Query 045217
Match_columns 224
No_of_seqs 193 out of 1074
Neff 7.1
Searched_HMMs 46136
Date Fri Mar 29 11:00:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045217.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045217hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK05776 DNA topoisomerase I; 100.0 2.3E-63 4.9E-68 479.4 24.0 216 8-224 188-406 (670)
2 TIGR01057 topA_arch DNA topois 100.0 9.9E-63 2.1E-67 472.5 24.6 218 7-224 184-402 (618)
3 PRK08173 DNA topoisomerase III 100.0 3E-62 6.5E-67 481.5 23.3 215 7-224 188-423 (862)
4 PRK07219 DNA topoisomerase I; 100.0 1.3E-61 2.9E-66 476.7 23.3 217 8-224 190-411 (822)
5 PRK07220 DNA topoisomerase I; 100.0 3.3E-61 7.1E-66 469.1 23.3 213 8-224 190-403 (740)
6 TIGR01056 topB DNA topoisomera 100.0 4.3E-61 9.3E-66 463.2 22.3 217 6-224 188-414 (660)
7 PRK14724 DNA topoisomerase III 100.0 4.3E-61 9.4E-66 478.1 22.7 213 9-224 198-433 (987)
8 PRK14973 DNA topoisomerase I; 100.0 1.1E-60 2.4E-65 472.0 23.5 215 6-224 187-402 (936)
9 PRK07726 DNA topoisomerase III 100.0 1.1E-60 2.3E-65 461.0 22.7 217 6-224 183-412 (658)
10 COG0550 TopA Topoisomerase IA 100.0 1.5E-60 3.3E-65 450.6 20.4 210 9-224 166-385 (570)
11 PF01131 Topoisom_bac: DNA top 100.0 1E-60 2.2E-65 438.6 12.4 212 7-224 31-247 (403)
12 TIGR01051 topA_bact DNA topois 100.0 6.1E-58 1.3E-62 438.6 21.4 208 8-224 156-388 (610)
13 PRK05582 DNA topoisomerase I; 100.0 4.1E-57 8.8E-62 435.9 21.2 208 8-224 160-389 (650)
14 PRK08780 DNA topoisomerase I; 100.0 5.4E-57 1.2E-61 441.1 22.0 212 6-224 162-400 (780)
15 cd00186 TOP1Ac DNA Topoisomera 100.0 3.1E-57 6.6E-62 412.9 16.8 178 8-224 33-216 (381)
16 PRK07561 DNA topoisomerase I s 100.0 3.8E-56 8.3E-61 439.5 21.8 209 6-224 171-397 (859)
17 PRK06599 DNA topoisomerase I; 100.0 1.4E-55 3E-60 426.6 22.1 209 7-224 162-396 (675)
18 PTZ00407 DNA topoisomerase IA; 100.0 1.9E-55 4.1E-60 426.0 22.2 216 6-224 215-472 (805)
19 PRK06319 DNA topoisomerase I/S 100.0 1.7E-55 3.7E-60 434.5 21.5 206 9-224 162-406 (860)
20 PRK09401 reverse gyrase; Revie 100.0 4.3E-51 9.4E-56 412.4 18.0 192 8-224 807-1015(1176)
21 TIGR01054 rgy reverse gyrase. 100.0 2.8E-50 6E-55 406.8 19.8 192 8-224 807-1014(1171)
22 KOG1956 DNA topoisomerase III 100.0 3.1E-48 6.7E-53 360.0 17.8 217 6-222 201-419 (758)
23 smart00437 TOP1Ac Bacterial DN 100.0 4.5E-42 9.8E-47 298.4 11.7 136 87-224 2-143 (259)
24 COG1110 Reverse gyrase [DNA re 100.0 1E-36 2.2E-41 295.6 13.8 191 7-223 822-1027(1187)
25 PRK14701 reverse gyrase; Provi 100.0 1.1E-28 2.4E-33 255.2 12.1 124 8-153 788-913 (1638)
26 KOG1957 DNA topoisomerase III 99.8 8.6E-23 1.9E-27 184.6 -0.1 171 7-223 184-354 (555)
27 PRK14701 reverse gyrase; Provi 99.6 1.9E-15 4.1E-20 157.6 5.1 81 131-224 1381-1477(1638)
28 smart00436 TOP1Bc Bacterial DN 99.6 1.4E-15 3.1E-20 111.9 2.7 33 8-40 57-89 (89)
29 PF01131 Topoisom_bac: DNA top 96.8 0.0064 1.4E-07 56.3 9.1 119 14-134 223-351 (403)
30 smart00437 TOP1Ac Bacterial DN 96.7 0.0087 1.9E-07 52.3 8.5 113 18-132 123-244 (259)
31 TIGR01051 topA_bact DNA topois 96.0 0.041 8.9E-07 53.7 9.5 112 19-132 369-495 (610)
32 cd00186 TOP1Ac DNA Topoisomera 96.0 0.028 6.1E-07 51.6 7.8 113 18-132 196-317 (381)
33 PRK07219 DNA topoisomerase I; 95.9 0.035 7.6E-07 56.0 8.7 113 17-131 390-510 (822)
34 PRK05582 DNA topoisomerase I; 95.4 0.064 1.4E-06 52.7 8.4 112 19-132 370-489 (650)
35 TIGR01057 topA_arch DNA topois 95.4 0.056 1.2E-06 52.8 7.9 114 16-132 380-502 (618)
36 TIGR01056 topB DNA topoisomera 95.1 0.09 2E-06 51.8 8.4 118 14-132 390-535 (660)
37 PRK07220 DNA topoisomerase I; 95.0 0.065 1.4E-06 53.5 7.2 115 15-132 380-503 (740)
38 PRK06599 DNA topoisomerase I; 95.0 0.12 2.7E-06 50.9 9.0 112 19-132 377-503 (675)
39 PRK14973 DNA topoisomerase I; 95.0 0.086 1.9E-06 53.9 7.9 115 16-132 380-502 (936)
40 PRK05776 DNA topoisomerase I; 95.0 0.1 2.2E-06 51.5 8.3 115 15-132 383-508 (670)
41 PRK07726 DNA topoisomerase III 95.0 0.11 2.4E-06 51.1 8.5 113 19-132 393-532 (658)
42 PRK08173 DNA topoisomerase III 94.4 0.16 3.5E-06 51.5 8.1 114 18-132 403-540 (862)
43 PRK07561 DNA topoisomerase I s 93.8 0.4 8.8E-06 48.7 9.7 115 17-133 376-503 (859)
44 PRK06319 DNA topoisomerase I/S 93.4 0.68 1.5E-05 47.1 10.5 115 16-132 384-513 (860)
45 COG0550 TopA Topoisomerase IA 92.7 0.5 1.1E-05 45.9 8.1 118 19-141 366-493 (570)
46 PRK14724 DNA topoisomerase III 92.3 0.55 1.2E-05 48.4 8.2 123 19-144 414-569 (987)
47 PRK08780 DNA topoisomerase I; 91.5 1.7 3.7E-05 43.8 10.6 113 18-132 380-509 (780)
48 TIGR02647 DNA conserved hypoth 91.0 0.21 4.5E-06 35.5 2.5 44 98-144 17-60 (77)
49 TIGR00373 conserved hypothetic 90.6 0.25 5.3E-06 40.0 3.0 35 98-136 29-63 (158)
50 PF08259 Periviscerokin: Periv 89.5 0.15 3.2E-06 22.9 0.5 9 128-136 3-11 (11)
51 PRK06266 transcription initiat 88.7 0.5 1.1E-05 39.0 3.5 29 107-135 42-70 (178)
52 PF02002 TFIIE_alpha: TFIIE al 88.5 0.46 1E-05 35.4 2.9 31 105-135 31-61 (105)
53 COG1675 TFA1 Transcription ini 82.6 1.4 3.1E-05 36.4 3.2 31 106-136 37-67 (176)
54 PF13412 HTH_24: Winged helix- 81.7 2.5 5.4E-05 26.6 3.5 29 104-132 20-48 (48)
55 PRK09401 reverse gyrase; Revie 81.3 4.6 9.9E-05 42.6 7.1 108 15-132 992-1107(1176)
56 PTZ00407 DNA topoisomerase IA; 80.4 2.6 5.7E-05 42.5 4.9 52 80-132 561-613 (805)
57 PF01047 MarR: MarR family; I 78.9 3.3 7.1E-05 27.0 3.5 30 106-135 22-51 (59)
58 COG1321 TroR Mn-dependent tran 77.5 3.3 7.1E-05 33.4 3.8 40 104-143 27-66 (154)
59 PF01325 Fe_dep_repress: Iron 77.3 3.5 7.7E-05 27.7 3.3 30 106-135 27-56 (60)
60 PF03962 Mnd1: Mnd1 family; I 75.6 2.8 6E-05 34.9 3.0 39 94-132 8-46 (188)
61 smart00419 HTH_CRP helix_turn_ 75.3 5.9 0.00013 24.3 3.8 31 104-134 11-41 (48)
62 PF09851 SHOCT: Short C-termin 73.1 2.7 5.8E-05 24.5 1.6 17 116-132 2-18 (31)
63 PF01022 HTH_5: Bacterial regu 72.6 5.9 0.00013 24.9 3.3 33 97-133 15-47 (47)
64 PF04182 B-block_TFIIIC: B-blo 71.2 4.8 0.0001 28.1 2.9 30 103-132 20-49 (75)
65 cd07377 WHTH_GntR Winged helix 71.0 8.7 0.00019 25.0 4.1 29 106-134 30-58 (66)
66 smart00418 HTH_ARSR helix_turn 70.3 7.6 0.00016 24.7 3.6 29 106-134 15-43 (66)
67 cd00092 HTH_CRP helix_turn_hel 67.3 11 0.00024 24.8 4.0 30 106-135 30-59 (67)
68 TIGR01054 rgy reverse gyrase. 66.6 24 0.00052 37.4 8.0 111 15-133 991-1109(1171)
69 PF01978 TrmB: Sugar-specific 65.1 9.9 0.00021 25.6 3.4 28 106-133 27-54 (68)
70 PF13730 HTH_36: Helix-turn-he 63.8 11 0.00023 24.2 3.3 29 99-131 27-55 (55)
71 smart00345 HTH_GNTR helix_turn 63.6 14 0.00029 23.5 3.8 29 105-133 24-52 (60)
72 PF03965 Penicillinase_R: Peni 63.4 10 0.00022 28.5 3.5 41 98-138 18-58 (115)
73 PF01726 LexA_DNA_bind: LexA D 62.0 12 0.00027 25.5 3.4 29 106-134 30-59 (65)
74 PF10872 DUF2740: Protein of u 59.6 12 0.00025 23.4 2.6 28 196-223 3-31 (48)
75 PF03444 HrcA_DNA-bdg: Winged 57.4 20 0.00043 25.7 3.9 36 109-144 31-67 (78)
76 TIGR02698 CopY_TcrY copper tra 56.2 22 0.00047 27.6 4.3 38 98-135 19-56 (130)
77 TIGR01889 Staph_reg_Sar staphy 56.0 18 0.00038 26.9 3.7 32 105-136 47-78 (109)
78 smart00420 HTH_DEOR helix_turn 55.8 21 0.00045 21.9 3.6 33 98-134 15-47 (53)
79 PF10007 DUF2250: Uncharacteri 55.5 18 0.0004 26.6 3.6 27 107-133 27-53 (92)
80 COG4840 Uncharacterized protei 55.1 24 0.00052 24.5 3.8 28 99-126 40-67 (71)
81 PF13463 HTH_27: Winged helix 54.8 24 0.00051 23.3 3.9 28 105-132 22-49 (68)
82 PF04337 DUF480: Protein of un 54.7 12 0.00026 30.0 2.6 46 88-133 15-66 (148)
83 PF12802 MarR_2: MarR family; 54.6 21 0.00045 23.1 3.5 27 106-132 26-52 (62)
84 PF13545 HTH_Crp_2: Crp-like h 53.8 22 0.00048 24.1 3.7 40 93-136 24-63 (76)
85 PF09339 HTH_IclR: IclR helix- 53.2 24 0.00051 22.5 3.5 33 97-133 18-50 (52)
86 PF05402 PqqD: Coenzyme PQQ sy 52.8 32 0.0007 22.9 4.3 35 98-132 30-68 (68)
87 smart00550 Zalpha Z-DNA-bindin 52.3 26 0.00055 23.9 3.7 34 97-134 22-55 (68)
88 PRK03902 manganese transport t 52.1 21 0.00045 27.8 3.7 39 105-143 26-64 (142)
89 PF00325 Crp: Bacterial regula 48.9 34 0.00075 20.1 3.4 27 105-131 6-32 (32)
90 PRK11239 hypothetical protein; 48.7 30 0.00065 29.5 4.3 46 87-132 18-69 (215)
91 PF12840 HTH_20: Helix-turn-he 48.1 28 0.00061 22.9 3.3 33 96-132 23-55 (61)
92 cd04449 DEP_DEPDC5-like DEP (D 47.8 99 0.0021 21.9 6.4 61 70-132 4-66 (83)
93 PF02082 Rrf2: Transcriptional 46.7 28 0.0006 24.5 3.3 34 98-135 26-59 (83)
94 PF14178 YppF: YppF-like prote 46.5 40 0.00088 22.9 3.8 35 98-132 1-38 (60)
95 KOG1956 DNA topoisomerase III 45.3 46 0.00099 33.0 5.4 66 77-143 466-532 (758)
96 PRK09391 fixK transcriptional 45.1 31 0.00067 28.9 3.9 32 104-135 182-213 (230)
97 PF08784 RPA_C: Replication pr 45.0 34 0.00073 25.0 3.7 23 109-131 73-95 (102)
98 TIGR03697 NtcA_cyano global ni 44.5 34 0.00073 27.2 3.9 34 104-137 146-179 (193)
99 PF00376 MerR: MerR family reg 44.5 19 0.00041 21.8 1.9 31 105-140 3-35 (38)
100 smart00529 HTH_DTXR Helix-turn 43.9 36 0.00078 24.2 3.6 32 104-135 2-33 (96)
101 KOG3433 Protein involved in me 43.9 13 0.00029 30.9 1.4 37 98-135 25-61 (203)
102 smart00531 TFIIE Transcription 43.1 27 0.00058 27.6 3.0 30 106-135 20-51 (147)
103 PF12793 SgrR_N: Sugar transpo 42.7 43 0.00092 25.5 4.0 37 94-134 16-52 (115)
104 PRK13918 CRP/FNR family transc 42.3 38 0.00083 27.3 4.0 34 104-137 152-185 (202)
105 PF11834 DUF3354: Domain of un 42.2 23 0.00049 24.7 2.2 24 95-118 23-46 (69)
106 PF09397 Ftsk_gamma: Ftsk gamm 42.2 39 0.00084 23.2 3.3 36 98-137 21-56 (65)
107 PF13061 DUF3923: Protein of u 41.7 14 0.00031 25.5 1.1 16 8-23 26-41 (66)
108 PRK00215 LexA repressor; Valid 41.5 45 0.00098 27.4 4.3 35 104-138 26-61 (205)
109 COG1522 Lrp Transcriptional re 41.5 38 0.00082 26.2 3.7 29 104-132 25-53 (154)
110 smart00344 HTH_ASNC helix_turn 39.8 44 0.00096 24.3 3.7 27 106-132 22-48 (108)
111 PF05848 CtsR: Firmicute trans 39.5 37 0.00079 27.4 3.3 31 102-132 80-112 (152)
112 PF09012 FeoC: FeoC like trans 38.8 46 0.00099 22.5 3.3 26 107-132 20-45 (69)
113 PF01726 LexA_DNA_bind: LexA D 38.8 40 0.00088 22.9 3.0 26 196-221 2-27 (65)
114 PF10141 ssDNA-exonuc_C: Singl 38.5 59 0.0013 26.9 4.6 37 97-133 112-148 (195)
115 smart00843 Ftsk_gamma This dom 38.0 40 0.00088 23.1 2.9 34 99-136 21-54 (63)
116 PRK11753 DNA-binding transcrip 38.0 49 0.0011 26.7 4.0 35 103-137 170-204 (211)
117 cd04789 HTH_Cfa Helix-Turn-Hel 37.9 36 0.00079 25.1 2.9 30 106-140 6-36 (102)
118 PRK11161 fumarate/nitrate redu 37.8 47 0.001 27.5 4.0 33 104-136 187-219 (235)
119 cd04783 HTH_MerR1 Helix-Turn-H 36.5 38 0.00082 25.9 2.9 31 105-140 4-36 (126)
120 TIGR02337 HpaR homoprotocatech 36.5 48 0.001 24.7 3.4 30 104-133 45-74 (118)
121 cd04775 HTH_Cfa-like Helix-Tur 36.3 41 0.00088 24.8 2.9 30 106-140 6-36 (102)
122 COG5204 SPT4 Transcription elo 35.9 30 0.00065 25.8 2.1 20 120-139 91-110 (112)
123 COG3682 Predicted transcriptio 35.6 56 0.0012 25.4 3.6 45 97-141 20-64 (123)
124 PRK11512 DNA-binding transcrip 35.0 55 0.0012 25.3 3.7 29 104-132 57-85 (144)
125 smart00347 HTH_MARR helix_turn 33.5 70 0.0015 22.2 3.8 31 106-136 29-59 (101)
126 COG1110 Reverse gyrase [DNA re 33.3 2.3E+02 0.0051 29.9 8.5 116 9-133 990-1122(1187)
127 PF13601 HTH_34: Winged helix 33.1 73 0.0016 22.4 3.7 29 108-136 21-49 (80)
128 TIGR03882 cyclo_dehyd_2 bacter 33.1 69 0.0015 26.5 4.1 34 98-133 43-76 (193)
129 PRK14165 winged helix-turn-hel 33.0 60 0.0013 27.7 3.8 31 104-134 24-54 (217)
130 cd04770 HTH_HMRTR Helix-Turn-H 32.3 51 0.0011 24.9 3.0 35 105-144 4-42 (123)
131 COG1654 BirA Biotin operon rep 32.3 66 0.0014 23.0 3.3 27 106-132 24-50 (79)
132 PF00610 DEP: Domain found in 31.9 55 0.0012 22.2 2.9 41 98-138 18-61 (74)
133 PF13309 HTH_22: HTH domain 31.6 48 0.001 22.4 2.4 20 113-132 21-40 (64)
134 COG2975 Uncharacterized protei 31.6 46 0.00099 22.6 2.2 22 116-141 4-25 (64)
135 PRK11179 DNA-binding transcrip 31.2 69 0.0015 25.2 3.7 34 106-139 28-63 (153)
136 PF10557 Cullin_Nedd8: Cullin 30.5 68 0.0015 21.8 3.1 28 106-133 35-62 (68)
137 COG1414 IclR Transcriptional r 30.3 83 0.0018 27.0 4.3 44 95-142 17-60 (246)
138 PRK02079 pyrroloquinoline quin 30.2 1.1E+02 0.0023 22.2 4.2 49 65-133 36-87 (88)
139 cd04371 DEP DEP domain, named 30.1 1.6E+02 0.0035 19.9 5.1 46 91-136 22-68 (81)
140 TIGR01610 phage_O_Nterm phage 30.0 76 0.0016 23.0 3.5 29 104-132 50-78 (95)
141 PRK03573 transcriptional regul 29.7 72 0.0016 24.5 3.5 32 104-135 49-80 (144)
142 COG1777 Predicted transcriptio 29.1 60 0.0013 27.7 3.0 28 106-133 33-60 (217)
143 COG1497 Predicted transcriptio 28.6 76 0.0016 27.7 3.6 29 104-132 28-56 (260)
144 PRK11169 leucine-responsive tr 28.4 79 0.0017 25.2 3.6 28 105-132 32-59 (164)
145 PF14268 YoaP: YoaP-like 28.4 29 0.00063 22.0 0.8 22 80-101 2-23 (44)
146 smart00540 LEM in nuclear memb 28.0 21 0.00045 22.7 0.1 34 99-133 7-40 (44)
147 COG1339 Transcriptional regula 27.9 60 0.0013 27.5 2.8 30 106-135 24-53 (214)
148 COG2345 Predicted transcriptio 27.2 81 0.0018 27.0 3.6 29 106-134 30-58 (218)
149 COG0789 SoxR Predicted transcr 26.8 72 0.0016 23.7 3.0 28 106-138 5-33 (124)
150 PRK10402 DNA-binding transcrip 26.8 89 0.0019 25.9 3.8 32 104-135 172-203 (226)
151 cd01388 SOX-TCF_HMG-box SOX-TC 26.7 92 0.002 21.1 3.3 28 196-223 41-71 (72)
152 PF13447 Multi-haem_cyto: Seve 26.5 69 0.0015 28.2 3.1 30 100-133 232-261 (267)
153 PF08221 HTH_9: RNA polymerase 26.5 1.1E+02 0.0023 20.5 3.4 31 100-134 30-60 (62)
154 cd00090 HTH_ARSR Arsenical Res 26.3 1.1E+02 0.0025 19.5 3.7 27 107-133 26-52 (78)
155 COG1846 MarR Transcriptional r 26.1 90 0.0019 22.4 3.3 33 105-137 40-72 (126)
156 TIGR02431 pcaR_pcaU beta-ketoa 26.0 1.1E+02 0.0023 26.0 4.2 40 96-141 23-62 (248)
157 PRK11569 transcriptional repre 25.6 1.2E+02 0.0026 26.3 4.5 34 96-133 42-75 (274)
158 COG2512 Predicted membrane-ass 25.5 87 0.0019 27.4 3.6 30 103-132 212-241 (258)
159 PF00392 GntR: Bacterial regul 25.3 1.2E+02 0.0025 20.0 3.5 26 107-132 30-55 (64)
160 PF04282 DUF438: Family of unk 24.6 1.6E+02 0.0035 20.6 4.1 31 99-129 14-45 (71)
161 TIGR02944 suf_reg_Xantho FeS a 24.5 99 0.0022 23.4 3.4 33 97-133 25-57 (130)
162 PF09105 SelB-wing_1: Elongati 24.5 78 0.0017 20.7 2.3 34 106-139 22-55 (61)
163 PRK13777 transcriptional regul 24.1 1E+02 0.0022 25.5 3.6 30 104-133 62-91 (185)
164 smart00049 DEP Domain found in 23.8 2.4E+02 0.0051 19.0 5.0 47 90-136 13-60 (77)
165 PRK10163 DNA-binding transcrip 23.6 1.2E+02 0.0026 26.2 4.2 42 97-142 40-81 (271)
166 PRK10870 transcriptional repre 23.4 1.1E+02 0.0024 24.7 3.7 31 105-135 75-105 (176)
167 cd07153 Fur_like Ferric uptake 23.2 2E+02 0.0043 21.0 4.8 39 95-133 14-53 (116)
168 smart00411 BHL bacterial (prok 23.1 1.6E+02 0.0034 20.6 4.1 29 99-127 2-30 (90)
169 COG1706 FlgI Flagellar basal-b 23.1 1.2E+02 0.0027 27.8 4.1 33 99-132 327-359 (365)
170 PRK00082 hrcA heat-inducible t 22.9 1.6E+02 0.0036 26.6 5.0 36 110-145 36-71 (339)
171 PRK12789 flgI flagellar basal 22.7 1.9E+02 0.0041 26.8 5.3 32 99-131 329-360 (367)
172 PRK15090 DNA-binding transcrip 22.7 1.3E+02 0.0029 25.6 4.2 41 97-141 28-68 (257)
173 PRK11050 manganese transport r 22.0 1.5E+02 0.0032 23.4 4.1 40 104-143 54-93 (152)
174 cd04777 HTH_MerR-like_sg1 Heli 21.6 99 0.0022 22.7 2.8 29 105-139 4-33 (107)
175 PF13518 HTH_28: Helix-turn-he 21.4 1.5E+02 0.0032 18.1 3.3 25 105-129 16-40 (52)
176 TIGR02702 SufR_cyano iron-sulf 21.4 1.3E+02 0.0028 24.8 3.7 28 106-133 20-47 (203)
177 PF03428 RP-C: Replication pro 21.2 1.5E+02 0.0032 24.5 3.9 27 107-133 77-103 (177)
178 smart00346 HTH_ICLR helix_turn 21.1 2.1E+02 0.0044 19.7 4.3 34 97-134 20-53 (91)
179 PF10711 DUF2513: Hypothetical 21.1 1.2E+02 0.0027 22.2 3.2 29 106-134 25-53 (102)
180 PF05584 Sulfolobus_pRN: Sulfo 20.9 1.7E+02 0.0038 20.5 3.7 27 106-132 23-49 (72)
181 cd04441 DEP_2_DEP6 DEP (Dishev 20.7 97 0.0021 22.4 2.5 40 94-133 29-69 (85)
182 TIGR00498 lexA SOS regulatory 20.7 1.4E+02 0.003 24.4 3.7 31 104-134 28-59 (199)
183 cd01389 MATA_HMG-box MATA_HMG- 20.5 1.5E+02 0.0032 20.3 3.3 28 196-223 41-71 (77)
184 cd04448 DEP_PIKfyve DEP (Dishe 20.5 99 0.0021 21.9 2.5 40 93-132 24-64 (81)
185 COG3355 Predicted transcriptio 20.2 1.5E+02 0.0033 23.1 3.6 32 97-132 42-73 (126)
186 PF03368 Dicer_dimer: Dicer di 20.1 63 0.0014 23.3 1.4 17 117-133 63-79 (90)
No 1
>PRK05776 DNA topoisomerase I; Provisional
Probab=100.00 E-value=2.3e-63 Score=479.37 Aligned_cols=216 Identities=30% Similarity=0.507 Sum_probs=195.6
Q ss_pred CccccCcchhHHHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEeccccCCHHHHHHHHHHHccCCceEEEEEee
Q 045217 8 LILIYGPCQTPTLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWERQKLFDFDVATMFQKLVMQDRILEVIDISE 87 (224)
Q Consensus 8 ~~lS~GRVQTPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~ 87 (224)
.++|+||||||||+|||+||+||++|+|++||+|.+.+..+++.|.+.|..++++|+++|+.+.+.+.+.+.++|++|++
T Consensus 188 ~~lS~GRVQsptL~lVveRe~eI~~Fvp~~yw~i~~~~~~~~~~f~~~~~~~~~~~~~~a~~i~~~~~~~~~~~V~~v~~ 267 (670)
T PRK05776 188 VILSAGRVQSPTLKYVVEREIERNLFVPLPYFSVSIIIEKNGYEFTLKYENKKFETKEEAKEILEEIKKTGYLKVTKVEV 267 (670)
T ss_pred cceecceecCchhhHhHhhHHHHHcCCCCcceEEEEEEecCCceEEEEEcCCccCCHHHHHHHHHHhcCCCCEEEEEEEe
Confidence 47999999999999999999999999999999999999888888999998778999999999999997634799999999
Q ss_pred ecccccCCCcccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceeccCCCCcccCCCcChHHHHHHHhcCCchHHHHHHH
Q 045217 88 KQESKVRPCGLNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISYPRTESTAYPSSFDFRGTLSALANNPVWGDYVERL 167 (224)
Q Consensus 88 k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRTds~~l~~~~~~~~~l~~l~~~~~~~~~~~~~ 167 (224)
++++.+||+||||++||++||++|||||++||++||+|||+||||||||||++||+++++.++++.|.+.+.|+.++..+
T Consensus 268 k~~~~~pP~pf~ts~LQ~~As~~lg~sa~ktm~iAQ~LYe~glISYPRTDs~~ls~~~~~~~~~~~l~~~~~~~~~~~~~ 347 (670)
T PRK05776 268 KIEILEPPPPFNLGDLQVEAARIYGFSPYKTQSIAEDLYLDGLISYPRTNSQKLPPTLNIRNILKGLSRSPQYRPLVNLL 347 (670)
T ss_pred eeEEcCCCCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHhcCceecCCCccCCCChhhCHHHHHHHHhcchhHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999988889999998877788877766
Q ss_pred hhc--CCCCCCCCCCC-CCCCCcccCCCCCcCCCCHHHHHHHHHHHHHHHHhcCcCcccC
Q 045217 168 LAE--GYAKPRSGTDA-GDHPPITPMRSATEDMLGKDAWRLYSYVCQHFLGTVSPDCKYI 224 (224)
Q Consensus 168 ~~~--~~~~~~~~~k~-~aH~AI~PT~~~~~~~L~~~e~~iY~lI~~r~la~f~~~a~y~ 224 (224)
+.. ...++++++++ +|||||+||+. .+++|+++|++||+|||+||||+||+||+|+
T Consensus 348 l~~~~~~~~~~~~~k~~~aH~AI~PT~~-~p~~L~~de~klY~LI~rRflA~~~~~a~~~ 406 (670)
T PRK05776 348 LKETKGVLKPVQGPKDDPAHPAIYPTGE-PPKNLSKDEFKLYDLIVRRFLASFAAPAVLS 406 (670)
T ss_pred hcccCCccccCCCCCCCCCCCCCCCCCC-CcccCCHHHHHHHHHHHHHHHHHhChhheEE
Confidence 542 23345555554 59999999998 4568999999999999999999999999984
No 2
>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=9.9e-63 Score=472.55 Aligned_cols=218 Identities=28% Similarity=0.478 Sum_probs=194.2
Q ss_pred CCccccCcchhHHHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEeccccCCHHHHHHHHHHHccCCceEEEEEe
Q 045217 7 TLILIYGPCQTPTLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWERQKLFDFDVATMFQKLVMQDRILEVIDIS 86 (224)
Q Consensus 7 ~~~lS~GRVQTPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~ 86 (224)
+.++|+||||||||+|||+||+||+||+|++||.|.+.+..+|+.|.+.|.++++++++.|+.+.+.+.+...++|++|+
T Consensus 184 ~~~lS~GRVQtPtL~lvv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~ 263 (618)
T TIGR01057 184 WVILSAGRVQGPTLAFLVEREREINLFVPKPYWVIKATLEKGGGVFDARPEKWKIWSEEEAKSIKEELKKSPWAAVEEVR 263 (618)
T ss_pred cccccccccchhHHHHHHHhHHHHHcCcCCccEEEEEEEecCCceEEEEEccCCcCCHHHHHHHHHHHhCCCCeEEEEEE
Confidence 45799999999999999999999999999999999999988888899999888999999999999999864379999999
Q ss_pred eecccccCCCcccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceeccCCCCcccCCCcChHHHHHHHhcCCchHHHHHH
Q 045217 87 EKQESKVRPCGLNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISYPRTESTAYPSSFDFRGTLSALANNPVWGDYVER 166 (224)
Q Consensus 87 ~k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRTds~~l~~~~~~~~~l~~l~~~~~~~~~~~~ 166 (224)
+++++..||+||||++||++||++|||||++||++||+|||+||||||||||+|||+++++.++++++...+.|+.++..
T Consensus 264 ~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~iaQ~LYe~g~ISYPRTds~~l~~~~~~~~~l~~l~~~~~~~~~~~~ 343 (618)
T TIGR01057 264 SERSILKPPPPFDLGTLQREAYRIFGFSPKKTQSIAQELYEEALISYPRTSSQKLPPSINYRAILDNLAKGPLYREAAER 343 (618)
T ss_pred eeeeeccCCCCccHHHHHHHHHHhcCCCHHHHHHHHHHHHhcCceeecCcccCccCHHHhHHHHHHHHhcccchHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999987778889988766667766554
Q ss_pred HhhcCCCCCCCCCCC-CCCCCcccCCCCCcCCCCHHHHHHHHHHHHHHHHhcCcCcccC
Q 045217 167 LLAEGYAKPRSGTDA-GDHPPITPMRSATEDMLGKDAWRLYSYVCQHFLGTVSPDCKYI 224 (224)
Q Consensus 167 ~~~~~~~~~~~~~k~-~aH~AI~PT~~~~~~~L~~~e~~iY~lI~~r~la~f~~~a~y~ 224 (224)
+......++++++++ +||||||||.......|+++|++||+||++||||+|||||+|+
T Consensus 344 ~~~~~~~~~~~~~~~~~aH~aI~PT~~~~~~~L~~~e~~iY~lI~~r~la~~~~~a~~~ 402 (618)
T TIGR01057 344 LLETGVLKPVEGKKEDPAHPAIHPTGEIPSQELSKDEKKVYDLIVRRFLAAFSEEAIRE 402 (618)
T ss_pred hhcccccccCCCCCCCCCCCCcCccCCCccccCCHHHHHHHHHHHHHHHHHhChhhhee
Confidence 433334456677765 4999999998642237999999999999999999999999984
No 3
>PRK08173 DNA topoisomerase III; Validated
Probab=100.00 E-value=3e-62 Score=481.53 Aligned_cols=215 Identities=23% Similarity=0.416 Sum_probs=188.2
Q ss_pred CCccccCcchhHHHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEe--------------ccccCCHHHHHHHHH
Q 045217 7 TLILIYGPCQTPTLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWE--------------RQKLFDFDVATMFQK 72 (224)
Q Consensus 7 ~~~lS~GRVQTPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~--------------~~~~~~~~~a~~~~~ 72 (224)
..++|+||||||||+|||+||+||+||+|++||+|.+.+...++.|.+.|. .++++|++.|+.+.+
T Consensus 188 ~~~lSvGRVQTPtL~lVv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~d~~~A~~i~~ 267 (862)
T PRK08173 188 FFLTTVGRVQTPTLSIVVEREEKIRRFVPRDYWEVRAEFVAAAGFYEGRWFDPKFKKDEFDPEKRASRLWSEAAAEAIVA 267 (862)
T ss_pred ccccccccchhhHHHHHHHHHHHHHcCCCCccEEEEEEEecCCccEEEEEeccccccccccccccccccCCHHHHHHHHH
Confidence 347999999999999999999999999999999999999887778888883 257999999999999
Q ss_pred HHccCCceEEEEEeeecccccCCCcccHHHHHHHHHHhCCCCHHHHHHHHHHHhhc-cceeccCCCCcccCCCc--ChHH
Q 045217 73 LVMQDRILEVIDISEKQESKVRPCGLNTVNLLKVASSALGYGPQMAMQLAERLYTQ-GFISYPRTESTAYPSSF--DFRG 149 (224)
Q Consensus 73 ~~~~~~~~~V~~v~~k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~-glITYPRTds~~l~~~~--~~~~ 149 (224)
.|.+ +.++|++ +.+++++.||+||||++||++||++|||||++||+|||+|||+ |+||||||||+|||+++ +++.
T Consensus 268 ~~~~-~~~~V~~-~~k~~~~~pP~~f~Lt~LQ~~A~~~~g~sa~~tL~iaQ~LYE~~k~iTYPRTDs~~l~~~~~~~~~~ 345 (862)
T PRK08173 268 ACRG-KPGTVTE-ESKPSTQLSPLLFDLTSLQREANGRFGFSAKNTLGLAQALYEKHKVLTYPRTDSRALPEDYLGTVKQ 345 (862)
T ss_pred HhcC-CCcEEEE-eeeEEecCCCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHHhcCCEEEecCCCCccCCHHHHHHHHH
Confidence 9987 5789999 8899999999999999999999999999999999999999996 89999999999999986 5888
Q ss_pred HHHHHhcCCchHHHHHHHhhcC----CCCCCCCCCCCCCCCcccCCCCCcCCCCHHHHHHHHHHHHHHHHhcCcCcccC
Q 045217 150 TLSALANNPVWGDYVERLLAEG----YAKPRSGTDAGDHPPITPMRSATEDMLGKDAWRLYSYVCQHFLGTVSPDCKYI 224 (224)
Q Consensus 150 ~l~~l~~~~~~~~~~~~~~~~~----~~~~~~~~k~~aH~AI~PT~~~~~~~L~~~e~~iY~lI~~r~la~f~~~a~y~ 224 (224)
+|+.|...+.|..++..++... ..+.+++++++||||||||... +..|+++|++||+||++||||+|||||+|+
T Consensus 346 ~l~~l~~~~~~~~~~~~~~~~~~~~~~~r~~~~~kv~dH~AIiPT~~~-~~~Ls~~E~~iY~lI~rRfla~f~~~a~~~ 423 (862)
T PRK08173 346 TLEMLKESNNYLPHAKQILDKGWVKPNKRIFDNSKISDHFAIIPTLQA-PKSLSEPEQKLYDLVVKRFLAVFFPAAEFL 423 (862)
T ss_pred HHHHHhCCcccHHHHHHhhcccccCCCCCcCCCCCCCCCCCcCccCCC-cccCCHHHHHHHHHHHHHHHHHhCchheEE
Confidence 8988875455666655444321 1233467889999999999874 346999999999999999999999999984
No 4
>PRK07219 DNA topoisomerase I; Validated
Probab=100.00 E-value=1.3e-61 Score=476.74 Aligned_cols=217 Identities=32% Similarity=0.612 Sum_probs=190.6
Q ss_pred CccccCcchhHHHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEE----eccccCCHHHHHHHHHHHccCCceEEE
Q 045217 8 LILIYGPCQTPTLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEW----ERQKLFDFDVATMFQKLVMQDRILEVI 83 (224)
Q Consensus 8 ~~lS~GRVQTPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~----~~~~~~~~~~a~~~~~~~~~~~~~~V~ 83 (224)
.++|+||||||||+|||+||+||+||+|++||+|.+.+..++..|.+.| ..++++|++.|+++.+.+.+...++|+
T Consensus 190 ~~lS~GRVQtPtL~lIv~Re~eI~~F~p~~yw~i~~~~~~~~~~~~~~~~~~~~~~r~~d~~~a~~~~~~~~~~~~~~V~ 269 (822)
T PRK07219 190 DFLSVGRVQTPTLAFIVDREREIRAFDPEDYWKIEALLDKEAQYFYRDLIGGHEAEKFWDEEEAEEIYEKLKGAKEATVS 269 (822)
T ss_pred CccccccccchhhHHHHHHHHHHHcCCCcccEEEEEEEEecCcceeeecccccccCccCCHHHHHHHHHHhcCCCCeEEE
Confidence 4799999999999999999999999999999999999976655666665 346899999999999999764479999
Q ss_pred EEeeecccccCCCcccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceeccCCCCcccCCCcChHHHHHHHhcCCchHHH
Q 045217 84 DISEKQESKVRPCGLNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISYPRTESTAYPSSFDFRGTLSALANNPVWGDY 163 (224)
Q Consensus 84 ~v~~k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRTds~~l~~~~~~~~~l~~l~~~~~~~~~ 163 (224)
+|++++++.+||+||||++||++||++|||||++||++||+|||+||||||||||++||++++++++++.+.....|+.+
T Consensus 270 ~v~~~~~~~~pP~pf~t~~Lq~~a~~~~g~sa~~tm~iaQ~LYe~glITYpRTds~~l~~~~~~~~~~~~l~~~~~~~~~ 349 (822)
T PRK07219 270 SVKKRERTISPPAPFNTTEFLREASKIFGISPKRAMEIAEKLYTAGYISYPRTDNTVYPDDLDPKELLKKLSKKKEYGPY 349 (822)
T ss_pred EEEEeeEEccCCCCccHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCceeccCcccccCCHHHHHHHHHHHhhcccchhhH
Confidence 99999999999999999999999999999999999999999999999999999999999987777888888766678877
Q ss_pred HHHHhhcCCCCCCCC-CCCCCCCCcccCCCCCcCCCCHHHHHHHHHHHHHHHHhcCcCcccC
Q 045217 164 VERLLAEGYAKPRSG-TDAGDHPPITPMRSATEDMLGKDAWRLYSYVCQHFLGTVSPDCKYI 224 (224)
Q Consensus 164 ~~~~~~~~~~~~~~~-~k~~aH~AI~PT~~~~~~~L~~~e~~iY~lI~~r~la~f~~~a~y~ 224 (224)
+..++.....+++++ ++++||||||||+....+.|+++|++||+||++||||+||+||+|+
T Consensus 350 ~~~~l~~~~~~~~~~~~~~~aH~aI~PT~~~~~~~L~~~e~~lY~LI~rrfla~~~~~a~~~ 411 (822)
T PRK07219 350 AESILEQENIKPTEGKKETTDHPPIHPVDVPKREELSDDEWKVYELIVRRFLATLADPAEWE 411 (822)
T ss_pred hhhhcccCCcccCCCCCCCCCCCCCCCcCCCCcccCCHHHHHHHHHHHHHHHHHhCccceee
Confidence 665553333345554 4589999999999853378999999999999999999999999984
No 5
>PRK07220 DNA topoisomerase I; Validated
Probab=100.00 E-value=3.3e-61 Score=469.14 Aligned_cols=213 Identities=30% Similarity=0.596 Sum_probs=190.0
Q ss_pred CccccCcchhHHHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEeccccCCHHHHHHHHHHHccCCceEEEEEee
Q 045217 8 LILIYGPCQTPTLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWERQKLFDFDVATMFQKLVMQDRILEVIDISE 87 (224)
Q Consensus 8 ~~lS~GRVQTPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~ 87 (224)
+++|+||||||||+|||+||+||+||+|++||+|.+.+..++..|.+.|..++++|++.|+.+.+.+ + ..++|++|++
T Consensus 190 ~~lS~GRVQtptL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~r~~~~~~a~~~~~~~-~-~~~~V~~v~~ 267 (740)
T PRK07220 190 MFLSVGRVQSPTLALIVDREKEREAFVPTPYWEIYATLENNGETFVAQHSTRRFWEKEEADRVFEKL-G-KTAEVTEVEK 267 (740)
T ss_pred ccccccccchhhhHHHHhhHHHHHhCCCCccEEEEEEEEcCCceEEEEeccCcCCCHHHHHHHHHhh-C-CCeEEEEEee
Confidence 4799999999999999999999999999999999999987778899999888999999999999988 4 4799999999
Q ss_pred ecccccCCCcccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceeccCCCCcccCCCcChHHHHHHHhcCCchHHHHHHH
Q 045217 88 KQESKVRPCGLNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISYPRTESTAYPSSFDFRGTLSALANNPVWGDYVERL 167 (224)
Q Consensus 88 k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRTds~~l~~~~~~~~~l~~l~~~~~~~~~~~~~ 167 (224)
++++..||+||||++||++||+ +||||++||++||+|||+||||||||||++||+++++.++++.+.. ..|+.++..+
T Consensus 268 ~~~~~~pP~pf~ts~Lq~~a~~-~g~s~~~tm~iaQ~LYe~g~ITYPRTDs~~l~~~~~~~~~i~~l~~-~~~~~~~~~~ 345 (740)
T PRK07220 268 GTKTDKPPTPFNTTEFISAANS-IGFSAANAMRIAESLYTNGYISYPRTDNTVYPESLDLREQIEIFAE-GPFGEYAQKL 345 (740)
T ss_pred eeEecCCCCCcCHHHHHHHHHH-cCCCHHHHHHHHHHHHhCCceeecccCCeecCchhhHHHHHHHHHH-HHHHHHHHHh
Confidence 9999999999999999999996 8999999999999999999999999999999998888888888875 3577776655
Q ss_pred hhcCCCC-CCCCCCCCCCCCcccCCCCCcCCCCHHHHHHHHHHHHHHHHhcCcCcccC
Q 045217 168 LAEGYAK-PRSGTDAGDHPPITPMRSATEDMLGKDAWRLYSYVCQHFLGTVSPDCKYI 224 (224)
Q Consensus 168 ~~~~~~~-~~~~~k~~aH~AI~PT~~~~~~~L~~~e~~iY~lI~~r~la~f~~~a~y~ 224 (224)
+...... .+++++++||||||||+....+.|+++|++||+||||||||+||+||+|+
T Consensus 346 l~~~~~~~~~~~~~~~~H~aI~PT~~~~~~~L~~de~~lY~LI~rRfla~~~~~a~~~ 403 (740)
T PRK07220 346 LEKGELVPTRGKKETTDHPPIYPASLAKKSELKEDEWKVYELVVRRFFATFAGPAEWE 403 (740)
T ss_pred cccCCccCCCCCCCCCCCCCCCcccCCCcccCCHHHHHHHHHHHHHHHHHhCchheEE
Confidence 5432222 23456788999999999865568999999999999999999999999984
No 6
>TIGR01056 topB DNA topoisomerase III, bacteria and conjugative plasmid. This model describes topoisomerase III from bacteria and its equivalents encoded on plasmids. The gene is designated topB if found in the bacterial chromosome, traE on conjugative plasmid RP4, etc. These enzymes are involved in the control of DNA topology. DNA topoisomerase III belongs to the type I topoisomerases, which are ATP-independent.
Probab=100.00 E-value=4.3e-61 Score=463.18 Aligned_cols=217 Identities=22% Similarity=0.296 Sum_probs=183.2
Q ss_pred cCCccccCcchhHHHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEec-----cccCCHHHHHHHHHHHccCCce
Q 045217 6 VTLILIYGPCQTPTLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWER-----QKLFDFDVATMFQKLVMQDRIL 80 (224)
Q Consensus 6 ~~~~lS~GRVQTPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~-----~~~~~~~~a~~~~~~~~~~~~~ 80 (224)
.+.++|+||||||||+|||+||+||+||+|++||+|.+.+..++..|.+.|.+ .+++|++.|+.+.+.+.+ ..+
T Consensus 188 ~~~~lS~GRVQtptL~lIveRe~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~i~~~~~~-~~~ 266 (660)
T TIGR01056 188 NDGVLSVGRVQTPTLAMVVKRENEIKNFVGKPFYEVSATINKDEQEFTTEWQPYKDEEERELHEFLAENVVTDLTQ-KPA 266 (660)
T ss_pred CCCceecccchhhhhHHHHHHHHHHHcCCCCccEEEEEEEEcCCceEEEEEeccCCcccCcCCHHHHHHHHHHhhC-CCe
Confidence 55689999999999999999999999999999999999998777789999963 478999999999999976 469
Q ss_pred EEEEEeeecccccCCCcccHHHHHHHHHHhCCCCHHHHHHHHHHHhhc-cceeccCCCCcccCCCc--ChHHHHHHHhcC
Q 045217 81 EVIDISEKQESKVRPCGLNTVNLLKVASSALGYGPQMAMQLAERLYTQ-GFISYPRTESTAYPSSF--DFRGTLSALANN 157 (224)
Q Consensus 81 ~V~~v~~k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~-glITYPRTds~~l~~~~--~~~~~l~~l~~~ 157 (224)
+|.+|++++++..||+||||++||++||++|||||++||++||+|||+ ||||||||||++||+++ ++.++++.+...
T Consensus 267 ~V~~v~~k~~~~~pP~pf~ts~LQ~~as~~~g~s~~~tm~iAQ~LYE~~glITYpRTDS~~ls~~~~~~~~~~i~~~~~~ 346 (660)
T TIGR01056 267 LVTDIEKERKKTSAPLFYDLSALQEDANKRFGISAKRTLDIAQKLYETHKLITYPRTDSRYLPEDEKEMLLEVLDALKVI 346 (660)
T ss_pred EEEEEEeeeeecCCCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHHHhCCEEEEecCCCccCCHHHHHHHHHHHHHhhcc
Confidence 999999999999999999999999999999999999999999999998 99999999999999986 466666666432
Q ss_pred CchHHHHHHHhh-cCCCCCCCCCCCCCCCCcccCCCC-CcCCCCHHHHHHHHHHHHHHHHhcCcCcccC
Q 045217 158 PVWGDYVERLLA-EGYAKPRSGTDAGDHPPITPMRSA-TEDMLGKDAWRLYSYVCQHFLGTVSPDCKYI 224 (224)
Q Consensus 158 ~~~~~~~~~~~~-~~~~~~~~~~k~~aH~AI~PT~~~-~~~~L~~~e~~iY~lI~~r~la~f~~~a~y~ 224 (224)
. +..+...... ....+..++++++||||||||+.. ..+.|+++|++||+|||+||||+||+||+|+
T Consensus 347 ~-~~~~~~~~~~~~~~~~~~~~~~~~aH~AI~PT~~~~~~~~L~~de~klY~LI~~Rflas~~~~a~~~ 414 (660)
T TIGR01056 347 T-PALLPIKKRDELTNNRLWNDKKIEDHHAIIPTGNDFNLSDLSEEERNVYKLIAQNYLMQFMPKEEYE 414 (660)
T ss_pred c-hhhhcccccccccccCcCCCCccCCcCCccccCCccccccCCHHHHHHHHHHHHHHHHHhCchhEEE
Confidence 1 2111100000 011223456678999999999873 4568999999999999999999999999984
No 7
>PRK14724 DNA topoisomerase III; Provisional
Probab=100.00 E-value=4.3e-61 Score=478.15 Aligned_cols=213 Identities=23% Similarity=0.412 Sum_probs=184.8
Q ss_pred ccccCcchhHHHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEe--------------ccccCCHHHHHHHHHHH
Q 045217 9 ILIYGPCQTPTLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWE--------------RQKLFDFDVATMFQKLV 74 (224)
Q Consensus 9 ~lS~GRVQTPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~--------------~~~~~~~~~a~~~~~~~ 74 (224)
++|+||||||||+|||+||+||+||+|++||+|.+.+...++.|.+.|. .+++++++.|+.+.+.+
T Consensus 198 ~lSvGRVQTPtL~lVv~Re~eI~~F~p~~Y~~i~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~A~~i~~~~ 277 (987)
T PRK14724 198 LTTVGRVQTPTLSLVVEREEKIRKFVSRDYWEIHAGFHAEAGEYLGKWFDPQWKKASDDPEARADRVWSEREARAIADAV 277 (987)
T ss_pred eeccccchhHHHHHHHHHHHHHHhCCCCccEEEEEEEecCCCceeEEEeecccccccccccccccccCCHHHHHHHHHHh
Confidence 6899999999999999999999999999999999999887778888773 14789999999999999
Q ss_pred ccCCceEEEEEeeecccccCCCcccHHHHHHHHHHhCCCCHHHHHHHHHHHhhc-cceeccCCCCcccCCCc--ChHHHH
Q 045217 75 MQDRILEVIDISEKQESKVRPCGLNTVNLLKVASSALGYGPQMAMQLAERLYTQ-GFISYPRTESTAYPSSF--DFRGTL 151 (224)
Q Consensus 75 ~~~~~~~V~~v~~k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~-glITYPRTds~~l~~~~--~~~~~l 151 (224)
.+ +.++|++ +.+++++.||+||||++||++||++|||||++||+|||+|||+ ||||||||||+|||+++ +++.+|
T Consensus 278 ~~-~~~~V~~-~~k~~~~~pP~pf~Lt~LQ~eA~~~~g~Sa~~TL~iAQ~LYE~~klITYPRTDS~~l~~~~~~~~~~il 355 (987)
T PRK14724 278 RG-KAATVTE-ESKPTTQASPLLFDLTSLQREANGKFGFSAKTTLALAQSLYERHKALTYPRTDSRALPEDYLPVAKQTF 355 (987)
T ss_pred cC-CCeEEEE-eeeeEecCCCCCCcHHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCeEeecCcCCccCCHHHHHHHHHHH
Confidence 86 5789999 9999999999999999999999999999999999999999996 99999999999999986 577888
Q ss_pred HHHhcC--CchHHHHHHHhhcC----CCCCCCCCCCCCCCCcccCCCCCcCCCCHHHHHHHHHHHHHHHHhcCcCcccC
Q 045217 152 SALANN--PVWGDYVERLLAEG----YAKPRSGTDAGDHPPITPMRSATEDMLGKDAWRLYSYVCQHFLGTVSPDCKYI 224 (224)
Q Consensus 152 ~~l~~~--~~~~~~~~~~~~~~----~~~~~~~~k~~aH~AI~PT~~~~~~~L~~~e~~iY~lI~~r~la~f~~~a~y~ 224 (224)
+.|... +.|..++...+... ..+.+++++++||||||||... ++.|+++|++||+||++||||+|||||+|+
T Consensus 356 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~Kv~~H~AIiPT~~~-p~~Ls~~E~kiY~lI~rRfla~f~~~a~~~ 433 (987)
T PRK14724 356 EMLATSGMRHLAPFAQQALDGNYVRPSKRIFDNSKVSDHFAIIPTTQA-PSGLSEAEQKLYDLVVRRFMAVFFPSAEYQ 433 (987)
T ss_pred HHHhcccchhHHHHHHHHhcccccCCCCCcCCCCCCCCcCCcCCCCCC-cccCCHHHHHHHHHHHHHHHHHhCchhEEE
Confidence 888643 33444444333211 1233467889999999999874 478999999999999999999999999984
No 8
>PRK14973 DNA topoisomerase I; Provisional
Probab=100.00 E-value=1.1e-60 Score=472.04 Aligned_cols=215 Identities=34% Similarity=0.594 Sum_probs=186.3
Q ss_pred cCCccccCcchhHHHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEeccccCCHHHHHHHHHHHccCCceEEEEE
Q 045217 6 VTLILIYGPCQTPTLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWERQKLFDFDVATMFQKLVMQDRILEVIDI 85 (224)
Q Consensus 6 ~~~~lS~GRVQTPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v 85 (224)
.+.+||+||||||||+|||+||+||+||+|++||+|.+.+..+|..|.+.|..++++|++.|+.+.+.+. ..++|++|
T Consensus 187 ~~~~lS~GRVQTPtL~lIveRe~EI~~Fvp~~Yw~I~~~~~~~~~~~~a~~~~~r~~d~~~A~~i~~~~~--~~~~V~~v 264 (936)
T PRK14973 187 GDNILSVGRVQSPTLAMIVDREKEIEAFVPEKYWMLSLATEKDGEGIEARHTHGRFTDSAAAEAAYDATK--EPLVVTEV 264 (936)
T ss_pred CCcceeeccccchHHHHHHhHHHHHHcCCCCceEEEEEEEecCCceEEEEEcCCCCCCHHHHHHHHHHcC--CCeEEEEE
Confidence 3457999999999999999999999999999999999999877888999998889999999999998874 47899999
Q ss_pred eeecccccCCCcccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceeccCCCCcccCCCcChHHHHHHHhcCCchHHHHH
Q 045217 86 SEKQESKVRPCGLNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISYPRTESTAYPSSFDFRGTLSALANNPVWGDYVE 165 (224)
Q Consensus 86 ~~k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRTds~~l~~~~~~~~~l~~l~~~~~~~~~~~ 165 (224)
+++++++.||+||||++||++|++ |||||++||++||+|||+||||||||||++||+++++.+++..+... .|+.++.
T Consensus 265 ~~k~~~~~pP~Pf~ts~LQ~~ask-lg~Sa~kTm~iAQ~LYE~glITYPRTDS~~l~~~~~~~~il~~l~~~-~~~~~~~ 342 (936)
T PRK14973 265 KEGHKVDRAPTPFDTTTFIVAASR-LGFSAANAMRIAEDLYMNGYISYPRTDNTIYPKSLDLNGVLATLAKG-AFSKDVA 342 (936)
T ss_pred EeeeEeccCCCCccHHHHHHHHHH-cCCCHHHHHHHHHHHHhCCeeeccCcccccCchhhhHHHHHHHHHHh-hhHHHHH
Confidence 999999999999999999999985 99999999999999999999999999999999987788888877642 3555443
Q ss_pred HHhhcCCCCCCCCCC-CCCCCCcccCCCCCcCCCCHHHHHHHHHHHHHHHHhcCcCcccC
Q 045217 166 RLLAEGYAKPRSGTD-AGDHPPITPMRSATEDMLGKDAWRLYSYVCQHFLGTVSPDCKYI 224 (224)
Q Consensus 166 ~~~~~~~~~~~~~~k-~~aH~AI~PT~~~~~~~L~~~e~~iY~lI~~r~la~f~~~a~y~ 224 (224)
.+.......+.++++ ++|||||+||+..+...|+++|++||+|||+||||+|||||+|+
T Consensus 343 ~l~~~~~~~~~~~kk~~~aH~AI~PT~~~~~~~Ls~de~klY~LI~rRfLA~~~~~a~~~ 402 (936)
T PRK14973 343 WVKDNRRPVPTRGKKSSTDHPPIHPTGVATREELGDDRWKLYELVVRRFLATLSPDAEWA 402 (936)
T ss_pred HHhhcCCccCCCCCCCcCCcCCccCcCCcChhhCCHHHHHHHHHHHHHHHHHhChhheEE
Confidence 332222112334444 89999999999865567999999999999999999999999984
No 9
>PRK07726 DNA topoisomerase III; Provisional
Probab=100.00 E-value=1.1e-60 Score=460.98 Aligned_cols=217 Identities=22% Similarity=0.404 Sum_probs=188.6
Q ss_pred cCCccccCcchhHHHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEec--------cccCCHHHHHHHHHHHccC
Q 045217 6 VTLILIYGPCQTPTLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWER--------QKLFDFDVATMFQKLVMQD 77 (224)
Q Consensus 6 ~~~~lS~GRVQTPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~--------~~~~~~~~a~~~~~~~~~~ 77 (224)
.++++|+||||||||+|||+||+||+||+|++||+|.+.+ .+|+.|.+.|.. ++++|++.|+.+.+.+.+
T Consensus 183 ~~~~lS~GRVQTPtL~lVv~Re~eI~~F~p~~y~~i~~~~-~~~~~~~~~~~~~~~~~~~~~r~~~~~~a~~~~~~~~~- 260 (658)
T PRK07726 183 YNGVLSVGRVQTPTLALVVRRDEEIENFVPKPYWEVEAHL-TPGERFTAKWQPSEPYQDEEGRLLDRPLAEQVVARIQG- 260 (658)
T ss_pred CCcceeecccccchhHHHHHHHHHHHcCCCcccEEEEEEE-cCCCeEEEEEeccccccccccccCCHHHHHHHHHHhcC-
Confidence 4568999999999999999999999999999999999999 667789999962 579999999999999976
Q ss_pred CceEEEEEeeecccccCCCcccHHHHHHHHHHhCCCCHHHHHHHHHHHhhc-cceeccCCCCcccCCCc--ChHHHHHHH
Q 045217 78 RILEVIDISEKQESKVRPCGLNTVNLLKVASSALGYGPQMAMQLAERLYTQ-GFISYPRTESTAYPSSF--DFRGTLSAL 154 (224)
Q Consensus 78 ~~~~V~~v~~k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~-glITYPRTds~~l~~~~--~~~~~l~~l 154 (224)
..++|++|+++++++.||+||||++||++||++|||||++||++||+|||+ ||||||||||++||+++ +++.+++.+
T Consensus 261 ~~~~V~~v~~k~~~~~pP~pf~ls~Lq~~a~~~~g~s~~~tl~iaQ~LYE~~glITYPRTds~~ls~~~~~~~~~~l~~l 340 (658)
T PRK07726 261 QPAKVTEVETKRKKEYAPLLYDLSELQIDANKRFGLSAKETLDIAQSLYETHKLITYPRTDSRYLPEDMVATLPEVLNAI 340 (658)
T ss_pred CCeEEEEEEeeEEecCCCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCEEEecCCCCccCCHHHHHHHHHHHHHH
Confidence 479999999999999999999999999999999999999999999999997 99999999999999986 678888888
Q ss_pred hcCCchHHHHHHHhhcCC-CCCCCCCCCCCCCCcccCCCC-CcCCCCHHHHHHHHHHHHHHHHhcCcCcccC
Q 045217 155 ANNPVWGDYVERLLAEGY-AKPRSGTDAGDHPPITPMRSA-TEDMLGKDAWRLYSYVCQHFLGTVSPDCKYI 224 (224)
Q Consensus 155 ~~~~~~~~~~~~~~~~~~-~~~~~~~k~~aH~AI~PT~~~-~~~~L~~~e~~iY~lI~~r~la~f~~~a~y~ 224 (224)
.....|..++..++.... .+..++++++|||||+||+.. +.++|+++|++||+||++||||+|||||+|+
T Consensus 341 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aH~AI~PT~~~~~~~~L~~~e~~iY~lI~~r~la~~~~~~~~~ 412 (658)
T PRK07726 341 SKVDPYLLLAPPVLDPSIRSRAWNDKKVTAHHAIIPTEQPPNLSKLSEDERKVYDLIARRYLAQFLPPAEYD 412 (658)
T ss_pred hccCcchhhhhhhhccccccCcCCCCcCCCCCCcCccCCCCCcccCCHHHHHHHHHHHHHHHHHhCchhEEE
Confidence 755556544333332211 233466789999999999874 4468999999999999999999999999874
No 10
>COG0550 TopA Topoisomerase IA [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.5e-60 Score=450.62 Aligned_cols=210 Identities=26% Similarity=0.437 Sum_probs=173.5
Q ss_pred ccccCcchhHHHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEec------cccCCHHHHHHHHHHHccCCceEE
Q 045217 9 ILIYGPCQTPTLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWER------QKLFDFDVATMFQKLVMQDRILEV 82 (224)
Q Consensus 9 ~lS~GRVQTPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~------~~~~~~~~a~~~~~~~~~~~~~~V 82 (224)
+||+||||||||+|||+||+||++|+|++||+|.+.+..+++.|.+.|.. .++.+...|..+++.+++ +.+.|
T Consensus 166 ~LSaGRVQSpaL~lVveRE~EI~~F~p~~yw~i~a~~~~~~~~f~a~~~~~~~~~~~~~~~~~~a~~~~~~l~~-~~~~V 244 (570)
T COG0550 166 VLSAGRVQSPALRLVVEREREIEAFVPEEYWEIKAIFEKGGGEFSARLTEIEGKKEGRLKDKDEAEEIVNKLKG-KPAKV 244 (570)
T ss_pred CCCCccccchhhhhhHhhHHHHHhCCCCcceEEEEEEecCCccEEEEEeccccccccccccHHHHHHHHHHccC-CceEE
Confidence 59999999999999999999999999999999999998877669988862 367788889999999985 58999
Q ss_pred EEEeeecccccCCCcccHHHHHHHHHHhCCCCHHHHHHHHHHHhhc-cceeccCCCCcccCCCcChHHHHHHHhcCCchH
Q 045217 83 IDISEKQESKVRPCGLNTVNLLKVASSALGYGPQMAMQLAERLYTQ-GFISYPRTESTAYPSSFDFRGTLSALANNPVWG 161 (224)
Q Consensus 83 ~~v~~k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~-glITYPRTds~~l~~~~~~~~~l~~l~~~~~~~ 161 (224)
+++++++++..||+||+|++||++||++|||||++||++||+|||. ||||||||||++||+++.... ...+.... |+
T Consensus 245 ~~ve~k~~~~~pp~Pf~tstLQq~As~~lgfs~kktm~iAQ~LYE~~glITYpRTDs~~ls~~~~~~~-~~~i~~~~-yg 322 (570)
T COG0550 245 VSVEKKPKKRSPPPPFTTSTLQQEASRKLGFSAKKTMDIAQKLYEGHGLITYPRTDSTRLSEEALAEA-RLYILAIA-YG 322 (570)
T ss_pred EEEeeeeeccCCCCCCcHHHHHHHHHHhCCCCHHHHHHHHHHHhcCCCcEEecCCCCCcCCHHHHHHH-HHHHHhhc-cH
Confidence 9999999999999999999999999999999999999999999997 999999999999999862211 11111111 55
Q ss_pred HHHHHHhhc-CCCCC-CCCCCCCCCCCcccCCCCCcCCCC-HHHHHHHHHHHHHHHHhcCcCcccC
Q 045217 162 DYVERLLAE-GYAKP-RSGTDAGDHPPITPMRSATEDMLG-KDAWRLYSYVCQHFLGTVSPDCKYI 224 (224)
Q Consensus 162 ~~~~~~~~~-~~~~~-~~~~k~~aH~AI~PT~~~~~~~L~-~~e~~iY~lI~~r~la~f~~~a~y~ 224 (224)
+ .+++. ....+ +++++++||||||||+...+..+. .+|++||+|||||||||||+||+|+
T Consensus 323 ~---~~l~~~~~~~~~~~~~~q~AHeAIrPT~~~~p~~~~~~de~klY~LI~rrflAs~m~~A~~~ 385 (570)
T COG0550 323 K---EYLPLKPRRYPSKGKKAQEAHEAIRPTDFETPESLKAYDELKLYDLIWRRFLASQMPDAIYE 385 (570)
T ss_pred H---hhcccccccCCCCCCCCcCCCCCcCCCCCCCcccccchhHHHHHHHHHHHHHHHhCchhhhe
Confidence 3 33432 11222 345678999999999721233333 7999999999999999999999985
No 11
>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=1e-60 Score=438.59 Aligned_cols=212 Identities=29% Similarity=0.485 Sum_probs=157.5
Q ss_pred CCccccCcchhHHHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEeccccCCHHHHHHHHHHHccCCceEEEEEe
Q 045217 7 TLILIYGPCQTPTLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWERQKLFDFDVATMFQKLVMQDRILEVIDIS 86 (224)
Q Consensus 7 ~~~lS~GRVQTPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~ 86 (224)
++++|+||||||||+|||+||+||+||+|++||+|.+.+..++.. ...+.+.+++++++|+.+++.+.+. +|++++
T Consensus 31 ~~~ls~GRVQtp~L~li~~Re~ei~~f~~~~y~~i~~~~~~~~~~-~~~~~~~~~~~~~~a~~~~~~~~~~---~v~~~~ 106 (403)
T PF01131_consen 31 NGVLSVGRVQTPTLGLIVEREREIENFKPEPYYEIKAQFKKGGFE-FKNDDKKRFDDKEEAEQILEKLKNS---KVTEVE 106 (403)
T ss_dssp STT-TTHTTHHHHHHHHHHHHHHHHCEEEEEEEEEEEEEETCCS--EETTEES-CTSHHHHHHHHHHHHHC---EEEEEE
T ss_pred CCccccCcccchHHHHHHHHHhhhhccCCCceEEEEEEecccccc-cccccccccccHHHHHHHhhcccCc---eEEEEE
Confidence 689999999999999999999999999999999999998765544 2334567899999999999999862 899999
Q ss_pred eecccccCCCcccHHHHHHHHHHhCCCCHHHHHHHHHHHhhc-cceeccCCCCcccCCCcChHHHHHHHhcC-C-chHHH
Q 045217 87 EKQESKVRPCGLNTVNLLKVASSALGYGPQMAMQLAERLYTQ-GFISYPRTESTAYPSSFDFRGTLSALANN-P-VWGDY 163 (224)
Q Consensus 87 ~k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~-glITYPRTds~~l~~~~~~~~~l~~l~~~-~-~~~~~ 163 (224)
+++++..||+||||++||++||++|||||++||++||+|||+ ||||||||||++||++.++..+++.+... + .|..+
T Consensus 107 ~~~~~~~pP~p~~l~~Lq~~a~k~~g~s~~~tl~iaQ~LYE~~g~ISYPRTds~~l~~~~~~~~i~~~l~~~~~~~~~~~ 186 (403)
T PF01131_consen 107 EKEKKKPPPLPFNLSTLQKEASKKLGFSAKETLDIAQKLYEKHGLISYPRTDSRYLPEDEDLKEILKYLKKHYGEDYFPE 186 (403)
T ss_dssp EEEEEE----SB-HHHHHHHHHHHH---HHHHHHHHHHHHHTTTSBS-SS-S---B-HHHGHHHHHHHHHHHTTGGGS-S
T ss_pred EEEeeecCCChHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhhhheeeeeccchhhhcchhhHHHHHHHHHHhcccccccc
Confidence 999999999999999999999999999999999999999997 99999999999999986678888888752 2 12222
Q ss_pred HHHHhhcCCCCCCCCCCCCCCCCcccCCCC--CcCCCCHHHHHHHHHHHHHHHHhcCcCcccC
Q 045217 164 VERLLAEGYAKPRSGTDAGDHPPITPMRSA--TEDMLGKDAWRLYSYVCQHFLGTVSPDCKYI 224 (224)
Q Consensus 164 ~~~~~~~~~~~~~~~~k~~aH~AI~PT~~~--~~~~L~~~e~~iY~lI~~r~la~f~~~a~y~ 224 (224)
+..... ..+.+++++++||||||||... +.++|+++|++||+||++|||++|||||+|+
T Consensus 187 ~~~~~~--~~~~~~~~kv~aH~AI~PT~~~~~~~~~Ls~~e~~vY~LI~rr~la~~~~~~~~~ 247 (403)
T PF01131_consen 187 APNLLK--SPKSKNDSKVTAHHAIIPTGKIPPDLSNLSEDERKVYDLIARRFLAAFMPDAKYE 247 (403)
T ss_dssp S--TTS--SSTTC-CCC-SSSS-B-BSSSTTHCGHHCHHHHHHHHHHHHHHHHHHTS--EEEE
T ss_pred chhhhh--cccccCCccccCCCCccccccCccchhhcCHHHHHHHHHHHHHHHHHHHHHHhee
Confidence 211111 1122356778999999999774 3468999999999999999999999999984
No 12
>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=6.1e-58 Score=438.58 Aligned_cols=208 Identities=27% Similarity=0.391 Sum_probs=175.5
Q ss_pred CccccCcchhHHHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEe--------ccccCCHHHHHHHHHHHccCCc
Q 045217 8 LILIYGPCQTPTLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWE--------RQKLFDFDVATMFQKLVMQDRI 79 (224)
Q Consensus 8 ~~lS~GRVQTPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~--------~~~~~~~~~a~~~~~~~~~~~~ 79 (224)
..+|+||||||||+|||+||+||+||+|++||+|.+.+..+|+.|.+.|. .++++|++.|+++.+.+.+ ..
T Consensus 156 ~~lSvGRVQtPtL~lvv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~-~~ 234 (610)
T TIGR01051 156 KGLSAGRVQSVALRLIVDREREIKRFVPEEYWTIDATFQKGEETFEALLTEVNGKKLKAGSDLDEAEATALKEQLKG-EE 234 (610)
T ss_pred CCCCcceehHHHHHHHHHHHHHHHhcCCCceEEEEEEEecCCcceEEEEEecCCccccccccCCHHHHHHHHHHhcC-CC
Confidence 45999999999999999999999999999999999999877778988773 2478899999999999876 57
Q ss_pred eEEEEEeeecccccCCCcccHHHHHHHHHHhCCCCHHHHHHHHHHHhhc--------cceeccCCCCcccCCCc--ChHH
Q 045217 80 LEVIDISEKQESKVRPCGLNTVNLLKVASSALGYGPQMAMQLAERLYTQ--------GFISYPRTESTAYPSSF--DFRG 149 (224)
Q Consensus 80 ~~V~~v~~k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~--------glITYPRTds~~l~~~~--~~~~ 149 (224)
++|++|+.++++..||+||||++||++||++|||||++||++||+|||+ |+||||||||+|||+++ ++..
T Consensus 235 ~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~S~~~tl~iaQ~LYe~~~~~~~~~g~iSYPRTds~~l~~~~~~~~~~ 314 (610)
T TIGR01051 235 LVVEEIEKKPKKSRPPPPFTTSTLQQEASRKLGFSAKKTMMIAQRLYEGVSTGDGTIGLITYMRTDSTRLSNQAVNEARN 314 (610)
T ss_pred eEEEEEeeceeeeCCCCCcCHHHHHHHHHHhcCCCHHHHHHHHHHHHhcccccCCceeEEeecCcCccccCHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999 99999999999999975 3444
Q ss_pred HHHHHhcCCchHHHHHHHhhcCCCCCCCCCC-C-CCCCCcccCCCC-Cc----CCCCHHHHHHHHHHHHHHHHhcCcCcc
Q 045217 150 TLSALANNPVWGDYVERLLAEGYAKPRSGTD-A-GDHPPITPMRSA-TE----DMLGKDAWRLYSYVCQHFLGTVSPDCK 222 (224)
Q Consensus 150 ~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~k-~-~aH~AI~PT~~~-~~----~~L~~~e~~iY~lI~~r~la~f~~~a~ 222 (224)
++..+. +. .++.....+..++++ + +||||||||... .+ ++|+++|++||+||++||||+|||||+
T Consensus 315 ~l~~~~-----~~---~~~~~~~~~~~~~~k~~~~~H~aI~Pt~~~~~~~~~~~~Ls~~e~~iY~lI~rr~la~~~~~~~ 386 (610)
T TIGR01051 315 LIDKNY-----GK---EYLGPKPKRYKSKEKNAQEAHEAIRPTSVFRTPEELKDYLKRDEFRLYELIWKRFVASQMADAR 386 (610)
T ss_pred HHHHhh-----hH---hhccccCcccCCCCCCCCCCcCCCCCCCCCcChhhhhccCCHHHHHHHHHHHHHHHHHhCccce
Confidence 444432 21 112111223334444 5 899999999863 12 469999999999999999999999998
Q ss_pred cC
Q 045217 223 YI 224 (224)
Q Consensus 223 y~ 224 (224)
|+
T Consensus 387 ~~ 388 (610)
T TIGR01051 387 YD 388 (610)
T ss_pred EE
Confidence 84
No 13
>PRK05582 DNA topoisomerase I; Validated
Probab=100.00 E-value=4.1e-57 Score=435.88 Aligned_cols=208 Identities=21% Similarity=0.347 Sum_probs=174.6
Q ss_pred CccccCcchhHHHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEe-----ccccCCHHHHHHHHHHHccCCceEE
Q 045217 8 LILIYGPCQTPTLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWE-----RQKLFDFDVATMFQKLVMQDRILEV 82 (224)
Q Consensus 8 ~~lS~GRVQTPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~-----~~~~~~~~~a~~~~~~~~~~~~~~V 82 (224)
..+|+||||||||+|||+||+||+||+|++||+|.+.+..+++.|.+.|. .++++|+++|+++.+.+.+ +.++|
T Consensus 160 ~~ls~GRVQtPtL~lvv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~-~~~~v 238 (650)
T PRK05582 160 KGLSAGRVQSVALKLIIDREKEIRAFVPEEYWTIDAEFKKGKKKFEASFYGYKGKKIELKNEEDVKEILAELKK-KDFKV 238 (650)
T ss_pred CCCccccchHhHHHHHHhHHHHHHhCCCCccEEEEEEEecCCccEEEEEEecCCCccccCCHHHHHHHHHHhcC-CCeEE
Confidence 35999999999999999999999999999999999999766667888773 3589999999999999976 57999
Q ss_pred EEEeeecccccCCCcccHHHHHHHHHHhCCCCHHHHHHHHHHHhh---------ccceeccCCCCcccCCCc--ChHHHH
Q 045217 83 IDISEKQESKVRPCGLNTVNLLKVASSALGYGPQMAMQLAERLYT---------QGFISYPRTESTAYPSSF--DFRGTL 151 (224)
Q Consensus 83 ~~v~~k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE---------~glITYPRTds~~l~~~~--~~~~~l 151 (224)
++|++++++..||+||||++||++||++|||||++||++||+||| +||||||||||++||+++ ++..++
T Consensus 239 ~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~~aQ~LYe~~~~~~~~~~gliSYPRTds~~l~~~~~~~~~~~~ 318 (650)
T PRK05582 239 SKVKKKERKRNPPPPFTTSTLQQEAARKLNFSTKKTMMIAQQLYEGIDLGKQGTVGLITYMRTDSTRISDTAQEEAREFI 318 (650)
T ss_pred EEEeeeeeecCCCCCccHHHHHHHHHHHcCCCHHHHHHHHHHHhcccccCCCCceEEEEecCCCcccCCHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999 699999999999999975 234444
Q ss_pred HHHhcCCchHHHHHHHhhcCCCCCCCCCCC-CCCCCcccCCCC-Cc----CCCCHHHHHHHHHHHHHHHHhcCcCcccC
Q 045217 152 SALANNPVWGDYVERLLAEGYAKPRSGTDA-GDHPPITPMRSA-TE----DMLGKDAWRLYSYVCQHFLGTVSPDCKYI 224 (224)
Q Consensus 152 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~-~aH~AI~PT~~~-~~----~~L~~~e~~iY~lI~~r~la~f~~~a~y~ 224 (224)
..+ ++. .+......+.++++++ +|||||+||+.. .+ ++|+++|++||+||++||||+|||||+|+
T Consensus 319 ~~~-----~~~---~~~~~~~~~~~~~~k~~~~H~aI~PT~~~~~p~~~~~~L~~~e~~iY~lI~~rfla~~~~~~~~~ 389 (650)
T PRK05582 319 EEK-----YGK---EYLPKKPKVYKKKSGAQDAHEAIRPTSVFLTPESAKKYLTKDQLKLYKLIWNRFVASQMAPAVFD 389 (650)
T ss_pred HHH-----hHH---HhhccCCcccCCCcCCCCCCCCEeecCCCcChhHHhccCCHHHHHHHHHHHHHHHHHhCchhhee
Confidence 332 121 1121111223455555 699999999862 22 47999999999999999999999999984
No 14
>PRK08780 DNA topoisomerase I; Provisional
Probab=100.00 E-value=5.4e-57 Score=441.14 Aligned_cols=212 Identities=23% Similarity=0.356 Sum_probs=173.3
Q ss_pred cCCccccCcchhHHHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEec--------cccCCHHHHHHHHHHHcc-
Q 045217 6 VTLILIYGPCQTPTLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWER--------QKLFDFDVATMFQKLVMQ- 76 (224)
Q Consensus 6 ~~~~lS~GRVQTPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~--------~~~~~~~~a~~~~~~~~~- 76 (224)
..+.+|+||||||||+|||+||+||+||+|++||+|.+.+..++..|.+.|.. .+++|++.|+.+.+.|.+
T Consensus 162 ~~~~lSaGRVQspaL~lIveRE~eI~~F~p~~yw~i~~~~~~~~~~f~a~~~~~~~~~~~~~~~~~~~~a~~i~~~~~~~ 241 (780)
T PRK08780 162 IQRGLSAGRVQSPALRMIVEREEEIEAFIAREYWSIEADCAHPSQPFNAKLIKLDGQKFEQFTITDGDTAEAARLRIQQA 241 (780)
T ss_pred hCCCCcccccHHHHHHHHHHHHHHHHhCCCcceEEEEEEEecCCceEEEEEEecCCccccccccCCHHHHHHHHHHHhhc
Confidence 34569999999999999999999999999999999999998777778877742 358899999999998864
Q ss_pred -CCceEEEEEeeecccccCCCcccHHHHHHHHHHhCCCCHHHHHHHHHHHhhc---------cceeccCCCCcccCCCc-
Q 045217 77 -DRILEVIDISEKQESKVRPCGLNTVNLLKVASSALGYGPQMAMQLAERLYTQ---------GFISYPRTESTAYPSSF- 145 (224)
Q Consensus 77 -~~~~~V~~v~~k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~---------glITYPRTds~~l~~~~- 145 (224)
...++|.+|++++++.+||+||+|++||++||++|||||++||++||+|||+ ||||||||||++||++.
T Consensus 242 ~~~~~~V~~v~~k~~~~~pp~Pf~tstLQq~As~klg~s~~~Tm~iAQ~LYE~~~~~~~~~~glITYpRTDS~~ls~~~~ 321 (780)
T PRK08780 242 AQGTLHVTDVESKERKRNPAPPFTTSTLQQEASRKLGFTTRRTMQVAQKLYEGVDLGDEGSVGLITYMRTDSVNLSQDAL 321 (780)
T ss_pred cCCCeEEEEEEeeeeecCCCCCccHHHHHHHHHHHcCCCHHHHHHHHHHHHhhcccccCCceeEEEecccCCccCCHHHH
Confidence 2478999999999999999999999999999999999999999999999997 99999999999999874
Q ss_pred -ChHHHHHHHhcCCchH-HHHHHHhhcCCCCCCCCCCCCCCCCcccCCCC-Cc----CCCCHHHHHHHHHHHHHHHHhcC
Q 045217 146 -DFRGTLSALANNPVWG-DYVERLLAEGYAKPRSGTDAGDHPPITPMRSA-TE----DMLGKDAWRLYSYVCQHFLGTVS 218 (224)
Q Consensus 146 -~~~~~l~~l~~~~~~~-~~~~~~~~~~~~~~~~~~k~~aH~AI~PT~~~-~~----~~L~~~e~~iY~lI~~r~la~f~ 218 (224)
++...+..+ |+ .++.. ....+ +.+....++||||||||+.. .+ ..|+++|++||+|||+||||+||
T Consensus 322 ~~~~~~i~~~-----~g~~~~~~-~~~~~-~~~~~~~q~aHeAI~PT~~~~~p~~~~~~L~~de~klY~LI~~R~lAs~m 394 (780)
T PRK08780 322 AEIRDVIARD-----YGTASLPD-QPNTY-KTKSKNAQEAHEAVRPTSALRTPAQVARFLSDDQRRLYELIWKRAVACQM 394 (780)
T ss_pred HHHHHHHHHH-----hChhhhhh-ccccc-CCCCCCCcCCCCCCCCCCCCcChhhhhccCCHHHHHHHHHHHHHHHHHhC
Confidence 233333332 33 22111 01111 11112347899999999763 22 47999999999999999999999
Q ss_pred cCcccC
Q 045217 219 PDCKYI 224 (224)
Q Consensus 219 ~~a~y~ 224 (224)
+||+|+
T Consensus 395 ~~a~~~ 400 (780)
T PRK08780 395 IPATLN 400 (780)
T ss_pred chhEEE
Confidence 999874
No 15
>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=3.1e-57 Score=412.90 Aligned_cols=178 Identities=33% Similarity=0.561 Sum_probs=150.6
Q ss_pred CccccCcchhHHHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEeccccCCHHHHHHHHHHHccCCceEEEEEee
Q 045217 8 LILIYGPCQTPTLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWERQKLFDFDVATMFQKLVMQDRILEVIDISE 87 (224)
Q Consensus 8 ~~lS~GRVQTPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~ 87 (224)
+++|+||||||||+|||+||+||+||+|++||.| +.++|+++++
T Consensus 33 ~~lS~GRVQtPtL~liv~Re~ei~~F~p~~y~~i------------------------------------~~~~v~~~~~ 76 (381)
T cd00186 33 GVLSAGRVQSPTLGLIVEREREIKAFVPEDYWEI------------------------------------KEAVVVSVEK 76 (381)
T ss_pred CCCccccchhhHhHHHHHHHHHHHhCCCcceEEe------------------------------------eeEEEEEEEe
Confidence 5799999999999999999999999999999998 2578999999
Q ss_pred ecccccCCCcccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceeccCCCCcccCCCc--ChHHHHHHHhcCCchHHHHH
Q 045217 88 KQESKVRPCGLNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISYPRTESTAYPSSF--DFRGTLSALANNPVWGDYVE 165 (224)
Q Consensus 88 k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~~~~ 165 (224)
++++..||+||||++||++||++|||||++||++||+|||+||||||||||++||+++ +...++..+.... .....
T Consensus 77 ~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~iaQ~LYe~glISYPRTds~~ls~~~~~~~~~~~~~~~~~~--~~~~~ 154 (381)
T cd00186 77 KEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYEAGLITYPRTDSTRLSEEAILEAREYIQAIYGKE--YLYPA 154 (381)
T ss_pred eeeecCCCCCcCHHHHHHHHHHhcCCCHHHHHHHHHHHHcCCeeeecCCCCccCCHHHHHHHHHHHHHhcCcc--ccchh
Confidence 9999999999999999999999999999999999999999999999999999999986 3445555543321 11111
Q ss_pred HHhhcCCCCCCCCCCCCCCCCcccCCCCC----cCCCCHHHHHHHHHHHHHHHHhcCcCcccC
Q 045217 166 RLLAEGYAKPRSGTDAGDHPPITPMRSAT----EDMLGKDAWRLYSYVCQHFLGTVSPDCKYI 224 (224)
Q Consensus 166 ~~~~~~~~~~~~~~k~~aH~AI~PT~~~~----~~~L~~~e~~iY~lI~~r~la~f~~~a~y~ 224 (224)
... ....+.+++++++|||||+||+... ..+|+++|++||+||+|||||+|||||+|+
T Consensus 155 ~~~-~~~~~~~~~~~~~aH~AI~PT~~~~~~~~~~~l~~~e~~iY~LI~rrfla~~~~~~~~~ 216 (381)
T cd00186 155 PLL-GRRNPKRGKKEQGAHEAIRPTKVAPTPELEANLSEDEFKLYELIWRRFLASQMADAKYE 216 (381)
T ss_pred hcc-ccccccCCCCCcCCCCCCCcCCCCcCchhhccCCHHHHHHHHHHHHHHHHHhCchhhEE
Confidence 111 1123345678899999999998853 368999999999999999999999999884
No 16
>PRK07561 DNA topoisomerase I subunit omega; Validated
Probab=100.00 E-value=3.8e-56 Score=439.52 Aligned_cols=209 Identities=25% Similarity=0.403 Sum_probs=172.8
Q ss_pred cCCccccCcchhHHHHHHHHHHHHHHcCcCcceEEEEEEEEe-cCeEEEEEEec---c-----ccCCHHHHHHHHHHHcc
Q 045217 6 VTLILIYGPCQTPTLGFCVQRYLQITSFKPEKFWTLHPYLVQ-NGYELKLEWER---Q-----KLFDFDVATMFQKLVMQ 76 (224)
Q Consensus 6 ~~~~lS~GRVQTPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~-~~~~~~~~~~~---~-----~~~~~~~a~~~~~~~~~ 76 (224)
....+|+||||||||+|||+||+||++|+|++||+|.+.+.. +|..|.+.|.. . +++|++.|+++.+.+.+
T Consensus 171 ~~~~lSaGRVQsp~L~lIv~Re~eI~~F~p~~yw~i~~~~~~~~~~~f~a~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~ 250 (859)
T PRK07561 171 IARGLSAGRVQSVAVRLIVEREREIEAFVPEEYWDIHADLTTPRGDAFEARLTHLDGKKFAPVDLLNEAQAEAAVAALEG 250 (859)
T ss_pred hccCCCcccchhhhhHHHHHHHHHHHhcCCCccEEEEEEEEecCCCeEEEEEEeeCCceecccccCCHHHHHHHHHHhcC
Confidence 345699999999999999999999999999999999999976 56678876631 2 37899999999999976
Q ss_pred CCceEEEEEeeecccccCCCcccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceeccCCCCcccCCCc--ChHHHHHHH
Q 045217 77 DRILEVIDISEKQESKVRPCGLNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISYPRTESTAYPSSF--DFRGTLSAL 154 (224)
Q Consensus 77 ~~~~~V~~v~~k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRTds~~l~~~~--~~~~~l~~l 154 (224)
..++|++|++++++.+||+||+|++||++||++|||||++||++||+|||.||||||||||++||++. +++.++..+
T Consensus 251 -~~~~V~~v~~k~~~~~pp~pf~ts~LQ~~As~klg~s~~~tm~~aQ~LYE~glITYpRTDs~~ls~~~~~~~~~~i~~~ 329 (859)
T PRK07561 251 -ARYSVASVEDKPTTRKPSAPFTTSTLQQEASRKLGFSVKKTMRIAQRLYEAGYITYMRTDSTNLSQEAINAARGYIGDN 329 (859)
T ss_pred -CCeEEEEEEeceeEecCCCCccHHHHHHHHHHhcCCCHHHHHHHHHHHHhCCeEEecCCCCCcCCHHHHHHHHHHHHHH
Confidence 47999999999999999999999999999999999999999999999999999999999999999874 344444432
Q ss_pred hcCCchHHHHHHHhhcCCCCCCCCC-C--CCCCCCcccCCCC-Cc---CCCCHHHHHHHHHHHHHHHHhcCcCcccC
Q 045217 155 ANNPVWGDYVERLLAEGYAKPRSGT-D--AGDHPPITPMRSA-TE---DMLGKDAWRLYSYVCQHFLGTVSPDCKYI 224 (224)
Q Consensus 155 ~~~~~~~~~~~~~~~~~~~~~~~~~-k--~~aH~AI~PT~~~-~~---~~L~~~e~~iY~lI~~r~la~f~~~a~y~ 224 (224)
|+. .+++... +..+++ + ++||||||||+.. .+ ..|+++|++||+|||+||||+||+||+|+
T Consensus 330 -----~g~---~~~~~~~-r~~~~~~k~~q~aHeAI~Pt~~~~~~~~~~~L~~~e~~lY~LI~~R~lAs~m~~a~~~ 397 (859)
T PRK07561 330 -----YGK---KYLPEKP-RQYSSKAKNAQEAHEAIRPSDVFRTPDQLKGLEGDAQRLYELIWKRFVASQMAPARYD 397 (859)
T ss_pred -----hhh---hhcccCC-ccCCCcCCCCCCCcCCcccCCCCcChhhhccCCHHHHHHHHHHHHHHHHHhCchheEE
Confidence 331 1222111 112222 3 5899999999752 22 46999999999999999999999999874
No 17
>PRK06599 DNA topoisomerase I; Validated
Probab=100.00 E-value=1.4e-55 Score=426.62 Aligned_cols=209 Identities=22% Similarity=0.332 Sum_probs=172.2
Q ss_pred CCccccCcchhHHHHHHHHHHHHHHcCcCcceEEEEEEEEe-cCeEEEEEEec------c--ccCCHHHHHHHHHHHccC
Q 045217 7 TLILIYGPCQTPTLGFCVQRYLQITSFKPEKFWTLHPYLVQ-NGYELKLEWER------Q--KLFDFDVATMFQKLVMQD 77 (224)
Q Consensus 7 ~~~lS~GRVQTPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~-~~~~~~~~~~~------~--~~~~~~~a~~~~~~~~~~ 77 (224)
+..+|+||||||||+|||+||+||+||+|++||.|.+.+.. +|..|.+.|.. + +++|++.|+.+.+.+.+
T Consensus 162 ~~~lS~GRVQtPtL~lvv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~a~~~~~~~~~- 240 (675)
T PRK06599 162 RRGLSAGRVQSVALRLICEREDEIEAFIPQEYWTIEADLATSNGEPFTAKLVEVNGKKLEKFSITNEEQAKALVKALEG- 240 (675)
T ss_pred cCCCccceeHHHHhHHHHHhHHHHHhcCCCceEEEEEEEEcCCCCeeEEEEEeccCccccccCCCCHHHHHHHHHHhcC-
Confidence 34699999999999999999999999999999999999976 46678776531 2 68999999999999976
Q ss_pred CceEEEEEeeecccccCCCcccHHHHHHHHHHhCCCCHHHHHHHHHHHhhc--------cceeccCCCCcccCCCc--Ch
Q 045217 78 RILEVIDISEKQESKVRPCGLNTVNLLKVASSALGYGPQMAMQLAERLYTQ--------GFISYPRTESTAYPSSF--DF 147 (224)
Q Consensus 78 ~~~~V~~v~~k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~--------glITYPRTds~~l~~~~--~~ 147 (224)
..++|++|++++++..||+||||++||++||++|||||++||++||+|||+ ||||||||||+|||+++ ++
T Consensus 241 ~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~~aQ~LYe~~~~~~~~~g~iSYPRTds~~l~~~~~~~~ 320 (675)
T PRK06599 241 QAYTVDKIEKKERKRNPPPPFITSTLQQEASRKLGFSAKKTMRIAQKLYEGIDLGEGTVGLITYMRTDSVRLSNEALDEA 320 (675)
T ss_pred CCeEEEEEEeeEEecCCCCCCcHHHHHHHHHHHcCCCHHHHHHHHHHHHhccccccccceeEEeccCCCccCCHHHHHHH
Confidence 478999999999999999999999999999999999999999999999995 99999999999999874 34
Q ss_pred HHHHHHHhcCCchHHHHHHHhhcCCCCCCCCCC--CCCCCCcccCCCC-Cc----CCCCHHHHHHHHHHHHHHHHhcCcC
Q 045217 148 RGTLSALANNPVWGDYVERLLAEGYAKPRSGTD--AGDHPPITPMRSA-TE----DMLGKDAWRLYSYVCQHFLGTVSPD 220 (224)
Q Consensus 148 ~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~k--~~aH~AI~PT~~~-~~----~~L~~~e~~iY~lI~~r~la~f~~~ 220 (224)
..+++.+.. . .+ ........+++++ ++|||||+||+.. .+ +.|+++|++||+||++||||+||||
T Consensus 321 ~~~l~~~~~-~---~~----~~~~~~~~~~~~~~~~~aH~aI~Pt~~~~~~~~~~~~l~~~e~~iY~lI~~rfla~~~~~ 392 (675)
T PRK06599 321 RKYITKKYG-K---EY----LPAKPRVYKKKSKNAQEAHEAIRPTSINRTPESLKPYLTPDQFKLYELIWKRTVASQMAP 392 (675)
T ss_pred HHHHHHHhc-h---hh----ccccCcccCCCCCCCCCCCCCCccCCCCCChhHhhccCCHHHHHHHHHHHHHHHHHhCch
Confidence 555544322 1 11 1111111122233 3899999999863 22 4799999999999999999999999
Q ss_pred cccC
Q 045217 221 CKYI 224 (224)
Q Consensus 221 a~y~ 224 (224)
|+|+
T Consensus 393 ~~~~ 396 (675)
T PRK06599 393 AILD 396 (675)
T ss_pred heEE
Confidence 9984
No 18
>PTZ00407 DNA topoisomerase IA; Provisional
Probab=100.00 E-value=1.9e-55 Score=425.99 Aligned_cols=216 Identities=19% Similarity=0.212 Sum_probs=166.7
Q ss_pred cCCccccCcchhHHHHHHHHHHHHHHcCcCc--ceEEEEEEEEe---cCeEEEEEEe------c--cccCCHHHHHHHHH
Q 045217 6 VTLILIYGPCQTPTLGFCVQRYLQITSFKPE--KFWTLHPYLVQ---NGYELKLEWE------R--QKLFDFDVATMFQK 72 (224)
Q Consensus 6 ~~~~lS~GRVQTPtL~lIv~Re~eI~~F~p~--~y~~i~~~~~~---~~~~~~~~~~------~--~~~~~~~~a~~~~~ 72 (224)
..+.+|+||||||||+|||+||+||++|+|+ +||+|.+.+.. +|..|.+.|. . .++.++++|+++++
T Consensus 215 ~~~~lSaGRVQTPtL~LIVeRE~EIe~Fkpee~~Yw~I~a~~~~~~~~g~~F~a~~~~~~~~~~~~~~~~~~~eA~~~~~ 294 (805)
T PTZ00407 215 NSQMRSIGRVQTPALILINEREDKIKAFLESNKSTFEVQAMCQFPSPHGTTFSQVVTITPDRKGGASHWATEAEARRCLE 294 (805)
T ss_pred ccCceeecccchHHHHHHHHHHHHHHhcCCccCceEEEEEEEeecCCCCcceeEEeeccccccccccccCCHHHHHHHHH
Confidence 3457999999999999999999999999999 59999988753 3566776653 1 25668888988887
Q ss_pred HHc--cCCceEEE-EEeeecccccCCCcccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceeccCCCCcccCCCcChHH
Q 045217 73 LVM--QDRILEVI-DISEKQESKVRPCGLNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISYPRTESTAYPSSFDFRG 149 (224)
Q Consensus 73 ~~~--~~~~~~V~-~v~~k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRTds~~l~~~~~~~~ 149 (224)
.++ +...+.|. .+++++++++||+||||++||++||++|||||++||++||+|||+||||||||||++||+++ +.+
T Consensus 295 ~~~~~~~~~~~V~~~v~~k~kk~~PP~PF~tstLQqeAsrkLG~Sa~kTM~iAQ~LYE~GlITYPRTDS~~l~~e~-~~~ 373 (805)
T PTZ00407 295 QWKLNNCTGFSVPLEPKPQPSVVPPPQPFTMATAIAKANRQLKYSSEMVSGCLQDLFQLGHITYPRTDSTRIDESA-LPD 373 (805)
T ss_pred HhhhccCCcEEEEEEEEEEEEEcCCCCCccHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCceeccCCCCCcCCHHH-HHH
Confidence 764 22346663 46778999999999999999999999999999999999999999999999999999999986 445
Q ss_pred HHHHHhcCCchH-HHHHHH----h--hcCCCC------------CCCCC---CCC-CCCCcccCCCC-Cc--CCCCHHHH
Q 045217 150 TLSALANNPVWG-DYVERL----L--AEGYAK------------PRSGT---DAG-DHPPITPMRSA-TE--DMLGKDAW 203 (224)
Q Consensus 150 ~l~~l~~~~~~~-~~~~~~----~--~~~~~~------------~~~~~---k~~-aH~AI~PT~~~-~~--~~L~~~e~ 203 (224)
+...|.. .|+ +++..+ . ...... ..+++ +++ ||||||||+.. .+ ..|+++|+
T Consensus 374 i~~~I~~--~~g~~~l~~~~~~~~~~~~~~~~~k~~k~~~~~~k~~~d~~~~kvqeAHeAIrPT~~~~~~~~~~Ls~de~ 451 (805)
T PTZ00407 374 IYAAVKK--EFGKEFLYRLEDRTVSAQEGKGSKKTGKKRSTKQKKGADTPVGNVEDAHEAIRPTNIDTTGESLSLSPPTR 451 (805)
T ss_pred HHHHHHH--hhhhhhhhhhcccccccccccccccccccccccccccccccccCCCCCcCCCCccCCCCChhhccCCHHHH
Confidence 5555543 233 222000 0 111100 01222 554 79999999874 23 36999999
Q ss_pred HHHHHHHHHHHHhcCcCcccC
Q 045217 204 RLYSYVCQHFLGTVSPDCKYI 224 (224)
Q Consensus 204 ~iY~lI~~r~la~f~~~a~y~ 224 (224)
+||+|||+||||+||+||+|+
T Consensus 452 kLYdLI~rRfLAs~m~~a~~e 472 (805)
T PTZ00407 452 AVYDLVRRNTLAVFMIPMKTE 472 (805)
T ss_pred HHHHHHHHHHHHHhCchhEEE
Confidence 999999999999999999974
No 19
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=100.00 E-value=1.7e-55 Score=434.48 Aligned_cols=206 Identities=20% Similarity=0.297 Sum_probs=170.1
Q ss_pred ccccCcchhHHHHHHHHHHHHHHcCcCcceEEEEEEEEec--CeEEEEEEec-------------------cccCCHHHH
Q 045217 9 ILIYGPCQTPTLGFCVQRYLQITSFKPEKFWTLHPYLVQN--GYELKLEWER-------------------QKLFDFDVA 67 (224)
Q Consensus 9 ~lS~GRVQTPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~--~~~~~~~~~~-------------------~~~~~~~~a 67 (224)
.+|+||||||||+|||+||+||+||+|++||+|.+.+..+ +..|.+.|.. .++.|++.|
T Consensus 162 ~lSaGRVQsp~L~lIveRe~eI~~F~p~~yw~i~~~~~~~~~~~~f~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a 241 (860)
T PRK06319 162 GVSAGRVQSVALKLVVDREKAIEAFVPVEYWNIRVHLKDPKTQKTFWAHLYSVDGKKWEKEIPEGKTEDEVLLINSKEKA 241 (860)
T ss_pred CCcCCccchhhhHHHHHHHHHHHcCCCCceEEEEEEEecCCCCcceEEEeecccCcccccccccccccccccccCCHHHH
Confidence 6999999999999999999999999999999999999753 4568877631 136789999
Q ss_pred HHHHHHHccCCceEEEEEeeecccccCCCcccHHHHHHHHHHhCCCCHHHHHHHHHHHhhc---------cceeccCCCC
Q 045217 68 TMFQKLVMQDRILEVIDISEKQESKVRPCGLNTVNLLKVASSALGYGPQMAMQLAERLYTQ---------GFISYPRTES 138 (224)
Q Consensus 68 ~~~~~~~~~~~~~~V~~v~~k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~---------glITYPRTds 138 (224)
+++.+.+.+ ..++|++|++++++.+||+||+|++||++||++|||||++||++||+|||. ||||||||||
T Consensus 242 ~~i~~~l~~-~~~~V~~v~~k~~~~~pp~pf~ts~LQ~~As~~~g~sa~~tm~iAQ~LYE~~~~~~~~~~glITYpRTDs 320 (860)
T PRK06319 242 DHIVELLES-ATYTVTRVESKEKRRNAYPPFITSTLQQEASRHFRFSSSRTMNIAQTLYEGVDLDSEGATGLITYMRTDS 320 (860)
T ss_pred HHHHHHhcC-CCeEEEEEEeeEeecCCCCCccHHHHHHHHHHHcCCCHHHHHHHHHHHHhccccccCCceeEEeecCcCc
Confidence 999999976 479999999999999999999999999999999999999999999999994 9999999999
Q ss_pred cccCCCc--ChHHHHHHHhcCCchHHHHHHHhhcCCCCCCCCCC--CCCCCCcccCCCC-Cc----CCCCHHHHHHHHHH
Q 045217 139 TAYPSSF--DFRGTLSALANNPVWGDYVERLLAEGYAKPRSGTD--AGDHPPITPMRSA-TE----DMLGKDAWRLYSYV 209 (224)
Q Consensus 139 ~~l~~~~--~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~k--~~aH~AI~PT~~~-~~----~~L~~~e~~iY~lI 209 (224)
++||++. +++.++..+ |+. ++++.. .+..++++ ++||||||||+.. .+ ..|+++|++||+||
T Consensus 321 ~~ls~~~~~~~~~~i~~~-----~g~---~~~~~~-~~~~~~~k~~q~aH~AI~PT~~~~~p~~~~~~L~~de~klY~LI 391 (860)
T PRK06319 321 VRTDPEALKQVRKYIEGT-----FGK---EFLPSS-PNVYTTKKMAQDAHEAIRPTDITLTPEKLRSKLTEDQYKLYSLI 391 (860)
T ss_pred ccCCHHHHHHHHHHHHHh-----hhh---hhcccC-CcccCCCCCCCCCcCCCccCCCCcChhHhhccCCHHHHHHHHHH
Confidence 9999875 344444433 221 122211 11223333 4799999999863 23 47999999999999
Q ss_pred HHHHHHhcCcCcccC
Q 045217 210 CQHFLGTVSPDCKYI 224 (224)
Q Consensus 210 ~~r~la~f~~~a~y~ 224 (224)
|+||||+||+||+|+
T Consensus 392 ~~RflAs~m~~a~~~ 406 (860)
T PRK06319 392 WKRFVASQMIPAIYD 406 (860)
T ss_pred HHHHHHHhCchhheE
Confidence 999999999999974
No 20
>PRK09401 reverse gyrase; Reviewed
Probab=100.00 E-value=4.3e-51 Score=412.44 Aligned_cols=192 Identities=30% Similarity=0.378 Sum_probs=157.5
Q ss_pred CccccCcchhHHHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEeccccCCHHHHHHHHHHHccCCceEEEEEee
Q 045217 8 LILIYGPCQTPTLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWERQKLFDFDVATMFQKLVMQDRILEVIDISE 87 (224)
Q Consensus 8 ~~lS~GRVQTPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~ 87 (224)
..+|+||||||||+|||+||+||++|++ ||.+ .. ..+|..|.+.| ++.+++.|+.+.+.+. +|.++++
T Consensus 807 ~~lSaGRVQTPtL~~IVeRe~ei~~f~~--~~~~-~~-~~~~~~~~~~~---~~~~~~~a~~~~~~l~-----~V~~v~~ 874 (1176)
T PRK09401 807 RNLSAGRVQTPVLGWIVERYKEYKKSKG--YVLV-IK-LENGGGLELEG---EFSEKEEAEKFYNNLI-----EVEKVEE 874 (1176)
T ss_pred cCccccccccchhhhhhhhHHHhcccCC--EEEE-EE-ecCCceEEEEE---eeCCHHHHHHHHHhCC-----eeeEEEe
Confidence 4699999999999999999999999975 5544 32 23455676664 5789999988888763 7899999
Q ss_pred ecccccCCCcccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceeccCCCCcccCCCc--ChHHHHHHHhcCCchHHHHH
Q 045217 88 KQESKVRPCGLNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISYPRTESTAYPSSF--DFRGTLSALANNPVWGDYVE 165 (224)
Q Consensus 88 k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~~~~ 165 (224)
++++.+||+||||++||++||++|||||++||++||+|||+||||||||||+++|++. .+++.++.+..
T Consensus 875 k~~~~~pP~Pf~t~~Lq~~As~~lg~Sa~~tm~iAQ~LYE~glITYpRTDS~~ls~~~~~~a~~~l~~~~~--------- 945 (1176)
T PRK09401 875 KEEELNPLPPYTTDTLLSDASRKLRLSAQETMRIAQDLFELGLITYHRTDSTRVSDVGISVAKEYLEKRGG--------- 945 (1176)
T ss_pred eEEEecCCCCCccHHHHHHHHHHcCCCHHHHHHHHHHHHhCCceeecCCCCCcCCHHHHHHHHHHHHHhhC---------
Confidence 9999999999999999999999999999999999999999999999999999999763 23333333221
Q ss_pred HHhhcCCCCCCCCCCCCCCCCcccCCCCCc---------------CCCCHHHHHHHHHHHHHHHHhcCcCcccC
Q 045217 166 RLLAEGYAKPRSGTDAGDHPPITPMRSATE---------------DMLGKDAWRLYSYVCQHFLGTVSPDCKYI 224 (224)
Q Consensus 166 ~~~~~~~~~~~~~~k~~aH~AI~PT~~~~~---------------~~L~~~e~~iY~lI~~r~la~f~~~a~y~ 224 (224)
.....++..++++|||||+||...+. ..|+++|++||+||+|||||+||+||+|+
T Consensus 946 ----~~~~~~r~~~~~~aH~AI~PT~~~~~~~l~~~~~~g~~~~~~~Lt~~e~~lY~LI~rRflAs~~~~a~~~ 1015 (1176)
T PRK09401 946 ----EEYFVPRSWGEGGAHEAIRPTRPLDAEELRQMIEEGILKLSEGLTKNHLRLYDLIFRRFMASQMKPAKVR 1015 (1176)
T ss_pred ----ccccCCCCCCCCCCcCCcCccCCCCchhhhhhhccccccccccCCHHHHHHHHHHHHHHHHHhCchhEEE
Confidence 11234555566899999999986321 47899999999999999999999999874
No 21
>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=2.8e-50 Score=406.79 Aligned_cols=192 Identities=28% Similarity=0.380 Sum_probs=155.7
Q ss_pred CccccCcchhHHHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEeccccCCHHHHHHHHHHHccCCceEEEEEee
Q 045217 8 LILIYGPCQTPTLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWERQKLFDFDVATMFQKLVMQDRILEVIDISE 87 (224)
Q Consensus 8 ~~lS~GRVQTPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~ 87 (224)
+.+|+||||||||+|||+||+||++|+ +||.+.+.. ++..+...| .+++.|+.+.+.+. .++|.+|++
T Consensus 807 ~~lSaGRVQTPtL~lIVeRe~ei~~~~--~~~~i~~~~--~~~~~~~~~-----~~~~~a~~~~~~~~---~~~V~~v~~ 874 (1171)
T TIGR01054 807 RWLSAGRVQTPVLGWIIDRYRESREKR--GYLLIFALE--SDFRLGLEH-----DNRLEAKEFEKDLT---WLDVEDIAE 874 (1171)
T ss_pred CCcccceecchhhHHHHHHHHHHhCCC--ceEEEEEec--CCeEEEEEe-----CCHHHHHHHHHhCC---CcEEEEEEe
Confidence 469999999999999999999999965 599987643 333444444 47778888777763 578999999
Q ss_pred ecccccCCCcccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceeccCCCCcccCCCc--ChHHHHHHHhcCCchHHHHH
Q 045217 88 KQESKVRPCGLNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISYPRTESTAYPSSF--DFRGTLSALANNPVWGDYVE 165 (224)
Q Consensus 88 k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~~~~ 165 (224)
++++.+||+||+|++||++||++|||||++||++||+|||+||||||||||++||++. ..++.+..+
T Consensus 875 k~~~~~pP~Pf~t~~Lq~~As~~lg~sa~~tm~iAQ~LYE~GlITYpRTDS~~ls~~~~~~~~~~l~~~----------- 943 (1171)
T TIGR01054 875 REEERNPLPPYTTDTMLEDANRKLGLSVKETMQIAQELFENGLITYHRTDSTRVSDVGMRVAKEYLASR----------- 943 (1171)
T ss_pred eEEeccCCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHHhCCEEEecCCCCCcCCHHHHHHHHHHHHHH-----------
Confidence 9999999999999999999999999999999999999999999999999999999863 223333221
Q ss_pred HHhhcCCCCCCCCCCCCCCCCcccCCCCCc--------------CCCCHHHHHHHHHHHHHHHHhcCcCcccC
Q 045217 166 RLLAEGYAKPRSGTDAGDHPPITPMRSATE--------------DMLGKDAWRLYSYVCQHFLGTVSPDCKYI 224 (224)
Q Consensus 166 ~~~~~~~~~~~~~~k~~aH~AI~PT~~~~~--------------~~L~~~e~~iY~lI~~r~la~f~~~a~y~ 224 (224)
.......++..++++|||||+||...++ ..|+++|++||+||+|||||+|||||+|+
T Consensus 944 --~~~~~~~~r~~~~~~aHeAI~PT~~~~~~~l~~~~~~g~~~~~~Ls~~e~~lY~LI~rRflAs~~~~a~~~ 1014 (1171)
T TIGR01054 944 --LGGEYFYPREWGEGGAHECIRPTRPLDVDDLQRLILEGVIELEGLTREHLRLYDLIFRRFMASQMRPAKVD 1014 (1171)
T ss_pred --hcccccCCCCCCCCCCcCCcCCcCCCChhhhhhhhcccccccccCCHHHHHHHHHHHHHHHHHhCchheEE
Confidence 1111223444456799999999986332 36899999999999999999999999874
No 22
>KOG1956 consensus DNA topoisomerase III alpha [Replication, recombination and repair]
Probab=100.00 E-value=3.1e-48 Score=359.96 Aligned_cols=217 Identities=38% Similarity=0.743 Sum_probs=201.1
Q ss_pred cCCccccCcchhHHHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEeccccCCHHHHHHHHHHHccCCceEEEEE
Q 045217 6 VTLILIYGPCQTPTLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWERQKLFDFDVATMFQKLVMQDRILEVIDI 85 (224)
Q Consensus 6 ~~~~lS~GRVQTPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v 85 (224)
.++++|+|+||.|||++||+|++||++|+|+.||+|.+.....|+...++|.++++||...+..+.+.|...+.+.|+++
T Consensus 201 ~~~viSyG~cQfpTLgfVvdR~~eIe~FvPEefWtl~~~~~~~~~~~~fnw~R~~lfdr~s~~~~~e~c~e~k~a~Vv~~ 280 (758)
T KOG1956|consen 201 GEQVISYGPCQFPTLGFVVDRYKEIENFVPEEFWTLKFKHTHKGGLTEFNWKRGHLFDRLSVVILYEICVEEKEATVVKV 280 (758)
T ss_pred hccccccccccCcceeeeeehHHHHhccCCcceEEEEEEEeccCceeEEeecccccccHHHHHHHHHHHhcccceeEEec
Confidence 34899999999999999999999999999999999999999999999999999999999988888898888788999999
Q ss_pred eeecccccCCCcccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceeccCCCCcccCCCcChHHHHHHHhcCCchHHHHH
Q 045217 86 SEKQESKVRPCGLNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISYPRTESTAYPSSFDFRGTLSALANNPVWGDYVE 165 (224)
Q Consensus 86 ~~k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRTds~~l~~~~~~~~~l~~l~~~~~~~~~~~ 165 (224)
..++++++||+|++|.+||+.|+++|.+|+++||+||++||.+|+||||||++..+|.+++++.+++.+...+.|+.|+.
T Consensus 281 ~kkpktKyrP~pl~TvELqK~~s~~lrlSak~TM~iAE~ly~~gfisyprtetd~F~s~~~lk~lv~~qt~~~~wg~yA~ 360 (758)
T KOG1956|consen 281 TKKPKTKYRPLPLDTVELQKLASRKLRLSAKHTMKIAEKLYQKGFISYPRTETDNFPSDMDLKALVEKQTQDPAWGSYAQ 360 (758)
T ss_pred ccCCccCCCCCcchHHHHHhhhhhheeccHHHHHHHHHHHHhccceeccccccccCCCcCchHHHHHhhccCchhHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999988899999999
Q ss_pred HHhhcCCCCCCCCC-CCCCCCCcccCCCCC-cCCCCHHHHHHHHHHHHHHHHhcCcCcc
Q 045217 166 RLLAEGYAKPRSGT-DAGDHPPITPMRSAT-EDMLGKDAWRLYSYVCQHFLGTVSPDCK 222 (224)
Q Consensus 166 ~~~~~~~~~~~~~~-k~~aH~AI~PT~~~~-~~~L~~~e~~iY~lI~~r~la~f~~~a~ 222 (224)
.++......|+|++ .+.||++|+||.... ..+++.++++||++|+||||||.+.||+
T Consensus 361 ~ll~~~~r~Prng~~~d~Ahppihp~k~~s~~~~~s~d~~~vye~v~rhflAc~S~dak 419 (758)
T KOG1956|consen 361 RLLQPENRNPRNGKHNDKAHPPIHPTKFTSREANLSGDHRKVYELVVRHFLACCSQDAK 419 (758)
T ss_pred HhhccCCCCCCCCccccccCCCccceeeccccccCCcchHHHHHHHHHHHHHhhccccc
Confidence 98865545677754 578999999998853 3589999999999999999999999885
No 23
>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=4.5e-42 Score=298.42 Aligned_cols=136 Identities=31% Similarity=0.490 Sum_probs=110.9
Q ss_pred eecccccCCCcccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceeccCCCCcccCCCc--ChHHHHHHHhcCCchHHHH
Q 045217 87 EKQESKVRPCGLNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISYPRTESTAYPSSF--DFRGTLSALANNPVWGDYV 164 (224)
Q Consensus 87 ~k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~~~ 164 (224)
+++++..||+||||++||++||++|||||++||++||+|||+||||||||||+|||+++ ++..++..+.. +.|..++
T Consensus 2 ~~~~~~~pP~pf~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYe~g~iTYPRTds~~l~~~~~~~~~~~l~~~~~-~~~~~~~ 80 (259)
T smart00437 2 EKEKKKNPPPPFTTSTLQQEASRKLGFSAKKTMQIAQKLYEKGLITYPRTDSTRLSEEAVLEARNYISKHYG-KEYLPLA 80 (259)
T ss_pred CCcccCCCCCCccHHHHHHHHHHhcCCCHHHHHHHHHHHHhCCeeEecCCCCCcCCHHHHHHHHHHHHHhhc-hhhhhhh
Confidence 56788899999999999999999999999999999999999999999999999999986 45555655543 3343332
Q ss_pred HHHhhcCCCCCCCCCCCCCCCCcccCCCCC----cCCCCHHHHHHHHHHHHHHHHhcCcCcccC
Q 045217 165 ERLLAEGYAKPRSGTDAGDHPPITPMRSAT----EDMLGKDAWRLYSYVCQHFLGTVSPDCKYI 224 (224)
Q Consensus 165 ~~~~~~~~~~~~~~~k~~aH~AI~PT~~~~----~~~L~~~e~~iY~lI~~r~la~f~~~a~y~ 224 (224)
..+. ....+.+++++++||||||||+... ..+|+++|++||+||+|||||+|||||+|+
T Consensus 81 ~~~~-~~~~~~~~~~k~~~H~aI~PT~~~~~~~~~~~L~~~e~~iY~lI~rr~la~~~~~~~~~ 143 (259)
T smart00437 81 VSLL-KPRKPRWGKKEQGAHEAIRPTKPIPTPELEKELSEDEKKLYELIWRRFLASQMPDAKYE 143 (259)
T ss_pred hhhc-cCccccCCCCCCCCCCCCCccCCCCCchhhhhCCHHHHHHHHHHHHHHHHHhChhheEE
Confidence 2111 1122345778899999999998842 257999999999999999999999999984
No 24
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=100.00 E-value=1e-36 Score=295.59 Aligned_cols=191 Identities=27% Similarity=0.402 Sum_probs=144.0
Q ss_pred CCccccCcchhHHHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEeccccCCHHHHHHHHHHHccCCceEEEEEe
Q 045217 7 TLILIYGPCQTPTLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWERQKLFDFDVATMFQKLVMQDRILEVIDIS 86 (224)
Q Consensus 7 ~~~lS~GRVQTPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~ 86 (224)
+..||+||||||+|+|||+|++|-+.=+. |..+. ..+... +-+...++.+...+.. ..+.|.++.
T Consensus 822 ~~nLsAGRVQTPVLGWIV~Ry~e~~~~~~--~~~~~-------~~~~~~-----~~~~~~~~~~~~~~~~-~~v~v~~~~ 886 (1187)
T COG1110 822 NKNLSAGRVQTPVLGWIVNRYEEYKEKRG--YLVIQ-------LDLDLP-----SGNREEVENVKRKLKL-IVVEVVDVV 886 (1187)
T ss_pred ccCccccccccccceeehhhHHHHhhccc--eeEee-------ccceee-----ccchhhhhhhhhhccc-ceEEEeehh
Confidence 46799999999999999999999886554 44431 111111 1233444444444433 346666766
Q ss_pred eecccccCCCcccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceeccCCCCcccCCCcChHHHHHHHhcCCchHHHHHH
Q 045217 87 EKQESKVRPCGLNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISYPRTESTAYPSSFDFRGTLSALANNPVWGDYVER 166 (224)
Q Consensus 87 ~k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRTds~~l~~~~~~~~~l~~l~~~~~~~~~~~~ 166 (224)
++++-.+||+||+|+++.++||++||+|+++||+|||.|+|.|||||+||||+++|+.- ..+.. +|+..
T Consensus 887 e~ee~~~PlPPyTTDt~L~dAs~~L~lsa~~~M~iaQdLFE~GlITYHRTDSTrVS~~G--i~vAr---------eyl~~ 955 (1187)
T COG1110 887 EREEEKNPLPPYTTDTMLRDASRRLRLSADETMQIAQDLFEGGLITYHRTDSTRVSDVG--IRVAR---------EYLRK 955 (1187)
T ss_pred hhhhccCCCCCcCcchHHHHHHHHhCCChhHHHHHHHHHHhccceEEeecCCcccchhh--HHHHH---------HHHHH
Confidence 66777899999999999999999999999999999999999999999999999999752 01111 22222
Q ss_pred HhhcCCCCCCCCCCCCCCCCcccCCCCC---------------cCCCCHHHHHHHHHHHHHHHHhcCcCccc
Q 045217 167 LLAEGYAKPRSGTDAGDHPPITPMRSAT---------------EDMLGKDAWRLYSYVCQHFLGTVSPDCKY 223 (224)
Q Consensus 167 ~~~~~~~~~~~~~k~~aH~AI~PT~~~~---------------~~~L~~~e~~iY~lI~~r~la~f~~~a~y 223 (224)
-.......|+.+...+||+||+||...+ +..|+..+.+||+||.|||+|++|.|++.
T Consensus 956 ~~~e~~f~pR~Wge~GAHEaIRPtrPid~~eL~~~i~~G~i~~~~~Lt~~HlrvYdLIFrRFmASQm~pa~v 1027 (1187)
T COG1110 956 EFGEEYFRPRSWGEEGAHEAIRPTRPIDVEELITLIEEGVIQLPIRLTKNHLRVYDLIFRRFMASQMRPAKV 1027 (1187)
T ss_pred hhccccccCCccccCCcccccCCCCCCCHHHHHHHHHcCCeeccchhhHHHHHHHHHHHHHHHHhhCCceeE
Confidence 2223345788888899999999998753 13589999999999999999999999863
No 25
>PRK14701 reverse gyrase; Provisional
Probab=99.95 E-value=1.1e-28 Score=255.15 Aligned_cols=124 Identities=24% Similarity=0.274 Sum_probs=101.3
Q ss_pred CccccCcchhHHHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEeccccCCHHHHHHHHHHHccCCceEEEEEee
Q 045217 8 LILIYGPCQTPTLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWERQKLFDFDVATMFQKLVMQDRILEVIDISE 87 (224)
Q Consensus 8 ~~lS~GRVQTPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~ 87 (224)
..+|+||||||||+|||+||+||+| +|++||++.+.. + +.+.|.. +++. ..++|.+|++
T Consensus 788 ~~lS~GRVQTPtL~~Iv~Re~ei~~-~~~~~~~i~~~~---~--~~~~~~~----~~~~-----------~~~~V~~v~~ 846 (1638)
T PRK14701 788 RNLSAGRVQTPVLGWIIQRYKEFTE-SKVPFLGIILEN---D--LTVTIED----SKDE-----------VEVEVELVEE 846 (1638)
T ss_pred CceeecccccchhhhhHhhHHHHhc-CCCceEEEEEcC---c--eEEEecc----cccC-----------CeEEEEEEEe
Confidence 4699999999999999999999999 599999986442 2 3333321 1110 2578999999
Q ss_pred ecccccCCCcccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceeccCCCCcccCCCc--ChHHHHHH
Q 045217 88 KQESKVRPCGLNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISYPRTESTAYPSSF--DFRGTLSA 153 (224)
Q Consensus 88 k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRTds~~l~~~~--~~~~~l~~ 153 (224)
++++.+||+||||++||++||++|||||++||++||+|||+|++|||||.. .+++.. .+.++.+.
T Consensus 847 k~~~~~pP~pf~t~~Lq~~As~~~g~s~~~tm~iAQ~LYE~g~~~~p~t~V-~l~dG~~~~I~el~e~ 913 (1638)
T PRK14701 847 EEKERNPLPPYTTDTMLRDASAFLKLSAKETMKLAQDLFEAGLCVTPDTYV-SLHDGRIKEIDEIVEG 913 (1638)
T ss_pred eEEEccCCCCcCHHHHHHHHHHhcCCCHHHHHHHHHHHHhCceeeCCCcee-ecCchHHHHHHHHHhh
Confidence 999999999999999999999999999999999999999999999999987 355553 45555544
No 26
>KOG1957 consensus DNA topoisomerase III beta [Replication, recombination and repair]
Probab=99.85 E-value=8.6e-23 Score=184.56 Aligned_cols=171 Identities=49% Similarity=0.851 Sum_probs=145.0
Q ss_pred CCccccCcchhHHHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEeccccCCHHHHHHHHHHHccCCceEEEEEe
Q 045217 7 TLILIYGPCQTPTLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWERQKLFDFDVATMFQKLVMQDRILEVIDIS 86 (224)
Q Consensus 7 ~~~lS~GRVQTPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~ 86 (224)
+..+|+|.||||||++.|+|...|+.|||+.||.+...+..++ +...|+++|+||.+.|..++++++..+.+.|.+|.
T Consensus 184 s~~isygpcqtptlgfcv~rhd~i~tfkpe~~w~l~~~~~~~~--~~lew~r~rvfd~eia~~f~~~vk~~~~a~v~~vs 261 (555)
T KOG1957|consen 184 SSLISYGPCQTPTLGFCVTRHDQIQTFKPEQYWVLQTNFTTDD--LSLEWQRGRVFDAEIARVFLNRVKECKTALVEDVS 261 (555)
T ss_pred hcceeecCCCCCcceeeeeehhhhhccCccceEEEeeecCCCC--ccchhhhcchhhHHHHHHHHHHHHhhhhheehhhh
Confidence 4689999999999999999999999999999999999987665 88999999999999999999999988899999999
Q ss_pred eecccccCCCcccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceeccCCCCcccCCCcChHHHHHHHhcCCchHHHHHH
Q 045217 87 EKQESKVRPCGLNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISYPRTESTAYPSSFDFRGTLSALANNPVWGDYVER 166 (224)
Q Consensus 87 ~k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRTds~~l~~~~~~~~~l~~l~~~~~~~~~~~~ 166 (224)
+|++.+..|.-+||.+|.+.| +|+++.+|.++|-. ..
T Consensus 262 ~ke~~k~rp~alntvel~rv~---------------------------itett~y~~nfd~s--------i~-------- 298 (555)
T KOG1957|consen 262 KKEARKERPCALNTVELMRVA---------------------------ITETTAYPANFDTS--------II-------- 298 (555)
T ss_pred hhHHhhcCCcccchhheeeee---------------------------EeecccCccccccc--------cc--------
Confidence 999999999999999998887 48999999987510 01
Q ss_pred HhhcCCCCCCCCCCCCCCCCcccCCCCCcCCCCHHHHHHHHHHHHHHHHhcCcCccc
Q 045217 167 LLAEGYAKPRSGTDAGDHPPITPMRSATEDMLGKDAWRLYSYVCQHFLGTVSPDCKY 223 (224)
Q Consensus 167 ~~~~~~~~~~~~~k~~aH~AI~PT~~~~~~~L~~~e~~iY~lI~~r~la~f~~~a~y 223 (224)
+.+++..+..+...++|++|.|-+..+-...+.+-++||..++++|++.-+.+++|
T Consensus 299 -~~D~L~~~s~gtdAgdgpPitpmr~~~R~m~~~dtkRLY~~vCqhf~~tp~~~~~k 354 (555)
T KOG1957|consen 299 -LGDTLFEASFGTDAGDGPPITPMRKCNRYMKSGDTKRLYCYVCQHFYATPQFKCKK 354 (555)
T ss_pred -cccccccccccCcCCCCCCcCcccccccccccccceeecchhhhhheeccCcCceE
Confidence 11222333444556789999999886555567788899999999999998888765
No 27
>PRK14701 reverse gyrase; Provisional
Probab=99.56 E-value=1.9e-15 Score=157.58 Aligned_cols=81 Identities=30% Similarity=0.417 Sum_probs=58.3
Q ss_pred eeccCCCCcccCCCc--ChHHHHHHHhcCCchHHHHHHHhhcCCCCCCCCCCCCCCCCcccCCCC-Cc------------
Q 045217 131 ISYPRTESTAYPSSF--DFRGTLSALANNPVWGDYVERLLAEGYAKPRSGTDAGDHPPITPMRSA-TE------------ 195 (224)
Q Consensus 131 ITYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~~aH~AI~PT~~~-~~------------ 195 (224)
+|||||||.+||+++ .+++.+. ..||. . +..++..+.++||+||+||+.. .+
T Consensus 1381 ~TY~RTDS~~lS~~~~~~~~~~i~-----~~~g~---~-----y~~~r~~~~q~AHeAIrPT~~~~~~~~~~~~~~~~~~ 1447 (1638)
T PRK14701 1381 CTYHRTDSTRVSNTGIRVAREYLT-----QENGE---D-----YFKPRDWFMEGAHECIRPTRPIDTDRLIQLIREGIIQ 1447 (1638)
T ss_pred cccccCCCCccCHHHHHHHHHHHH-----HhhCh---h-----hcCcccCCCcCCcCCCCCCCCCcChhhhhcccccccc
Confidence 399999999999874 1222222 12331 1 1123434568999999999763 11
Q ss_pred -CCCCHHHHHHHHHHHHHHHHhcCcCcccC
Q 045217 196 -DMLGKDAWRLYSYVCQHFLGTVSPDCKYI 224 (224)
Q Consensus 196 -~~L~~~e~~iY~lI~~r~la~f~~~a~y~ 224 (224)
..|+++|++||+|||+||||+|||||+|+
T Consensus 1448 ~~~Ls~de~klY~LI~rRflAs~m~~a~~~ 1477 (1638)
T PRK14701 1448 VPGLTRNHLRLYDLIFRRFMASQMKPAKVL 1477 (1638)
T ss_pred cccCCHHHHHHHHHHHHHHHHHhCchheEE
Confidence 25899999999999999999999999874
No 28
>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=99.56 E-value=1.4e-15 Score=111.94 Aligned_cols=33 Identities=42% Similarity=0.763 Sum_probs=31.4
Q ss_pred CccccCcchhHHHHHHHHHHHHHHcCcCcceEE
Q 045217 8 LILIYGPCQTPTLGFCVQRYLQITSFKPEKFWT 40 (224)
Q Consensus 8 ~~lS~GRVQTPtL~lIv~Re~eI~~F~p~~y~~ 40 (224)
+.+|+||||||||+|||+||+||+||+|++||+
T Consensus 57 ~~ls~GRVQtptL~lIv~R~~ei~~F~~~~y~~ 89 (89)
T smart00436 57 GVLSAGRVQTPTLGLIVEREREIKNFVPKPYWE 89 (89)
T ss_pred CCcceecchHHHHHHHHHHHHHHHcCCCCCCCC
Confidence 379999999999999999999999999999994
No 29
>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=96.85 E-value=0.0064 Score=56.27 Aligned_cols=119 Identities=16% Similarity=0.231 Sum_probs=77.6
Q ss_pred cchhHHHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEec----c--ccCCHHHHH-H--HHHHHccCCceEEEE
Q 045217 14 PCQTPTLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWER----Q--KLFDFDVAT-M--FQKLVMQDRILEVID 84 (224)
Q Consensus 14 RVQTPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~----~--~~~~~~~a~-~--~~~~~~~~~~~~V~~ 84 (224)
..+--+-.||++|..+. -..|..|-+..+.+..++..|.+.+.. | .++.....+ . .+..+..+..+.+.+
T Consensus 223 ~~e~~vY~LI~rr~la~-~~~~~~~~~t~v~~~~~~~~F~~~g~~~~~~Gw~~~~~~~~~~~~~~~lp~l~~g~~~~~~~ 301 (403)
T PF01131_consen 223 EDERKVYDLIARRFLAA-FMPDAKYEKTTVTFEVGGEEFKASGKVIIDPGWKKVYPYEEEEDEEEDLPSLKEGDEIPIED 301 (403)
T ss_dssp HHHHHHHHHHHHHHHHH-TS--EEEEEEEEEEEETTEEEEEEEEEEEEHGGGGCS-HCHCCTTSBB-----TTEEEEEEE
T ss_pred HHHHHHHHHHHHHHHHH-HHHHHheeeEEEEEEecCcEEEEEEeEEEECceeEEEEcccccccccccccccCCcEEeecc
Confidence 44456778999988776 235666777778888888889887531 1 233211111 0 122344444677888
Q ss_pred EeeecccccCCCcccHHHHHHHHHHhCCCCHHHHH-HHHHHHhhccceecc
Q 045217 85 ISEKQESKVRPCGLNTVNLLKVASSALGYGPQMAM-QLAERLYTQGFISYP 134 (224)
Q Consensus 85 v~~k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl-~iaQ~LYE~glITYP 134 (224)
++.++++..||.+|+-++|...+ .+.|+...-|. .|...|.+.|||.--
T Consensus 302 ~~~~e~~TkPP~~~Te~~Ll~~M-e~~GIGTpATra~iI~~L~~r~Yi~~~ 351 (403)
T PF01131_consen 302 VEIKEKKTKPPKRYTEASLLKAM-EKAGIGTPATRASIIEKLIKRGYIERS 351 (403)
T ss_dssp EEEEEEEEESS--EBHHHHHHHH-HHTTSS-TTTHHHHHHHHHHTTSEEE-
T ss_pred cchhhhccCCCCCCCHHHHHhhh-hhcCCCccccHHHHHHHhhccceeecc
Confidence 99999999999999999999998 55699755554 589999999999863
No 30
>smart00437 TOP1Ac Bacterial DNA topoisomerase I DNA-binding domain. Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit
Probab=96.72 E-value=0.0087 Score=52.27 Aligned_cols=113 Identities=14% Similarity=0.242 Sum_probs=76.0
Q ss_pred HHHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEe----cc--ccCCHHHHH--HHHHHHccCCceEEEEEeeec
Q 045217 18 PTLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWE----RQ--KLFDFDVAT--MFQKLVMQDRILEVIDISEKQ 89 (224)
Q Consensus 18 PtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~----~~--~~~~~~~a~--~~~~~~~~~~~~~V~~v~~k~ 89 (224)
-+-.||++|..+--- .+.-|-...+.+..++..|.+... .| .++..+..+ ..+-.+..+..+.+.+++..+
T Consensus 123 ~iY~lI~rr~la~~~-~~~~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~~~~~~~lp~~~~g~~~~~~~~~~~e 201 (259)
T smart00437 123 KLYELIWRRFLASQM-PDAKYEETKVIIKIGGEKFKAKGKTLLFDGWLKVYPEEKKEEEIELPTLKKGDELKVEEVEVEE 201 (259)
T ss_pred HHHHHHHHHHHHHhC-hhheEEEEEEEEEECCeEEEEEEEEEeECCHHHhhcccccCccccCCCcCCCCEeeeeeeEEEe
Confidence 345688888765432 345566667777778878887643 11 122211111 111223334567888999999
Q ss_pred ccccCCCcccHHHHHHHHHHhCCCCHHHHH-HHHHHHhhcccee
Q 045217 90 ESKVRPCGLNTVNLLKVASSALGYGPQMAM-QLAERLYTQGFIS 132 (224)
Q Consensus 90 ~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl-~iaQ~LYE~glIT 132 (224)
++..||.+|+-++|..+|.+ .|+.-.-|. .|.+.|.+.|||.
T Consensus 202 ~~TkPP~~~Te~tLl~~Me~-~GIGTpATra~iIe~L~~r~Yi~ 244 (259)
T smart00437 202 KKTKPPARYTEASLIKLMEK-RGIGRPSTYAEIIETLLDRGYVT 244 (259)
T ss_pred cccCCCCCCCHHHHHHHHHH-CCCCchhhHHHHHHHHHhCCcEE
Confidence 99999999999999999965 699755555 4899999999996
No 31
>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=96.01 E-value=0.041 Score=53.68 Aligned_cols=112 Identities=12% Similarity=0.220 Sum_probs=74.3
Q ss_pred HHHHHHHHHHHHHcCcCcceEEEEEEEEe--cCeEEEEEEe----cc--ccCCH------HHHHHHHHHHccCCceEEEE
Q 045217 19 TLGFCVQRYLQITSFKPEKFWTLHPYLVQ--NGYELKLEWE----RQ--KLFDF------DVATMFQKLVMQDRILEVID 84 (224)
Q Consensus 19 tL~lIv~Re~eI~~F~p~~y~~i~~~~~~--~~~~~~~~~~----~~--~~~~~------~~a~~~~~~~~~~~~~~V~~ 84 (224)
+-.||++|..+.-. .|.-|-+..+.+.. ++..|.++.. .| .++.. +..+..+-.+..+..+.+.+
T Consensus 369 iY~lI~rr~la~~~-~~~~~~~t~v~~~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~~~~~~~~~~~Lp~l~~g~~~~~~~ 447 (610)
T TIGR01051 369 LYELIWKRFVASQM-ADARYDSTSVRLTNEDGEYVFKATGRKLIFDGYYKVYVEGSDDPLEEKDRILPPLKEGDAVKLVE 447 (610)
T ss_pred HHHHHHHHHHHHhC-ccceEEEEEEEEEEcCCCeEEEEEEEEEEeCCHHHhcccccccccccccccCCCCCCCCEeEeee
Confidence 34678888775442 45556666777776 6667776532 11 11110 11111122233334677888
Q ss_pred EeeecccccCCCcccHHHHHHHHHHhCCCCHHHHHH-HHHHHhhcccee
Q 045217 85 ISEKQESKVRPCGLNTVNLLKVASSALGYGPQMAMQ-LAERLYTQGFIS 132 (224)
Q Consensus 85 v~~k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~-iaQ~LYE~glIT 132 (224)
++..+++..||.+|+-++|..+|-+ .|+...-|.. |.+.|.+.|||.
T Consensus 448 ~~~~~~~T~PP~~yTe~tLl~~Me~-~GIGTpATra~iIe~L~~r~Yi~ 495 (610)
T TIGR01051 448 VKPNQHFTQPPARYTEASLVKELEE-LGIGRPSTYASIISTIQDRGYVK 495 (610)
T ss_pred eeeccccccCCCCCCHHHHHHHHhc-CCCCccccHHHHHHHHhhCCeEE
Confidence 8888999999999999999999854 5997666655 899999999997
No 32
>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=95.98 E-value=0.028 Score=51.65 Aligned_cols=113 Identities=14% Similarity=0.196 Sum_probs=77.5
Q ss_pred HHHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEe----cc--ccCCH--HHHHHHHHHHccCCceEEEEEeeec
Q 045217 18 PTLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWE----RQ--KLFDF--DVATMFQKLVMQDRILEVIDISEKQ 89 (224)
Q Consensus 18 PtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~----~~--~~~~~--~~a~~~~~~~~~~~~~~V~~v~~k~ 89 (224)
-+-.||++|..+.-- .+.-|=...+.+..+|..|.+... .| .++.. ...+...-.+..+..+.+.+++..+
T Consensus 196 ~iY~LI~rrfla~~~-~~~~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~~~~~~~~p~l~~g~~~~~~~~~~~~ 274 (381)
T cd00186 196 KLYELIWRRFLASQM-ADAKYEETTVTLEIGGEKFKASGKVLLEDGWLEVYPEEKDDEEEEPPPLKEGDELKLEEVELEE 274 (381)
T ss_pred HHHHHHHHHHHHHhC-chhhEEEEEEEEEECCeEEEEEEEEEeeCCHHHHhCcccccccccCCCCCCCCEEeeeeeeeee
Confidence 356788888876553 455676777788777778877542 11 12111 1111111123333567788899999
Q ss_pred ccccCCCcccHHHHHHHHHHhCCCCHHHHHH-HHHHHhhcccee
Q 045217 90 ESKVRPCGLNTVNLLKVASSALGYGPQMAMQ-LAERLYTQGFIS 132 (224)
Q Consensus 90 ~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~-iaQ~LYE~glIT 132 (224)
+...||.+|+-++|.+++-+ .|+...-|.. |.+.|.+.|||.
T Consensus 275 ~~T~PP~~~Te~~Li~~Me~-~GIGTpATra~iI~~L~~r~Yi~ 317 (381)
T cd00186 275 KETQPPPRYTEASLIKLMEK-RGIGRPSTYASIIETLLDRGYVE 317 (381)
T ss_pred cccCCCCCCCHHHHHHHHHh-CCCCccccHHHHHHHHHhCCcEE
Confidence 99999999999999999854 5997666665 899999999997
No 33
>PRK07219 DNA topoisomerase I; Validated
Probab=95.90 E-value=0.035 Score=55.98 Aligned_cols=113 Identities=19% Similarity=0.274 Sum_probs=77.8
Q ss_pred hHHHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEe----cc--ccCCHHHH-HHHHHHHccCCceEEEEEeeec
Q 045217 17 TPTLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWE----RQ--KLFDFDVA-TMFQKLVMQDRILEVIDISEKQ 89 (224)
Q Consensus 17 TPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~----~~--~~~~~~~a-~~~~~~~~~~~~~~V~~v~~k~ 89 (224)
--+-.||++|..+-.. .|..|=+..+.+..++..|.+... .| .++..+.. +..+-.+..+..+.+.+++.++
T Consensus 390 ~~lY~LI~rrfla~~~-~~a~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~vy~~~~~~~~~lP~l~~G~~~~~~~~~~~~ 468 (822)
T PRK07219 390 WKVYELIVRRFLATLA-DPAEWEYLKVELDVNGEIFKASGSRLVEEGWHEVYPYEKFDEKELPDLEEGEKLKVNKIEIEA 468 (822)
T ss_pred HHHHHHHHHHHHHHhC-ccceeeEEEEEEEeCCeEEEEEEEEEccCCcHhhcCccccccccCCCCCCCCEeeeeeeEecc
Confidence 3456789988876654 566676777888878888887642 11 12211111 1111223333567888888899
Q ss_pred ccccCCCcccHHHHHHHHHHhCCCCHHHHH-HHHHHHhhccce
Q 045217 90 ESKVRPCGLNTVNLLKVASSALGYGPQMAM-QLAERLYTQGFI 131 (224)
Q Consensus 90 ~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl-~iaQ~LYE~glI 131 (224)
+...||.+|+-++|.+.|-+ .|+...-|. .|.+.|++.|||
T Consensus 469 ~~T~PP~rytea~Li~~Me~-~GIGT~ATra~iI~~L~~R~Yv 510 (822)
T PRK07219 469 KETQPPKRYTQSSLIKEMEK-RGLGTKATRHDIIEKLYKRGYV 510 (822)
T ss_pred cccCCCCCCCHHHHHHHHHh-CCCCCCccHHHHHHHHHhcCcE
Confidence 99999999999999999855 599655555 489999999998
No 34
>PRK05582 DNA topoisomerase I; Validated
Probab=95.43 E-value=0.064 Score=52.70 Aligned_cols=112 Identities=15% Similarity=0.224 Sum_probs=75.7
Q ss_pred HHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEe----cc--ccCCH-HHHHHHHHHHccCCceEEEEEeeeccc
Q 045217 19 TLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWE----RQ--KLFDF-DVATMFQKLVMQDRILEVIDISEKQES 91 (224)
Q Consensus 19 tL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~----~~--~~~~~-~~a~~~~~~~~~~~~~~V~~v~~k~~~ 91 (224)
+-.||++|..+.-. .|.-|=+..+.+..++..|.++.. .| .++.. +..+..+-.+..+..+.+.+++.++++
T Consensus 370 iY~lI~~rfla~~~-~~~~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~~~~~~~~~~~~lp~l~~g~~~~~~~~~~~~~~ 448 (650)
T PRK05582 370 LYKLIWNRFVASQM-APAVFDTVSVDLENNGVKFRASGSKVKFDGFMKVYVGDEEKDKMLPELEEGEKVKLKKIEPEQHF 448 (650)
T ss_pred HHHHHHHHHHHHhC-chhheeEEEEEEEeCCEEEEEEEEEEeeCChHhhcCCcccccccCCCCCCCCEeEEEEeeecccc
Confidence 45678888765433 455566677788888878887643 11 22211 111111222333346778888888899
Q ss_pred ccCCCcccHHHHHHHHHHhCCCCHHHHHH-HHHHHhhcccee
Q 045217 92 KVRPCGLNTVNLLKVASSALGYGPQMAMQ-LAERLYTQGFIS 132 (224)
Q Consensus 92 ~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~-iaQ~LYE~glIT 132 (224)
..||.+|+-++|...|-+ .|+...-|.. |.+.|.+.|||.
T Consensus 449 T~PP~~~Te~~Ll~~Me~-~GIGT~ATra~iI~~L~~r~Yi~ 489 (650)
T PRK05582 449 TQPPARYTEASLIKTLEE-LGIGRPSTYAPTISTIQKRGYVK 489 (650)
T ss_pred cCCCCCCCHHHHHHHHHH-cCCCCcccHHHHHHHHHhCCeEE
Confidence 999999999999999855 5997666654 899999999997
No 35
>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=95.41 E-value=0.056 Score=52.81 Aligned_cols=114 Identities=15% Similarity=0.249 Sum_probs=78.5
Q ss_pred hhHHHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEe----cc--ccCCH--HHHHHHHHHHccCCceEEEEEee
Q 045217 16 QTPTLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWE----RQ--KLFDF--DVATMFQKLVMQDRILEVIDISE 87 (224)
Q Consensus 16 QTPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~----~~--~~~~~--~~a~~~~~~~~~~~~~~V~~v~~ 87 (224)
+--+-.||++|..+.-- .+.-|=...+.+..++..|.+... .| .++.. .....+- .+..+..+.+.+++.
T Consensus 380 e~~iY~lI~~r~la~~~-~~a~~~~t~v~~~~~~~~F~~~g~~~~~~Gw~~v~~~~~~~~~~lp-~~~~gd~~~~~~~~~ 457 (618)
T TIGR01057 380 EKKVYDLIVRRFLAAFS-EEAIREKSKVLLRIGQEKFRLSGLRVVKLGWLEYYHYSKFEEKELP-PLDRGDKIKVVRVDV 457 (618)
T ss_pred HHHHHHHHHHHHHHHhC-hhhheeEEEEEEEECCeEEEEEEEEEEeCCcceeccCcccccccCC-CCCCCCEeeeeeeee
Confidence 33456789988886653 566677777888777777887642 11 22211 1111111 233334678888999
Q ss_pred ecccccCCCcccHHHHHHHHHHhCCCCHHHHH-HHHHHHhhcccee
Q 045217 88 KQESKVRPCGLNTVNLLKVASSALGYGPQMAM-QLAERLYTQGFIS 132 (224)
Q Consensus 88 k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl-~iaQ~LYE~glIT 132 (224)
.+++..||.+|+-++|.++|-+ .|+...-|. .|.+.|.+.|||.
T Consensus 458 ~e~~TkPP~~~Te~tLi~~Me~-~GIGTpATra~iIe~L~~r~Yi~ 502 (618)
T TIGR01057 458 RVKETQPPARYDKASLIREMES-RGLGTKATRARIIETLYKRGYIE 502 (618)
T ss_pred cccccCCCCCCCHHHHHHHHHh-CCCCCCCcHHHHHHHHHhCCcEe
Confidence 9999999999999999999855 598655555 4899999999997
No 36
>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=95.15 E-value=0.09 Score=51.82 Aligned_cols=118 Identities=15% Similarity=0.193 Sum_probs=79.4
Q ss_pred cchhHHHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEe----cc--ccCCH-----HHHHHHHHHHccCCceEE
Q 045217 14 PCQTPTLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWE----RQ--KLFDF-----DVATMFQKLVMQDRILEV 82 (224)
Q Consensus 14 RVQTPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~----~~--~~~~~-----~~a~~~~~~~~~~~~~~V 82 (224)
.-+--+-.||++|..+..- .+--|-+..+.+..++..|.+... .| .++.. +..+..+-.+..+..+.+
T Consensus 390 ~de~klY~LI~~Rflas~~-~~a~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~~~~~~~~~~LP~l~~G~~~~~ 468 (660)
T TIGR01056 390 EEERNVYKLIAQNYLMQFM-PKEEYETTTIEIAIGKLMFEAKGKILQDNGWKALLGKQEEDEETEDTTLPAFQKGDELDV 468 (660)
T ss_pred HHHHHHHHHHHHHHHHHhC-chhEEEEEEEEEEECCEEEEEEEEEEcccCHHHHhcccccccccccccCCCCCCCCEeee
Confidence 3444567789999887654 556677777888888888887642 11 12211 000111112333346778
Q ss_pred EEEeeecccccCCCcccHHHHHHHHHH----------------hCCCCHHHHH-HHHHHHhhcccee
Q 045217 83 IDISEKQESKVRPCGLNTVNLLKVASS----------------ALGYGPQMAM-QLAERLYTQGFIS 132 (224)
Q Consensus 83 ~~v~~k~~~~~pP~p~~l~~Lq~~a~~----------------~~g~sa~~tl-~iaQ~LYE~glIT 132 (224)
.+++..++...||..|+-++|.+++-+ ..|+.-.-|. .|.+.|.+.|||.
T Consensus 469 ~~~~~~~~~TkPP~ryTeasLi~~Me~~~k~v~d~~l~~~l~e~~GIGtpATrA~iI~~L~~R~Yv~ 535 (660)
T TIGR01056 469 ETLELLEKQTKPPARYTEGTLLSAMTNPAAFVQDKGLKKTLKETKGLGTEATRADIIENLFKRGFIQ 535 (660)
T ss_pred eecccccCcCCCCCCcCHHHHHHHHHhhhhcccCHHHHHHhhhccCCCCcccHHHHHHHHHhCCCEE
Confidence 888888999999999999999999862 5688644444 5899999999997
No 37
>PRK07220 DNA topoisomerase I; Validated
Probab=95.05 E-value=0.065 Score=53.49 Aligned_cols=115 Identities=15% Similarity=0.224 Sum_probs=79.1
Q ss_pred chhHHHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEe----cc--ccCC--HHHHHHHHHHHccCCceEEEEEe
Q 045217 15 CQTPTLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWE----RQ--KLFD--FDVATMFQKLVMQDRILEVIDIS 86 (224)
Q Consensus 15 VQTPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~----~~--~~~~--~~~a~~~~~~~~~~~~~~V~~v~ 86 (224)
=|=-+-.||++|..+-.- .+.-|=+..+.+..++..|.+... .| .++. .... ..+-.+..+..+.|.+++
T Consensus 380 de~~lY~LI~rRfla~~~-~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~vy~~~~~~~-~~LP~l~~Ge~~~~~~~~ 457 (740)
T PRK07220 380 DEWKVYELVVRRFFATFA-GPAEWETMKLRFDIGGEEFRANGSRLTEPGWRWYYPYNAPED-RLLPELSEGEELKVKKKE 457 (740)
T ss_pred HHHHHHHHHHHHHHHHhC-chheEEEEEEEEEECCeEEEEeeeEEeeCChHHHcCcccccc-ccCCCCCCCCEeeeeeee
Confidence 344456789998886554 566676777888888878887542 11 1221 1111 112223334567888899
Q ss_pred eecccccCCCcccHHHHHHHHHHhCCCCHHHHH-HHHHHHhhcccee
Q 045217 87 EKQESKVRPCGLNTVNLLKVASSALGYGPQMAM-QLAERLYTQGFIS 132 (224)
Q Consensus 87 ~k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl-~iaQ~LYE~glIT 132 (224)
..++...||..|+-++|.+.+-+ .|+.-.-|. .|.+.|++.|||.
T Consensus 458 ~~ek~TkPP~ryTea~Li~~Me~-~GIGTpATra~iI~~L~~R~Yi~ 503 (740)
T PRK07220 458 MLDKETQPPGRYGQGRLIKLMED-LGLGTKATRHEIISKLYSRAYIH 503 (740)
T ss_pred ecccccCCCCCCCHHHHHHHHHh-CCCCCCCcHHHHHHHHHhcCCcc
Confidence 99999999999999999999854 588655555 4899999999996
No 38
>PRK06599 DNA topoisomerase I; Validated
Probab=95.03 E-value=0.12 Score=50.94 Aligned_cols=112 Identities=12% Similarity=0.137 Sum_probs=73.1
Q ss_pred HHHHHHHHHHHHHcCcCcceEEEEEEEEe--cCeEEEEEEe----cc--ccCCH--H----HHHHHHHHHccCCceEEEE
Q 045217 19 TLGFCVQRYLQITSFKPEKFWTLHPYLVQ--NGYELKLEWE----RQ--KLFDF--D----VATMFQKLVMQDRILEVID 84 (224)
Q Consensus 19 tL~lIv~Re~eI~~F~p~~y~~i~~~~~~--~~~~~~~~~~----~~--~~~~~--~----~a~~~~~~~~~~~~~~V~~ 84 (224)
+-.||++|..+--- .+--|-...+.+.. ++..|.++.. .| .++.. . ..+..+-.+..+..+.+.+
T Consensus 377 iY~lI~~rfla~~~-~~~~~~~t~v~~~~~~~~~~F~a~g~~~~~~Gw~~~~~~~~~~~~~~~~~~lp~~~~g~~~~~~~ 455 (675)
T PRK06599 377 LYELIWKRTVASQM-APAILDQTSVDIASENGKYVFRATGSVILFPGFLKVYGESKDDEEEDDEKLLPPLKEGEKLKLDE 455 (675)
T ss_pred HHHHHHHHHHHHhC-chheEEEEEEEEEEcCCCeEEEEEEEEEEecCeeeeeccccccccccccccCCCCCCCCEeeeee
Confidence 34678877764332 34456666677776 6667776532 11 12111 0 1111111233335677888
Q ss_pred EeeecccccCCCcccHHHHHHHHHHhCCCCHHHHHH-HHHHHhhcccee
Q 045217 85 ISEKQESKVRPCGLNTVNLLKVASSALGYGPQMAMQ-LAERLYTQGFIS 132 (224)
Q Consensus 85 v~~k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~-iaQ~LYE~glIT 132 (224)
++..++...||..|+-++|..+|-+ .|+...-|.. |.+.|.+.|||.
T Consensus 456 ~~~~~~~T~PP~r~te~tLi~~Me~-~GIGT~ATra~iIe~L~~r~Yi~ 503 (675)
T PRK06599 456 LLPEQHFTEPPPRYSEASLVKKLEE-YGIGRPSTYASIISTLQDREYVE 503 (675)
T ss_pred eeecccccCCCCCCCHHHHHHHHhh-CCCCccccHHHHHHHHhhCCeEE
Confidence 8888899999999999999999854 5997666655 899999999996
No 39
>PRK14973 DNA topoisomerase I; Provisional
Probab=94.99 E-value=0.086 Score=53.89 Aligned_cols=115 Identities=12% Similarity=0.226 Sum_probs=78.1
Q ss_pred hhHHHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEe----cc--ccCCHH-HHHHHHHHHccCCceEEEEEeee
Q 045217 16 QTPTLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWE----RQ--KLFDFD-VATMFQKLVMQDRILEVIDISEK 88 (224)
Q Consensus 16 QTPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~----~~--~~~~~~-~a~~~~~~~~~~~~~~V~~v~~k 88 (224)
|--+--||++|..+..- .+.-|-+..+.+..++..|.++.. .| .++..+ ..+..+-.+..+..+.+.+++.+
T Consensus 380 e~klY~LI~rRfLA~~~-~~a~~~~t~v~~~~~~~~F~a~G~~i~~~Gw~~vy~~~~~~~~~LP~l~~Ge~~~~~~~~~~ 458 (936)
T PRK14973 380 RWKLYELVVRRFLATLS-PDAEWATMKVNFDAGGEPYTATGGRLLEAGWRTVYPYSEAKENILPAFALGEKLPILAVNLE 458 (936)
T ss_pred HHHHHHHHHHHHHHHhC-hhheEEEEEEEEEECCEEEEEEEEEEeecCeeEeecccccccccCCCccCCCEEEeeeeEEe
Confidence 34456789999887654 555576777777777777876542 11 222211 11111222333356778889999
Q ss_pred cccccCCCcccHHHHHHHHHHhCCCCHHHHH-HHHHHHhhcccee
Q 045217 89 QESKVRPCGLNTVNLLKVASSALGYGPQMAM-QLAERLYTQGFIS 132 (224)
Q Consensus 89 ~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl-~iaQ~LYE~glIT 132 (224)
++...||.+|+-++|.+.|-+ .|+.-.-|. .|.+.|++.|||.
T Consensus 459 e~~T~PP~ryTEatLik~ME~-~GIGTpATrA~II~~L~~R~Yve 502 (936)
T PRK14973 459 EKETQPPARYSQSRLIQRMEE-LGLGTKSTRHEVIGKLVSRKYIE 502 (936)
T ss_pred ecCCCCCCCCCHHHHHHHhcc-CCCCCcccHHHHHHHHHHccCee
Confidence 999999999999999999854 599655555 4899999999994
No 40
>PRK05776 DNA topoisomerase I; Provisional
Probab=94.98 E-value=0.1 Score=51.53 Aligned_cols=115 Identities=17% Similarity=0.296 Sum_probs=79.9
Q ss_pred chhHHHHHHHHHHHHHHcCcCcceEEEEEEEEecCe--EEEEEEe----cc--ccCC--HHHHHHHHHHHccCCceEEEE
Q 045217 15 CQTPTLGFCVQRYLQITSFKPEKFWTLHPYLVQNGY--ELKLEWE----RQ--KLFD--FDVATMFQKLVMQDRILEVID 84 (224)
Q Consensus 15 VQTPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~--~~~~~~~----~~--~~~~--~~~a~~~~~~~~~~~~~~V~~ 84 (224)
-|--+-.||++|..+-.- .|.-|-+..+.+..++. .|.++-. .| .+++ .+....+ -.+..+..+.+.+
T Consensus 383 de~klY~LI~rRflA~~~-~~a~~~~t~v~~~~~~~~~~F~a~G~~i~~~Gw~~vy~~~~~~~~~L-P~l~~G~~~~~~~ 460 (670)
T PRK05776 383 DEFKLYDLIVRRFLASFA-APAVLSNTIVTLRVPGFPLVFSASGQRIEERGWLKYYPFHKFDEEEL-PLLKKGERVKIVD 460 (670)
T ss_pred HHHHHHHHHHHHHHHHhC-hhheEEEEEEEEEECCeEEEEEEEEEEEEECCceeecccCccccccC-CCcCCCCEeEeee
Confidence 344467899999887653 56667777888877777 6776532 11 2221 1111112 2233345688889
Q ss_pred EeeecccccCCCcccHHHHHHHHHHhCCCCHHHHH-HHHHHHhhcccee
Q 045217 85 ISEKQESKVRPCGLNTVNLLKVASSALGYGPQMAM-QLAERLYTQGFIS 132 (224)
Q Consensus 85 v~~k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl-~iaQ~LYE~glIT 132 (224)
++.+++...||..|+-++|.+.+- ..|+.-.-|. .|.+.|++.|||.
T Consensus 461 ~~~~~~~TkPP~ryTeasLi~~ME-~~GIGtpATra~iI~~L~~R~Yv~ 508 (670)
T PRK05776 461 VKVRKSYTKPPSRYSKASLLKWME-SVGIGTEATRARIIETLFKRGYLT 508 (670)
T ss_pred eeeeccccCCCCCCCHHHHHHHHh-hCCCCCCccHHHHHHHHHhCCCEE
Confidence 999999999999999999999985 4598655554 4899999999996
No 41
>PRK07726 DNA topoisomerase III; Provisional
Probab=94.96 E-value=0.11 Score=51.15 Aligned_cols=113 Identities=16% Similarity=0.194 Sum_probs=76.7
Q ss_pred HHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEe----cc--ccCCH----HHHHHHHHHHccCCceEEEEEeee
Q 045217 19 TLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWE----RQ--KLFDF----DVATMFQKLVMQDRILEVIDISEK 88 (224)
Q Consensus 19 tL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~----~~--~~~~~----~~a~~~~~~~~~~~~~~V~~v~~k 88 (224)
+-.||++|..+.-. .|.-|-...+.+..++..|.+... .| .++.. ++....+-.+..+..+.+.+++.+
T Consensus 393 iY~lI~~r~la~~~-~~~~~~~t~v~~~~~~~~F~~~g~~i~~~Gw~~v~~~~~~~~~~~~~lp~l~~g~~~~~~~~~~~ 471 (658)
T PRK07726 393 VYDLIARRYLAQFL-PPAEYDKTTIELEIAGGTFIAKGKQVVEAGWKALLGKKEEDEEKEQPLPVLAKGDELKVEKGEVK 471 (658)
T ss_pred HHHHHHHHHHHHhC-chhEEEEEEEEEEECCEEEEEEEEEEccCCHHHHcccccccccccccCCCcCCCCEeeecccccc
Confidence 56789888876553 566677777888888888877642 11 12210 000111112333346777888888
Q ss_pred cccccCCCcccHHHHHHHHHHh----------------CCCCHHHHHH-HHHHHhhcccee
Q 045217 89 QESKVRPCGLNTVNLLKVASSA----------------LGYGPQMAMQ-LAERLYTQGFIS 132 (224)
Q Consensus 89 ~~~~~pP~p~~l~~Lq~~a~~~----------------~g~sa~~tl~-iaQ~LYE~glIT 132 (224)
++...||.+|+-++|.+.|-+. .|+.-.-|.. |.+.|.+.|||.
T Consensus 472 e~~TkPP~~yTe~tLi~~Me~~~k~v~d~~~~~~l~e~~GIGTpATra~iIe~L~~R~Yi~ 532 (658)
T PRK07726 472 EGQTQPPKRFTEGTLLSAMENIARFVQDKELKKTLKETDGLGTEATRAGIIEKLFKRGYLE 532 (658)
T ss_pred cccCCCCCCcCHHHHHHHHHhhhhhccCHHHHHhhcccCCCCccccHHHHHHHHHhCCCEE
Confidence 9999999999999999998543 3886555554 899999999997
No 42
>PRK08173 DNA topoisomerase III; Validated
Probab=94.35 E-value=0.16 Score=51.53 Aligned_cols=114 Identities=16% Similarity=0.196 Sum_probs=75.0
Q ss_pred HHHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEe----cc--ccCCHHH--HHHHHHHHccCCceEEEEEeeec
Q 045217 18 PTLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWE----RQ--KLFDFDV--ATMFQKLVMQDRILEVIDISEKQ 89 (224)
Q Consensus 18 PtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~----~~--~~~~~~~--a~~~~~~~~~~~~~~V~~v~~k~ 89 (224)
-+--|||+|..+.-- .|.-|=...+.+..+|..|.++.. .| .++..+. .+..+-.+..+..+.+.+++.++
T Consensus 403 ~iY~lI~rRfla~f~-~~a~~~~t~v~~~v~~~~F~a~G~~~~~~Gw~~vy~~~~~~~~~~LP~l~~Ge~~~~~~~~~~e 481 (862)
T PRK08173 403 KLYDLVVKRFLAVFF-PAAEFLVTTRITEVAGHHFKTEGKVLVNPGWLAVYGKEAQGADANLVPVQKGEKVKTDKIEAVA 481 (862)
T ss_pred HHHHHHHHHHHHHhC-chheEEEEEEEEEeCCcEEEEEEEEEeeCChHHHhCcccccccccCCCcCCCCEeeeeeeeecc
Confidence 456788888875432 344455555677777878887642 11 1211100 01111223333567788899999
Q ss_pred ccccCCCcccHHHHHHHHHH---------------hCCCCHHHHH-HHHHHHhhcccee
Q 045217 90 ESKVRPCGLNTVNLLKVASS---------------ALGYGPQMAM-QLAERLYTQGFIS 132 (224)
Q Consensus 90 ~~~~pP~p~~l~~Lq~~a~~---------------~~g~sa~~tl-~iaQ~LYE~glIT 132 (224)
+...||.+|+=++|.++|-+ ..|+.-.-|. .|.+.|.+.|||.
T Consensus 482 ~~TkPP~ryTEatLl~aMe~~gk~v~D~el~~~~~~~GIGTpATRA~IIe~L~~r~Yi~ 540 (862)
T PRK08173 482 LTTKPPARYNEATLLSAMEGAGKLVEDDELREAMAEKGLGTPATRAAIIEGLLGEKYLV 540 (862)
T ss_pred cccCCCCCcCHHHHHHHHHhhhhccccHHHHhhhhcCCCCchhhHHHHHHHHHhCCcEE
Confidence 99999999999999998863 4688655554 5999999999997
No 43
>PRK07561 DNA topoisomerase I subunit omega; Validated
Probab=93.82 E-value=0.4 Score=48.70 Aligned_cols=115 Identities=13% Similarity=0.185 Sum_probs=77.4
Q ss_pred hHHHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEe----cc--ccCCH------HHHHHHHHHHccCCceEEEE
Q 045217 17 TPTLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWE----RQ--KLFDF------DVATMFQKLVMQDRILEVID 84 (224)
Q Consensus 17 TPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~----~~--~~~~~------~~a~~~~~~~~~~~~~~V~~ 84 (224)
--+-.||++|..+-.- .+.-|=+..+.+..++..|.++.. .| .++.. ++.+..+-.+..+..+.+.+
T Consensus 376 ~~lY~LI~~R~lAs~m-~~a~~~~~~v~~~~~~~~F~a~g~~i~~~G~~~vy~~~~~~~~~~~~~~LP~l~~g~~~~~~~ 454 (859)
T PRK07561 376 QRLYELIWKRFVASQM-APARYDSTTVTIAAGDAELRATGRVLRFDGFLKVYVEGRDDALDDEDRRLPALKVGDALTLEK 454 (859)
T ss_pred HHHHHHHHHHHHHHhC-chheEEEEEEEEEeCCEEEEEEEEEEeeCCchheeccccccccccccccCCCCCCCCEeeeee
Confidence 3456788888876553 455577777888777777776532 11 12110 11111222233334677888
Q ss_pred EeeecccccCCCcccHHHHHHHHHHhCCCCHHHHHH-HHHHHhhccceec
Q 045217 85 ISEKQESKVRPCGLNTVNLLKVASSALGYGPQMAMQ-LAERLYTQGFISY 133 (224)
Q Consensus 85 v~~k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~-iaQ~LYE~glITY 133 (224)
++..++...||..|+-++|.+.+- ..|+.-.-|.. |.+.|.+.|||.-
T Consensus 455 ~~~~~~~T~PP~ryTeasLv~~me-~~GIGtpsT~a~iI~~L~~R~Yv~~ 503 (859)
T PRK07561 455 LDPTQHFTKPPARYSEASLVKELE-KLGIGRPSTYASIISTIQDRGYVRL 503 (859)
T ss_pred eEecccccCCCCCCCHHHHHHHHH-hcCCCcchhHHHHHHHHhhcCeEEe
Confidence 888899999999999999999986 46997555554 8999999999863
No 44
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=93.40 E-value=0.68 Score=47.10 Aligned_cols=115 Identities=12% Similarity=0.172 Sum_probs=78.5
Q ss_pred hhHHHHHHHHHHHHHHcCcCcceEEEEEEEEecC-eEEEEEEe----cc--ccCC-----HH--HHHHHHHHHccCCceE
Q 045217 16 QTPTLGFCVQRYLQITSFKPEKFWTLHPYLVQNG-YELKLEWE----RQ--KLFD-----FD--VATMFQKLVMQDRILE 81 (224)
Q Consensus 16 QTPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~-~~~~~~~~----~~--~~~~-----~~--~a~~~~~~~~~~~~~~ 81 (224)
|--+--||++|..+-.- .|.-|-+..+.+..++ ..|.++.. .| .++. .+ +....+-.+..+..+.
T Consensus 384 e~klY~LI~~RflAs~m-~~a~~~~t~v~~~~~~~~~F~a~G~~i~~~G~~~vy~~~~~~~~~~~~~~~LP~l~~Ge~~~ 462 (860)
T PRK06319 384 QYKLYSLIWKRFVASQM-IPAIYDTLAIRITTNKGIDLRATGSLLKFKGFLAVYEEKRDDEGDEEENIHLPKLHEQDVLT 462 (860)
T ss_pred HHHHHHHHHHHHHHHhC-chhheEEEEEEEEeCCeeEEEEEeEEEeeCCHHHHhCccccccccccccccCCCCCCCCEee
Confidence 33456789999887653 6777888888887765 35776532 11 1211 01 1111122233345677
Q ss_pred EEEEeeecccccCCCcccHHHHHHHHHHhCCCCHHHHHH-HHHHHhhcccee
Q 045217 82 VIDISEKQESKVRPCGLNTVNLLKVASSALGYGPQMAMQ-LAERLYTQGFIS 132 (224)
Q Consensus 82 V~~v~~k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~-iaQ~LYE~glIT 132 (224)
+.+++.+++...||..|+-++|.+.+- .+|+.-.-|.. |.+.|.+.|||.
T Consensus 463 ~~~~~~~~~~T~PP~ryTeasLvk~me-~~GIGtpsT~A~iI~~L~~R~Yv~ 513 (860)
T PRK06319 463 KEELSAEQAFTKPLPRFTEASLVKELE-KSGIGRPSTYATIMNKIQSREYTL 513 (860)
T ss_pred eeeeeecccccCCCCCCCHHHHHHHHH-hcCCCchhhHHHHHHHHhhCCeEE
Confidence 888888899999999999999999985 57997655555 899999999996
No 45
>COG0550 TopA Topoisomerase IA [DNA replication, recombination, and repair]
Probab=92.74 E-value=0.5 Score=45.90 Aligned_cols=118 Identities=14% Similarity=0.177 Sum_probs=78.9
Q ss_pred HHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEe----cc--ccCC---HHHHHHHHHHHccCCceEEEEEeeec
Q 045217 19 TLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWE----RQ--KLFD---FDVATMFQKLVMQDRILEVIDISEKQ 89 (224)
Q Consensus 19 tL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~----~~--~~~~---~~~a~~~~~~~~~~~~~~V~~v~~k~ 89 (224)
+=-||++|...-.- .+-.|=+..+.+..+++.|.+.-. .| +++. .+..+..+-.++.+..+.+.+++..+
T Consensus 366 lY~LI~rrflAs~m-~~A~~~~~~v~l~~~~~~F~a~g~~~~~~Gw~~vy~~~~~~~~~~~lP~l~~gd~l~~~~~~~~~ 444 (570)
T COG0550 366 LYDLIWRRFLASQM-PDAIYEKTTVTLEVAGEKFKASGKVLKFDGWLKVYGEDKDEEEDKELPELKEGDELKVEKLEVEE 444 (570)
T ss_pred HHHHHHHHHHHHhC-chhhheEEEEEEEecCcEEEEeeeEEecCcHHHhhcccccccccccCCCCCCCCeeEEeeeeecc
Confidence 44578888875442 344455666777766667776532 11 1111 11222222234444578899999999
Q ss_pred ccccCCCcccHHHHHHHHHHhCCCCHHHHH-HHHHHHhhccceeccCCCCccc
Q 045217 90 ESKVRPCGLNTVNLLKVASSALGYGPQMAM-QLAERLYTQGFISYPRTESTAY 141 (224)
Q Consensus 90 ~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl-~iaQ~LYE~glITYPRTds~~l 141 (224)
....||..|+=++|.+.+ ...|+.-.-|. .|...|++.|||. .+.+.+
T Consensus 445 ~~T~PP~rytEasLvk~m-E~~GIGrpSTyA~iI~~L~~RgYv~---~~~~~~ 493 (570)
T COG0550 445 HFTKPPPRYTEASLVKAM-EKLGIGTPSTYASIIETLQKRGYVE---KKGKRL 493 (570)
T ss_pred cccCCcCCCCHHHHHHHH-HhCCCCCcccHHHHHHHHhcCCcEE---ecCCee
Confidence 999999999999999998 56799766665 4999999999998 444444
No 46
>PRK14724 DNA topoisomerase III; Provisional
Probab=92.30 E-value=0.55 Score=48.43 Aligned_cols=123 Identities=15% Similarity=0.165 Sum_probs=77.1
Q ss_pred HHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEe----cc--ccCCHH-----------HHHHHHHHHccCCceE
Q 045217 19 TLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWE----RQ--KLFDFD-----------VATMFQKLVMQDRILE 81 (224)
Q Consensus 19 tL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~----~~--~~~~~~-----------~a~~~~~~~~~~~~~~ 81 (224)
+--||++|..+.-- .|.-|-...+.+..++..|.++.. .| .++..+ .....+-.+..+..+.
T Consensus 414 iY~lI~rRfla~f~-~~a~~~~t~v~~~~~~~~F~a~G~~i~~~GW~~vy~~~~~~~~~~~~~~~~~~~LP~l~~Ge~v~ 492 (987)
T PRK14724 414 LYDLVVRRFMAVFF-PSAEYQVTTRISQVVGHSFKTEGKVLVKPGWLAIYGKEAANEVEDAKDGDKGQPLVPVKPGEMVR 492 (987)
T ss_pred HHHHHHHHHHHHhC-chhEEEEEEEEEEecCcEEEEEEEEECcCChHHHhCccccccccccccccccccCCCcCCCCEee
Confidence 56789988876542 444455556677777777877532 11 121110 0001111233334677
Q ss_pred EEEEeeecccccCCCcccHHHHHHHHHH---------------hCCCCHHHHH-HHHHHHhhccceeccCCCCcccCCC
Q 045217 82 VIDISEKQESKVRPCGLNTVNLLKVASS---------------ALGYGPQMAM-QLAERLYTQGFISYPRTESTAYPSS 144 (224)
Q Consensus 82 V~~v~~k~~~~~pP~p~~l~~Lq~~a~~---------------~~g~sa~~tl-~iaQ~LYE~glITYPRTds~~l~~~ 144 (224)
+.+++.+++...||.+|+=++|.++|-+ ..|+.-.-|. .|.+.|.+.|||. |-....+|.+
T Consensus 493 ~~~~~~~e~~TkPP~ryTEatLl~aME~~gk~v~d~el~~~~~~~GIGTpATRA~IIe~L~~r~Yi~--~~~k~l~pT~ 569 (987)
T PRK14724 493 TEFAEAKGLKTKPPARYSEATLLGAMESAGKQIDDDELREAMQEKGLGTPATRAAIIEGLLTEKYML--REGRELIPTA 569 (987)
T ss_pred eeeccccccccCCCCCcCHHHHHHHHHhhhhcccchhhhhhhhcCCCCCcccHHHHHHHHHhCCcEE--ecCCEEeEcH
Confidence 8888889999999999999999998862 4577544443 5899999999997 3333334443
No 47
>PRK08780 DNA topoisomerase I; Provisional
Probab=91.55 E-value=1.7 Score=43.80 Aligned_cols=113 Identities=11% Similarity=0.091 Sum_probs=76.3
Q ss_pred HHHHHHHHHHHHHHcCcCcceEEEEEEEEecC-eEEEEEEe----cc--ccCC----H---H--HHHHHHHHHccCCceE
Q 045217 18 PTLGFCVQRYLQITSFKPEKFWTLHPYLVQNG-YELKLEWE----RQ--KLFD----F---D--VATMFQKLVMQDRILE 81 (224)
Q Consensus 18 PtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~-~~~~~~~~----~~--~~~~----~---~--~a~~~~~~~~~~~~~~ 81 (224)
-+-.||++|..+-.- .|..|-+..+.+..++ ..|.++-. .| +++. . + .....+-.+..+..+.
T Consensus 380 klY~LI~~R~lAs~m-~~a~~~~t~v~~~~~~~~~F~a~G~~i~~~G~~~vy~~~~~~~~~~~~~~~~~LP~l~~G~~~~ 458 (780)
T PRK08780 380 RLYELIWKRAVACQM-IPATLNTVSVDLAAGSEHVFRATGSTVVVPGFLAVYEEGKDDKSAEDEDEGRKLPPMKEGDNVP 458 (780)
T ss_pred HHHHHHHHHHHHHhC-chhEEEEEEEEEEeCCeeEEEEEEEEEeEcCeEEeeccccccccccccchhccCCCcCCCCEee
Confidence 346789888876654 5556777777777665 46665421 11 1211 0 0 1112222344445678
Q ss_pred EEEEeeecccccCCCcccHHHHHHHHHHhCCCCHHHHHH-HHHHHhhcccee
Q 045217 82 VIDISEKQESKVRPCGLNTVNLLKVASSALGYGPQMAMQ-LAERLYTQGFIS 132 (224)
Q Consensus 82 V~~v~~k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~-iaQ~LYE~glIT 132 (224)
+.+++..++...||..|+-++|.+.+-+ .|+.-.-|.. |.+.|.+.|||.
T Consensus 459 ~~~~~~~~~~T~PP~ryTEasLik~mE~-~GIGtpST~A~iI~~L~~R~Yv~ 509 (780)
T PRK08780 459 LERIRAEQHFTEPPPRYTEASLVKALEE-YGIGRPSTYASIISTLQFRKYVE 509 (780)
T ss_pred eeeeeeeeeecCCCCCCCHHHHHHHHHh-CCCCchhhHHHHHHHHHhCCcEe
Confidence 8888889999999999999999999865 6997666655 899999999996
No 48
>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=90.99 E-value=0.21 Score=35.48 Aligned_cols=44 Identities=18% Similarity=0.140 Sum_probs=29.9
Q ss_pred ccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceeccCCCCcccCCC
Q 045217 98 LNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISYPRTESTAYPSS 144 (224)
Q Consensus 98 ~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRTds~~l~~~ 144 (224)
|++++.|.- -|...=-+.+...++++|||+||||=|.- .||+++
T Consensus 17 F~~~S~~~G-IKvH~dA~p~~i~a~~RLheKGLI~~pdG--gyLT~~ 60 (77)
T TIGR02647 17 FNLSSTQEG-IKVHSTASPAAVAAAARLHEKGLTTQPDG--GYLTSL 60 (77)
T ss_pred CCchhhhcC-ccccccCCHHHHHHHHHHHHcCCccCCCC--CEecHH
Confidence 556555542 23333334667789999999999998754 488875
No 49
>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=90.61 E-value=0.25 Score=40.02 Aligned_cols=35 Identities=23% Similarity=0.338 Sum_probs=29.3
Q ss_pred ccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceeccCC
Q 045217 98 LNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISYPRT 136 (224)
Q Consensus 98 ~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRT 136 (224)
.+-.+| +..+|++...+-+++++|||.||++|-|.
T Consensus 29 ~tdEeL----a~~Lgi~~~~VRk~L~~L~e~~Lv~~~r~ 63 (158)
T TIGR00373 29 FTDEEI----SLELGIKLNEVRKALYALYDAGLADYKRR 63 (158)
T ss_pred CCHHHH----HHHHCCCHHHHHHHHHHHHHCCCceeeee
Confidence 444555 45679999999999999999999999984
No 50
>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=89.49 E-value=0.15 Score=22.88 Aligned_cols=9 Identities=44% Similarity=1.132 Sum_probs=7.9
Q ss_pred ccceeccCC
Q 045217 128 QGFISYPRT 136 (224)
Q Consensus 128 ~glITYPRT 136 (224)
.|+|++|||
T Consensus 3 sGlI~fpR~ 11 (11)
T PF08259_consen 3 SGLIPFPRV 11 (11)
T ss_pred ccccccCCC
Confidence 489999997
No 51
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=88.66 E-value=0.5 Score=39.05 Aligned_cols=29 Identities=17% Similarity=0.315 Sum_probs=26.5
Q ss_pred HHHhCCCCHHHHHHHHHHHhhccceeccC
Q 045217 107 ASSALGYGPQMAMQLAERLYTQGFISYPR 135 (224)
Q Consensus 107 a~~~~g~sa~~tl~iaQ~LYE~glITYPR 135 (224)
.+..+|++...+-++++.|||.|||+|-|
T Consensus 42 LA~~Lgi~~~~VRk~L~~L~e~gLv~~~r 70 (178)
T PRK06266 42 IAEQTGIKLNTVRKILYKLYDARLADYKR 70 (178)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCCeEEee
Confidence 35678999999999999999999999987
No 52
>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=88.54 E-value=0.46 Score=35.38 Aligned_cols=31 Identities=29% Similarity=0.582 Sum_probs=25.2
Q ss_pred HHHHHhCCCCHHHHHHHHHHHhhccceeccC
Q 045217 105 KVASSALGYGPQMAMQLAERLYTQGFISYPR 135 (224)
Q Consensus 105 ~~a~~~~g~sa~~tl~iaQ~LYE~glITYPR 135 (224)
.+.++.+|++++++-.+++.|++.|||+|.|
T Consensus 31 e~la~~~~l~~~~vRkiL~~L~~~~lv~~~~ 61 (105)
T PF02002_consen 31 EDLAKKLGLKPKEVRKILYKLYEDGLVSYRR 61 (105)
T ss_dssp HHHHHTT-S-HHHHHHHHHHHHHHSS-EEEE
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHCCCeEEEE
Confidence 4667889999999999999999999999985
No 53
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=82.57 E-value=1.4 Score=36.37 Aligned_cols=31 Identities=26% Similarity=0.423 Sum_probs=27.7
Q ss_pred HHHHhCCCCHHHHHHHHHHHhhccceeccCC
Q 045217 106 VASSALGYGPQMAMQLAERLYTQGFISYPRT 136 (224)
Q Consensus 106 ~a~~~~g~sa~~tl~iaQ~LYE~glITYPRT 136 (224)
+.+..+|+....+..+...|||.|+|+|.|.
T Consensus 37 ela~~l~i~~~~vrriL~~L~e~~li~~~k~ 67 (176)
T COG1675 37 ELAELLGIKKNEVRRILYALYEDGLISYRKK 67 (176)
T ss_pred HHHHHhCccHHHHHHHHHHHHhCCceEEEee
Confidence 3467899999999999999999999999854
No 54
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=81.65 E-value=2.5 Score=26.59 Aligned_cols=29 Identities=21% Similarity=0.300 Sum_probs=24.5
Q ss_pred HHHHHHhCCCCHHHHHHHHHHHhhcccee
Q 045217 104 LKVASSALGYGPQMAMQLAERLYTQGFIS 132 (224)
Q Consensus 104 q~~a~~~~g~sa~~tl~iaQ~LYE~glIT 132 (224)
|.+.++.+|+|...+-.+.++|-++|+|.
T Consensus 20 ~~ela~~~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 20 QKELAEKLGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHCcCcC
Confidence 45667888999999999999999999984
No 55
>PRK09401 reverse gyrase; Reviewed
Probab=81.28 E-value=4.6 Score=42.65 Aligned_cols=108 Identities=18% Similarity=0.238 Sum_probs=67.5
Q ss_pred chhHHHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEE-Ee----cc--ccCCHHHHHHHHHHHccCCceEEEEEee
Q 045217 15 CQTPTLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLE-WE----RQ--KLFDFDVATMFQKLVMQDRILEVIDISE 87 (224)
Q Consensus 15 VQTPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~-~~----~~--~~~~~~~a~~~~~~~~~~~~~~V~~v~~ 87 (224)
-+--+--||++|..+-.- .|..|-...+.+..++..|.++ .. .| .++..+. ...+..+..+. + .
T Consensus 992 ~e~~lY~LI~rRflAs~~-~~a~~~~t~v~~~~~~~~f~~~~g~~i~~~Gw~~v~~~~~----~p~~~~g~~~~---~-~ 1062 (1176)
T PRK09401 992 NHLRLYDLIFRRFMASQM-KPAKVRYQKVLIKADGKELELELVVEILEDGFNKVLPLKL----YPLLEGKVKVK---E-K 1062 (1176)
T ss_pred HHHHHHHHHHHHHHHHhC-chhEEEEEEEEEEECCEEEEEeeeeEEeeCChheeecccc----CCCCCCCCEee---e-e
Confidence 334455688888876553 5666767777777788788876 32 11 1221110 11122222222 2 4
Q ss_pred ecccccCCCcccHHHHHHHHHHhCCCCHHHH-HHHHHHHhhcccee
Q 045217 88 KQESKVRPCGLNTVNLLKVASSALGYGPQMA-MQLAERLYTQGFIS 132 (224)
Q Consensus 88 k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~t-l~iaQ~LYE~glIT 132 (224)
+.++++||.+|+-++|.+.|- ..|+.-.-| -.|.+.|.+.|||.
T Consensus 1063 ~~~~~~pp~~yTea~Li~~Me-~~GIGtpAT~A~IIe~L~~R~YV~ 1107 (1176)
T PRK09401 1063 KTYKKSKVPLYTQGDLISEMK-ERGIGRPSTYAKIVETLLRRGYVI 1107 (1176)
T ss_pred ccccCCCcCCCCHHHHHHHHH-hCCCCCcCcHHHHHHHHhccCcEE
Confidence 455666789999999999985 458854444 45899999999996
No 56
>PTZ00407 DNA topoisomerase IA; Provisional
Probab=80.39 E-value=2.6 Score=42.53 Aligned_cols=52 Identities=17% Similarity=0.311 Sum_probs=43.4
Q ss_pred eEEEEEeeecccccCCCcccHHHHHHHHHHhCCCCHHHHHH-HHHHHhhcccee
Q 045217 80 LEVIDISEKQESKVRPCGLNTVNLLKVASSALGYGPQMAMQ-LAERLYTQGFIS 132 (224)
Q Consensus 80 ~~V~~v~~k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~-iaQ~LYE~glIT 132 (224)
..+.+++..+++..||.+|+=++|.+.|-+ .|+.-.-|.. |.+.|.+.|||.
T Consensus 561 ~~i~~~~l~ek~TkPPpryTEAtLIk~ME~-~GIGTPATrAsIIetL~~R~YV~ 613 (805)
T PTZ00407 561 FELRSPQVRENRPVPPLPHSEGTLIEELKN-NGVGRPSTYPMIVKTLLARGYIA 613 (805)
T ss_pred eecceeeeecccCCCCCCCCHHHHHHHHHh-CCCCCcccHHHHHHHHHhcCCEE
Confidence 446778888889999999999999999854 5997555554 899999999997
No 57
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=78.87 E-value=3.3 Score=26.99 Aligned_cols=30 Identities=23% Similarity=0.377 Sum_probs=25.1
Q ss_pred HHHHhCCCCHHHHHHHHHHHhhccceeccC
Q 045217 106 VASSALGYGPQMAMQLAERLYTQGFISYPR 135 (224)
Q Consensus 106 ~a~~~~g~sa~~tl~iaQ~LYE~glITYPR 135 (224)
+.++.+|+++..+-.++.+|.++|||+--+
T Consensus 22 ~la~~~~~~~~~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 22 ELAEKLGISRSTVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp HHHHHHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHCCChhHHHHHHHHHHHCCCEEecc
Confidence 456778999999999999999999997544
No 58
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=77.51 E-value=3.3 Score=33.36 Aligned_cols=40 Identities=18% Similarity=0.270 Sum_probs=31.6
Q ss_pred HHHHHHhCCCCHHHHHHHHHHHhhccceeccCCCCcccCC
Q 045217 104 LKVASSALGYGPQMAMQLAERLYTQGFISYPRTESTAYPS 143 (224)
Q Consensus 104 q~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRTds~~l~~ 143 (224)
.++.++.+|.||.-+.+.+++|.+.|||.|-+-.--.|.+
T Consensus 27 ~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~y~gi~LT~ 66 (154)
T COG1321 27 TKDIAERLKVSPPSVTEMLKRLERLGLVEYEPYGGVTLTE 66 (154)
T ss_pred HHHHHHHhCCCcHHHHHHHHHHHHCCCeEEecCCCeEECh
Confidence 3466788999999999999999999999994333333654
No 59
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=77.33 E-value=3.5 Score=27.71 Aligned_cols=30 Identities=23% Similarity=0.489 Sum_probs=25.5
Q ss_pred HHHHhCCCCHHHHHHHHHHHhhccceeccC
Q 045217 106 VASSALGYGPQMAMQLAERLYTQGFISYPR 135 (224)
Q Consensus 106 ~a~~~~g~sa~~tl~iaQ~LYE~glITYPR 135 (224)
+.++.+|.|+.-+-+.+++|=++|||.|-+
T Consensus 27 ~iA~~L~vs~~tvt~ml~~L~~~GlV~~~~ 56 (60)
T PF01325_consen 27 DIAERLGVSPPTVTEMLKRLAEKGLVEYEP 56 (60)
T ss_dssp HHHHHHTS-HHHHHHHHHHHHHTTSEEEET
T ss_pred HHHHHHCCChHHHHHHHHHHHHCCCEEecC
Confidence 346788999999999999999999999854
No 60
>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast). The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].
Probab=75.58 E-value=2.8 Score=34.90 Aligned_cols=39 Identities=15% Similarity=0.120 Sum_probs=35.7
Q ss_pred CCCcccHHHHHHHHHHhCCCCHHHHHHHHHHHhhcccee
Q 045217 94 RPCGLNTVNLLKVASSALGYGPQMAMQLAERLYTQGFIS 132 (224)
Q Consensus 94 pP~p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glIT 132 (224)
-.-.|+|-+|.+.|.+.=|+++..+-+++|+|-+.|+|.
T Consensus 8 ~~~~y~lKELEK~~pK~~gI~~~~VKdvlq~LvDDglV~ 46 (188)
T PF03962_consen 8 SKDFYTLKELEKLAPKEKGIVSMSVKDVLQSLVDDGLVH 46 (188)
T ss_pred cCCcccHHHHHHHcccccCCchhhHHHHHHHHhccccch
Confidence 345799999999999967999999999999999999997
No 61
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=75.31 E-value=5.9 Score=24.27 Aligned_cols=31 Identities=23% Similarity=0.277 Sum_probs=27.0
Q ss_pred HHHHHHhCCCCHHHHHHHHHHHhhccceecc
Q 045217 104 LKVASSALGYGPQMAMQLAERLYTQGFISYP 134 (224)
Q Consensus 104 q~~a~~~~g~sa~~tl~iaQ~LYE~glITYP 134 (224)
+.+.++.+|+|...+..+.+.|-+.|+|.+-
T Consensus 11 ~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~ 41 (48)
T smart00419 11 RQEIAELLGLTRETVSRTLKRLEKEGLISRE 41 (48)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 4566788899999999999999999999864
No 62
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=73.07 E-value=2.7 Score=24.53 Aligned_cols=17 Identities=29% Similarity=0.454 Sum_probs=14.7
Q ss_pred HHHHHHHHHHhhcccee
Q 045217 116 QMAMQLAERLYTQGFIS 132 (224)
Q Consensus 116 ~~tl~iaQ~LYE~glIT 132 (224)
.+.|..++.||+.|.||
T Consensus 2 ~~~L~~L~~l~~~G~Is 18 (31)
T PF09851_consen 2 EDRLEKLKELYDKGEIS 18 (31)
T ss_pred hHHHHHHHHHHHcCCCC
Confidence 45688999999999997
No 63
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=72.61 E-value=5.9 Score=24.91 Aligned_cols=33 Identities=18% Similarity=0.314 Sum_probs=26.4
Q ss_pred cccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceec
Q 045217 97 GLNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISY 133 (224)
Q Consensus 97 p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITY 133 (224)
|.+..+| ++.+|+|...+-.....|.+.|+|+|
T Consensus 15 ~~~~~el----~~~l~~s~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 15 PLTVSEL----AEELGLSQSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp SEEHHHH----HHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred CCchhhH----HHhccccchHHHHHHHHHHHCcCeeC
Confidence 4555555 56679999999999999999999986
No 64
>PF04182 B-block_TFIIIC: B-block binding subunit of TFIIIC; InterPro: IPR007309 Yeast transcription factor IIIC (TFIIIC) is a multisubunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding []. Although defined as a yeast protein, it is also found in a number of other organisms.
Probab=71.18 E-value=4.8 Score=28.15 Aligned_cols=30 Identities=23% Similarity=0.290 Sum_probs=26.9
Q ss_pred HHHHHHHhCCCCHHHHHHHHHHHhhcccee
Q 045217 103 LLKVASSALGYGPQMAMQLAERLYTQGFIS 132 (224)
Q Consensus 103 Lq~~a~~~~g~sa~~tl~iaQ~LYE~glIT 132 (224)
+|.+..+.+|.++...--+.++|.+.|||+
T Consensus 20 ~q~~L~~~~~~D~r~i~~~~k~L~~~gLI~ 49 (75)
T PF04182_consen 20 TQSDLSKLLGIDPRSIFYRLKKLEKKGLIV 49 (75)
T ss_pred ehhHHHHHhCCCchHHHHHHHHHHHCCCEE
Confidence 466777889999999999999999999995
No 65
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=70.96 E-value=8.7 Score=24.99 Aligned_cols=29 Identities=14% Similarity=0.208 Sum_probs=25.2
Q ss_pred HHHHhCCCCHHHHHHHHHHHhhccceecc
Q 045217 106 VASSALGYGPQMAMQLAERLYTQGFISYP 134 (224)
Q Consensus 106 ~a~~~~g~sa~~tl~iaQ~LYE~glITYP 134 (224)
+.++.+|+|...+.++...|-+.|+|++-
T Consensus 30 ~la~~~~is~~~v~~~l~~L~~~G~i~~~ 58 (66)
T cd07377 30 ELAEELGVSRTTVREALRELEAEGLVERR 58 (66)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 44677899999999999999999999853
No 66
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=70.27 E-value=7.6 Score=24.73 Aligned_cols=29 Identities=14% Similarity=0.226 Sum_probs=25.1
Q ss_pred HHHHhCCCCHHHHHHHHHHHhhccceecc
Q 045217 106 VASSALGYGPQMAMQLAERLYTQGFISYP 134 (224)
Q Consensus 106 ~a~~~~g~sa~~tl~iaQ~LYE~glITYP 134 (224)
+.++.+|+|...+..+++.|.+.|+|+.-
T Consensus 15 ~i~~~l~is~~~v~~~l~~L~~~g~i~~~ 43 (66)
T smart00418 15 ELAEILGLSQSTVSHHLKKLREAGLVESR 43 (66)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCeeee
Confidence 45677899999999999999999999853
No 67
>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=67.30 E-value=11 Score=24.80 Aligned_cols=30 Identities=20% Similarity=0.221 Sum_probs=26.2
Q ss_pred HHHHhCCCCHHHHHHHHHHHhhccceeccC
Q 045217 106 VASSALGYGPQMAMQLAERLYTQGFISYPR 135 (224)
Q Consensus 106 ~a~~~~g~sa~~tl~iaQ~LYE~glITYPR 135 (224)
+.+..+|+|...+-.+.+.|=+.|+|.+-+
T Consensus 30 ela~~~g~s~~tv~r~l~~L~~~g~i~~~~ 59 (67)
T cd00092 30 EIADYLGLTRETVSRTLKELEEEGLISRRG 59 (67)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 446678999999999999999999998765
No 68
>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=66.64 E-value=24 Score=37.43 Aligned_cols=111 Identities=13% Similarity=0.138 Sum_probs=67.2
Q ss_pred chhHHHHHHHHHHHHHHcCcCcceEEEEEEEEecC-eEEEEEEe----cc--ccCCHHHHHHHHHHHccCCceEEEEEee
Q 045217 15 CQTPTLGFCVQRYLQITSFKPEKFWTLHPYLVQNG-YELKLEWE----RQ--KLFDFDVATMFQKLVMQDRILEVIDISE 87 (224)
Q Consensus 15 VQTPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~-~~~~~~~~----~~--~~~~~~~a~~~~~~~~~~~~~~V~~v~~ 87 (224)
-+--+-.||++|..+-.- .|..|=...+.+..+| ..|.+.+. .| .++..+... .+..+..+.+.+++.
T Consensus 991 ~e~~lY~LI~rRflAs~~-~~a~~~~t~v~~~~~~~~~f~~~g~~i~~~Gw~~v~~~~~~~----~~~~G~~~~~~~~~~ 1065 (1171)
T TIGR01054 991 EHLRLYDLIFRRFMASQM-RPAKVDTKEITLKADGKEAEEEGIVEIVERGFELVYPLWRKN----ELEKGSTFIVKDKEL 1065 (1171)
T ss_pred HHHHHHHHHHHHHHHHhC-chheEEEEEEEEEeCCeeEEEEEEEEEeeCCHHHHcCccccc----cccCCCEeeeeccee
Confidence 344566788988887664 6666767777777655 46665543 11 122211111 112223445555444
Q ss_pred ecccccCCCcccHHHHHHHHHHhCCCCHHHHH-HHHHHHhhccceec
Q 045217 88 KQESKVRPCGLNTVNLLKVASSALGYGPQMAM-QLAERLYTQGFISY 133 (224)
Q Consensus 88 k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl-~iaQ~LYE~glITY 133 (224)
.++ .||.+|+-++|.+.|-+ .|+.-.-|. .|.+.|.+.|||.-
T Consensus 1066 ~~~--~~~p~yTe~~Li~~Me~-~GIGtpsT~A~II~~L~~R~YV~~ 1109 (1171)
T TIGR01054 1066 RSV--PKVYPYTQGEIVQEMKE-RGIGRPSTYATIVEKLLRRGYVVE 1109 (1171)
T ss_pred eec--CCCCCCCHHHHHHHHHh-CCCCCcccHHHHHHHhhccCcEEe
Confidence 433 24448999999999865 588655554 58999999999963
No 69
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=65.14 E-value=9.9 Score=25.62 Aligned_cols=28 Identities=14% Similarity=0.245 Sum_probs=24.5
Q ss_pred HHHHhCCCCHHHHHHHHHHHhhccceec
Q 045217 106 VASSALGYGPQMAMQLAERLYTQGFISY 133 (224)
Q Consensus 106 ~a~~~~g~sa~~tl~iaQ~LYE~glITY 133 (224)
+.++.+|++...+-++..+|.++|+|.-
T Consensus 27 eIa~~l~i~~~~v~~~L~~L~~~GlV~~ 54 (68)
T PF01978_consen 27 EIAEELGISRSTVYRALKSLEEKGLVER 54 (68)
T ss_dssp HHHHHHTSSHHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 3466779999999999999999999964
No 70
>PF13730 HTH_36: Helix-turn-helix domain
Probab=63.77 E-value=11 Score=24.16 Aligned_cols=29 Identities=21% Similarity=0.318 Sum_probs=23.7
Q ss_pred cHHHHHHHHHHhCCCCHHHHHHHHHHHhhccce
Q 045217 99 NTVNLLKVASSALGYGPQMAMQLAERLYTQGFI 131 (224)
Q Consensus 99 ~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glI 131 (224)
+..+|+ +.+|+|...+.++...|=+.|+|
T Consensus 27 S~~~la----~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 27 SQETLA----KDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CHHHHH----HHHCcCHHHHHHHHHHHHHCcCC
Confidence 455554 45599999999999999999987
No 71
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=63.57 E-value=14 Score=23.50 Aligned_cols=29 Identities=17% Similarity=0.304 Sum_probs=25.0
Q ss_pred HHHHHhCCCCHHHHHHHHHHHhhccceec
Q 045217 105 KVASSALGYGPQMAMQLAERLYTQGFISY 133 (224)
Q Consensus 105 ~~a~~~~g~sa~~tl~iaQ~LYE~glITY 133 (224)
.+.+..||+|..-+.++.+.|-+.|+|+.
T Consensus 24 ~~la~~~~vs~~tv~~~l~~L~~~g~i~~ 52 (60)
T smart00345 24 RELAAQLGVSRTTVREALSRLEAEGLVQR 52 (60)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 34567889999999999999999999963
No 72
>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=63.37 E-value=10 Score=28.52 Aligned_cols=41 Identities=12% Similarity=0.226 Sum_probs=33.8
Q ss_pred ccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceeccCCCC
Q 045217 98 LNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISYPRTES 138 (224)
Q Consensus 98 ~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRTds 138 (224)
-+..++...+....+++..-++.+..+|.++|+|+.-+..-
T Consensus 18 ~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~gr 58 (115)
T PF03965_consen 18 ATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTREKIGR 58 (115)
T ss_dssp EEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEEETT
T ss_pred CCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEeecCC
Confidence 57788888888888999999999999999999999876543
No 73
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=61.98 E-value=12 Score=25.50 Aligned_cols=29 Identities=21% Similarity=0.276 Sum_probs=24.1
Q ss_pred HHHHhCCCC-HHHHHHHHHHHhhccceecc
Q 045217 106 VASSALGYG-PQMAMQLAERLYTQGFISYP 134 (224)
Q Consensus 106 ~a~~~~g~s-a~~tl~iaQ~LYE~glITYP 134 (224)
+..+.+|++ +.-+...++.|-++|+|...
T Consensus 30 EIa~~~g~~S~~tv~~~L~~Le~kG~I~r~ 59 (65)
T PF01726_consen 30 EIAEALGLKSTSTVQRHLKALERKGYIRRD 59 (65)
T ss_dssp HHHHHHTSSSHHHHHHHHHHHHHTTSEEEG
T ss_pred HHHHHhCCCChHHHHHHHHHHHHCcCccCC
Confidence 445667996 99999999999999999853
No 74
>PF10872 DUF2740: Protein of unknown function (DUF2740); InterPro: IPR022626 This entry is represented by Bacteriophage P22, Orf48. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family of proteins with unknown function has a highly conserved sequence. They are found in Enterobacteria and Enterobacteria phages.
Probab=59.62 E-value=12 Score=23.44 Aligned_cols=28 Identities=11% Similarity=0.216 Sum_probs=21.6
Q ss_pred CCCCHHHHHHHHHHHH-HHHHhcCcCccc
Q 045217 196 DMLGKDAWRLYSYVCQ-HFLGTVSPDCKY 223 (224)
Q Consensus 196 ~~L~~~e~~iY~lI~~-r~la~f~~~a~y 223 (224)
..||+++-+|-.-|.| |||++|-.|..|
T Consensus 3 kqlsp~qdk~hk~ilrdrflssfkqpgrf 31 (48)
T PF10872_consen 3 KQLSPYQDKIHKHILRDRFLSSFKQPGRF 31 (48)
T ss_pred cccCccHHHHHHHHHHHHHHHHhcCcchH
Confidence 4578888888877765 999999877654
No 75
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=57.43 E-value=20 Score=25.70 Aligned_cols=36 Identities=19% Similarity=0.339 Sum_probs=32.3
Q ss_pred HhCCCCHHHHHHHHHHHhhcccee-ccCCCCcccCCC
Q 045217 109 SALGYGPQMAMQLAERLYTQGFIS-YPRTESTAYPSS 144 (224)
Q Consensus 109 ~~~g~sa~~tl~iaQ~LYE~glIT-YPRTds~~l~~~ 144 (224)
+.+|+|+.-+-+.++.|-+-|||. =|=|.+-|+|.+
T Consensus 31 ~~l~~s~aTIRN~M~~Le~lGlve~~p~~s~GriPT~ 67 (78)
T PF03444_consen 31 EELGRSPATIRNEMADLEELGLVESQPHPSGGRIPTD 67 (78)
T ss_pred HHHCCChHHHHHHHHHHHHCCCccCCCCCCCCCCcCH
Confidence 347999999999999999999995 799999999985
No 76
>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=56.19 E-value=22 Score=27.61 Aligned_cols=38 Identities=11% Similarity=0.288 Sum_probs=32.4
Q ss_pred ccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceeccC
Q 045217 98 LNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISYPR 135 (224)
Q Consensus 98 ~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYPR 135 (224)
-+..++...++...|++..-++.++..|.++|+|+.-+
T Consensus 19 ~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~k 56 (130)
T TIGR02698 19 TTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTTEK 56 (130)
T ss_pred CCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceeeec
Confidence 36678887788888999999999999999999998653
No 77
>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=55.96 E-value=18 Score=26.91 Aligned_cols=32 Identities=16% Similarity=0.278 Sum_probs=26.3
Q ss_pred HHHHHhCCCCHHHHHHHHHHHhhccceeccCC
Q 045217 105 KVASSALGYGPQMAMQLAERLYTQGFISYPRT 136 (224)
Q Consensus 105 ~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRT 136 (224)
++.+..++++...+-.+...|.++|||+=-|.
T Consensus 47 ~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~~ 78 (109)
T TIGR01889 47 KEIIKEILIKQSALVKIIKKLSKKGYLSKERS 78 (109)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEeccCC
Confidence 34467789999999999999999999984433
No 78
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=55.78 E-value=21 Score=21.92 Aligned_cols=33 Identities=18% Similarity=0.223 Sum_probs=27.1
Q ss_pred ccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceecc
Q 045217 98 LNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISYP 134 (224)
Q Consensus 98 ~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYP 134 (224)
++..+|. +.+|+|...+-...+.|-+.|+|...
T Consensus 15 ~s~~~l~----~~l~~s~~tv~~~l~~L~~~g~i~~~ 47 (53)
T smart00420 15 VSVEELA----ELLGVSEMTIRRDLNKLEEQGLLTRV 47 (53)
T ss_pred cCHHHHH----HHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 5666664 45699999999999999999999754
No 79
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=55.52 E-value=18 Score=26.62 Aligned_cols=27 Identities=15% Similarity=0.144 Sum_probs=24.6
Q ss_pred HHHhCCCCHHHHHHHHHHHhhccceec
Q 045217 107 ASSALGYGPQMAMQLAERLYTQGFISY 133 (224)
Q Consensus 107 a~~~~g~sa~~tl~iaQ~LYE~glITY 133 (224)
.++.++++.+++..++.+|-+.|||.+
T Consensus 27 ia~~l~~~~~~v~~~l~~Le~~GLler 53 (92)
T PF10007_consen 27 IARRLKIPLEEVREALEKLEEMGLLER 53 (92)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCCeEE
Confidence 467789999999999999999999985
No 80
>COG4840 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.14 E-value=24 Score=24.49 Aligned_cols=28 Identities=11% Similarity=0.278 Sum_probs=25.6
Q ss_pred cHHHHHHHHHHhCCCCHHHHHHHHHHHh
Q 045217 99 NTVNLLKVASSALGYGPQMAMQLAERLY 126 (224)
Q Consensus 99 ~l~~Lq~~a~~~~g~sa~~tl~iaQ~LY 126 (224)
+|+.+..-.-++-.|||.+...|||.|-
T Consensus 40 dLtdiy~mvkkkenfSpsEmqaiA~eL~ 67 (71)
T COG4840 40 DLTDIYDMVKKKENFSPSEMQAIADELG 67 (71)
T ss_pred HHHHHHHHHHHhccCCHHHHHHHHHHHH
Confidence 6889999889999999999999999984
No 81
>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=54.76 E-value=24 Score=23.29 Aligned_cols=28 Identities=14% Similarity=0.319 Sum_probs=22.7
Q ss_pred HHHHHhCCCCHHHHHHHHHHHhhcccee
Q 045217 105 KVASSALGYGPQMAMQLAERLYTQGFIS 132 (224)
Q Consensus 105 ~~a~~~~g~sa~~tl~iaQ~LYE~glIT 132 (224)
.+.++.+|++...+-.+.++|-++|||.
T Consensus 22 ~~l~~~~~~~~~~vs~~i~~L~~~glv~ 49 (68)
T PF13463_consen 22 SDLAERLGISKSTVSRIIKKLEEKGLVE 49 (68)
T ss_dssp HHHHHHTT--HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 3446789999999999999999999994
No 82
>PF04337 DUF480: Protein of unknown function, DUF480; InterPro: IPR007432 This family consists of several proteins of uncharacterised function.; PDB: 3BZ6_A.
Probab=54.65 E-value=12 Score=30.01 Aligned_cols=46 Identities=11% Similarity=0.104 Sum_probs=35.0
Q ss_pred ecccccCCCcccHHHHHHHHHHhCC------CCHHHHHHHHHHHhhccceec
Q 045217 88 KQESKVRPCGLNTVNLLKVASSALG------YGPQMAMQLAERLYTQGFISY 133 (224)
Q Consensus 88 k~~~~~pP~p~~l~~Lq~~a~~~~g------~sa~~tl~iaQ~LYE~glITY 133 (224)
|+....=--|++|.+|...||.|-. ++-.++..+...|-++|+++=
T Consensus 15 K~~TTPd~YPLtLNaL~~aCNQKsnR~PVm~l~e~eV~~ald~L~~~~Lv~~ 66 (148)
T PF04337_consen 15 KEVTTPDQYPLTLNALTTACNQKSNREPVMNLSESEVQAALDELRAKGLVRE 66 (148)
T ss_dssp HHHH-GGG-SEEHHHHHHHHT-SSS-SS-----HHHHHHHHHHHHHTTSEEE
T ss_pred ecccCCCcCcchHHHHHHHhccccccCccccCCHHHHHHHHHHHHHCcCeee
Confidence 3444455578999999999999865 788999999999999999986
No 83
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=54.62 E-value=21 Score=23.13 Aligned_cols=27 Identities=19% Similarity=0.380 Sum_probs=23.0
Q ss_pred HHHHhCCCCHHHHHHHHHHHhhcccee
Q 045217 106 VASSALGYGPQMAMQLAERLYTQGFIS 132 (224)
Q Consensus 106 ~a~~~~g~sa~~tl~iaQ~LYE~glIT 132 (224)
+..+.+|+++.-+-.++..|=++|||.
T Consensus 26 ~la~~l~~~~~~vs~~v~~L~~~Glv~ 52 (62)
T PF12802_consen 26 ELAERLGISKSTVSRIVKRLEKKGLVE 52 (62)
T ss_dssp HHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 446778999999999999999999996
No 84
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=53.78 E-value=22 Score=24.07 Aligned_cols=40 Identities=23% Similarity=0.355 Sum_probs=31.7
Q ss_pred cCCCcccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceeccCC
Q 045217 93 VRPCGLNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISYPRT 136 (224)
Q Consensus 93 ~pP~p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRT 136 (224)
.-|.|++..+| +...|.|...+..+...|=+.|+|++-|.
T Consensus 24 ~~~~~lt~~~i----A~~~g~sr~tv~r~l~~l~~~g~I~~~~~ 63 (76)
T PF13545_consen 24 RIPLPLTQEEI----ADMLGVSRETVSRILKRLKDEGIIEVKRG 63 (76)
T ss_dssp EEEEESSHHHH----HHHHTSCHHHHHHHHHHHHHTTSEEEETT
T ss_pred eEEecCCHHHH----HHHHCCCHHHHHHHHHHHHHCCCEEEcCC
Confidence 34555665544 67789999999999999999999997555
No 85
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=53.22 E-value=24 Score=22.50 Aligned_cols=33 Identities=21% Similarity=0.384 Sum_probs=26.6
Q ss_pred cccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceec
Q 045217 97 GLNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISY 133 (224)
Q Consensus 97 p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITY 133 (224)
+.++++| ++.+|++...+-.+++.|-+.||+..
T Consensus 18 ~~t~~ei----a~~~gl~~stv~r~L~tL~~~g~v~~ 50 (52)
T PF09339_consen 18 PLTLSEI----ARALGLPKSTVHRLLQTLVEEGYVER 50 (52)
T ss_dssp CEEHHHH----HHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred CCCHHHH----HHHHCcCHHHHHHHHHHHHHCcCeec
Confidence 3577766 56679999999999999999999864
No 86
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=52.82 E-value=32 Score=22.87 Aligned_cols=35 Identities=14% Similarity=0.288 Sum_probs=23.1
Q ss_pred ccHHHHHHHHHHhCCCCHH----HHHHHHHHHhhcccee
Q 045217 98 LNTVNLLKVASSALGYGPQ----MAMQLAERLYTQGFIS 132 (224)
Q Consensus 98 ~~l~~Lq~~a~~~~g~sa~----~tl~iaQ~LYE~glIT 132 (224)
.+..++-+....+|+.+++ .+....+.|.++|+|.
T Consensus 30 ~t~~ei~~~l~~~y~~~~~~~~~dv~~fl~~L~~~glIe 68 (68)
T PF05402_consen 30 RTVEEIVDALAEEYDVDPEEAEEDVEEFLEQLREKGLIE 68 (68)
T ss_dssp S-HHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT---
T ss_pred CCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCcCcC
Confidence 5678888888888999886 4566788888889874
No 87
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=52.32 E-value=26 Score=23.94 Aligned_cols=34 Identities=15% Similarity=0.173 Sum_probs=28.1
Q ss_pred cccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceecc
Q 045217 97 GLNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISYP 134 (224)
Q Consensus 97 p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYP 134 (224)
.++..+| ++.+|++...+-.+..+|=+.|+|..-
T Consensus 22 ~~ta~eL----a~~lgl~~~~v~r~L~~L~~~G~V~~~ 55 (68)
T smart00550 22 TSTALQL----AKNLGLPKKEVNRVLYSLEKKGKVCKQ 55 (68)
T ss_pred CcCHHHH----HHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 4665555 677899999999999999999999863
No 88
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=52.13 E-value=21 Score=27.79 Aligned_cols=39 Identities=13% Similarity=0.279 Sum_probs=31.8
Q ss_pred HHHHHhCCCCHHHHHHHHHHHhhccceeccCCCCcccCC
Q 045217 105 KVASSALGYGPQMAMQLAERLYTQGFISYPRTESTAYPS 143 (224)
Q Consensus 105 ~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRTds~~l~~ 143 (224)
.+.++.+|+|+..+-..++.|-++|||.|-|...-.|++
T Consensus 26 ~ela~~l~vs~~svs~~l~~L~~~Gli~~~~~~~i~LT~ 64 (142)
T PRK03902 26 SDIAEALSVHPSSVTKMVQKLDKDEYLIYEKYRGLVLTP 64 (142)
T ss_pred HHHHHHhCCChhHHHHHHHHHHHCCCEEEecCceEEECH
Confidence 566788999999999999999999999987654444554
No 89
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=48.89 E-value=34 Score=20.13 Aligned_cols=27 Identities=22% Similarity=0.359 Sum_probs=22.5
Q ss_pred HHHHHhCCCCHHHHHHHHHHHhhccce
Q 045217 105 KVASSALGYGPQMAMQLAERLYTQGFI 131 (224)
Q Consensus 105 ~~a~~~~g~sa~~tl~iaQ~LYE~glI 131 (224)
++.+..+|.|.+-+-.+.-+|-++|+|
T Consensus 6 ~diA~~lG~t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 6 QDIADYLGLTRETVSRILKKLERQGLI 32 (32)
T ss_dssp HHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHhCCcHHHHHHHHHHHHHcCCC
Confidence 455678999999999999999999987
No 90
>PRK11239 hypothetical protein; Provisional
Probab=48.73 E-value=30 Score=29.47 Aligned_cols=46 Identities=11% Similarity=0.166 Sum_probs=38.8
Q ss_pred eecccccCCCcccHHHHHHHHHHhCC------CCHHHHHHHHHHHhhcccee
Q 045217 87 EKQESKVRPCGLNTVNLLKVASSALG------YGPQMAMQLAERLYTQGFIS 132 (224)
Q Consensus 87 ~k~~~~~pP~p~~l~~Lq~~a~~~~g------~sa~~tl~iaQ~LYE~glIT 132 (224)
+|+.+.+=--|++|.+|.-.||.|-+ +|-.++..+...|-.+|+++
T Consensus 18 EKe~TTPd~YPLSLNaL~~aCNQKsnRePVm~lsE~eV~~ald~L~~~~Lv~ 69 (215)
T PRK11239 18 EKQVTTPEQYPLSVNGVVTACNQKTNREPVMNLSESEVQEQLDNLVKRHYLR 69 (215)
T ss_pred hhcccCCCcCcchHHHHHHHhccccccCccccCCHHHHHHHHHHHHhCcCee
Confidence 34455566679999999999999865 78899999999999999996
No 91
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=48.11 E-value=28 Score=22.89 Aligned_cols=33 Identities=18% Similarity=0.243 Sum_probs=26.3
Q ss_pred CcccHHHHHHHHHHhCCCCHHHHHHHHHHHhhcccee
Q 045217 96 CGLNTVNLLKVASSALGYGPQMAMQLAERLYTQGFIS 132 (224)
Q Consensus 96 ~p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glIT 132 (224)
.|.+.++|. +.+|++...+-...+.|-+.|+|+
T Consensus 23 ~~~t~~ela----~~l~~~~~t~s~hL~~L~~aGli~ 55 (61)
T PF12840_consen 23 GPMTVSELA----EELGISQSTVSYHLKKLEEAGLIE 55 (61)
T ss_dssp STBEHHHHH----HHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred CCCCHHHHH----HHHCCCHHHHHHHHHHHHHCCCeE
Confidence 356777764 455999999999999999999996
No 92
>cd04449 DEP_DEPDC5-like DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in DEPDC5-like proteins. DEPDC5, in human also known as KIAA0645, is a DEP domain containing protein of unknown function.
Probab=47.75 E-value=99 Score=21.92 Aligned_cols=61 Identities=10% Similarity=0.126 Sum_probs=42.8
Q ss_pred HHHHHccCCceEEEEEeeecccccCCCcccHHHHHHHHHHhCC--CCHHHHHHHHHHHhhcccee
Q 045217 70 FQKLVMQDRILEVIDISEKQESKVRPCGLNTVNLLKVASSALG--YGPQMAMQLAERLYTQGFIS 132 (224)
Q Consensus 70 ~~~~~~~~~~~~V~~v~~k~~~~~pP~p~~l~~Lq~~a~~~~g--~sa~~tl~iaQ~LYE~glIT 132 (224)
+.+.+.+.....|.. .......+|.=|.-+++=.=.-+.++ -|-.++..++|.|-+.|+|.
T Consensus 4 i~~~m~~~~~~~i~~--r~~~~~~~~~cF~G~e~VdWL~~~~~~~~~r~eAv~lgq~Ll~~g~I~ 66 (83)
T cd04449 4 IAEAMRDPSGIGIFD--RSWHKGLPSNCFIGSEAVSWLINNFEDVDTREEAVELGQELMNEGLIE 66 (83)
T ss_pred HHHHHhCCCCCceee--chhcCccCCcceEhHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCCCEE
Confidence 444454432223443 23456778888988888776666665 47889999999999999996
No 93
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=46.72 E-value=28 Score=24.47 Aligned_cols=34 Identities=21% Similarity=0.464 Sum_probs=26.9
Q ss_pred ccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceeccC
Q 045217 98 LNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISYPR 135 (224)
Q Consensus 98 ~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYPR 135 (224)
.+..+| ++.+|.++..+-++.|.|-+.|+|.=-|
T Consensus 26 ~s~~ei----A~~~~i~~~~l~kil~~L~~~Gli~s~~ 59 (83)
T PF02082_consen 26 VSSKEI----AERLGISPSYLRKILQKLKKAGLIESSR 59 (83)
T ss_dssp BEHHHH----HHHHTS-HHHHHHHHHHHHHTTSEEEET
T ss_pred CCHHHH----HHHHCcCHHHHHHHHHHHhhCCeeEecC
Confidence 555555 5678999999999999999999996444
No 94
>PF14178 YppF: YppF-like protein
Probab=46.48 E-value=40 Score=22.87 Aligned_cols=35 Identities=29% Similarity=0.334 Sum_probs=27.4
Q ss_pred ccHHHHHHHHHHhCCCC---HHHHHHHHHHHhhcccee
Q 045217 98 LNTVNLLKVASSALGYG---PQMAMQLAERLYTQGFIS 132 (224)
Q Consensus 98 ~~l~~Lq~~a~~~~g~s---a~~tl~iaQ~LYE~glIT 132 (224)
+++.+|++.-....++. ..+-|+-|+.+|=.|-||
T Consensus 1 M~l~eLk~~F~~~k~y~p~~~NeLLDFar~~Yi~gei~ 38 (60)
T PF14178_consen 1 MNLHELKQKFMQKKKYEPEDMNELLDFARKLYIQGEIS 38 (60)
T ss_pred CCHHHHHHHHHHHhccCcccHHHHHHHHHHHHHhCccc
Confidence 36778888766666765 578899999999998887
No 95
>KOG1956 consensus DNA topoisomerase III alpha [Replication, recombination and repair]
Probab=45.28 E-value=46 Score=33.01 Aligned_cols=66 Identities=14% Similarity=0.290 Sum_probs=54.9
Q ss_pred CCceEEEEEeeecccccCCCcccHHHHHHHHHHhCCCCHHHHHH-HHHHHhhccceeccCCCCcccCC
Q 045217 77 DRILEVIDISEKQESKVRPCGLNTVNLLKVASSALGYGPQMAMQ-LAERLYTQGFISYPRTESTAYPS 143 (224)
Q Consensus 77 ~~~~~V~~v~~k~~~~~pP~p~~l~~Lq~~a~~~~g~sa~~tl~-iaQ~LYE~glITYPRTds~~l~~ 143 (224)
+..+.+..++-+.....||.+++=.+|...+ .+.|+..+-|+. +.++|-+.||++=-+-+.+.+|+
T Consensus 466 ge~fq~~~lem~~g~T~~P~~ltEaeLI~lM-dk~GIGtdAT~aehi~kiq~R~Yv~~~~~~~~~~P~ 532 (758)
T KOG1956|consen 466 GELFQPGELEMKDGETSPPKYLTEAELISLM-DKNGIGTDATIAEHIEKIQERGYVTKKNKVGRFVPT 532 (758)
T ss_pred ccccccceEEeccCccCCCCccCHHHHHHHH-HHcCCCCchhHHHHHHHHHhhcceeeeccccccCch
Confidence 3467788899999999999999999999888 467998888875 89999999999976666665554
No 96
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=45.05 E-value=31 Score=28.89 Aligned_cols=32 Identities=16% Similarity=0.209 Sum_probs=28.7
Q ss_pred HHHHHHhCCCCHHHHHHHHHHHhhccceeccC
Q 045217 104 LKVASSALGYGPQMAMQLAERLYTQGFISYPR 135 (224)
Q Consensus 104 q~~a~~~~g~sa~~tl~iaQ~LYE~glITYPR 135 (224)
|++.+..+|.++..+-.+.++|-+.|+|.+-+
T Consensus 182 ~~~IA~~lGisretlsR~L~~L~~~GlI~~~~ 213 (230)
T PRK09391 182 RRDIADYLGLTIETVSRALSQLQDRGLIGLSG 213 (230)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCCcEEecC
Confidence 66667889999999999999999999999864
No 97
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=44.97 E-value=34 Score=24.99 Aligned_cols=23 Identities=22% Similarity=0.303 Sum_probs=20.1
Q ss_pred HhCCCCHHHHHHHHHHHhhccce
Q 045217 109 SALGYGPQMAMQLAERLYTQGFI 131 (224)
Q Consensus 109 ~~~g~sa~~tl~iaQ~LYE~glI 131 (224)
+++|++..++.++++.|-+.|+|
T Consensus 73 ~~l~~~~~~v~~al~~L~~eG~I 95 (102)
T PF08784_consen 73 QQLGMSENEVRKALDFLSNEGHI 95 (102)
T ss_dssp HHSTS-HHHHHHHHHHHHHTTSE
T ss_pred HHhCcCHHHHHHHHHHHHhCCeE
Confidence 45599999999999999999998
No 98
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=44.49 E-value=34 Score=27.24 Aligned_cols=34 Identities=18% Similarity=0.207 Sum_probs=29.8
Q ss_pred HHHHHHhCCCCHHHHHHHHHHHhhccceeccCCC
Q 045217 104 LKVASSALGYGPQMAMQLAERLYTQGFISYPRTE 137 (224)
Q Consensus 104 q~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRTd 137 (224)
|++.+..+|.|...+-.+.++|=+.|+|++-|-.
T Consensus 146 ~~~iA~~lG~tretvsR~l~~l~~~g~I~~~~~~ 179 (193)
T TIGR03697 146 HQAIAEAIGSTRVTITRLLGDLRKKKLISIHKKK 179 (193)
T ss_pred HHHHHHHhCCcHHHHHHHHHHHHHCCCEEecCCE
Confidence 5666788999999999999999999999997743
No 99
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=44.47 E-value=19 Score=21.84 Aligned_cols=31 Identities=29% Similarity=0.479 Sum_probs=20.8
Q ss_pred HHHHHhCCCCHHHHHHHHHHHhh-ccce-eccCCCCcc
Q 045217 105 KVASSALGYGPQMAMQLAERLYT-QGFI-SYPRTESTA 140 (224)
Q Consensus 105 ~~a~~~~g~sa~~tl~iaQ~LYE-~glI-TYPRTds~~ 140 (224)
.++++.+|.|++.. .-|| .|+| +-.||++.|
T Consensus 3 ~e~A~~~gvs~~tl-----R~ye~~Gll~~~~r~~~g~ 35 (38)
T PF00376_consen 3 GEVAKLLGVSPRTL-----RYYEREGLLPPPERTEGGY 35 (38)
T ss_dssp HHHHHHHTS-HHHH-----HHHHHTTSS-SSEETTTS-
T ss_pred HHHHHHHCCCHHHH-----HHHHHCCCCCCCccCCCCe
Confidence 35678889887643 3466 4999 888988764
No 100
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=43.89 E-value=36 Score=24.15 Aligned_cols=32 Identities=19% Similarity=0.372 Sum_probs=28.0
Q ss_pred HHHHHHhCCCCHHHHHHHHHHHhhccceeccC
Q 045217 104 LKVASSALGYGPQMAMQLAERLYTQGFISYPR 135 (224)
Q Consensus 104 q~~a~~~~g~sa~~tl~iaQ~LYE~glITYPR 135 (224)
+.++++.+|+|+.-+..+.+.|=++|||.--+
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~~glI~r~~ 33 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEKDGLVEYEP 33 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHHCCCEEEcC
Confidence 45678899999999999999999999998644
No 101
>KOG3433 consensus Protein involved in meiotic recombination/predicted coiled-coil protein [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=43.89 E-value=13 Score=30.92 Aligned_cols=37 Identities=19% Similarity=0.206 Sum_probs=30.9
Q ss_pred ccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceeccC
Q 045217 98 LNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISYPR 135 (224)
Q Consensus 98 ~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYPR 135 (224)
|-|-+|-+.+++ -|+-..-+-++.|+||+.|++.--+
T Consensus 25 f~LkelEKlG~k-KgIv~~tvKdvLQsLvDD~lV~~eK 61 (203)
T KOG3433|consen 25 FQLKELEKLGSK-KGIVWQTVKDVLQSLVDDGLVIKEK 61 (203)
T ss_pred HHHHHHHHhCCc-cceehhHHHHHHHHHhccchHHHHH
Confidence 667788888777 5999999999999999998887544
No 102
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=43.11 E-value=27 Score=27.64 Aligned_cols=30 Identities=23% Similarity=0.348 Sum_probs=24.1
Q ss_pred HHHHhCCCCHHHHHHHHHHHhhccc--eeccC
Q 045217 106 VASSALGYGPQMAMQLAERLYTQGF--ISYPR 135 (224)
Q Consensus 106 ~a~~~~g~sa~~tl~iaQ~LYE~gl--ITYPR 135 (224)
+.+..+|++.+++-+++..|||.|+ +.|-|
T Consensus 20 dLa~~l~i~~n~vRkiL~~L~ed~~~~~~~~~ 51 (147)
T smart00531 20 DLAELLGIKQKQLRKILYLLYDEKLIKIDYKR 51 (147)
T ss_pred HHHHHhCCCHHHHHHHHHHHHhhhcchhheee
Confidence 4567789999999999999999655 45543
No 103
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=42.74 E-value=43 Score=25.54 Aligned_cols=37 Identities=19% Similarity=0.346 Sum_probs=30.9
Q ss_pred CCCcccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceecc
Q 045217 94 RPCGLNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISYP 134 (224)
Q Consensus 94 pP~p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYP 134 (224)
.|.+.++++| +..+..|...|-.+.++|=|.|+|+|-
T Consensus 16 ~~~~vtl~el----A~~l~cS~Rn~r~lLkkm~~~gWi~W~ 52 (115)
T PF12793_consen 16 QPVEVTLDEL----AELLFCSRRNARTLLKKMQEEGWITWQ 52 (115)
T ss_pred CCcceeHHHH----HHHhCCCHHHHHHHHHHHHHCCCeeee
Confidence 4555666666 567899999999999999999999995
No 104
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=42.27 E-value=38 Score=27.25 Aligned_cols=34 Identities=15% Similarity=0.188 Sum_probs=29.5
Q ss_pred HHHHHHhCCCCHHHHHHHHHHHhhccceeccCCC
Q 045217 104 LKVASSALGYGPQMAMQLAERLYTQGFISYPRTE 137 (224)
Q Consensus 104 q~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRTd 137 (224)
|++.+..+|.|+..+-.+..+|-+.|+|++.|--
T Consensus 152 ~~~iA~~lG~tretvsR~l~~l~~~g~I~~~~~~ 185 (202)
T PRK13918 152 HDELAAAVGSVRETVTKVIGELSREGYIRSGYGK 185 (202)
T ss_pred HHHHHHHhCccHHHHHHHHHHHHHCCCEEcCCCE
Confidence 5566789999999999999999999999986543
No 105
>PF11834 DUF3354: Domain of unknown function (DUF3354); InterPro: IPR021789 Potassium channels take part in important processes of higher plants, including opening and closing of stomatal pores and leaf movement. Inward rectifying potassium (K(+)in) channels play an important role in turgor regulation and ion uptake in higher plants. All of them comprise, from their N-terminal to their C-terminal ends: a short hydrophilic region, a hydrophobic region structurally analogous and partially homologous to the transmembrane domain of voltage-gated animal channels from the Shaker superfamily, a putative cyclic nucleotide-binding domain, and a conserved C-terminal KHA domain. Between these last two regions, some of them (AKT1, AKT2 and SKT1) contain an ankyrin-repeat domain with six repeats homologous to those of human erythrocyte ankyrin. This entry represents the KHA domain which is unique to plant K(+)in channels. The KHA domain contains two high-homology blocks enriched for hydrophobic and acidic residues, respectively. The KHA domain is essential for interaction of plant K(+)in channels. The KHA domain mediates tetramerization and/or stabilisation of the heteromers [, , ].
Probab=42.25 E-value=23 Score=24.70 Aligned_cols=24 Identities=25% Similarity=0.256 Sum_probs=20.2
Q ss_pred CCcccHHHHHHHHHHhCCCCHHHH
Q 045217 95 PCGLNTVNLLKVASSALGYGPQMA 118 (224)
Q Consensus 95 P~p~~l~~Lq~~a~~~~g~sa~~t 118 (224)
.+|=|+.+|.+.|+++||+++.+.
T Consensus 23 ~lP~SleeLl~ia~~kfg~~~~~v 46 (69)
T PF11834_consen 23 WLPDSLEELLKIASEKFGFSATKV 46 (69)
T ss_pred EcCccHHHHHHHHHHHhCCCceEE
Confidence 467899999999999999986443
No 106
>PF09397 Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541 This domain directs oriented DNA translocation and forms a winged helix structure []. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding []. ; PDB: 2VE9_B 2VE8_E 2J5O_A 2J5P_A.
Probab=42.24 E-value=39 Score=23.24 Aligned_cols=36 Identities=17% Similarity=0.201 Sum_probs=25.7
Q ss_pred ccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceeccCCC
Q 045217 98 LNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISYPRTE 137 (224)
Q Consensus 98 ~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRTd 137 (224)
-+++.|| ++|+++-.++-.++..|-+.|+|+-+-..
T Consensus 21 ~S~S~lQ----R~~rIGynrAariid~LE~~GiVs~~~~~ 56 (65)
T PF09397_consen 21 ASISLLQ----RKFRIGYNRAARIIDQLEEEGIVSPANGS 56 (65)
T ss_dssp ECHHHHH----HHHT--HHHHHHHHHHHHHCTSBE---TT
T ss_pred ccHHHHH----HHhCCCHHHHHHHHHHHHHCCCCCCCCCC
Confidence 3677787 45788999999999999999999976544
No 107
>PF13061 DUF3923: Protein of unknown function (DUF3923)
Probab=41.69 E-value=14 Score=25.49 Aligned_cols=16 Identities=31% Similarity=0.243 Sum_probs=13.1
Q ss_pred CccccCcchhHHHHHH
Q 045217 8 LILIYGPCQTPTLGFC 23 (224)
Q Consensus 8 ~~lS~GRVQTPtL~lI 23 (224)
++=..|.||||.+.++
T Consensus 26 ~vDgaGv~qT~~~k~i 41 (66)
T PF13061_consen 26 KVDGAGVVQTPELKLI 41 (66)
T ss_pred eccccccccCHHHHHH
Confidence 3446899999999887
No 108
>PRK00215 LexA repressor; Validated
Probab=41.48 E-value=45 Score=27.43 Aligned_cols=35 Identities=26% Similarity=0.344 Sum_probs=29.2
Q ss_pred HHHHHHhCCC-CHHHHHHHHHHHhhccceeccCCCC
Q 045217 104 LKVASSALGY-GPQMAMQLAERLYTQGFISYPRTES 138 (224)
Q Consensus 104 q~~a~~~~g~-sa~~tl~iaQ~LYE~glITYPRTds 138 (224)
+++.++.+|+ |..-+..+++.|-++|+|+.-..+.
T Consensus 26 ~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~~~~ 61 (205)
T PRK00215 26 RREIADALGLRSPSAVHEHLKALERKGFIRRDPGRS 61 (205)
T ss_pred HHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCCCCc
Confidence 4455788999 9999999999999999998866554
No 109
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=41.48 E-value=38 Score=26.21 Aligned_cols=29 Identities=21% Similarity=0.360 Sum_probs=25.3
Q ss_pred HHHHHHhCCCCHHHHHHHHHHHhhcccee
Q 045217 104 LKVASSALGYGPQMAMQLAERLYTQGFIS 132 (224)
Q Consensus 104 q~~a~~~~g~sa~~tl~iaQ~LYE~glIT 132 (224)
+.+.++++|+|+..+.+-.++|=+.|+|.
T Consensus 25 ~~eia~~lglS~~~v~~Ri~~L~~~GiI~ 53 (154)
T COG1522 25 NAELAERVGLSPSTVLRRIKRLEEEGVIK 53 (154)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCCcee
Confidence 34667889999999999999999998773
No 110
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=39.83 E-value=44 Score=24.27 Aligned_cols=27 Identities=22% Similarity=0.380 Sum_probs=24.4
Q ss_pred HHHHhCCCCHHHHHHHHHHHhhcccee
Q 045217 106 VASSALGYGPQMAMQLAERLYTQGFIS 132 (224)
Q Consensus 106 ~a~~~~g~sa~~tl~iaQ~LYE~glIT 132 (224)
+.++.+|+|+..+....+.|-+.|+|.
T Consensus 22 ~la~~l~~s~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 22 ELAKKVGLSPSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred HHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence 456778999999999999999999998
No 111
>PF05848 CtsR: Firmicute transcriptional repressor of class III stress genes (CtsR); InterPro: IPR008463 This family consists of several Firmicute transcriptional repressor of class III stress gene (CtsR) proteins. CtsR of Listeria monocytogenes negatively regulates the clpC, clpP and clpE genes belonging to the CtsR regulon [].; PDB: 3H0D_A.
Probab=39.51 E-value=37 Score=27.43 Aligned_cols=31 Identities=29% Similarity=0.485 Sum_probs=21.7
Q ss_pred HHHHHHHHhCC--CCHHHHHHHHHHHhhcccee
Q 045217 102 NLLKVASSALG--YGPQMAMQLAERLYTQGFIS 132 (224)
Q Consensus 102 ~Lq~~a~~~~g--~sa~~tl~iaQ~LYE~glIT 132 (224)
+++....+..| +|.+++..+.+.|+|.|+||
T Consensus 80 ~~~~~l~~~ig~~is~~~a~~ii~~L~e~~~it 112 (152)
T PF05848_consen 80 DLLDHLIESIGDSISQQDAEDIIQRLLEEGLIT 112 (152)
T ss_dssp HHHHHHHCCS-S---HHHHHHHHHHHHHTTSS-
T ss_pred HHHHHHHHHhcCcCCHHHHHHHHHHHHHCCCCC
Confidence 44555555554 89999999999999999997
No 112
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=38.83 E-value=46 Score=22.54 Aligned_cols=26 Identities=23% Similarity=0.530 Sum_probs=21.4
Q ss_pred HHHhCCCCHHHHHHHHHHHhhcccee
Q 045217 107 ASSALGYGPQMAMQLAERLYTQGFIS 132 (224)
Q Consensus 107 a~~~~g~sa~~tl~iaQ~LYE~glIT 132 (224)
.++.||+|++.+......|-.+|+|-
T Consensus 20 La~~~~~s~~~ve~mL~~l~~kG~I~ 45 (69)
T PF09012_consen 20 LAREFGISPEAVEAMLEQLIRKGYIR 45 (69)
T ss_dssp HHHHTT--HHHHHHHHHHHHCCTSCE
T ss_pred HHHHHCcCHHHHHHHHHHHHHCCcEE
Confidence 36889999999999999999999885
No 113
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=38.77 E-value=40 Score=22.93 Aligned_cols=26 Identities=8% Similarity=0.074 Sum_probs=17.5
Q ss_pred CCCCHHHHHHHHHHHHHHHHhcCcCc
Q 045217 196 DMLGKDAWRLYSYVCQHFLGTVSPDC 221 (224)
Q Consensus 196 ~~L~~~e~~iY~lI~~r~la~f~~~a 221 (224)
..|++.|+.|++.|....-..-+||.
T Consensus 2 ~~LT~rQ~~vL~~I~~~~~~~G~~Pt 27 (65)
T PF01726_consen 2 KELTERQKEVLEFIREYIEENGYPPT 27 (65)
T ss_dssp ----HHHHHHHHHHHHHHHHHSS---
T ss_pred CCCCHHHHHHHHHHHHHHHHcCCCCC
Confidence 46899999999999998888777764
No 114
>PF10141 ssDNA-exonuc_C: Single-strand DNA-specific exonuclease, C terminal domain; InterPro: IPR018779 This entry represents a domain found at the C terminus of a set of single-stranded DNA-specific exonucleases, including RecJ. Its function has not, as yet, been determined.
Probab=38.46 E-value=59 Score=26.90 Aligned_cols=37 Identities=16% Similarity=0.371 Sum_probs=31.9
Q ss_pred cccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceec
Q 045217 97 GLNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISY 133 (224)
Q Consensus 97 p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITY 133 (224)
++++..-....++.+||++....-+.|=..|-|+||.
T Consensus 112 ~~~l~~~~~~La~~l~i~~~~l~fml~VF~EL~FVti 148 (195)
T PF10141_consen 112 NFDLKEQLQALAKYLGISPDTLKFMLKVFFELGFVTI 148 (195)
T ss_pred CCCHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCcEEE
Confidence 4777766677789999999999999999999999884
No 115
>smart00843 Ftsk_gamma This domain directs oriented DNA translocation and forms a winged helix structure. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding.
Probab=38.03 E-value=40 Score=23.06 Aligned_cols=34 Identities=24% Similarity=0.293 Sum_probs=27.4
Q ss_pred cHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceeccCC
Q 045217 99 NTVNLLKVASSALGYGPQMAMQLAERLYTQGFISYPRT 136 (224)
Q Consensus 99 ~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRT 136 (224)
++|-||+ +|++.-.++-.++..|-+.|+|+=+..
T Consensus 21 S~S~lQR----~~~IGynrAariid~lE~~GiV~p~~g 54 (63)
T smart00843 21 STSLLQR----RLRIGYNRAARLIDQLEEEGIVGPANG 54 (63)
T ss_pred ChHHHHH----HHhcchhHHHHHHHHHHHCcCCCCCCC
Confidence 6778876 567788888999999999999985543
No 116
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=37.95 E-value=49 Score=26.74 Aligned_cols=35 Identities=20% Similarity=0.200 Sum_probs=29.9
Q ss_pred HHHHHHHhCCCCHHHHHHHHHHHhhccceeccCCC
Q 045217 103 LLKVASSALGYGPQMAMQLAERLYTQGFISYPRTE 137 (224)
Q Consensus 103 Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRTd 137 (224)
-|++.+..+|+|+..+-.+..+|-+.|+|+..|-.
T Consensus 170 t~~~lA~~lG~tr~tvsR~l~~l~~~gii~~~~~~ 204 (211)
T PRK11753 170 TRQEIGRIVGCSREMVGRVLKMLEDQGLISAHGKT 204 (211)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHCCCEEecCCE
Confidence 35666788999999999999999999999987643
No 117
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=37.85 E-value=36 Score=25.07 Aligned_cols=30 Identities=17% Similarity=0.284 Sum_probs=22.8
Q ss_pred HHHHhCCCCHHHHHHHHHHHhhc-cceeccCCCCcc
Q 045217 106 VASSALGYGPQMAMQLAERLYTQ-GFISYPRTESTA 140 (224)
Q Consensus 106 ~a~~~~g~sa~~tl~iaQ~LYE~-glITYPRTds~~ 140 (224)
++++.+|+|+...- .||+ |+|.-+|++..|
T Consensus 6 eva~~~gvs~~tlR-----~ye~~Gll~~~r~~~g~ 36 (102)
T cd04789 6 ELAEKAGISRSTLL-----YYEKLGLITGTRNANGY 36 (102)
T ss_pred HHHHHHCcCHHHHH-----HHHHCCCCCCCcCCCCC
Confidence 55788999986543 6875 999878988654
No 118
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=37.84 E-value=47 Score=27.50 Aligned_cols=33 Identities=15% Similarity=0.174 Sum_probs=29.3
Q ss_pred HHHHHHhCCCCHHHHHHHHHHHhhccceeccCC
Q 045217 104 LKVASSALGYGPQMAMQLAERLYTQGFISYPRT 136 (224)
Q Consensus 104 q~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRT 136 (224)
|++.+..+|.|...+-.+.++|-++|+|.+.|-
T Consensus 187 ~~~iA~~lG~sr~tvsR~l~~l~~~g~I~~~~~ 219 (235)
T PRK11161 187 RGDIGNYLGLTVETISRLLGRFQKSGMLAVKGK 219 (235)
T ss_pred HHHHHHHhCCcHHHHHHHHHHHHHCCCEEecCC
Confidence 556678899999999999999999999998774
No 119
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=36.51 E-value=38 Score=25.86 Aligned_cols=31 Identities=26% Similarity=0.449 Sum_probs=23.4
Q ss_pred HHHHHhCCCCHHHHHHHHHHHhhc-ccee-ccCCCCcc
Q 045217 105 KVASSALGYGPQMAMQLAERLYTQ-GFIS-YPRTESTA 140 (224)
Q Consensus 105 ~~a~~~~g~sa~~tl~iaQ~LYE~-glIT-YPRTds~~ 140 (224)
.+.++.+|+|+.. + .-||+ |+|. -.|+++.|
T Consensus 4 ~e~a~~~gvs~~t-l----R~Ye~~GLl~~~~r~~~gy 36 (126)
T cd04783 4 GELAKAAGVNVET-I----RYYQRRGLLPEPPRPEGGY 36 (126)
T ss_pred HHHHHHHCcCHHH-H----HHHHHCCCCCCCCcCCCCC
Confidence 3567899999984 3 77886 9998 56877655
No 120
>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=36.49 E-value=48 Score=24.65 Aligned_cols=30 Identities=10% Similarity=0.083 Sum_probs=25.8
Q ss_pred HHHHHHhCCCCHHHHHHHHHHHhhccceec
Q 045217 104 LKVASSALGYGPQMAMQLAERLYTQGFISY 133 (224)
Q Consensus 104 q~~a~~~~g~sa~~tl~iaQ~LYE~glITY 133 (224)
+.+.++.+|++...+-.++.+|-++|||+=
T Consensus 45 ~~ela~~~~~~~~tvs~~l~~Le~~GlI~r 74 (118)
T TIGR02337 45 FTQLANQACILRPSLTGILARLERDGLVTR 74 (118)
T ss_pred HHHHHHHhCCCchhHHHHHHHHHHCCCEEe
Confidence 346678899999999999999999999974
No 121
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=36.34 E-value=41 Score=24.75 Aligned_cols=30 Identities=23% Similarity=0.347 Sum_probs=23.0
Q ss_pred HHHHhCCCCHHHHHHHHHHHhhc-cceeccCCCCcc
Q 045217 106 VASSALGYGPQMAMQLAERLYTQ-GFISYPRTESTA 140 (224)
Q Consensus 106 ~a~~~~g~sa~~tl~iaQ~LYE~-glITYPRTds~~ 140 (224)
++++.+|+|++.. .-||+ |+|.-.|++..|
T Consensus 6 eva~~~gvs~~tL-----R~ye~~Gll~~~r~~~g~ 36 (102)
T cd04775 6 QMSRKFGVSRSTL-----LYYESIGLIPSARSEANY 36 (102)
T ss_pred HHHHHHCcCHHHH-----HHHHHCCCCCCCCCCCCC
Confidence 5578889998765 67885 999767887754
No 122
>COG5204 SPT4 Transcription elongation factor SPT4 [Transcription]
Probab=35.92 E-value=30 Score=25.82 Aligned_cols=20 Identities=45% Similarity=0.599 Sum_probs=16.6
Q ss_pred HHHHHHhhccceeccCCCCc
Q 045217 120 QLAERLYTQGFISYPRTEST 139 (224)
Q Consensus 120 ~iaQ~LYE~glITYPRTds~ 139 (224)
+..+.|-.+|.|-||||.|.
T Consensus 91 dvve~L~~~g~~Y~pR~gs~ 110 (112)
T COG5204 91 DVVEDLEQHGRIYYPRTGSF 110 (112)
T ss_pred HHHHHHHHhCccccCCCCcc
Confidence 45677777899999999986
No 123
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=35.56 E-value=56 Score=25.45 Aligned_cols=45 Identities=9% Similarity=0.149 Sum_probs=35.6
Q ss_pred cccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceeccCCCCccc
Q 045217 97 GLNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISYPRTESTAY 141 (224)
Q Consensus 97 p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRTds~~l 141 (224)
|-+-.++-....+...||..-+.-+..+|+.+|+||--|-.-.|+
T Consensus 20 ~~t~~eI~~~l~~~~ews~sTV~TLl~RL~KKg~l~~~kdgr~~~ 64 (123)
T COG3682 20 PATVREIIEELPADREWSYSTVKTLLNRLVKKGLLTRKKDGRAFR 64 (123)
T ss_pred CccHHHHHHHHhhcccccHHHHHHHHHHHHhccchhhhhcCCeee
Confidence 344556666667778999999999999999999999777665554
No 124
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=34.96 E-value=55 Score=25.28 Aligned_cols=29 Identities=14% Similarity=0.217 Sum_probs=25.8
Q ss_pred HHHHHHhCCCCHHHHHHHHHHHhhcccee
Q 045217 104 LKVASSALGYGPQMAMQLAERLYTQGFIS 132 (224)
Q Consensus 104 q~~a~~~~g~sa~~tl~iaQ~LYE~glIT 132 (224)
|.+.++.+|+++.-+-.++..|-++|||.
T Consensus 57 ~~eLa~~l~i~~~tvsr~l~~Le~~GlI~ 85 (144)
T PRK11512 57 PVELKKVLSVDLGALTRMLDRLVCKGWVE 85 (144)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 44567888999999999999999999997
No 125
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=33.48 E-value=70 Score=22.21 Aligned_cols=31 Identities=23% Similarity=0.382 Sum_probs=25.9
Q ss_pred HHHHhCCCCHHHHHHHHHHHhhccceeccCC
Q 045217 106 VASSALGYGPQMAMQLAERLYTQGFISYPRT 136 (224)
Q Consensus 106 ~a~~~~g~sa~~tl~iaQ~LYE~glITYPRT 136 (224)
+....+++|...+..+..+|=+.|+|+..+.
T Consensus 29 ~la~~~~~s~~~i~~~l~~L~~~g~v~~~~~ 59 (101)
T smart00347 29 ELAKRLGVSPSTVTRVLDRLEKKGLIRRLPS 59 (101)
T ss_pred HHHHHHCCCchhHHHHHHHHHHCCCeEecCC
Confidence 4456679999999999999999999986544
No 126
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=33.30 E-value=2.3e+02 Score=29.95 Aligned_cols=116 Identities=16% Similarity=0.283 Sum_probs=69.8
Q ss_pred ccccCcchhH---------HHHHHHHHHHHHHcCcCcceEEEEEEEEecCeEEEEEEe-----cc--ccCCHHHHHHHHH
Q 045217 9 ILIYGPCQTP---------TLGFCVQRYLQITSFKPEKFWTLHPYLVQNGYELKLEWE-----RQ--KLFDFDVATMFQK 72 (224)
Q Consensus 9 ~lS~GRVQTP---------tL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~-----~~--~~~~~~~a~~~~~ 72 (224)
.+..|.+|.| +..||-+|..+-+ -+|.......+.+..++......-. .+ .+.. -....
T Consensus 990 ~i~~G~i~~~~~Lt~~HlrvYdLIFrRFmASQ-m~pa~v~~~~~~i~~~~~~~~~e~~ve~~~~G~~~vy~----~~~~p 1064 (1187)
T COG1110 990 LIEEGVIQLPIRLTKNHLRVYDLIFRRFMASQ-MRPAKVLKEKAEVKADGKDVELEALVEILEDGFALVYP----TRVLP 1064 (1187)
T ss_pred HHHcCCeeccchhhHHHHHHHHHHHHHHHHhh-CCceeEEEEEEEEecCcceeeeeehhhhhccchhhhcc----ccccC
Confidence 4788999999 6889999977654 4677776667777655433222100 00 0111 01111
Q ss_pred HHccCCceEEEEEeeecccccCCCcccHHHHHHHHHHhCCCC-HHHHHHHHHHHhhccceec
Q 045217 73 LVMQDRILEVIDISEKQESKVRPCGLNTVNLLKVASSALGYG-PQMAMQLAERLYTQGFISY 133 (224)
Q Consensus 73 ~~~~~~~~~V~~v~~k~~~~~pP~p~~l~~Lq~~a~~~~g~s-a~~tl~iaQ~LYE~glITY 133 (224)
.+..+ ...|+.++.... +--.||+-+++-+.|-.+ |+. |..=-+|.|.|.+.||+=.
T Consensus 1065 ~l~~g-~l~v~~~~~~~~--~kv~lytqg~vi~~MKer-GIGRPSTYAkive~L~~RgYvie 1122 (1187)
T COG1110 1065 ELEKG-TLKVTEVEIRKV--SKVYLYTQGEVVEEMKER-GIGRPSTYAKIVETLLRRGYVIE 1122 (1187)
T ss_pred ccCCC-ceeeeeeEEEEc--ccccccccchHHHHHHhc-CCCCCcHHHHHHHHHhcCCeEEE
Confidence 22222 355544444433 334569999999998554 775 4566689999999999843
No 127
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=33.09 E-value=73 Score=22.45 Aligned_cols=29 Identities=14% Similarity=0.262 Sum_probs=23.4
Q ss_pred HHhCCCCHHHHHHHHHHHhhccceeccCC
Q 045217 108 SSALGYGPQMAMQLAERLYTQGFISYPRT 136 (224)
Q Consensus 108 ~~~~g~sa~~tl~iaQ~LYE~glITYPRT 136 (224)
.+.+|+|....-...+.|-+.|||++-+.
T Consensus 21 ~~~l~lt~g~Ls~hL~~Le~~GyV~~~k~ 49 (80)
T PF13601_consen 21 KEELGLTDGNLSKHLKKLEEAGYVEVEKE 49 (80)
T ss_dssp HHHTT--HHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHhCcCHHHHHHHHHHHHHCCCEEEEEe
Confidence 45689999999999999999999998654
No 128
>TIGR03882 cyclo_dehyd_2 bacteriocin biosynthesis cyclodehydratase domain. This model describes a ThiF-like domain of a fusion protein found in clusters associated with the production of TOMMs (thiazole/oxazole-modified microcins), small bacteriocins with characteristic heterocycle modifications. This domain is presumed to act as a cyclodehydratase, as do members of the SagC family modeled by TIGR03603.
Probab=33.06 E-value=69 Score=26.50 Aligned_cols=34 Identities=9% Similarity=0.224 Sum_probs=29.1
Q ss_pred ccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceec
Q 045217 98 LNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISY 133 (224)
Q Consensus 98 ~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITY 133 (224)
.++.++...+.. ++++.++.++...|.++|+|+.
T Consensus 43 rt~~eI~~~l~~--~~p~~~v~~~L~~L~~~G~l~~ 76 (193)
T TIGR03882 43 RTLDEIIAALAG--RFPAEEVLYALDRLERRGYLVE 76 (193)
T ss_pred CCHHHHHHHhhc--cCCHHHHHHHHHHHHHCCCEec
Confidence 467788777766 5789999999999999999995
No 129
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=33.00 E-value=60 Score=27.68 Aligned_cols=31 Identities=16% Similarity=0.282 Sum_probs=27.0
Q ss_pred HHHHHHhCCCCHHHHHHHHHHHhhccceecc
Q 045217 104 LKVASSALGYGPQMAMQLAERLYTQGFISYP 134 (224)
Q Consensus 104 q~~a~~~~g~sa~~tl~iaQ~LYE~glITYP 134 (224)
|++.++.+|+|++.+-.++++|=++|||+.-
T Consensus 24 ~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~ 54 (217)
T PRK14165 24 SSEFANHTGTSSKTAARILKQLEDEGYITRT 54 (217)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence 4566788899999999999999999999863
No 130
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=32.35 E-value=51 Score=24.88 Aligned_cols=35 Identities=26% Similarity=0.506 Sum_probs=24.1
Q ss_pred HHHHHhCCCCHHHHHHHHHHHhhc-ccee-ccCCCCcc--cCCC
Q 045217 105 KVASSALGYGPQMAMQLAERLYTQ-GFIS-YPRTESTA--YPSS 144 (224)
Q Consensus 105 ~~a~~~~g~sa~~tl~iaQ~LYE~-glIT-YPRTds~~--l~~~ 144 (224)
.++++.+|+|+. |+ .-||+ |+|. -.|+++.| ++++
T Consensus 4 ~eva~~~gvs~~-tL----RyYe~~GLl~p~~r~~~gyR~Y~~~ 42 (123)
T cd04770 4 GELAKAAGVSPD-TI----RYYERIGLLPPPQRSENGYRLYGEA 42 (123)
T ss_pred HHHHHHHCcCHH-HH----HHHHHCCCCCCCCCCCCCCccCCHH
Confidence 356789999987 44 34885 9998 45777654 5543
No 131
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=32.29 E-value=66 Score=22.96 Aligned_cols=27 Identities=15% Similarity=0.164 Sum_probs=22.9
Q ss_pred HHHHhCCCCHHHHHHHHHHHhhcccee
Q 045217 106 VASSALGYGPQMAMQLAERLYTQGFIS 132 (224)
Q Consensus 106 ~a~~~~g~sa~~tl~iaQ~LYE~glIT 132 (224)
+.+..+|+|-.-+.+.+|+|-+.|+==
T Consensus 24 ~La~~LgiSRtaVwK~Iq~Lr~~G~~I 50 (79)
T COG1654 24 KLAEELGISRTAVWKHIQQLREEGVDI 50 (79)
T ss_pred HHHHHHCccHHHHHHHHHHHHHhCCce
Confidence 346789999999999999999988643
No 132
>PF00610 DEP: Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP); InterPro: IPR000591 This entry represents the DEP (Dishevelled, Egl-10 and Pleckstrin) domain, a globular domain of about 80 residues that is found in over 50 proteins involved in G-protein signalling pathways. It was named after the three proteins it was initially found in: Dishevelled (Dsh and Dvl), which play a key role in the transduction of the Wg/Wnt signal from the cell surface to the nucleus; it is a segment polarity protein required to establish coherent arrays of polarized cells and segments in embryos, and plays a role in wingless signalling. Egl-10, which regulates G-protein signalling in the central nervous system. Pleckstrin, the major substrate of protein kinase C in platelets; Pleckstrin contains two PH domains flanking the DEP domain. Mammalian regulators of G-protein signalling also contain these domains, and regulate signal transduction by increasing the GTPase activity of G-protein alpha subunits, thereby driving them into their inactive GDP-bound form. It has been proposed that the DEP domain could play a selective role in targeting DEP domain-containing proteins to specific subcellular membranous sites, perhaps even to specific G protein-coupled signaling pathways [, ]. Nuclear magnetic resonance spectroscopy has revealed that the DEP domain comprises a three-helix bundle, a beta-hairpin 'arm' composed of two beta-strands and two short beta-strands in the C-terminal region [].; GO: 0035556 intracellular signal transduction; PDB: 1UHW_A 1V3F_A 2YSR_A 2CSO_A 1W4M_A 2PBI_C 1O7F_A 2BYV_E 1FSH_A 3ML6_D ....
Probab=31.90 E-value=55 Score=22.16 Aligned_cols=41 Identities=20% Similarity=0.242 Sum_probs=29.2
Q ss_pred ccHHHHHHHHHH---hCCCCHHHHHHHHHHHhhccceeccCCCC
Q 045217 98 LNTVNLLKVASS---ALGYGPQMAMQLAERLYTQGFISYPRTES 138 (224)
Q Consensus 98 ~~l~~Lq~~a~~---~~g~sa~~tl~iaQ~LYE~glITYPRTds 138 (224)
|+=.++-.-.-+ .+..+..++..++|.|-+.|+|..--.+.
T Consensus 18 F~G~e~v~WL~~~~~~~~~~r~eA~~l~q~Ll~~g~i~~v~~~~ 61 (74)
T PF00610_consen 18 FTGSEAVDWLMDNFEGFVRDREEAVQLGQELLDHGFIEHVSDKS 61 (74)
T ss_dssp EEHHHHHHHHHHTSCTSTSSHHHHHHHHHHHHHCTSEEESSSSS
T ss_pred eEhHHHHHHHHHhccccccCHHHHHHHHHHHHHCCCEEECCCCC
Confidence 444444333333 34689999999999999999998765555
No 133
>PF13309 HTH_22: HTH domain
Probab=31.62 E-value=48 Score=22.42 Aligned_cols=20 Identities=15% Similarity=0.399 Sum_probs=17.6
Q ss_pred CCHHHHHHHHHHHhhcccee
Q 045217 113 YGPQMAMQLAERLYTQGFIS 132 (224)
Q Consensus 113 ~sa~~tl~iaQ~LYE~glIT 132 (224)
++.++-+++.+.||++|+--
T Consensus 21 l~~~~k~~iV~~L~~~G~F~ 40 (64)
T PF13309_consen 21 LSKEEKKEIVRQLYEKGIFL 40 (64)
T ss_pred CCHHHHHHHHHHHHHCCCcc
Confidence 78899999999999998754
No 134
>COG2975 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.60 E-value=46 Score=22.58 Aligned_cols=22 Identities=27% Similarity=0.572 Sum_probs=17.6
Q ss_pred HHHHHHHHHHhhccceeccCCCCccc
Q 045217 116 QMAMQLAERLYTQGFISYPRTESTAY 141 (224)
Q Consensus 116 ~~tl~iaQ~LYE~glITYPRTds~~l 141 (224)
..+.+||..||+ .||-.|-+++
T Consensus 4 tD~~~Iae~Lyd----~~pdvDPktv 25 (64)
T COG2975 4 TDSQEIAEALYD----AYPDVDPKTV 25 (64)
T ss_pred chHHHHHHHHHh----cCCCCCccee
Confidence 367899999999 6888886654
No 135
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=31.19 E-value=69 Score=25.19 Aligned_cols=34 Identities=15% Similarity=0.231 Sum_probs=27.8
Q ss_pred HHHHhCCCCHHHHHHHHHHHhhcccee-c-cCCCCc
Q 045217 106 VASSALGYGPQMAMQLAERLYTQGFIS-Y-PRTEST 139 (224)
Q Consensus 106 ~a~~~~g~sa~~tl~iaQ~LYE~glIT-Y-PRTds~ 139 (224)
+.++.+|+|+..+..=.++|-+.|.|. | .-.|..
T Consensus 28 eiA~~lglS~~tV~~Ri~rL~~~GvI~~~~~~v~~~ 63 (153)
T PRK11179 28 ELAKQFGVSPGTIHVRVEKMKQAGIITGTRVDVNPK 63 (153)
T ss_pred HHHHHHCcCHHHHHHHHHHHHHCCCeeeEEEEECHH
Confidence 457889999999999999999999997 4 344433
No 136
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=30.51 E-value=68 Score=21.76 Aligned_cols=28 Identities=11% Similarity=0.011 Sum_probs=20.0
Q ss_pred HHHHhCCCCHHHHHHHHHHHhhccceec
Q 045217 106 VASSALGYGPQMAMQLAERLYTQGFISY 133 (224)
Q Consensus 106 ~a~~~~g~sa~~tl~iaQ~LYE~glITY 133 (224)
...+.|..+........+.|-|++||.-
T Consensus 35 ~l~~~f~~~~~~ik~~Ie~LIekeyi~R 62 (68)
T PF10557_consen 35 ELKKRFPPSVSDIKKRIESLIEKEYIER 62 (68)
T ss_dssp HTTTTS---HHHHHHHHHHHHHTTSEEE
T ss_pred HhcCCcCCCHHHHHHHHHHHHHhhhhhc
Confidence 3344667788889999999999999973
No 137
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=30.27 E-value=83 Score=26.99 Aligned_cols=44 Identities=20% Similarity=0.331 Sum_probs=35.5
Q ss_pred CCcccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceeccCCCCcccC
Q 045217 95 PCGLNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISYPRTESTAYP 142 (224)
Q Consensus 95 P~p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRTds~~l~ 142 (224)
|.+.++++| ++++|++...+-.+++.|-+.||+.+-..|.+|..
T Consensus 17 ~~~l~l~el----a~~~glpksT~~RlL~tL~~~G~v~~d~~~g~Y~L 60 (246)
T COG1414 17 PGGLSLAEL----AERLGLPKSTVHRLLQTLVELGYVEQDPEDGRYRL 60 (246)
T ss_pred CCCCCHHHH----HHHhCcCHHHHHHHHHHHHHCCCEEEcCCCCcEee
Confidence 444556655 57789999999999999999999999887766644
No 138
>PRK02079 pyrroloquinoline quinone biosynthesis protein PqqD; Provisional
Probab=30.22 E-value=1.1e+02 Score=22.24 Aligned_cols=49 Identities=10% Similarity=0.120 Sum_probs=31.7
Q ss_pred HHHHHHHHHHccCCceEEEEEeeecccccCCCcccHHHHHHHHHHhC-CC--CHHHHHHHHHHHhhccceec
Q 045217 65 DVATMFQKLVMQDRILEVIDISEKQESKVRPCGLNTVNLLKVASSAL-GY--GPQMAMQLAERLYTQGFISY 133 (224)
Q Consensus 65 ~~a~~~~~~~~~~~~~~V~~v~~k~~~~~pP~p~~l~~Lq~~a~~~~-g~--sa~~tl~iaQ~LYE~glITY 133 (224)
+.|..+.+.|.+.+ |..++-......| .- =.+++....+.|.++|+|.|
T Consensus 36 etg~~Iw~~~DG~~--------------------tv~eIi~~L~~~y~~~~~~~~DV~~fl~~L~~~g~i~~ 87 (88)
T PRK02079 36 ESAGEILGLIDGKR--------------------TVAAIIAELQQQFPDVPGLDEDVLEFLEVARAKHWIEL 87 (88)
T ss_pred hHHHHHHHHccCCC--------------------CHHHHHHHHHHHccchhhHHHHHHHHHHHHHHCcCEEe
Confidence 45667777776532 2334444445555 22 14778889999999999986
No 139
>cd04371 DEP DEP domain, named after Dishevelled, Egl-10, and Pleckstrin, where this domain was first discovered. The function of this domain is still not clear, but it is believed to be important for the membrane association of the signaling proteins in which it is present. New studies show that the DEP domain of Sst2, a yeast RGS protein is necessary and sufficient for receptor interaction.
Probab=30.14 E-value=1.6e+02 Score=19.94 Aligned_cols=46 Identities=20% Similarity=0.219 Sum_probs=35.7
Q ss_pred cccCCCcccHHHHHHHHHHhCC-CCHHHHHHHHHHHhhccceeccCC
Q 045217 91 SKVRPCGLNTVNLLKVASSALG-YGPQMAMQLAERLYTQGFISYPRT 136 (224)
Q Consensus 91 ~~~pP~p~~l~~Lq~~a~~~~g-~sa~~tl~iaQ~LYE~glITYPRT 136 (224)
....+.=|+-+++-.-...... .+..++..++|.|-+.|+|..---
T Consensus 22 ~~~~~~~F~G~e~v~WL~~~~~~~~r~ea~~~~~~ll~~g~i~~v~~ 68 (81)
T cd04371 22 LKTYPNCFTGSELVDWLLDNLEAITREEAVELGQALLKHGLIHHVSD 68 (81)
T ss_pred CEECCceeEcHHHHHHHHHhCCCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence 4455567887777766666555 799999999999999999986543
No 140
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=30.02 E-value=76 Score=23.03 Aligned_cols=29 Identities=14% Similarity=0.094 Sum_probs=25.2
Q ss_pred HHHHHHhCCCCHHHHHHHHHHHhhcccee
Q 045217 104 LKVASSALGYGPQMAMQLAERLYTQGFIS 132 (224)
Q Consensus 104 q~~a~~~~g~sa~~tl~iaQ~LYE~glIT 132 (224)
|++.+...|+|...+-.+..+|=++|+|.
T Consensus 50 ~~eLa~~~g~sr~tVsr~L~~Le~~GlI~ 78 (95)
T TIGR01610 50 ATVIAELTGLSRTHVSDAIKSLARRRIIF 78 (95)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence 44556788999999999999999999996
No 141
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=29.70 E-value=72 Score=24.51 Aligned_cols=32 Identities=19% Similarity=0.233 Sum_probs=27.7
Q ss_pred HHHHHHhCCCCHHHHHHHHHHHhhccceeccC
Q 045217 104 LKVASSALGYGPQMAMQLAERLYTQGFISYPR 135 (224)
Q Consensus 104 q~~a~~~~g~sa~~tl~iaQ~LYE~glITYPR 135 (224)
|.+.++.+|+++.-+-.++.+|-++|||+=-+
T Consensus 49 ~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~ 80 (144)
T PRK03573 49 QIQLAKAIGIEQPSLVRTLDQLEEKGLISRQT 80 (144)
T ss_pred HHHHHHHhCCChhhHHHHHHHHHHCCCEeeec
Confidence 55778889999999999999999999998543
No 142
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=29.08 E-value=60 Score=27.68 Aligned_cols=28 Identities=18% Similarity=0.240 Sum_probs=25.4
Q ss_pred HHHHhCCCCHHHHHHHHHHHhhccceec
Q 045217 106 VASSALGYGPQMAMQLAERLYTQGFISY 133 (224)
Q Consensus 106 ~a~~~~g~sa~~tl~iaQ~LYE~glITY 133 (224)
+.|+.+|+|++-++++.+-|=+.|+|+-
T Consensus 33 EiS~~lgvsqkAVl~HL~~LE~AGlveS 60 (217)
T COG1777 33 EISRELGVSQKAVLKHLRILERAGLVES 60 (217)
T ss_pred HHHhhcCcCHHHHHHHHHHHHHcCCchh
Confidence 4588899999999999999999999975
No 143
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=28.64 E-value=76 Score=27.74 Aligned_cols=29 Identities=24% Similarity=0.289 Sum_probs=27.3
Q ss_pred HHHHHHhCCCCHHHHHHHHHHHhhcccee
Q 045217 104 LKVASSALGYGPQMAMQLAERLYTQGFIS 132 (224)
Q Consensus 104 q~~a~~~~g~sa~~tl~iaQ~LYE~glIT 132 (224)
|++-++++|+|++-+-+..-+|-..|||-
T Consensus 28 q~eIA~~lgiT~QaVsehiK~Lv~eG~i~ 56 (260)
T COG1497 28 QKEIAKKLGITLQAVSEHIKELVKEGLIE 56 (260)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHhcccee
Confidence 78889999999999999999999999994
No 144
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=28.36 E-value=79 Score=25.22 Aligned_cols=28 Identities=32% Similarity=0.483 Sum_probs=25.4
Q ss_pred HHHHHhCCCCHHHHHHHHHHHhhcccee
Q 045217 105 KVASSALGYGPQMAMQLAERLYTQGFIS 132 (224)
Q Consensus 105 ~~a~~~~g~sa~~tl~iaQ~LYE~glIT 132 (224)
.+.++..|+|+.-+..=.++|-+.|.|.
T Consensus 32 ~eiA~~lglS~~tv~~Ri~rL~~~GvI~ 59 (164)
T PRK11169 32 VELSKRVGLSPTPCLERVRRLERQGFIQ 59 (164)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence 3567889999999999999999999997
No 145
>PF14268 YoaP: YoaP-like
Probab=28.35 E-value=29 Score=22.03 Aligned_cols=22 Identities=23% Similarity=0.545 Sum_probs=17.5
Q ss_pred eEEEEEeeecccccCCCcccHH
Q 045217 80 LEVIDISEKQESKVRPCGLNTV 101 (224)
Q Consensus 80 ~~V~~v~~k~~~~~pP~p~~l~ 101 (224)
+.+..++..++-++.|.||++=
T Consensus 2 ~~~i~i~t~e~Aq~~P~pft~y 23 (44)
T PF14268_consen 2 FKLIKIDTLEKAQNAPCPFTTY 23 (44)
T ss_pred cEEEEeccHHHHhcCCCceeEE
Confidence 4567788888889999998753
No 146
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=27.98 E-value=21 Score=22.69 Aligned_cols=34 Identities=15% Similarity=0.227 Sum_probs=20.2
Q ss_pred cHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceec
Q 045217 99 NTVNLLKVASSALGYGPQMAMQLAERLYTQGFISY 133 (224)
Q Consensus 99 ~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITY 133 (224)
+-.+|...+ +.||+.+-=+.+...++||++|.-+
T Consensus 7 Sd~eL~~~L-~~~G~~~gPIt~sTR~vy~kkL~~~ 40 (44)
T smart00540 7 SDAELRAEL-KQYGLPPGPITDTTRKLYEKKLRKL 40 (44)
T ss_pred CHHHHHHHH-HHcCCCCCCcCcchHHHHHHHHHHH
Confidence 334555554 4567766666666667777665443
No 147
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=27.94 E-value=60 Score=27.48 Aligned_cols=30 Identities=23% Similarity=0.307 Sum_probs=25.9
Q ss_pred HHHHhCCCCHHHHHHHHHHHhhccceeccC
Q 045217 106 VASSALGYGPQMAMQLAERLYTQGFISYPR 135 (224)
Q Consensus 106 ~a~~~~g~sa~~tl~iaQ~LYE~glITYPR 135 (224)
+.++++|.|++.+....+.|=+.|+|+=-+
T Consensus 24 ela~~l~~S~qta~R~l~~le~~~~I~R~~ 53 (214)
T COG1339 24 ELAKRLGVSSQTAARKLKELEDEGYITRTI 53 (214)
T ss_pred HHHHHhCcCcHHHHHHHHhhccCCcEEEEe
Confidence 446789999999999999999999998433
No 148
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=27.25 E-value=81 Score=26.97 Aligned_cols=29 Identities=17% Similarity=0.318 Sum_probs=25.5
Q ss_pred HHHHhCCCCHHHHHHHHHHHhhccceecc
Q 045217 106 VASSALGYGPQMAMQLAERLYTQGFISYP 134 (224)
Q Consensus 106 ~a~~~~g~sa~~tl~iaQ~LYE~glITYP 134 (224)
++++++|+|+..+..+.|.|=+.|++..-
T Consensus 30 elA~~Lgis~~avR~HL~~Le~~Glv~~~ 58 (218)
T COG2345 30 ELAEELGISPMAVRRHLDDLEAEGLVEVE 58 (218)
T ss_pred HHHHHhCCCHHHHHHHHHHHHhCcceeee
Confidence 45788999999999999999999998643
No 149
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=26.84 E-value=72 Score=23.71 Aligned_cols=28 Identities=21% Similarity=0.406 Sum_probs=21.5
Q ss_pred HHHHhCCCCHHHHHHHHHHHhhc-cceeccCCCC
Q 045217 106 VASSALGYGPQMAMQLAERLYTQ-GFISYPRTES 138 (224)
Q Consensus 106 ~a~~~~g~sa~~tl~iaQ~LYE~-glITYPRTds 138 (224)
++++..|+|+... ..||+ |+|.-||.+.
T Consensus 5 eva~~~gvs~~tL-----RyYE~~GLl~p~~~~~ 33 (124)
T COG0789 5 EVAKLTGVSVRTL-----RFYERKGLLSPERRDE 33 (124)
T ss_pred HHHHHhCCCHHHH-----HHHHHcCCCCCcccCC
Confidence 5677889998654 46885 9999997774
No 150
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=26.82 E-value=89 Score=25.91 Aligned_cols=32 Identities=13% Similarity=0.262 Sum_probs=29.2
Q ss_pred HHHHHHhCCCCHHHHHHHHHHHhhccceeccC
Q 045217 104 LKVASSALGYGPQMAMQLAERLYTQGFISYPR 135 (224)
Q Consensus 104 q~~a~~~~g~sa~~tl~iaQ~LYE~glITYPR 135 (224)
|.+.+..+|.|...+-.+..+|-+.|+|...+
T Consensus 172 ~~~lA~~lG~sretvsR~L~~L~~~G~I~~~~ 203 (226)
T PRK10402 172 HTQAAEYLGVSYRHLLYVLAQFIQDGYLKKSK 203 (226)
T ss_pred HHHHHHHHCCcHHHHHHHHHHHHHCCCEEeeC
Confidence 67778899999999999999999999999865
No 151
>cd01388 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and transcription factor-like proteins, TCF-1, -3, -4, and LEF-1. They appear to bind the minor groove of the A/T C A A A G/C-motif.
Probab=26.71 E-value=92 Score=21.08 Aligned_cols=28 Identities=18% Similarity=0.243 Sum_probs=24.1
Q ss_pred CCCCHHHHHHHHHHHHHHHHhc---CcCccc
Q 045217 196 DMLGKDAWRLYSYVCQHFLGTV---SPDCKY 223 (224)
Q Consensus 196 ~~L~~~e~~iY~lI~~r~la~f---~~~a~y 223 (224)
..|+++|+..|.-.+++-...+ +|++.|
T Consensus 41 k~ls~~eK~~y~~~a~~~k~~y~~~~p~y~y 71 (72)
T cd01388 41 KALSNEEKQPYYEEAKKLKELHMKLYPDYKW 71 (72)
T ss_pred HcCCHHHHHHHHHHHHHHHHHHHHHCcCCCC
Confidence 5799999999999999888876 777776
No 152
>PF13447 Multi-haem_cyto: Seven times multi-haem cytochrome CxxCH; PDB: 1FGJ_B.
Probab=26.53 E-value=69 Score=28.17 Aligned_cols=30 Identities=20% Similarity=0.236 Sum_probs=21.1
Q ss_pred HHHHHHHHHHhCCCCHHHHHHHHHHHhhccceec
Q 045217 100 TVNLLKVASSALGYGPQMAMQLAERLYTQGFISY 133 (224)
Q Consensus 100 l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITY 133 (224)
+.....+++++ .+++.+|+..||++||++=
T Consensus 232 ~D~~v~~~n~~----~~eA~~iv~~L~~~GLL~~ 261 (267)
T PF13447_consen 232 MDKGVKEYNKK----YKEAKKIVEDLYKDGLLDP 261 (267)
T ss_dssp HHHHHHHHHHH----HHHHHHHHHHHHHCT-STT
T ss_pred HHHHHHHHHHH----HHHHHHHHHHHHHcCCCCC
Confidence 34444455555 4789999999999999863
No 153
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 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. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=26.47 E-value=1.1e+02 Score=20.55 Aligned_cols=31 Identities=13% Similarity=0.252 Sum_probs=23.1
Q ss_pred HHHHHHHHHHhCCCCHHHHHHHHHHHhhccceecc
Q 045217 100 TVNLLKVASSALGYGPQMAMQLAERLYTQGFISYP 134 (224)
Q Consensus 100 l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYP 134 (224)
+.+|. +.-|++++++....=.|..+++++|-
T Consensus 30 l~~i~----~~t~l~~~~Vk~~L~~LiQh~~v~y~ 60 (62)
T PF08221_consen 30 LREIV----RRTGLSPKQVKKALVVLIQHNLVQYF 60 (62)
T ss_dssp HHHHH----HHHT--HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHH----HHhCCCHHHHHHHHHHHHHcCCeeee
Confidence 45554 34469999999999999999999983
No 154
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=26.27 E-value=1.1e+02 Score=19.46 Aligned_cols=27 Identities=15% Similarity=0.272 Sum_probs=23.0
Q ss_pred HHHhCCCCHHHHHHHHHHHhhccceec
Q 045217 107 ASSALGYGPQMAMQLAERLYTQGFISY 133 (224)
Q Consensus 107 a~~~~g~sa~~tl~iaQ~LYE~glITY 133 (224)
..+.+|++...+-.++..|-+.|+|..
T Consensus 26 i~~~~~i~~~~i~~~l~~L~~~g~i~~ 52 (78)
T cd00090 26 LAERLGLSQSTVSRHLKKLEEAGLVES 52 (78)
T ss_pred HHHHHCcCHhHHHHHHHHHHHCCCeEE
Confidence 456779999999999999999999975
No 155
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=26.06 E-value=90 Score=22.38 Aligned_cols=33 Identities=27% Similarity=0.361 Sum_probs=27.9
Q ss_pred HHHHHhCCCCHHHHHHHHHHHhhccceeccCCC
Q 045217 105 KVASSALGYGPQMAMQLAERLYTQGFISYPRTE 137 (224)
Q Consensus 105 ~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRTd 137 (224)
.+.++.++++..-+-.+..+|-++|||.--|..
T Consensus 40 ~~la~~l~i~~~~vt~~l~~Le~~glv~r~~~~ 72 (126)
T COG1846 40 KELAERLGLDRSTVTRLLKRLEDKGLIERLRDP 72 (126)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCc
Confidence 566788999999999999999999999755443
No 156
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=26.03 E-value=1.1e+02 Score=25.99 Aligned_cols=40 Identities=15% Similarity=0.204 Sum_probs=31.6
Q ss_pred CcccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceeccCCCCccc
Q 045217 96 CGLNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISYPRTESTAY 141 (224)
Q Consensus 96 ~p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRTds~~l 141 (224)
.|.++++| ++.+|++...+..+++.|=+.||+.. .+..|-
T Consensus 23 ~~~~l~ei----a~~lglpksT~~RlL~tL~~~G~l~~--~~~~Y~ 62 (248)
T TIGR02431 23 PRLTLTDV----AEATGLTRAAARRFLLTLVELGYVTS--DGRLFW 62 (248)
T ss_pred CCCCHHHH----HHHHCcCHHHHHHHHHHHHHCCCEEe--CCCEEE
Confidence 35777766 66789999999999999999999984 344443
No 157
>PRK11569 transcriptional repressor IclR; Provisional
Probab=25.64 E-value=1.2e+02 Score=26.26 Aligned_cols=34 Identities=18% Similarity=0.286 Sum_probs=29.3
Q ss_pred CcccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceec
Q 045217 96 CGLNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISY 133 (224)
Q Consensus 96 ~p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITY 133 (224)
.|.++++| ++.+|++...+..+++.|-+.||+..
T Consensus 42 ~~~~lsei----a~~lglpksTv~RlL~tL~~~G~l~~ 75 (274)
T PRK11569 42 GSVALTEL----AQQAGLPNSTTHRLLTTMQQQGFVRQ 75 (274)
T ss_pred CCcCHHHH----HHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 34677666 67789999999999999999999986
No 158
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=25.50 E-value=87 Score=27.41 Aligned_cols=30 Identities=23% Similarity=0.313 Sum_probs=27.5
Q ss_pred HHHHHHHhCCCCHHHHHHHHHHHhhcccee
Q 045217 103 LLKVASSALGYGPQMAMQLAERLYTQGFIS 132 (224)
Q Consensus 103 Lq~~a~~~~g~sa~~tl~iaQ~LYE~glIT 132 (224)
.|++..|.+|+|-..+-.+.++|=..|+|-
T Consensus 212 ~Q~eL~r~lglsktTvsR~L~~LEk~GlIe 241 (258)
T COG2512 212 TQAELRRALGLSKTTVSRILRRLEKRGLIE 241 (258)
T ss_pred eHHHHHHhhCCChHHHHHHHHHHHhCCceE
Confidence 388999999999999999999999999984
No 159
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=25.31 E-value=1.2e+02 Score=19.96 Aligned_cols=26 Identities=19% Similarity=0.298 Sum_probs=22.4
Q ss_pred HHHhCCCCHHHHHHHHHHHhhcccee
Q 045217 107 ASSALGYGPQMAMQLAERLYTQGFIS 132 (224)
Q Consensus 107 a~~~~g~sa~~tl~iaQ~LYE~glIT 132 (224)
.++.||.|..-+.++...|=+.|+|+
T Consensus 30 la~~~~vsr~tvr~al~~L~~~g~i~ 55 (64)
T PF00392_consen 30 LAERYGVSRTTVREALRRLEAEGLIE 55 (64)
T ss_dssp HHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHhccCCcHHHHHHHHHHHCCcEE
Confidence 36789999999999999999999995
No 160
>PF04282 DUF438: Family of unknown function (DUF438); InterPro: IPR007380 This is a a group of uncharacterised proteins.
Probab=24.56 E-value=1.6e+02 Score=20.57 Aligned_cols=31 Identities=6% Similarity=0.081 Sum_probs=25.0
Q ss_pred cHHHHHHHHHHhCC-CCHHHHHHHHHHHhhcc
Q 045217 99 NTVNLLKVASSALG-YGPQMAMQLAERLYTQG 129 (224)
Q Consensus 99 ~l~~Lq~~a~~~~g-~sa~~tl~iaQ~LYE~g 129 (224)
+..+++++-.+.|+ .||.+.+.+-|.|-+.|
T Consensus 14 ~~e~vk~~F~~~~~~Vs~~EI~~~Eq~Li~eG 45 (71)
T PF04282_consen 14 DPEEVKEEFKKLFSDVSASEISAAEQELIQEG 45 (71)
T ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcC
Confidence 34567777766665 89999999999999887
No 161
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=24.53 E-value=99 Score=23.40 Aligned_cols=33 Identities=9% Similarity=0.258 Sum_probs=28.0
Q ss_pred cccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceec
Q 045217 97 GLNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISY 133 (224)
Q Consensus 97 p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITY 133 (224)
+.+..+| +.++|+|+.-+.++++.|=+.|+|.-
T Consensus 25 ~~s~~ei----a~~l~is~~~v~~~l~~L~~~Gli~~ 57 (130)
T TIGR02944 25 PYSAAEI----AEQTGLNAPTVSKILKQLSLAGIVTS 57 (130)
T ss_pred CccHHHH----HHHHCcCHHHHHHHHHHHHHCCcEEe
Confidence 4566665 67789999999999999999999964
No 162
>PF09105 SelB-wing_1: Elongation factor SelB, winged helix ; InterPro: IPR015189 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 1". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; PDB: 2V9V_A 1LVA_A 2PLY_A.
Probab=24.50 E-value=78 Score=20.66 Aligned_cols=34 Identities=15% Similarity=0.205 Sum_probs=25.9
Q ss_pred HHHHhCCCCHHHHHHHHHHHhhccceeccCCCCc
Q 045217 106 VASSALGYGPQMAMQLAERLYTQGFISYPRTEST 139 (224)
Q Consensus 106 ~a~~~~g~sa~~tl~iaQ~LYE~glITYPRTds~ 139 (224)
+|..+-.+|-++|-++.|++--.|-+|--|.+..
T Consensus 22 eaatraslsleetrkllqsmaaagqvtllrvend 55 (61)
T PF09105_consen 22 EAATRASLSLEETRKLLQSMAAAGQVTLLRVEND 55 (61)
T ss_dssp HHHHHHT--HHHHHHHHHHHHHTTSEEEEEETTE
T ss_pred HHHHHhhccHHHHHHHHHHHHhcCceEEEEeccc
Confidence 3445568999999999999999999998887654
No 163
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=24.12 E-value=1e+02 Score=25.48 Aligned_cols=30 Identities=10% Similarity=0.258 Sum_probs=25.8
Q ss_pred HHHHHHhCCCCHHHHHHHHHHHhhccceec
Q 045217 104 LKVASSALGYGPQMAMQLAERLYTQGFISY 133 (224)
Q Consensus 104 q~~a~~~~g~sa~~tl~iaQ~LYE~glITY 133 (224)
|++.++.++++...+-.++++|-++|||+=
T Consensus 62 q~eLa~~l~l~~sTvtr~l~rLE~kGlI~R 91 (185)
T PRK13777 62 ISEIAKFGVMHVSTAFNFSKKLEERGYLTF 91 (185)
T ss_pred HHHHHHHHCCCHhhHHHHHHHHHHCCCEEe
Confidence 556677889998888899999999999984
No 164
>smart00049 DEP Domain found in Dishevelled, Egl-10, and Pleckstrin. Domain of unknown function present in signalling proteins that contain PH, rasGEF, rhoGEF, rhoGAP, RGS, PDZ domains. DEP domain in Drosophila dishevelled is essential to rescue planar polarity defects and induce JNK signalling (Cell 94, 109-118).
Probab=23.83 E-value=2.4e+02 Score=19.05 Aligned_cols=47 Identities=19% Similarity=0.184 Sum_probs=35.7
Q ss_pred ccccCCCcccHHHHHHHHHHhCC-CCHHHHHHHHHHHhhccceeccCC
Q 045217 90 ESKVRPCGLNTVNLLKVASSALG-YGPQMAMQLAERLYTQGFISYPRT 136 (224)
Q Consensus 90 ~~~~pP~p~~l~~Lq~~a~~~~g-~sa~~tl~iaQ~LYE~glITYPRT 136 (224)
..+..|.=|+-.++-.-...... .+..++..++|.|-+.|+|..-..
T Consensus 13 ~~~~~~~~F~G~e~v~wL~~~~~~~~r~eA~~l~~~ll~~g~i~~v~~ 60 (77)
T smart00049 13 FLKTYPNCFTGSELVDWLMDNLEIIDREEAVHLGQLLLDEGLIHHVNG 60 (77)
T ss_pred CCEECcceeEcHHHHHHHHHcCCcCCHHHHHHHHHHHHHCCCEEEeCC
Confidence 33456666777777666655555 589999999999999999998764
No 165
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=23.64 E-value=1.2e+02 Score=26.19 Aligned_cols=42 Identities=12% Similarity=0.023 Sum_probs=33.9
Q ss_pred cccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceeccCCCCcccC
Q 045217 97 GLNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISYPRTESTAYP 142 (224)
Q Consensus 97 p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRTds~~l~ 142 (224)
+.++++| ++.+|++...+..+++.|-+.||+.+...+..|..
T Consensus 40 ~~tl~eI----a~~lglpkStv~RlL~tL~~~G~l~~~~~~~~Y~l 81 (271)
T PRK10163 40 SSSVSDI----SLNLDLPLSTTFRLLKVLQAADFVYQDSQLGWWHI 81 (271)
T ss_pred CcCHHHH----HHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCeEEe
Confidence 4666666 67789999999999999999999988765555543
No 166
>PRK10870 transcriptional repressor MprA; Provisional
Probab=23.41 E-value=1.1e+02 Score=24.74 Aligned_cols=31 Identities=29% Similarity=0.370 Sum_probs=26.1
Q ss_pred HHHHHhCCCCHHHHHHHHHHHhhccceeccC
Q 045217 105 KVASSALGYGPQMAMQLAERLYTQGFISYPR 135 (224)
Q Consensus 105 ~~a~~~~g~sa~~tl~iaQ~LYE~glITYPR 135 (224)
.+.++.+|++...+-.++.+|-++|||.=-+
T Consensus 75 ~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~ 105 (176)
T PRK10870 75 SELSCALGSSRTNATRIADELEKRGWIERRE 105 (176)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 3557788999999999999999999998543
No 167
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=23.19 E-value=2e+02 Score=21.00 Aligned_cols=39 Identities=10% Similarity=0.046 Sum_probs=32.2
Q ss_pred CCcccHHHHHHHHHHh-CCCCHHHHHHHHHHHhhccceec
Q 045217 95 PCGLNTVNLLKVASSA-LGYGPQMAMQLAERLYTQGFISY 133 (224)
Q Consensus 95 P~p~~l~~Lq~~a~~~-~g~sa~~tl~iaQ~LYE~glITY 133 (224)
+.|++-.++...+.+. .++|..-+-.+.+.|-|.|+|.=
T Consensus 14 ~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~ 53 (116)
T cd07153 14 DGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVRE 53 (116)
T ss_pred CCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEE
Confidence 5678999998887665 36899999999999999999863
No 168
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=23.15 E-value=1.6e+02 Score=20.60 Aligned_cols=29 Identities=10% Similarity=0.179 Sum_probs=24.0
Q ss_pred cHHHHHHHHHHhCCCCHHHHHHHHHHHhh
Q 045217 99 NTVNLLKVASSALGYGPQMAMQLAERLYT 127 (224)
Q Consensus 99 ~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE 127 (224)
|..+|-...+.+.|++.+++..+.+.|.+
T Consensus 2 tk~eli~~ia~~~~~~~~~v~~vl~~l~~ 30 (90)
T smart00411 2 TKSELIDAIAEKAGLSKKDAKAAVDAFLE 30 (90)
T ss_pred CHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 56777778888889999999888888876
No 169
>COG1706 FlgI Flagellar basal-body P-ring protein [Cell motility and secretion]
Probab=23.11 E-value=1.2e+02 Score=27.79 Aligned_cols=33 Identities=24% Similarity=0.401 Sum_probs=26.4
Q ss_pred cHHHHHHHHHHhCCCCHHHHHHHHHHHhhcccee
Q 045217 99 NTVNLLKVASSALGYGPQMAMQLAERLYTQGFIS 132 (224)
Q Consensus 99 ~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glIT 132 (224)
+|..|=+.. +.+|-+|++-+.|.|.|++.|.+.
T Consensus 327 ~l~~lV~aL-n~iGa~P~diiaILQalk~AGal~ 359 (365)
T COG1706 327 TLNNLVRAL-NAIGATPQDIIAILQALKSAGALQ 359 (365)
T ss_pred cHHHHHHHH-HHhcCCHHHHHHHHHHHHHcCccc
Confidence 455565555 567999999999999999988764
No 170
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=22.87 E-value=1.6e+02 Score=26.59 Aligned_cols=36 Identities=22% Similarity=0.273 Sum_probs=33.1
Q ss_pred hCCCCHHHHHHHHHHHhhccceeccCCCCcccCCCc
Q 045217 110 ALGYGPQMAMQLAERLYTQGFISYPRTESTAYPSSF 145 (224)
Q Consensus 110 ~~g~sa~~tl~iaQ~LYE~glITYPRTds~~l~~~~ 145 (224)
.+|+|+.-.-+-...|=+.|++.=|.|-+.++|.+.
T Consensus 36 ~l~~S~aTIR~dm~~Le~~G~l~~~h~sagrIPT~k 71 (339)
T PRK00082 36 GLGVSSATIRNDMADLEELGLLEKPHTSSGRIPTDK 71 (339)
T ss_pred CCCCChHHHHHHHHHHHhCCCcCCCcCCCCCCcCHH
Confidence 489999999999999988999999999999999864
No 171
>PRK12789 flgI flagellar basal body P-ring protein; Reviewed
Probab=22.73 E-value=1.9e+02 Score=26.76 Aligned_cols=32 Identities=16% Similarity=0.335 Sum_probs=26.0
Q ss_pred cHHHHHHHHHHhCCCCHHHHHHHHHHHhhccce
Q 045217 99 NTVNLLKVASSALGYGPQMAMQLAERLYTQGFI 131 (224)
Q Consensus 99 ~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glI 131 (224)
++.+|=... +.+|.+|.+.+.|.|.|.+.|.+
T Consensus 329 tl~~lV~aL-N~lG~tp~DlIsILqalk~aGAL 360 (367)
T PRK12789 329 DLQTLVRGL-NQIGLKPSDIIAILQAIKTAGAL 360 (367)
T ss_pred CHHHHHHHH-HHcCCChHHHHHHHHHHHhcCcc
Confidence 666665554 56899999999999999998765
No 172
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=22.70 E-value=1.3e+02 Score=25.58 Aligned_cols=41 Identities=10% Similarity=0.167 Sum_probs=32.5
Q ss_pred cccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceeccCCCCccc
Q 045217 97 GLNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISYPRTESTAY 141 (224)
Q Consensus 97 p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRTds~~l 141 (224)
|.++++| ++.+|++...+..+++.|-+.||+.+...+..|.
T Consensus 28 ~l~l~ei----a~~lgl~kstv~Rll~tL~~~G~l~~~~~~~~Y~ 68 (257)
T PRK15090 28 EIGITEL----SQRVMMSKSTVYRFLQTMKTLGYVAQEGESEKYS 68 (257)
T ss_pred CCCHHHH----HHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCcEE
Confidence 4677665 6677999999999999999999999864444443
No 173
>PRK11050 manganese transport regulator MntR; Provisional
Probab=21.99 E-value=1.5e+02 Score=23.40 Aligned_cols=40 Identities=13% Similarity=0.180 Sum_probs=30.7
Q ss_pred HHHHHHhCCCCHHHHHHHHHHHhhccceeccCCCCcccCC
Q 045217 104 LKVASSALGYGPQMAMQLAERLYTQGFISYPRTESTAYPS 143 (224)
Q Consensus 104 q~~a~~~~g~sa~~tl~iaQ~LYE~glITYPRTds~~l~~ 143 (224)
+.+.++.+|+|+.-+-.+.+.|-+.|+|..-+...-++++
T Consensus 54 ~~eLA~~l~is~stVsr~l~~Le~~GlI~r~~~~~v~LT~ 93 (152)
T PRK11050 54 QVDIAARLGVSQPTVAKMLKRLARDGLVEMRPYRGVFLTP 93 (152)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCceEECc
Confidence 3466888999999999999999999999864333334444
No 174
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=21.59 E-value=99 Score=22.71 Aligned_cols=29 Identities=14% Similarity=0.242 Sum_probs=21.4
Q ss_pred HHHHHhCCCCHHHHHHHHHHHhhc-cceeccCCCCc
Q 045217 105 KVASSALGYGPQMAMQLAERLYTQ-GFISYPRTEST 139 (224)
Q Consensus 105 ~~a~~~~g~sa~~tl~iaQ~LYE~-glITYPRTds~ 139 (224)
.+.++++|+|++ |+ .-||+ |||. ||+++.
T Consensus 4 ge~a~~~gvs~~-tl----RyYe~~GLl~-p~~~~g 33 (107)
T cd04777 4 GKFAKKNNITID-TV----RHYIDLGLLI-PEKKGG 33 (107)
T ss_pred HHHHHHHCcCHH-HH----HHHHHCCCcC-CccCCC
Confidence 356788999987 44 45885 9997 887664
No 175
>PF13518 HTH_28: Helix-turn-helix domain
Probab=21.45 E-value=1.5e+02 Score=18.15 Aligned_cols=25 Identities=12% Similarity=0.234 Sum_probs=17.7
Q ss_pred HHHHHhCCCCHHHHHHHHHHHhhcc
Q 045217 105 KVASSALGYGPQMAMQLAERLYTQG 129 (224)
Q Consensus 105 ~~a~~~~g~sa~~tl~iaQ~LYE~g 129 (224)
.++++.||+|...+-...+..-+.|
T Consensus 16 ~~~a~~~gis~~tv~~w~~~y~~~G 40 (52)
T PF13518_consen 16 REIAREFGISRSTVYRWIKRYREGG 40 (52)
T ss_pred HHHHHHHCCCHhHHHHHHHHHHhcC
Confidence 4577899998877766666655545
No 176
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=21.38 E-value=1.3e+02 Score=24.84 Aligned_cols=28 Identities=32% Similarity=0.480 Sum_probs=24.6
Q ss_pred HHHHhCCCCHHHHHHHHHHHhhccceec
Q 045217 106 VASSALGYGPQMAMQLAERLYTQGFISY 133 (224)
Q Consensus 106 ~a~~~~g~sa~~tl~iaQ~LYE~glITY 133 (224)
+..+.+|+|+.-+..+++.|-++|+|..
T Consensus 20 eLA~~lgis~~tV~~~L~~Le~~GlV~r 47 (203)
T TIGR02702 20 ALAEALAISPQAVRRHLKDLETEGLIEY 47 (203)
T ss_pred HHHHHHCcCHHHHHHHHHHHHHCCCeEE
Confidence 3456789999999999999999999975
No 177
>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []. They may be involved in plasmid replication and stabilisation functions.
Probab=21.19 E-value=1.5e+02 Score=24.47 Aligned_cols=27 Identities=22% Similarity=0.224 Sum_probs=23.5
Q ss_pred HHHhCCCCHHHHHHHHHHHhhccceec
Q 045217 107 ASSALGYGPQMAMQLAERLYTQGFISY 133 (224)
Q Consensus 107 a~~~~g~sa~~tl~iaQ~LYE~glITY 133 (224)
|.+..|+|....-.+.-.|.|.|||.+
T Consensus 77 a~r~~G~s~~tlrR~l~~LveaGLI~r 103 (177)
T PF03428_consen 77 AERLNGMSERTLRRHLARLVEAGLIVR 103 (177)
T ss_pred HHHHcCCCHHHHHHHHHHHHHCCCeee
Confidence 334449999999999999999999997
No 178
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=21.10 E-value=2.1e+02 Score=19.74 Aligned_cols=34 Identities=26% Similarity=0.440 Sum_probs=28.2
Q ss_pred cccHHHHHHHHHHhCCCCHHHHHHHHHHHhhccceecc
Q 045217 97 GLNTVNLLKVASSALGYGPQMAMQLAERLYTQGFISYP 134 (224)
Q Consensus 97 p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glITYP 134 (224)
+.+.++| ++.+|++...+-.+.+.|-+.|+|..-
T Consensus 20 ~~t~~~i----a~~l~i~~~tv~r~l~~L~~~g~l~~~ 53 (91)
T smart00346 20 GLTLAEL----AERLGLSKSTAHRLLNTLQELGYVEQD 53 (91)
T ss_pred CcCHHHH----HHHhCCCHHHHHHHHHHHHHCCCeeec
Confidence 5777766 455699999999999999999999753
No 179
>PF10711 DUF2513: Hypothetical protein (DUF2513); InterPro: IPR019650 The function of this family is not known.
Probab=21.07 E-value=1.2e+02 Score=22.21 Aligned_cols=29 Identities=17% Similarity=0.125 Sum_probs=24.2
Q ss_pred HHHHhCCCCHHHHHHHHHHHhhccceecc
Q 045217 106 VASSALGYGPQMAMQLAERLYTQGFISYP 134 (224)
Q Consensus 106 ~a~~~~g~sa~~tl~iaQ~LYE~glITYP 134 (224)
.....-|++.++..-+.+.|.|.|||.-.
T Consensus 25 ~~~~~~~y~~~~i~YHl~lL~eagli~~~ 53 (102)
T PF10711_consen 25 EEDEIDGYSKEEIAYHLKLLDEAGLIEGS 53 (102)
T ss_pred chhcccCCCHHHHHHHHHHHHHCCCeeec
Confidence 34456689999999999999999999654
No 180
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=20.87 E-value=1.7e+02 Score=20.54 Aligned_cols=27 Identities=19% Similarity=0.254 Sum_probs=23.6
Q ss_pred HHHHhCCCCHHHHHHHHHHHhhcccee
Q 045217 106 VASSALGYGPQMAMQLAERLYTQGFIS 132 (224)
Q Consensus 106 ~a~~~~g~sa~~tl~iaQ~LYE~glIT 132 (224)
+...+.|++-.+.+-..-.|++.|+|+
T Consensus 23 eL~ekTgi~k~~LlV~LsrL~k~GiI~ 49 (72)
T PF05584_consen 23 ELEEKTGISKNTLLVYLSRLAKRGIIE 49 (72)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCee
Confidence 345678999999999999999999996
No 181
>cd04441 DEP_2_DEP6 DEP (Dishevelled, Egl-10, and Pleckstrin) domain 2 found in DEP6-like proteins. DEP6 proteins contain two DEP and a PDZ domain. Their function is unknown.
Probab=20.69 E-value=97 Score=22.41 Aligned_cols=40 Identities=18% Similarity=0.125 Sum_probs=29.4
Q ss_pred CCCcccHHHHHHHHHHhCC-CCHHHHHHHHHHHhhccceec
Q 045217 94 RPCGLNTVNLLKVASSALG-YGPQMAMQLAERLYTQGFISY 133 (224)
Q Consensus 94 pP~p~~l~~Lq~~a~~~~g-~sa~~tl~iaQ~LYE~glITY 133 (224)
=|.=|.=++|-.=.-.... -|-.++..++|.|-++|+|-=
T Consensus 29 y~~cF~GsElVdWL~~~~~~~sR~eAv~lgq~Ll~~gii~H 69 (85)
T cd04441 29 YERTFVGSEFIDWLLQEGEAESRREAVQLCRRLLEHGIIQH 69 (85)
T ss_pred cCCEeEchHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCEEe
Confidence 4445777777655444433 388999999999999999963
No 182
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=20.65 E-value=1.4e+02 Score=24.37 Aligned_cols=31 Identities=23% Similarity=0.390 Sum_probs=26.3
Q ss_pred HHHHHHhCCCC-HHHHHHHHHHHhhccceecc
Q 045217 104 LKVASSALGYG-PQMAMQLAERLYTQGFISYP 134 (224)
Q Consensus 104 q~~a~~~~g~s-a~~tl~iaQ~LYE~glITYP 134 (224)
+++.++.+|++ +.-+-...+.|=++|+|..-
T Consensus 28 ~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~ 59 (199)
T TIGR00498 28 IREIARAVGLRSPSAAEEHLKALERKGYIERD 59 (199)
T ss_pred HHHHHHHhCCCChHHHHHHHHHHHHCCCEecC
Confidence 44557889998 88899999999999999963
No 183
>cd01389 MATA_HMG-box MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include the fungal mating type gene products MC, MATA1 and Ste11.
Probab=20.49 E-value=1.5e+02 Score=20.30 Aligned_cols=28 Identities=18% Similarity=0.186 Sum_probs=22.6
Q ss_pred CCCCHHHHHHHHHHHHHHHHhc---CcCccc
Q 045217 196 DMLGKDAWRLYSYVCQHFLGTV---SPDCKY 223 (224)
Q Consensus 196 ~~L~~~e~~iY~lI~~r~la~f---~~~a~y 223 (224)
..|+++|+..|...+..-...+ +|+|.|
T Consensus 41 k~ls~eeK~~y~~~A~~~k~~~~~~~p~Yky 71 (77)
T cd01389 41 RSESPEVKAYYKELAEEEKERHAREYPDYKY 71 (77)
T ss_pred hhCCHHHHHHHHHHHHHHHHHHHHHCCCCcc
Confidence 6799999999998888776655 677766
No 184
>cd04448 DEP_PIKfyve DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in fungal RhoGEF (GDP/GTP exchange factor) PIKfyve-like proteins. PIKfyve contains N-terminal Fyve finger and DEP domains, a central chaperonin-like domain and a C-terminal PIPK (phosphatidylinositol phosphate kinase) domain. PIKfyve-like proteins are important phosphatidylinositol (3)-monophosphate (PtdIns(3)P)-5-kinases, producing PtdIns(3,5)P2, which plays a major role in multivesicular body (MVB) sorting and control of retrograde traffic from the vacuole back to the endosome and/or Golgi. PIKfyve itself has been shown to be play a role in regulating early-endosome-to-trans-Golgi network (TGN) retrograde trafficking.
Probab=20.49 E-value=99 Score=21.94 Aligned_cols=40 Identities=13% Similarity=0.083 Sum_probs=28.4
Q ss_pred cCCCcccHHHHHHHHHHhC-CCCHHHHHHHHHHHhhcccee
Q 045217 93 VRPCGLNTVNLLKVASSAL-GYGPQMAMQLAERLYTQGFIS 132 (224)
Q Consensus 93 ~pP~p~~l~~Lq~~a~~~~-g~sa~~tl~iaQ~LYE~glIT 132 (224)
.=|.=|.=++|-.=.-..- -.|-.++..++|.|-++|+|.
T Consensus 24 ~y~~cF~GselVdWL~~~~~~~~R~eAv~~gq~Ll~~g~i~ 64 (81)
T cd04448 24 TYTNCILGKELVNWLIRQGKAATRVQAIAIGQALLDAGWIE 64 (81)
T ss_pred EcCcccChHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCEE
Confidence 3444576666655443332 368889999999999999996
No 185
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=20.16 E-value=1.5e+02 Score=23.14 Aligned_cols=32 Identities=16% Similarity=0.239 Sum_probs=26.7
Q ss_pred cccHHHHHHHHHHhCCCCHHHHHHHHHHHhhcccee
Q 045217 97 GLNTVNLLKVASSALGYGPQMAMQLAERLYTQGFIS 132 (224)
Q Consensus 97 p~~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYE~glIT 132 (224)
|.+..+| +..++.|-.-+-...|+|-+.|+|-
T Consensus 42 ~~tvdel----ae~lnr~rStv~rsl~~L~~~GlV~ 73 (126)
T COG3355 42 PLTVDEL----AEILNRSRSTVYRSLQNLLEAGLVE 73 (126)
T ss_pred CcCHHHH----HHHHCccHHHHHHHHHHHHHcCCee
Confidence 4677776 5567889999999999999999985
No 186
>PF03368 Dicer_dimer: Dicer dimerisation domain; InterPro: IPR005034 This domain is found in members of the Dicer protein family of dsRNA nucleases. This entry represents a dsRNA-binding domain. RNA interference (RNAi) is an ancient gene-silencing process that plays a fundamental role in diverse eukaryotic functions including viral defence, chromatin remodelling, genome rearrangement, developmental timing, brain morphogenesis, and stem cell maintenance. All RNAi pathways require the multidomain ribonuclease Dicer, which initiates RNAi by cleaving double-stranded RNA (dsRNA) substrates into small fragments ~25 nuleotides in length. A typical eukaryotic Dicer consists of a helicase domain (PDOC51192 from PROSITEDOC), a domain of unknown function, and a PAZ domain (PDOC50821 from PROSITEDOC) at the amino (N)-terminus as well as two ribonuclease III domains (PDOC00448 from PROSITEDOC) and a dsRNA-binding domain (dsRBD) (PDOC50137 from PROSITEDOC) at the carboxy (C)-terminus. The domain of unknown function of ~100 amino acids is predicted to adopt the canonical alpha-beta-beta-beta-alpha-fold found in all dsRBDs [, , , ].; GO: 0016891 endoribonuclease activity, producing 5'-phosphomonoesters; PDB: 2KOU_A.
Probab=20.12 E-value=63 Score=23.29 Aligned_cols=17 Identities=18% Similarity=0.255 Sum_probs=12.6
Q ss_pred HHHHHHHHHhhccceec
Q 045217 117 MAMQLAERLYTQGFISY 133 (224)
Q Consensus 117 ~tl~iaQ~LYE~glITY 133 (224)
-++++++.||+.|+|+.
T Consensus 63 AAf~Ac~~L~~~g~ldd 79 (90)
T PF03368_consen 63 AAFEACKKLHEAGELDD 79 (90)
T ss_dssp HHHHHHHHHHHH-S-TT
T ss_pred HHHHHHHHHHHcCCCcc
Confidence 46899999999999863
Done!