHHHHHHHHHHHhHhhhhhccHHHHhhCC-CccccCcchhHHHHHHH
Q 001106 449 ALHENITVARVVFHEITEASIKVALQAAREIDANLVQAYLARRALDYLIGFNISPLLWRKLP-GCQSAGRVQSAALSLIC 527 (1157)
Q Consensus 449 ~~~~~k~vkRl~fsslT~~aI~~A~~nlr~~d~~L~~A~~AR~~lD~LiG~nlSR~lt~k~~-~~lS~GRVQTPtL~LVv 527 (1157)
.+..|+|+.||++|+.+|.+|++|++++|.||+.||..||+.|++|||.||+.||..++ ..||+||||||+|++||
T Consensus 763 ---y~~nikR~eFHEVTrrAIleAl~n~r~vd~nlVkAQiVRRIeDRWIGF~LS~~Lw~~F~~~nLsAGRVQTPVLGWIV 839 (1187)
T COG1110 763 ---YNPNVKRIEFHEVTRRAILEALKNPRDVDENLVKAQIVRRIEDRWIGFELSQKLWDVFNNKNLSAGRVQTPVLGWIV 839 (1187)
T ss_pred ---CCCceeEEEeeeecHHHHHHHHhCccccchhhhHHHhhhhhhhcccceeecHHHHHHhCccCccccccccccceeeh
Confidence 46789999999999999999999999999999999999999999999999999999986 47999999999999999
Q ss_pred hHHHHHHhcCCcceEEEEEEEecCcCCCCCCceeeeeecccccccccccccCCHHHHHHHHHHHccCCeEEEEeeeeeee
Q 001106 528 DREMEIDEFKPQEYWTVEAVLDKKESHSLDTFSFPAHLTHFQSKRLNQLSIGSHTEAKDIEQKINSANFQVIKNSKRSMV 607 (1157)
Q Consensus 528 eRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~g~~f~a~l~~~~~~~~~~~~i~d~e~Ae~i~~~l~~~~~~V~~v~~k~~~ 607 (1157)
+|+.|-+.-+. |..+...+ .+ .+.+...++.+...+....+.|.++..++..
T Consensus 840 ~Ry~e~~~~~~--~~~~~~~~-----------~~---------------~~~~~~~~~~~~~~~~~~~v~v~~~~e~ee~ 891 (1187)
T COG1110 840 NRYEEYKEKRG--YLVIQLDL-----------DL---------------PSGNREEVENVKRKLKLIVVEVVDVVEREEE 891 (1187)
T ss_pred hhHHHHhhccc--eeEeeccc-----------ee---------------eccchhhhhhhhhhcccceEEEeehhhhhhc
Confidence 99999776444 44441111 11 1223344555555555555677777667777
Q ss_pred ecCCCCcchHHHHHHHHHHcCCCHHHHHHHHHHHhhcccCCCCCceEEEEEEccCCcCCCHHHHHHHHHHHHHHhCCCCC
Q 001106 608 RKNPTPYITSTLQQDAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFERYGSHHA 687 (1157)
Q Consensus 608 ~~PP~Pf~ts~LQ~~AskklG~Sa~~Tm~iAQ~LYE~~k~~~~~~~GlITYPRTDS~~Ls~~~~~~i~~~i~~~~g~~~~ 687 (1157)
.+|||||+|++|+++||++||+|+++||+|||.|||. |||||+||||+++|+..+..++.+|...++..+.
T Consensus 892 ~~PlPPyTTDt~L~dAs~~L~lsa~~~M~iaQdLFE~---------GlITYHRTDSTrVS~~Gi~vAreyl~~~~~e~~f 962 (1187)
T COG1110 892 KNPLPPYTTDTMLRDASRRLRLSADETMQIAQDLFEG---------GLITYHRTDSTRVSDVGIRVAREYLRKEFGEEYF 962 (1187)
T ss_pred cCCCCCcCcchHHHHHHHHhCCChhHHHHHHHHHHhc---------cceEEeecCCcccchhhHHHHHHHHHHhhccccc
Confidence 8999999999999999999999999999999999996 9999999999999999999999999988887764
Q ss_pred CCCCCCccccccccccccCCCCCCCcccCChhh-----------hhCCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEEE
Q 001106 688 PEEGPRKYFKKVKNAQEAHEAIRPTDIRRLPAM-----------LSGLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVD 756 (1157)
Q Consensus 688 ~~~~~r~~~~k~k~~q~AH~AI~PT~~~~~p~~-----------l~~~Ls~dE~klY~LI~rRfLAs~~~~a~~e~t~v~ 756 (1157)
.||.|.. ..||+|||||.+.+. +. ++..|+..+.+||+||.|||||+||.|+++....+.
T Consensus 963 ---~pR~Wge-----~GAHEaIRPtrPid~-~eL~~~i~~G~i~~~~~Lt~~HlrvYdLIFrRFmASQm~pa~v~~~~~~ 1033 (1187)
T COG1110 963 ---RPRSWGE-----EGAHEAIRPTRPIDV-EELITLIEEGVIQLPIRLTKNHLRVYDLIFRRFMASQMRPAKVLKEKAE 1033 (1187)
T ss_pred ---cCCcccc-----CCcccccCCCCCCCH-HHHHHHHHcCCeeccchhhHHHHHHHHHHHHHHHHhhCCceeEEEEEEE
Confidence 4788743 469999999976432 21 223489999999999999999999999999888888
Q ss_pred EEecCccEEEEEEEEEEEEcCceecccccchhhhccccccchhhhhHHHhccCCCCCCeEEeeeEEeeecccCCCCCCCH
Q 001106 757 IGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSE 836 (1157)
Q Consensus 757 i~~~~~~~~F~asg~~i~~~Gw~~vy~~~~~~~~~~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTE 836 (1157)
+..++.+... -....+...||..+|+. ..+|.|..|+ +.+....+...-.. ..|||
T Consensus 1034 i~~~~~~~~~-e~~ve~~~~G~~~vy~~--------------------~~~p~l~~g~-l~v~~~~~~~~~kv--~lytq 1089 (1187)
T COG1110 1034 VKADGKDVEL-EALVEILEDGFALVYPT--------------------RVLPELEKGT-LKVTEVEIRKVSKV--YLYTQ 1089 (1187)
T ss_pred EecCcceeee-eehhhhhccchhhhccc--------------------cccCccCCCc-eeeeeeEEEEcccc--ccccc
Confidence 8775433222 22344567999999863 2478899998 77766666655443 46999
Q ss_pred HHHHHHHHhcCCCCCCchHHHHHhccccceEEEcCc--eeecccchhhhhhhhhcccccccChhhhHHHHHHhhhHhhcC
Q 001106 837 GSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKSR--ILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGL 914 (1157)
Q Consensus 837 asLI~~MEk~GIGTpATrA~IIe~L~~R~YV~~k~k--~L~PT~lG~~vi~~L~~~f~~l~~p~~TA~~E~~Ld~Ia~G~ 914 (1157)
+++|+.|++.|||||||||.||++|.+||||...++ +++||.+|+.|+++|...|+.+++.+.|.++|+.||+|+.|+
T Consensus 1090 g~vi~~MKerGIGRPSTYAkive~L~~RgYvie~kg~~~lipTk~Gi~Vy~yL~~~~~~lVSEerTR~LEe~MD~vE~gk 1169 (1187)
T COG1110 1090 GEVVEEMKERGIGRPSTYAKIVETLLRRGYVIESKGRKKLIPTKLGIEVYEYLSEKYKKLVSEERTRRLEEIMDKVEEGK 1169 (1187)
T ss_pred chHHHHHHhcCCCCCcHHHHHHHHHhcCCeEEEecCceEeccccccHHHHHHHHHhcccccchhHHHHHHHHHHHHHhcc
Confidence 999999999999999999999999999999976543 399999999999999999999999999999999999999999
Q ss_pred ccHHHHHHHHHHHhhh
Q 001106 915 TEWKGLLVDYWSRFSS 930 (1157)
Q Consensus 915 ~~~~~~l~~F~~~f~~ 930 (1157)
.++.++|.+.|+++..
T Consensus 1170 ~dy~~vL~ely~ei~~ 1185 (1187)
T COG1110 1170 ADYQEVLKELYEEIKS 1185 (1187)
T ss_pred cCHHHHHHHHHHHHHh
Confidence 9999999999887654
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=525.60 Aligned_cols=255 Identities=44% Similarity=0.601 Sum_probs=216.1
Q ss_pred eeeeeecCCCCcchHHHHHHHHHHcCCCHHHHHHHHHHHhhcccCCCCCceEEEEEEccCCcCCCHHHHHHHHHHHHHHh
Q 001106 603 KRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFERY 682 (1157)
Q Consensus 603 ~k~~~~~PP~Pf~ts~LQ~~AskklG~Sa~~Tm~iAQ~LYE~~k~~~~~~~GlITYPRTDS~~Ls~~~~~~i~~~i~~~~ 682 (1157)
+++++..||+||||++||++||++|||||++||++||+|||+ ||||||||||+|||+++..++..++....
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 89999999999999999999888887655
Q ss_pred CCCCCCC---CCCCccccccccccccCCCCCCCcccCChhhhhCCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEEEEEe
Q 001106 683 GSHHAPE---EGPRKYFKKVKNAQEAHEAIRPTDIRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGN 759 (1157)
Q Consensus 683 g~~~~~~---~~~r~~~~k~k~~q~AH~AI~PT~~~~~p~~l~~~Ls~dE~klY~LI~rRfLAs~~~~a~~e~t~v~i~~ 759 (1157)
+..|... ....+........++||||||||+....++.+ ..|+++|++||+||+|||||+||++|+|++++|.+.+
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 4333221 01111111112246899999999864332222 3499999999999999999999999999999999988
Q ss_pred cCccEEEEEEEEEEEEcCceecccccchhhhccccccchhhhhHHHhccCCCCCCeEEeeeEEeeecccCCCCCCCHHHH
Q 001106 760 ADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSEGSL 839 (1157)
Q Consensus 760 ~~~~~~F~asg~~i~~~Gw~~vy~~~~~~~~~~~e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasL 839 (1157)
++ +.|.++|++++++||+.||++.+. + + ...||.+++||.+.+.++.+.+++|+||+||||++|
T Consensus 152 ~~--~~F~a~g~~i~~~Gw~~v~~~~~~------~-~-------~~~lp~~~~g~~~~~~~~~~~e~~TkPP~~~Te~tL 215 (259)
T smart00437 152 GG--EKFKAKGKTLLFDGWLKVYPEEKK------E-E-------EIELPTLKKGDELKVEEVEVEEKKTKPPARYTEASL 215 (259)
T ss_pred CC--eEEEEEEEEEeECCHHHhhccccc------C-c-------cccCCCcCCCCEeeeeeeEEEecccCCCCCCCHHHH
Confidence 64 589999999999999999975311 0 0 135999999999999999999999999999999999
Q ss_pred HHHHHhcCCCCCCchHHHHHhccccceEEEcCceeecccchhhh
Q 001106 840 VKKLEELGIGRPSTYASTLKVLQDRNYVTVKSRILYPEFRGRMV 883 (1157)
Q Consensus 840 I~~MEk~GIGTpATrA~IIe~L~~R~YV~~k~k~L~PT~lG~~v 883 (1157)
|++||+.|||||||||+||++|++||||.++++.|+||++|+.|
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=7.1e-54 Score=477.75 Aligned_cols=493 Identities=21% Similarity=0.239 Sum_probs=387.6
Q ss_pred CCeEEEEecchHHHHHHhhcCC------------------------CEEEEEecccccccccc-----CCCCCCCCCCcc
Q 001106 348 GKSVVVVESVTKAKVIQGYLGD------------------------MYEVLPSYGHVRDLAAR-----SGSVRPDDDFSM 398 (1157)
Q Consensus 348 ~k~LiIaEkPskAk~Ia~~LG~------------------------~y~V~~s~GHl~dL~~~-----~~~v~p~~~f~~ 398 (1157)
.-.|.|||||+.|..||++|.. .|.||+..||++.|..+ |..|||.+.|..
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 38899999999999775 456777766653
Q ss_pred eEe--cccchHHHHHHHHHHhccCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhc
Q 001106 399 VWE--VPSAAWTHLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAA 476 (1157)
Q Consensus 399 ~~~--v~~~kk~~lk~Lk~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fsslT~~aI~~A~~nl 476 (1157)
.-+ -...|....+.|...+++||.+|||.|+|+|||+|.+||++..+.... .....++|++||+||+++|.+||+||
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 111 112255678889999999999999999999999999999998876432 33457899999999999999999999
Q ss_pred ccccHhHHHHHHHHHHHhHhhhhhccHHHHhhCCCccccCcchhHHHHHHHhHHHHHHhcCCcceEEEEEEEecCcCCCC
Q 001106 477 REIDANLVQAYLARRALDYLIGFNISPLLWRKLPGCQSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSL 556 (1157)
Q Consensus 477 r~~d~~L~~A~~AR~~lD~LiG~nlSR~lt~k~~~~lS~GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~ 556 (1157)
.++|.|.+.+..|||++|+.| .....+|+|.||||||++.|+|...|+.|+|+.||.+.+.+...
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 CCceeeeeecccccccccccccCCHHHHHHHHHHHcc-CCeEEEEeeeeeeeecCCCCcchHHHHHHHHHHcCCCHHHHH
Q 001106 557 DTFSFPAHLTHFQSKRLNQLSIGSHTEAKDIEQKINS-ANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTM 635 (1157)
Q Consensus 557 ~g~~f~a~l~~~~~~~~~~~~i~d~e~Ae~i~~~l~~-~~~~V~~v~~k~~~~~PP~Pf~ts~LQ~~AskklG~Sa~~Tm 635 (1157)
.+...| +..|+.|.|.|..+.+.++. +.+.|.+|.+++..+..|..+||.+|.+.|
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 34688999999999998874 679999999999999999999999998776
Q ss_pred HHHHHHhhcccCCCCCceEEEEEEccCCcCCCHHHHHHHHHHHHHHhCCCCCCCCCCCccccccccccccCCCCCCCccc
Q 001106 636 KLAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFERYGSHHAPEEGPRKYFKKVKNAQEAHEAIRPTDIR 715 (1157)
Q Consensus 636 ~iAQ~LYE~~k~~~~~~~GlITYPRTDS~~Ls~~~~~~i~~~i~~~~g~~~~~~~~~r~~~~k~k~~q~AH~AI~PT~~~ 715 (1157)
+|+.+.+|..+-..+ + .+..+.. + +.. ...++|+||.|-..-
T Consensus 283 ------------------------itett~y~~nfd~si---~---~~D~L~~---~----s~g-tdAgdgpPitpmr~~ 324 (555)
T KOG1957|consen 283 ------------------------ITETTAYPANFDTSI---I---LGDTLFE---A----SFG-TDAGDGPPITPMRKC 324 (555)
T ss_pred ------------------------EeecccCcccccccc---c---ccccccc---c----ccc-CcCCCCCCcCccccc
Confidence 256666665431111 0 0110100 1 111 112579999998742
Q ss_pred CChhhhhCCCCHHHHHHHHHHHHHHHHccCCCcEEEEEEEEEEecCccEEEE--EEEEEEEEcCceecccccchhhhccc
Q 001106 716 RLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGNADESIVFR--SSCSRVEFLGFQAAYEDVDAGAIRYK 793 (1157)
Q Consensus 716 ~~p~~l~~~Ls~dE~klY~LI~rRfLAs~~~~a~~e~t~v~i~~~~~~~~F~--asg~~i~~~Gw~~vy~~~~~~~~~~~ 793 (1157)
.. ...+.+-++||..++++|++.-+...+|..+++...++++ .|. .+|+++.+.||..+-.....-.-...
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 2356677899999999999999999999999998887654 677 99999999999998652110000000
Q ss_pred cccchhhhhHHHhccCCCCCCeEEeeeEEeeecccCCCCCCCHHHHHHHHHhcCCCCCCchHHHHHhccccceEEEc-Cc
Q 001106 794 ENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVK-SR 872 (1157)
Q Consensus 794 e~~e~~~~~~~~~LP~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk~GIGTpATrA~IIe~L~~R~YV~~k-~k 872 (1157)
.++.. ...-...|.-+--|+.+.+.++.+-+.+|.||-++|+..|+..||++||||.+..+-+|..+-+|+||.++ +|
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 00001123334459999999999999999999999999999999999999999999999999999999986 77
Q ss_pred eeecccchhhhhhhhhcccccccChhhhHHHHHHhhhHhhcCccHHHHHHHHH
Q 001106 873 ILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKGLLVDYW 925 (1157)
Q Consensus 873 ~L~PT~lG~~vi~~L~~~f~~l~~p~~TA~~E~~Ld~Ia~G~~~~~~~l~~F~ 925 (1157)
.+.||++|+.+......-.|++.-|.+.+..|.++-.++.|..+.++++..+.
T Consensus 477 ~~~Pt~Lg~~l~~Gy~~~DP~l~lpt~r~~~es~~~lvA~G~A~~q~v~R~r~ 529 (555)
T KOG1957|consen 477 ALVPTPLGETLVRGYVKCDPELVLPTMRKEAESQLPLVAGGPADFQDVWRNRG 529 (555)
T ss_pred ccCCCccchhhhcCceeeCcceechhHHHHHHhhchhhhCCccchhhhhhcce
Confidence 89999999988766655558899999999999999999999999877776544
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=0.704 Sum_probs=109.8
Q ss_pred CeEEEEecchHHHHHHhhcCCCEEEEEeccccccccccCCCCCCCCC-CcceEecccchHHHHHHHHHHhccCCeEEEcc
Q 001106 349 KSVVVVESVTKAKVIQGYLGDMYEVLPSYGHVRDLAARSGSVRPDDD-FSMVWEVPSAAWTHLKSIKVALSGAENLILAS 427 (1157)
Q Consensus 349 k~LiIaEkPskAk~Ia~~LG~~y~V~~s~GHl~dL~~~~~~v~p~~~-f~~~~~v~~~kk~~lk~Lk~l~k~ad~IIlAT 427 (1157)
|+|||+|||++|++|+++||.+|+|+||.|||++|++|+...++.+. |.+.|.+.+.++++++.|+++++++|+|||||
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 67999999999999999999999999999999999987665433322 56678887788999999999999999999999
Q ss_pred CCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhc
Q 001106 428 DPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAA 476 (1157)
Q Consensus 428 DpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fsslT~~aI~~A~~nl 476 (1157)
|||||||+|+|+|+++++ ++.+|+|+|||++|+++|++||+||
T Consensus 81 D~drEGe~i~~~i~~~~~------~~~~v~Rl~~sslt~~~I~~A~~n~ 123 (123)
T cd03363 81 DPDREGEAIAWHLAEVLK------LKKNVKRVVFNEITKEAIKEALKNP 123 (123)
T ss_pred CCCcchHHHHHHHHHHcC------CCCCeEEEEEccCCHHHHHHHHhCc
Confidence 999999999999999985 3579999999999999999999986
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=9e-30 Score=257.61 Aligned_cols=123 Identities=37% Similarity=0.531 Sum_probs=105.7
Q ss_pred CeEEEEecchHHHHHHhhcCC------------CEEEEEeccccccccccCCCCCCCC-------CCcceEecccchHHH
Q 001106 349 KSVVVVESVTKAKVIQGYLGD------------MYEVLPSYGHVRDLAARSGSVRPDD-------DFSMVWEVPSAAWTH 409 (1157)
Q Consensus 349 k~LiIaEkPskAk~Ia~~LG~------------~y~V~~s~GHl~dL~~~~~~v~p~~-------~f~~~~~v~~~kk~~ 409 (1157)
+.|||||||++|++|+++||. .|+|+||.|||++|++++....... .+.+.|.+...+.++
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 123346666778999
Q ss_pred HHHHHHHhccCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhc
Q 001106 410 LKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAA 476 (1157)
Q Consensus 410 lk~Lk~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fsslT~~aI~~A~~nl 476 (1157)
++.|++++++||+||||||||||||+|||||+++++. .+++++|+|||+||+++|++||+||
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=3.3e-29 Score=256.03 Aligned_cols=124 Identities=26% Similarity=0.316 Sum_probs=105.4
Q ss_pred CeEEEEecchHHHHHHhhcC------------------CCEEEEEeccccccccccCCC--C---CCC----CCCcceEe
Q 001106 349 KSVVVVESVTKAKVIQGYLG------------------DMYEVLPSYGHVRDLAARSGS--V---RPD----DDFSMVWE 401 (1157)
Q Consensus 349 k~LiIaEkPskAk~Ia~~LG------------------~~y~V~~s~GHl~dL~~~~~~--v---~p~----~~f~~~~~ 401 (1157)
|.|||||||++|++|+++|| .+|+|+|+.|||++|+.|+.. + .+. ..+.+.|.
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 1 111 12344566
Q ss_pred cccchHHHHHHHHHHhccCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhc
Q 001106 402 VPSAAWTHLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAA 476 (1157)
Q Consensus 402 v~~~kk~~lk~Lk~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fsslT~~aI~~A~~nl 476 (1157)
+...++++++.|++++++||.||||||||||||+|||+|+++++.. .+++|+|+|||++|+++|++||+||
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=8.6e-30 Score=237.63 Aligned_cols=88 Identities=56% Similarity=0.844 Sum_probs=84.7
Q ss_pred EEEEEEcccCHHHHHHHHHhcccccHhHHHHHHHHHHHhHhhhhhccHHHHhhCCC-ccccCcchhHHHHHHHhHHHHHH
Q 001106 456 VARVVFHEITEASIKVALQAAREIDANLVQAYLARRALDYLIGFNISPLLWRKLPG-CQSAGRVQSAALSLICDREMEID 534 (1157)
Q Consensus 456 vkRl~fsslT~~aI~~A~~nlr~~d~~L~~A~~AR~~lD~LiG~nlSR~lt~k~~~-~lS~GRVQTPtL~LVveRe~EI~ 534 (1157)
|+|+|||++|+++|++||+|+++.+.+|++|++||+++|||+|||+||++|.+++. .+|+||||||||+|||+||+||+
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 001106 535 EFKPQEYWT 543 (1157)
Q Consensus 535 ~Fkp~~Yw~ 543 (1157)
+|+|++||.
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=8.9e-27 Score=242.48 Aligned_cols=122 Identities=30% Similarity=0.516 Sum_probs=101.2
Q ss_pred eEEEEecchHHHHHHhhcCCC-------------------EEEEEeccccccccccCCCC--CCC-CCCcceEec-----
Q 001106 350 SVVVVESVTKAKVIQGYLGDM-------------------YEVLPSYGHVRDLAARSGSV--RPD-DDFSMVWEV----- 402 (1157)
Q Consensus 350 ~LiIaEkPskAk~Ia~~LG~~-------------------y~V~~s~GHl~dL~~~~~~v--~p~-~~f~~~~~v----- 402 (1157)
.|||||||++|++|+++||.. |+|+|+.|||++|+.++... ... ..|.+.|..
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 001106 403 --------------------PSAAWTHLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFH 462 (1157)
Q Consensus 403 --------------------~~~kk~~lk~Lk~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fs 462 (1157)
.+++++|++.|++++++||+||||||||||||+|+|||+++++. .+.+++|+|||
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 001106 463 EITEASIKVALQAA 476 (1157)
Q Consensus 463 slT~~aI~~A~~nl 476 (1157)
+||+++|++||+||
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=4.2e-26 Score=246.08 Aligned_cols=169 Identities=33% Similarity=0.585 Sum_probs=144.0
Q ss_pred CCCCCCCCCceEEEEecccCceeEEecCCCCCCcccccCCCCCCchhhhhhhccCCCCCcccCCCCCccceeeeccCCCc
Q 001106 963 DRSCPVCGEGTLIFKVSRFGAGYFIGCNQHPRCNYIAKTLYGDDDEEDTLQRNTNVDEPKLIGHHPASKEKVLLKSGPYG 1042 (1157)
Q Consensus 963 ~g~CPkCGkg~lv~K~gr~G~~~F~GCsnyP~Ck~t~~~~~~~~~~~e~~~~~~~~~~Pr~LG~cPkcGk~V~lK~GrfG 1042 (1157)
...||.|+.+.+.++.|+||+ |++|+|||.|.+...+.....+..+. .....|++||.+|.+|.+|+++.||||
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 478999999999999999999 89999999999876543322221111 122346899999999999999999999
Q ss_pred ceEEeCCCCCCCCCccccCCCCCCccccCHHHHHHHhcCCcccCCCCCCCcCeEEeeccCcceeecCCe-eeecCCCCCC
Q 001106 1043 FYVQLGEDRTGYLPKRASVSHIKDVDSITLEDALELLRYPVNLGNHPKDGQPIMLRLARAGFSVRHRRT-IASVPKNMKP 1121 (1157)
Q Consensus 1043 ~yv~c~~d~kg~~~k~~slpk~~~~~sItLe~Al~ll~~pk~lG~cP~cG~~v~v~~GryG~yi~~~~~-~~~ipk~~~~ 1121 (1157)
|||+..-+..+.+|+++|||+.+++++||||.||.||.+|+.+|+||+.|+.|.+..||||||+.+.+. .++|.++.++
T Consensus 97 PYVq~~lg~~~~kpkraSLpkg~~~e~ItLE~AL~LLsLPR~iG~hp~sge~I~ag~GRfGPyv~k~Gsd~~sL~~~dd~ 176 (298)
T COG1754 97 PYVQEQLGDPKPKPKRASLPKGWKPETITLEKALKLLSLPRVIGKHPDSGEEISAGLGRFGPYVKKRGSDYRSLKSEDDV 176 (298)
T ss_pred ceeeeecCCCCCCcccccCCCCCChhhCcHHHHHHHHcCchhhCCCCCCCcEEEecccccCcceeecCccccccccccce
Confidence 999862222247899999999999999999999999999999999999999999999999999966655 8999999999
Q ss_pred CCCCHHHHHHHhcccc
Q 001106 1122 NDVTLEKALEFLSGKD 1137 (1157)
Q Consensus 1122 ~~itle~A~~LL~~k~ 1137 (1157)
.+|+|++|+.||++++
T Consensus 177 ftItL~rA~~liaEk~ 192 (298)
T COG1754 177 FTITLDRALKLIAEKR 192 (298)
T ss_pred eeecHHHHHHHHHhhh
Confidence 9999999999999944
No 33
>COG1754 Uncharacterized C-terminal domain of topoisomerase IA [General function prediction only]
Probab=99.87 E-value=2.5e-22 Score=217.11 Aligned_cols=171 Identities=30% Similarity=0.446 Sum_probs=146.8
Q ss_pred CCCCCCCCCCCceEEEEecccCceeE--EecC-CCCCCcccccCCCCCCchhhhhhhccCCCCCcccCCCCCccceeeec
Q 001106 961 NKDRSCPVCGEGTLIFKVSRFGAGYF--IGCN-QHPRCNYIAKTLYGDDDEEDTLQRNTNVDEPKLIGHHPASKEKVLLK 1037 (1157)
Q Consensus 961 ~~~g~CPkCGkg~lv~K~gr~G~~~F--~GCs-nyP~Ck~t~~~~~~~~~~~e~~~~~~~~~~Pr~LG~cPkcGk~V~lK 1037 (1157)
...+..|..|. .+..|.||||+|++ +|-. -.|+.....+.+..++++.|.+. .++++||.+|.||++|+.|++.
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 35789999996 88999999999986 4766 33555555666667777777665 5789999999999999999999
Q ss_pred cCCCcceEEeCCCCCCCCCccccCCCCCCccccCHHHHHHHhcCCc----------ccCCCCCCCcCeEEeeccCcceee
Q 001106 1038 SGPYGFYVQLGEDRTGYLPKRASVSHIKDVDSITLEDALELLRYPV----------NLGNHPKDGQPIMLRLARAGFSVR 1107 (1157)
Q Consensus 1038 ~GrfG~yv~c~~d~kg~~~k~~slpk~~~~~sItLe~Al~ll~~pk----------~lG~cP~cG~~v~v~~GryG~yi~ 1107 (1157)
.|||||||.... ..++||...+++++|+|++|+.||+.++ .+|.||+.|++|+|+.||||||+.
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 999999996431 1378999999999999999999997654 478899999999999999999999
Q ss_pred cCCeeeecCCCCCCCCCCHHHHHHHhccccccc
Q 001106 1108 HRRTIASVPKNMKPNDVTLEKALEFLSGKDVRR 1140 (1157)
Q Consensus 1108 ~~~~~~~ipk~~~~~~itle~A~~LL~~k~~k~ 1140 (1157)
++..|++||++.++.+||+++|++||+++.++-
T Consensus 227 ~Gk~Na~Lpkg~d~~sit~e~A~~LLaer~a~~ 259 (298)
T COG1754 227 DGKTNATLPKGKDPASITLEEALELLAERRAKG 259 (298)
T ss_pred cccccccCCCCCCccccCHHHHHHHHHHhcccC
Confidence 999999999999999999999999999876543
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=5.4e-21 Score=182.30 Aligned_cols=99 Identities=36% Similarity=0.636 Sum_probs=83.9
Q ss_pred eEEEEecchHHHHHHhhcC-CCEEEEEeccccccccccCCCCCCCCCCcceEecccchHHHHHHHHHHhccCCeEEEccC
Q 001106 350 SVVVVESVTKAKVIQGYLG-DMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILASD 428 (1157)
Q Consensus 350 ~LiIaEkPskAk~Ia~~LG-~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~kk~~lk~Lk~l~k~ad~IIlATD 428 (1157)
.|||||+|++|++|+++|+ ..|.|+|+.||++++..++.. .. ..+.++++.|+++++++|.||||||
T Consensus 1 ~liIvE~ps~a~~i~~~l~~~~~~v~~~~Ghl~~~~~~~~~-------~~-----~~~~~~i~~l~~~~~~~~~iiiatD 68 (100)
T PF01751_consen 1 ELIIVEKPSDAKAIAKALGGEEYIVIATSGHLLELAKPEDY-------DP-----KDKKKQIKNLKKLLKKADEIIIATD 68 (100)
T ss_dssp EEEEESSHHHHHHHHHHSSTTTEEEEEESSSSEESTTSSHH-------HC-----HTTHHHHHHHHHHHHSCSEEEEEC-
T ss_pred CEEEEeCHHHHHHHHHHcCCCCEEEEEeCCccccccccccc-------cc-----ccccccchhhHHHhhhccEeeecCC
Confidence 5999999999999999998 569999999999999764321 11 4688999999999999999999999
Q ss_pred CCccccHHHHHHHHHHhhcccccCCccEEEEEEccc
Q 001106 429 PDREGEAIAWHIVEMLQQQDALHENITVARVVFHEI 464 (1157)
Q Consensus 429 pDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fssl 464 (1157)
||||||+|+|+|+++++... +.. ++|+|||+|
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
>PRK08780 DNA topoisomerase I; Provisional
Probab=99.66 E-value=1.9e-16 Score=198.57 Aligned_cols=119 Identities=31% Similarity=0.471 Sum_probs=108.7
Q ss_pred CcccCCCCCccceeeeccCCCcceEEeCCCCCCCCCccccCCCCCCccccCHHHHHHHhcCCcccCCCCCCCcCeEEeec
Q 001106 1021 PKLIGHHPASKEKVLLKSGPYGFYVQLGEDRTGYLPKRASVSHIKDVDSITLEDALELLRYPVNLGNHPKDGQPIMLRLA 1100 (1157)
Q Consensus 1021 Pr~LG~cPkcGk~V~lK~GrfG~yv~c~~d~kg~~~k~~slpk~~~~~sItLe~Al~ll~~pk~lG~cP~cG~~v~v~~G 1100 (1157)
++.+|.||+||..|+++.||||+||+|++...+..|+++|||+..++++|||++|++||.+|+.+|.||+ |++|+++.|
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 789999999
Q ss_pred cCcceeecCCeeeecCCCCCCCCCCHHHHHHHhccccccc
Q 001106 1101 RAGFSVRHRRTIASVPKNMKPNDVTLEKALEFLSGKDVRR 1140 (1157)
Q Consensus 1101 ryG~yi~~~~~~~~ipk~~~~~~itle~A~~LL~~k~~k~ 1140 (1157)
|||||+++++.+.+||+..++.++|+++|++||+++..+.
T Consensus 667 RfGpYv~~~~~~~sl~k~~~~~~itle~A~~ll~~k~~~~ 706 (780)
T PRK08780 667 RFGPFVKRGSKYASLKKEDDPYTIDLARALFLIEEKEEIA 706 (780)
T ss_pred CCCCeEeeCCcccCCCCCCCcccCCHHHHHHHHHhhhhcc
Confidence 9999999999999999999999999999999999876443
No 36
>PRK07561 DNA topoisomerase I subunit omega; Validated
Probab=99.65 E-value=4.3e-16 Score=197.63 Aligned_cols=156 Identities=33% Similarity=0.541 Sum_probs=124.4
Q ss_pred CCCCCCCCCCceEEEEecccCceeEEe----------c-CCCCCCcccccCCCCCCchhhhhhhccCCCCCcccCCCCCc
Q 001106 962 KDRSCPVCGEGTLIFKVSRFGAGYFIG----------C-NQHPRCNYIAKTLYGDDDEEDTLQRNTNVDEPKLIGHHPAS 1030 (1157)
Q Consensus 962 ~~g~CPkCGkg~lv~K~gr~G~~~F~G----------C-snyP~Ck~t~~~~~~~~~~~e~~~~~~~~~~Pr~LG~cPkc 1030 (1157)
..+.||.||. .++++.||||++++.+ | +.+|.|... +.+. .++.+|+.+|.||+|
T Consensus 644 ~lg~~P~cg~-~i~~r~Gr~Gpyv~~~~~~~~~~~sic~~~~p~c~~~-----------e~a~--~ll~~pr~lg~cPec 709 (859)
T PRK07561 644 ALGADPECGT-AMVLRSGRFGPYVQEGEGDKPRRLSLPKGNNPECVGL-----------EIAL--GLLSLPRPVGEHPEC 709 (859)
T ss_pred ccCCCCCCCC-eeEEecCCCCCeeecccCCCCceeccCCCCCCCcCCH-----------HHHH--hhhccccccCcCCCC
Confidence 4578999997 5777899999843311 6 456666432 1121 244668999999999
Q ss_pred cceeeeccCCCcceEEeCCCCCCCCCccccCCCCCCccccCHHHHHHHhcCC----------cccCCCCCCCcCeEEeec
Q 001106 1031 KEKVLLKSGPYGFYVQLGEDRTGYLPKRASVSHIKDVDSITLEDALELLRYP----------VNLGNHPKDGQPIMLRLA 1100 (1157)
Q Consensus 1031 Gk~V~lK~GrfG~yv~c~~d~kg~~~k~~slpk~~~~~sItLe~Al~ll~~p----------k~lG~cP~cG~~v~v~~G 1100 (1157)
|.+|+++.|+||+||+|+. .+.+++...++.++++++|+.+|..| +.+| ||.||++|.+..|
T Consensus 710 g~~i~~k~gr~G~yl~c~~-------~~~sc~~~~~~~~i~l~~a~~ll~~~~~~~~~~~~~k~~g-~p~~g~~i~~~~G 781 (859)
T PRK07561 710 GSEIQAKIGRFGPYVKCGG-------TYASLKNTRKVLTIGLNRAVELLAEPKRPKEDPVPLPELG-CPKSGAPFVLRDG 781 (859)
T ss_pred CCeeEEecCCCCCeEEeCC-------CcCCCCCCCccccCCHHHHHHHHhcccccccccccccccC-CCCCCCeEEEecC
Confidence 9999999999999999953 23455555678889999999999888 3343 6999999999999
Q ss_pred cCcceeecCCeeeecCCCCCCCCCCHHHHHHHhcccccc
Q 001106 1101 RAGFSVRHRRTIASVPKNMKPNDVTLEKALEFLSGKDVR 1139 (1157)
Q Consensus 1101 ryG~yi~~~~~~~~ipk~~~~~~itle~A~~LL~~k~~k 1139 (1157)
|||+|+.|++.++++|++.++.++|+++|++||+++..+
T Consensus 782 r~Gpyi~~~~~~~slpk~~~~~~itle~a~~li~~~~~~ 820 (859)
T PRK07561 782 RYGPYVKHGKANATLPKGRETRAPTVEEALELLAEKPEK 820 (859)
T ss_pred CCCccccccchhccCCCCCCcccCCHHHHHHHHhhcchh
Confidence 999999999999999999999999999999999877433
No 37
>PF13368 Toprim_C_rpt: Topoisomerase C-terminal repeat
Probab=98.69 E-value=2.2e-08 Score=87.78 Aligned_cols=50 Identities=42% Similarity=0.740 Sum_probs=46.4
Q ss_pred CCCCCcCeEEeeccCcceeecCCeeeecCCCCCCCCCCHHHHHHHhccccc
Q 001106 1088 HPKDGQPIMLRLARAGFSVRHRRTIASVPKNMKPNDVTLEKALEFLSGKDV 1138 (1157)
Q Consensus 1088 cP~cG~~v~v~~GryG~yi~~~~~~~~ipk~~~~~~itle~A~~LL~~k~~ 1138 (1157)
||+.|.+| |+.|||||||.++..+++||++.++.++|+++|++||++++.
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 68888777 799999999999999999999999999999999999998754
No 38
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=98.64 E-value=1.1e-07 Score=96.56 Aligned_cols=100 Identities=21% Similarity=0.481 Sum_probs=69.8
Q ss_pred CCCCCCCCCCCceEEEEecccCceeEEecCCCCCCcccccCCCCCCchhhhhhhccCCCCCcccCCCCCcc-ceeeeccC
Q 001106 961 NKDRSCPVCGEGTLIFKVSRFGAGYFIGCNQHPRCNYIAKTLYGDDDEEDTLQRNTNVDEPKLIGHHPASK-EKVLLKSG 1039 (1157)
Q Consensus 961 ~~~g~CPkCGkg~lv~K~gr~G~~~F~GCsnyP~Ck~t~~~~~~~~~~~e~~~~~~~~~~Pr~LG~cPkcG-k~V~lK~G 1039 (1157)
...+.||+||+ .|+++.+++| .|+||++||+|++- +.. .. ......+.||+|| ..++++.|
T Consensus 15 ~~~~~Cp~Cg~-~m~~~~~~~g--~f~gCs~yP~C~~~-~~~--~~------------~~~~~~~~Cp~C~~~~~~~k~~ 76 (140)
T COG0551 15 KTGQICPKCGK-NMVKKFGKYG--IFLGCSNYPKCDYY-EPE--KA------------IAEKTGVKCPKCGKGLLVLKKG 76 (140)
T ss_pred ccCccCCcCCC-eeEEEEccCC--eEEEeCCCCCCCCC-ccc--cc------------ccccCceeCCCCCCCceEEEec
Confidence 34679999997 7888889988 69999999999971 110 00 0112345699999 68999999
Q ss_pred CCc-ceEEeCCCCCCCCCccccCCCCCCccccCHHHHHHHhcCCcccCCCCCCCcCeEEeec
Q 001106 1040 PYG-FYVQLGEDRTGYLPKRASVSHIKDVDSITLEDALELLRYPVNLGNHPKDGQPIMLRLA 1100 (1157)
Q Consensus 1040 rfG-~yv~c~~d~kg~~~k~~slpk~~~~~sItLe~Al~ll~~pk~lG~cP~cG~~v~v~~G 1100 (1157)
+|| .|+.|. .+|+|..+.... .....||+||.+.++.+.
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 799887 457777644322 122349999975555444
No 39
>smart00493 TOPRIM topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins.
Probab=98.58 E-value=2.1e-07 Score=83.98 Aligned_cols=73 Identities=36% Similarity=0.499 Sum_probs=63.0
Q ss_pred CeEEEEecchHHHHHHhhcCCCEEEEEeccccccccccCCCCCCCCCCcceEecccchHHHHHHHHHHhccCCeEEEccC
Q 001106 349 KSVVVVESVTKAKVIQGYLGDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILASD 428 (1157)
Q Consensus 349 k~LiIaEkPskAk~Ia~~LG~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~kk~~lk~Lk~l~k~ad~IIlATD 428 (1157)
+.|+|||.|.-|.++..+++.++.+.++.||+. ..++++.|++...+ +.||||+|
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 001106 429 PDREGEAIAWHIVEMLQQ 446 (1157)
Q Consensus 429 pDREGE~Ia~~Ile~l~~ 446 (1157)
+|+||+.+++++.+++..
T Consensus 56 ~D~~G~~~~~~i~~~l~~ 73 (76)
T smart00493 56 PDREGEAIAWKLAELLKP 73 (76)
T ss_pred CChhHHHHHHHHHHHhhh
Confidence 999999999999998753
No 40
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=98.40 E-value=3.3e-07 Score=117.39 Aligned_cols=119 Identities=13% Similarity=0.099 Sum_probs=69.2
Q ss_pred hhHHHHHHHhHHHHHHhcCCcceEEEEEEEecCcCCCCCCceeeeeeccc--ccc-cccccccCCHH--HHHHHHHHH-c
Q 001106 519 QSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDTFSFPAHLTHF--QSK-RLNQLSIGSHT--EAKDIEQKI-N 592 (1157)
Q Consensus 519 QTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~g~~f~a~l~~~--~~~-~~~~~~i~d~e--~Ae~i~~~l-~ 592 (1157)
|--+-.||++|-.... ..|.-|-...+.+..+. +..|.+.-... .+- .+-...-.+.+ +.+..+-.+ .
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 3344578888887744 25666777777776421 12465532111 110 00000000000 111111112 3
Q ss_pred cCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHHcCCCHHHHHH-HHHHHhhc
Q 001106 593 SANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMK-LAQKLYEG 644 (1157)
Q Consensus 593 ~~~~~V~~v~~k~~~~~PP~Pf~ts~LQ~~AskklG~Sa~~Tm~-iAQ~LYE~ 644 (1157)
+..+.+.+++..++...||+.|+-++|.+++-+ +|+.-.-|.. |.+.|.+.
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 456778888888888999999999999999864 7887766665 78889885
No 41
>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=98.38 E-value=3.6e-07 Score=73.17 Aligned_cols=36 Identities=36% Similarity=0.993 Sum_probs=31.9
Q ss_pred CCCCCCCCceEEEEecccCceeEEecCCCCCCcccccCC
Q 001106 964 RSCPVCGEGTLIFKVSRFGAGYFIGCNQHPRCNYIAKTL 1002 (1157)
Q Consensus 964 g~CPkCGkg~lv~K~gr~G~~~F~GCsnyP~Ck~t~~~~ 1002 (1157)
..||.|| +.|+.|.+++| .||||++||.|+++.++.
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 5799999 58999999999 599999999999998654
No 42
>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=98.37 E-value=1.4e-06 Score=85.23 Aligned_cols=88 Identities=31% Similarity=0.493 Sum_probs=66.1
Q ss_pred CeEEEEecchHHHHHHh---hcCCCEEEEEeccccccccccCCCCCCCCCCcceEecccchHHHHHHHHHHhcc--CCeE
Q 001106 349 KSVVVVESVTKAKVIQG---YLGDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSG--AENL 423 (1157)
Q Consensus 349 k~LiIaEkPskAk~Ia~---~LG~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~kk~~lk~Lk~l~k~--ad~I 423 (1157)
+.|.|||.|....+|.+ |.|. |.|. .||+-.++ ++.|+ + -.++.|.+.+++ .++|
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 67877664 23343 1 123445555543 5899
Q ss_pred EEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEE
Q 001106 424 ILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVF 461 (1157)
Q Consensus 424 IlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~f 461 (1157)
|+|||||+|||+++++|.+.++. ...+|.|+-+
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 43
>PF13368 Toprim_C_rpt: Topoisomerase C-terminal repeat
Probab=98.35 E-value=5.8e-07 Score=78.88 Aligned_cols=55 Identities=40% Similarity=0.620 Sum_probs=48.1
Q ss_pred CCCccceeeeccCCCcceEEeCCCCCCCCCccccCCCCCCccccCHHHHHHHhcCCcccCCCC
Q 001106 1027 HPASKEKVLLKSGPYGFYVQLGEDRTGYLPKRASVSHIKDVDSITLEDALELLRYPVNLGNHP 1089 (1157)
Q Consensus 1027 cPkcGk~V~lK~GrfG~yv~c~~d~kg~~~k~~slpk~~~~~sItLe~Al~ll~~pk~lG~cP 1089 (1157)
||++|..| ++.||||+||+++. .+++||+..++++|++++|++||+.|+..+...
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 58899888 79999999999974 567999999999999999999999887766543
No 44
>PRK07219 DNA topoisomerase I; Validated
Probab=97.96 E-value=1.2e-05 Score=103.21 Aligned_cols=70 Identities=24% Similarity=0.470 Sum_probs=54.7
Q ss_pred CCCCCCCCCceEEEEecccCceeEEecCCCCCCcccccCCCCCCchhhhhhhccCCCCCcccCCCCCccceeeeccCCCc
Q 001106 963 DRSCPVCGEGTLIFKVSRFGAGYFIGCNQHPRCNYIAKTLYGDDDEEDTLQRNTNVDEPKLIGHHPASKEKVLLKSGPYG 1042 (1157)
Q Consensus 963 ~g~CPkCGkg~lv~K~gr~G~~~F~GCsnyP~Ck~t~~~~~~~~~~~e~~~~~~~~~~Pr~LG~cPkcGk~V~lK~GrfG 1042 (1157)
...||.||+ .+..+.+++|. ||+|++||.|+++.++...... ..+...||+||.+++.+.+++|
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 67778899987 9999999999988765422111 0123469999999999999999
Q ss_pred ceEEeC
Q 001106 1043 FYVQLG 1048 (1157)
Q Consensus 1043 ~yv~c~ 1048 (1157)
.|+.|.
T Consensus 752 ~~~~Cs 757 (822)
T PRK07219 752 DELGCC 757 (822)
T ss_pred ceeeeC
Confidence 999996
No 45
>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=97.51 E-value=0.00077 Score=59.78 Aligned_cols=82 Identities=32% Similarity=0.420 Sum_probs=62.7
Q ss_pred CeEEEEecchHHHHHHhhcCCCEEEEEeccccccccccCCCCCCCCCCcceEecccchHHHHHHHHHHhccCCeEEEccC
Q 001106 349 KSVVVVESVTKAKVIQGYLGDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILASD 428 (1157)
Q Consensus 349 k~LiIaEkPskAk~Ia~~LG~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~kk~~lk~Lk~l~k~ad~IIlATD 428 (1157)
+.|||||.++-+..+..+...++.|+++.||... .....+..+++....|++++|
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 3689999999999999998777778888887553 223344555555789999999
Q ss_pred CCccccHHHHHHHHHHhhcccccCCccEEEEE
Q 001106 429 PDREGEAIAWHIVEMLQQQDALHENITVARVV 460 (1157)
Q Consensus 429 pDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~ 460 (1157)
+|.+|+.+++.+.+.+.. ....+.|++
T Consensus 56 ~D~~g~~~~~~~~~~~~~-----~~~~~~~~~ 82 (83)
T cd00188 56 ADREGEAIALRLLELLKS-----LGKKVRRLL 82 (83)
T ss_pred CChhHHHHHHHHHHHHHh-----cCCceEEee
Confidence 999999999999988753 134566654
No 46
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=97.37 E-value=0.00017 Score=73.52 Aligned_cols=103 Identities=17% Similarity=0.100 Sum_probs=65.9
Q ss_pred cccCCCCCccceeeeccCCCcceEEeCCCCCCCCCccccCCCCCCccccCHHHHHHHhcCCcccCCCCCCC-cCeEEeec
Q 001106 1022 KLIGHHPASKEKVLLKSGPYGFYVQLGEDRTGYLPKRASVSHIKDVDSITLEDALELLRYPVNLGNHPKDG-QPIMLRLA 1100 (1157)
Q Consensus 1022 r~LG~cPkcGk~V~lK~GrfG~yv~c~~d~kg~~~k~~slpk~~~~~sItLe~Al~ll~~pk~lG~cP~cG-~~v~v~~G 1100 (1157)
+..+.||+||..|+++.++||.|++|++ +|+|.. ..+. .+ ........||+|| ..++++.|
T Consensus 15 ~~~~~Cp~Cg~~m~~~~~~~g~f~gCs~-----------yP~C~~-~~~~--~~----~~~~~~~~Cp~C~~~~~~~k~~ 76 (140)
T COG0551 15 KTGQICPKCGKNMVKKFGKYGIFLGCSN-----------YPKCDY-YEPE--KA----IAEKTGVKCPKCGKGLLVLKKG 76 (140)
T ss_pred ccCccCCcCCCeeEEEEccCCeEEEeCC-----------CCCCCC-Cccc--cc----ccccCceeCCCCCCCceEEEec
Confidence 4567899999999999999999999984 566664 1110 00 0112345799999 68899999
Q ss_pred cCc-ce--eecCCeeeecCCCCCCCCCCHHHHHHHhcccccccCC
Q 001106 1101 RAG-FS--VRHRRTIASVPKNMKPNDVTLEKALEFLSGKDVRRCG 1142 (1157)
Q Consensus 1101 ryG-~y--i~~~~~~~~ipk~~~~~~itle~A~~LL~~k~~k~~g 1142 (1157)
+|| .| +...+.|-.+.+.......++.+....+..++.++.|
T Consensus 77 ~~~~~f~~~~~~Pkc~~~~~~~~~~~~cp~c~~~~~~~k~~~~~~ 121 (140)
T COG0551 77 RFGKNFLGCSNYPKCRFTEKPKPKEKKCPKCGSRKLVEKKEKKKG 121 (140)
T ss_pred cCCceEEeecCCCcCceeecCCcccccCCcCCCceeEEEeeecce
Confidence 998 34 3334445444444444445777776444444444433
No 47
>PRK00076 recR recombination protein RecR; Reviewed
Probab=97.34 E-value=0.0012 Score=70.83 Aligned_cols=106 Identities=28% Similarity=0.441 Sum_probs=74.2
Q ss_pred CeEEEEecchHHHHHHh--hcCCCEEEEEeccccccccccCCCCCCCCCCcceEecccchHHHHHHHHHHhccCCeEEEc
Q 001106 349 KSVVVVESVTKAKVIQG--YLGDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILA 426 (1157)
Q Consensus 349 k~LiIaEkPskAk~Ia~--~LG~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~kk~~lk~Lk~l~k~ad~IIlA 426 (1157)
..|.|||.|.-..+|.+ .+.+-|.|.. ||+--|. ++.|+ ++.. .+.++.| -.+..+||+|
T Consensus 79 ~~icVVE~~~Dv~aiE~s~~y~G~YhVL~--G~ispl~----gi~p~-~l~i--------~~L~~ri---~~~v~EVIlA 140 (196)
T PRK00076 79 SLICVVESPADVLAIERTGEYRGLYHVLG--GLLSPLD----GIGPE-DLNI--------DELLERL---DGEVKEVILA 140 (196)
T ss_pred CEEEEECCHHHHHHHHhhCcCceEEEEec--CCcCCCC----CCCcc-ccCH--------HHHHHHH---hCCCCEEEEe
Confidence 56999999999999987 2334488886 7776553 34554 3331 2444444 2468899999
Q ss_pred cCCCccccHHHHHHHHHHhhcccccCCccEEEEEE--------cccCHHHHHHHHHhcc
Q 001106 427 SDPDREGEAIAWHIVEMLQQQDALHENITVARVVF--------HEITEASIKVALQAAR 477 (1157)
Q Consensus 427 TDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~f--------sslT~~aI~~A~~nlr 477 (1157)
|+|+.|||+.+++|.+.++. ...+|.|+-. .=++.-.+.+||++.+
T Consensus 141 ~~pt~EGe~Ta~yi~~~lk~-----~~ikvtRiA~GiP~G~~ley~D~~TL~~Al~~R~ 194 (196)
T PRK00076 141 TNPTVEGEATAHYIARLLKP-----LGVKVTRLAHGVPVGGELEYVDEGTLSRALEGRR 194 (196)
T ss_pred CCCCchHHHHHHHHHHHHHH-----cCCCeeeeeeCCCCCcceeeCCHHHHHHHHHhCc
Confidence 99999999999999999874 2457888754 2345555666666543
No 48
>PRK14973 DNA topoisomerase I; Provisional
Probab=97.31 E-value=0.00027 Score=91.44 Aligned_cols=54 Identities=17% Similarity=0.354 Sum_probs=45.6
Q ss_pred CeEEeeeEEeeecccCCCCCCCHHHHHHHHHhcCCCCCCchHHHHHhccccceEE
Q 001106 814 DPLYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVT 868 (1157)
Q Consensus 814 d~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk~GIGTpATrA~IIe~L~~R~YV~ 868 (1157)
..+.|.++..++.++.||.+|+-.+|.++.-+.|+...-|. .|.+.|++.|||.
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 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=96.86 E-value=0.0057 Score=56.93 Aligned_cols=79 Identities=24% Similarity=0.356 Sum_probs=56.7
Q ss_pred CeEEEEecchHHHHHHhhcCCCEEEEEeccccccccccCCCCCCCCCCcceEecccchHHHHHHHHHHhccCCeEEEccC
Q 001106 349 KSVVVVESVTKAKVIQGYLGDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILASD 428 (1157)
Q Consensus 349 k~LiIaEkPskAk~Ia~~LG~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~kk~~lk~Lk~l~k~ad~IIlATD 428 (1157)
+.+||||-..-+.++.++..+ ..+.++.|..+ ..++++.|++. .+.||++||
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 468999999988888887532 34555655332 12455566655 689999999
Q ss_pred CCccccHHHHHHHHHHhhcccccCCccEEEEE
Q 001106 429 PDREGEAIAWHIVEMLQQQDALHENITVARVV 460 (1157)
Q Consensus 429 pDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~ 460 (1157)
+|+.||.|.+.+.++++. +...++|+.
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=96.74 E-value=0.0016 Score=82.36 Aligned_cols=54 Identities=19% Similarity=0.370 Sum_probs=42.4
Q ss_pred CeEEeeeEEeeecccCCCCCCCHHHHHHHHH-hcCCCCCCchHHHHHhcccc--------ceEE
Q 001106 814 DPLYLGEVELKQHHTQPPARYSEGSLVKKLE-ELGIGRPSTYASTLKVLQDR--------NYVT 868 (1157)
Q Consensus 814 d~v~~~~~~i~e~~TkPP~ryTEasLI~~ME-k~GIGTpATrA~IIe~L~~R--------~YV~ 868 (1157)
..+.|.++..++.+..||.+|+-++|.+.+- +.|+.-.-|. .|++.|++. |||.
T Consensus 241 ~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl-~~aQ~LYe~~~~~~~~~g~iS 303 (675)
T PRK06599 241 QAYTVDKIEKKERKRNPPPPFITSTLQQEASRKLGFSAKKTM-RIAQKLYEGIDLGEGTVGLIT 303 (675)
T ss_pred CCeEEEEEEeeEEecCCCCCCcHHHHHHHHHHHcCCCHHHHH-HHHHHHHhccccccccceeEE
Confidence 4466778888999999999999999999885 4577655554 488999985 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=96.46 E-value=0.0027 Score=51.06 Aligned_cols=35 Identities=14% Similarity=0.299 Sum_probs=29.9
Q ss_pred CCCCCccceeeeccCCCcceEEeCCCCCCCCCccccCCCCCCcccc
Q 001106 1025 GHHPASKEKVLLKSGPYGFYVQLGEDRTGYLPKRASVSHIKDVDSI 1070 (1157)
Q Consensus 1025 G~cPkcGk~V~lK~GrfG~yv~c~~d~kg~~~k~~slpk~~~~~sI 1070 (1157)
..||+||..|+++.+++|.||+|+ ++|+|..+..+
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 46888876554
No 52
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=95.16 E-value=0.11 Score=56.16 Aligned_cols=95 Identities=27% Similarity=0.391 Sum_probs=68.2
Q ss_pred eEEEEecchHHHHHHhhc-----CCCEEEEEeccccccccccCCCCCCCCCCcceEecccchHHHHHHHHHHhccCCeEE
Q 001106 350 SVVVVESVTKAKVIQGYL-----GDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLI 424 (1157)
Q Consensus 350 ~LiIaEkPskAk~Ia~~L-----G~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~kk~~lk~Lk~l~k~ad~II 424 (1157)
.=||||-.|-+.+|.++| |..|.||-+ ++.|. ..+..-+..+.+||.|+
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 458999999999888765 888877654 12232 12334567889999999
Q ss_pred EccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEc------ccCHHHHHHHHHh
Q 001106 425 LASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFH------EITEASIKVALQA 475 (1157)
Q Consensus 425 lATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fs------slT~~aI~~A~~n 475 (1157)
||||+||-|--+|....+.|.. --..|-||.+. -++.+-|++-++|
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 2555555555554
No 53
>PF13662 Toprim_4: Toprim domain; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=94.60 E-value=0.085 Score=48.63 Aligned_cols=79 Identities=29% Similarity=0.330 Sum_probs=44.3
Q ss_pred CeEEEEecchHHHHHHhhcCCCEEEEEeccccc-cccccCCCCCCCCCCcceEecccchHHHHHHHHHHhccCCeEEEcc
Q 001106 349 KSVVVVESVTKAKVIQGYLGDMYEVLPSYGHVR-DLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILAS 427 (1157)
Q Consensus 349 k~LiIaEkPskAk~Ia~~LG~~y~V~~s~GHl~-dL~~~~~~v~p~~~f~~~~~v~~~kk~~lk~Lk~l~k~ad~IIlAT 427 (1157)
+.|||||-+.=+.++.+. |-...| ++.|+.+ .+ +++...+.. ....+||+|+
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 469999999999999998 654433 3344332 11 111100100 0157899999
Q ss_pred CCCccccHHHHHHHHHHhhcccccCCccEEEE
Q 001106 428 DPDREGEAIAWHIVEMLQQQDALHENITVARV 459 (1157)
Q Consensus 428 DpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl 459 (1157)
|+|.+|+..+.++.+.|.. ...+|+|+
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 23456554
No 54
>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=94.54 E-value=0.046 Score=41.37 Aligned_cols=32 Identities=34% Similarity=0.766 Sum_probs=20.4
Q ss_pred CCCCCCCceEEEEecccCceeEEecCCCCCCcc
Q 001106 965 SCPVCGEGTLIFKVSRFGAGYFIGCNQHPRCNY 997 (1157)
Q Consensus 965 ~CPkCGkg~lv~K~gr~G~~~F~GCsnyP~Ck~ 997 (1157)
-||+||-|.++--...+|.-..+.|+| |.|++
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 599999988877666667666789998 88976
No 55
>PRK07220 DNA topoisomerase I; Validated
Probab=94.34 E-value=0.063 Score=68.82 Aligned_cols=66 Identities=18% Similarity=0.382 Sum_probs=51.5
Q ss_pred CCeEEeeeEEeeecccCCCCCCCHHHHHHHHHhcCCCCCCchHHHHHhccccceEE--EcCceeecccc
Q 001106 813 GDPLYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVT--VKSRILYPEFR 879 (1157)
Q Consensus 813 Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk~GIGTpATrA~IIe~L~~R~YV~--~k~k~L~PT~l 879 (1157)
+..+.|.++..+++...||.+|+-.+|.+++-+.|+. |..--.|.+.|++.|||. +.....+|.+.
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 344456999999999996 33444555543
No 56
>PRK13844 recombination protein RecR; Provisional
Probab=94.31 E-value=0.27 Score=53.29 Aligned_cols=106 Identities=24% Similarity=0.380 Sum_probs=69.3
Q ss_pred CeEEEEecchHHHHHHh--hcCCCEEEEEeccccccccccCCCCCCCCCCcceEecccchHHHHHHHHHHhccCCeEEEc
Q 001106 349 KSVVVVESVTKAKVIQG--YLGDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILA 426 (1157)
Q Consensus 349 k~LiIaEkPskAk~Ia~--~LG~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~kk~~lk~Lk~l~k~ad~IIlA 426 (1157)
..|.|||.|.-..+|.+ .+.+-|.|.. ||+=-| .++.|+ ++. -.+.++.|++ .+..+||+|
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 56999999999999976 3455676652 333222 133343 221 1133344432 257899999
Q ss_pred cCCCccccHHHHHHHHHHhhcccccCCccEEEEEE--------cccCHHHHHHHHHhcc
Q 001106 427 SDPDREGEAIAWHIVEMLQQQDALHENITVARVVF--------HEITEASIKVALQAAR 477 (1157)
Q Consensus 427 TDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~f--------sslT~~aI~~A~~nlr 477 (1157)
|.|+-|||+-+.+|.+.++. ..+|.|+=. .=+++..+.+||++.+
T Consensus 146 t~~t~EGe~Ta~yi~~~lk~------~vkvtRlA~GiP~G~~ley~D~~TL~~Al~~R~ 198 (200)
T PRK13844 146 ISPTVEGETTAHFISQMIAK------DIKISRIGFGVPFGGELEYLDQQTLLHAFNART 198 (200)
T ss_pred CCCCccHHHHHHHHHHHhcC------CCcEEeeeecCcCCcceeecCHHHHHHHHHhCc
Confidence 99999999999999999863 457888743 2345666777776654
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=93.90 E-value=0.42 Score=50.68 Aligned_cols=104 Identities=23% Similarity=0.308 Sum_probs=68.7
Q ss_pred CCeEEEEecchHHHHHHhhcCCCEEEEEeccccccccccCCCCCCCCCCcceEecccchHHHHHHHHHHhccCCeEEEcc
Q 001106 348 GKSVVVVESVTKAKVIQGYLGDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILAS 427 (1157)
Q Consensus 348 ~k~LiIaEkPskAk~Ia~~LG~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~kk~~lk~Lk~l~k~ad~IIlAT 427 (1157)
-+.+||||=-+-...|..++. ..+..|-|..+ ..+.++.|+.+.++ .-||+-|
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 23556677776654 5699999
Q ss_pred CCCccccHHHHHHHHHHhhccc--ccCCccE---EEEEEcccCHHHHHHHHHhccc
Q 001106 428 DPDREGEAIAWHIVEMLQQQDA--LHENITV---ARVVFHEITEASIKVALQAARE 478 (1157)
Q Consensus 428 DpDREGE~Ia~~Ile~l~~~~~--~~~~k~v---kRl~fsslT~~aI~~A~~nlr~ 478 (1157)
|||.-||.|=..|.+++..... +.....+ .-+=+-..++++|++||.+...
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=93.60 E-value=0.25 Score=53.34 Aligned_cols=105 Identities=29% Similarity=0.444 Sum_probs=67.1
Q ss_pred CeEEEEecchHHHHHHh--hcCCCEEEEEeccccccccccCCCCCCCCCCcceEecccchHHHHHHHHHHhccCCeEEEc
Q 001106 349 KSVVVVESVTKAKVIQG--YLGDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILA 426 (1157)
Q Consensus 349 k~LiIaEkPskAk~Ia~--~LG~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~kk~~lk~Lk~l~k~ad~IIlA 426 (1157)
..|.|||.|.-.-+|.+ .+.+-|.|.. ||+=-| .++.|+ ++. -.+.++.|++ .+..+||+|
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 56899999999999976 3456676652 333322 233343 222 1133333332 257899999
Q ss_pred cCCCccccHHHHHHHHHHhhcccccCCccEEEEEE--------cccCHHHHHHHHHh
Q 001106 427 SDPDREGEAIAWHIVEMLQQQDALHENITVARVVF--------HEITEASIKVALQA 475 (1157)
Q Consensus 427 TDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~f--------sslT~~aI~~A~~n 475 (1157)
|+|+-|||+-+.+|.+.++. ...+|.|+=. .=++...+.+||++
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 22344555555544
No 59
>PRK05582 DNA topoisomerase I; Validated
Probab=92.75 E-value=0.15 Score=64.54 Aligned_cols=54 Identities=17% Similarity=0.332 Sum_probs=47.2
Q ss_pred CeEEeeeEEeeecccCCCCCCCHHHHHHHHH-hcCCCCCCchHHHHHhccc---------cceEE
Q 001106 814 DPLYLGEVELKQHHTQPPARYSEGSLVKKLE-ELGIGRPSTYASTLKVLQD---------RNYVT 868 (1157)
Q Consensus 814 d~v~~~~~~i~e~~TkPP~ryTEasLI~~ME-k~GIGTpATrA~IIe~L~~---------R~YV~ 868 (1157)
..+.+.++..+++++.||.+|+-++|.+.|- +.|+...-|. .|++.|++ .|||.
T Consensus 234 ~~~~v~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl-~~aQ~LYe~~~~~~~~~~gliS 297 (650)
T PRK05582 234 KDFKVSKVKKKERKRNPPPPFTTSTLQQEAARKLNFSTKKTM-MIAQQLYEGIDLGKQGTVGLIT 297 (650)
T ss_pred CCeEEEEEeeeeeecCCCCCccHHHHHHHHHHHcCCCHHHHH-HHHHHHhcccccCCCCceEEEE
Confidence 5577788999999999999999999998885 5699888888 69999999 68986
No 60
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=92.67 E-value=0.48 Score=47.94 Aligned_cols=102 Identities=22% Similarity=0.256 Sum_probs=67.0
Q ss_pred CeEEEEecchHHHHHHhhcCCCEEEEEeccccccccccCCCCCCCCCCcceEecccchHHHHHHHHHHhccCCeEEEccC
Q 001106 349 KSVVVVESVTKAKVIQGYLGDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILASD 428 (1157)
Q Consensus 349 k~LiIaEkPskAk~Ia~~LG~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~kk~~lk~Lk~l~k~ad~IIlATD 428 (1157)
+.+||||=.+-...|..+.-.+-+++.+.|+.. ..-++.|+++.+. ..|||-||
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 578999999988899988766544554433221 1233445554443 46999999
Q ss_pred CCccccHHHHHHHHHHhh-cccccCC----cc---EEE-EEEcccCHHHHHHHHHhcc
Q 001106 429 PDREGEAIAWHIVEMLQQ-QDALHEN----IT---VAR-VVFHEITEASIKVALQAAR 477 (1157)
Q Consensus 429 pDREGE~Ia~~Ile~l~~-~~~~~~~----k~---vkR-l~fsslT~~aI~~A~~nlr 477 (1157)
||+.||-|...+.+++.. .+. ..+ .+ ..| +-+-++...+++.||.+..
T Consensus 64 ~D~~Ge~Irk~l~~~l~~~~~~-~id~~~~~~~~~~~~i~gVE~~~~~~~~~~l~~~~ 120 (127)
T COG1658 64 PDRKGERIRKKLKEYLPGAKGA-FIDREIRNKLKINGKIIGVEEASSEALRKALKEVP 120 (127)
T ss_pred CCcchHHHHHHHHHHhcccccc-cccHHHhhhcccccccccceecChHHHHHHHHhCC
Confidence 999999999999999975 211 111 11 222 2344677888888887765
No 61
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=91.28 E-value=1.1 Score=48.14 Aligned_cols=88 Identities=27% Similarity=0.507 Sum_probs=60.5
Q ss_pred CeEEEEecchHHHHHHhh--cCCCEEEEEeccccccccccCCCCCCCCCCcceEecccchHHHHHH-HHHHhccC-CeEE
Q 001106 349 KSVVVVESVTKAKVIQGY--LGDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKS-IKVALSGA-ENLI 424 (1157)
Q Consensus 349 k~LiIaEkPskAk~Ia~~--LG~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~kk~~lk~-Lk~l~k~a-d~II 424 (1157)
..|.|||.|.-.-+|.+. +.+-|.|.. |||--|. ++.|+ +.. ++. ++++.... ++||
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 579999999999998864 355677763 5554332 34443 111 122 23344443 3999
Q ss_pred EccCCCccccHHHHHHHHHHhhcccccCCccEEEEE
Q 001106 425 LASDPDREGEAIAWHIVEMLQQQDALHENITVARVV 460 (1157)
Q Consensus 425 lATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~ 460 (1157)
+||+|--|||+-|..|.++|+.. ..+|.|+-
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=82.41 E-value=1.7 Score=51.53 Aligned_cols=65 Identities=18% Similarity=0.198 Sum_probs=46.1
Q ss_pred HHHHhccCCeEEEccCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHhcccccH
Q 001106 413 IKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAAREIDA 481 (1157)
Q Consensus 413 Lk~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fsslT~~aI~~A~~nlr~~d~ 481 (1157)
++.+++ .+.||+++|+|+-||.|.+++++.+... .+ ...| .-.-+-++++++|.+||.+..++.+
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 7899999999999999999998853211 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=81.34 E-value=3.9 Score=51.81 Aligned_cols=58 Identities=21% Similarity=0.288 Sum_probs=50.2
Q ss_pred CCCCCeEEeeeEEeeecccCCCCCCCHHHHHHHHH-hcCCCCCCchHHHHHhccccceEE
Q 001106 810 LKTGDPLYLGEVELKQHHTQPPARYSEGSLVKKLE-ELGIGRPSTYASTLKVLQDRNYVT 868 (1157)
Q Consensus 810 l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~ME-k~GIGTpATrA~IIe~L~~R~YV~ 868 (1157)
++..+...+.++.-+++.+.||.+|+-++|.+.|- +.|++..-|. .|.+.|++.|||.
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 44333677888999999999999999999999886 5699999888 7999999999996
No 64
>smart00437 TOP1Ac Bacterial DNA topoisomerase I DNA-binding domain. Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit
Probab=78.30 E-value=6.3 Score=44.63 Aligned_cols=51 Identities=14% Similarity=0.182 Sum_probs=43.2
Q ss_pred cCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHHcCCCHHHHHH-HHHHHhhc
Q 001106 593 SANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMK-LAQKLYEG 644 (1157)
Q Consensus 593 ~~~~~V~~v~~k~~~~~PP~Pf~ts~LQ~~AskklG~Sa~~Tm~-iAQ~LYE~ 644 (1157)
+..+.|.+++..+.+..||++|+-++|..+|-+ .|+.-.-|.. |.+.|.+.
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 65
>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=75.29 E-value=8.8 Score=40.15 Aligned_cols=73 Identities=19% Similarity=0.188 Sum_probs=50.9
Q ss_pred CCeEEEEecchHHHHHHhhcCCC-EEEEEeccccccccccCCCCCCCCCCcceEecccchHHHHHHHHHHhccCCeEEEc
Q 001106 348 GKSVVVVESVTKAKVIQGYLGDM-YEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILA 426 (1157)
Q Consensus 348 ~k~LiIaEkPskAk~Ia~~LG~~-y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~kk~~lk~Lk~l~k~ad~IIlA 426 (1157)
...++|+|.|++-..++..+|.. .-++++.||. ....+.-|..|...--.++.+
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 34599999999999999987652 2334444431 112333444454443489999
Q ss_pred cCCCccccHHHHHHHHHHh
Q 001106 427 SDPDREGEAIAWHIVEMLQ 445 (1157)
Q Consensus 427 TDpDREGE~Ia~~Ile~l~ 445 (1157)
+|.|-||=.|+..+++..+
T Consensus 73 GDfDp~Gl~IA~~l~~r~~ 91 (152)
T PF09664_consen 73 GDFDPEGLRIANRLIQRYG 91 (152)
T ss_pred cCCCHHHHHHHHHHHHHhC
Confidence 9999999999999988754
No 66
>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=73.02 E-value=6.9 Score=46.96 Aligned_cols=121 Identities=16% Similarity=0.207 Sum_probs=69.3
Q ss_pred hhHHHHHHHhHHHHHHhcCC-cceEEEEEEEecCcCCCCCCceeeeeecccccccccccccCCHHHHH----HHHHHHcc
Q 001106 519 QSAALSLICDREMEIDEFKP-QEYWTVEAVLDKKESHSLDTFSFPAHLTHFQSKRLNQLSIGSHTEAK----DIEQKINS 593 (1157)
Q Consensus 519 QTPtL~LVveRe~EI~~Fkp-~~Yw~I~a~~~~~~~~~~~g~~f~a~l~~~~~~~~~~~~i~d~e~Ae----~i~~~l~~ 593 (1157)
+--+-.||+.|-... |-| ..|-...+.+.. ++..|.+.....-...+.. +......+ .+-..-.+
T Consensus 225 e~~vY~LI~rr~la~--~~~~~~~~~t~v~~~~------~~~~F~~~g~~~~~~Gw~~--~~~~~~~~~~~~~lp~l~~g 294 (403)
T PF01131_consen 225 ERKVYDLIARRFLAA--FMPDAKYEKTTVTFEV------GGEEFKASGKVIIDPGWKK--VYPYEEEEDEEEDLPSLKEG 294 (403)
T ss_dssp HHHHHHHHHHHHHHH--TS--EEEEEEEEEEEE------TTEEEEEEEEEEEEHGGGG--CS-HCHCCTTSBB-----TT
T ss_pred HHHHHHHHHHHHHHH--HHHHHheeeEEEEEEe------cCcEEEEEEeEEEECceeE--EEEcccccccccccccccCC
Confidence 345667888888764 544 445555666654 2456765432211111100 11100000 12222234
Q ss_pred CCeEEEEeeeeeeeecCCCCcchHHHHHHHHHHcCCCHHHHHH-HHHHHhhcccCCCCCceEEEEEE
Q 001106 594 ANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMK-LAQKLYEGVQLPDGTAAGLITYM 659 (1157)
Q Consensus 594 ~~~~V~~v~~k~~~~~PP~Pf~ts~LQ~~AskklG~Sa~~Tm~-iAQ~LYE~~k~~~~~~~GlITYP 659 (1157)
..+.+.++..++.+..||++|+-++|...+-+ .|+.-.-|.. |.+.|.+. |||.--
T Consensus 295 ~~~~~~~~~~~e~~TkPP~~~Te~~Ll~~Me~-~GIGTpATra~iI~~L~~r---------~Yi~~~ 351 (403)
T PF01131_consen 295 DEIPIEDVEIKEKKTKPPKRYTEASLLKAMEK-AGIGTPATRASIIEKLIKR---------GYIERS 351 (403)
T ss_dssp EEEEEEEEEEEEEEEESS--EBHHHHHHHHHH-TTSS-TTTHHHHHHHHHHT---------TSEEE-
T ss_pred cEEeecccchhhhccCCCCCCCHHHHHhhhhh-cCCCccccHHHHHHHhhcc---------ceeecc
Confidence 45778888899999999999999999999855 6988766665 88999985 688774
No 67
>PRK04017 hypothetical protein; Provisional
Probab=67.53 E-value=5.8 Score=40.59 Aligned_cols=69 Identities=28% Similarity=0.365 Sum_probs=46.3
Q ss_pred eEEEEecchHHHHHHhhcCCCEEEEEeccccccccccCCCCCCCCCCcceEecccchHHHHHHHHHHhccCCeEEEccCC
Q 001106 350 SVVVVESVTKAKVIQGYLGDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILASDP 429 (1157)
Q Consensus 350 ~LiIaEkPskAk~Ia~~LG~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~kk~~lk~Lk~l~k~ad~IIlATDp 429 (1157)
.+||||=..-..++.++ |-++.++.+-|. .+. + .. +.| +.+...|||.|||
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 322233334332 110 0 01 112 4567789999999
Q ss_pred CccccHHHHHHHHHHhhc
Q 001106 430 DREGEAIAWHIVEMLQQQ 447 (1157)
Q Consensus 430 DREGE~Ia~~Ile~l~~~ 447 (1157)
|.-||-|...|.+++...
T Consensus 75 D~~GekIr~~l~~~l~~~ 92 (132)
T PRK04017 75 DRKGEELAKKLSEYLQGY 92 (132)
T ss_pred CcchHHHHHHHHHHHHhC
Confidence 999999999999998764
No 68
>COG0550 TopA Topoisomerase IA [DNA replication, recombination, and repair]
Probab=67.52 E-value=16 Score=45.89 Aligned_cols=71 Identities=25% Similarity=0.360 Sum_probs=54.8
Q ss_pred CCCCCCeEEeeeEEeeecccCCCCCCCHHHHHHHHHh-cCCCCCCchHHHHHhcccc-ceEEE---cCceeecccchh
Q 001106 809 SLKTGDPLYLGEVELKQHHTQPPARYSEGSLVKKLEE-LGIGRPSTYASTLKVLQDR-NYVTV---KSRILYPEFRGR 881 (1157)
Q Consensus 809 ~l~~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk-~GIGTpATrA~IIe~L~~R-~YV~~---k~k~L~PT~lG~ 881 (1157)
.++ |+...|.++.-+.+...||++|+-++|.+..-+ .|++..-|. .|-++|++. |||+- +...|-++-...
T Consensus 236 ~l~-~~~~~V~~ve~k~~~~~pp~Pf~tstLQq~As~~lgfs~kktm-~iAQ~LYE~~glITYpRTDs~~ls~~~~~~ 311 (570)
T COG0550 236 KLK-GKPAKVVSVEKKPKKRSPPPPFTTSTLQQEASRKLGFSAKKTM-DIAQKLYEGHGLITYPRTDSTRLSEEALAE 311 (570)
T ss_pred Hcc-CCceEEEEEeeeeeccCCCCCCcHHHHHHHHHHhCCCCHHHHH-HHHHHHhcCCCcEEecCCCCCcCCHHHHHH
Confidence 344 888999999999999999999999999998865 478777665 588999998 99862 444444444333
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=66.47 E-value=17 Score=46.68 Aligned_cols=55 Identities=20% Similarity=0.364 Sum_probs=47.0
Q ss_pred CCeEEeeeEEeeecccCCCCCCCHHHHHHHHHh-cCCCCCCchHHHHHhcccc-ceEE
Q 001106 813 GDPLYLGEVELKQHHTQPPARYSEGSLVKKLEE-LGIGRPSTYASTLKVLQDR-NYVT 868 (1157)
Q Consensus 813 Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk-~GIGTpATrA~IIe~L~~R-~YV~ 868 (1157)
|..+.|.++..+++.+.||++|+-++|.+.+-+ .|+...-|. .|.+.|++. |||.
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 698766666 799999998 9996
No 70
>PRK05776 DNA topoisomerase I; Provisional
Probab=65.06 E-value=17 Score=46.59 Aligned_cols=142 Identities=12% Similarity=0.137 Sum_probs=82.3
Q ss_pred CcchhHHHHHHHhHHHHHHhcCCcceEEEEEEEecCcCCCCCCc--eeeeeecccccccccccccC--CHHHHHHHHHHH
Q 001106 516 GRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDTF--SFPAHLTHFQSKRLNQLSIG--SHTEAKDIEQKI 591 (1157)
Q Consensus 516 GRVQTPtL~LVveRe~EI~~Fkp~~Yw~I~a~~~~~~~~~~~g~--~f~a~l~~~~~~~~~~~~i~--d~e~Ae~i~~~l 591 (1157)
...|--+-.||++|-.... ..|.-|-...+.+..+ +. .|.+.-.......+- .+. +.++.+.+-..-
T Consensus 381 ~~de~klY~LI~rRflA~~-~~~a~~~~t~v~~~~~------~~~~~F~a~G~~i~~~Gw~--~vy~~~~~~~~~LP~l~ 451 (670)
T PRK05776 381 SKDEFKLYDLIVRRFLASF-AAPAVLSNTIVTLRVP------GFPLVFSASGQRIEERGWL--KYYPFHKFDEEELPLLK 451 (670)
T ss_pred CHHHHHHHHHHHHHHHHHh-ChhheEEEEEEEEEEC------CeEEEEEEEEEEEEECCce--eecccCccccccCCCcC
Confidence 3344445688999888743 2455566766766542 23 465542211110000 010 001111111111
Q ss_pred ccCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHHcCCCHHHHHH-HHHHHhhcccCCCCCceEEEEEEccCCcCCCHHH
Q 001106 592 NSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMK-LAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEA 670 (1157)
Q Consensus 592 ~~~~~~V~~v~~k~~~~~PP~Pf~ts~LQ~~AskklG~Sa~~Tm~-iAQ~LYE~~k~~~~~~~GlITYPRTDS~~Ls~~~ 670 (1157)
.+..+.|.+++..++...||+.|+-++|.+.+-+ .|+.-.-|.. |.+.|++. |||.- -....+|.+.
T Consensus 452 ~G~~~~~~~~~~~~~~TkPP~ryTeasLi~~ME~-~GIGtpATra~iI~~L~~R---------~Yv~~--~~k~l~pT~~ 519 (670)
T PRK05776 452 KGERVKIVDVKVRKSYTKPPSRYSKASLLKWMES-VGIGTEATRARIIETLFKR---------GYLTS--NGKYIEVTPL 519 (670)
T ss_pred CCCEeEeeeeeeeccccCCCCCCCHHHHHHHHhh-CCCCCCccHHHHHHHHHhC---------CCEEe--eCCEEeECHH
Confidence 2456788888889999999999999999998865 6887777765 88999996 78863 3333444443
Q ss_pred HHHHHHHH
Q 001106 671 AKEIRSLI 678 (1157)
Q Consensus 671 ~~~i~~~i 678 (1157)
-..+.+.+
T Consensus 520 G~~v~~~L 527 (670)
T PRK05776 520 GFGVAEVL 527 (670)
T ss_pred HHHHHHHH
Confidence 33334444
No 71
>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=64.16 E-value=2.2 Score=25.29 Aligned_cols=9 Identities=44% Similarity=0.859 Sum_probs=8.0
Q ss_pred eEEEEEEcc
Q 001106 653 AGLITYMRT 661 (1157)
Q Consensus 653 ~GlITYPRT 661 (1157)
.|||++|||
T Consensus 3 sGlI~fpR~ 11 (11)
T PF08259_consen 3 SGLIPFPRV 11 (11)
T ss_pred ccccccCCC
Confidence 489999997
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=63.21 E-value=22 Score=45.25 Aligned_cols=55 Identities=24% Similarity=0.466 Sum_probs=47.3
Q ss_pred CCeEEeeeEEeeecccCCCCCCCHHHHHHHHH-hcCCCCCCchHHHHHhcccc--------ceEE
Q 001106 813 GDPLYLGEVELKQHHTQPPARYSEGSLVKKLE-ELGIGRPSTYASTLKVLQDR--------NYVT 868 (1157)
Q Consensus 813 Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~ME-k~GIGTpATrA~IIe~L~~R--------~YV~ 868 (1157)
|....+.++..+++++.||.+|+-.+|.+.+- +.|+...-|.. |++.|++. |||.
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
>PRK14724 DNA topoisomerase III; Provisional
Probab=62.21 E-value=5.9 Score=52.79 Aligned_cols=54 Identities=24% Similarity=0.334 Sum_probs=45.1
Q ss_pred CCeEEeeeEEeeecccCCCCCCCHHHHHHHHH-hcCCCCCCchHHHHHhcccc-ceEE
Q 001106 813 GDPLYLGEVELKQHHTQPPARYSEGSLVKKLE-ELGIGRPSTYASTLKVLQDR-NYVT 868 (1157)
Q Consensus 813 Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~ME-k~GIGTpATrA~IIe~L~~R-~YV~ 868 (1157)
|....|.+ ..+++.+.||.+|+-.+|-+.+- +.|+.-.-|.. |.+.|++. +||.
T Consensus 279 ~~~~~V~~-~~k~~~~~pP~pf~Lt~LQ~eA~~~~g~Sa~~TL~-iAQ~LYE~~klIT 334 (987)
T PRK14724 279 GKAATVTE-ESKPTTQASPLLFDLTSLQREANGKFGFSAKTTLA-LAQSLYERHKALT 334 (987)
T ss_pred CCCeEEEE-eeeeEecCCCCCCcHHHHHHHHHHHcCCCHHHHHH-HHHHHHHcCCeEe
Confidence 45566777 88999999999999999999995 56888777764 89999997 8996
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=61.87 E-value=19 Score=42.96 Aligned_cols=55 Identities=11% Similarity=0.201 Sum_probs=46.8
Q ss_pred cCCeEEEEeeeeeeeecCCCCcchHHHHHHHHHHcCCCHHHHHH-HHHHHhhcccCCCCCceEEEE
Q 001106 593 SANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMK-LAQKLYEGVQLPDGTAAGLIT 657 (1157)
Q Consensus 593 ~~~~~V~~v~~k~~~~~PP~Pf~ts~LQ~~AskklG~Sa~~Tm~-iAQ~LYE~~k~~~~~~~GlIT 657 (1157)
+..+.+.+++..+....||++|+-++|..++-+ .|+.-.-|+. |.+.|.+. |||.
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 455778888888999999999999999999865 5998877776 89999985 8997
No 75
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=59.76 E-value=7.4 Score=39.53 Aligned_cols=51 Identities=16% Similarity=0.247 Sum_probs=39.1
Q ss_pred CCHHHHHHHHHhcCCCCCCchHHHHHhccccceEEEc-------Cceeecccchhhhhhhhh
Q 001106 834 YSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVK-------SRILYPEFRGRMVSAFLS 888 (1157)
Q Consensus 834 yTEasLI~~MEk~GIGTpATrA~IIe~L~~R~YV~~k-------~k~L~PT~lG~~vi~~L~ 888 (1157)
.|..+|.+.| |+ +++|-..+|+.|.++|||++. ...|.+|+.|+.+.+.+.
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 3556666665 44 456899999999999999874 136999999998877654
No 76
>PRK08173 DNA topoisomerase III; Validated
Probab=55.23 E-value=40 Score=44.67 Aligned_cols=121 Identities=11% Similarity=0.126 Sum_probs=70.9
Q ss_pred hHHHHHHHhHHHHHHhcCCcceEE-EEEEEecCcCCCCCCceeeeeeccccccccccc-ccCCHHHHHHHHHHHccCCeE
Q 001106 520 SAALSLICDREMEIDEFKPQEYWT-VEAVLDKKESHSLDTFSFPAHLTHFQSKRLNQL-SIGSHTEAKDIEQKINSANFQ 597 (1157)
Q Consensus 520 TPtL~LVveRe~EI~~Fkp~~Yw~-I~a~~~~~~~~~~~g~~f~a~l~~~~~~~~~~~-~i~d~e~Ae~i~~~l~~~~~~ 597 (1157)
--+-.||++|... .|-|.--|. ..+.+.. .+..|.+.-...-...+-.+ .-.+.+..+.+-..-.+..+.
T Consensus 402 ~~iY~lI~rRfla--~f~~~a~~~~t~v~~~v------~~~~F~a~G~~~~~~Gw~~vy~~~~~~~~~~LP~l~~Ge~~~ 473 (862)
T PRK08173 402 QKLYDLVVKRFLA--VFFPAAEFLVTTRITEV------AGHHFKTEGKVLVNPGWLAVYGKEAQGADANLVPVQKGEKVK 473 (862)
T ss_pred HHHHHHHHHHHHH--HhCchheEEEEEEEEEe------CCcEEEEEEEEEeeCChHHHhCcccccccccCCCcCCCCEee
Confidence 3456788888876 565554344 3444443 24467654322111110000 000000001122122345677
Q ss_pred EEEeeeeeeeecCCCCcchHHHHHHHHH---------------HcCCCHHHHHH-HHHHHhhcccCCCCCceEEEE
Q 001106 598 VIKNSKRSMVRKNPTPYITSTLQQDAAN---------------KLNFSATYTMK-LAQKLYEGVQLPDGTAAGLIT 657 (1157)
Q Consensus 598 V~~v~~k~~~~~PP~Pf~ts~LQ~~Ask---------------klG~Sa~~Tm~-iAQ~LYE~~k~~~~~~~GlIT 657 (1157)
+.+++..++...||++|+=++|..+|-+ ..|+.-.-|.. |.+.|++. |||.
T Consensus 474 ~~~~~~~e~~TkPP~ryTEatLl~aMe~~gk~v~D~el~~~~~~~GIGTpATRA~IIe~L~~r---------~Yi~ 540 (862)
T PRK08173 474 TDKIEAVALTTKPPARYNEATLLSAMEGAGKLVEDDELREAMAEKGLGTPATRAAIIEGLLGE---------KYLV 540 (862)
T ss_pred eeeeeecccccCCCCCcCHHHHHHHHHhhhhccccHHHHhhhhcCCCCchhhHHHHHHHHHhC---------CcEE
Confidence 8888889999999999999999998863 45776666655 89999995 8997
No 77
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=54.00 E-value=11 Score=38.30 Aligned_cols=50 Identities=14% Similarity=0.105 Sum_probs=38.0
Q ss_pred CCHHHHHHHHHhcCCCCCCchHHHHHhccccceEEEc-------Cceeecccchhhhhhhh
Q 001106 834 YSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVK-------SRILYPEFRGRMVSAFL 887 (1157)
Q Consensus 834 yTEasLI~~MEk~GIGTpATrA~IIe~L~~R~YV~~k-------~k~L~PT~lG~~vi~~L 887 (1157)
.|..+|-..| || +++|-..+|+.|.++|||++. ...|.+|+.|+.+.+.+
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 23689999999876554
No 78
>PRK10870 transcriptional repressor MprA; Provisional
Probab=53.45 E-value=14 Score=39.23 Aligned_cols=54 Identities=13% Similarity=0.089 Sum_probs=40.0
Q ss_pred CCCCCHHHHHHHHHhcCCCCCCchHHHHHhccccceEEEc-------Cceeecccchhhhhhhhh
Q 001106 831 PARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVK-------SRILYPEFRGRMVSAFLS 888 (1157)
Q Consensus 831 P~ryTEasLI~~MEk~GIGTpATrA~IIe~L~~R~YV~~k-------~k~L~PT~lG~~vi~~L~ 888 (1157)
+...|..+|-+.| |+ +++|-..+|+.|.++|||++. ...|.+|+.|+.+++-+.
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 3445566676666 33 347889999999999999873 236999999998776553
No 79
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=52.88 E-value=8 Score=35.61 Aligned_cols=38 Identities=21% Similarity=0.195 Sum_probs=31.3
Q ss_pred CchHHHHHhccccceEEEcCceeecccchhhhhhhhhc
Q 001106 852 STYASTLKVLQDRNYVTVKSRILYPEFRGRMVSAFLSH 889 (1157)
Q Consensus 852 ATrA~IIe~L~~R~YV~~k~k~L~PT~lG~~vi~~L~~ 889 (1157)
.+-..+|+.|.++|+|...++.+..|++|..+.+.+..
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 80
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=52.45 E-value=12 Score=35.04 Aligned_cols=43 Identities=28% Similarity=0.363 Sum_probs=36.0
Q ss_pred HhcCCCCCCchHHHHHhccccceEEEcC-ceeecccchhhhhhhh
Q 001106 844 EELGIGRPSTYASTLKVLQDRNYVTVKS-RILYPEFRGRMVSAFL 887 (1157)
Q Consensus 844 Ek~GIGTpATrA~IIe~L~~R~YV~~k~-k~L~PT~lG~~vi~~L 887 (1157)
+..|| .++|-..++..|.+.|||.+.. +.+.+|+.|..+...+
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 34577 7889999999999999999876 5899999999876544
No 81
>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=52.45 E-value=66 Score=33.60 Aligned_cols=98 Identities=16% Similarity=0.110 Sum_probs=60.2
Q ss_pred eEEEEecchHHHHHHhhc---CCCEEEEEeccccccccccCCCCCCCCCCcceEecccchHHHHHHHHHHhccCCeEEEc
Q 001106 350 SVVVVESVTKAKVIQGYL---GDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILA 426 (1157)
Q Consensus 350 ~LiIaEkPskAk~Ia~~L---G~~y~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~kk~~lk~Lk~l~k~ad~IIlA 426 (1157)
.++||||+++...+-..- ..+.+++++.|- |+ ...+..++.|.+.. + =.+++.
T Consensus 2 ~ilvVEk~avf~~L~~~~~~~~~~~ilit~kG~------------P~----------~~tr~~l~~L~~~~-~-~~~~~l 57 (160)
T cd00223 2 FVLVVEKEAVFQRLIEEGFHERNNCILITGKGY------------PD----------RATRRFLRRLHEEL-D-LPVYIL 57 (160)
T ss_pred EEEEEecHHHHHHHHHcCccccCCEEEEEcCCc------------CC----------HHHHHHHHHHHHhh-C-CCEEEE
Confidence 589999999999887642 234455554330 21 13456666665555 2 359999
Q ss_pred cCCCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHH
Q 001106 427 SDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKV 471 (1157)
Q Consensus 427 TDpDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fsslT~~aI~~ 471 (1157)
+|.|-.|=.|+..+..-............+.++.+-.+.++++.+
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 999999999988876521110000111224578877888888755
No 82
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=51.49 E-value=23 Score=38.24 Aligned_cols=51 Identities=20% Similarity=0.079 Sum_probs=38.1
Q ss_pred CCHHHHHHHHHhcCCCCCCchHHHHHhccccceEEEc-------Cceeecccchhhhhhhhh
Q 001106 834 YSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVK-------SRILYPEFRGRMVSAFLS 888 (1157)
Q Consensus 834 yTEasLI~~MEk~GIGTpATrA~IIe~L~~R~YV~~k-------~k~L~PT~lG~~vi~~L~ 888 (1157)
.|..+|-+.| ++ +++|-..+|++|.++|||.+. .+.+.+|+.|+.+.+-+.
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 4555555533 33 568999999999999999974 236999999998776553
No 83
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=50.03 E-value=17 Score=34.74 Aligned_cols=39 Identities=23% Similarity=0.221 Sum_probs=32.2
Q ss_pred CCCchHHHHHhccccceEEEc-------Cceeecccchhhhhhhhh
Q 001106 850 RPSTYASTLKVLQDRNYVTVK-------SRILYPEFRGRMVSAFLS 888 (1157)
Q Consensus 850 TpATrA~IIe~L~~R~YV~~k-------~k~L~PT~lG~~vi~~L~ 888 (1157)
+++|-..+|+.|.++|||.+. ...+..|+.|+.++..+.
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 578889999999999999873 236999999998776654
No 84
>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=49.69 E-value=22 Score=29.46 Aligned_cols=35 Identities=31% Similarity=0.757 Sum_probs=23.1
Q ss_pred CCCCCCCceEEEEecc-cCc---eeEEecCCCC--CCcccccC
Q 001106 965 SCPVCGEGTLIFKVSR-FGA---GYFIGCNQHP--RCNYIAKT 1001 (1157)
Q Consensus 965 ~CPkCGkg~lv~K~gr-~G~---~~F~GCsnyP--~Ck~t~~~ 1001 (1157)
.|+ ||. ..+++..+ .+. ..||.|.++. .|+|..|.
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 588 985 44444443 332 2699999886 49987664
No 85
>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=49.23 E-value=34 Score=33.55 Aligned_cols=51 Identities=24% Similarity=0.192 Sum_probs=37.7
Q ss_pred CCHHHHHHHHHhcCCCCCCchHHHHHhccccceEEEc-----C--ceeecccchhhhhhhhh
Q 001106 834 YSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVK-----S--RILYPEFRGRMVSAFLS 888 (1157)
Q Consensus 834 yTEasLI~~MEk~GIGTpATrA~IIe~L~~R~YV~~k-----~--k~L~PT~lG~~vi~~L~ 888 (1157)
.|..+|-+.| ||-++ |-..+|++|.++|||++. + ..+.+|+.|+.+++.+.
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 66655 889999999999999873 2 36999999998776654
No 86
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=49.15 E-value=20 Score=36.59 Aligned_cols=55 Identities=22% Similarity=0.260 Sum_probs=41.1
Q ss_pred cCCCCCCchHHHHHhccccceEEE-cCceeecccchhhhhhhhhcccccccChhhhHHHHHHhhhH
Q 001106 846 LGIGRPSTYASTLKVLQDRNYVTV-KSRILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNV 910 (1157)
Q Consensus 846 ~GIGTpATrA~IIe~L~~R~YV~~-k~k~L~PT~lG~~vi~~L~~~f~~l~~p~~TA~~E~~Ld~I 910 (1157)
.|+ +++|-..+|..|.++|||.. ..+.+.+|+.|+.+...+. .--..||.-|+.+
T Consensus 32 l~v-s~~svs~~l~~L~~~Gli~~~~~~~i~LT~~G~~~a~~~~---------~~h~~~e~~l~~l 87 (142)
T PRK03902 32 LSV-HPSSVTKMVQKLDKDEYLIYEKYRGLVLTPKGKKIGKRLV---------YRHELLEQFLRII 87 (142)
T ss_pred hCC-ChhHHHHHHHHHHHCCCEEEecCceEEECHHHHHHHHHHH---------HHHHHHHHHHHHh
Confidence 478 58888899999999999985 4578999999997655442 2235667666544
No 87
>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=48.70 E-value=17 Score=35.51 Aligned_cols=55 Identities=16% Similarity=0.201 Sum_probs=41.8
Q ss_pred CCCCCCHHHHHHHHHhcCCCCCCchHHHHHhccccceEEEc-----C--ceeecccchhhhhhhhh
Q 001106 830 PPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVK-----S--RILYPEFRGRMVSAFLS 888 (1157)
Q Consensus 830 PP~ryTEasLI~~MEk~GIGTpATrA~IIe~L~~R~YV~~k-----~--k~L~PT~lG~~vi~~L~ 888 (1157)
++...|..+|-..| ++- ++|-..+|+.|.++|||.+. + ..+.+|+.|+.+++.+.
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 44556677777666 454 78999999999999999863 2 25889999998776654
No 88
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=47.93 E-value=11 Score=37.45 Aligned_cols=33 Identities=30% Similarity=0.877 Sum_probs=23.8
Q ss_pred CCCCCCCCCceE-----EEEecccCceeEEecCCCCCCccc
Q 001106 963 DRSCPVCGEGTL-----IFKVSRFGAGYFIGCNQHPRCNYI 998 (1157)
Q Consensus 963 ~g~CPkCGkg~l-----v~K~gr~G~~~F~GCsnyP~Ck~t 998 (1157)
..+||+||...| .+|..--|..+||-| |+|++.
T Consensus 74 ~~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC---~kC~~k 111 (116)
T KOG2907|consen 74 KHKCPKCGHEEMSYHTLQLRSADEGQTVFYTC---PKCKYK 111 (116)
T ss_pred hccCcccCCchhhhhhhhcccccCCceEEEEc---Ccccee
Confidence 468999997543 456555577789999 458874
No 89
>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=46.18 E-value=7.8 Score=35.37 Aligned_cols=47 Identities=19% Similarity=0.270 Sum_probs=32.8
Q ss_pred CCCHHHHHHHHHhcCCCCCCchHHHHHhccccceEEEcCc----eeecccch
Q 001106 833 RYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKSR----ILYPEFRG 880 (1157)
Q Consensus 833 ryTEasLI~~MEk~GIGTpATrA~IIe~L~~R~YV~~k~k----~L~PT~lG 880 (1157)
...-++||..|+..||..+|+|..+ ..|.++|.++..+. ....|+.|
T Consensus 20 ~i~~~~Li~ll~~~Gv~e~avR~al-sRl~~~G~L~~~r~Gr~~~Y~Lt~~g 70 (70)
T PF07848_consen 20 WIWVASLIRLLAAFGVSESAVRTAL-SRLVRRGWLESERRGRRSYYRLTERG 70 (70)
T ss_dssp -EEHHHHHHHHCCTT--HHHHHHHH-HHHHHTTSEEEECCCTEEEEEE-HHH
T ss_pred ceeHHHHHHHHHHcCCChHHHHHHH-HHHHHcCceeeeecCccceEeeCCCC
Confidence 3445899999999999999999875 57889999986532 24455543
No 90
>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=45.87 E-value=15 Score=32.34 Aligned_cols=36 Identities=22% Similarity=0.370 Sum_probs=26.6
Q ss_pred cCCCCCCchHHHHHhccccceEEEcCceeecccchh
Q 001106 846 LGIGRPSTYASTLKVLQDRNYVTVKSRILYPEFRGR 881 (1157)
Q Consensus 846 ~GIGTpATrA~IIe~L~~R~YV~~k~k~L~PT~lG~ 881 (1157)
.|.--...+...|+.+++.|+|+.+++.|.+|+.|+
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 354444555788999999999999999999999997
No 91
>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=45.83 E-value=17 Score=33.75 Aligned_cols=49 Identities=20% Similarity=0.190 Sum_probs=33.3
Q ss_pred cchHHHHHHHHHHcCCCHHHHHHHHHHHhhcccCCCCCceEEEEEEccCCcCCCHHHHHHH
Q 001106 614 YITSTLQQDAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEI 674 (1157)
Q Consensus 614 f~ts~LQ~~AskklG~Sa~~Tm~iAQ~LYE~~k~~~~~~~GlITYPRTDS~~Ls~~~~~~i 674 (1157)
|++++.|.- -|...=-+.+...++++|||+ ||||=| |..||+++.++.+
T Consensus 17 F~~~S~~~G-IKvH~dA~p~~i~a~~RLheK---------GLI~~p--dGgyLT~~G~~~a 65 (77)
T TIGR02647 17 FNLSSTQEG-IKVHSTASPAAVAAAARLHEK---------GLTTQP--DGGYLTSLGLEAA 65 (77)
T ss_pred CCchhhhcC-ccccccCCHHHHHHHHHHHHc---------CCccCC--CCCEecHHHHHHH
Confidence 666666642 233333345677899999997 999987 4559999865543
No 92
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=45.24 E-value=50 Score=42.82 Aligned_cols=22 Identities=23% Similarity=0.307 Sum_probs=15.9
Q ss_pred HHHHHHHHHHhHhhhhhccHHH
Q 001106 484 VQAYLARRALDYLIGFNISPLL 505 (1157)
Q Consensus 484 ~~A~~AR~~lD~LiG~nlSR~l 505 (1157)
+.....++.+||+..+-++++-
T Consensus 72 ~l~~~~~~L~~w~s~yy~~~~g 93 (730)
T COG1198 72 VLTPELLRLIEWAADYYLSPLG 93 (730)
T ss_pred CCCHHHHHHHHHHHHhhcCcHH
Confidence 3445677888888888888753
No 93
>PRK07726 DNA topoisomerase III; Provisional
Probab=42.08 E-value=28 Score=44.67 Aligned_cols=56 Identities=23% Similarity=0.366 Sum_probs=47.7
Q ss_pred CCCeEEeeeEEeeecccCCCCCCCHHHHHHHHHh-cCCCCCCchHHHHHhcccc-ceEE
Q 001106 812 TGDPLYLGEVELKQHHTQPPARYSEGSLVKKLEE-LGIGRPSTYASTLKVLQDR-NYVT 868 (1157)
Q Consensus 812 ~Gd~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk-~GIGTpATrA~IIe~L~~R-~YV~ 868 (1157)
.|..+.|.++..+++.+.||.+|+-++|.+.+-+ .|+...-|.. |.+.|++. |||.
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 94
>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=41.63 E-value=23 Score=37.19 Aligned_cols=30 Identities=27% Similarity=0.371 Sum_probs=26.1
Q ss_pred HHHHcCCCHHHHHHHHHHHhhcccCCCCCceEEEEEEcc
Q 001106 623 AANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRT 661 (1157)
Q Consensus 623 AskklG~Sa~~Tm~iAQ~LYE~~k~~~~~~~GlITYPRT 661 (1157)
.+..+|++...+-+++++|||. |||+|-|+
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 89999884
No 95
>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=41.22 E-value=32 Score=28.86 Aligned_cols=33 Identities=27% Similarity=0.684 Sum_probs=20.8
Q ss_pred CCCCCCCceEEEEeccc----CceeEEecCCCCCCcccc
Q 001106 965 SCPVCGEGTLIFKVSRF----GAGYFIGCNQHPRCNYIA 999 (1157)
Q Consensus 965 ~CPkCGkg~lv~K~gr~----G~~~F~GCsnyP~Ck~t~ 999 (1157)
.||.||. ....+.++. ....++.|.| +.|..+.
T Consensus 1 ~CP~Cg~-~a~ir~S~~~s~~~~~~Y~qC~N-~~Cg~tf 37 (47)
T PF04606_consen 1 RCPHCGS-KARIRTSRQLSPLTRELYCQCTN-PECGHTF 37 (47)
T ss_pred CcCCCCC-eeEEEEchhhCcceEEEEEEECC-CcCCCEE
Confidence 4999997 445554433 2234778988 6787643
No 96
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=40.70 E-value=19 Score=39.84 Aligned_cols=51 Identities=24% Similarity=0.303 Sum_probs=41.5
Q ss_pred CCCCCHHHHHHHHHhcCCCCCCchHHHHHhccccceEEEc----Cceeecccchhhhhh
Q 001106 831 PARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVK----SRILYPEFRGRMVSA 885 (1157)
Q Consensus 831 P~ryTEasLI~~MEk~GIGTpATrA~IIe~L~~R~YV~~k----~k~L~PT~lG~~vi~ 885 (1157)
|...|.++|-+.| |+ +++|-+.+|..|.+.|||++. +..+.+|+.|+.+.+
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 3456777887777 56 789999999999999999874 567999999997653
No 97
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=40.37 E-value=33 Score=29.81 Aligned_cols=32 Identities=25% Similarity=0.853 Sum_probs=19.6
Q ss_pred CCCCCCCCCceEEEEeccc-Cce--eEEecCCCCCCcc
Q 001106 963 DRSCPVCGEGTLIFKVSRF-GAG--YFIGCNQHPRCNY 997 (1157)
Q Consensus 963 ~g~CPkCGkg~lv~K~gr~-G~~--~F~GCsnyP~Ck~ 997 (1157)
+.+||.||...+..+.... +.+ +++-|.+ |..
T Consensus 3 LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~---Cga 37 (61)
T PF14354_consen 3 LKPCPFCGSADVLIRQDEGFDYGMYYYVECTD---CGA 37 (61)
T ss_pred CcCCCCCCCcceEeecccCCCCCCEEEEEcCC---CCC
Confidence 4689999876665553221 111 6777875 765
No 98
>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=39.00 E-value=94 Score=35.74 Aligned_cols=32 Identities=25% Similarity=0.632 Sum_probs=13.8
Q ss_pred CCCCCCCCCceEEEEeccc---CceeEEecCCCCCCccc
Q 001106 963 DRSCPVCGEGTLIFKVSRF---GAGYFIGCNQHPRCNYI 998 (1157)
Q Consensus 963 ~g~CPkCGkg~lv~K~gr~---G~~~F~GCsnyP~Ck~t 998 (1157)
.+.||.||........... |. .|+-|+- |.+.
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 5888974 6653
No 99
>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=37.69 E-value=41 Score=30.71 Aligned_cols=36 Identities=31% Similarity=0.414 Sum_probs=28.2
Q ss_pred HHHHHHHHHhccCCeEEEccCCCccccHHHHHHHHHHhh
Q 001106 408 THLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQ 446 (1157)
Q Consensus 408 ~~lk~Lk~l~k~ad~IIlATDpDREGE~Ia~~Ile~l~~ 446 (1157)
.++..|+.. ...||+|+|.|..|..-+..+.+.+..
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 100
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=36.82 E-value=38 Score=31.28 Aligned_cols=50 Identities=26% Similarity=0.343 Sum_probs=35.8
Q ss_pred CCHHHHHHHHHhcCCCCCCchHHHHHhccccceEEEcC-------ceeecccchhhhhhhh
Q 001106 834 YSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKS-------RILYPEFRGRMVSAFL 887 (1157)
Q Consensus 834 yTEasLI~~MEk~GIGTpATrA~IIe~L~~R~YV~~k~-------k~L~PT~lG~~vi~~L 887 (1157)
.|-..|...| +| +++|-..+|..|.++|||+... ..+.+|+.|..+...+
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 4555565554 56 3566779999999999998642 2588899998766544
No 101
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=36.45 E-value=40 Score=30.44 Aligned_cols=32 Identities=28% Similarity=0.623 Sum_probs=21.1
Q ss_pred CCCCCCCCCceEEEEecccCceeEEecCCCCCCcccc
Q 001106 963 DRSCPVCGEGTLIFKVSRFGAGYFIGCNQHPRCNYIA 999 (1157)
Q Consensus 963 ~g~CPkCGkg~lv~K~gr~G~~~F~GCsnyP~Ck~t~ 999 (1157)
+.+||.||...+.++.. +.++++-|. +|....
T Consensus 6 lKPCPFCG~~~~~v~~~--~g~~~v~C~---~CgA~~ 37 (64)
T PRK09710 6 VKPCPFCGCPSVTVKAI--SGYYRAKCN---GCESRT 37 (64)
T ss_pred ccCCCCCCCceeEEEec--CceEEEEcC---CCCcCc
Confidence 56899999876666643 444556674 466543
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=35.57 E-value=35 Score=46.62 Aligned_cols=52 Identities=15% Similarity=0.356 Sum_probs=45.2
Q ss_pred EEeeeEEeeecccCCCCCCCHHHHHHHHH-hcCCCCCCchHHHHHhccccceEE
Q 001106 816 LYLGEVELKQHHTQPPARYSEGSLVKKLE-ELGIGRPSTYASTLKVLQDRNYVT 868 (1157)
Q Consensus 816 v~~~~~~i~e~~TkPP~ryTEasLI~~ME-k~GIGTpATrA~IIe~L~~R~YV~ 868 (1157)
+.+.++..++.+..||++||-.+|++.+- +.|++..-|.. |.+.|++.|||.
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 56778888999999999999999999886 46998877764 899999999997
No 103
>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=35.37 E-value=54 Score=28.14 Aligned_cols=35 Identities=17% Similarity=0.646 Sum_probs=19.1
Q ss_pred CCCCCCCCceEEEEec--ccCceeEEecCCCCCCcccccC
Q 001106 964 RSCPVCGEGTLIFKVS--RFGAGYFIGCNQHPRCNYIAKT 1001 (1157)
Q Consensus 964 g~CPkCGkg~lv~K~g--r~G~~~F~GCsnyP~Ck~t~~~ 1001 (1157)
.+||.||+....++.+ ..+...++.|+ .|....+.
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~---~Cga~~~~ 38 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECS---TCGASGPV 38 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECC---CCCCCccc
Confidence 4799999755534422 11222233775 47766543
No 104
>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=34.84 E-value=1.9e+02 Score=29.38 Aligned_cols=96 Identities=19% Similarity=0.256 Sum_probs=56.9
Q ss_pred CCHHHHHHHHHh-cCCCCCCchHHHHHhccccceEEEcCceeecccchhhhhhhhhcccccccChhh-hHHHHHHhhhHh
Q 001106 834 YSEGSLVKKLEE-LGIGRPSTYASTLKVLQDRNYVTVKSRILYPEFRGRMVSAFLSHYFSEVTDYSF-TADMETELDNVS 911 (1157)
Q Consensus 834 yTEasLI~~MEk-~GIGTpATrA~IIe~L~~R~YV~~k~k~L~PT~lG~~vi~~L~~~f~~l~~p~~-TA~~E~~Ld~Ia 911 (1157)
.|-.+++..|.+ .|+. .+|-.++|..|.++|||.+++ .|+.. .+.|-+..-++ ...+...++.+-
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 24421 12233444445 345566666676
Q ss_pred hcCccHHHHHHHHHHHhhhhhhhccchhHHHHHHHHHh
Q 001106 912 AGLTEWKGLLVDYWSRFSSYCTCAQSLHIHQVEKMLEK 949 (1157)
Q Consensus 912 ~G~~~~~~~l~~F~~~f~~~v~~~~~~~i~~V~k~l~~ 949 (1157)
.|.. ..+|..|.+. + .......+.+.+++++
T Consensus 86 ~gs~--~~ll~~l~~~--~---~ls~eele~L~~li~~ 116 (130)
T TIGR02698 86 SRKV--GAVIADLIEE--S---PLSQTDIEKLEKLLSE 116 (130)
T ss_pred CCCH--HHHHHHHHhc--C---CCCHHHHHHHHHHHHh
Confidence 6754 4577776552 1 1122234555666654
No 105
>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=34.38 E-value=51 Score=29.70 Aligned_cols=27 Identities=37% Similarity=0.460 Sum_probs=23.2
Q ss_pred CCeEEEccCCCccccHHHHHHHHHHhh
Q 001106 420 AENLILASDPDREGEAIAWHIVEMLQQ 446 (1157)
Q Consensus 420 ad~IIlATDpDREGE~Ia~~Ile~l~~ 446 (1157)
...||+|.|.|..|+..+..+.+.+..
T Consensus 43 ~~~vii~~D~D~~G~~~~~~~~~~~~~ 69 (79)
T cd01029 43 ARTVILAFDNDEAGKKAAARALELLLA 69 (79)
T ss_pred CCEEEEEECCCHHHHHHHHHHHHHHHH
Confidence 478999999999999888888887753
No 106
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=34.19 E-value=39 Score=36.32 Aligned_cols=30 Identities=27% Similarity=0.414 Sum_probs=26.4
Q ss_pred HHHHHcCCCHHHHHHHHHHHhhcccCCCCCceEEEEEEc
Q 001106 622 DAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMR 660 (1157)
Q Consensus 622 ~AskklG~Sa~~Tm~iAQ~LYE~~k~~~~~~~GlITYPR 660 (1157)
+++..+|++...+-+++++|||. |||+|-|
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 107
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.28 E-value=17 Score=32.58 Aligned_cols=30 Identities=37% Similarity=0.852 Sum_probs=17.0
Q ss_pred CCCCCCCCCceEEEEecccCceeEEecCCCCCCccc
Q 001106 963 DRSCPVCGEGTLIFKVSRFGAGYFIGCNQHPRCNYI 998 (1157)
Q Consensus 963 ~g~CPkCGkg~lv~K~gr~G~~~F~GCsnyP~Ck~t 998 (1157)
..+||.||+.....-.+.|-+ | |+ ..|+.+
T Consensus 7 ~v~CP~Cgkpv~w~~~s~frP--F--CS--kRCklI 36 (65)
T COG3024 7 TVPCPTCGKPVVWGEESPFRP--F--CS--KRCKLI 36 (65)
T ss_pred cccCCCCCCcccccccCCcCc--c--hh--Hhhhhc
Confidence 468999998543333334333 4 65 356553
No 108
>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=32.19 E-value=35 Score=33.01 Aligned_cols=32 Identities=41% Similarity=0.643 Sum_probs=25.4
Q ss_pred HHHHHHcCCCHHHHHHHHHHHhhcccCCCCCceEEEEEEcc
Q 001106 621 QDAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRT 661 (1157)
Q Consensus 621 ~~AskklG~Sa~~Tm~iAQ~LYE~~k~~~~~~~GlITYPRT 661 (1157)
.+.++.+|+++.++-++++.||+. |||+|-|.
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 109
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=31.94 E-value=74 Score=27.65 Aligned_cols=30 Identities=23% Similarity=0.176 Sum_probs=20.8
Q ss_pred ccCCCCCCCcCeEEeeccCc------ceeecCCeee
Q 001106 1084 NLGNHPKDGQPIMLRLARAG------FSVRHRRTIA 1113 (1157)
Q Consensus 1084 ~lG~cP~cG~~v~v~~GryG------~yi~~~~~~~ 1113 (1157)
.|..||-||.+.+......+ .||.|..+.+
T Consensus 2 ~LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 46679999877666555444 5688777654
No 110
>PRK14701 reverse gyrase; Provisional
Probab=31.77 E-value=53 Score=46.43 Aligned_cols=65 Identities=14% Similarity=0.218 Sum_probs=54.4
Q ss_pred eEEeeeEEeeecccCCCCCCCHHHHHHHHHh-cCCCCCCchHHHHHhccccceEEEcCceeecccchh
Q 001106 815 PLYLGEVELKQHHTQPPARYSEGSLVKKLEE-LGIGRPSTYASTLKVLQDRNYVTVKSRILYPEFRGR 881 (1157)
Q Consensus 815 ~v~~~~~~i~e~~TkPP~ryTEasLI~~MEk-~GIGTpATrA~IIe~L~~R~YV~~k~k~L~PT~lG~ 881 (1157)
.+.+.++..+++...||++||-.+|.+.+-+ .|++..-|. .|.+.|++.||+. -.+..+.|+-|.
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 3567788899999999999999999999965 599877776 4899999999986 456677888886
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=31.56 E-value=1.5e+02 Score=35.75 Aligned_cols=88 Identities=20% Similarity=0.220 Sum_probs=56.0
Q ss_pred eEEEEecchHHHHHHhhcCCCE-EEEEeccccccccccCCCCCCCCCCcceEecccchHHHHHHHHHHhccCCeEEEccC
Q 001106 350 SVVVVESVTKAKVIQGYLGDMY-EVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILASD 428 (1157)
Q Consensus 350 ~LiIaEkPskAk~Ia~~LG~~y-~V~~s~GHl~dL~~~~~~v~p~~~f~~~~~v~~~kk~~lk~Lk~l~k~ad~IIlATD 428 (1157)
.++|||-|++-..+...++... -++++.|. . +.....-|.++...-..|+-.+|
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 34444431 1 22344455556543333454599
Q ss_pred CCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHHHHh
Q 001106 429 PDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQA 475 (1157)
Q Consensus 429 pDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fsslT~~aI~~A~~n 475 (1157)
.|-||=.|+.++....+ -+.| -++.++-++|+.+
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 99999999999987542 1223 3456666666553
No 112
>KOG1956 consensus DNA topoisomerase III alpha [Replication, recombination and repair]
Probab=29.28 E-value=40 Score=42.36 Aligned_cols=56 Identities=13% Similarity=-0.140 Sum_probs=48.2
Q ss_pred eeecCCCCCCCCCCCCCCCeEEEEecchHHHHHHhhcCCCEEEEEecccccccccc
Q 001106 331 VIVPRGQNTQNPLYPPSGKSVVVVESVTKAKVIQGYLGDMYEVLPSYGHVRDLAAR 386 (1157)
Q Consensus 331 ~~~~~~~~~~~~~~~~~~k~LiIaEkPskAk~Ia~~LG~~y~V~~s~GHl~dL~~~ 386 (1157)
+++---..-|.++++++++..|..++|.++..+.-+++..+.+.-..|||.+++..
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 113
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=29.26 E-value=56 Score=35.17 Aligned_cols=31 Identities=29% Similarity=0.502 Sum_probs=27.1
Q ss_pred HHHHHcCCCHHHHHHHHHHHhhcccCCCCCceEEEEEEcc
Q 001106 622 DAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRT 661 (1157)
Q Consensus 622 ~AskklG~Sa~~Tm~iAQ~LYE~~k~~~~~~~GlITYPRT 661 (1157)
+.+..+|+....+.++.+.|||. |+|+|.|.
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 89998773
No 114
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=28.59 E-value=14 Score=34.43 Aligned_cols=41 Identities=32% Similarity=0.443 Sum_probs=29.6
Q ss_pred HhcCCCCCCchHHHHHhccccceEEEcC----c----eeecccchhhhhh
Q 001106 844 EELGIGRPSTYASTLKVLQDRNYVTVKS----R----ILYPEFRGRMVSA 885 (1157)
Q Consensus 844 Ek~GIGTpATrA~IIe~L~~R~YV~~k~----k----~L~PT~lG~~vi~ 885 (1157)
+..|| |+++-..|+++|.+.|||..++ + .+..|+.|+...+
T Consensus 22 ~~l~l-t~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~ 70 (80)
T PF13601_consen 22 EELGL-TDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAFE 70 (80)
T ss_dssp HHTT---HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHHH
T ss_pred HHhCc-CHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHHH
Confidence 34678 8899999999999999998742 2 3788999986443
No 115
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=28.41 E-value=56 Score=25.94 Aligned_cols=29 Identities=31% Similarity=0.679 Sum_probs=19.0
Q ss_pred CCCCCCCceEEEEecccCceeEEecCCCCCCccccc
Q 001106 965 SCPVCGEGTLIFKVSRFGAGYFIGCNQHPRCNYIAK 1000 (1157)
Q Consensus 965 ~CPkCGkg~lv~K~gr~G~~~F~GCsnyP~Ck~t~~ 1000 (1157)
-||.||. +|..+.++.+. . .|. .|.+..+
T Consensus 3 FCp~C~n-lL~p~~~~~~~--~-~C~---~C~Y~~~ 31 (35)
T PF02150_consen 3 FCPECGN-LLYPKEDKEKR--V-ACR---TCGYEEP 31 (35)
T ss_dssp BETTTTS-BEEEEEETTTT--E-EES---SSS-EEE
T ss_pred eCCCCCc-cceEcCCCccC--c-CCC---CCCCccC
Confidence 4999996 77777666554 2 674 4777543
No 116
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=28.05 E-value=76 Score=42.82 Aligned_cols=42 Identities=24% Similarity=0.097 Sum_probs=29.0
Q ss_pred CCccccHHHHHHHHHHhhcccccCCccEEEEEEcccCHHHHHHH
Q 001106 429 PDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVA 472 (1157)
Q Consensus 429 pDREGE~Ia~~Ile~l~~~~~~~~~k~vkRl~fsslT~~aI~~A 472 (1157)
.-|+..+|+..|.+...... ....+.+|+-||.=|+=+=..|
T Consensus 309 f~~~l~m~i~~I~ei~~~~r--~D~~~eKRVELh~HTkMS~mDa 350 (1444)
T COG2176 309 FTRDLTMIINDINEIENAKR--KDLAKEKRVELHFHTKMSQMDA 350 (1444)
T ss_pred cccceEEEhhhhhhhhcccc--cccCccceEEEEeccchhhhcc
Confidence 35889999999988764432 2345799999998776443333
No 117
>PRK00420 hypothetical protein; Validated
Probab=27.61 E-value=46 Score=33.32 Aligned_cols=11 Identities=45% Similarity=1.147 Sum_probs=8.3
Q ss_pred CCCCCCCCCce
Q 001106 963 DRSCPVCGEGT 973 (1157)
Q Consensus 963 ~g~CPkCGkg~ 973 (1157)
...||.||.+.
T Consensus 23 ~~~CP~Cg~pL 33 (112)
T PRK00420 23 SKHCPVCGLPL 33 (112)
T ss_pred cCCCCCCCCcc
Confidence 35899999643
No 118
>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=27.35 E-value=94 Score=30.58 Aligned_cols=79 Identities=18% Similarity=0.217 Sum_probs=51.2
Q ss_pred CCHHHHHHHHHhc-CCCCCCchHHHHHhccccceEEEcCceeecccchhhhhhhhhcccccccChhhh-HHHHHHhhhHh
Q 001106 834 YSEGSLVKKLEEL-GIGRPSTYASTLKVLQDRNYVTVKSRILYPEFRGRMVSAFLSHYFSEVTDYSFT-ADMETELDNVS 911 (1157)
Q Consensus 834 yTEasLI~~MEk~-GIGTpATrA~IIe~L~~R~YV~~k~k~L~PT~lG~~vi~~L~~~f~~l~~p~~T-A~~E~~Ld~Ia 911 (1157)
.|-.++++.|.+. ++ .++|-.+.+..|.++|||..+. .|+..+ +.|-+..-++. ..+...++.+.
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 144211 22333333433 46777778887
Q ss_pred hcCccHHHHHHHHHHH
Q 001106 912 AGLTEWKGLLVDYWSR 927 (1157)
Q Consensus 912 ~G~~~~~~~l~~F~~~ 927 (1157)
.| +...++..|.+.
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 455677776653
No 119
>PHA00626 hypothetical protein
Probab=26.93 E-value=59 Score=28.68 Aligned_cols=11 Identities=55% Similarity=1.422 Sum_probs=8.4
Q ss_pred CCCCCCCceEE
Q 001106 965 SCPVCGEGTLI 975 (1157)
Q Consensus 965 ~CPkCGkg~lv 975 (1157)
.||.||...++
T Consensus 2 ~CP~CGS~~Iv 12 (59)
T PHA00626 2 SCPKCGSGNIA 12 (59)
T ss_pred CCCCCCCceee
Confidence 59999985544
No 120
>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=26.20 E-value=1.3e+02 Score=28.89 Aligned_cols=52 Identities=12% Similarity=0.245 Sum_probs=38.6
Q ss_pred CHHHHHHHHHhcC-----CCCCCchHHHHHhccccceEEEc---------Cceeecccchhhhhhhh
Q 001106 835 SEGSLVKKLEELG-----IGRPSTYASTLKVLQDRNYVTVK---------SRILYPEFRGRMVSAFL 887 (1157)
Q Consensus 835 TEasLI~~MEk~G-----IGTpATrA~IIe~L~~R~YV~~k---------~k~L~PT~lG~~vi~~L 887 (1157)
+=-+|.+.|++.. |+ ++|--.++..|.+.|||+.. .+.+..|+.|+.+.+.+
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 4457788887642 33 47888999999999999862 25689999999765543
No 121
>PF13362 Toprim_3: Toprim domain
Probab=25.21 E-value=2.1e+02 Score=26.93 Aligned_cols=65 Identities=23% Similarity=0.429 Sum_probs=42.6
Q ss_pred eEEEEecchHHHHHHhhcCCCEEEEEec--cccccccccCCCCCCCCCCcceEecccchHHHHHHHHHHhccCCeEEEcc
Q 001106 350 SVVVVESVTKAKVIQGYLGDMYEVLPSY--GHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILAS 427 (1157)
Q Consensus 350 ~LiIaEkPskAk~Ia~~LG~~y~V~~s~--GHl~dL~~~~~~v~p~~~f~~~~~v~~~kk~~lk~Lk~l~k~ad~IIlAT 427 (1157)
+|+|+|-..-|-+++ +...++.|.++. |+|.... ++ .....||||.
T Consensus 1 tl~i~EG~etals~~-~~~~~~~~~a~~~~~nl~~~~-----------------~~--------------~~~~~vii~~ 48 (96)
T PF13362_consen 1 TLIIAEGIETALSIA-QQATGVPVVAALGAGNLKNVA-----------------IP--------------EPGRRVIIAA 48 (96)
T ss_pred CEEEEEhHHHHHHHH-HhcCCCeEEEEEChhhhhhhc-----------------CC--------------CCCCeEEEEE
Confidence 589999888888882 333444444443 3333211 00 2346789999
Q ss_pred CCCcc--ccHHHHHHHHHHhh
Q 001106 428 DPDRE--GEAIAWHIVEMLQQ 446 (1157)
Q Consensus 428 DpDRE--GE~Ia~~Ile~l~~ 446 (1157)
|.|.. |+.=+..+.+.+..
T Consensus 49 D~D~~~~G~~~a~~~~~~~~~ 69 (96)
T PF13362_consen 49 DNDKANEGQKAAEKAAERLEA 69 (96)
T ss_pred CCCCchhhHHHHHHHHHHHHh
Confidence 99999 99988888887754
No 122
>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=24.92 E-value=77 Score=27.35 Aligned_cols=42 Identities=17% Similarity=0.235 Sum_probs=30.9
Q ss_pred CCCHHHHHHHHHhcCCCCCCchHHHHHhccccceEEEcC-ceeeccc
Q 001106 833 RYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKS-RILYPEF 878 (1157)
Q Consensus 833 ryTEasLI~~MEk~GIGTpATrA~IIe~L~~R~YV~~k~-k~L~PT~ 878 (1157)
.+|..+|-+.+ |+ +++|-..+|..|.+.|||...+ +.+.+++
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 66 5677888999999999999876 6666653
No 123
>PRK09401 reverse gyrase; Reviewed
Probab=24.89 E-value=59 Score=44.58 Aligned_cols=51 Identities=20% Similarity=0.277 Sum_probs=44.6
Q ss_pred EeeeEEeeecccCCCCCCCHHHHHHHHHh-cCCCCCCchHHHHHhccccceEE
Q 001106 817 YLGEVELKQHHTQPPARYSEGSLVKKLEE-LGIGRPSTYASTLKVLQDRNYVT 868 (1157)
Q Consensus 817 ~~~~~~i~e~~TkPP~ryTEasLI~~MEk-~GIGTpATrA~IIe~L~~R~YV~ 868 (1157)
.+..+..++.+..||++||-.+|.+.+-+ .|++..-|.. |.+.|++.|||.
T Consensus 868 ~V~~v~~k~~~~~pP~Pf~t~~Lq~~As~~lg~Sa~~tm~-iAQ~LYE~glIT 919 (1176)
T PRK09401 868 EVEKVEEKEEELNPLPPYTTDTLLSDASRKLRLSAQETMR-IAQDLFELGLIT 919 (1176)
T ss_pred eeeEEEeeEEEecCCCCCccHHHHHHHHHHcCCCHHHHHH-HHHHHHhCCcee
Confidence 56678889999999999999999999864 6998887775 899999999996
No 124
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=24.76 E-value=1.5e+02 Score=31.22 Aligned_cols=51 Identities=20% Similarity=0.404 Sum_probs=41.1
Q ss_pred HHHHHHHcCCCHHHHHHHHHHHhhcccCCCCCceEEEEEEccCCcCCCHHHHHHHHHHHH
Q 001106 620 QQDAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIF 679 (1157)
Q Consensus 620 Q~~AskklG~Sa~~Tm~iAQ~LYE~~k~~~~~~~GlITYPRTDS~~Ls~~~~~~i~~~i~ 679 (1157)
+.+.+..|+.+|.-+.+.+++|.+. |||.|-+=..-.|++.....+..++.
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 99999777777888766555555443
No 125
>KOG1589 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.40 E-value=32 Score=34.03 Aligned_cols=14 Identities=43% Similarity=0.857 Sum_probs=9.3
Q ss_pred hhhhhhhhccCCCC
Q 001106 38 FMATHRAFWNHQGI 51 (1157)
Q Consensus 38 ~~~~~~~~~~~~~~ 51 (1157)
||++.|.|||||+-
T Consensus 6 ~~~k~r~~WnhpaG 19 (118)
T KOG1589|consen 6 FVAKLRPLWNHPAG 19 (118)
T ss_pred HHHHHHHHhcCCCC
Confidence 55667777777763
No 126
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=24.24 E-value=59 Score=27.23 Aligned_cols=29 Identities=34% Similarity=0.699 Sum_probs=16.4
Q ss_pred CCCCCCCceEEEEecccCceeEEecCCCCCCcccc
Q 001106 965 SCPVCGEGTLIFKVSRFGAGYFIGCNQHPRCNYIA 999 (1157)
Q Consensus 965 ~CPkCGkg~lv~K~gr~G~~~F~GCsnyP~Ck~t~ 999 (1157)
-||.||. +|..+..... ..+.|. .|.+..
T Consensus 2 FCp~Cg~-~l~~~~~~~~--~~~vC~---~Cg~~~ 30 (52)
T smart00661 2 FCPKCGN-MLIPKEGKEK--RRFVCR---KCGYEE 30 (52)
T ss_pred CCCCCCC-ccccccCCCC--CEEECC---cCCCeE
Confidence 4999986 5554432211 256674 577654
No 127
>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=23.90 E-value=65 Score=37.03 Aligned_cols=52 Identities=21% Similarity=0.215 Sum_probs=42.2
Q ss_pred CCCHHHHHHHHHhcCCCCCCchHHHHHhccccceEEEcC----ceeecccchhhhhh
Q 001106 833 RYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKS----RILYPEFRGRMVSA 885 (1157)
Q Consensus 833 ryTEasLI~~MEk~GIGTpATrA~IIe~L~~R~YV~~k~----k~L~PT~lG~~vi~ 885 (1157)
...-++||+.|+..||...+.|. ++..|.++|+|+... +....|+.|+...+
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 577999999998753 46889999986544
No 128
>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=23.61 E-value=30 Score=30.15 Aligned_cols=30 Identities=20% Similarity=0.227 Sum_probs=22.4
Q ss_pred CCchHHHHHhccccceEEEc-----C--ceeecccch
Q 001106 851 PSTYASTLKVLQDRNYVTVK-----S--RILYPEFRG 880 (1157)
Q Consensus 851 pATrA~IIe~L~~R~YV~~k-----~--k~L~PT~lG 880 (1157)
.+|-..+|+.|.++|||++. + +.+.+|+.|
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 358888876
No 129
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=22.72 E-value=55 Score=34.36 Aligned_cols=40 Identities=20% Similarity=0.153 Sum_probs=32.3
Q ss_pred CCCCCCchHHHHHhccccceEEE-cCceeecccchhhhhhhh
Q 001106 847 GIGRPSTYASTLKVLQDRNYVTV-KSRILYPEFRGRMVSAFL 887 (1157)
Q Consensus 847 GIGTpATrA~IIe~L~~R~YV~~-k~k~L~PT~lG~~vi~~L 887 (1157)
++ .|+|-..++++|.+.|||.. +.+.+..|+.|..+...+
T Consensus 35 ~V-sp~sVt~ml~rL~~~GlV~~~~y~gi~LT~~G~~~a~~~ 75 (154)
T COG1321 35 KV-SPPSVTEMLKRLERLGLVEYEPYGGVTLTEKGREKAKEL 75 (154)
T ss_pred CC-CcHHHHHHHHHHHHCCCeEEecCCCeEEChhhHHHHHHH
Confidence 44 47788999999999999987 567899999999655433
No 130
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=22.58 E-value=1.8e+02 Score=29.62 Aligned_cols=48 Identities=25% Similarity=0.344 Sum_probs=39.3
Q ss_pred HHHHHHcCCCHHHHHHHHHHHhhcccCCCCCceEEEEEEccCCcCCCHHHHHHHHHH
Q 001106 621 QDAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSL 677 (1157)
Q Consensus 621 ~~AskklG~Sa~~Tm~iAQ~LYE~~k~~~~~~~GlITYPRTDS~~Ls~~~~~~i~~~ 677 (1157)
.+.+..+++|+.-+....++|-+. |||.|-|...-.|++.....+..+
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 131
>PLN03122 Poly [ADP-ribose] polymerase; Provisional
Probab=22.41 E-value=1.9e+02 Score=38.24 Aligned_cols=33 Identities=24% Similarity=0.561 Sum_probs=22.4
Q ss_pred CCCCCCCCCceEEEEecccCceeEEecCC----CCCCcccccCC
Q 001106 963 DRSCPVCGEGTLIFKVSRFGAGYFIGCNQ----HPRCNYIAKTL 1002 (1157)
Q Consensus 963 ~g~CPkCGkg~lv~K~gr~G~~~F~GCsn----yP~Ck~t~~~~ 1002 (1157)
..+||.|++ .++...+ .|.|++ |.+|.++...+
T Consensus 111 l~~Cp~C~g-~l~~~g~------~Y~C~G~iSeWtKC~y~T~~P 147 (815)
T PLN03122 111 LEKCPLCGG-ALECDGH------RYTCTGFISEWSSCTFSTKNP 147 (815)
T ss_pred CCCCCCCCC-eEEEcCC------eeEeccccCCCcccccccCCC
Confidence 568999995 6666532 567865 57898865333
No 132
>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=22.23 E-value=60 Score=25.99 Aligned_cols=20 Identities=20% Similarity=0.213 Sum_probs=14.4
Q ss_pred hcCCcccCCCCCCCcCeEEe
Q 001106 1079 LRYPVNLGNHPKDGQPIMLR 1098 (1157)
Q Consensus 1079 l~~pk~lG~cP~cG~~v~v~ 1098 (1157)
+..|+.-|+|..||++++.+
T Consensus 15 ~~pP~~~~~Cd~cg~~L~qR 34 (36)
T PF05191_consen 15 FNPPKVEGVCDNCGGELVQR 34 (36)
T ss_dssp TB--SSTTBCTTTTEBEBEE
T ss_pred cCCCCCCCccCCCCCeeEeC
Confidence 34577889999999987755
No 133
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=22.19 E-value=90 Score=26.41 Aligned_cols=27 Identities=19% Similarity=0.543 Sum_probs=18.2
Q ss_pred CCCCCCCCceEEEEecccCceeEEecCCC
Q 001106 964 RSCPVCGEGTLIFKVSRFGAGYFIGCNQH 992 (1157)
Q Consensus 964 g~CPkCGkg~lv~K~gr~G~~~F~GCsny 992 (1157)
..|+.||. .|..+... +.+.+|-|.++
T Consensus 6 l~C~~CG~-~m~~~~~~-~~~~yy~C~~~ 32 (58)
T PF13408_consen 6 LRCGHCGS-KMTRRKRK-GKYRYYRCSNR 32 (58)
T ss_pred EEcccCCc-EeEEEECC-CCceEEEcCCC
Confidence 47999997 45544433 44467899875
No 134
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=22.15 E-value=99 Score=31.99 Aligned_cols=51 Identities=14% Similarity=0.191 Sum_probs=40.6
Q ss_pred CHHHHHHHHHhcCCCC----CCchHHHHHhccccceEEE-----cCceeecccchhhhhh
Q 001106 835 SEGSLVKKLEELGIGR----PSTYASTLKVLQDRNYVTV-----KSRILYPEFRGRMVSA 885 (1157)
Q Consensus 835 TEasLI~~MEk~GIGT----pATrA~IIe~L~~R~YV~~-----k~k~L~PT~lG~~vi~ 885 (1157)
.=-.|++.|++.|+|. ++|-=.++.+|.+.|||.. ..+.+.+|+.|+....
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 3457888888888775 7899999999999999975 2467889999996544
No 135
>PHA02998 RNA polymerase subunit; Provisional
Probab=21.68 E-value=1.2e+02 Score=32.65 Aligned_cols=35 Identities=14% Similarity=0.270 Sum_probs=21.9
Q ss_pred CCCCCCCCCCceE-----EEEecccCceeEEecCCCCCCcccc
Q 001106 962 KDRSCPVCGEGTL-----IFKVSRFGAGYFIGCNQHPRCNYIA 999 (1157)
Q Consensus 962 ~~g~CPkCGkg~l-----v~K~gr~G~~~F~GCsnyP~Ck~t~ 999 (1157)
....||+||.... +.|.+--+...|+-|.+ |....
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~---CG~~w 181 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRD---CKKHF 181 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCC---CCCcc
Confidence 4679999997542 33333334457899954 87654
No 136
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=21.65 E-value=84 Score=29.09 Aligned_cols=33 Identities=21% Similarity=0.567 Sum_probs=21.1
Q ss_pred CCCCCCCceEEEEecccC-c---eeEEecCCCCCCcccc
Q 001106 965 SCPVCGEGTLIFKVSRFG-A---GYFIGCNQHPRCNYIA 999 (1157)
Q Consensus 965 ~CPkCGkg~lv~K~gr~G-~---~~F~GCsnyP~Ck~t~ 999 (1157)
.||.||... .++.+++- . ..+..|.| ++|..+.
T Consensus 3 ~CP~Cg~~a-~irtSr~~s~~~~~~Y~qC~N-~eCg~tF 39 (72)
T PRK09678 3 HCPLCQHAA-HARTSRYITDTTKERYHQCQN-VNCSATF 39 (72)
T ss_pred cCCCCCCcc-EEEEChhcChhhheeeeecCC-CCCCCEE
Confidence 699999755 55555442 1 23667887 6787643
No 137
>PF08063 PADR1: PADR1 (NUC008) domain; InterPro: IPR012982 This domain is found in poly(ADP-ribose)-synthetases []. The function of this domain is unknown.; GO: 0003950 NAD+ ADP-ribosyltransferase activity, 0005634 nucleus; PDB: 2JVN_A 4DQY_E 2RIQ_A.
Probab=21.60 E-value=40 Score=29.45 Aligned_cols=31 Identities=32% Similarity=0.696 Sum_probs=17.0
Q ss_pred CCCCCCCCCceEEEEecccCceeEEecCC----CCCCcccc
Q 001106 963 DRSCPVCGEGTLIFKVSRFGAGYFIGCNQ----HPRCNYIA 999 (1157)
Q Consensus 963 ~g~CPkCGkg~lv~K~gr~G~~~F~GCsn----yP~Ck~t~ 999 (1157)
..+||.|+++.++.... .+.|.+ |-+|.+..
T Consensus 14 l~~Cp~C~~~~l~~~~~------~Y~C~G~~sewtkC~~~t 48 (55)
T PF08063_consen 14 LEPCPKCKGGQLYFDGS------GYKCTGYISEWTKCTYST 48 (55)
T ss_dssp E---SSSSE-EEEEETT------EEEEESECCTTCEEEEEE
T ss_pred CCCCCCCCCCeEEecCC------ccEeCcccCceeEcccCc
Confidence 35899999876665432 355654 56787754
No 138
>PTZ00407 DNA topoisomerase IA; Provisional
Probab=20.83 E-value=1.7e+02 Score=38.53 Aligned_cols=72 Identities=15% Similarity=0.125 Sum_probs=51.7
Q ss_pred eEEEEeeeeeeeecCCCCcchHHHHHHHHHHcCCCHHHHHH-HHHHHhhcccCCCCCceEEEEEEccCCc-CCCHHHHHH
Q 001106 596 FQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMK-LAQKLYEGVQLPDGTAAGLITYMRTDGL-HISDEAAKE 673 (1157)
Q Consensus 596 ~~V~~v~~k~~~~~PP~Pf~ts~LQ~~AskklG~Sa~~Tm~-iAQ~LYE~~k~~~~~~~GlITYPRTDS~-~Ls~~~~~~ 673 (1157)
+.|.+++..+++..||++|+=++|.+++-+ .|+.-.-|.. |.+.|.+. |||. +.+.. .+|.+.-..
T Consensus 561 ~~i~~~~l~ek~TkPPpryTEAtLIk~ME~-~GIGTPATrAsIIetL~~R---------~YV~--~~~kkrl~PT~lG~~ 628 (805)
T PTZ00407 561 FELRSPQVRENRPVPPLPHSEGTLIEELKN-NGVGRPSTYPMIVKTLLAR---------GYIA--VNPKGRCETTPVGRM 628 (805)
T ss_pred eecceeeeecccCCCCCCCCHHHHHHHHHh-CCCCCcccHHHHHHHHHhc---------CCEE--eccCceeeecHHHHH
Confidence 456777778888899999999999998866 6997777776 79999995 8996 33233 445544334
Q ss_pred HHHHHH
Q 001106 674 IRSLIF 679 (1157)
Q Consensus 674 i~~~i~ 679 (1157)
+.+++.
T Consensus 629 Li~~L~ 634 (805)
T PTZ00407 629 LVETAK 634 (805)
T ss_pred HHHHHH
Confidence 444443
Done!