Query gi|254780620|ref|YP_003065033.1| iron-responsive transcriptional regulator [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 144
No_of_seqs 108 out of 2328
Neff 7.2
Searched_HMMs 39220
Date Sun May 29 21:11:06 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780620.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK11920 rirA iron-responsive 100.0 3E-42 0 270.5 15.7 143 1-143 1-143 (153)
2 PRK10857 DNA-binding transcrip 100.0 2.6E-41 0 265.0 14.9 137 1-139 1-138 (164)
3 TIGR00738 rrf2_super rrf2 fami 100.0 2.2E-41 0 265.4 13.0 130 1-132 1-133 (133)
4 PRK11014 transcriptional repre 100.0 1.8E-40 4.2E-45 260.1 15.1 139 1-143 1-140 (141)
5 COG1959 Predicted transcriptio 100.0 1.2E-38 3E-43 249.3 15.7 133 1-134 1-134 (150)
6 TIGR02010 IscR iron-sulfur clu 100.0 3.6E-38 9.3E-43 246.4 11.0 135 1-135 1-139 (140)
7 TIGR02944 suf_reg_Xantho FeS a 100.0 1.6E-32 4E-37 213.2 8.2 129 1-130 2-130 (130)
8 pfam02082 Rrf2 Transcriptional 99.9 3.9E-25 9.9E-30 169.5 8.7 81 2-82 1-82 (82)
9 PRK04214 rbn ribonuclease BN/u 98.7 2.1E-07 5.4E-12 64.8 10.3 113 8-132 291-405 (411)
10 COG2524 Predicted transcriptio 98.6 8.3E-08 2.1E-12 67.2 6.3 68 2-69 3-70 (294)
11 pfam03444 DUF293 Domain of unk 98.6 1E-07 2.6E-12 66.7 6.7 65 3-67 2-66 (79)
12 PRK11886 biotin--protein ligas 97.7 0.00026 6.7E-09 46.5 8.2 72 6-81 2-74 (319)
13 cd00090 HTH_ARSR Arsenical Res 97.2 0.0017 4.3E-08 41.8 7.2 56 10-68 9-65 (78)
14 smart00418 HTH_ARSR helix_turn 97.1 0.0014 3.4E-08 42.3 6.1 54 13-69 2-56 (66)
15 smart00346 HTH_ICLR helix_turn 97.1 0.0026 6.6E-08 40.7 7.3 60 7-68 4-63 (91)
16 COG3355 Predicted transcriptio 97.1 0.0023 6E-08 40.9 6.6 60 15-74 32-97 (126)
17 PRK10163 DNA-binding transcrip 97.0 0.004 1E-07 39.5 7.3 63 5-69 22-84 (271)
18 PRK09834 DNA-binding transcrip 97.0 0.0045 1.1E-07 39.2 7.4 63 6-70 9-71 (264)
19 COG1725 Predicted transcriptio 96.9 0.0022 5.6E-08 41.1 5.3 59 12-72 19-81 (125)
20 pfam08279 HTH_11 HTH domain. T 96.9 0.0037 9.3E-08 39.8 6.4 51 12-65 4-55 (55)
21 COG1654 BirA Biotin operon rep 96.9 0.006 1.5E-07 38.5 7.4 58 19-78 14-72 (79)
22 PRK11569 transcriptional repre 96.8 0.006 1.5E-07 38.5 7.3 61 6-68 26-86 (274)
23 pfam01978 TrmB Sugar-specific 96.8 0.0038 9.7E-08 39.7 5.9 62 7-71 7-68 (68)
24 COG1321 TroR Mn-dependent tran 96.7 0.0076 1.9E-07 37.9 7.1 75 6-84 8-84 (154)
25 PRK03902 manganese transport t 96.7 0.003 7.6E-08 40.3 5.0 77 4-84 4-82 (142)
26 PRK10141 DNA-binding transcrip 96.6 0.0064 1.6E-07 38.3 6.1 58 11-70 17-75 (106)
27 PRK09464 pdhR transcriptional 96.6 0.0099 2.5E-07 37.2 7.0 48 20-69 29-77 (254)
28 pfam09339 HTH_IclR IclR helix- 96.5 0.0068 1.7E-07 38.2 5.6 48 8-56 3-50 (52)
29 PRK11050 manganese transport r 96.5 0.005 1.3E-07 39.0 4.9 60 12-74 43-102 (155)
30 COG1414 IclR Transcriptional r 96.4 0.017 4.3E-07 35.8 7.1 61 7-69 3-63 (246)
31 PRK09990 DNA-binding transcrip 96.4 0.024 6.2E-07 34.9 7.8 59 10-69 15-75 (251)
32 PRK10421 DNA-binding transcrip 96.2 0.03 7.8E-07 34.3 7.7 65 4-70 4-70 (253)
33 COG2378 Predicted transcriptio 96.0 0.038 9.7E-07 33.8 7.3 69 11-81 11-84 (311)
34 pfam01047 MarR MarR family. Th 95.9 0.028 7.1E-07 34.6 6.2 49 11-61 6-54 (59)
35 smart00347 HTH_MARR helix_turn 95.9 0.065 1.7E-06 32.4 7.9 64 11-76 13-78 (101)
36 COG1378 Predicted transcriptio 95.8 0.02 5.2E-07 35.4 5.2 64 6-72 14-77 (247)
37 PRK12423 LexA repressor; Provi 95.8 0.059 1.5E-06 32.6 7.4 69 3-71 4-73 (202)
38 pfam01022 HTH_5 Bacterial regu 95.7 0.021 5.3E-07 35.3 4.9 43 11-56 5-47 (47)
39 PRK10225 DNA-binding transcrip 95.6 0.041 1.1E-06 33.6 6.2 63 11-74 18-82 (257)
40 PRK11534 DNA-binding transcrip 95.6 0.046 1.2E-06 33.2 6.3 63 19-84 25-90 (224)
41 pfam00392 GntR Bacterial regul 95.6 0.026 6.5E-07 34.8 4.9 42 20-61 19-61 (64)
42 pfam01325 Fe_dep_repress Iron 95.6 0.034 8.6E-07 34.1 5.5 47 11-58 8-54 (58)
43 PRK03837 transcriptional regul 95.5 0.056 1.4E-06 32.8 6.5 46 19-65 32-78 (243)
44 COG2345 Predicted transcriptio 95.5 0.045 1.2E-06 33.3 6.1 53 20-72 21-79 (218)
45 smart00345 HTH_GNTR helix_turn 95.5 0.03 7.6E-07 34.4 4.9 42 20-61 15-57 (60)
46 PRK11523 DNA-binding transcrip 95.4 0.087 2.2E-06 31.6 7.1 52 20-72 27-79 (258)
47 cd07377 WHTH_GntR Winged helix 95.2 0.042 1.1E-06 33.5 5.0 44 20-65 20-64 (66)
48 PRK00215 LexA repressor; Valid 95.1 0.13 3.3E-06 30.6 7.3 69 4-72 3-72 (204)
49 TIGR01884 cas_HTH CRISPR locus 95.1 0.088 2.2E-06 31.6 6.5 62 6-68 167-229 (231)
50 smart00529 HTH_DTXR Helix-turn 95.1 0.032 8.1E-07 34.2 4.1 46 27-74 2-47 (96)
51 pfam01726 LexA_DNA_bind LexA D 95.0 0.13 3.4E-06 30.6 7.1 58 3-60 4-62 (65)
52 TIGR03338 phnR_burk phosphonat 95.0 0.19 5E-06 29.6 7.9 72 11-84 20-94 (212)
53 smart00419 HTH_CRP helix_turn_ 94.9 0.047 1.2E-06 33.2 4.6 36 24-59 8-43 (48)
54 COG1420 HrcA Transcriptional r 94.8 0.098 2.5E-06 31.3 6.0 58 1-58 2-61 (346)
55 COG1802 GntR Transcriptional r 94.7 0.1 2.6E-06 31.2 5.8 66 19-86 34-101 (230)
56 pfam09202 Rio2_N Rio2, N-termi 94.4 0.23 5.8E-06 29.2 7.1 66 6-71 6-71 (82)
57 COG4189 Predicted transcriptio 94.3 0.11 2.9E-06 30.9 5.4 52 11-64 26-79 (308)
58 PRK11753 cAMP-regulatory prote 94.2 0.17 4.2E-06 30.0 6.1 48 12-60 147-203 (211)
59 TIGR03337 phnR transcriptional 94.2 0.11 2.7E-06 31.1 5.0 60 21-82 21-87 (231)
60 COG1497 Predicted transcriptio 94.2 0.18 4.7E-06 29.7 6.1 66 4-72 6-71 (260)
61 PRK10079 putative transcriptio 94.1 0.12 3E-06 30.8 5.0 47 21-68 31-78 (241)
62 PRK09764 DNA-binding transcrip 94.0 0.13 3.2E-06 30.7 5.0 53 21-75 25-78 (239)
63 PRK00082 hrcA heat-inducible t 94.0 0.23 5.8E-06 29.2 6.3 55 3-57 4-60 (339)
64 PRK11402 DNA-binding transcrip 93.9 0.13 3.4E-06 30.5 5.0 45 21-66 31-76 (243)
65 PRK10430 DNA-binding transcrip 93.9 0.23 5.9E-06 29.1 6.2 60 15-76 169-234 (239)
66 PRK10434 srlR DNA-bindng trans 93.8 0.27 6.9E-06 28.7 6.5 59 12-75 9-67 (256)
67 pfam02002 TFIIE_alpha TFIIE al 93.8 0.19 4.8E-06 29.6 5.7 50 10-61 15-64 (105)
68 PRK10710 DNA-binding transcrip 93.6 0.23 6E-06 29.1 5.9 61 10-72 165-238 (240)
69 COG1846 MarR Transcriptional r 93.6 0.25 6.5E-06 28.9 6.0 51 11-63 25-75 (126)
70 COG4465 CodY Pleiotropic trans 93.6 0.12 3E-06 30.9 4.3 63 3-65 180-246 (261)
71 PRK06474 hypothetical protein; 93.6 0.3 7.6E-06 28.5 6.3 64 11-74 14-84 (180)
72 PRK04984 fatty acid metabolism 93.5 0.32 8.1E-06 28.3 6.4 42 20-61 26-68 (239)
73 PRK10336 DNA-binding transcrip 93.4 0.26 6.6E-06 28.8 5.8 55 11-68 155-218 (219)
74 pfam01475 FUR Ferric uptake re 93.3 0.48 1.2E-05 27.3 7.1 60 1-64 4-68 (120)
75 PRK13509 transcriptional repre 93.3 0.35 8.8E-06 28.1 6.3 54 12-69 9-62 (251)
76 COG2512 Predicted membrane-ass 93.1 0.29 7.5E-06 28.5 5.7 58 11-69 198-256 (258)
77 PRK10402 DNA-binding transcrip 93.1 0.52 1.3E-05 27.0 7.0 52 18-73 149-201 (213)
78 PRK10906 DNA-binding transcrip 92.9 0.45 1.1E-05 27.4 6.4 56 12-72 9-64 (252)
79 TIGR02431 pcaR_pcaU beta-ketoa 92.8 0.25 6.3E-06 29.0 5.0 63 10-78 11-73 (252)
80 PRK11414 putative DNA-binding 92.8 0.9 2.3E-05 25.6 9.8 71 10-84 19-94 (221)
81 PRK11161 fumarate/nitrate redu 92.7 0.22 5.6E-06 29.3 4.6 45 24-72 184-228 (235)
82 PRK09954 hypothetical protein; 92.6 0.22 5.7E-06 29.2 4.5 49 21-74 14-62 (362)
83 COG1349 GlpR Transcriptional r 92.5 0.42 1.1E-05 27.6 5.8 55 13-72 10-64 (253)
84 PRK13918 CRP/FNR family transc 92.4 0.25 6.4E-06 28.9 4.6 45 24-72 145-189 (201)
85 TIGR02325 C_P_lyase_phnF phosp 92.4 0.21 5.3E-06 29.4 4.2 46 20-66 27-73 (240)
86 PRK11179 DNA-binding transcrip 92.3 0.5 1.3E-05 27.2 6.0 79 11-93 12-101 (153)
87 cd00383 trans_reg_C Effector d 92.3 0.39 9.9E-06 27.8 5.4 56 9-66 27-95 (95)
88 PRK09213 purine operon repress 92.2 0.69 1.8E-05 26.3 6.7 88 1-90 1-99 (274)
89 PRK03573 transcriptional regul 92.2 0.55 1.4E-05 26.9 6.1 49 12-61 35-83 (144)
90 PRK10701 DNA-binding transcrip 92.1 0.77 2E-05 26.1 6.8 62 6-71 164-238 (240)
91 cd00092 HTH_CRP helix_turn_hel 91.9 0.29 7.3E-06 28.6 4.4 46 12-57 7-58 (67)
92 PRK13626 transcriptional regul 91.9 0.78 2E-05 26.0 6.7 62 22-83 21-86 (551)
93 PRK10161 transcriptional regul 91.8 0.62 1.6E-05 26.6 6.0 56 11-68 160-227 (229)
94 smart00550 Zalpha Z-DNA-bindin 91.8 0.57 1.5E-05 26.8 5.8 51 10-60 8-58 (68)
95 PRK04158 transcriptional repre 91.8 0.29 7.3E-06 28.6 4.3 44 22-65 199-243 (256)
96 PRK10870 transcriptional repre 91.7 0.53 1.3E-05 27.0 5.6 62 13-74 60-123 (176)
97 COG2188 PhnF Transcriptional r 91.5 0.42 1.1E-05 27.6 4.9 62 21-83 27-94 (236)
98 COG1522 Lrp Transcriptional re 91.4 0.94 2.4E-05 25.5 6.6 85 7-93 7-101 (154)
99 smart00862 Trans_reg_C Transcr 91.3 0.93 2.4E-05 25.6 6.5 55 10-66 10-78 (78)
100 PRK11169 leucine-responsive tr 91.3 0.4 1E-05 27.7 4.6 81 11-93 17-108 (164)
101 COG5340 Predicted transcriptio 91.3 0.36 9.3E-06 28.0 4.4 66 12-79 18-87 (269)
102 PRK11639 zinc uptake transcrip 91.2 0.99 2.5E-05 25.4 6.5 55 12-68 30-89 (169)
103 TIGR02404 trehalos_R_Bsub treh 91.2 0.32 8.1E-06 28.3 4.0 59 21-80 20-79 (236)
104 PRK03911 heat-inducible transc 91.2 0.66 1.7E-05 26.4 5.6 52 8-59 5-58 (258)
105 smart00531 TFIIE Transcription 91.1 0.26 6.6E-06 28.8 3.5 34 23-56 14-47 (147)
106 smart00420 HTH_DEOR helix_turn 91.0 0.74 1.9E-05 26.2 5.7 45 13-59 5-49 (53)
107 COG1339 Transcriptional regula 90.9 0.67 1.7E-05 26.4 5.4 75 10-85 5-84 (214)
108 COG1777 Predicted transcriptio 90.8 0.52 1.3E-05 27.0 4.8 42 12-56 19-60 (217)
109 smart00344 HTH_ASNC helix_turn 90.7 0.43 1.1E-05 27.5 4.3 78 11-92 6-94 (108)
110 pfam09182 PuR_N Bacterial puri 90.7 0.77 2E-05 26.1 5.6 59 7-66 3-68 (70)
111 COG2186 FadR Transcriptional r 90.7 0.5 1.3E-05 27.2 4.6 46 21-67 30-76 (241)
112 TIGR02787 codY_Gpos GTP-sensin 90.6 0.16 4.1E-06 30.1 2.0 54 11-64 186-243 (255)
113 PRK11512 DNA-binding transcrip 90.6 0.81 2.1E-05 25.9 5.7 49 13-63 45-93 (144)
114 PRK09391 fixK transcriptional 90.6 0.54 1.4E-05 27.0 4.7 45 13-57 156-206 (224)
115 PRK09468 ompR osmolarity respo 90.6 1.1 2.8E-05 25.1 6.3 62 6-71 164-238 (239)
116 PRK09836 DNA-binding transcrip 90.5 1.1 2.8E-05 25.1 6.3 60 6-69 153-224 (226)
117 CHL00148 orf27 Ycf27; Reviewed 90.5 1 2.6E-05 25.3 6.1 61 6-70 164-239 (240)
118 TIGR02812 fadR_gamma fatty aci 90.5 0.2 5E-06 29.5 2.4 63 21-87 26-93 (275)
119 COG2390 DeoR Transcriptional r 90.5 0.91 2.3E-05 25.6 5.8 34 24-57 26-59 (321)
120 PRK10046 dpiA two-component re 90.4 1.2 3.1E-05 24.8 6.5 42 16-58 170-211 (225)
121 pfam08220 HTH_DeoR DeoR-like h 90.3 0.93 2.4E-05 25.6 5.8 50 13-67 5-54 (57)
122 PRK11832 putative DNA-binding 90.3 0.34 8.7E-06 28.1 3.5 58 11-70 142-204 (207)
123 cd07153 Fur_like Ferric uptake 90.2 1.2 3.2E-05 24.8 6.3 53 14-67 7-66 (116)
124 pfam05732 RepL Firmicute plasm 90.2 0.5 1.3E-05 27.2 4.3 73 11-85 58-141 (165)
125 pfam00486 Trans_reg_C Transcri 90.2 1.2 3.1E-05 24.9 6.2 55 10-66 10-77 (77)
126 pfam07848 PaaX PaaX-like prote 90.1 0.51 1.3E-05 27.1 4.3 49 20-68 16-68 (70)
127 pfam05158 RNA_pol_Rpc34 RNA po 90.1 1.4 3.6E-05 24.5 6.5 62 14-75 87-156 (313)
128 COG1510 Predicted transcriptio 90.1 0.26 6.6E-06 28.8 2.8 55 11-68 31-87 (177)
129 PRK11517 transcriptional regul 90.0 1.3 3.3E-05 24.7 6.2 60 6-69 150-221 (223)
130 PRK09462 fur ferric uptake reg 89.8 1.6 4E-05 24.2 6.6 54 15-68 24-84 (148)
131 TIGR02928 TIGR02928 orc1/cdc6 89.8 1.2 3.2E-05 24.8 6.0 61 3-63 301-376 (383)
132 pfam08222 HTH_CodY CodY helix- 89.8 0.5 1.3E-05 27.1 4.0 45 23-67 2-47 (60)
133 COG4565 CitB Response regulato 89.8 1.3 3.4E-05 24.6 6.2 49 10-58 159-207 (224)
134 pfam09079 Cdc6_C CDC6, C termi 89.4 0.94 2.4E-05 25.5 5.2 62 12-73 2-81 (85)
135 PRK10219 DNA-binding transcrip 89.4 0.93 2.4E-05 25.6 5.1 44 12-55 9-52 (107)
136 PRK06266 transcription initiat 89.3 0.71 1.8E-05 26.2 4.5 53 21-73 33-90 (178)
137 PRK11173 two-component respons 89.1 1.7 4.4E-05 24.0 6.3 60 7-70 164-236 (237)
138 PRK10411 DNA-binding transcrip 88.9 1.2 3.1E-05 24.9 5.5 46 12-59 8-53 (240)
139 PRK11511 DNA-binding transcrip 88.9 0.94 2.4E-05 25.5 4.9 45 11-55 12-56 (127)
140 COG4109 Predicted transcriptio 88.9 1.5 3.9E-05 24.3 5.9 74 12-86 6-84 (432)
141 pfam09940 DUF2172 Domain of un 88.7 1.1 2.9E-05 25.0 5.2 40 39-78 183-224 (384)
142 PRK00411 cdc6 cell division co 88.7 2.2 5.7E-05 23.3 7.8 78 3-85 294-387 (394)
143 PRK10955 DNA-binding transcrip 88.6 1.5 3.7E-05 24.4 5.7 60 6-69 159-231 (232)
144 PRK09802 DNA-binding transcrip 88.5 2.2 5.5E-05 23.4 6.5 59 4-67 13-71 (269)
145 COG0735 Fur Fe2+/Zn2+ uptake r 88.1 2.1 5.2E-05 23.5 6.2 59 11-70 24-89 (145)
146 COG4738 Predicted transcriptio 88.0 0.58 1.5E-05 26.8 3.3 59 13-73 32-97 (124)
147 TIGR02702 SufR_cyano iron-sulf 87.8 0.39 1E-05 27.8 2.4 125 13-139 6-140 (215)
148 COG4533 ABC-type uncharacteriz 87.5 2.6 6.7E-05 22.9 7.7 60 24-83 23-86 (564)
149 PRK11083 DNA-binding response 87.0 2.6 6.6E-05 22.9 6.2 54 12-67 162-228 (229)
150 PRK10572 DNA-binding transcrip 86.9 2 5E-05 23.7 5.5 47 9-55 184-230 (290)
151 TIGR02073 PBP_1c penicillin-bi 86.6 1.5 3.7E-05 24.4 4.7 68 23-90 375-456 (786)
152 PRK13856 two-component respons 86.5 2.5 6.3E-05 23.1 5.9 62 6-71 158-232 (241)
153 COG3327 PaaX Phenylacetic acid 86.3 0.95 2.4E-05 25.5 3.6 54 16-70 18-75 (291)
154 COG4753 Response regulator con 86.2 1.6 4.1E-05 24.1 4.8 69 12-83 376-448 (475)
155 pfam00888 Cullin Cullin family 85.9 3.2 8.3E-05 22.4 6.3 44 11-54 538-581 (605)
156 TIGR01889 Staph_reg_Sar staphy 85.8 2.1 5.3E-05 23.5 5.1 53 6-58 25-80 (112)
157 pfam06971 Put_DNA-bind_N Putat 85.8 1.1 2.8E-05 25.1 3.8 35 11-45 14-48 (49)
158 COG1675 TFA1 Transcription ini 85.8 2.4 6.2E-05 23.1 5.5 38 24-61 32-69 (176)
159 PRK10816 DNA-binding transcrip 85.6 2.3 5.9E-05 23.2 5.3 54 12-67 156-221 (223)
160 PRK05472 redox-sensing transcr 85.5 2.3 5.8E-05 23.3 5.2 50 11-66 19-68 (211)
161 TIGR00331 hrcA heat-inducible 85.4 1.3 3.4E-05 24.6 4.0 50 9-58 6-57 (343)
162 pfam00325 Crp Bacterial regula 85.3 1.1 2.7E-05 25.2 3.5 31 24-54 2-32 (32)
163 PRK10643 DNA-binding transcrip 85.1 3.2 8.3E-05 22.4 5.9 61 6-71 152-221 (222)
164 PRK11642 exoribonuclease R; Pr 84.9 3.4 8.6E-05 22.3 5.9 54 13-69 24-81 (813)
165 PRK09392 ftrB transcriptional 84.8 1.7 4.3E-05 24.0 4.3 45 24-73 173-217 (236)
166 COG3682 Predicted transcriptio 84.7 2.6 6.6E-05 22.9 5.2 59 24-82 20-83 (123)
167 COG3710 CadC DNA-binding winge 82.8 4 0.0001 21.8 5.6 66 7-74 33-110 (148)
168 PRK11564 stationary phase indu 82.5 4.5 0.00012 21.5 7.2 71 3-75 11-85 (426)
169 smart00351 PAX Paired Box doma 82.4 2.6 6.6E-05 22.9 4.5 47 13-64 25-71 (125)
170 COG3432 Predicted transcriptio 82.3 1.2 3.2E-05 24.8 2.8 68 4-73 12-81 (95)
171 pfam04703 FaeA FaeA-like prote 82.2 4.2 0.00011 21.7 5.5 54 12-66 4-60 (61)
172 COG0745 OmpR Response regulato 82.0 4.8 0.00012 21.4 5.9 57 11-69 159-228 (229)
173 TIGR00373 TIGR00373 conserved 82.0 2.6 6.6E-05 22.9 4.3 82 9-92 17-115 (168)
174 PRK04172 pheS phenylalanyl-tRN 81.7 4.7 0.00012 21.4 5.6 59 8-68 6-64 (501)
175 PRK09643 RNA polymerase sigma 80.8 4.4 0.00011 21.6 5.2 13 119-131 142-154 (197)
176 PRK09863 putative frv operon r 79.3 5.9 0.00015 20.8 5.8 44 23-68 16-63 (585)
177 PRK10371 DNA-binding transcrip 79.1 5.8 0.00015 20.9 5.3 45 11-55 194-238 (302)
178 TIGR02063 RNase_R ribonuclease 79.1 6 0.00015 20.8 5.4 59 12-71 6-69 (755)
179 PRK10681 DNA-binding transcrip 78.9 6 0.00015 20.8 6.3 51 11-69 10-60 (252)
180 PRK13503 transcriptional activ 78.6 4.5 0.00011 21.5 4.6 22 111-132 173-195 (278)
181 pfam09012 FeoC FeoC like trans 78.5 5.1 0.00013 21.2 4.9 42 16-59 8-49 (68)
182 cd00131 PAX Paired Box domain 78.1 4.2 0.00011 21.7 4.4 48 13-65 25-72 (128)
183 COG1695 Predicted transcriptio 77.6 4.2 0.00011 21.7 4.3 74 8-82 9-93 (138)
184 pfam05584 Sulfolobus_pRN Sulfo 77.5 4.4 0.00011 21.6 4.3 50 11-63 8-57 (72)
185 TIGR01016 sucCoAbeta succinyl- 77.3 2.4 6.1E-05 23.2 2.9 49 25-73 6-69 (389)
186 pfam00292 PAX 'Paired box' dom 77.1 4.6 0.00012 21.5 4.3 48 13-65 25-72 (125)
187 PRK10529 DNA-binding transcrip 77.0 6.9 0.00018 20.4 5.9 58 6-67 154-224 (225)
188 COG3415 Transposase and inacti 76.9 6.5 0.00017 20.6 5.1 59 11-76 9-67 (138)
189 pfam04079 DUF387 Putative tran 76.6 5.5 0.00014 21.0 4.6 64 11-82 3-71 (159)
190 COG1373 Predicted ATPase (AAA+ 76.5 7.1 0.00018 20.3 6.6 70 7-77 219-291 (398)
191 pfam03428 RP-C Replication pro 76.4 5.8 0.00015 20.9 4.7 55 26-85 72-128 (177)
192 PRK00135 scpB segregation and 76.1 5.3 0.00013 21.1 4.4 56 22-82 11-72 (182)
193 PRK10736 hypothetical protein; 76.0 7.3 0.00019 20.3 5.7 50 17-69 304-354 (364)
194 PRK09393 ftrA transcriptional 76.0 5.8 0.00015 20.9 4.6 39 12-50 220-258 (320)
195 KOG2165 consensus 75.9 7.4 0.00019 20.3 6.6 61 7-77 602-662 (765)
196 PTZ00326 phenylalanyl-tRNA syn 75.8 7.4 0.00019 20.2 6.2 63 5-69 3-65 (505)
197 COG2865 Predicted transcriptio 75.4 5.4 0.00014 21.1 4.3 50 14-64 407-456 (467)
198 TIGR02846 spore_sigmaK RNA pol 74.7 2.4 6.1E-05 23.1 2.4 27 20-46 191-217 (228)
199 pfam05848 CtsR Firmicute trans 74.1 1.5 3.7E-05 24.4 1.1 61 25-86 25-92 (151)
200 cd04774 HTH_YfmP Helix-Turn-He 73.6 8.5 0.00022 19.9 5.2 62 25-91 1-63 (96)
201 COG0664 Crp cAMP-binding prote 73.2 7.3 0.00019 20.3 4.5 37 24-60 171-207 (214)
202 pfam04492 Phage_rep_O Bacterio 73.2 8.7 0.00022 19.8 5.8 33 23-55 53-85 (100)
203 pfam10007 DUF2250 Uncharacteri 73.0 8.7 0.00022 19.8 5.6 52 7-60 7-58 (93)
204 COG4463 CtsR Transcriptional r 72.7 1.6 4.1E-05 24.1 1.1 63 3-68 4-72 (153)
205 TIGR02277 PaaX_trns_reg phenyl 72.7 2.2 5.7E-05 23.3 1.8 50 26-75 22-72 (287)
206 smart00342 HTH_ARAC helix_turn 72.6 5.1 0.00013 21.2 3.6 32 24-55 1-32 (84)
207 COG4977 Transcriptional regula 72.5 8.4 0.00021 19.9 4.7 41 11-51 223-263 (328)
208 pfam04539 Sigma70_r3 Sigma-70 71.6 8.8 0.00022 19.8 4.6 60 13-81 9-68 (78)
209 pfam04182 B-block_TFIIIC B-blo 70.9 9.7 0.00025 19.5 4.8 48 10-57 4-51 (73)
210 COG5631 Predicted transcriptio 70.8 8.8 0.00022 19.8 4.5 44 15-58 89-133 (199)
211 PRK13500 transcriptional activ 70.4 9.6 0.00025 19.6 4.6 41 12-52 210-250 (312)
212 PRK13412 fkp bifunctional fuco 69.8 6.1 0.00016 20.7 3.5 38 35-72 900-940 (974)
213 TIGR02154 PhoB phosphate regul 69.5 2.7 6.8E-05 22.9 1.6 55 11-67 160-226 (226)
214 COG4519 Uncharacterized protei 69.4 11 0.00027 19.3 6.0 64 1-68 1-71 (95)
215 cd02417 Peptidase_C39_likeA A 69.0 6.4 0.00016 20.6 3.5 51 5-55 3-55 (121)
216 KOG3411 consensus 68.9 5.8 0.00015 20.9 3.3 37 32-70 91-127 (143)
217 PRK13182 racA polar chromosome 68.9 11 0.00028 19.3 9.4 110 26-141 2-134 (178)
218 KOG2268 consensus 68.8 5.7 0.00015 20.9 3.2 77 11-87 16-101 (465)
219 pfam01399 PCI PCI domain. This 68.6 11 0.00028 19.2 5.3 48 12-60 49-96 (105)
220 pfam08784 RPA_C Replication pr 68.1 11 0.00029 19.2 6.5 51 7-57 46-99 (103)
221 COG3177 Fic family protein [Fu 68.1 11 0.00029 19.2 6.1 45 21-65 301-345 (348)
222 COG1733 Predicted transcriptio 67.9 11 0.00029 19.1 7.1 70 9-83 24-98 (120)
223 cd04787 HTH_HMRTR_unk Helix-Tu 67.8 11 0.00029 19.1 6.3 62 25-91 1-63 (133)
224 COG4742 Predicted transcriptio 67.1 12 0.0003 19.0 7.2 73 12-90 17-94 (260)
225 pfam00376 MerR MerR family reg 66.8 6.8 0.00017 20.5 3.3 37 26-66 1-37 (38)
226 PRK09685 DNA-binding transcrip 66.2 12 0.00031 18.9 4.9 36 12-47 202-238 (303)
227 TIGR02997 Sig70-cyanoRpoD RNA 65.5 13 0.00032 18.9 4.8 63 15-86 204-267 (336)
228 PRK09775 hypothetical protein; 64.0 14 0.00035 18.7 4.6 64 23-87 11-75 (443)
229 COG1386 scpB Chromosome segreg 63.8 14 0.00035 18.7 5.9 56 21-82 20-81 (184)
230 COG2238 RPS19A Ribosomal prote 63.8 11 0.00027 19.3 3.8 51 22-77 65-129 (147)
231 PRK00696 sucC succinyl-CoA syn 63.4 12 0.00029 19.1 3.9 25 49-73 45-69 (388)
232 PRK09334 30S ribosomal protein 63.3 12 0.00031 19.0 4.0 38 21-58 59-96 (107)
233 TIGR02545 ATP_syn_fliI flagell 62.8 14 0.00036 18.6 7.5 122 16-144 266-393 (439)
234 TIGR02018 his_ut_repres histid 62.7 13 0.00033 18.8 4.0 61 21-83 21-86 (234)
235 pfam01638 HxlR HxlR-like helix 62.5 14 0.00037 18.5 7.2 70 9-83 6-80 (90)
236 COG4901 Ribosomal protein S25 62.0 13 0.00034 18.8 4.0 39 21-59 56-94 (107)
237 TIGR02937 sigma70-ECF RNA poly 61.5 15 0.00038 18.4 4.9 35 14-50 122-156 (162)
238 smart00088 PINT motif in prote 61.5 15 0.00038 18.4 5.5 58 11-69 12-69 (88)
239 smart00753 PAM PCI/PINT associ 61.5 15 0.00038 18.4 5.5 58 11-69 12-69 (88)
240 cd04786 HTH_MerR-like_sg7 Heli 61.3 15 0.00039 18.4 7.7 62 25-91 1-63 (131)
241 COG5111 RPC34 DNA-directed RNA 61.2 11 0.00028 19.2 3.5 59 3-61 80-138 (301)
242 PRK00423 tfb transcription ini 60.5 16 0.0004 18.3 5.6 46 6-51 163-209 (310)
243 cd04773 HTH_TioE_rpt2 Second H 60.1 16 0.00041 18.3 6.7 63 25-91 1-63 (108)
244 COG1813 Predicted transcriptio 60.0 16 0.0004 18.3 4.1 72 6-81 77-162 (165)
245 COG4367 Uncharacterized protei 59.9 16 0.00041 18.3 5.6 46 1-48 1-47 (97)
246 COG1167 ARO8 Transcriptional r 59.7 16 0.00041 18.2 6.0 54 7-60 9-64 (459)
247 PRK06654 fliL flagellar basal 59.2 17 0.00042 18.2 6.1 109 26-138 11-148 (177)
248 TIGR02607 antidote_HigA addict 58.7 8.9 0.00023 19.8 2.6 22 25-46 21-42 (81)
249 COG4310 Uncharacterized protei 58.4 13 0.00033 18.8 3.5 44 37-80 230-275 (435)
250 pfam01090 Ribosomal_S19e Ribos 57.6 14 0.00037 18.5 3.6 50 24-77 66-129 (140)
251 COG4190 Predicted transcriptio 57.1 18 0.00046 18.0 4.6 40 20-59 74-113 (144)
252 TIGR02147 Fsuc_second hypothet 56.9 18 0.00046 17.9 6.0 59 10-72 131-192 (281)
253 COG2344 AT-rich DNA-binding pr 56.7 18 0.00047 17.9 4.9 42 11-52 19-60 (211)
254 TIGR02337 HpaR homoprotocatech 56.5 15 0.00038 18.4 3.5 51 11-63 31-81 (130)
255 TIGR01764 excise DNA binding d 56.4 11 0.00027 19.3 2.7 40 25-69 2-41 (49)
256 COG4861 Uncharacterized protei 55.5 10 0.00026 19.4 2.5 60 10-72 148-208 (345)
257 COG0789 SoxR Predicted transcr 54.7 20 0.0005 17.7 4.4 62 25-91 1-63 (124)
258 COG0758 Smf Predicted Rossmann 54.5 20 0.00051 17.7 5.6 43 17-59 302-344 (350)
259 KOG3233 consensus 54.4 5.6 0.00014 20.9 1.0 42 18-59 94-135 (297)
260 pfam05331 DUF742 Protein of un 54.3 6.9 0.00018 20.4 1.5 36 23-58 54-89 (114)
261 PRK13239 alkylmercury lyase; P 54.1 20 0.00051 17.7 5.6 54 19-74 31-86 (206)
262 PRK09526 lacI lac repressor; R 54.0 14 0.00035 18.6 3.0 25 22-46 3-27 (342)
263 PRK08583 RNA polymerase sigma 53.8 17 0.00045 18.0 3.5 35 17-51 125-159 (257)
264 pfam12324 HTH_15 Helix-turn-he 53.4 21 0.00053 17.6 4.7 39 11-50 26-64 (77)
265 pfam09205 DUF1955 Domain of un 53.2 21 0.00053 17.6 4.3 52 1-53 80-134 (160)
266 PRK10014 DNA-binding transcrip 53.1 15 0.00038 18.4 3.1 25 22-46 4-28 (342)
267 COG3413 Predicted DNA binding 53.0 21 0.00054 17.6 5.4 16 24-39 178-193 (215)
268 COG0640 ArsR Predicted transcr 53.0 21 0.00054 17.6 5.9 46 11-58 28-73 (110)
269 TIGR02403 trehalose_treC alpha 52.7 3.5 9E-05 22.1 -0.2 62 58-130 188-251 (555)
270 cd04447 DEP_BRCC3 DEP (Disheve 52.4 17 0.00044 18.1 3.2 28 35-62 52-79 (92)
271 cd01105 HTH_GlnR-like Helix-Tu 52.3 22 0.00055 17.5 4.3 61 25-89 2-62 (88)
272 PRK12529 RNA polymerase sigma 50.5 23 0.00059 17.3 4.5 14 36-49 67-80 (178)
273 PRK09492 treR trehalose repres 50.5 16 0.00041 18.2 2.9 24 23-46 3-26 (315)
274 COG3398 Uncharacterized protei 50.4 23 0.00059 17.3 5.1 55 21-78 112-166 (240)
275 PRK13890 conjugal transfer pro 50.4 15 0.00039 18.4 2.7 50 21-89 15-64 (119)
276 TIGR02716 C20_methyl_CrtF C-20 50.3 23 0.00059 17.3 5.9 46 22-70 21-66 (306)
277 cd04767 HTH_HspR-like_MBC Heli 50.3 23 0.00059 17.3 4.3 58 25-88 2-60 (120)
278 PRK06811 RNA polymerase factor 49.3 24 0.00061 17.2 4.8 14 119-132 139-152 (185)
279 TIGR02980 SigBFG RNA polymeras 49.2 16 0.00042 18.2 2.7 67 14-86 97-165 (229)
280 cd04766 HTH_HspR Helix-Turn-He 49.0 23 0.00059 17.3 3.5 51 25-81 2-52 (91)
281 pfam03297 Ribosomal_S25 S25 ri 48.7 25 0.00063 17.2 4.5 41 22-62 56-96 (104)
282 pfam08221 HTH_9 RNA polymerase 48.6 25 0.00063 17.1 4.5 48 6-55 11-58 (62)
283 PRK09943 DNA-binding transcrip 48.5 14 0.00036 18.6 2.3 24 22-45 18-41 (185)
284 KOG2167 consensus 48.3 25 0.00064 17.1 5.3 53 11-63 499-551 (661)
285 pfam07037 DUF1323 Putative tra 48.3 23 0.00059 17.3 3.4 37 25-64 1-38 (122)
286 pfam02980 FokI_C Restriction e 48.2 23 0.00059 17.3 3.4 54 28-82 72-125 (142)
287 PRK09333 30S ribosomal protein 48.1 22 0.00056 17.4 3.3 44 24-70 67-124 (150)
288 pfam00464 SHMT Serine hydroxym 47.8 25 0.00065 17.1 5.1 57 27-87 180-251 (380)
289 pfam03965 Pencillinase_R Penic 47.7 26 0.00065 17.1 5.7 61 23-83 16-81 (115)
290 COG3711 BglG Transcriptional a 47.5 26 0.00066 17.0 6.3 59 14-73 9-71 (491)
291 cd00378 SHMT Serine-glycine hy 47.3 26 0.00066 17.0 4.7 34 47-86 211-249 (402)
292 pfam03551 PadR Transcriptional 46.7 26 0.00067 17.0 4.1 36 28-63 22-61 (81)
293 COG0045 SucC Succinyl-CoA synt 46.3 19 0.00049 17.8 2.7 26 49-74 45-70 (387)
294 pfam04967 HTH_10 HTH DNA bindi 46.1 27 0.00069 16.9 5.3 25 23-47 22-46 (53)
295 pfam05491 RuvB_C Holliday junc 45.8 27 0.0007 16.9 4.5 50 11-60 10-62 (75)
296 PRK12532 RNA polymerase sigma 45.8 27 0.0007 16.9 4.7 14 119-132 147-160 (195)
297 PRK07405 RNA polymerase sigma 44.8 28 0.00072 16.8 3.7 36 15-50 176-211 (318)
298 TIGR02989 Sig-70_gvs1 RNA poly 44.6 29 0.00073 16.8 4.8 37 12-50 121-157 (163)
299 pfam04545 Sigma70_r4 Sigma-70, 43.8 29 0.00075 16.7 4.6 33 13-47 11-43 (50)
300 PRK12525 RNA polymerase sigma 43.6 30 0.00076 16.7 4.6 14 119-132 129-142 (168)
301 COG0478 RIO-like serine/threon 43.3 30 0.00076 16.7 6.3 76 11-86 16-99 (304)
302 pfam00165 HTH_AraC Bacterial r 43.3 26 0.00067 17.0 3.0 27 23-49 7-34 (43)
303 COG1974 LexA SOS-response tran 43.2 30 0.00077 16.6 6.8 49 21-69 22-71 (201)
304 PRK12370 invasion protein regu 43.0 30 0.00077 16.6 5.9 60 10-71 40-110 (553)
305 PRK07500 rpoH2 RNA polymerase 42.9 30 0.00078 16.6 4.9 28 25-52 149-176 (289)
306 pfam09681 Phage_rep_org_N N-te 42.8 30 0.00078 16.6 4.3 44 23-68 52-95 (121)
307 TIGR02985 Sig70_bacteroi1 RNA 42.3 31 0.00079 16.6 4.4 33 12-46 125-157 (167)
308 pfam01418 HTH_6 Helix-turn-hel 42.2 31 0.0008 16.5 3.6 45 11-55 19-65 (106)
309 KOG1511 consensus 42.1 31 0.0008 16.5 4.9 45 29-73 303-348 (397)
310 pfam10078 DUF2316 Uncharacteri 42.1 31 0.0008 16.5 5.6 46 1-48 1-47 (89)
311 KOG0538 consensus 41.5 21 0.00053 17.6 2.3 84 47-133 242-351 (363)
312 PRK09958 DNA-binding transcrip 41.5 32 0.00082 16.5 3.4 25 59-85 95-120 (204)
313 PRK11778 putative periplasmic 41.4 24 0.00061 17.2 2.6 64 10-74 91-159 (317)
314 cd04761 HTH_MerR-SF Helix-Turn 41.2 32 0.00082 16.5 3.5 39 25-68 1-39 (49)
315 PRK08295 RNA polymerase factor 40.2 33 0.00085 16.4 3.6 12 121-132 167-178 (209)
316 PRK10401 DNA-binding transcrip 39.9 28 0.00071 16.9 2.7 20 26-45 3-22 (346)
317 PRK12523 RNA polymerase sigma 39.8 34 0.00087 16.3 4.5 14 119-132 130-143 (172)
318 cd04763 HTH_MlrA-like Helix-Tu 39.8 34 0.00087 16.3 3.8 60 25-88 1-60 (68)
319 COG0112 GlyA Glycine/serine hy 39.8 19 0.00049 17.8 1.9 55 27-87 186-255 (413)
320 pfam00356 LacI Bacterial regul 39.7 27 0.00069 16.9 2.6 21 26-46 1-21 (46)
321 cd06171 Sigma70_r4 Sigma70, re 39.7 34 0.00087 16.3 4.7 36 12-49 16-51 (55)
322 cd04772 HTH_TioE_rpt1 First He 39.2 35 0.00089 16.3 3.5 53 26-83 2-54 (99)
323 pfam05567 Neisseria_PilC Neiss 39.2 20 0.00052 17.7 1.9 37 36-72 567-603 (1039)
324 pfam09286 Pro-kuma_activ Pro-k 38.9 35 0.00089 16.2 4.8 64 22-90 45-108 (141)
325 PRK09483 response regulator; P 38.9 35 0.0009 16.2 3.5 26 59-86 97-123 (216)
326 pfam08461 HTH_12 Ribonuclease 38.8 35 0.0009 16.2 4.8 52 13-67 3-59 (66)
327 TIGR03433 padR_acidobact trans 38.8 35 0.0009 16.2 4.4 52 11-62 7-63 (100)
328 pfam00984 UDPG_MGDP_dh UDP-glu 38.5 23 0.00058 17.3 2.1 47 27-73 25-72 (96)
329 cd01109 HTH_YyaN Helix-Turn-He 37.9 36 0.00093 16.1 4.9 62 25-90 1-62 (113)
330 pfam08100 dimerization dimeriz 37.8 37 0.00093 16.1 4.0 32 17-49 15-50 (50)
331 pfam08442 ATP-grasp_2 ATP-gras 37.4 12 0.0003 19.0 0.5 26 49-74 44-69 (202)
332 COG2005 ModE N-terminal domain 37.3 37 0.00095 16.1 4.5 47 26-72 33-84 (130)
333 PRK09430 djlA Dna-J like membr 37.1 38 0.00096 16.1 4.9 72 10-83 131-209 (269)
334 cd04446 DEP_DEPDC4 DEP (Dishev 37.1 37 0.00095 16.1 3.0 29 35-63 51-79 (95)
335 PRK05949 RNA polymerase sigma 36.9 38 0.00096 16.1 3.5 35 16-50 186-220 (327)
336 PRK13824 replication initiatio 36.8 38 0.00097 16.1 4.6 49 8-56 55-115 (404)
337 COG0616 SppA Periplasmic serin 36.4 17 0.00044 18.1 1.2 35 40-74 117-154 (317)
338 PRK07239 bifunctional uroporph 36.2 39 0.00099 16.0 6.3 57 14-72 315-378 (381)
339 TIGR01743 purR_Bsub pur operon 36.0 39 0.001 16.0 3.6 71 11-82 8-85 (269)
340 PRK10840 transcriptional regul 35.8 39 0.001 16.0 3.2 29 58-88 101-130 (216)
341 cd01107 HTH_BmrR Helix-Turn-He 35.6 40 0.001 15.9 4.3 63 25-91 1-64 (108)
342 cd04768 HTH_BmrR-like Helix-Tu 35.4 40 0.001 15.9 5.6 63 25-91 1-63 (96)
343 TIGR02663 nifX nitrogen fixati 35.3 17 0.00042 18.2 1.0 24 22-45 97-125 (125)
344 PRK10727 DNA-binding transcrip 35.1 37 0.00093 16.1 2.7 20 26-45 3-22 (342)
345 cd01108 HTH_CueR Helix-Turn-He 35.0 41 0.001 15.9 6.8 60 25-88 1-60 (127)
346 cd04770 HTH_HMRTR Helix-Turn-H 35.0 41 0.001 15.9 7.0 61 25-90 1-62 (123)
347 PRK12520 RNA polymerase sigma 34.5 41 0.0011 15.8 4.5 14 119-132 142-155 (191)
348 pfam00382 TFIIB Transcription 34.3 39 0.00099 16.0 2.7 25 13-37 42-67 (71)
349 COG5647 Cullin, a subunit of E 34.2 42 0.0011 15.8 5.1 83 3-91 603-685 (773)
350 PRK09935 transcriptional regul 34.0 42 0.0011 15.8 3.5 27 58-86 98-125 (210)
351 PRK12515 RNA polymerase sigma 33.7 43 0.0011 15.7 4.9 14 119-132 142-155 (189)
352 PRK11041 DNA-binding transcrip 33.6 39 0.001 16.0 2.7 23 24-46 9-31 (341)
353 pfam07638 Sigma70_ECF ECF sigm 33.6 43 0.0011 15.7 4.9 14 119-132 146-159 (185)
354 COG1737 RpiR Transcriptional r 33.5 43 0.0011 15.7 3.9 99 12-132 22-122 (281)
355 cd00592 HTH_MerR-like Helix-Tu 33.3 43 0.0011 15.7 5.6 62 25-91 1-62 (100)
356 smart00354 HTH_LACI helix_turn 33.1 39 0.001 16.0 2.6 21 26-46 2-22 (70)
357 PRK12516 RNA polymerase sigma 32.8 44 0.0011 15.7 4.9 13 119-131 130-142 (190)
358 COG2197 CitB Response regulato 32.8 44 0.0011 15.7 3.3 26 58-85 95-121 (211)
359 COG2169 Ada Adenosine deaminas 32.8 44 0.0011 15.7 5.1 49 6-55 80-128 (187)
360 cd04775 HTH_Cfa-like Helix-Tur 32.7 44 0.0011 15.7 7.7 62 25-91 2-63 (102)
361 pfam09397 Ftsk_gamma Ftsk gamm 32.5 45 0.0011 15.6 3.6 39 22-60 19-57 (67)
362 PRK12527 RNA polymerase sigma 32.4 45 0.0011 15.6 4.6 13 120-132 117-129 (159)
363 COG4800 Predicted transcriptio 32.3 45 0.0011 15.6 2.9 23 24-46 29-51 (170)
364 pfam06413 Neugrin Neugrin. Thi 32.2 45 0.0012 15.6 4.6 51 8-58 13-79 (225)
365 PRK10703 DNA-binding transcrip 31.9 43 0.0011 15.7 2.7 19 36-54 28-46 (335)
366 PRK11303 DNA-binding transcrip 31.9 40 0.001 15.9 2.5 19 36-54 30-48 (330)
367 pfam08281 Sigma70_r4_2 Sigma-7 31.8 46 0.0012 15.6 4.6 37 12-50 16-52 (54)
368 cd04762 HTH_MerR-trunc Helix-T 31.6 46 0.0012 15.5 3.4 37 25-66 1-37 (49)
369 PRK11924 RNA polymerase sigma 31.5 46 0.0012 15.5 4.4 12 121-132 138-149 (180)
370 cd04788 HTH_NolA-AlbR Helix-Tu 31.2 47 0.0012 15.5 5.0 63 25-91 1-63 (96)
371 PRK09390 fixJ response regulat 30.9 36 0.00093 16.2 2.1 11 59-71 97-107 (202)
372 PRK09651 RNA polymerase sigma 30.8 48 0.0012 15.5 4.6 14 119-132 130-143 (172)
373 PRK05602 RNA polymerase sigma 30.7 48 0.0012 15.4 4.7 14 119-132 139-152 (186)
374 pfam07106 TBPIP Tat binding pr 30.6 48 0.0012 15.4 8.1 113 13-138 6-122 (169)
375 PRK10403 transcriptional regul 30.6 48 0.0012 15.4 3.4 27 58-86 101-128 (215)
376 cd04790 HTH_Cfa-like_unk Helix 30.2 49 0.0012 15.4 7.6 63 25-91 2-64 (172)
377 PRK06596 RNA polymerase factor 30.2 49 0.0012 15.4 4.9 24 26-49 153-176 (284)
378 PRK10130 transcriptional regul 29.4 50 0.0013 15.3 4.9 26 108-133 239-265 (350)
379 PRK07921 RNA polymerase sigma 29.4 51 0.0013 15.3 4.5 29 21-49 182-210 (320)
380 cd06170 LuxR_C_like C-terminal 29.3 51 0.0013 15.3 3.6 35 11-49 6-44 (57)
381 cd04780 HTH_MerR-like_sg5 Heli 29.3 51 0.0013 15.3 4.9 62 25-91 1-64 (95)
382 pfam02796 HTH_7 Helix-turn-hel 28.9 37 0.00095 16.1 1.9 23 25-47 22-44 (45)
383 PRK04338 N(2),N(2)-dimethylgua 28.9 52 0.0013 15.3 4.5 57 25-82 317-373 (376)
384 PRK11337 DNA-binding transcrip 28.9 52 0.0013 15.3 3.8 44 12-55 33-78 (293)
385 PTZ00095 40S ribosomal protein 28.9 52 0.0013 15.3 3.4 44 24-68 91-148 (169)
386 pfam10668 Phage_terminase Phag 28.9 52 0.0013 15.3 2.8 32 8-43 10-41 (60)
387 PRK10339 DNA-binding transcrip 28.7 52 0.0013 15.3 2.6 10 44-53 38-47 (327)
388 TIGR02392 rpoH_proteo alternat 28.6 52 0.0013 15.2 2.7 23 22-44 242-265 (279)
389 cd04789 HTH_Cfa Helix-Turn-Hel 28.1 53 0.0014 15.2 7.4 62 25-91 2-63 (102)
390 PRK11557 putative DNA-binding 27.7 54 0.0014 15.1 3.7 45 11-55 19-65 (282)
391 smart00843 Ftsk_gamma This dom 27.4 55 0.0014 15.1 4.9 39 22-60 17-55 (63)
392 PRK10651 transcriptional regul 27.4 55 0.0014 15.1 3.5 28 58-87 101-129 (216)
393 PRK10360 DNA-binding transcrip 27.0 38 0.00097 16.0 1.7 27 58-86 93-120 (196)
394 PRK07075 isochorismate-pyruvat 27.0 56 0.0014 15.1 2.5 27 26-52 60-86 (101)
395 pfam02005 TRM N2,N2-dimethylgu 26.6 57 0.0014 15.0 3.4 22 34-55 129-150 (375)
396 pfam00538 Linker_histone linke 26.6 57 0.0014 15.0 6.0 44 25-68 22-77 (77)
397 PRK07037 extracytoplasmic-func 26.5 57 0.0015 15.0 4.7 14 119-132 134-147 (183)
398 pfam07381 DUF1495 Winged helix 26.3 57 0.0015 15.0 6.0 63 5-67 6-80 (90)
399 PRK13558 bacterio-opsin activa 26.1 58 0.0015 15.0 5.2 36 50-85 552-588 (674)
400 TIGR02999 Sig-70_X6 RNA polyme 26.1 58 0.0015 15.0 3.3 20 25-44 162-181 (194)
401 cd01279 HTH_HspR-like Helix-Tu 26.0 58 0.0015 15.0 4.3 60 25-89 2-62 (98)
402 PRK12528 RNA polymerase sigma 25.7 59 0.0015 14.9 4.6 26 8-33 18-43 (167)
403 cd04784 HTH_CadR-PbrR Helix-Tu 25.7 59 0.0015 14.9 6.5 61 26-90 2-62 (127)
404 cd04781 HTH_MerR-like_sg6 Heli 25.6 59 0.0015 14.9 5.2 62 25-91 1-62 (120)
405 cd04782 HTH_BltR Helix-Turn-He 25.6 59 0.0015 14.9 4.1 63 25-91 1-63 (97)
406 PRK12427 flagellar biosynthesi 25.5 60 0.0015 14.9 5.2 31 17-47 108-138 (229)
407 COG3357 Predicted transcriptio 25.3 60 0.0015 14.9 6.1 50 19-68 13-70 (97)
408 PRK09415 RNA polymerase factor 25.3 60 0.0015 14.9 4.8 14 119-132 138-151 (177)
409 cd02421 Peptidase_C39_likeD A 25.3 60 0.0015 14.9 3.0 61 6-74 4-66 (124)
410 pfam04645 DUF603 Protein of un 25.3 60 0.0015 14.9 3.6 37 16-52 11-47 (181)
411 TIGR03026 NDP-sugDHase nucleot 25.1 55 0.0014 15.1 2.2 45 28-72 226-271 (411)
412 PRK00117 recX recombination re 25.1 60 0.0015 14.9 4.1 41 13-56 36-79 (184)
413 PRK13749 transcriptional regul 25.0 61 0.0015 14.8 3.2 43 24-70 3-45 (121)
414 COG2207 AraC AraC-type DNA-bin 25.0 61 0.0016 14.8 5.4 43 12-54 24-66 (127)
415 pfam07900 DUF1670 Protein of u 24.9 61 0.0016 14.8 5.8 50 11-60 89-142 (220)
416 PRK12517 RNA polymerase sigma 24.9 61 0.0016 14.8 4.9 14 119-132 139-152 (188)
417 pfam03979 Sigma70_r1_1 Sigma-7 24.3 63 0.0016 14.8 5.3 48 7-55 5-55 (79)
418 smart00530 HTH_XRE Helix-turn- 24.0 63 0.0016 14.7 2.8 22 24-45 10-31 (56)
419 PRK05927 hypothetical protein; 23.7 65 0.0016 14.7 5.2 75 6-83 107-192 (350)
420 cd01392 HTH_LacI Helix-turn-he 23.6 46 0.0012 15.5 1.6 21 34-54 22-42 (52)
421 PRK11064 wecC UDP-N-acetyl-D-m 23.5 61 0.0015 14.9 2.2 43 27-71 229-272 (415)
422 PRK06986 fliA flagellar biosyn 23.4 65 0.0017 14.7 4.0 30 22-51 109-138 (234)
423 PRK11302 DNA-binding transcrip 23.3 66 0.0017 14.6 3.8 44 12-55 20-65 (284)
424 KOG2908 consensus 23.2 66 0.0017 14.6 5.4 46 10-55 277-325 (380)
425 pfam08535 KorB KorB domain. Th 22.9 67 0.0017 14.6 3.6 52 25-84 4-57 (93)
426 COG2522 Predicted transcriptio 22.5 68 0.0017 14.6 3.9 43 8-60 7-49 (119)
427 cd00093 HTH_XRE Helix-turn-hel 22.5 68 0.0017 14.6 2.5 23 24-46 12-34 (58)
428 cd04776 HTH_GnyR Helix-Turn-He 22.4 68 0.0017 14.5 5.4 61 25-91 1-61 (118)
429 PRK08184 enoyl-CoA hydratase; 22.3 22 0.00056 17.4 -0.3 43 34-77 116-160 (558)
430 PRK10100 DNA-binding transcrip 22.1 69 0.0018 14.5 3.3 29 58-88 102-131 (216)
431 TIGR00311 aIF-2beta translatio 22.1 69 0.0018 14.5 2.9 58 26-92 42-102 (134)
432 cd04783 HTH_MerR1 Helix-Turn-H 22.0 70 0.0018 14.5 7.3 62 25-91 1-63 (126)
433 PRK09047 RNA polymerase factor 21.9 70 0.0018 14.5 4.3 13 119-131 117-129 (161)
434 pfam08888 HopJ HopJ type III e 21.9 55 0.0014 15.1 1.7 77 65-141 8-96 (110)
435 smart00421 HTH_LUXR helix_turn 21.9 70 0.0018 14.5 3.6 35 11-49 9-43 (58)
436 smart00422 HTH_MERR helix_turn 21.9 70 0.0018 14.5 4.4 53 25-82 1-53 (70)
437 pfam04552 Sigma54_DBD Sigma-54 21.8 70 0.0018 14.5 2.6 33 23-59 48-80 (160)
438 PRK12544 RNA polymerase sigma 21.7 71 0.0018 14.5 4.7 12 120-131 161-172 (207)
439 PRK07408 RNA polymerase sigma 21.6 71 0.0018 14.4 4.9 40 15-54 120-159 (256)
440 PRK10188 DNA-binding transcrip 21.5 71 0.0018 14.4 3.5 29 42-70 104-139 (240)
441 PRK12524 RNA polymerase sigma 21.5 71 0.0018 14.4 4.6 13 119-131 147-159 (196)
442 PRK05911 RNA polymerase sigma 21.5 71 0.0018 14.4 3.6 33 22-54 124-156 (257)
443 PRK13413 mpi multiple promoter 21.4 72 0.0018 14.4 3.2 47 30-82 41-87 (200)
444 TIGR02207 lipid_A_htrB lipid A 21.4 48 0.0012 15.4 1.3 32 39-70 222-256 (308)
445 PRK05658 RNA polymerase sigma 21.4 72 0.0018 14.4 4.7 45 8-53 10-57 (620)
446 pfam09639 YjcQ YjcQ protein. Y 21.3 72 0.0018 14.4 5.6 24 34-57 20-43 (88)
447 PRK09637 RNA polymerase sigma 21.2 72 0.0018 14.4 4.7 12 120-131 118-129 (181)
448 TIGR01958 nuoE_fam NADH-quinon 21.1 73 0.0019 14.4 2.3 39 7-45 16-58 (153)
449 COG3811 Uncharacterized protei 20.9 64 0.0016 14.7 1.9 63 1-69 1-73 (85)
450 PRK12545 RNA polymerase sigma 20.9 74 0.0019 14.4 4.5 12 120-131 151-162 (201)
451 PRK09652 RNA polymerase sigma 20.9 74 0.0019 14.3 4.8 12 121-132 150-161 (192)
452 PRK05657 RNA polymerase sigma 20.8 74 0.0019 14.3 5.4 37 11-47 179-215 (328)
453 TIGR03070 couple_hipB transcri 20.8 74 0.0019 14.3 2.8 22 23-44 14-35 (58)
454 pfam05043 Mga Mga helix-turn-h 20.7 74 0.0019 14.3 5.4 39 10-50 18-56 (87)
455 PRK07122 RNA polymerase sigma 20.7 74 0.0019 14.3 3.6 33 21-53 139-171 (263)
No 1
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=100.00 E-value=3e-42 Score=270.53 Aligned_cols=143 Identities=58% Similarity=0.991 Sum_probs=137.7
Q ss_pred CCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHH
Q ss_conf 97645689999999999855986335999999819978999999999932590573156545400023721260999999
Q gi|254780620|r 1 MHLTKRTDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVK 80 (144)
Q Consensus 1 Mkis~~~~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~ 80 (144)
||||+++|||||+|+|||.++++.+++++||+.+++|.+||+||++.|+++|||+|+||++|||+|+++|++||++||++
T Consensus 1 Mkls~~~dYAlr~l~~LA~~~~~~~~~~~Ia~~~~is~~~l~kIl~~L~~~Glv~S~RG~~GGy~Lar~p~~Isl~dIi~ 80 (153)
T PRK11920 1 MRLTKQTNYAIRMLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLVEAGLVETVRGRNGGVRLGKPAADISLFDVVR 80 (153)
T ss_pred CCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCEEECCCHHHCCHHHHHH
T ss_conf 98861882999999999828999767999998889199999999999998898784588988635448989899999999
Q ss_pred HHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHCHHHHHHHHCC
Q ss_conf 971876311146887788876566447999999999999998417999999158989995278
Q gi|254780620|r 81 ATEESFFVAECFASHKIDCPLVGSCGLTSVLRKALNAFFDVLTQYSIECLVRNRSSIKKIFNA 143 (144)
Q Consensus 81 aie~~~~~~~C~~~~~~~C~~~~~c~~~~~~~~~~~~~~~~L~~~TL~dl~~~~~~~~~l~~~ 143 (144)
++||++.+++|+..+...|+..+.|.++.+|.+++++|.+.|+++||+||++++.+++.++..
T Consensus 81 a~eg~~~~~~C~~~~~~~C~~~~~C~~~~~w~~~~~~~~~~L~~~TLaDLi~~~~~~r~l~~~ 143 (153)
T PRK11920 81 VTEDNFSMAECFENDASECPLVDSCGLNAALRKALNAFFAVLSKYSIADLVKARPNVRFLLGL 143 (153)
T ss_pred HHCCCCCEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHCCCHHHHHHHCC
T ss_conf 974898812368899999999998756799999999999999159199997488879987199
No 2
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=100.00 E-value=2.6e-41 Score=264.99 Aligned_cols=137 Identities=26% Similarity=0.406 Sum_probs=129.7
Q ss_pred CCCCHHHHHHHHHHHHHHHCC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHH
Q ss_conf 976456899999999998559-8633599999981997899999999993259057315654540002372126099999
Q gi|254780620|r 1 MHLTKRTDYGIRVLMYCAIHN-DYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVV 79 (144)
Q Consensus 1 Mkis~~~~yAi~~l~~La~~~-~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~ 79 (144)
||||+++|||+|+|+|||.++ ++++++++||+.++||.+||+||++.|+++|||+|+||++|||+|+|+|++||++||+
T Consensus 1 MkLS~kt~YAlraL~~LA~~~~~~~vsi~eIAe~~~Is~~~LekIl~~L~kaGlV~S~RG~~GGY~Lar~p~~Itl~dIi 80 (164)
T PRK10857 1 MRLTSKGRYAVTAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGPGGGYLLGKDASSIAVGEVI 80 (164)
T ss_pred CCCCCHHHHHHHHHHHHHHCCCCCEECHHHHHHHHCCCHHHHHHHHHHHHHCCCCEECCCCCCCCCCCCCHHHCCHHHHH
T ss_conf 97873887999999999818899809499999887919999999999998678506326888880336998989999999
Q ss_pred HHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHCHHHHHH
Q ss_conf 997187631114688778887656644799999999999999841799999915898999
Q gi|254780620|r 80 KATEESFFVAECFASHKIDCPLVGSCGLTSVLRKALNAFFDVLTQYSIECLVRNRSSIKK 139 (144)
Q Consensus 80 ~aie~~~~~~~C~~~~~~~C~~~~~c~~~~~~~~~~~~~~~~L~~~TL~dl~~~~~~~~~ 139 (144)
+++||++.+++|..+. .|+..+.|.++.+|.++++++.++|+++||+||+++.+.+.-
T Consensus 81 ~aiEG~i~~~~C~~~~--~C~~~~~C~t~~~W~~l~~ai~~~Ld~iTLaDLv~~~~~l~~ 138 (164)
T PRK10857 81 SAVDESVDATRCQGKG--GCQGGDKCLTHALWRDLSDRLTGFLNNITLGELVNNQEVLDV 138 (164)
T ss_pred HHHCCCCCCCCCCCCC--CCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHCCHHHHHH
T ss_conf 9965887640689999--989989667779999999999999806919999768778899
No 3
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator); InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulphovibrio 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 strain PCC 6803 hypothetical protein slr0846. These are small proteins of 12 to 18 kD which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators..
Probab=100.00 E-value=2.2e-41 Score=265.41 Aligned_cols=130 Identities=41% Similarity=0.629 Sum_probs=122.9
Q ss_pred CCCCHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHH
Q ss_conf 97645689999999999855986-33599999981997899999999993259057315654540002372126099999
Q gi|254780620|r 1 MHLTKRTDYGIRVLMYCAIHNDY-PNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVV 79 (144)
Q Consensus 1 Mkis~~~~yAi~~l~~La~~~~~-~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~ 79 (144)
||+|++++||+++|++||.++++ ++++++||++++||++||+|||+.|+|+|+|+|+||++|||+|+|||++||++|||
T Consensus 1 M~lt~~~~YAl~al~~LA~~~~~~~v~~~~ia~~~~Is~~yL~K~l~~L~~~GlV~S~rG~~GGY~L~~~~~~I~~~dvv 80 (133)
T TIGR00738 1 MKLTKKSEYALRALLDLALNADEGPVSVKEIAERQGISRSYLEKVLRTLRKAGLVESVRGPGGGYRLARPPEEITVGDVV 80 (133)
T ss_pred CCCCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCCHHHCCHHHHH
T ss_conf 98871157799999999722688760789999884899879999999887707642115898563107753430498888
Q ss_pred HHHCCCCCCCCCCCCCCCCCC--CCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHH
Q ss_conf 997187631114688778887--65664479999999999999984179999991
Q gi|254780620|r 80 KATEESFFVAECFASHKIDCP--LVGSCGLTSVLRKALNAFFDVLTQYSIECLVR 132 (144)
Q Consensus 80 ~aie~~~~~~~C~~~~~~~C~--~~~~c~~~~~~~~~~~~~~~~L~~~TL~dl~~ 132 (144)
+++|++..++.|...+. |+ ....|.++.+|.++++++.++|+++||+||++
T Consensus 81 ~a~e~~~~~~~c~~~~~--c~~~~~~~C~~~~~w~~~~~~~~~~L~~~TL~DL~~ 133 (133)
T TIGR00738 81 RAVEGSLAPVQCIGGNG--CHNVGEPVCLLHAVWRELEDAIEDVLREITLADLVK 133 (133)
T ss_pred HHHCCCCCHHCCCCCCC--CCCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHCC
T ss_conf 75368510001445788--864444422589999999999999852775788519
No 4
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=100.00 E-value=1.8e-40 Score=260.08 Aligned_cols=139 Identities=35% Similarity=0.596 Sum_probs=131.3
Q ss_pred CCCCHHHHHHHHHHHHHHHCC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHH
Q ss_conf 976456899999999998559-8633599999981997899999999993259057315654540002372126099999
Q gi|254780620|r 1 MHLTKRTDYGIRVLMYCAIHN-DYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVV 79 (144)
Q Consensus 1 Mkis~~~~yAi~~l~~La~~~-~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~ 79 (144)
||||+++|||+|+|+|||.++ ++++++++||+.+++|++||+||++.|+++|||.|+||++|||+|++||++||++||+
T Consensus 1 Mkls~~tdYAlraL~~LA~~~~~~~~~~~eIae~~~Ip~~~L~KIl~~L~~aGlv~S~RG~~GGy~Lar~p~~Itl~dVi 80 (141)
T PRK11014 1 MQLTSFTDYGLRALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRGKNGGIRLGKPASTIRIGDVV 80 (141)
T ss_pred CCCCCHHHHHHHHHHHHHHCCCCCEECHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCEECCCCHHHCCHHHHH
T ss_conf 98872886999999999839999847499999987949999999999998879567204799883214898879799999
Q ss_pred HHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHCHHHHHHHHCC
Q ss_conf 9971876311146887788876566447999999999999998417999999158989995278
Q gi|254780620|r 80 KATEESFFVAECFASHKIDCPLVGSCGLTSVLRKALNAFFDVLTQYSIECLVRNRSSIKKIFNA 143 (144)
Q Consensus 80 ~aie~~~~~~~C~~~~~~~C~~~~~c~~~~~~~~~~~~~~~~L~~~TL~dl~~~~~~~~~l~~~ 143 (144)
+++| +..+++|.. ..|+..+.|.++++|.++++++.+.|+++||+||+++.+.+.+++..
T Consensus 81 ~aiE-~~~~~~C~~---~~C~~~~~C~l~~~~~~~~~~~~~~L~~~TLadli~~~~~l~~l~~~ 140 (141)
T PRK11014 81 RELE-PLSLVNCSS---EFCHITPACRLKQALSKAVQSFLKELDNYTLADLVEENQPLYKLLLV 140 (141)
T ss_pred HHHC-CCCCCCCCC---CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHCCCHHHHHHHCC
T ss_conf 9946-765436799---99999998845499999999999999429299997496758998675
No 5
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=100.00 E-value=1.2e-38 Score=249.34 Aligned_cols=133 Identities=41% Similarity=0.683 Sum_probs=126.3
Q ss_pred CCCCHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHH
Q ss_conf 97645689999999999855986-33599999981997899999999993259057315654540002372126099999
Q gi|254780620|r 1 MHLTKRTDYGIRVLMYCAIHNDY-PNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVV 79 (144)
Q Consensus 1 Mkis~~~~yAi~~l~~La~~~~~-~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~ 79 (144)
||+|++++||+|+|+|||.++++ ++|+++||+++++|++||+||++.|+++|||+|+||++|||+|+|||++||++||+
T Consensus 1 Mklt~~~~yal~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG~~GGy~Lar~~~~Isl~dVv 80 (150)
T COG1959 1 MKLTSKGEYALRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKAGLVKSVRGKGGGYRLARPPEEITLGDVV 80 (150)
T ss_pred CCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCEECCCCHHHCCHHHHH
T ss_conf 96654899999999999848898846499999998919999999999998779878520799892023897979099999
Q ss_pred HHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHCH
Q ss_conf 9971876311146887788876566447999999999999998417999999158
Q gi|254780620|r 80 KATEESFFVAECFASHKIDCPLVGSCGLTSVLRKALNAFFDVLTQYSIECLVRNR 134 (144)
Q Consensus 80 ~aie~~~~~~~C~~~~~~~C~~~~~c~~~~~~~~~~~~~~~~L~~~TL~dl~~~~ 134 (144)
+|+|++..+++|+......|. ...|.++..|.++.+++.+.|+++||+|++.+.
T Consensus 81 ~ave~~~~~~~c~~~~~~~~~-~~~C~i~~~~~~~~~~~~~~L~~~tladl~~~~ 134 (150)
T COG1959 81 RALEGPLALVECFSITNNECN-TPTCGIRAAWLKALDAFLEVLDNITLADLVEDT 134 (150)
T ss_pred HHHCCCCCCCCCCCCCCCCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 997686665225577777889-997459999999999999999984699998623
No 6
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR; InterPro: IPR010242 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly . The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen . This entry describes IscR, an iron-sulphur binding transcription factor of the ISC iron-sulphur cluster assembly system.; GO: 0003690 double-stranded DNA binding, 0003700 transcription factor activity, 0006355 regulation of transcription DNA-dependent.
Probab=100.00 E-value=3.6e-38 Score=246.42 Aligned_cols=135 Identities=30% Similarity=0.459 Sum_probs=129.1
Q ss_pred CCCCHHHHHHHHHHHHHHHCC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHH
Q ss_conf 976456899999999998559-8633599999981997899999999993259057315654540002372126099999
Q gi|254780620|r 1 MHLTKRTDYGIRVLMYCAIHN-DYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVV 79 (144)
Q Consensus 1 Mkis~~~~yAi~~l~~La~~~-~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~ 79 (144)
||||+|.+||+-||+.||.|. .+||+..+||++|+||-+||||++++|+|+|||+|+|||+|||.|.+++++|++++|+
T Consensus 1 MrLTtKGRYAVTAmLDlA~~~~~GPV~La~IS~RQ~ISLSYLEQLFaKLRk~gLV~SvRGPGGGY~L~~~~~~I~va~ii 80 (140)
T TIGR02010 1 MRLTTKGRYAVTAMLDLALNAETGPVTLADISERQNISLSYLEQLFAKLRKAGLVKSVRGPGGGYQLGRPAEQISVADII 80 (140)
T ss_pred CCCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHCCCCHHHHHHHHHHHCHHCCCEECCCCCCCCCCCCCCCCCCHHHHH
T ss_conf 98876236899999999973058991667654421613567989988632101312101777413125530001287788
Q ss_pred HHHCCCCCCCCCCCCCCCCC---CCCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHCHH
Q ss_conf 99718763111468877888---765664479999999999999984179999991589
Q gi|254780620|r 80 KATEESFFVAECFASHKIDC---PLVGSCGLTSVLRKALNAFFDVLTQYSIECLVRNRS 135 (144)
Q Consensus 80 ~aie~~~~~~~C~~~~~~~C---~~~~~c~~~~~~~~~~~~~~~~L~~~TL~dl~~~~~ 135 (144)
.|+|+++..+.|.......| +....|..|.+|.++.+.|.+||+++||++|++++.
T Consensus 81 ~AV~E~~daT~C~~Kg~~~Cgg~~~g~~ClTH~LW~~L~~~i~~yL~~isL~~l~~~~~ 139 (140)
T TIGR02010 81 DAVDESVDATRCQKKGKGNCGGVRSGTRCLTHDLWEDLSKHIRDYLESISLADLVNKQN 139 (140)
T ss_pred HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHC
T ss_conf 75238731010522356678888798855467888775389998725755789985205
No 7
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator; InterPro: IPR014290 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly . The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen . This entry represents proteins belonging to the Rtf2 family of transcriptional regulators and are found, typically, as the first gene of the SUF operon. They are found only in a subset of the genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role..
Probab=99.97 E-value=1.6e-32 Score=213.16 Aligned_cols=129 Identities=32% Similarity=0.506 Sum_probs=124.3
Q ss_pred CCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHH
Q ss_conf 97645689999999999855986335999999819978999999999932590573156545400023721260999999
Q gi|254780620|r 1 MHLTKRTDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVK 80 (144)
Q Consensus 1 Mkis~~~~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~ 80 (144)
.||||-+|||+-+|..||...+++.|+.+||+..+++.|.++|||..|.+||||+|.||.+|||+|+++|++||+.||++
T Consensus 2 LkiSkL~DYA~~vl~~lA~~~~~~ySAA~lA~~tgL~~pTvsK~Lk~L~~A~lV~S~RGv~GGY~La~~~~~itv~~Iv~ 81 (130)
T TIGR02944 2 LKISKLTDYATVVLTVLAQADEQTYSAAELAEQTGLEAPTVSKILKALSEAGLVTSKRGVEGGYTLARAPEDITVADIVK 81 (130)
T ss_pred CCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCCCCCCCCHHHHHHCCCCCCCHHHHHH
T ss_conf 50135876799999998528997006888786459886047899887642875324346430046200545543654543
Q ss_pred HHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCHHHH
Q ss_conf 97187631114688778887656644799999999999999841799999
Q gi|254780620|r 81 ATEESFFVAECFASHKIDCPLVGSCGLTSVLRKALNAFFDVLTQYSIECL 130 (144)
Q Consensus 81 aie~~~~~~~C~~~~~~~C~~~~~c~~~~~~~~~~~~~~~~L~~~TL~dl 130 (144)
|+|||+.++||..+.+ .|.....|.++..|+-++..+.+.|+++||+|+
T Consensus 82 Aveg~~alTECs~~~~-~C~~~~~C~Vr~~W~viN~~v~~~L~~~~Ladm 130 (130)
T TIGR02944 82 AVEGPVALTECSDDQK-KCELANSCGVRSNWKVINSLVLDLLESVSLADM 130 (130)
T ss_pred HHCCCCCCCCCHHHHH-HCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 2059965120215674-133467787316789999999989754112039
No 8
>pfam02082 Rrf2 Transcriptional regulator. This family is related to pfam001022 and other transcription regulation families (personal obs: Yeats C).
Probab=99.92 E-value=3.9e-25 Score=169.49 Aligned_cols=81 Identities=48% Similarity=0.775 Sum_probs=77.6
Q ss_pred CCCHHHHHHHHHHHHHHHCC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHH
Q ss_conf 76456899999999998559-86335999999819978999999999932590573156545400023721260999999
Q gi|254780620|r 2 HLTKRTDYGIRVLMYCAIHN-DYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVK 80 (144)
Q Consensus 2 kis~~~~yAi~~l~~La~~~-~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~ 80 (144)
|||+++|||+|+|+|||.++ ++++|+++||+.+++|++|++|||+.|+++|+|+|+||++|||.|+|+|++|||+||++
T Consensus 1 kls~~~~yAl~~l~~La~~~~~~~~s~~~iA~~~~i~~~~l~kil~~L~~~gli~s~rG~~GGy~L~k~~~~Itl~dIi~ 80 (82)
T pfam02082 1 KLSTKTDYALHALLYLALHPGEGPVTSEEIAERQNISPVYLRKILAKLRKAGLVKSVRGPGGGYRLARPPEEITLLDVVR 80 (82)
T ss_pred CCCHHHHHHHHHHHHHHHCCCCCEECHHHHHHHHCCCHHHHHHHHHHHHCCCCEEECCCCCCCCCCCCCHHHCCHHHHHH
T ss_conf 98819999999999998189998495999998789099999999998102798256589998811348989895999998
Q ss_pred HH
Q ss_conf 97
Q gi|254780620|r 81 AT 82 (144)
Q Consensus 81 ai 82 (144)
|+
T Consensus 81 ai 82 (82)
T pfam02082 81 AV 82 (82)
T ss_pred HC
T ss_conf 79
No 9
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=98.71 E-value=2.1e-07 Score=64.77 Aligned_cols=113 Identities=21% Similarity=0.206 Sum_probs=79.2
Q ss_pred HHHHHHHHHHH--HCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHHHCCC
Q ss_conf 99999999998--5598633599999981997899999999993259057315654540002372126099999997187
Q gi|254780620|r 8 DYGIRVLMYCA--IHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKATEES 85 (144)
Q Consensus 8 ~yAi~~l~~La--~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~aie~~ 85 (144)
.-++.+|..++ .+.|+..+..+++...+.++..+..++..|.++|+|. |+..|+|.|++||++||+.|+++.+.-.
T Consensus 291 ~~~l~vl~~~~~a~~~g~~~~~~~l~~~~~~~~~~~~~~l~~L~~~~~v~--~~~~~~~vl~rd~~~i~l~~l~~~~~~~ 368 (411)
T PRK04214 291 YDLLRLLLLLDAARKHGKGLDEDEIRRLEPMGYDELGELLCELARIGYLR--RGERGQWVLARDADSIPLAELFELFVYR 368 (411)
T ss_pred HHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCE--ECCCCCEEEECCHHHCCHHHHHHHCCCC
T ss_conf 99999999999998758999999999772898689999999999789816--6688976884387758199999865789
Q ss_pred CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHH
Q ss_conf 63111468877888765664479999999999999984179999991
Q gi|254780620|r 86 FFVAECFASHKIDCPLVGSCGLTSVLRKALNAFFDVLTQYSIECLVR 132 (144)
Q Consensus 86 ~~~~~C~~~~~~~C~~~~~c~~~~~~~~~~~~~~~~L~~~TL~dl~~ 132 (144)
+..|.+++- .-.....+++..+...+.|++ .+.|+..
T Consensus 369 --p~~~~~~~~-------~~~~~~~l~~~~~~~~~~l~~-~~~~~~~ 405 (411)
T PRK04214 369 --PLPCRDDHV-------GQAADAALEQLLQPLRSVLAQ-PVGDLYT 405 (411)
T ss_pred --CCCCCCCHH-------HHHHHHHHHHHHHHHHHHHHC-HHHHHHH
T ss_conf --998677677-------789999999999899999705-1788721
No 10
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=98.63 E-value=8.3e-08 Score=67.17 Aligned_cols=68 Identities=24% Similarity=0.238 Sum_probs=59.6
Q ss_pred CCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCC
Q ss_conf 76456899999999998559863359999998199789999999999325905731565454000237
Q gi|254780620|r 2 HLTKRTDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRP 69 (144)
Q Consensus 2 kis~~~~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~ 69 (144)
-||.-..--|++|+.|-.+.++++.++|||+..+.++-+++..||.|+.-|+|+|+.||+|||.=.-.
T Consensus 3 ~LT~~QkeIL~aLi~LY~~~~r~IKgeeIA~~l~rnpGTVRNqmq~LkaLgLVegvpGPkGGY~PT~k 70 (294)
T COG2524 3 ELTSSQKEILQALINLYRRKKRPIKGEEIAEVLNRNPGTVRNQMQSLKALGLVEGVPGPKGGYKPTSK 70 (294)
T ss_pred CCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCHH
T ss_conf 42188999999999999853788555999998745961699999998852752256689889653389
No 11
>pfam03444 DUF293 Domain of unknown function. This domain is always found with a pair of CBS domains pfam00571. this region may be distantly related to the HrcA proteins of prokaryotes (Bateman A pers. obs.).
Probab=98.63 E-value=1e-07 Score=66.66 Aligned_cols=65 Identities=22% Similarity=0.194 Sum_probs=57.3
Q ss_pred CCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEEC
Q ss_conf 64568999999999985598633599999981997899999999993259057315654540002
Q gi|254780620|r 3 LTKRTDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLC 67 (144)
Q Consensus 3 is~~~~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~La 67 (144)
+|..-.--+.+|+.+-...++|+.+++||+..+.++..++..|+.|+.-|||+|++|+.|||.=.
T Consensus 2 LT~~Qr~IL~aLI~lY~~~~~pVks~~IAe~l~~spgTIRN~M~~L~~LGLVe~~pgp~gGy~PT 66 (79)
T pfam03444 2 LTPVQKEILQALINLYRKKGRAVKGEEIADIIGRNPGTVRNQMQSLKALGLVEGVPGPKGGYKPT 66 (79)
T ss_pred CCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC
T ss_conf 77899999999999999729986679999998789088999999999858865788998887658
No 12
>PRK11886 biotin--protein ligase; Provisional
Probab=97.71 E-value=0.00026 Score=46.53 Aligned_cols=72 Identities=24% Similarity=0.302 Sum_probs=56.5
Q ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCC-EEECCCCCCCCEECCCHHHCCHHHHHHH
Q ss_conf 689999999999855986335999999819978999999999932590-5731565454000237212609999999
Q gi|254780620|r 6 RTDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGI-VETVRGRRGGVRLCRPADQITILDVVKA 81 (144)
Q Consensus 6 ~~~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agl-i~S~rG~~GGy~Lak~~~~Itl~dI~~a 81 (144)
..+-.+++|-.|+ .++.+|-++||+.+++|++-+-|-++.|++.|| |+|.+++ ||+|..+++-+.-..|-..
T Consensus 2 ~~~~~~~lL~~L~--~g~~~SGe~la~~LgvSR~aVwK~i~~L~~~G~~I~s~~~~--GYrL~~~~~~l~~~~i~~~ 74 (319)
T PRK11886 2 TYEKMLQLLSLLA--DGDFHSGEQLAEELGISRAAIWKHIQTLEEWGLDIFSVKGK--GYRLATPLSLLDEERIQQL 74 (319)
T ss_pred HHHHHHHHHHHHH--CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECCC--CEEECCCCCCCCHHHHHHC
T ss_conf 1789999999973--79929699999987988999999999999779739997898--7387877566899999732
No 13
>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=97.22 E-value=0.0017 Score=41.76 Aligned_cols=56 Identities=32% Similarity=0.388 Sum_probs=46.1
Q ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECC-CCCCCCEECC
Q ss_conf 9999999985598633599999981997899999999993259057315-6545400023
Q gi|254780620|r 10 GIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVR-GRRGGVRLCR 68 (144)
Q Consensus 10 Ai~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~r-G~~GGy~Lak 68 (144)
-++++.+|... +.++.+||+..++|++.+.+-+..|.++|+|+..+ |+...|.++.
T Consensus 9 r~~Il~~L~~~---~~~~~eia~~l~is~~~vs~hL~~L~~~Gli~~~~~~~~~~y~l~~ 65 (78)
T cd00090 9 RLRILRLLLEG---PLTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREGRRVYYSLTD 65 (78)
T ss_pred HHHHHHHHHHC---CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEECCEEEEEECC
T ss_conf 99999999848---9069999877784878999999999988986899988999999799
No 14
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=97.15 E-value=0.0014 Score=42.32 Aligned_cols=54 Identities=28% Similarity=0.298 Sum_probs=45.1
Q ss_pred HHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECC-CCCCCCEECCC
Q ss_conf 9999985598633599999981997899999999993259057315-65454000237
Q gi|254780620|r 13 VLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVR-GRRGGVRLCRP 69 (144)
Q Consensus 13 ~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~r-G~~GGy~Lak~ 69 (144)
++.+|+ +++.++.|||+..++|++.+.+-|+.|+++|+|++.+ |+.=-|+++.+
T Consensus 2 Il~~L~---~~~~~~~ela~~l~is~~tvs~HL~~L~~~Glv~~~~~G~~~~Y~i~~~ 56 (66)
T smart00418 2 ILKLLA---EGELCVCELAEILGLSQSTVSHHLKKLREAGLVESRREGKRVYYSLTDE 56 (66)
T ss_pred HHHHHH---CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEECCEEEEEECCH
T ss_conf 588977---3996699999998829888879999999889268999868999998948
No 15
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=97.11 E-value=0.0026 Score=40.66 Aligned_cols=60 Identities=27% Similarity=0.297 Sum_probs=50.5
Q ss_pred HHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECC
Q ss_conf 89999999999855986335999999819978999999999932590573156545400023
Q gi|254780620|r 7 TDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCR 68 (144)
Q Consensus 7 ~~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak 68 (144)
.+=|+.+|-+++.++ ++++..|||+..++|.+-+.++++.|...|+|.-. +..|.|+|.-
T Consensus 4 l~ral~IL~~l~~~~-~~~sl~eia~~~~l~ksT~~RlL~tL~~~G~l~~~-~~~~~Y~lG~ 63 (91)
T smart00346 4 LERGLAVLRALAEEP-GGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQD-GQNGRYRLGP 63 (91)
T ss_pred HHHHHHHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEE-CCCCEEEECH
T ss_conf 999999999997289-99899999999890999999999999988996884-9999775309
No 16
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=97.05 E-value=0.0023 Score=40.90 Aligned_cols=60 Identities=27% Similarity=0.400 Sum_probs=46.7
Q ss_pred HHHHH-CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECC--CCCCCCEE---CCCHHHCC
Q ss_conf 99985-598633599999981997899999999993259057315--65454000---23721260
Q gi|254780620|r 15 MYCAI-HNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVR--GRRGGVRL---CRPADQIT 74 (144)
Q Consensus 15 ~~La~-~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~r--G~~GGy~L---ak~~~~It 74 (144)
+|.+. ..++|.++.+||+..+.+.+.+.|-++.|..+|+|.=.+ .++|||.- +.|+++++
T Consensus 32 v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~i~~ee~k 97 (126)
T COG3355 32 VYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKPIDPEEIK 97 (126)
T ss_pred HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEECCCCCCEEEEEECCCHHHHH
T ss_conf 999998646995799999997831999999999999858866664226788614887117999999
No 17
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=96.98 E-value=0.004 Score=39.54 Aligned_cols=63 Identities=19% Similarity=0.184 Sum_probs=50.8
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCC
Q ss_conf 56899999999998559863359999998199789999999999325905731565454000237
Q gi|254780620|r 5 KRTDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRP 69 (144)
Q Consensus 5 ~~~~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~ 69 (144)
+..+=|+.+|-+++..+ .+.|..|||+..++|++-+.++|+.|.+.|||. ..+..|.|+|...
T Consensus 22 qsl~Ral~IL~~la~~~-~~ltl~eia~~lglpksT~~RlL~tL~~~G~v~-~d~~~~~Y~lG~~ 84 (271)
T PRK10163 22 QALERGIAILQYLEKSG-GSSSVSDISLNLDLPLSTTFRLLKVLQAADFVY-QDSQLGWWHIGLG 84 (271)
T ss_pred CHHHHHHHHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE-EECCCCCEECCHH
T ss_conf 29999999999997479-997999999997919999999999999689889-8489991764789
No 18
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=96.97 E-value=0.0045 Score=39.23 Aligned_cols=63 Identities=19% Similarity=0.186 Sum_probs=50.9
Q ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCH
Q ss_conf 68999999999985598633599999981997899999999993259057315654540002372
Q gi|254780620|r 6 RTDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPA 70 (144)
Q Consensus 6 ~~~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~ 70 (144)
..+=|+.+|-.++.. +.+.+..|||+..++|++-+.++|+.|...|||.-. +..|.|+|.-..
T Consensus 9 sl~Ral~ILe~l~~~-~~~lslsela~~lglpksTv~RlL~tL~~~G~l~~~-~~~~~Y~LG~~~ 71 (264)
T PRK09834 9 GLSRGLMVLRALNRL-DGGATVGLLAELTGLHRTTVRRLLETLQEEGYVRRS-ASDDSFRLTLKV 71 (264)
T ss_pred HHHHHHHHHHHHHHC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEE-CCCCCEECCHHH
T ss_conf 999999999987417-999799999999790999999999999978998996-799976516079
No 19
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=96.89 E-value=0.0022 Score=41.07 Aligned_cols=59 Identities=22% Similarity=0.271 Sum_probs=46.6
Q ss_pred HHHHHHHH---CCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHH
Q ss_conf 99999985---598-63359999998199789999999999325905731565454000237212
Q gi|254780620|r 12 RVLMYCAI---HND-YPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQ 72 (144)
Q Consensus 12 ~~l~~La~---~~~-~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~ 72 (144)
++...++. .+| +.-|+.++|...+++|..+.|..+.|.++|+|.+.||. |+..+.++.+
T Consensus 19 qIk~~I~~g~l~pGdkLPSvRelA~~~~VNpnTv~raY~eLE~eG~i~t~rg~--G~fV~~~~~~ 81 (125)
T COG1725 19 QIKEQIASGELKPGDKLPSVRELAKDLGVNPNTVQRAYQELEREGIVETKRGK--GTFVTEDAKE 81 (125)
T ss_pred HHHHHHHHCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCE--EEEECCCCHH
T ss_conf 99999980886888889759999998198988999999999978877986670--5797477145
No 20
>pfam08279 HTH_11 HTH domain. This family includes helix-turn-helix domains in a wide variety of proteins.
Probab=96.89 E-value=0.0037 Score=39.76 Aligned_cols=51 Identities=24% Similarity=0.272 Sum_probs=41.9
Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC-CEEECCCCCCCCE
Q ss_conf 99999985598633599999981997899999999993259-0573156545400
Q gi|254780620|r 12 RVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAG-IVETVRGRRGGVR 65 (144)
Q Consensus 12 ~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~ag-li~S~rG~~GGy~ 65 (144)
.+|..|-. .++++|+++||+..++|..-+.+=++.|...| -|.|.+|+ ||+
T Consensus 4 ~il~~L~~-~~~~vt~~~La~~l~VSr~TV~rdi~~L~~~G~~I~s~~g~--GY~ 55 (55)
T pfam08279 4 QILELLLQ-AREPISGQELAEKLGVSRRTIRRDIKALEALGVPIESEPGR--GYR 55 (55)
T ss_pred HHHHHHHH-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCEEECCCC--CCC
T ss_conf 99999997-69991899999996988999999999999889978846899--998
No 21
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=96.87 E-value=0.006 Score=38.48 Aligned_cols=58 Identities=26% Similarity=0.311 Sum_probs=47.7
Q ss_pred HCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCC-EEECCCCCCCCEECCCHHHCCHHHH
Q ss_conf 55986335999999819978999999999932590-5731565454000237212609999
Q gi|254780620|r 19 IHNDYPNRISQIAEACCISELFLFKILQPLVKAGI-VETVRGRRGGVRLCRPADQITILDV 78 (144)
Q Consensus 19 ~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agl-i~S~rG~~GGy~Lak~~~~Itl~dI 78 (144)
...+.++|-++||+.+++|+.-+.|-++.|+..|+ |.|++++ ||+|...|+-..-..|
T Consensus 14 ~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~I~s~~~k--GY~L~~~~~ll~~~~i 72 (79)
T COG1654 14 LLTGNFVSGEKLAEELGISRTAVWKHIQQLREEGVDIESVRGK--GYLLPQLPDLLPQEII 72 (79)
T ss_pred HCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCEEECCCC--CEECCCCCCCCCHHHH
T ss_conf 7379966689999997865999999999999809716860788--6365675010758888
No 22
>PRK11569 transcriptional repressor IclR; Provisional
Probab=96.85 E-value=0.006 Score=38.49 Aligned_cols=61 Identities=18% Similarity=0.308 Sum_probs=49.8
Q ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECC
Q ss_conf 689999999999855986335999999819978999999999932590573156545400023
Q gi|254780620|r 6 RTDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCR 68 (144)
Q Consensus 6 ~~~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak 68 (144)
..+=|+.+|-.++..+ .+++..|||+..++|++-+.++++.|...|||+-. +..|.|+|.-
T Consensus 26 sl~Ral~IL~~la~~~-~~lsl~eia~~lglpksT~~RlL~tL~~~G~v~~~-~~~~~Y~LG~ 86 (274)
T PRK11569 26 SLTRGLKLLEWIAESN-GSVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQV-GELGHWAIGA 86 (274)
T ss_pred HHHHHHHHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEC-CCCCEECCCH
T ss_conf 9999999999996389-99899999998791999999999999976987786-9988022457
No 23
>pfam01978 TrmB Sugar-specific transcriptional regulator TrmB. One member of this family, TrmB, has been shown to be a sugar-specific transcriptional regulator of the trehalose/maltose ABC transporter in Thermococcus litoralis.
Probab=96.79 E-value=0.0038 Score=39.66 Aligned_cols=62 Identities=23% Similarity=0.339 Sum_probs=47.2
Q ss_pred HHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHH
Q ss_conf 89999999999855986335999999819978999999999932590573156545400023721
Q gi|254780620|r 7 TDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPAD 71 (144)
Q Consensus 7 ~~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~ 71 (144)
++|-.++-+.|.. .++.++.+||+..++|++.+..+|+.|.+.|+|...+|..- ..-+.|||
T Consensus 7 s~~E~~vY~~Ll~--~g~~t~~eia~~~~i~r~~vY~~L~~L~~kGlv~~~~~~p~-~y~a~~Pe 68 (68)
T pfam01978 7 SEYEAKVYLALLK--LGPATADEIAEESGVPRSKVYEVLRSLEKKGLVEREKGRPK-KYRAVDPE 68 (68)
T ss_pred CHHHHHHHHHHHH--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCCC-EEEECCCC
T ss_conf 9999999999998--19988999999959889899999999998898898679744-79815969
No 24
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=96.74 E-value=0.0076 Score=37.90 Aligned_cols=75 Identities=25% Similarity=0.345 Sum_probs=55.2
Q ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHC--CHHHHHHHHC
Q ss_conf 68999999999985598633599999981997899999999993259057315654540002372126--0999999971
Q gi|254780620|r 6 RTDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQI--TILDVVKATE 83 (144)
Q Consensus 6 ~~~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~I--tl~dI~~aie 83 (144)
.-+| +.+ +|.....++++.+.+||+.++++++-+.+.+++|.+.|+|+= =+.||+.|...-+++ .+..-.+.++
T Consensus 8 ~edY-L~~-Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~--~~y~gi~LT~~G~~~a~~~~r~hrlle 83 (154)
T COG1321 8 EEDY-LET-IYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEY--EPYGGVTLTEKGREKAKELLRKHRLLE 83 (154)
T ss_pred HHHH-HHH-HHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCEEE--ECCCCEEECCCHHHHHHHHHHHHHHHH
T ss_conf 8999-999-999984368751999999858992789999999987899788--458886788354899999999999999
Q ss_pred C
Q ss_conf 8
Q gi|254780620|r 84 E 84 (144)
Q Consensus 84 ~ 84 (144)
-
T Consensus 84 ~ 84 (154)
T COG1321 84 R 84 (154)
T ss_pred H
T ss_conf 9
No 25
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=96.74 E-value=0.003 Score=40.29 Aligned_cols=77 Identities=22% Similarity=0.212 Sum_probs=56.2
Q ss_pred CHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCC--HHHHHHH
Q ss_conf 45689999999999855986335999999819978999999999932590573156545400023721260--9999999
Q gi|254780620|r 4 TKRTDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQIT--ILDVVKA 81 (144)
Q Consensus 4 s~~~~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~It--l~dI~~a 81 (144)
.+.-|| |.++..|.. .++.+++.+||+.++++++-+.+-+++|.+.|||. ..++||..|...-.++- +..=.+.
T Consensus 4 ~s~EdY-Le~Iy~L~~-~~~~vr~~dIA~~L~Vs~~SVs~mikkL~~~Glv~--~~~y~~i~LT~~G~~~A~~i~~rHrl 79 (142)
T PRK03902 4 PSMEDY-IEQIYLLIE-EKGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLI--YEKYRGLVLTPKGKKIGKRLVYRHEL 79 (142)
T ss_pred CHHHHH-HHHHHHHHH-CCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCCE--ECCCCCEEECHHHHHHHHHHHHHHHH
T ss_conf 429999-999999982-58971299999997899533999999999879924--55898756898799999999999999
Q ss_pred HCC
Q ss_conf 718
Q gi|254780620|r 82 TEE 84 (144)
Q Consensus 82 ie~ 84 (144)
++.
T Consensus 80 le~ 82 (142)
T PRK03902 80 LEQ 82 (142)
T ss_pred HHH
T ss_conf 999
No 26
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=96.63 E-value=0.0064 Score=38.34 Aligned_cols=58 Identities=14% Similarity=0.114 Sum_probs=47.9
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECC-CCCCCCEECCCH
Q ss_conf 999999985598633599999981997899999999993259057315-654540002372
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVR-GRRGGVRLCRPA 70 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~r-G~~GGy~Lak~~ 70 (144)
++++..|..+ +..++.+|++..+++.+-+++-|+.|+++|+|++.| |..==|+|+.+.
T Consensus 17 l~Il~lL~~~--gelcV~eL~~~l~~sQs~vS~HL~~L~~aGlV~~rr~G~~vyY~Ln~~~ 75 (106)
T PRK10141 17 LGIVLLLRES--GELCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQGKWVHYRLSPHI 75 (106)
T ss_pred HHHHHHHHHC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCEEEECCEEEEEEECCCC
T ss_conf 9999999874--9956999998869988899999999998897303741417998779988
No 27
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=96.62 E-value=0.0099 Score=37.21 Aligned_cols=48 Identities=19% Similarity=0.178 Sum_probs=39.8
Q ss_pred CCCCCCCH-HHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCC
Q ss_conf 59863359-999998199789999999999325905731565454000237
Q gi|254780620|r 20 HNDYPNRI-SQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRP 69 (144)
Q Consensus 20 ~~~~~~s~-~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~ 69 (144)
.+|.+.++ .+||+..++|++-|+.-|..|...|+|++.+| ||+....+
T Consensus 29 ~pGd~LPsE~eLA~~lgVSR~~VREAL~~L~~~GlV~~r~g--~G~~V~~~ 77 (254)
T PRK09464 29 RPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQG--GGTFVQSS 77 (254)
T ss_pred CCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCEEEECC--CCEEECCC
T ss_conf 99396936999999868995599999999998899897178--71364677
No 28
>pfam09339 HTH_IclR IclR helix-turn-helix domain.
Probab=96.52 E-value=0.0068 Score=38.19 Aligned_cols=48 Identities=25% Similarity=0.261 Sum_probs=42.3
Q ss_pred HHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Q ss_conf 9999999999855986335999999819978999999999932590573
Q gi|254780620|r 8 DYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVET 56 (144)
Q Consensus 8 ~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S 56 (144)
+=|+++|-+++.++ ++++.+|||+..++|++-+.++++.|.+.|||.-
T Consensus 3 ~r~l~iL~~~~~~~-~~~~l~eia~~~gl~kstv~RlL~tL~~~G~v~~ 50 (52)
T pfam09339 3 DRALAILEALAEAP-GGLSLTEIARRTGLPKSTAHRLLQTLVELGYVEQ 50 (52)
T ss_pred HHHHHHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCCC
T ss_conf 99999999986289-9989999999989199999999999998819116
No 29
>PRK11050 manganese transport regulator MntR; Provisional
Probab=96.51 E-value=0.005 Score=38.96 Aligned_cols=60 Identities=22% Similarity=0.237 Sum_probs=48.1
Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCC
Q ss_conf 999999855986335999999819978999999999932590573156545400023721260
Q gi|254780620|r 12 RVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQIT 74 (144)
Q Consensus 12 ~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~It 74 (144)
-++..|.. .++.+.+.+||+.+|++++-+.+.+++|.+.|||. ..++||..|...-.++-
T Consensus 43 E~I~~L~~-~~G~aR~~DIA~~LgVs~pSVt~mlkrL~~~GlV~--~~~Y~~I~LT~~G~~~A 102 (155)
T PRK11050 43 ELIADLIA-EVGEARQVDIAARLGVSQPTVAKMLKRLARDGLVE--MRPYRGVFLTPEGEKLA 102 (155)
T ss_pred HHHHHHHH-CCCCEEHHHHHHHHCCCCHHHHHHHHHHHHCCCEE--ECCCCCEEECHHHHHHH
T ss_conf 99999998-26956499999890999331999999998789988--71898846897799999
No 30
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=96.41 E-value=0.017 Score=35.83 Aligned_cols=61 Identities=23% Similarity=0.238 Sum_probs=48.6
Q ss_pred HHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCC
Q ss_conf 899999999998559863359999998199789999999999325905731565454000237
Q gi|254780620|r 7 TDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRP 69 (144)
Q Consensus 7 ~~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~ 69 (144)
.+=|+.+|-+++.++ ...+..|||+..++|++-+.++|+.|...|||+-. +..|=|+|.-.
T Consensus 3 l~ral~iL~~l~~~~-~~l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d-~~~grY~Lg~~ 63 (246)
T COG1414 3 LERALAILDLLAEGP-GGLSLAELAERLGLPKSTVHRLLQTLVELGYVEQD-PEDGRYRLGPR 63 (246)
T ss_pred HHHHHHHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEC-CCCCEEEECHH
T ss_conf 899999999997188-88879999998791988999999999978988897-99996985789
No 31
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=96.38 E-value=0.024 Score=34.90 Aligned_cols=59 Identities=24% Similarity=0.209 Sum_probs=43.9
Q ss_pred HHHHHHHHH-HCCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCC
Q ss_conf 999999998-5598633-59999998199789999999999325905731565454000237
Q gi|254780620|r 10 GIRVLMYCA-IHNDYPN-RISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRP 69 (144)
Q Consensus 10 Ai~~l~~La-~~~~~~~-s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~ 69 (144)
.|+-.+.=. ..+|.+. +-.+||+..|+|++-++--|..|...|+|++.+|+ |.|.-..+
T Consensus 15 ~ir~~I~~g~l~pG~~LP~E~eLae~~gVSR~~VREAL~~L~~~GlV~~~~g~-G~~V~~~~ 75 (251)
T PRK09990 15 RIERLIVDGVLKVGQALPSERRLTEKLGVSRSALREGLKVLRGRGIIETAQGR-GSFVARLN 75 (251)
T ss_pred HHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCC-CCEEECCC
T ss_conf 99999980999992979239999999897959999999999988997985798-50671587
No 32
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=96.24 E-value=0.03 Score=34.33 Aligned_cols=65 Identities=22% Similarity=0.235 Sum_probs=45.6
Q ss_pred CHHHHHHHHHHHHHH-HCCCCCCCH-HHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCH
Q ss_conf 456899999999998-559863359-9999981997899999999993259057315654540002372
Q gi|254780620|r 4 TKRTDYGIRVLMYCA-IHNDYPNRI-SQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPA 70 (144)
Q Consensus 4 s~~~~yAi~~l~~La-~~~~~~~s~-~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~ 70 (144)
+...-=.|+-.+.=. ..+|.+..+ .+||+..|+|++-|+.-|..|...|+|++.+| +|+....++
T Consensus 4 ~e~V~e~Lr~~I~~g~l~pG~~LP~E~eLae~~GVSRt~VREAL~~L~~eGlV~~~~g--~G~~V~~~~ 70 (253)
T PRK10421 4 SDEVADRVRALIEEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRG--GGTFIRWQH 70 (253)
T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEC--CEEEECCCC
T ss_conf 9999999999998199998595933999999979698999999999998898799757--824873476
No 33
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=96.03 E-value=0.038 Score=33.77 Aligned_cols=69 Identities=20% Similarity=0.328 Sum_probs=51.6
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCC-EEECCCCCCCCEECC----CHHHCCHHHHHHH
Q ss_conf 9999999855986335999999819978999999999932590-573156545400023----7212609999999
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGI-VETVRGRRGGVRLCR----PADQITILDVVKA 81 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agl-i~S~rG~~GGy~Lak----~~~~Itl~dI~~a 81 (144)
+.++.+|.. ... +|+.++|+..++|...+.+=+..|..+|+ |.+.+|++|||.+.. ||-..|--++.-.
T Consensus 11 ~~ii~~L~~-~~~-vta~~lA~~~~VS~RTi~RDi~~L~~~gvPI~~e~G~~~gy~~~~~~~L~pl~ft~~E~~Al 84 (311)
T COG2378 11 LQIIQILRA-KET-VTAAELADEFEVSVRTIYRDIATLRAAGVPIEGERGKGGGYRLRPGFKLPPLMFTEEEAEAL 84 (311)
T ss_pred HHHHHHHHH-CCC-CHHHHHHHHHCCCHHHHHHHHHHHHHCCCCEEECCCCCCCEEECCCCCCCCCCCCHHHHHHH
T ss_conf 999999985-760-45999998729889999999999997699765325886318960577788666898799999
No 34
>pfam01047 MarR MarR family. The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif.
Probab=95.92 E-value=0.028 Score=34.55 Aligned_cols=49 Identities=24% Similarity=0.383 Sum_probs=40.9
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCC
Q ss_conf 999999985598633599999981997899999999993259057315654
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRR 61 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~ 61 (144)
.++|..|..++ +++..+||+..+++++.+.+++.+|.+.|||.-.+-+.
T Consensus 6 ~~vL~~l~~~~--~~s~~~la~~~~~~~~~vs~~i~~Le~~glv~R~~~~~ 54 (59)
T pfam01047 6 FHILRILYEHG--PLTVSELAEKLGVDRSTVTRVLDRLEKKGLIERSRSPE 54 (59)
T ss_pred HHHHHHHHHCC--CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCC
T ss_conf 99999999469--92999999998858654999999998897988627999
No 35
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=95.88 E-value=0.065 Score=32.39 Aligned_cols=64 Identities=17% Similarity=0.237 Sum_probs=47.7
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCC--CEECCCHHHCCHH
Q ss_conf 99999998559863359999998199789999999999325905731565454--0002372126099
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGG--VRLCRPADQITIL 76 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GG--y~Lak~~~~Itl~ 76 (144)
.++|.+|+.++ ++|..+||+..+++++.+.+++..|.+.|||...+.+.-+ +.+.-.++-..+.
T Consensus 13 ~~vL~~l~~~~--~~t~~~la~~l~~~~~~vs~~v~~L~~~glv~r~~~~~D~R~~~i~LT~~G~~~~ 78 (101)
T smart00347 13 FLVLRILYEEG--PLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEEGRELI 78 (101)
T ss_pred HHHHHHHHHCC--CCCHHHHHHHHCCCHHHHHHHHHHHHCCCCEEEEECCCCCCEEEEEECHHHHHHH
T ss_conf 99999999769--9799999999896887999999999458938982189998858989998999999
No 36
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=95.82 E-value=0.02 Score=35.38 Aligned_cols=64 Identities=23% Similarity=0.369 Sum_probs=51.3
Q ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHH
Q ss_conf 6899999999998559863359999998199789999999999325905731565454000237212
Q gi|254780620|r 6 RTDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQ 72 (144)
Q Consensus 6 ~~~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~ 72 (144)
.++|=.++-+.|-.. ++.|++|||+..++|++.+..||..|.+.|+|+...|+--=| =+.||++
T Consensus 14 lt~yEa~vY~aLl~~--g~~tA~eis~~sgvP~~kvY~vl~sLe~kG~v~~~~g~P~~y-~av~p~~ 77 (247)
T COG1378 14 LTEYEAKVYLALLCL--GEATAKEISEASGVPRPKVYDVLRSLEKKGLVEVIEGRPKKY-RAVPPEE 77 (247)
T ss_pred CCHHHHHHHHHHHHH--CCCCHHHHHHHCCCCCHHHHHHHHHHHHCCCEEECCCCCCEE-EECCHHH
T ss_conf 978899999999981--887799999865999322999999998788778407998448-8579999
No 37
>PRK12423 LexA repressor; Provisional
Probab=95.79 E-value=0.059 Score=32.64 Aligned_cols=69 Identities=26% Similarity=0.302 Sum_probs=49.5
Q ss_pred CCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCC-CHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHH
Q ss_conf 6456899999999998559863359999998199-78999999999932590573156545400023721
Q gi|254780620|r 3 LTKRTDYGIRVLMYCAIHNDYPNRISQIAEACCI-SELFLFKILQPLVKAGIVETVRGRRGGVRLCRPAD 71 (144)
Q Consensus 3 is~~~~yAi~~l~~La~~~~~~~s~~eIA~~~~i-~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~ 71 (144)
||.+-.--+..+..--...+.+-|.+||++..++ |+.-+.+-++.|.+.|+|+-..|..=|++|..++.
T Consensus 4 LT~kQ~~iL~fI~~~~~~~G~~Pt~rEI~~~~g~~S~~~v~~hl~~L~~kG~i~r~~~~~R~i~l~~~~~ 73 (202)
T PRK12423 4 LTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEAGLIEVVPNQARGIRLPGGAG 73 (202)
T ss_pred CCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHCCCEECCCCCCEEEEECCCCC
T ss_conf 0899999999999999962989889999998299986789999999998879970699953799368778
No 38
>pfam01022 HTH_5 Bacterial regulatory protein, arsR family. Members of this family contains a DNA binding 'helix-turn-helix' motif. This family includes other proteins which are not included in the Prosite definition.
Probab=95.73 E-value=0.021 Score=35.31 Aligned_cols=43 Identities=23% Similarity=0.279 Sum_probs=36.9
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Q ss_conf 9999999855986335999999819978999999999932590573
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVET 56 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S 56 (144)
++++..|+. ++.++.+||+..+++++-+.+-|+.|+++|+|++
T Consensus 5 l~Il~~L~~---~~~~v~el~~~l~~sq~~vS~HL~~L~~~GlV~~ 47 (47)
T pfam01022 5 LKILYLLSE---GELCVCELAEILGLSQSTVSHHLKKLREAGLVEK 47 (47)
T ss_pred HHHHHHHHC---CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCCC
T ss_conf 999999980---8996999999989588699999999989809689
No 39
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=95.64 E-value=0.041 Score=33.55 Aligned_cols=63 Identities=25% Similarity=0.182 Sum_probs=46.5
Q ss_pred HHHHHHHH-HCCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCC
Q ss_conf 99999998-5598633-5999999819978999999999932590573156545400023721260
Q gi|254780620|r 11 IRVLMYCA-IHNDYPN-RISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQIT 74 (144)
Q Consensus 11 i~~l~~La-~~~~~~~-s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~It 74 (144)
|+-++.=. ..+|.+. +=.+||+..|+|++-|+.-|+.|...|+|++.+|. |-|....++..+.
T Consensus 18 Lr~~I~~G~l~PGdrLP~EreLAe~lgVSRt~VREAL~~Le~~GLV~~r~G~-Gt~V~~~~~~~~~ 82 (257)
T PRK10225 18 IRDLIIKTPYNPGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEVRRGA-GIYVLDSSGSHNT 82 (257)
T ss_pred HHHHHHHCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECC-EEEEECCCHHHHC
T ss_conf 9999982899997939529999999798878999999999988997996488-7788268704210
No 40
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=95.61 E-value=0.046 Score=33.25 Aligned_cols=63 Identities=22% Similarity=0.301 Sum_probs=47.2
Q ss_pred HCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHH---HHCC
Q ss_conf 55986335999999819978999999999932590573156545400023721260999999---9718
Q gi|254780620|r 19 IHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVK---ATEE 84 (144)
Q Consensus 19 ~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~---aie~ 84 (144)
..+|..++-.+||+..|+|+.=|+.-|+.|...|+|+..+++ |+..+ +++.-.+.|+|+ ++|+
T Consensus 25 l~PG~~L~e~~Lae~lgVSRtPVREAL~rL~~eGLV~~~p~r--G~~V~-~~s~~~i~ei~~~R~~LE~ 90 (224)
T PRK11534 25 FQPDEKLRMSLLTSRYALGVGPLREALSQLVAERLVTVVNQK--GYRVA-SMSEQELLDIFDARANMEA 90 (224)
T ss_pred CCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCC--EEEEE-ECCCHHHHHHHHHHHHHHH
T ss_conf 899395589999999798858999999999987998874797--36982-2750109999999999999
No 41
>pfam00392 GntR Bacterial regulatory proteins, gntR family. This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector-binding/oligomerisation domain. The GntR-like proteins include the following sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA, DevA, DasR. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships. The DasR regulator has been shown to be a global regulator of primary metabolism and development in Streptomyces coelicolor.
Probab=95.58 E-value=0.026 Score=34.77 Aligned_cols=42 Identities=21% Similarity=0.204 Sum_probs=37.0
Q ss_pred CCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCC
Q ss_conf 598633-599999981997899999999993259057315654
Q gi|254780620|r 20 HNDYPN-RISQIAEACCISELFLFKILQPLVKAGIVETVRGRR 61 (144)
Q Consensus 20 ~~~~~~-s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~ 61 (144)
.+|... |..++|+..++|+.-+++.++.|...|+|.+.+|++
T Consensus 19 ~~G~~LPs~~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~g~G 61 (64)
T pfam00392 19 RPGDKLPSERELAAEFGVSRTTVREALRRLEAEGLVERRPGRG 61 (64)
T ss_pred CCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCE
T ss_conf 9929984799999997969999999999999889389977953
No 42
>pfam01325 Fe_dep_repress Iron dependent repressor, N-terminal DNA binding domain. This family includes the Diphtheria toxin repressor. DNA binding is through a helix-turn-helix motif.
Probab=95.57 E-value=0.034 Score=34.05 Aligned_cols=47 Identities=17% Similarity=0.130 Sum_probs=39.5
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECC
Q ss_conf 999999985598633599999981997899999999993259057315
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVR 58 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~r 58 (144)
|.++..|.. .++++++.+||+.++++++-+.+-+++|.+.|||.-.+
T Consensus 8 Lk~Iy~l~~-~~~~v~~~~iA~~L~Vs~~SVt~mlkkL~~~GlV~~e~ 54 (58)
T pfam01325 8 LETIYTLSE-EKGVVKTKDLAERLNVSPSTVSEMLKKLEKDGYVVYEP 54 (58)
T ss_pred HHHHHHHHC-CCCCEEHHHHHHHHCCCCHHHHHHHHHHHHCCCEEEEC
T ss_conf 999999882-69961299999995999252999999999889978532
No 43
>PRK03837 transcriptional regulator NanR; Provisional
Probab=95.54 E-value=0.056 Score=32.78 Aligned_cols=46 Identities=15% Similarity=0.144 Sum_probs=38.7
Q ss_pred HCCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCE
Q ss_conf 5598633-5999999819978999999999932590573156545400
Q gi|254780620|r 19 IHNDYPN-RISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVR 65 (144)
Q Consensus 19 ~~~~~~~-s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~ 65 (144)
..+|.+. +-.+||+..|+|++-++.-|+.|...|+|+..+|++ +|.
T Consensus 32 l~pG~rLp~E~eLae~lgVSRtpVREAL~~L~~~GlV~~~~g~g-~~V 78 (243)
T PRK03837 32 FGPGEQLPSERELMAFFGVGRPSVREALQALKRKGLVQISHGER-ARV 78 (243)
T ss_pred CCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECCC-CEE
T ss_conf 99949793599999997969789999999999889989950897-068
No 44
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=95.54 E-value=0.045 Score=33.32 Aligned_cols=53 Identities=28% Similarity=0.389 Sum_probs=43.7
Q ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCC-C-----CEECCCHHH
Q ss_conf 5986335999999819978999999999932590573156545-4-----000237212
Q gi|254780620|r 20 HNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRG-G-----VRLCRPADQ 72 (144)
Q Consensus 20 ~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~G-G-----y~Lak~~~~ 72 (144)
...+++|+.+||+.+++|+.-+++-|..|...|+|++.+.+.| | |+|..+-.+
T Consensus 21 ~~~g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~~~~~g~GRP~~~y~Lt~~g~~ 79 (218)
T COG2345 21 KKSGPVSADELAEELGISPMAVRRHLDDLEAEGLVEVERQQGGRGRPAKLYRLTEKGRE 79 (218)
T ss_pred HCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECCCCCCCCCEEEEECCCCHH
T ss_conf 31698249999988599989999999999868666876425789997333220026265
No 45
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=95.45 E-value=0.03 Score=34.38 Aligned_cols=42 Identities=17% Similarity=0.133 Sum_probs=36.9
Q ss_pred CCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCC
Q ss_conf 598633-599999981997899999999993259057315654
Q gi|254780620|r 20 HNDYPN-RISQIAEACCISELFLFKILQPLVKAGIVETVRGRR 61 (144)
Q Consensus 20 ~~~~~~-s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~ 61 (144)
.+|... |..++|+..++|+.-+++.+..|...|+|.+.+|++
T Consensus 15 ~~G~~LPs~~~la~~~~vSr~tvr~A~~~L~~~G~i~~~~g~G 57 (60)
T smart00345 15 RPGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRRPGSG 57 (60)
T ss_pred CCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCE
T ss_conf 9839881099999998949999999999999889789966854
No 46
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=95.38 E-value=0.087 Score=31.63 Aligned_cols=52 Identities=17% Similarity=0.077 Sum_probs=41.6
Q ss_pred CCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHH
Q ss_conf 598633-59999998199789999999999325905731565454000237212
Q gi|254780620|r 20 HNDYPN-RISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQ 72 (144)
Q Consensus 20 ~~~~~~-s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~ 72 (144)
.+|... |=.++|+..|+|++-++.-++.|...|+|++.+|. |.|....+|..
T Consensus 27 ~pGdrLPsEreLAe~fGVSRt~VREAL~~Le~~GlVe~r~G~-Gt~V~~~~~~~ 79 (258)
T PRK11523 27 LVGDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVEVRKGS-GIHVVSNQPRH 79 (258)
T ss_pred CCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECC-EEEECCCCCCC
T ss_conf 997909669999999798879999999999988998996378-15874588411
No 47
>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=95.22 E-value=0.042 Score=33.53 Aligned_cols=44 Identities=25% Similarity=0.251 Sum_probs=37.9
Q ss_pred CCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCE
Q ss_conf 598633-5999999819978999999999932590573156545400
Q gi|254780620|r 20 HNDYPN-RISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVR 65 (144)
Q Consensus 20 ~~~~~~-s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~ 65 (144)
.+|.+. |..+||+..++|+.-+++.+..|...|+|.+.+|+ ||.
T Consensus 20 ~~G~~LPs~~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~g~--G~~ 64 (66)
T cd07377 20 KPGDRLPSERELAEELGVSRTTVREALRELEAEGLVERRPGR--GTF 64 (66)
T ss_pred CCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCC--EEE
T ss_conf 991999279999999798889999999999988958997382--788
No 48
>PRK00215 LexA repressor; Validated
Probab=95.14 E-value=0.13 Score=30.61 Aligned_cols=69 Identities=19% Similarity=0.242 Sum_probs=49.1
Q ss_pred CHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCC-CHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHH
Q ss_conf 456899999999998559863359999998199-789999999999325905731565454000237212
Q gi|254780620|r 4 TKRTDYGIRVLMYCAIHNDYPNRISQIAEACCI-SELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQ 72 (144)
Q Consensus 4 s~~~~yAi~~l~~La~~~~~~~s~~eIA~~~~i-~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~ 72 (144)
|.+-.--+..+..--...+-+-|.+|||+..++ |+.-+.+.++.|.+.|+|+-..|+.=|.++..++..
T Consensus 3 T~kQ~~il~fI~~~~~~~g~~Ps~rEI~~~~g~~S~~tV~~~l~~Le~kG~i~r~~~~~R~i~i~~~~~~ 72 (204)
T PRK00215 3 TARQQEILDFIKDRIEETGYPPSRREIADALGLRSPSAVHEHLKALERKGFIRRDPGRSRAIEVLPAEAA 72 (204)
T ss_pred CHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHCCCEECCCCCCCEEEEECCCCC
T ss_conf 9899999999999999748899899999980999818999999999879788706999733897157665
No 49
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein; InterPro: IPR010163 Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity..
Probab=95.13 E-value=0.088 Score=31.60 Aligned_cols=62 Identities=18% Similarity=0.156 Sum_probs=49.0
Q ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCC-CCCCCEECC
Q ss_conf 689999999999855986335999999819978999999999932590573156-545400023
Q gi|254780620|r 6 RTDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRG-RRGGVRLCR 68 (144)
Q Consensus 6 ~~~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG-~~GGy~Lak 68 (144)
.++--+.+|-+|....| ..+++.||+.++.+.+.+.+.+..|.+.|||++..+ +.=+|.+.+
T Consensus 167 ~s~~~~~vL~~L~~~~G-e~~v~~iA~~lg~s~~T~~~~~~~Lek~gLv~~~~~~k~~~~~~t~ 229 (231)
T TIGR01884 167 LSREELKVLEALKAEKG-EKSVKNIAKKLGKSLSTISRHLAELEKKGLVESKGRGKGKRYSVTK 229 (231)
T ss_pred CCHHHHHHHHHHHCCCC-EECHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECCCCCCCEECC
T ss_conf 88999999999850788-0528779988578887999999988744754563046787200013
No 50
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=95.08 E-value=0.032 Score=34.23 Aligned_cols=46 Identities=28% Similarity=0.372 Sum_probs=40.8
Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCC
Q ss_conf 999999819978999999999932590573156545400023721260
Q gi|254780620|r 27 ISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQIT 74 (144)
Q Consensus 27 ~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~It 74 (144)
+.+||+..+++++-+.+.+++|.+.|||+ .-++||+.|...-.++-
T Consensus 2 ~~diA~~L~vs~~sVs~~l~~L~~~Gli~--~~~y~~i~LT~~G~~~A 47 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEKDGLVE--YEPYRGITLTEKGRRLA 47 (96)
T ss_pred HHHHHHHHCCCCHHHHHHHHHHHHCCCEE--ECCCCCEEECHHHHHHH
T ss_conf 78899884999167999999999888988--74998978898799999
No 51
>pfam01726 LexA_DNA_bind LexA DNA binding domain. This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins. The aligned region contains a variant form of the helix-turn-helix DNA binding motif. This domain is found associated with pfam00717 the auto-proteolytic domain of LexA EC:3.4.21.88.
Probab=95.02 E-value=0.13 Score=30.57 Aligned_cols=58 Identities=24% Similarity=0.272 Sum_probs=41.0
Q ss_pred CCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCC-CHHHHHHHHHHHHHCCCEEECCCC
Q ss_conf 6456899999999998559863359999998199-789999999999325905731565
Q gi|254780620|r 3 LTKRTDYGIRVLMYCAIHNDYPNRISQIAEACCI-SELFLFKILQPLVKAGIVETVRGR 60 (144)
Q Consensus 3 is~~~~yAi~~l~~La~~~~~~~s~~eIA~~~~i-~~~~l~kil~~L~~agli~S~rG~ 60 (144)
||.+-.--+..+..--...|-+-|..||++..|+ |++-+.+.+..|.+.|+|+-..|.
T Consensus 4 LT~rQ~~il~~I~~~~~~~G~~Pt~rEI~~~~g~~S~s~v~~~l~~Le~kG~I~r~~~~ 62 (65)
T pfam01726 4 LTERQREVLDFIKASIEETGYPPSRREIAQALGLRSPNAAEEHLKALERKGYIERDPGK 62 (65)
T ss_pred CCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHCCCEECCCCC
T ss_conf 37999999999999999828898799999993899809999999999998396348999
No 52
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=94.98 E-value=0.19 Score=29.57 Aligned_cols=72 Identities=19% Similarity=0.213 Sum_probs=48.4
Q ss_pred HHHHHHHH-HCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECC-CHHHC-CHHHHHHHHCC
Q ss_conf 99999998-55986335999999819978999999999932590573156545400023-72126-09999999718
Q gi|254780620|r 11 IRVLMYCA-IHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCR-PADQI-TILDVVKATEE 84 (144)
Q Consensus 11 i~~l~~La-~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak-~~~~I-tl~dI~~aie~ 84 (144)
|+-.+.-. ..+|...+-.+||+..|+|++-++.-|+.|...|+|+..+|+ |+.... +++++ -++++=.++|+
T Consensus 20 lr~~I~~g~l~pG~~L~E~~La~~~gVSRtpvREAL~~L~~eGlv~~~~~~--G~~V~~~~~~~~~ei~~~R~~lE~ 94 (212)
T TIGR03338 20 IERAILSGELPPGAKLNESDIAARLGVSRGPVREAFRALEEAGLVRNEKNR--GVFVREISLAEADEIYELRAVLDE 94 (212)
T ss_pred HHHHHHCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCHHEECCC--CEEEECCCHHHHHHHHHHHHHHHH
T ss_conf 999998399999098189999998896949999999999986963311677--615511768888789999999999
No 53
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=94.93 E-value=0.047 Score=33.21 Aligned_cols=36 Identities=25% Similarity=0.336 Sum_probs=32.6
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCC
Q ss_conf 335999999819978999999999932590573156
Q gi|254780620|r 24 PNRISQIAEACCISELFLFKILQPLVKAGIVETVRG 59 (144)
Q Consensus 24 ~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG 59 (144)
++|-++||+..|+++..+.++|++|.+.|+|+-.+|
T Consensus 8 ~lt~~~iA~~lG~tretvsR~l~~l~~~GlI~~~~~ 43 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLISREGG 43 (48)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCC
T ss_conf 379999999979979999999999998897997897
No 54
>COG1420 HrcA Transcriptional regulator of heat shock gene [Transcription]
Probab=94.80 E-value=0.098 Score=31.32 Aligned_cols=58 Identities=17% Similarity=0.189 Sum_probs=51.8
Q ss_pred CCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEECC
Q ss_conf 9764568999999999985598633599999981--997899999999993259057315
Q gi|254780620|r 1 MHLTKRTDYGIRVLMYCAIHNDYPNRISQIAEAC--CISELFLFKILQPLVKAGIVETVR 58 (144)
Q Consensus 1 Mkis~~~~yAi~~l~~La~~~~~~~s~~eIA~~~--~i~~~~l~kil~~L~~agli~S~r 58 (144)
|+++.+...=+++++..-...++|+.|+.+++.. ++|++.++..|+.|-+.|+|+..-
T Consensus 2 ~~l~~Rq~~IL~aIV~~Yi~t~ePVGSk~L~e~~~l~~SsATIRN~Ma~LE~~GlI~k~H 61 (346)
T COG1420 2 GKLDERQRLILRAIVEDYLATGEPVGSKTLSEKYNLDLSSATIRNEMADLEKLGLIEKPH 61 (346)
T ss_pred CCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCCCCC
T ss_conf 870079999999999999604991663999987388988462878999998777815765
No 55
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=94.71 E-value=0.1 Score=31.25 Aligned_cols=66 Identities=18% Similarity=0.164 Sum_probs=49.6
Q ss_pred HCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECC-CHHHC-CHHHHHHHHCCCC
Q ss_conf 55986335999999819978999999999932590573156545400023-72126-0999999971876
Q gi|254780620|r 19 IHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCR-PADQI-TILDVVKATEESF 86 (144)
Q Consensus 19 ~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak-~~~~I-tl~dI~~aie~~~ 86 (144)
..+|.+++-.+||+..++|+.-|+.-|..|...|+|... ++.|+..+. +++++ -++++-..+|+..
T Consensus 34 l~pG~~l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~~--p~rG~~V~~~~~~~~~ei~~~R~~lE~~a 101 (230)
T COG1802 34 LAPGERLSEEELAEELGVSRTPVREALRRLEAEGLVEIE--PNRGAFVAPLSLAEAREIFEVRELLEGAA 101 (230)
T ss_pred CCCCCEECHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEC--CCCCEEECCCCHHHHHHHHHHHHHHHHHH
T ss_conf 898298179999999888907999999999889794777--99832662899999999999999999999
No 56
>pfam09202 Rio2_N Rio2, N-terminal. Members of this family are found in Rio2, and are structurally homologous to the winged helix (wHTH) domain. They adopt a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains.
Probab=94.40 E-value=0.23 Score=29.15 Aligned_cols=66 Identities=17% Similarity=0.117 Sum_probs=51.3
Q ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHH
Q ss_conf 689999999999855986335999999819978999999999932590573156545400023721
Q gi|254780620|r 6 RTDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPAD 71 (144)
Q Consensus 6 ~~~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~ 71 (144)
+-|+-+-.-+.+...+-+-|+.+.|+...+++..-+.+.++.|.+.++|.-...+.-||+|.-..-
T Consensus 6 ~~dfRvL~aiE~gmrnhE~VP~~lI~~~s~L~~~~~~~~L~~L~k~kLv~~~~~~Y~GYrLT~~GY 71 (82)
T pfam09202 6 KEDFRVLTAVEMGMRNHEWVPTELITSISRLRAGGVNKRLSRLLKRKLVSRKNAKYDGYRLTYLGY 71 (82)
T ss_pred HHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEECCCCCCCEEEEEECCC
T ss_conf 999999999994446875478999999968886679999999976789533588853288710673
No 57
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=94.33 E-value=0.11 Score=30.92 Aligned_cols=52 Identities=29% Similarity=0.462 Sum_probs=41.2
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE--ECCCCCCCC
Q ss_conf 999999985598633599999981997899999999993259057--315654540
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVE--TVRGRRGGV 64 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~--S~rG~~GGy 64 (144)
+++|-.| |..+|..+.|||++.++|.+.+.--++.|.++|+|+ +++++.|--
T Consensus 26 v~Il~lL--~~k~plNvneiAe~lgLpqst~s~~ik~Le~aGlirT~t~karkG~Q 79 (308)
T COG4189 26 VAILQLL--HRKGPLNVNEIAEALGLPQSTMSANIKVLEKAGLIRTETVKARKGSQ 79 (308)
T ss_pred HHHHHHH--HHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEECCCCCCE
T ss_conf 9999999--87179878999988588656666557888864724631001336750
No 58
>PRK11753 cAMP-regulatory protein; Provisional
Probab=94.23 E-value=0.17 Score=29.99 Aligned_cols=48 Identities=19% Similarity=0.243 Sum_probs=36.9
Q ss_pred HHHHHHHHCCC------C---CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCC
Q ss_conf 99999985598------6---3359999998199789999999999325905731565
Q gi|254780620|r 12 RVLMYCAIHND------Y---PNRISQIAEACCISELFLFKILQPLVKAGIVETVRGR 60 (144)
Q Consensus 12 ~~l~~La~~~~------~---~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~ 60 (144)
+.|+.++...+ + ++|-++||+..|+++..+.++|+.|++.|+|+. +|+
T Consensus 147 ~~Ll~l~~~~~~~~~~~~~~i~lt~~eLA~~lG~sretvsR~L~~L~~~GlI~~-~~~ 203 (211)
T PRK11753 147 QTLLDLAKQPDAMTHPDGMQIKITRQEIGRIVGCSREMVGRVLKMLEDQGLISA-HGK 203 (211)
T ss_pred HHHHHHHHHCCCCCCCCCEEECCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE-CCC
T ss_conf 999999852288778984482469999998869989999999999998899998-599
No 59
>TIGR03337 phnR transcriptional regulator protein. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii.
Probab=94.18 E-value=0.11 Score=31.13 Aligned_cols=60 Identities=15% Similarity=0.149 Sum_probs=42.7
Q ss_pred CCCC-CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHH------CCHHHHHHHH
Q ss_conf 9863-359999998199789999999999325905731565454000237212------6099999997
Q gi|254780620|r 21 NDYP-NRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQ------ITILDVVKAT 82 (144)
Q Consensus 21 ~~~~-~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~------Itl~dI~~ai 82 (144)
+|.. -|=.+||+..++|+..++|-|+.|.+.|+|...+|+ |=|. +.++-. .++.+.+..-
T Consensus 21 ~G~~LPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~G~-GTfV-~~~~~~~~~~~~~~f~~~~~~~ 87 (231)
T TIGR03337 21 PGDKLPSERDLGERFNTTRVTIREALQQLEAEGLIYREDRR-GWFV-SPPRLRYNPTRTQNFHEYVREQ 87 (231)
T ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCC-EEEE-CCCCCCCCCHHCCCHHHHHHHC
T ss_conf 95978589999999797999999999999987996996686-6798-8885444800013448999965
No 60
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=94.15 E-value=0.18 Score=29.73 Aligned_cols=66 Identities=21% Similarity=0.331 Sum_probs=51.2
Q ss_pred CHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHH
Q ss_conf 456899999999998559863359999998199789999999999325905731565454000237212
Q gi|254780620|r 4 TKRTDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQ 72 (144)
Q Consensus 4 s~~~~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~ 72 (144)
+++-..-..+|..|+.+.. .++-+|||+.+++++.-+.--+..|++.|+|++ .|+ |-|.+.|.-.+
T Consensus 6 ~kk~~t~fqIL~ei~~~qp-~v~q~eIA~~lgiT~QaVsehiK~Lv~eG~i~~-~gR-~~Y~iTkkG~e 71 (260)
T COG1497 6 SKKNLTRFQILSEIAVRQP-RVKQKEIAKKLGITLQAVSEHIKELVKEGLIEK-EGR-GEYEITKKGAE 71 (260)
T ss_pred CCCCCHHHHHHHHHHHHCC-CCCHHHHHHHCCCCHHHHHHHHHHHHHCCCEEE-CCC-EEEEEEHHHHH
T ss_conf 4663159899999997588-778889998709879999999999986646661-487-25897266899
No 61
>PRK10079 putative transcriptional regulator; Provisional
Probab=94.07 E-value=0.12 Score=30.85 Aligned_cols=47 Identities=23% Similarity=0.207 Sum_probs=38.4
Q ss_pred CCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECC
Q ss_conf 98633-5999999819978999999999932590573156545400023
Q gi|254780620|r 21 NDYPN-RISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCR 68 (144)
Q Consensus 21 ~~~~~-s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak 68 (144)
.|... |=.+||+..++|+..++|-++.|.+.|+|...+|+ |=|...+
T Consensus 31 ~G~~LPsE~eLa~~y~VSR~TVR~Al~~L~~eGli~r~~G~-GtfV~~~ 78 (241)
T PRK10079 31 CGDYLPAEQQLAARFEVNRHTLRRAIDQLVERGWVQRRQGV-GVLVLMR 78 (241)
T ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCC-CEEEECC
T ss_conf 98919699999999798899999999999977987997696-2599357
No 62
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=93.96 E-value=0.13 Score=30.69 Aligned_cols=53 Identities=19% Similarity=0.201 Sum_probs=40.1
Q ss_pred CCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCH
Q ss_conf 98633-59999998199789999999999325905731565454000237212609
Q gi|254780620|r 21 NDYPN-RISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITI 75 (144)
Q Consensus 21 ~~~~~-s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl 75 (144)
+|... |=.+||+..++|+..++|-|..|...|+|...+|+ |=|. +.++-...+
T Consensus 25 ~G~~LPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~G~-GTfV-~~~~~~~~~ 78 (239)
T PRK09764 25 PGDALPTESALQTEFGVSRVTVRQALRQLVEQQILESIQGS-GTYV-KEERVNYDI 78 (239)
T ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCC-EEEE-CCCCCCCCH
T ss_conf 95999299999999797999999999999978999998687-7898-887577874
No 63
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=93.95 E-value=0.23 Score=29.18 Aligned_cols=55 Identities=18% Similarity=0.180 Sum_probs=47.4
Q ss_pred CCHHHHHHHHHHHHHHHCCCCCCCHHHHHHH--HCCCHHHHHHHHHHHHHCCCEEEC
Q ss_conf 6456899999999998559863359999998--199789999999999325905731
Q gi|254780620|r 3 LTKRTDYGIRVLMYCAIHNDYPNRISQIAEA--CCISELFLFKILQPLVKAGIVETV 57 (144)
Q Consensus 3 is~~~~yAi~~l~~La~~~~~~~s~~eIA~~--~~i~~~~l~kil~~L~~agli~S~ 57 (144)
+|.+-..=+++++.--...++|+.|+.|++. .++|++.++..|+.|-+.||++.-
T Consensus 4 Lt~R~~~IL~aiVe~Yi~tg~PVGSk~L~~~~~l~~SsATIRNeMa~LE~~G~L~qp 60 (339)
T PRK00082 4 LDERQREILRAIVEDYIATGEPVGSKTLSERYGLGVSSATIRNDMADLEELGLLEKP 60 (339)
T ss_pred CCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHCCCCCCC
T ss_conf 579999999999999851498556799997649997817899999999978783679
No 64
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=93.90 E-value=0.13 Score=30.53 Aligned_cols=45 Identities=16% Similarity=0.250 Sum_probs=37.5
Q ss_pred CCCC-CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEE
Q ss_conf 9863-359999998199789999999999325905731565454000
Q gi|254780620|r 21 NDYP-NRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRL 66 (144)
Q Consensus 21 ~~~~-~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~L 66 (144)
+|.. -|=.+||+..++|+..++|-+..|...|+|...+|+ |=|..
T Consensus 31 ~G~~LPsE~eLa~~y~VSR~TVR~Al~~L~~eGli~r~~G~-GtfV~ 76 (243)
T PRK11402 31 AGQQIPTENELCTQYNVSRITIRKAISDLVADGVLIRWQGK-GTFVQ 76 (243)
T ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCC-EEEEC
T ss_conf 97989399999999797999999999999978999997796-68995
No 65
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=93.87 E-value=0.23 Score=29.11 Aligned_cols=60 Identities=30% Similarity=0.335 Sum_probs=45.3
Q ss_pred HHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECC--CCCCC----CEECCCHHHCCHH
Q ss_conf 99985598633599999981997899999999993259057315--65454----0002372126099
Q gi|254780620|r 15 MYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVR--GRRGG----VRLCRPADQITIL 76 (144)
Q Consensus 15 ~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~r--G~~GG----y~Lak~~~~Itl~ 76 (144)
-.|..+++++.|++|+|+..|+|+..++|=|..|...|.+...- |.-|= |+|. |+..+++
T Consensus 169 ~~l~~~~~~~~sa~eva~~~giSRvTaRRYLe~L~~~g~~~~~~~YG~~GRP~~~Y~l~--~~~~~~~ 234 (239)
T PRK10430 169 QWIDAHQDYEFSTDELANEVNISRVSCRKYLIWLVNCHILFTSIHYGVTGRPVYRYRLQ--AEHYSLL 234 (239)
T ss_pred HHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEEEECCCCCCCCCEEEEEC--CCHHHHH
T ss_conf 99982799984699999885852988999999998689589983578999986578737--3144777
No 66
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=93.81 E-value=0.27 Score=28.71 Aligned_cols=59 Identities=24% Similarity=0.205 Sum_probs=45.4
Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCH
Q ss_conf 9999998559863359999998199789999999999325905731565454000237212609
Q gi|254780620|r 12 RVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITI 75 (144)
Q Consensus 12 ~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl 75 (144)
+++-+|..+ +.+++++||+..++|+..+++=|..|-+.|+|.-+ +||..+..+..+.+.
T Consensus 9 ~Il~~L~~~--g~v~v~eLa~~l~VS~~TIRRDL~~Le~~G~l~R~---hGGa~~~~~~~~~~~ 67 (256)
T PRK10434 9 AILEYLQKQ--GKCSVEELAQYFDTTGTTIRKDLVILEHAGTVIRT---YGGVVLNKEESDPPI 67 (256)
T ss_pred HHHHHHHHC--CCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEE---ECEEECCCCCCCCCH
T ss_conf 999999986--97999999998796998999849999878988999---473864777778788
No 67
>pfam02002 TFIIE_alpha TFIIE alpha subunit. 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 family consists of the conserved amino terminal region of eukaryotic TFIIE-alpha and proteins from archaebacteria that are presumed to be TFIIE-alpha subunits.
Probab=93.80 E-value=0.19 Score=29.64 Aligned_cols=50 Identities=26% Similarity=0.096 Sum_probs=39.3
Q ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCC
Q ss_conf 9999999985598633599999981997899999999993259057315654
Q gi|254780620|r 10 GIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRR 61 (144)
Q Consensus 10 Ai~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~ 61 (144)
++.++-.|..+ +-+|-++||+.+++....++|++.+|...+++...|-+.
T Consensus 15 ~v~vid~L~~~--~~v~dedLa~~l~~~~n~vRkiL~~L~e~~lv~~~r~kd 64 (105)
T pfam02002 15 AVLVLDALLRK--GEVTEEDLAELLGIDLNELRKLLYRLYDARLVKYRRRRD 64 (105)
T ss_pred HHHHHHHHHHC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEEEC
T ss_conf 89999999716--883899999997898889999999998788658897661
No 68
>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional
Probab=93.64 E-value=0.23 Score=29.10 Aligned_cols=61 Identities=15% Similarity=0.077 Sum_probs=46.3
Q ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCC---------CHHHHHHHHHHHHH----CCCEEECCCCCCCCEECCCHHH
Q ss_conf 999999998559863359999998199---------78999999999932----5905731565454000237212
Q gi|254780620|r 10 GIRVLMYCAIHNDYPNRISQIAEACCI---------SELFLFKILQPLVK----AGIVETVRGRRGGVRLCRPADQ 72 (144)
Q Consensus 10 Ai~~l~~La~~~~~~~s~~eIA~~~~i---------~~~~l~kil~~L~~----agli~S~rG~~GGy~Lak~~~~ 72 (144)
-..+|-+|+.++++.+|-++|.+...- =..++.++=++|.+ .++|+++||. ||++..++-.
T Consensus 165 E~~lL~~L~~~~g~vvSre~L~~~vw~~~~~~~~rsid~~I~rLRkKl~~~~~~~~~I~TvrG~--GYrf~~~~~~ 238 (240)
T PRK10710 165 EFRLLKTLSHEPGKVFSREQLLNHLYDDYRVVTDRTIDSHIKNLRRKLESLDAEQSFIRAVYGV--GYRWEADACR 238 (240)
T ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCEEEEECCC--CEEECCCCCC
T ss_conf 9999999997799739899999996288888884659999999999601069999819998985--5627710230
No 69
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=93.58 E-value=0.25 Score=28.89 Aligned_cols=51 Identities=18% Similarity=0.284 Sum_probs=41.0
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCC
Q ss_conf 99999998559863359999998199789999999999325905731565454
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGG 63 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GG 63 (144)
.++|.++..+++. +..+||+..+++++.+.+++..|.+.|+|+..+.+.-+
T Consensus 25 ~~~L~~l~~~~~~--~~~~la~~l~~~~~~vt~~l~~Le~~glv~r~~~~~Dr 75 (126)
T COG1846 25 YQVLLALYEAGGI--TVKELAERLGLDRSTVTRLLKRLEDKGLIERLRDPEDR 75 (126)
T ss_pred HHHHHHHHHCCCC--CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCCCC
T ss_conf 9999999984899--99999999787888899999999988993674388886
No 70
>COG4465 CodY Pleiotropic transcriptional repressor [Transcription]
Probab=93.58 E-value=0.12 Score=30.87 Aligned_cols=63 Identities=19% Similarity=0.211 Sum_probs=46.3
Q ss_pred CCHHHHHHHHHHHHHHH--C-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECC-CCCCCCE
Q ss_conf 64568999999999985--5-98633599999981997899999999993259057315-6545400
Q gi|254780620|r 3 LTKRTDYGIRVLMYCAI--H-NDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVR-GRRGGVR 65 (144)
Q Consensus 3 is~~~~yAi~~l~~La~--~-~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~r-G~~GGy~ 65 (144)
+|+-+---+.|+-++-. . +++...++.||++.||.++.+-.-|++|-.||+|+|.- |-+|-|.
T Consensus 180 i~tLSYSEleAve~I~eELdG~EG~lvASkiADrvGITRSVIVNALRKlESAGvIeSRSLGMKGTyi 246 (261)
T COG4465 180 ISTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRSLGMKGTYI 246 (261)
T ss_pred HHHCCHHHHHHHHHHHHHCCCCCCEEEEHHHHHHHCCHHHHHHHHHHHHHHCCCEEECCCCCCCEEE
T ss_conf 8542498999999999862886653630245565173399999999876543754312367662267
No 71
>PRK06474 hypothetical protein; Provisional
Probab=93.57 E-value=0.3 Score=28.49 Aligned_cols=64 Identities=9% Similarity=0.233 Sum_probs=48.2
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHH-CCCHHHHHHHHHHHHHCCCEEECCCCC-CC-----CEECCCHHHCC
Q ss_conf 999999985598633599999981-997899999999993259057315654-54-----00023721260
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEAC-CISELFLFKILQPLVKAGIVETVRGRR-GG-----VRLCRPADQIT 74 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~-~i~~~~l~kil~~L~~agli~S~rG~~-GG-----y~Lak~~~~It 74 (144)
+||+-.|........|+.+|++.+ ++|++-|.+-++.|..+|+++-+.=+. .| |+|..+...|.
T Consensus 14 mrI~q~l~~~~~~~lT~~eL~e~L~DVPqATLYRHv~~L~e~giL~Vv~E~kVRGavEk~Yal~~~~a~i~ 84 (180)
T PRK06474 14 MKICQALMRNKEEGLSPLEMVKVIKDVPQATLYRQIQTMVDSGILHVIKEKKVRSVSEKYYAINEEDAKIE 84 (180)
T ss_pred HHHHHHHHCCCCCCCCHHHHHHHCCCCCHHHHHHHHHHHHHCCCEEEEEEEEECCEEEEEEEECCCCCCCC
T ss_conf 99999996588788689999976569987999999999975674355454132453778875335445688
No 72
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=93.50 E-value=0.32 Score=28.31 Aligned_cols=42 Identities=17% Similarity=0.195 Sum_probs=36.2
Q ss_pred CCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCC
Q ss_conf 598633-599999981997899999999993259057315654
Q gi|254780620|r 20 HNDYPN-RISQIAEACCISELFLFKILQPLVKAGIVETVRGRR 61 (144)
Q Consensus 20 ~~~~~~-s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~ 61 (144)
.+|... +-.++|+..|+|++-++..|+.|...|+|+...|++
T Consensus 26 ~~G~~LP~EreLa~~~gVsR~tvReal~~L~~~G~v~~~~G~g 68 (239)
T PRK04984 26 PPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHGKP 68 (239)
T ss_pred CCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCC
T ss_conf 9999898899999997988899999999999889888855999
No 73
>PRK10336 DNA-binding transcriptional regulator QseB; Provisional
Probab=93.36 E-value=0.26 Score=28.82 Aligned_cols=55 Identities=18% Similarity=0.155 Sum_probs=41.2
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHH---------CCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECC
Q ss_conf 999999985598633599999981---------9978999999999932590573156545400023
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEAC---------CISELFLFKILQPLVKAGIVETVRGRRGGVRLCR 68 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~---------~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak 68 (144)
..+|.+|+.++++.+|-++|.+.. +.=..|+.++=++|. ..+|+++||. ||+|..
T Consensus 155 ~~lL~~L~~~~g~vvsre~l~~~vw~~~~~~~~~~vdv~I~rLRkKl~-~~~I~TvrG~--GY~l~e 218 (219)
T PRK10336 155 FALLELLMRNAGRVLPRKLIEEKLYTWDEEVTSNAVEVHVHHLRRKLG-SDFIRTVHGI--GYTLGE 218 (219)
T ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCC-CCCEEEECCC--CEEECC
T ss_conf 999999996899639799999996288988885819999999997679-8858981575--868662
No 74
>pfam01475 FUR Ferric uptake regulator family. This family includes metal ion uptake regulator proteins, that bind to the operator DNA and controls transcription of metal ion-responsive genes. This family is also known as the FUR family.
Probab=93.34 E-value=0.48 Score=27.25 Aligned_cols=60 Identities=22% Similarity=0.209 Sum_probs=42.6
Q ss_pred CCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHCCCEEECCCCCCCC
Q ss_conf 9764568999999999985598633599999981-----997899999999993259057315654540
Q gi|254780620|r 1 MHLTKRTDYGIRVLMYCAIHNDYPNRISQIAEAC-----CISELFLFKILQPLVKAGIVETVRGRRGGV 64 (144)
Q Consensus 1 Mkis~~~~yAi~~l~~La~~~~~~~s~~eIA~~~-----~i~~~~l~kil~~L~~agli~S~rG~~GGy 64 (144)
||+|+.=. + ++-.|.. .+++.|+.+|.+.. .++++-+.+.|..|...|+|....-.+|.+
T Consensus 4 lR~T~qR~-~--Il~~l~~-~~~~~ta~~i~~~l~~~~~~i~~~TVYR~L~~L~~~gli~~~~~~~~~~ 68 (120)
T pfam01475 4 LKITPQRL-K--ILEVLEK-SDEHLSAEEIYRELLEEDPNISLATVYRTLKLLEEAGIVKRLNFEGGES 68 (120)
T ss_pred CCCCHHHH-H--HHHHHHH-CCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCEEEEEECCCEE
T ss_conf 98888999-9--9999982-7999899999999996589987899999999999679469998479979
No 75
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=93.27 E-value=0.35 Score=28.10 Aligned_cols=54 Identities=19% Similarity=0.132 Sum_probs=41.2
Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCC
Q ss_conf 9999998559863359999998199789999999999325905731565454000237
Q gi|254780620|r 12 RVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRP 69 (144)
Q Consensus 12 ~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~ 69 (144)
.++-+|..+ +.++++|||+..++|+..++|=|..|.+.|++.-++| |+..+...
T Consensus 9 ~Il~~L~~~--g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~r~~G--GA~~~~~~ 62 (251)
T PRK13509 9 ILLDMLAQL--GFVTVEKVIERLGISPATARRDINKLDESGKLKKVRN--GAEAITQQ 62 (251)
T ss_pred HHHHHHHHC--CCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEC--CEEECCCC
T ss_conf 999999986--9898999999989699899983999987897899988--97977777
No 76
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=93.10 E-value=0.29 Score=28.51 Aligned_cols=58 Identities=22% Similarity=0.231 Sum_probs=44.3
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECC-CCCCCCEECCC
Q ss_conf 999999985598633599999981997899999999993259057315-65454000237
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVR-GRRGGVRLCRP 69 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~r-G~~GGy~Lak~ 69 (144)
.-+|-++..|+ +.++=+||.+..+.|.+-+.+++++|-|-|||+=.| |+.-=++|.++
T Consensus 198 ~~il~~i~~~G-Gri~Q~eL~r~lglsktTvsR~L~~LEk~GlIe~~K~G~~n~V~l~~~ 256 (258)
T COG2512 198 KEILDLIRERG-GRITQAELRRALGLSKTTVSRILRRLEKRGLIEKEKKGRTNIVELRDK 256 (258)
T ss_pred HHHHHHHHHHC-CEEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEECCEEEEEEECC
T ss_conf 99999999858-978699988860997677999999998689568887088069999336
No 77
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=93.07 E-value=0.52 Score=27.03 Aligned_cols=52 Identities=19% Similarity=0.242 Sum_probs=37.7
Q ss_pred HHCCCC-CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHC
Q ss_conf 855986-33599999981997899999999993259057315654540002372126
Q gi|254780620|r 18 AIHNDY-PNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQI 73 (144)
Q Consensus 18 a~~~~~-~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~I 73 (144)
..+++. ..+-.+||+..|+|+..|.++|+.|.+.|+|+..+ ++|. -.|.+..
T Consensus 149 ~~~~~~~~~~~~elA~~lG~Sretl~R~L~~f~~eGiI~~~~---~~i~-I~D~~~L 201 (213)
T PRK10402 149 TQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFCQDGYLIKSK---RGYL-IKNRKQL 201 (213)
T ss_pred HHCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECC---CEEE-EECHHHH
T ss_conf 610786666799999997988999999999999889889749---9999-9579999
No 78
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=92.93 E-value=0.45 Score=27.43 Aligned_cols=56 Identities=13% Similarity=0.135 Sum_probs=42.6
Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHH
Q ss_conf 9999998559863359999998199789999999999325905731565454000237212
Q gi|254780620|r 12 RVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQ 72 (144)
Q Consensus 12 ~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~ 72 (144)
+++-+|..+ +.+++.+||+..++|+..+++=|..|-+.|+|.=++ ||..+..+..+
T Consensus 9 ~Il~~l~~~--g~v~v~eLa~~~~VS~~TIRRDL~~Le~~G~l~R~h---GGA~~~~~~~~ 64 (252)
T PRK10906 9 AIIELVKQQ--GYVSTEELVEHFSVSPQTIRRDLNELAEQNLILRHH---GGAALPSSSVN 64 (252)
T ss_pred HHHHHHHHC--CCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEE---CEEEECCCCCC
T ss_conf 999999986--989999999987969989988299998789889995---84980687778
No 79
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; InterPro: IPR012794 Members 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.; GO: 0003677 DNA binding, 0016563 transcription activator activity, 0045941 positive regulation of transcription, 0046278 protocatechuate metabolic process.
Probab=92.83 E-value=0.25 Score=28.96 Aligned_cols=63 Identities=19% Similarity=0.160 Sum_probs=45.7
Q ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHH
Q ss_conf 999999998559863359999998199789999999999325905731565454000237212609999
Q gi|254780620|r 10 GIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDV 78 (144)
Q Consensus 10 Ai~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI 78 (144)
+|.++--...+ ....|..|+|+..|++++-.+++|-.|.+.||+++--+ =|+| -|+=..|+.=
T Consensus 11 GLaVi~aF~~~-~~~ltl~~vA~~TGL~RAaARR~LLTL~~LGY~~~Dg~---~F~L--TPrvL~LG~a 73 (252)
T TIGR02431 11 GLAVIEAFGEE-RPRLTLTDVAEATGLTRAAARRFLLTLVELGYVESDGR---LFWL--TPRVLRLGYA 73 (252)
T ss_pred HHHHHHHHCCC-CCCCCHHHHHHHHCCCCHHHHHHHHHHHHHCCEECCCC---CEEC--CHHHHHHHHH
T ss_conf 99999973103-78989899998758994798889984656230421798---3310--2467753322
No 80
>PRK11414 putative DNA-binding transcriptional regulator; Provisional
Probab=92.78 E-value=0.9 Score=25.64 Aligned_cols=71 Identities=11% Similarity=0.088 Sum_probs=50.3
Q ss_pred HHHHHHHHH-HCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECC-CHHHCCHHHHHH---HHCC
Q ss_conf 999999998-55986335999999819978999999999932590573156545400023-721260999999---9718
Q gi|254780620|r 10 GIRVLMYCA-IHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCR-PADQITILDVVK---ATEE 84 (144)
Q Consensus 10 Ai~~l~~La-~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak-~~~~Itl~dI~~---aie~ 84 (144)
.|+-.+.-. ..+|.+.+..+||+..|+|..=++--++.|...|+|+..+++ |+.... ++++ +.|+++ ++|+
T Consensus 19 ~Lr~~I~~G~l~PG~~L~e~~La~~lgVSRtPVREAL~rL~~eGLv~~~p~r--G~~V~~~s~~~--~~ei~~~R~~LE~ 94 (221)
T PRK11414 19 DLKHQLSIGALKPGARLITKNLAEQLGMSITPVREALLRLVSVNALSVAPAQ--AFTVPEVSLEQ--LDEINRIRYELEL 94 (221)
T ss_pred HHHHHHHCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCC--CEEEECCCHHH--HHHHHHHHHHHHH
T ss_conf 9999998399899597189999999799906899999999988895650487--33750798899--9999999999999
No 81
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=92.66 E-value=0.22 Score=29.25 Aligned_cols=45 Identities=13% Similarity=0.140 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHH
Q ss_conf 3359999998199789999999999325905731565454000237212
Q gi|254780620|r 24 PNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQ 72 (144)
Q Consensus 24 ~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~ 72 (144)
+.|-++||+..|+++..+.|+|+.|++.|+|+.. | +..--.|++.
T Consensus 184 ~lt~~dLA~~lG~trEtVsR~L~~L~~~GlI~~~-~---~~I~I~d~~~ 228 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETISRLLGRFQKSGMLAVK-G---KYITIENNDA 228 (235)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEC-C---CEEEECCHHH
T ss_conf 3789999988789899999999999978979973-9---9999878999
No 82
>PRK09954 hypothetical protein; Provisional
Probab=92.57 E-value=0.22 Score=29.22 Aligned_cols=49 Identities=18% Similarity=0.184 Sum_probs=40.8
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCC
Q ss_conf 986335999999819978999999999932590573156545400023721260
Q gi|254780620|r 21 NDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQIT 74 (144)
Q Consensus 21 ~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~It 74 (144)
++..+|-+|||+..|++++-++-.+..|.|.|+|. | .||.|..++.-.-
T Consensus 14 ~~p~i~q~ela~~lgisrs~va~hi~~l~~kg~i~---G--~gyi~~~~~~vvv 62 (362)
T PRK09954 14 RNPLIQQNEIADILQISRSRVAAHIMDLMRKGRIK---G--KGYILTEQEYCVV 62 (362)
T ss_pred HCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEC---C--CEEEECCCCCEEE
T ss_conf 78995899999997987999999999887547652---5--4688779971899
No 83
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=92.47 E-value=0.42 Score=27.63 Aligned_cols=55 Identities=22% Similarity=0.279 Sum_probs=43.1
Q ss_pred HHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHH
Q ss_conf 999998559863359999998199789999999999325905731565454000237212
Q gi|254780620|r 13 VLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQ 72 (144)
Q Consensus 13 ~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~ 72 (144)
++-+|.. .+.+++++||+..++|+..+++=|..|-+.|++.-+ +||-.+..++..
T Consensus 10 Il~~l~~--~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R~---hGGa~~~~~~~~ 64 (253)
T COG1349 10 ILELLKE--KGKVSVEELAELFGVSEMTIRRDLNELEEQGLLLRV---HGGAVLPDSESE 64 (253)
T ss_pred HHHHHHH--CCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCEEEEE---ECEEECCCCCCC
T ss_conf 9999998--596979999988597899998619999778928996---061883776655
No 84
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=92.39 E-value=0.25 Score=28.93 Aligned_cols=45 Identities=13% Similarity=0.089 Sum_probs=35.7
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHH
Q ss_conf 3359999998199789999999999325905731565454000237212
Q gi|254780620|r 24 PNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQ 72 (144)
Q Consensus 24 ~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~ 72 (144)
+.|=+|||...|+++..+.++|+.|++.|+|+..+| ...-.|++.
T Consensus 145 ~lT~~eLA~~iGttREtVsR~L~~l~~~GlI~~~~~----~I~I~D~~~ 189 (201)
T PRK13918 145 YATHDELAAAVGSVRETVTKVVGELSREGVIRSGYG----KIQLLDLKA 189 (201)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCC----EEEEECHHH
T ss_conf 579999998859868999999999998898896799----899928999
No 85
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF; InterPro: IPR012702 Members of this family are the PhnF protein associated with C-P lyase systems for utilization of phosphonates. These systems resemble phosphonatase-based systems in having a three-component ABC transporter, where IPR005769 from INTERPRO is the permease, IPR005770 from INTERPRO is the phosphonates binding protein, and IPR012693 from INTERPRO is the ATP-binding cassette (ABC) protein. They differ, however, in having, typically, ten or more additional genes, many of which are believed to form a membrane-associated C-P lyase complex. This protein (PhnF) is a predicted helix-turn-helix transcriptional regulatory protein of the broader GntR family, and is encoded in a gene cluster associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond. Its presence is apparently not required for phosphate utilisation to occur ..
Probab=92.38 E-value=0.21 Score=29.39 Aligned_cols=46 Identities=20% Similarity=0.276 Sum_probs=39.6
Q ss_pred CCCCCCCHH-HHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEE
Q ss_conf 598633599-99998199789999999999325905731565454000
Q gi|254780620|r 20 HNDYPNRIS-QIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRL 66 (144)
Q Consensus 20 ~~~~~~s~~-eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~L 66 (144)
+.|...+.+ +||++.++|+.-|++=+..|+..|+|+..+|+ |=|..
T Consensus 27 ~~G~~LP~E~~LAe~F~VNRHTvRrAiAaL~e~G~lr~~QGr-Gt~v~ 73 (240)
T TIGR02325 27 RAGDKLPAEMQLAERFGVNRHTVRRAIAALVERGLLRAEQGR-GTFVA 73 (240)
T ss_pred CCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHCCEEEECCCC-CHHHC
T ss_conf 333568877889856488735788999998753807510574-21210
No 86
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=92.29 E-value=0.5 Score=27.17 Aligned_cols=79 Identities=15% Similarity=0.132 Sum_probs=52.3
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCC----CCCCE------EC-CCHHHCCHHHHH
Q ss_conf 99999998559863359999998199789999999999325905731565----45400------02-372126099999
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGR----RGGVR------LC-RPADQITILDVV 79 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~----~GGy~------La-k~~~~Itl~dI~ 79 (144)
.++|-.|. .++..|..+||+..|+|++-+.+=+++|.++|+|+...-. .=||. +. +++. ...++.
T Consensus 12 ~~IL~~Lq--~d~R~s~~eiA~~lglS~stv~~Ri~rLe~~GvI~~~~~~id~~~lG~~~~a~i~i~~~~~~--~~~~~~ 87 (153)
T PRK11179 12 RGILEALM--ENARTPYAELAKQFGVSPGTIHVRVEKMKQAGIITGARIDVNPKQLGYDVCCFIGIILKSAK--DYPSAL 87 (153)
T ss_pred HHHHHHHH--HCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEEEECHHHHCCCEEEEEEEEECCCC--CHHHHH
T ss_conf 99999999--84899999999998929999999999999799658999997989939987999999984788--999999
Q ss_pred HHHCCCCCCCCCCC
Q ss_conf 99718763111468
Q gi|254780620|r 80 KATEESFFVAECFA 93 (144)
Q Consensus 80 ~aie~~~~~~~C~~ 93 (144)
+.+..-....+|..
T Consensus 88 ~~l~~~peV~~~~~ 101 (153)
T PRK11179 88 AKLESLDEVVEAYY 101 (153)
T ss_pred HHHHCCCHHEEEEE
T ss_conf 99748952118626
No 87
>cd00383 trans_reg_C Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and a response regulator. The former autophosphorylates in a histidine residue on detecting an external stimulus. The phosphate is then transferred to an invariant aspartate residue in a highly conserved receiver domain of the response regulator. Phosphorylation activates a variable effector domain of the response regulator, which triggers the cellular response. The C-terminal effector domain contains DNA and RNA polymerase binding sites. Several dimers or monomers bind head to tail to small tandem repeats upstream of the genes. The RNA polymerase binding sites interact with the alpha or sigma subunite of RNA polymerase.
Probab=92.29 E-value=0.39 Score=27.81 Aligned_cols=56 Identities=23% Similarity=0.284 Sum_probs=38.4
Q ss_pred HHHHHHHHHHHCCCCCCCHHHHHHHHC-----CCHH----HHHHHHHHHHHC----CCEEECCCCCCCCEE
Q ss_conf 999999999855986335999999819-----9789----999999999325----905731565454000
Q gi|254780620|r 9 YGIRVLMYCAIHNDYPNRISQIAEACC-----ISEL----FLFKILQPLVKA----GIVETVRGRRGGVRL 66 (144)
Q Consensus 9 yAi~~l~~La~~~~~~~s~~eIA~~~~-----i~~~----~l~kil~~L~~a----gli~S~rG~~GGy~L 66 (144)
.-..+|.+|..++++.+|-++|.+..- .+.. ++.++=++|.+. .+|++++|. ||+|
T Consensus 27 ~E~~lL~~L~~~~~~vvsr~~l~~~vw~~~~~~~~~~l~~~I~rLRkkl~~~~~~~~~I~tv~g~--GY~L 95 (95)
T cd00383 27 KEFELLELLARNPGRVLSREQLLEAVWGDDYDVDDRTVDVHISRLRKKLEDDPSNPRLIKTVRGV--GYRL 95 (95)
T ss_pred HHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCEEEECCCC--CCCC
T ss_conf 99999999987799745699999985397645574549999999999975268999859981885--5359
No 88
>PRK09213 purine operon repressor; Provisional
Probab=92.23 E-value=0.69 Score=26.32 Aligned_cols=88 Identities=15% Similarity=0.171 Sum_probs=60.8
Q ss_pred CCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHH-------HHHHHHHHHCCCEEECCCCCCCCEECC----C
Q ss_conf 97645689999999999855986335999999819978999-------999999932590573156545400023----7
Q gi|254780620|r 1 MHLTKRTDYGIRVLMYCAIHNDYPNRISQIAEACCISELFL-------FKILQPLVKAGIVETVRGRRGGVRLCR----P 69 (144)
Q Consensus 1 Mkis~~~~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l-------~kil~~L~~agli~S~rG~~GGy~Lak----~ 69 (144)
||+.+..+ =+.+.-||..|+.+.++....|++.+...+-+ .++++. ..-|.|++++|+.||.+..- .
T Consensus 1 mK~~RseR-lv~mt~~Ll~~P~~li~Lt~Fae~~~~AKSsISEDl~iik~~f~~-~g~G~leTv~GaaGGv~yiP~~~~~ 78 (274)
T PRK09213 1 MKLKRSER-LVDMTKYLLENPNKLISLTFFAERYGAAKSSISEDLVIIKETFEK-QGIGTLETIPGAAGGVKYIPYISEE 78 (274)
T ss_pred CCCCHHHH-HHHHHHHHHHCCCCEECHHHHHHHHCCCCCCCHHHHHHHHHHHHH-CCCCEEEEECCCCCCEEEEECCCHH
T ss_conf 98543468-999999998199846738999988561224214359999999987-3985499805877874997067989
Q ss_pred HHHCCHHHHHHHHCCCCCCCC
Q ss_conf 212609999999718763111
Q gi|254780620|r 70 ADQITILDVVKATEESFFVAE 90 (144)
Q Consensus 70 ~~~Itl~dI~~aie~~~~~~~ 90 (144)
-.+--+.++-+.+..+.++..
T Consensus 79 ~~~~fl~~l~~~L~~~~RiLP 99 (274)
T PRK09213 79 EAREFVEELCERLSEPDRILP 99 (274)
T ss_pred HHHHHHHHHHHHHCCCCCCCC
T ss_conf 999999999998468772766
No 89
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=92.22 E-value=0.55 Score=26.90 Aligned_cols=49 Identities=18% Similarity=0.132 Sum_probs=39.5
Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCC
Q ss_conf 99999985598633599999981997899999999993259057315654
Q gi|254780620|r 12 RVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRR 61 (144)
Q Consensus 12 ~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~ 61 (144)
.+|.+|...++ .+|-.+||+..++.++.+.+++..|-+.|||+=.+-+.
T Consensus 35 ~~L~~L~~~~~-g~tq~eLa~~l~v~~~t~tr~ld~LE~~GlI~R~~~~~ 83 (144)
T PRK03573 35 VTLHNIHQLPP-DQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCAS 83 (144)
T ss_pred HHHHHHHHCCC-CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCC
T ss_conf 99999997398-98999999997987836999999999888978622867
No 90
>PRK10701 DNA-binding transcriptional regulator RstA; Provisional
Probab=92.14 E-value=0.77 Score=26.06 Aligned_cols=62 Identities=16% Similarity=0.213 Sum_probs=43.3
Q ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHH-CC--------CHHHHHHHHHHHHHCC----CEEECCCCCCCCEECCCHH
Q ss_conf 68999999999985598633599999981-99--------7899999999993259----0573156545400023721
Q gi|254780620|r 6 RTDYGIRVLMYCAIHNDYPNRISQIAEAC-CI--------SELFLFKILQPLVKAG----IVETVRGRRGGVRLCRPAD 71 (144)
Q Consensus 6 ~~~yAi~~l~~La~~~~~~~s~~eIA~~~-~i--------~~~~l~kil~~L~~ag----li~S~rG~~GGy~Lak~~~ 71 (144)
..||. +|.+|+.++++.+|-++|.+.. +. =..|+.++=++|...+ +|+++||. ||+|+-++-
T Consensus 164 ~~E~~--lL~~L~~~~g~vvsre~L~~~vwg~~~~~~~rtvdv~I~rLRkKl~~~~~~~~~I~TvrG~--GY~f~p~a~ 238 (240)
T PRK10701 164 TADFE--LLWELATHAGQIMDRDALLKNLRGVSYDGLDRSVDVAISRLRKKLLDNAAEPYRIKTVRNK--GYLFAPHAW 238 (240)
T ss_pred HHHHH--HHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEECCC--CEEECCCCC
T ss_conf 89999--9999997799873899999985398878886789999999999875288999839998181--851857755
No 91
>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=91.95 E-value=0.29 Score=28.58 Aligned_cols=46 Identities=15% Similarity=0.247 Sum_probs=37.1
Q ss_pred HHHHHHHHCCC------CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEC
Q ss_conf 99999985598------63359999998199789999999999325905731
Q gi|254780620|r 12 RVLMYCAIHND------YPNRISQIAEACCISELFLFKILQPLVKAGIVETV 57 (144)
Q Consensus 12 ~~l~~La~~~~------~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~ 57 (144)
..|++|+...+ -|+|-+|||+..|+++..+.++|..|.+.|+|+..
T Consensus 7 ~~Ll~l~~~~g~~~~~~l~ltr~eiA~~lG~t~eTVsR~l~~l~~~G~I~~~ 58 (67)
T cd00092 7 SFLLNLSLRYGAGDLVQLPLTRQEIADYLGLTRETVSRTLKELEEEGLISRR 58 (67)
T ss_pred HHHHHHHHHHCCCCEEECCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEC
T ss_conf 9999999975899666617799999999789099999999999989948966
No 92
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=91.94 E-value=0.78 Score=26.00 Aligned_cols=62 Identities=10% Similarity=0.043 Sum_probs=49.3
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCC----CCCEECCCHHHCCHHHHHHHHC
Q ss_conf 8633599999981997899999999993259057315654----5400023721260999999971
Q gi|254780620|r 22 DYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRR----GGVRLCRPADQITILDVVKATE 83 (144)
Q Consensus 22 ~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~----GGy~Lak~~~~Itl~dI~~aie 83 (144)
+..+|..|||+...+++.+++.+|++|...|+|.=..|++ .-..+-++|+++....+-+.++
T Consensus 21 ~~~~tl~elA~~l~cS~Rn~r~lL~~m~~~gWl~W~p~~GRG~~S~L~~l~~~~~l~~~~a~~~l~ 86 (551)
T PRK13626 21 SQETTLNELAELLNCSRRHMRTLLNTMQDRGWLTWEAEVGRGKRSRLTFLYTGLALQQQRAEDLLE 86 (551)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCCCEEEEEECHHHHHHHHHHHHHH
T ss_conf 467439999998688857899999999988887860689989875699984899999999999997
No 93
>PRK10161 transcriptional regulator PhoB; Provisional
Probab=91.84 E-value=0.62 Score=26.61 Aligned_cols=56 Identities=20% Similarity=0.360 Sum_probs=39.6
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHC---------CCHHHHHHHHHHHHHC---CCEEECCCCCCCCEECC
Q ss_conf 9999999855986335999999819---------9789999999999325---90573156545400023
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACC---------ISELFLFKILQPLVKA---GIVETVRGRRGGVRLCR 68 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~---------i~~~~l~kil~~L~~a---gli~S~rG~~GGy~Lak 68 (144)
..+|.+|+.++++.+|-++|-+..- .=..|+.++=++|... .+|+++||. ||+|+.
T Consensus 160 ~~LL~~L~~~~g~vvsr~~L~~~vwg~~~~~~~rtldv~I~rLRkKl~~~~~~~~I~TvrG~--GYr~~~ 227 (229)
T PRK10161 160 FKLLHFFMTHPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEPGGHDRMVQTVRGT--GYRFST 227 (229)
T ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEECCC--CEEECC
T ss_conf 99999999779987979999998639998988473999999999974567999819986584--740571
No 94
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=91.82 E-value=0.57 Score=26.81 Aligned_cols=51 Identities=20% Similarity=0.197 Sum_probs=42.7
Q ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCC
Q ss_conf 999999998559863359999998199789999999999325905731565
Q gi|254780620|r 10 GIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGR 60 (144)
Q Consensus 10 Ai~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~ 60 (144)
.=+++-+|...++...++..||+..++|..-+-++|-.|.+.|-|....|-
T Consensus 8 eqkil~~L~~~g~~~~tA~~lak~lg~~Kk~vN~~LY~L~k~g~v~~~~~~ 58 (68)
T smart00550 8 EEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQGGT 58 (68)
T ss_pred HHHHHHHHHHCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHCCCEECCCCC
T ss_conf 999999999748864039999999499899999999999974883106998
No 95
>PRK04158 transcriptional repressor CodY; Validated
Probab=91.76 E-value=0.29 Score=28.58 Aligned_cols=44 Identities=25% Similarity=0.323 Sum_probs=35.4
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECC-CCCCCCE
Q ss_conf 8633599999981997899999999993259057315-6545400
Q gi|254780620|r 22 DYPNRISQIAEACCISELFLFKILQPLVKAGIVETVR-GRRGGVR 65 (144)
Q Consensus 22 ~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~r-G~~GGy~ 65 (144)
++...++.||++.||.++.+-.-|++|-.||+|+|.- |-+|-|.
T Consensus 199 EGlLVASkIADrvGITRSVIVNALRKlESAGVIESRSLGMKGTyI 243 (256)
T PRK04158 199 EGLLVASKIADRVGITRSVIVNALRKLESAGVIESRSLGMKGTYI 243 (256)
T ss_pred CCEEEEHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCEEE
T ss_conf 552754333443087156778777765314613512577771279
No 96
>PRK10870 transcriptional repressor MprA; Provisional
Probab=91.74 E-value=0.53 Score=27.01 Aligned_cols=62 Identities=16% Similarity=0.086 Sum_probs=43.9
Q ss_pred HHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCC--CEECCCHHHCC
Q ss_conf 999998559863359999998199789999999999325905731565454--00023721260
Q gi|254780620|r 13 VLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGG--VRLCRPADQIT 74 (144)
Q Consensus 13 ~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GG--y~Lak~~~~It 74 (144)
+|+.|...++.+.+-.+||+..+++++.+.+++-.|.+.|||+=.+-+.-. +.+.-.++-..
T Consensus 60 vL~~L~~~~~~~l~PseLa~~l~~s~a~iTr~vD~LEkkGlV~R~~s~~DRR~~~V~LT~~G~~ 123 (176)
T PRK10870 60 ALITLESQENHSIQPSELSCALGSSRTNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHE 123 (176)
T ss_pred HHHHHHCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCEEEEEECHHHHH
T ss_conf 9999971899985989999997787101999999999889978723712353478898988999
No 97
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=91.54 E-value=0.42 Score=27.59 Aligned_cols=62 Identities=21% Similarity=0.285 Sum_probs=45.3
Q ss_pred CCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECC----CHHHCC-HHHHHHHHC
Q ss_conf 98633-5999999819978999999999932590573156545400023----721260-999999971
Q gi|254780620|r 21 NDYPN-RISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCR----PADQIT-ILDVVKATE 83 (144)
Q Consensus 21 ~~~~~-s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak----~~~~It-l~dI~~aie 83 (144)
+|... |=.+||+..++|+..++|-+..|...|+|...+|+ |=|...+ +...++ +.+.+....
T Consensus 27 ~G~~LPsE~eLa~~f~VSR~TvRkAL~~L~~eGli~r~~G~-GtfV~~~~~~~~~~~~~~f~e~~~~~g 94 (236)
T COG2188 27 PGDKLPSERELAEQFGVSRMTVRKALDELVEEGLIVRRQGK-GTFVASPKEQSPLLELTSFSEELKSQG 94 (236)
T ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECC-EEEECCCCCCCHHHHHHHHHHHHHHCC
T ss_conf 98959598999999798899999999999989988995166-789887754233667764999999749
No 98
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=91.39 E-value=0.94 Score=25.52 Aligned_cols=85 Identities=18% Similarity=0.210 Sum_probs=55.8
Q ss_pred HHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCC----CCEE------CCCHHHCCHH
Q ss_conf 89999999999855986335999999819978999999999932590573156545----4000------2372126099
Q gi|254780620|r 7 TDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRG----GVRL------CRPADQITIL 76 (144)
Q Consensus 7 ~~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~G----Gy~L------ak~~~~Itl~ 76 (144)
.+.-.++|-.|.. +.+.|-.+||+..|+|++-+.+.+.+|.+.|+|......-. |+.+ ..++..-.+.
T Consensus 7 D~~D~~IL~~L~~--d~r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~~~~v~~~~~g~~~~a~v~v~~~~~~~~~~ 84 (154)
T COG1522 7 DDIDRRILRLLQE--DARISNAELAERVGLSPSTVLRRIKRLEEEGVIKGYTAVLDPEKLGLDLTAFVEVKLERSLEDLE 84 (154)
T ss_pred CHHHHHHHHHHHH--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEEEECHHHHCCCEEEEEEEECCCCHHHHH
T ss_conf 7999999999997--27657999999979798999999999998897699999998799199779999998177366899
Q ss_pred HHHHHHCCCCCCCCCCC
Q ss_conf 99999718763111468
Q gi|254780620|r 77 DVVKATEESFFVAECFA 93 (144)
Q Consensus 77 dI~~aie~~~~~~~C~~ 93 (144)
++.+.+.....+.+|..
T Consensus 85 ~~~~~~~~~p~V~~~~~ 101 (154)
T COG1522 85 EFAEALAKLPEVVECYR 101 (154)
T ss_pred HHHHHHHCCCCEEEEEE
T ss_conf 99999843987668999
No 99
>smart00862 Trans_reg_C Transcriptional regulatory protein, C terminal. This domain is almost always found associated with the response regulator receiver domain. It may play a role in DNA binding.
Probab=91.30 E-value=0.93 Score=25.56 Aligned_cols=55 Identities=24% Similarity=0.338 Sum_probs=37.7
Q ss_pred HHHHHHHHHHCCCCCCCHHHHHHHH-C-----CCH----HHHHHHHHHHHHC----CCEEECCCCCCCCEE
Q ss_conf 9999999985598633599999981-9-----978----9999999999325----905731565454000
Q gi|254780620|r 10 GIRVLMYCAIHNDYPNRISQIAEAC-C-----ISE----LFLFKILQPLVKA----GIVETVRGRRGGVRL 66 (144)
Q Consensus 10 Ai~~l~~La~~~~~~~s~~eIA~~~-~-----i~~----~~l~kil~~L~~a----gli~S~rG~~GGy~L 66 (144)
..++|.+|+.++++++|-++|.+.. + .+. .++.++=++|.+. .+|.+++|. ||+|
T Consensus 10 e~~lL~~L~~~~~~~vs~~~l~~~lw~~~~~~~~~~~l~~~I~~LR~kl~~~~~~~~~i~t~~g~--GY~l 78 (78)
T smart00862 10 EFRLLELLLRNPGRVVSREELLEAVWGDDDDDVDDNTLDVHISRLRKKLEDDGANPRLIETVRGV--GYRL 78 (78)
T ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEECCC--CCCC
T ss_conf 99999999847996296999998762888788886027899999999976458999959983795--6449
No 100
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=91.30 E-value=0.4 Score=27.72 Aligned_cols=81 Identities=11% Similarity=0.041 Sum_probs=53.0
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCC----CCCCEE------CC-CHHHCCHHHHH
Q ss_conf 99999998559863359999998199789999999999325905731565----454000------23-72126099999
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGR----RGGVRL------CR-PADQITILDVV 79 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~----~GGy~L------ak-~~~~Itl~dI~ 79 (144)
.++|-.|. .++..|..+||+..|+|++-+.+=+++|.+.|+|+..... .=||.+ .- +...-.+.++.
T Consensus 17 ~~IL~~Lq--~daR~s~~eLA~~vglS~stv~~RikrLe~~GiI~gy~a~id~~~lG~~~~a~v~i~l~~~~~~~~~~~~ 94 (164)
T PRK11169 17 RNILNELQ--KDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQGYTALLNPHYLDASLLVFVEITLNRGAPDVFEQFN 94 (164)
T ss_pred HHHHHHHH--HCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEEEECCCCCCCCEEEEEEEEECCCCHHHHHHHH
T ss_conf 99999999--8489999999999892999999999999978988668999760007987499999996588868999999
Q ss_pred HHHCCCCCCCCCCC
Q ss_conf 99718763111468
Q gi|254780620|r 80 KATEESFFVAECFA 93 (144)
Q Consensus 80 ~aie~~~~~~~C~~ 93 (144)
+++..-..+.+|..
T Consensus 95 ~~l~~~peV~~~~~ 108 (164)
T PRK11169 95 AAVQKLEEIQECHL 108 (164)
T ss_pred HHHHCCCCEEEEEE
T ss_conf 99842997899998
No 101
>COG5340 Predicted transcriptional regulator [Transcription]
Probab=91.29 E-value=0.36 Score=27.97 Aligned_cols=66 Identities=21% Similarity=0.140 Sum_probs=47.7
Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHH----HCCHHHHH
Q ss_conf 999999855986335999999819978999999999932590573156545400023721----26099999
Q gi|254780620|r 12 RVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPAD----QITILDVV 79 (144)
Q Consensus 12 ~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~----~Itl~dI~ 79 (144)
.-+.++|..+.+.+|+.+.++-.+++++.++++++.|-+.|+++ |=..|-|..---|. ++++-|-+
T Consensus 18 e~l~~laae~hkiiTirdvae~~ev~~n~lr~lasrLekkG~Le--Ri~rG~YlI~~lpage~~~~t~he~~ 87 (269)
T COG5340 18 ELLSHLAAEGHKIITIRDVAETLEVAPNTLRELASRLEKKGWLE--RILRGRYLIIPLPAGEEAVYTTHEYL 87 (269)
T ss_pred HHHHHHHHHHCCEEEEHHHHHHCCCCHHHHHHHHHHHHHCCHHH--HHCCCCEEEEECCCCCCCCEEEHHHH
T ss_conf 99999998747657717756631578889999986555342466--65186079865588765512303578
No 102
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=91.18 E-value=0.99 Score=25.41 Aligned_cols=55 Identities=18% Similarity=0.277 Sum_probs=42.0
Q ss_pred HHHHHHHHCCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECC
Q ss_conf 99999985598633599999981-----9978999999999932590573156545400023
Q gi|254780620|r 12 RVLMYCAIHNDYPNRISQIAEAC-----CISELFLFKILQPLVKAGIVETVRGRRGGVRLCR 68 (144)
Q Consensus 12 ~~l~~La~~~~~~~s~~eIA~~~-----~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak 68 (144)
.+|-.|.. .+++.|+.+|.+.. +++++.|.+.|..|...|+|.-..+.+ ||.+..
T Consensus 30 ~VL~~l~~-~~~~lsA~eI~~~l~~~~~~is~aTVYRtL~~L~e~Glv~ri~~~n-~y~~~~ 89 (169)
T PRK11639 30 EVLRLMSL-QDGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHKVESTN-SYVLCH 89 (169)
T ss_pred HHHHHHHH-CCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCEEEEECCC-CEEEEC
T ss_conf 99999995-7999999999999997589988277999999999789589970588-557722
No 103
>TIGR02404 trehalos_R_Bsub trehalose operon repressor; InterPro: IPR012770 This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from Escherichia coli..
Probab=91.18 E-value=0.32 Score=28.32 Aligned_cols=59 Identities=24% Similarity=0.302 Sum_probs=48.9
Q ss_pred CCCCCCH-HHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHH
Q ss_conf 9863359-99999819978999999999932590573156545400023721260999999
Q gi|254780620|r 21 NDYPNRI-SQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVK 80 (144)
Q Consensus 21 ~~~~~s~-~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~ 80 (144)
+|...+| .+|++..++|+-.++|-|..|..+|+|+=.||+ |=..|.+.+=+-.++.|+-
T Consensus 20 ~G~~LPSE~~L~~~Y~~SReTvRKAL~~L~~~GyIQKi~GK-GsiVl~~~~~~fP~SGivS 79 (236)
T TIGR02404 20 EGDLLPSEHELMEQYGASRETVRKALNLLTEAGYIQKIRGK-GSIVLNREKYEFPISGIVS 79 (236)
T ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECC-EEEEECCCCCCCCCCCCHH
T ss_conf 87738887899986068745889999999857871676152-3487667631048630011
No 104
>PRK03911 heat-inducible transcription repressor; Provisional
Probab=91.16 E-value=0.66 Score=26.45 Aligned_cols=52 Identities=10% Similarity=0.163 Sum_probs=41.4
Q ss_pred HHHHHHHHHHHHCCCCCCCHHHHHHHHC--CCHHHHHHHHHHHHHCCCEEECCC
Q ss_conf 9999999999855986335999999819--978999999999932590573156
Q gi|254780620|r 8 DYGIRVLMYCAIHNDYPNRISQIAEACC--ISELFLFKILQPLVKAGIVETVRG 59 (144)
Q Consensus 8 ~yAi~~l~~La~~~~~~~s~~eIA~~~~--i~~~~l~kil~~L~~agli~S~rG 59 (144)
+--+++++.--...+.|++|+.+++..+ +|++.++.+|+.|-+.|++...--
T Consensus 5 ~~IL~~iVe~Yi~t~~PVgSk~L~~~~~l~~SsATIRn~m~~LE~~G~L~~pHt 58 (258)
T PRK03911 5 DLILDSIIKTYLQDNEPIGSNELKSLMNLKIPASTIRVYFKKLSDEGLITQLHI 58 (258)
T ss_pred HHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCCCCC
T ss_conf 999999999995549814779999874999880899999999987867579867
No 105
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=91.10 E-value=0.26 Score=28.84 Aligned_cols=34 Identities=24% Similarity=0.109 Sum_probs=30.9
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Q ss_conf 6335999999819978999999999932590573
Q gi|254780620|r 23 YPNRISQIAEACCISELFLFKILQPLVKAGIVET 56 (144)
Q Consensus 23 ~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S 56 (144)
+-++-++||+.++++...++|+|..|...++|.+
T Consensus 14 ~~v~dedLa~~l~~~~n~vRkiL~~L~e~~lv~~ 47 (147)
T smart00531 14 GCVTEEDLAELLGIKQKQLRKILYLLYDEKLIKI 47 (147)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
T ss_conf 9707999999979999999999999997796468
No 106
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=91.02 E-value=0.74 Score=26.15 Aligned_cols=45 Identities=24% Similarity=0.326 Sum_probs=37.6
Q ss_pred HHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCC
Q ss_conf 99999855986335999999819978999999999932590573156
Q gi|254780620|r 13 VLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRG 59 (144)
Q Consensus 13 ~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG 59 (144)
++-++.. .+.+++.++|+..++|+..+++=+..|.+.|.|.-++|
T Consensus 5 Il~~l~~--~~~~~i~~La~~~~VS~~TiRRDl~~L~~~g~i~r~hG 49 (53)
T smart00420 5 ILELLAQ--QGKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTRVHG 49 (53)
T ss_pred HHHHHHH--CCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEC
T ss_conf 9999998--69797999999989799999996999998899899779
No 107
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=90.87 E-value=0.67 Score=26.42 Aligned_cols=75 Identities=15% Similarity=0.159 Sum_probs=48.9
Q ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCC-----HHHHHHHHCC
Q ss_conf 99999999855986335999999819978999999999932590573156545400023721260-----9999999718
Q gi|254780620|r 10 GIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQIT-----ILDVVKATEE 84 (144)
Q Consensus 10 Ai~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~It-----l~dI~~aie~ 84 (144)
+|..|..++..++-.+|++++|++.+.|....++.+..|...|+|.-..-+.|-+ +.-.-+-+. ..|.-++++.
T Consensus 5 ~lk~l~~~~a~~~~~~t~~ela~~l~~S~qta~R~l~~le~~~~I~R~~~~~Gq~-i~iTekG~~~L~~~~~d~~r~~~~ 83 (214)
T COG1339 5 LLKKLALRGAVRGVKVTSSELAKRLGVSSQTAARKLKELEDEGYITRTISKRGQL-ITITEKGIDLLYKEYEDLSRIFDS 83 (214)
T ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHCCCCCEEEEECCCCCE-EEEHHHHHHHHHHHHHHHHHHHCC
T ss_conf 9999987210037602089999885747077889988641178478883379848-981676899999999999999668
Q ss_pred C
Q ss_conf 7
Q gi|254780620|r 85 S 85 (144)
Q Consensus 85 ~ 85 (144)
+
T Consensus 84 ~ 84 (214)
T COG1339 84 G 84 (214)
T ss_pred C
T ss_conf 8
No 108
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=90.76 E-value=0.52 Score=27.04 Aligned_cols=42 Identities=31% Similarity=0.430 Sum_probs=35.1
Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Q ss_conf 999999855986335999999819978999999999932590573
Q gi|254780620|r 12 RVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVET 56 (144)
Q Consensus 12 ~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S 56 (144)
+++-.|+. .|+=+.+||...|+++.-+.+-|+.|-+||+|+|
T Consensus 19 ~Il~lLt~---~p~yvsEiS~~lgvsqkAVl~HL~~LE~AGlveS 60 (217)
T COG1777 19 RILQLLTR---RPCYVSEISRELGVSQKAVLKHLRILERAGLVES 60 (217)
T ss_pred HHHHHHHC---CCHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCHH
T ss_conf 99999854---7139998776608678999999999998587121
No 109
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=90.69 E-value=0.43 Score=27.53 Aligned_cols=78 Identities=14% Similarity=0.193 Sum_probs=48.9
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCC----CCCCC-----EECC--CHHHCCHHHHH
Q ss_conf 9999999855986335999999819978999999999932590573156----54540-----0023--72126099999
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRG----RRGGV-----RLCR--PADQITILDVV 79 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG----~~GGy-----~Lak--~~~~Itl~dI~ 79 (144)
.++|-.|.. ++..|..+||+..|+|++-+.+=+++|.+.|+|+.... ..-|| ...+ +++ .+-++.
T Consensus 6 ~~Il~~L~~--n~R~s~~~iA~~lg~S~~tv~~Ri~~L~~~GiI~~~~~~vd~~~lg~~~~a~v~i~v~~~~--~~~~v~ 81 (108)
T smart00344 6 RKILEELQK--DARISLAELAKKVGLSPSTVHNRVKRLEEEGVIKGYTAVINPKKLGLSVTAFVGVDLESPD--KLEEFL 81 (108)
T ss_pred HHHHHHHHH--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCCEEEEEECHHHHCCCEEEEEEEEECCCH--HHHHHH
T ss_conf 999999998--2899999999998939999999999996089732028998989929987999999986830--399999
Q ss_pred HHHCCCCCCCCCC
Q ss_conf 9971876311146
Q gi|254780620|r 80 KATEESFFVAECF 92 (144)
Q Consensus 80 ~aie~~~~~~~C~ 92 (144)
+.+..-.....|.
T Consensus 82 ~~l~~~peV~~~~ 94 (108)
T smart00344 82 EKLEKLPEVVEVY 94 (108)
T ss_pred HHHHCCHHHHEHH
T ss_conf 9986690111312
No 110
>pfam09182 PuR_N Bacterial purine repressor, N-terminal. The N-terminal domain of the bacterial purine repressor PuR is a winged-helix domain, a subdivision of the HTH structural family. It consists of a canonical arrangement of secondary structures: a1-b1-a2-T-a3-b2-W-b3, where a2-T-a3 is the HTH motif, a3 is the recognition helix, and W is the wing. The domain allows for recognition of a conserved CGAA sequence in the centre of a DNA PurBox, resulting in binding to the major groove of DNA.
Probab=90.68 E-value=0.77 Score=26.05 Aligned_cols=59 Identities=17% Similarity=0.221 Sum_probs=43.9
Q ss_pred HHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHH-------HHHHHHHHCCCEEECCCCCCCCEE
Q ss_conf 899999999998559863359999998199789999-------999999325905731565454000
Q gi|254780620|r 7 TDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLF-------KILQPLVKAGIVETVRGRRGGVRL 66 (144)
Q Consensus 7 ~~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~-------kil~~L~~agli~S~rG~~GGy~L 66 (144)
++==+.+.-||..|+.+.++....|+..+...+-++ +++++ ...|.|+.++|+.||.++
T Consensus 3 seRlv~mt~~Ll~~P~~li~L~~Fae~~~~AKSsISEDl~iik~~~~~-~g~G~leTi~GaaGGv~y 68 (70)
T pfam09182 3 SERLVAMTKYLLENPNKLIPLTYFAERFGSAKSSISEDLVIIKETFEK-FGLGKLETIPGAAGGVKY 68 (70)
T ss_pred CHHHHHHHHHHHHCCCCEECHHHHHHHHCCCCCHHHHHHHHHHHHHHH-CCCCEEEEECCCCCCEEE
T ss_conf 048999999998299855749999998660102037579999999987-398629984587778563
No 111
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=90.66 E-value=0.5 Score=27.16 Aligned_cols=46 Identities=22% Similarity=0.190 Sum_probs=38.9
Q ss_pred CCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEEC
Q ss_conf 98633-599999981997899999999993259057315654540002
Q gi|254780620|r 21 NDYPN-RISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLC 67 (144)
Q Consensus 21 ~~~~~-s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~La 67 (144)
+|... +=.++|+..|+|++-|+-.|+.|...|+|++.+|. |.|...
T Consensus 30 ~G~~LP~EreLae~fgVSR~~vREAl~~L~a~Glve~r~G~-Gt~V~~ 76 (241)
T COG2186 30 PGDRLPSERELAERFGVSRTVVREALKRLEAKGLVEIRQGS-GTFVRP 76 (241)
T ss_pred CCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCEECCCCC-CEEECC
T ss_conf 99999889999999789956899999999987886305899-827647
No 112
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY; InterPro: IPR014154 This entry represents pleiotropic repressors in Bacillus subtilis, CodY, and other Firmicutes (low-GC Gram-positive bacteria) that respond to intracellular levels of GTP and branched chain amino acids. All have a C-terminal helix-turn-helix DNA-binding region..
Probab=90.61 E-value=0.16 Score=30.07 Aligned_cols=54 Identities=20% Similarity=0.285 Sum_probs=44.2
Q ss_pred HHHHHHHH--HCC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECC-CCCCCC
Q ss_conf 99999998--559-8633599999981997899999999993259057315-654540
Q gi|254780620|r 11 IRVLMYCA--IHN-DYPNRISQIAEACCISELFLFKILQPLVKAGIVETVR-GRRGGV 64 (144)
Q Consensus 11 i~~l~~La--~~~-~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~r-G~~GGy 64 (144)
|+|+-++- .++ ++...++.||++.||.++-+-.-|+||=-||+|+|.= |=+|=|
T Consensus 186 L~AV~aIf~ELdG~EG~LvAS~IAD~vGITRSVIVNALRKlESAGvIESRSLGMKGTy 243 (255)
T TIGR02787 186 LEAVEAIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRSLGMKGTY 243 (255)
T ss_pred HHHHHHHHHHCCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHCCEEECCCCCCCHHH
T ss_conf 9999999842289966277530207126603355454344420764130237852014
No 113
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=90.61 E-value=0.81 Score=25.91 Aligned_cols=49 Identities=18% Similarity=0.099 Sum_probs=39.8
Q ss_pred HHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCC
Q ss_conf 999998559863359999998199789999999999325905731565454
Q gi|254780620|r 13 VLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGG 63 (144)
Q Consensus 13 ~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GG 63 (144)
+|..|.. .+++|..+||+..++.++-+.+++..|.+.|+|+-.+-+.-+
T Consensus 45 vL~~L~~--~~~~t~~eLa~~l~id~~tvt~~ldrLe~~GlI~R~~~p~Dr 93 (144)
T PRK11512 45 VLCSIRC--AACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDK 93 (144)
T ss_pred HHHHHHH--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCC
T ss_conf 9999998--699799999999788887899999999978796635798776
No 114
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=90.60 E-value=0.54 Score=26.98 Aligned_cols=45 Identities=16% Similarity=0.135 Sum_probs=35.3
Q ss_pred HHHHHHHCC--C----CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEC
Q ss_conf 999998559--8----63359999998199789999999999325905731
Q gi|254780620|r 13 VLMYCAIHN--D----YPNRISQIAEACCISELFLFKILQPLVKAGIVETV 57 (144)
Q Consensus 13 ~l~~La~~~--~----~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~ 57 (144)
.|+.++... + -+.|=++||...|+++..+.++|+.|++.|+|+-.
T Consensus 156 ~Ll~l~~~~~~~~~i~l~lT~~dLA~~lG~trETVsR~L~~L~~eGlI~~~ 206 (224)
T PRK09391 156 FLLEMDERLGGAGMMALPMSRRDIADYLGLTIETVSRALSQLKDRGVIGLS 206 (224)
T ss_pred HHHHHHHHHCCCEEEECCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEC
T ss_conf 999999973998089715799999988799799999999999988989965
No 115
>PRK09468 ompR osmolarity response regulator; Provisional
Probab=90.55 E-value=1.1 Score=25.14 Aligned_cols=62 Identities=13% Similarity=0.175 Sum_probs=40.7
Q ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHH-----CC----CHHHHHHHHHHHHHC----CCEEECCCCCCCCEECCCHH
Q ss_conf 68999999999985598633599999981-----99----789999999999325----90573156545400023721
Q gi|254780620|r 6 RTDYGIRVLMYCAIHNDYPNRISQIAEAC-----CI----SELFLFKILQPLVKA----GIVETVRGRRGGVRLCRPAD 71 (144)
Q Consensus 6 ~~~yAi~~l~~La~~~~~~~s~~eIA~~~-----~i----~~~~l~kil~~L~~a----gli~S~rG~~GGy~Lak~~~ 71 (144)
..|| .+|.+|+.++++.+|-++|.+.. .. =..|+.++=++|... .+|+++||. ||++.-+.+
T Consensus 164 ~~E~--~LL~~L~~~~g~vvsre~Ll~~vwg~~~~~~~rtidv~I~rLRkKl~~~~~~~~~I~TvrG~--GY~f~~dg~ 238 (239)
T PRK09468 164 TGEF--AVLKALVRHPREPLSRDKLMNLARGREYSAMERSIDVQISRLRRLIEPDPAHPRYIQTVWGL--GYVFVPDGA 238 (239)
T ss_pred HHHH--HHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEECCC--CEEECCCCC
T ss_conf 8999--99999997799667699999996298878884839999999999752078999849987580--868745898
No 116
>PRK09836 DNA-binding transcriptional activator CusR; Provisional
Probab=90.54 E-value=1.1 Score=25.10 Aligned_cols=60 Identities=20% Similarity=0.266 Sum_probs=41.8
Q ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHC-----CC----HHHHHHHHHHHHHC---CCEEECCCCCCCCEECCC
Q ss_conf 689999999999855986335999999819-----97----89999999999325---905731565454000237
Q gi|254780620|r 6 RTDYGIRVLMYCAIHNDYPNRISQIAEACC-----IS----ELFLFKILQPLVKA---GIVETVRGRRGGVRLCRP 69 (144)
Q Consensus 6 ~~~yAi~~l~~La~~~~~~~s~~eIA~~~~-----i~----~~~l~kil~~L~~a---gli~S~rG~~GGy~Lak~ 69 (144)
..|| .+|-+|+.++++.+|-++|.+..- .+ ..|+.++=++|.+. .+|+++||. ||+|..|
T Consensus 153 ~~E~--~lL~~L~~~~g~vvsre~l~~~vw~~~~~~~~~~vdv~I~rLR~Kl~~~~~~~~I~TvrG~--GY~l~~p 224 (226)
T PRK09836 153 SKEF--TLLEFFLRHQGEVLPRSLIASQVWDMNFDSDTNAIDVAVKRLRGKIDNDFEPKLIQTVRGV--GYMLEVP 224 (226)
T ss_pred HHHH--HHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCEEEEECCC--CEEEECC
T ss_conf 8999--9999998689964879999999628887888588999999999985788999839996681--5698448
No 117
>CHL00148 orf27 Ycf27; Reviewed
Probab=90.51 E-value=1 Score=25.29 Aligned_cols=61 Identities=13% Similarity=0.160 Sum_probs=42.8
Q ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHH-CC----------CHHHHHHHHHHHHH----CCCEEECCCCCCCCEECCCH
Q ss_conf 68999999999985598633599999981-99----------78999999999932----59057315654540002372
Q gi|254780620|r 6 RTDYGIRVLMYCAIHNDYPNRISQIAEAC-CI----------SELFLFKILQPLVK----AGIVETVRGRRGGVRLCRPA 70 (144)
Q Consensus 6 ~~~yAi~~l~~La~~~~~~~s~~eIA~~~-~i----------~~~~l~kil~~L~~----agli~S~rG~~GGy~Lak~~ 70 (144)
..||. +|.+|+.++++.+|-++|.+.. +. =..|+.++=++|.. ..+|+++||. ||.|.+.-
T Consensus 164 ~~E~~--lL~~L~~~~g~vvsre~L~~~vWg~~~~~~~~~r~vdv~I~rLRkKl~~~~~~~~~I~TvrG~--GY~~~~~~ 239 (240)
T CHL00148 164 GMEFS--LLELLISESGEIFSRATILKEVWGYTPERHIDTRVVDVHISRLRAKLEDDPSNPDLILTARGT--GYLFQRII 239 (240)
T ss_pred HHHHH--HHHHHHHCCCCCCCHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEECCC--CEEEEEEC
T ss_conf 99999--999999679974969999999728887667875579999999999741078999869997897--87896607
No 118
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR; InterPro: IPR014178 Members of this entry are transcriptional regulators of fatty acid metabolism (FadR), including both biosynthesis and beta-oxidation reactions, which are found exclusively in a subset of Gammaproteobacteria with strictly one copy per genome. Proteins have an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR when expressed in Escherichia coli shows differences in regulatory response and fatty acid binding profiles. All members of this entry are expected to have the same function.; GO: 0000062 acyl-CoA binding, 0003677 DNA binding, 0003700 transcription factor activity, 0019217 regulation of fatty acid metabolic process.
Probab=90.50 E-value=0.2 Score=29.55 Aligned_cols=63 Identities=14% Similarity=0.169 Sum_probs=49.5
Q ss_pred CCCCCCH-HHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCC----CCCCEECCCHHHCCHHHHHHHHCCCCC
Q ss_conf 9863359-999998199789999999999325905731565----454000237212609999999718763
Q gi|254780620|r 21 NDYPNRI-SQIAEACCISELFLFKILQPLVKAGIVETVRGR----RGGVRLCRPADQITILDVVKATEESFF 87 (144)
Q Consensus 21 ~~~~~s~-~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~----~GGy~Lak~~~~Itl~dI~~aie~~~~ 87 (144)
+|.-.++ .||||..|+.++.|+=|||+|.|=|+++-+=|+ +-=| +.+-.+++|.+-.+|+...
T Consensus 26 PGSiLPAERELsElIGVTRTTLREVLQRLARDGWLTIQHGKPTKVNnfW----ETSGLNILeTL~~LD~~~~ 93 (275)
T TIGR02812 26 PGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHGKPTKVNNFW----ETSGLNILETLIRLDGESV 93 (275)
T ss_pred CCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCHH----HCCCCCHHHHHHHHCCCCC
T ss_conf 5898724665754237663037899988764113436588998627624----3027357899986187777
No 119
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=90.49 E-value=0.91 Score=25.63 Aligned_cols=34 Identities=29% Similarity=0.253 Sum_probs=31.1
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEC
Q ss_conf 3359999998199789999999999325905731
Q gi|254780620|r 24 PNRISQIAEACCISELFLFKILQPLVKAGIVETV 57 (144)
Q Consensus 24 ~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~ 57 (144)
..|=.|||+++|+|+..+.+.++..++.|+|+-.
T Consensus 26 gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I~ 59 (321)
T COG2390 26 GLTQSEIAERLGISRATVSRLLAKAREEGIVKIS 59 (321)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEEE
T ss_conf 8879999988398899999999999987938999
No 120
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=90.44 E-value=1.2 Score=24.83 Aligned_cols=42 Identities=12% Similarity=0.039 Sum_probs=35.5
Q ss_pred HHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECC
Q ss_conf 9985598633599999981997899999999993259057315
Q gi|254780620|r 16 YCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVR 58 (144)
Q Consensus 16 ~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~r 58 (144)
.|. ..+++.|++|+|+..|+|+.-++|=|..|...|.++..-
T Consensus 170 ~l~-~~~~~~ta~eva~~~giSrvTaRRYLe~L~~~g~~~~~~ 211 (225)
T PRK10046 170 LFK-EPGVQHTAETVAQALTISRTTARRYLEYCASRHLIIAEI 211 (225)
T ss_pred HHH-CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEEEE
T ss_conf 997-179986899999985851999999999998689079983
No 121
>pfam08220 HTH_DeoR DeoR-like helix-turn-helix domain.
Probab=90.33 E-value=0.93 Score=25.55 Aligned_cols=50 Identities=20% Similarity=0.258 Sum_probs=39.8
Q ss_pred HHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEEC
Q ss_conf 9999985598633599999981997899999999993259057315654540002
Q gi|254780620|r 13 VLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLC 67 (144)
Q Consensus 13 ~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~La 67 (144)
++-+|.. .+.+++.+||+..++|...+++=+..|.+.|+|.-+ +||..+.
T Consensus 5 Il~~l~~--~~~v~i~~La~~f~VS~~TiRRDl~~L~~~g~i~R~---~GGA~~~ 54 (57)
T pfam08220 5 ILELLKQ--QGTLSVEELAELLGVSEMTIRRDLNELEEQGLLTRT---HGGAVSN 54 (57)
T ss_pred HHHHHHH--CCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEE---ECCEECC
T ss_conf 9999998--697979999999895999999969999988998997---4957758
No 122
>PRK11832 putative DNA-binding transcriptional regulator; Provisional
Probab=90.30 E-value=0.34 Score=28.13 Aligned_cols=58 Identities=24% Similarity=0.290 Sum_probs=40.7
Q ss_pred HHHH-HHHHHCCC---CCCCH-HHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCH
Q ss_conf 9999-99985598---63359-9999981997899999999993259057315654540002372
Q gi|254780620|r 11 IRVL-MYCAIHND---YPNRI-SQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPA 70 (144)
Q Consensus 11 i~~l-~~La~~~~---~~~s~-~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~ 70 (144)
||.. +.|...++ ..+++ .-|-+++++|++.+-||++.|++.|+|+-.||+- ..+.+=|
T Consensus 142 IR~~L~el~~~~e~~R~~i~v~~yI~~rT~lSRS~im~vls~Lk~ggyI~i~~G~L--~~i~~LP 204 (207)
T PRK11832 142 IRATLLSMIDWNEELRSRIGVMNYIHQRTRISRSVVAEVLAALRKGGYIEMNKGKL--VAINRLP 204 (207)
T ss_pred HHHHHHHHHHCCHHHHHHCCHHHHHHHHCCCCHHHHHHHHHHHHCCCCEEEECCEE--EECCCCC
T ss_conf 99999999838999983075999999874420999999999984499789863789--7714577
No 123
>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=90.23 E-value=1.2 Score=24.80 Aligned_cols=53 Identities=25% Similarity=0.231 Sum_probs=40.2
Q ss_pred HHHHHHCCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHCCCEEECCCCCCC--CEEC
Q ss_conf 999985598633599999981-----99789999999999325905731565454--0002
Q gi|254780620|r 14 LMYCAIHNDYPNRISQIAEAC-----CISELFLFKILQPLVKAGIVETVRGRRGG--VRLC 67 (144)
Q Consensus 14 l~~La~~~~~~~s~~eIA~~~-----~i~~~~l~kil~~L~~agli~S~rG~~GG--y~La 67 (144)
+-.|. ..+++.|+.+|-+.. +++++.+.+.|..|...|+|......+|. |.+.
T Consensus 7 l~~l~-~~~~h~sa~eI~~~l~~~~~~i~~~TVYR~L~~l~~~gli~~~~~~~~~~~y~~~ 66 (116)
T cd07153 7 LEVLL-ESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELGDGKARYELN 66 (116)
T ss_pred HHHHH-HCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCEEEEEECCCEEEEEEC
T ss_conf 99998-3798989999999999758999888999999999968956999816980599844
No 124
>pfam05732 RepL Firmicute plasmid replication protein (RepL). This family consists of Firmicute RepL proteins which are involved in plasmid replication.
Probab=90.19 E-value=0.5 Score=27.16 Aligned_cols=73 Identities=14% Similarity=0.155 Sum_probs=52.2
Q ss_pred HHHHHHHHHC--C-CC-CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECC-------CHHHCCHHHHH
Q ss_conf 9999999855--9-86-335999999819978999999999932590573156545400023-------72126099999
Q gi|254780620|r 11 IRVLMYCAIH--N-DY-PNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCR-------PADQITILDVV 79 (144)
Q Consensus 11 i~~l~~La~~--~-~~-~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak-------~~~~Itl~dI~ 79 (144)
++++.|+..+ . +. ..|.++||+..++|...+...|..|..+|++ .++.+|-|.+.- +-+.-.|+-=|
T Consensus 58 ~~Vv~yileN~nsnNtlI~T~R~lae~~gvs~~TV~~tmK~L~e~~fI--kk~t~GvymiNP~i~~kG~~~K~~ylL~~f 135 (165)
T pfam05732 58 TRLVFWLIDNLNSNNTLIMTQREIAEETGISLETVRQTMKALEEGNFL--KKKTSGVYMINPDLLFKGDDTKRLNLLLQF 135 (165)
T ss_pred HHHHHHHHHCCCCCCEEEEEHHHHHHHHCCCHHHHHHHHHHHHHCCCE--EEECCCEEEECHHHHHCCCHHHHHHHHHHH
T ss_conf 122566765368886499878999998395299999999999758926--861387699885895068727899999998
Q ss_pred HHHCCC
Q ss_conf 997187
Q gi|254780620|r 80 KATEES 85 (144)
Q Consensus 80 ~aie~~ 85 (144)
+.+|..
T Consensus 136 ~~~eqE 141 (165)
T pfam05732 136 RKFEQE 141 (165)
T ss_pred HHHCCC
T ss_conf 764027
No 125
>pfam00486 Trans_reg_C Transcriptional regulatory protein, C terminal.
Probab=90.17 E-value=1.2 Score=24.87 Aligned_cols=55 Identities=20% Similarity=0.264 Sum_probs=37.6
Q ss_pred HHHHHHHHHHCCCCCCCHHHHHHHH-----CCCHH----HHHHHHHHHHHC----CCEEECCCCCCCCEE
Q ss_conf 9999999985598633599999981-----99789----999999999325----905731565454000
Q gi|254780620|r 10 GIRVLMYCAIHNDYPNRISQIAEAC-----CISEL----FLFKILQPLVKA----GIVETVRGRRGGVRL 66 (144)
Q Consensus 10 Ai~~l~~La~~~~~~~s~~eIA~~~-----~i~~~----~l~kil~~L~~a----gli~S~rG~~GGy~L 66 (144)
...+|.+|..++++.+|-++|.+.. ..+.. ++.++=++|... .+|++++|. ||+|
T Consensus 10 E~~lL~~L~~~~~~~vsr~~l~~~iw~~~~~~~~~sl~~~I~rLR~kl~~~~~~~~~I~tv~g~--GY~L 77 (77)
T pfam00486 10 EFDLLELLARNPGRVVSREELLEEVWGEDFDVDDNTVDVHISRLRKKLEDDPRDPRLIKTVRGV--GYRL 77 (77)
T ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEECCC--CCCC
T ss_conf 9999999996799719799999996387666553309999999999875448999839984896--6449
No 126
>pfam07848 PaaX PaaX-like protein. This family contains proteins that are similar to the product of the paaX gene of Escherichia coli. This protein is involved in the regulation of expression of a group of proteins known to participate in the metabolism of phenylacetic acid. In fact, some members of this family are annotated by InterPro as containing a winged helix DNA-binding domain (Interpro:IPR009058).
Probab=90.11 E-value=0.51 Score=27.12 Aligned_cols=49 Identities=31% Similarity=0.306 Sum_probs=40.9
Q ss_pred CCCCCCC---HHHHHHHHCCCHHHHHHHHHHHHHCCCEEECC-CCCCCCEECC
Q ss_conf 5986335---99999981997899999999993259057315-6545400023
Q gi|254780620|r 20 HNDYPNR---ISQIAEACCISELFLFKILQPLVKAGIVETVR-GRRGGVRLCR 68 (144)
Q Consensus 20 ~~~~~~s---~~eIA~~~~i~~~~l~kil~~L~~agli~S~r-G~~GGy~Lak 68 (144)
+.++.++ .-++-+..++++.-++--++.|++.|++++.| |+.=+|.|+.
T Consensus 16 ~~gg~i~~~sLi~ll~~~Gi~~~avRtAlsRl~~~GwL~~~r~Gr~s~Y~LT~ 68 (70)
T pfam07848 16 PHGGAIWLGSLIRLLAGFGISERLVRTALSRLVKAGWLVRERVGRRSYYRLSD 68 (70)
T ss_pred CCCCEEEHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCEEEEECCCCCEEEECC
T ss_conf 58983748999999998399817899999999764864667518822366489
No 127
>pfam05158 RNA_pol_Rpc34 RNA polymerase Rpc34 subunit. Subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of yeast RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and is therefore participates in Pol III recruitment.
Probab=90.09 E-value=1.4 Score=24.50 Aligned_cols=62 Identities=19% Similarity=0.270 Sum_probs=45.3
Q ss_pred HHHHHHC--CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCC----CEECC--CHHHCCH
Q ss_conf 9999855--9863359999998199789999999999325905731565454----00023--7212609
Q gi|254780620|r 14 LMYCAIH--NDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGG----VRLCR--PADQITI 75 (144)
Q Consensus 14 l~~La~~--~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GG----y~Lak--~~~~Itl 75 (144)
|+|=..+ +.+.+-+++|-.+.+++.+.+.|+|..|-..++|+|++-.+-. |.|.- |.++||=
T Consensus 87 lVY~~Ie~ag~~GIW~k~i~~~tnL~~~~l~K~LK~LEsk~lIKsVksV~~~~rKvYmL~~LePS~eiTG 156 (313)
T pfam05158 87 LVYSIIEESGNEGIWTRTIKNRTNLHQSVLKKCLKSLESKKYIKSVKSVKAPTRKMYMLYNLEPSEEVTG 156 (313)
T ss_pred HHHHHHHHCCCCCEEHHHHHHHCCCCHHHHHHHHHHHHHCCCEEEECCCCCCCEEEEEEECCCCCCCCCC
T ss_conf 9999998627677449999988099889999999999756861542145678705999834774711148
No 128
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=90.09 E-value=0.26 Score=28.83 Aligned_cols=55 Identities=25% Similarity=0.266 Sum_probs=41.7
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEC--CCCCCCCEECC
Q ss_conf 99999998559863359999998199789999999999325905731--56545400023
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETV--RGRRGGVRLCR 68 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~--rG~~GGy~Lak 68 (144)
|-+++||+ .+|.|..||++.+|+|.+.++..+..|...|+|+=+ +|-.--|.-|-
T Consensus 31 iYgilyls---~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~~lV~~~~~~G~Rk~~F~a~ 87 (177)
T COG1510 31 IYGILYLS---RKPLTLDEIAEALGMSKSNVSMGLKKLQDWNLVKKVFEKGDRKDYFEAE 87 (177)
T ss_pred HHHHHEEC---CCCCCHHHHHHHHCCCCCHHHHHHHHHHHCCHHHHHHCCCCCHHHHCCC
T ss_conf 86540006---9996699999997778012889999998545688530467530100006
No 129
>PRK11517 transcriptional regulatory protein YedW; Provisional
Probab=89.95 E-value=1.3 Score=24.74 Aligned_cols=60 Identities=15% Similarity=0.202 Sum_probs=42.5
Q ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHC---------CCHHHHHHHHHHHHH---CCCEEECCCCCCCCEECCC
Q ss_conf 689999999999855986335999999819---------978999999999932---5905731565454000237
Q gi|254780620|r 6 RTDYGIRVLMYCAIHNDYPNRISQIAEACC---------ISELFLFKILQPLVK---AGIVETVRGRRGGVRLCRP 69 (144)
Q Consensus 6 ~~~yAi~~l~~La~~~~~~~s~~eIA~~~~---------i~~~~l~kil~~L~~---agli~S~rG~~GGy~Lak~ 69 (144)
..||. +|-+|+.++++.+|-++|.+..- .=..|+.++=++|.. ..+|+++||. ||+|..+
T Consensus 150 ~~E~~--LL~~L~~~~g~vvsre~l~~~vwg~~~~~~~~~idv~I~rLRkKl~~~~~~~~I~TvrG~--GYrl~a~ 221 (223)
T PRK11517 150 RKEFQ--LLWLLASRAGEIIPRTVIASEIWGINFDSDTNTVDVAIRRLRAKVDDPFPEKLIATIRGM--GYSFVAV 221 (223)
T ss_pred HHHHH--HHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEECCC--CEEEEEC
T ss_conf 99999--999998689985989999999629887888587999999999985788999958976681--6699531
No 130
>PRK09462 fur ferric uptake regulator; Provisional
Probab=89.82 E-value=1.6 Score=24.21 Aligned_cols=54 Identities=15% Similarity=0.124 Sum_probs=39.2
Q ss_pred HHHHHCCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHCCCEEECCCCCC--CCEECC
Q ss_conf 99985598633599999981-----9978999999999932590573156545--400023
Q gi|254780620|r 15 MYCAIHNDYPNRISQIAEAC-----CISELFLFKILQPLVKAGIVETVRGRRG--GVRLCR 68 (144)
Q Consensus 15 ~~La~~~~~~~s~~eIA~~~-----~i~~~~l~kil~~L~~agli~S~rG~~G--Gy~Lak 68 (144)
-+|....+.+.|+++|-+.. .++.+.|.+.|..|.++|+|....-.+| -|.++.
T Consensus 24 ~~L~~~~~~hlsaeeI~~~l~~~~~~is~aTVYRtL~~L~e~Glv~~~~~~~g~~~ye~~~ 84 (148)
T PRK09462 24 EVLQEPDNHHVSAEDLYKKLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVFELTQ 84 (148)
T ss_pred HHHHHCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCEEEEEECCCCEEEEECC
T ss_conf 9998179999999999999997589986662999999998689679999759957998169
No 131
>TIGR02928 TIGR02928 orc1/cdc6 family replication initiation protein; InterPro: IPR014277 This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. The proteins in this entry are found exclusively in the archaea. Several members may be found in a genome and interact with each other..
Probab=89.80 E-value=1.2 Score=24.82 Aligned_cols=61 Identities=23% Similarity=0.360 Sum_probs=48.8
Q ss_pred CCHHHHHHHHHHHHHHHC--CCCCCCH-------HHHHHHHC---CCHHHHHHHHHHHHHCCCEEECC---CCCCC
Q ss_conf 645689999999999855--9863359-------99999819---97899999999993259057315---65454
Q gi|254780620|r 3 LTKRTDYGIRVLMYCAIH--NDYPNRI-------SQIAEACC---ISELFLFKILQPLVKAGIVETVR---GRRGG 63 (144)
Q Consensus 3 is~~~~yAi~~l~~La~~--~~~~~s~-------~eIA~~~~---i~~~~l~kil~~L~~agli~S~r---G~~GG 63 (144)
|+....+.|.+++.++.. ++.++++ ++||+..+ ++...+..+|+.|.--|||.+.+ |++||
T Consensus 301 Lp~h~k~~L~A~~~l~~~~~~~~~~~t~~vY~~Y~~~c~~~~~dpl~~rR~~~~l~eL~~LG~~~~~~~~~G~g~G 376 (383)
T TIGR02928 301 LPTHSKLVLLAIANLAAESPEEDPFRTGEVYEVYKELCEDIGVDPLTQRRISDLLNELDMLGLVEAEERNKGRGGG 376 (383)
T ss_pred CCHHHHHHHHHHHHHHHHCCCCCEEEEHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCEEEEEEECCCCCC
T ss_conf 9867999999999998516788736612778999999876267766146799988767660733456774267764
No 132
>pfam08222 HTH_CodY CodY helix-turn-helix domain. This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk.
Probab=89.80 E-value=0.5 Score=27.13 Aligned_cols=45 Identities=27% Similarity=0.304 Sum_probs=38.5
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECC-CCCCCCEEC
Q ss_conf 633599999981997899999999993259057315-654540002
Q gi|254780620|r 23 YPNRISQIAEACCISELFLFKILQPLVKAGIVETVR-GRRGGVRLC 67 (144)
Q Consensus 23 ~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~r-G~~GGy~La 67 (144)
+...+..||++.++.++.+-.-+.+|-.||+|+|.- |-.|-|.=.
T Consensus 2 g~lvASkiAd~~giTRSVIVNAlRKlESAGvIesrSlGmKGTyikv 47 (60)
T pfam08222 2 GRLTASKIADRIGITRSVIVNALRKLESAGIIESRSLGMKGTYLKV 47 (60)
T ss_pred CEEEHHHHHHHHCCHHHHHHHHHHHHHHCCCEEECCCCCCCEEEEE
T ss_conf 5640556667629618999999987643472552146777158765
No 133
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=89.77 E-value=1.3 Score=24.64 Aligned_cols=49 Identities=22% Similarity=0.190 Sum_probs=39.5
Q ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECC
Q ss_conf 9999999985598633599999981997899999999993259057315
Q gi|254780620|r 10 GIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVR 58 (144)
Q Consensus 10 Ai~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~r 58 (144)
.++.+...-.+++.+.|++|+|+..++|+.-.+|=+..|...|++++.-
T Consensus 159 Tl~~i~~~~~~~~~~~Taeela~~~giSRvTaRRYLeyl~~~~~l~a~i 207 (224)
T COG4565 159 TLQKVREALKEPDQELTAEELAQALGISRVTARRYLEYLVSNGILEAEI 207 (224)
T ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEEEE
T ss_conf 9999999986757764799999883721999999999998468235786
No 134
>pfam09079 Cdc6_C CDC6, C terminal. The C terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity.
Probab=89.44 E-value=0.94 Score=25.53 Aligned_cols=62 Identities=23% Similarity=0.329 Sum_probs=41.7
Q ss_pred HHHHHHHHCCCCC-CCH-------HHHHHHHCCCH---HHHHHHHHHHHHCCCEEECC---CCCCC----CEECCCHHHC
Q ss_conf 9999998559863-359-------99999819978---99999999993259057315---65454----0002372126
Q gi|254780620|r 12 RVLMYCAIHNDYP-NRI-------SQIAEACCISE---LFLFKILQPLVKAGIVETVR---GRRGG----VRLCRPADQI 73 (144)
Q Consensus 12 ~~l~~La~~~~~~-~s~-------~eIA~~~~i~~---~~l~kil~~L~~agli~S~r---G~~GG----y~Lak~~~~I 73 (144)
.+++.+...++.+ +++ +++|+..+..| ..+..+++.|.-.|||.+.+ |+++| |.|..||++|
T Consensus 2 ~A~~~l~~~~~~~~~~tg~vy~~Y~~lc~~~~~~~lt~rr~~~~l~~L~~~gii~~~~~~~G~~~G~~~~~~L~~d~~~v 81 (85)
T pfam09079 2 YAIALLLKRGGTPETTTGEVYEVYKELCEELGVDPLTQRRISDLLSELEMLGILETEVVSRGRGGGRTKKISLNVDPDDV 81 (85)
T ss_pred HHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCEEEEECCCCCCCEEEEEEECCCHHHH
T ss_conf 88999997499998727899999999999829876529999999999996585005781488678647899833898999
No 135
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=89.36 E-value=0.93 Score=25.55 Aligned_cols=44 Identities=16% Similarity=0.326 Sum_probs=36.7
Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Q ss_conf 99999985598633599999981997899999999993259057
Q gi|254780620|r 12 RVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVE 55 (144)
Q Consensus 12 ~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~ 55 (144)
+++-|+..|-++++++++||+..++|+.++.++++......+.+
T Consensus 9 ~~~~yI~~h~~~~i~l~~lA~~~~~S~~~l~r~Fk~~~g~t~~~ 52 (107)
T PRK10219 9 TLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGD 52 (107)
T ss_pred HHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCHHH
T ss_conf 99999998669999999999898939999999999998909999
No 136
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=89.25 E-value=0.71 Score=26.24 Aligned_cols=53 Identities=21% Similarity=0.129 Sum_probs=42.3
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCC---CC--CEECCCHHHC
Q ss_conf 98633599999981997899999999993259057315654---54--0002372126
Q gi|254780620|r 21 NDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRR---GG--VRLCRPADQI 73 (144)
Q Consensus 21 ~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~---GG--y~Lak~~~~I 73 (144)
+.+-+|=.+||+.+++....++|+|..|-.+|++.-.|-+. |- |...-.++.|
T Consensus 33 ~~~evTDEeiAe~~gi~lN~VRk~LY~Lye~~La~yrR~KD~~tGWytY~W~~~~~~i 90 (178)
T PRK06266 33 KKGEVTDEEIAEQTGIKLNTVRKILYKLYDAGLADYKREKDEETNWYTYTWKPELEKL 90 (178)
T ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCEEEEEEECCCCEEEEEEEECHHHH
T ss_conf 5465789999999699789999999999857641366656368982899999668888
No 137
>PRK11173 two-component response regulator; Provisional
Probab=89.09 E-value=1.7 Score=23.98 Aligned_cols=60 Identities=12% Similarity=0.288 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHHHCCCCCCCHHHHHHHHC-----CC----HHHHHHHHHHHHHC----CCEEECCCCCCCCEECCCH
Q ss_conf 89999999999855986335999999819-----97----89999999999325----9057315654540002372
Q gi|254780620|r 7 TDYGIRVLMYCAIHNDYPNRISQIAEACC-----IS----ELFLFKILQPLVKA----GIVETVRGRRGGVRLCRPA 70 (144)
Q Consensus 7 ~~yAi~~l~~La~~~~~~~s~~eIA~~~~-----i~----~~~l~kil~~L~~a----gli~S~rG~~GGy~Lak~~ 70 (144)
.||. +|.+|+.+++..+|-++|.+..- .+ ..++.++=++|... .+|+++||. ||+|+-+.
T Consensus 164 ~E~~--lL~~L~~~~~~vvsR~~L~~~vwg~~~~~~~r~ld~~I~rLRkKl~~~~~~~~~I~TvrG~--GYrf~~~~ 236 (237)
T PRK11173 164 SEFR--AMLHFCENPGKIQSRAELLKKMTGRELKPHDRTVDVTIRRIRKHFESTPDTPEIIATIHGE--GYRFCGDL 236 (237)
T ss_pred HHHH--HHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEECCC--CEEECCCC
T ss_conf 9999--9999986799876899999996198878885869999999999765279999819978781--77978006
No 138
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=88.94 E-value=1.2 Score=24.86 Aligned_cols=46 Identities=17% Similarity=0.132 Sum_probs=38.1
Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCC
Q ss_conf 999999855986335999999819978999999999932590573156
Q gi|254780620|r 12 RVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRG 59 (144)
Q Consensus 12 ~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG 59 (144)
+++-+|..+ +.+++.+||+..++|+..+++=|..|.+.|+|.=++|
T Consensus 8 ~Il~~L~~~--g~v~v~eLa~~~~VS~~TIRRDL~~Le~~G~l~R~hG 53 (240)
T PRK10411 8 AIVDLLLNH--TSLTTEALAEQLNVSKETIRRDLNELQTQGKILRNHG 53 (240)
T ss_pred HHHHHHHHC--CCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEE
T ss_conf 999999986--9799999999889599899982998977898899942
No 139
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=88.88 E-value=0.94 Score=25.54 Aligned_cols=45 Identities=11% Similarity=0.168 Sum_probs=38.1
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Q ss_conf 999999985598633599999981997899999999993259057
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVE 55 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~ 55 (144)
-+++-|+..|-++++|+++||+..++|+.|+.++++......+.+
T Consensus 12 ~~i~~yI~~n~~~~lsl~~lA~~~~~S~~~l~r~Fk~~~G~s~~~ 56 (127)
T PRK11511 12 HSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQ 56 (127)
T ss_pred HHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCHHH
T ss_conf 999999998658999999999998959999999999998919999
No 140
>COG4109 Predicted transcriptional regulator containing CBS domains [Transcription]
Probab=88.86 E-value=1.5 Score=24.30 Aligned_cols=74 Identities=20% Similarity=0.343 Sum_probs=61.7
Q ss_pred HHHHHHH-HCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCC----HHHCCHHHHHHHHCCCC
Q ss_conf 9999998-559863359999998199789999999999325905731565454000237----21260999999971876
Q gi|254780620|r 12 RVLMYCA-IHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRP----ADQITILDVVKATEESF 86 (144)
Q Consensus 12 ~~l~~La-~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~----~~~Itl~dI~~aie~~~ 86 (144)
.+|-|+- +.-|+.+|+..||+.+++|.....+-...--+-|+|... -+-|-.|..+. .+.+|..+|++.+||..
T Consensus 6 qIL~Yie~L~vG~kISVR~Ia~~l~VSeGTAYRAIKeAen~G~V~Ti-~RvGTvRIekk~k~~Ie~LTf~Eiv~iidgqV 84 (432)
T COG4109 6 QILNYIESLEVGKKISVRGIAKHLKVSEGTAYRAIKEAENLGLVSTI-PRVGTVRIEKKGKKNIERLTFAEIVNIIDGQV 84 (432)
T ss_pred HHHHHHHHCCCCCEEEHHHHHHHCCCCCCHHHHHHHHHHHCCCEEEC-CCCEEEEEEECCCHHHHHHHHHHHHHHHCCCE
T ss_conf 99999971656656666776643776633588888888746856863-66506999861202565511999987623504
No 141
>pfam09940 DUF2172 Domain of unknown function (DUF2172). This domain, found in various hypothetical prokaryotic proteins, has no known function. An aminopeptidase domain is conserved within the family, but its relevance has not been established yet.
Probab=88.66 E-value=1.1 Score=25.04 Aligned_cols=40 Identities=35% Similarity=0.438 Sum_probs=29.9
Q ss_pred HHHHHHHHHH--HHCCCEEECCCCCCCCEECCCHHHCCHHHH
Q ss_conf 9999999999--325905731565454000237212609999
Q gi|254780620|r 39 LFLFKILQPL--VKAGIVETVRGRRGGVRLCRPADQITILDV 78 (144)
Q Consensus 39 ~~l~kil~~L--~~agli~S~rG~~GGy~Lak~~~~Itl~dI 78 (144)
.|+.|-...| ..+|++-+-=|-.|.|.+.+....=|+.|-
T Consensus 183 ~yl~kn~~~lk~v~~G~vltCvGd~~~~s~~~Sr~~ns~~D~ 224 (384)
T pfam09940 183 AYLSRNEEHLKRVKAGLVLTCLGDDGGYSYKRSRRGNTLIDR 224 (384)
T ss_pred HHHHHHHHHHHHHHEEEEEEEECCCCCEEEEECCCCCCHHHH
T ss_conf 999998998765102389998528994367878879978999
No 142
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=88.66 E-value=2.2 Score=23.32 Aligned_cols=78 Identities=17% Similarity=0.206 Sum_probs=48.2
Q ss_pred CCHHHHHHHHHHHHHHHCCCCCCCHH-------HHHHHHCC---CHHHHHHHHHHHHHCCCEEEC---CCCCCC---CEE
Q ss_conf 64568999999999985598633599-------99998199---789999999999325905731---565454---000
Q gi|254780620|r 3 LTKRTDYGIRVLMYCAIHNDYPNRIS-------QIAEACCI---SELFLFKILQPLVKAGIVETV---RGRRGG---VRL 66 (144)
Q Consensus 3 is~~~~yAi~~l~~La~~~~~~~s~~-------eIA~~~~i---~~~~l~kil~~L~~agli~S~---rG~~GG---y~L 66 (144)
++......+.+++.+...+...+++. ++++..++ +...+..+++.|...|+|++. +|+.|. +.|
T Consensus 294 L~~~~klvL~ai~~~~~~~~~~~~~g~vy~~Y~~lc~~~~~~~ls~~~~~~~l~~L~~~giI~~~~~~~G~~Gr~~~i~L 373 (394)
T PRK00411 294 LPLHEKLLLLAIVRLLEKGAPYVTTGEVYEEYKELCEELGYEPRSHTRFYEYLNKLDMLGLINTRYTGKGGRGRTRLISL 373 (394)
T ss_pred CCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEEEEEECCCCCCCEEEEEE
T ss_conf 89989999999999851788766389999999999997399888799999999999867985888754888885269996
Q ss_pred CCCHHHCCHHHHHHHHCCC
Q ss_conf 2372126099999997187
Q gi|254780620|r 67 CRPADQITILDVVKATEES 85 (144)
Q Consensus 67 ak~~~~Itl~dI~~aie~~ 85 (144)
..+|++ |.+++..+
T Consensus 374 ~~d~~~-----v~~~l~~d 387 (394)
T PRK00411 374 SYDPED-----VLERLLED 387 (394)
T ss_pred CCCHHH-----HHHHHHHH
T ss_conf 279999-----99999754
No 143
>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional
Probab=88.59 E-value=1.5 Score=24.39 Aligned_cols=60 Identities=17% Similarity=0.246 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHH---------CCCHHHHHHHHHHHHHC----CCEEECCCCCCCCEECCC
Q ss_conf 68999999999985598633599999981---------99789999999999325----905731565454000237
Q gi|254780620|r 6 RTDYGIRVLMYCAIHNDYPNRISQIAEAC---------CISELFLFKILQPLVKA----GIVETVRGRRGGVRLCRP 69 (144)
Q Consensus 6 ~~~yAi~~l~~La~~~~~~~s~~eIA~~~---------~i~~~~l~kil~~L~~a----gli~S~rG~~GGy~Lak~ 69 (144)
..||. +|.+|+.++++.+|-++|.+.. +.=..|+.++=++|... .+|+++||. ||.|..+
T Consensus 159 ~~E~~--lL~~L~~~~g~vvsre~L~~~vwg~~~~~~~rtidv~I~rLRkKL~~~~~~~~~I~TvrG~--GY~lvs~ 231 (232)
T PRK10955 159 GTEFT--LLYLLAQHLGQVVSREHLSQEVLGKRLTPFDRAIDMHISNLRRKLPDRKDGHPWFKTLRGR--GYLMVSA 231 (232)
T ss_pred HHHHH--HHHHHHHCCCCEECHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCEEEEECCC--CEEEEEC
T ss_conf 99999--9999997899509799999997188988885829999999999541168999819984570--6599867
No 144
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=88.47 E-value=2.2 Score=23.39 Aligned_cols=59 Identities=17% Similarity=0.235 Sum_probs=43.7
Q ss_pred CHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEEC
Q ss_conf 4568999999999985598633599999981997899999999993259057315654540002
Q gi|254780620|r 4 TKRTDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLC 67 (144)
Q Consensus 4 s~~~~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~La 67 (144)
++.++==-.++-+|..+ +.+++.+||+..++|...+++=|..|-+.|++.-++ ||..+.
T Consensus 13 ~~t~ER~~~Il~~L~~~--g~v~v~eLae~~~VS~~TIRRDL~~Le~~g~l~R~h---GGA~~~ 71 (269)
T PRK09802 13 TGTSERREQIIQRLRQQ--GSVQVNDLSALYGVSTVTIRNDLAFLEKQGIAVRAY---GGALIC 71 (269)
T ss_pred CCCHHHHHHHHHHHHHC--CCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEE---CCEEEC
T ss_conf 77099999999999986--989999999987969889998099998789869996---878976
No 145
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=88.13 E-value=2.1 Score=23.52 Aligned_cols=59 Identities=20% Similarity=0.200 Sum_probs=42.9
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHCCCEEECCCCCCC--CEECCCH
Q ss_conf 999999985598633599999981-----99789999999999325905731565454--0002372
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEAC-----CISELFLFKILQPLVKAGIVETVRGRRGG--VRLCRPA 70 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~-----~i~~~~l~kil~~L~~agli~S~rG~~GG--y~Lak~~ 70 (144)
+.++-+|..+++ +.|+++|-+.. +++++.|.+.|..|..+|+|....-.+|- |.+...+
T Consensus 24 ~~vl~~L~~~~~-~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~~~~~~~y~~~~~~ 89 (145)
T COG0735 24 LAVLELLLEADG-HLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEFEGGKTRYELNSEP 89 (145)
T ss_pred HHHHHHHHHCCC-CCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCEEEEEECCCEEEEEECCCC
T ss_conf 999999996689-999999999999748999887999999999988987999737977999707998
No 146
>COG4738 Predicted transcriptional regulator [Transcription]
Probab=88.04 E-value=0.58 Score=26.77 Aligned_cols=59 Identities=22% Similarity=0.241 Sum_probs=45.8
Q ss_pred HHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEC----CCC---CCCCEECCCHHHC
Q ss_conf 999998559863359999998199789999999999325905731----565---4540002372126
Q gi|254780620|r 13 VLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETV----RGR---RGGVRLCRPADQI 73 (144)
Q Consensus 13 ~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~----rG~---~GGy~Lak~~~~I 73 (144)
+|++|+. .+ -+|+.+|--..|+-.+-++=-|+.|+..|+|+-. +|+ --+|+|++|-++|
T Consensus 32 tlv~L~~-~~-E~sS~~IE~~sgLRQPEVSiAMr~Lre~gWV~~R~eKKkGKGRPik~Y~Lt~~~~eI 97 (124)
T COG4738 32 TLVCLAK-GD-EASSREIERVSGLRQPEVSIAMRYLRENGWVDEREEKKKGKGRPIKLYRLTVPFDEI 97 (124)
T ss_pred HHHHHHC-CC-CHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCHHHHCCCCCCCCCEEEEECCCHHHH
T ss_conf 8898751-76-222334377516788306899999987563006775136899971577742858999
No 147
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR; InterPro: IPR014075 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly . The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen . This entry represents members of the SufR cyanobacterial protein family of transcriptional regulators that control the SUF system. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to 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=87.79 E-value=0.39 Score=27.76 Aligned_cols=125 Identities=19% Similarity=0.139 Sum_probs=82.2
Q ss_pred HHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCC-------CEECCCHHHCCHHHHHH--HHC
Q ss_conf 999998559863359999998199789999999999325905731565454-------00023721260999999--971
Q gi|254780620|r 13 VLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGG-------VRLCRPADQITILDVVK--ATE 83 (144)
Q Consensus 13 ~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GG-------y~Lak~~~~Itl~dI~~--aie 83 (144)
||-||-.+ +-.|+.+||+.++|||.=++|-|.+|-..|||+-..-..|| |+|+|.-.+===..+.+ |.-
T Consensus 6 IL~~LL~~--Gq~sA~~lA~~L~iSpQAvRrHLKDLe~e~Lv~~~~~~~g~~GRPQy~Y~LS~qGRe~l~~~~~rqqa~~ 83 (215)
T TIGR02702 6 ILEYLLKE--GQASALALAEELAISPQAVRRHLKDLETEGLVEYKAVLQGTMGRPQYLYQLSRQGREQLPQLVLRQQADR 83 (215)
T ss_pred HHHHHHHH--HHHHHHHHHHHHCCCHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 99998860--0488999999727886788765433210103567777650478822542121776776366554541037
Q ss_pred CCCCCCCCCCCCC-CCCCCCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHCHHHHHH
Q ss_conf 8763111468877-8887656644799999999999999841799999915898999
Q gi|254780620|r 84 ESFFVAECFASHK-IDCPLVGSCGLTSVLRKALNAFFDVLTQYSIECLVRNRSSIKK 139 (144)
Q Consensus 84 ~~~~~~~C~~~~~-~~C~~~~~c~~~~~~~~~~~~~~~~L~~~TL~dl~~~~~~~~~ 139 (144)
.+.+-++-.+.-. .-.+-.=.-.+..-|..==+++.+.+.+=||+|=+.+--++++
T Consensus 84 ~~~FAl~LLdSl~etlG~~q~~~vL~~qW~RKA~~YR~q~G~G~L~~Rl~~Lv~LR~ 140 (215)
T TIGR02702 84 HGEFALSLLDSLAETLGPEQFEAVLQKQWQRKAEAYREQLGQGSLAERLAKLVALRQ 140 (215)
T ss_pred CCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH
T ss_conf 531678899988963787789999999998899999887189977899999999974
No 148
>COG4533 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=87.51 E-value=2.6 Score=22.89 Aligned_cols=60 Identities=15% Similarity=0.179 Sum_probs=47.3
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCC----CCCCEECCCHHHCCHHHHHHHHC
Q ss_conf 3359999998199789999999999325905731565----45400023721260999999971
Q gi|254780620|r 24 PNRISQIAEACCISELFLFKILQPLVKAGIVETVRGR----RGGVRLCRPADQITILDVVKATE 83 (144)
Q Consensus 24 ~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~----~GGy~Lak~~~~Itl~dI~~aie 83 (144)
.++..|||+....|+.+++.+|+++..+|.++=..|+ .+=..+.++|++......=+.+|
T Consensus 23 ~~tl~eLA~~lfCS~Rh~R~lL~q~q~~gWL~W~p~~GRGkrSrL~flr~~e~L~~q~a~~~le 86 (564)
T COG4533 23 ETTLNELADILFCSRRHARTLLRQMQEAGWLTWQPQAGRGKRSRLTFLRTPEALLLQLAEKLLE 86 (564)
T ss_pred EEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCCEEEEEECCHHHHHHHHHHHHHH
T ss_conf 3369999888626778999999999875977724677887621588824869999999999996
No 149
>PRK11083 DNA-binding response regulator CreB; Provisional
Probab=87.00 E-value=2.6 Score=22.94 Aligned_cols=54 Identities=15% Similarity=0.088 Sum_probs=33.0
Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHC---------CCHHHHHHHHHHHHHC----CCEEECCCCCCCCEEC
Q ss_conf 999999855986335999999819---------9789999999999325----9057315654540002
Q gi|254780620|r 12 RVLMYCAIHNDYPNRISQIAEACC---------ISELFLFKILQPLVKA----GIVETVRGRRGGVRLC 67 (144)
Q Consensus 12 ~~l~~La~~~~~~~s~~eIA~~~~---------i~~~~l~kil~~L~~a----gli~S~rG~~GGy~La 67 (144)
.+|.+|+.++++.+|-++|.+... .=..|+.++=++|... .+|+++||. ||+|.
T Consensus 162 ~LL~~L~~~~g~vvsr~~L~~~vw~~~~~~~~rtidv~I~rLR~KL~~~~~~~~~I~TvrG~--GY~l~ 228 (229)
T PRK11083 162 LLLKTLLLSPGRVFSRQQLMDIVWEDAQDSYDRTVDTHIKTLRAKLRAINPDLSPIRTHRGL--GYSLR 228 (229)
T ss_pred HHHHHHHHCCCCEECHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEECCC--CEEEC
T ss_conf 99999986799409699999985599888884669999999999875268999859997896--56973
No 150
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=86.87 E-value=2 Score=23.66 Aligned_cols=47 Identities=15% Similarity=0.176 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Q ss_conf 99999999985598633599999981997899999999993259057
Q gi|254780620|r 9 YGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVE 55 (144)
Q Consensus 9 yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~ 55 (144)
+-.+++-|+..|-.+++|+++||+..++|+.++.+++++-..-...+
T Consensus 184 ri~~a~~yI~~h~~~~isl~~lA~~~~lS~s~l~rlFk~~~G~sp~~ 230 (290)
T PRK10572 184 RVREACQYISDHLASEFDIESVAQHVCLSPSRLSHLFRQQLGISVLS 230 (290)
T ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCHHH
T ss_conf 99999999998637999999999896979999999999864989999
No 151
>TIGR02073 PBP_1c penicillin-binding protein 1C; InterPro: IPR011815 This entry contains penicillin binding proteins includes the member from Escherichia coli designated penicillin-binding protein 1C. Members have both transglycosylase and transpeptidase domains and are involved in forming cross-links in the late stages of peptidoglycan biosynthesis. All members of this entry are presumed to have the same basic function..
Probab=86.61 E-value=1.5 Score=24.40 Aligned_cols=68 Identities=18% Similarity=0.109 Sum_probs=55.5
Q ss_pred CCCCHHH-HHHHHCCCHHHH------HHHHHHHHHCCCEEECC-C-CCCCCEECCCHHHCCHHHHHHH---H--CCCCCC
Q ss_conf 6335999-999819978999------99999993259057315-6-5454000237212609999999---7--187631
Q gi|254780620|r 23 YPNRISQ-IAEACCISELFL------FKILQPLVKAGIVETVR-G-RRGGVRLCRPADQITILDVVKA---T--EESFFV 88 (144)
Q Consensus 23 ~~~s~~e-IA~~~~i~~~~l------~kil~~L~~agli~S~r-G-~~GGy~Lak~~~~Itl~dI~~a---i--e~~~~~ 88 (144)
++||+++ |+.+.|||...| .+....|+++|+=.-.+ + ...|++|+==..+|||.|+-++ + .|....
T Consensus 375 G~V~v~~AL~~SLNiPAV~ll~~~g~~~f~~~L~~~G~~~~~~~~~~~yGLSL~LGG~e~tL~dLa~lY~~LA~~G~~~p 454 (786)
T TIGR02073 375 GPVPVREALARSLNIPAVRLLERLGPPRFASFLRQAGLKLLKPKSRDYYGLSLILGGAEITLQDLANLYAMLANQGLSGP 454 (786)
T ss_pred CCCCHHHHHHHCCCCHHHHHHHHCCHHHHHHHHHHHCCCCCCHHHHCCCCCEEEECCCCCCHHHHHHHHHHHHHCCCCCC
T ss_conf 77639998643067148999974292689999997056557800002576013123017448999999999974266657
Q ss_pred CC
Q ss_conf 11
Q gi|254780620|r 89 AE 90 (144)
Q Consensus 89 ~~ 90 (144)
..
T Consensus 455 lr 456 (786)
T TIGR02073 455 LR 456 (786)
T ss_pred CC
T ss_conf 42
No 152
>PRK13856 two-component response regulator VirG; Provisional
Probab=86.54 E-value=2.5 Score=23.05 Aligned_cols=62 Identities=15% Similarity=0.203 Sum_probs=39.4
Q ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHC---------CCHHHHHHHHHHHHHC----CCEEECCCCCCCCEECCCHH
Q ss_conf 689999999999855986335999999819---------9789999999999325----90573156545400023721
Q gi|254780620|r 6 RTDYGIRVLMYCAIHNDYPNRISQIAEACC---------ISELFLFKILQPLVKA----GIVETVRGRRGGVRLCRPAD 71 (144)
Q Consensus 6 ~~~yAi~~l~~La~~~~~~~s~~eIA~~~~---------i~~~~l~kil~~L~~a----gli~S~rG~~GGy~Lak~~~ 71 (144)
..+|. +|.+|+.++++.+|-++|.+... .=..++.++=++|.+. .+|+++||. ||+|.-+-+
T Consensus 158 ~~E~~--lL~~L~~~~~~vvsRe~L~~~~~~~~~~~~~r~id~~I~rLRkKL~~~~~~~~~I~TvrG~--GY~f~~~~~ 232 (241)
T PRK13856 158 AGEFN--LLVAFLEKPRDVLSREQLLIASRVREEEVYDRSIDVLILRLRRKLEQDPANPQLIKTARGA--GYFFDADVD 232 (241)
T ss_pred HHHHH--HHHHHHHCCCCEEEHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEECCC--CEEEEECCC
T ss_conf 89999--9999987699438199999984456778886869999999999731388999809977371--549823246
No 153
>COG3327 PaaX Phenylacetic acid-responsive transcriptional repressor [Transcription]
Probab=86.28 E-value=0.95 Score=25.51 Aligned_cols=54 Identities=30% Similarity=0.234 Sum_probs=42.0
Q ss_pred HHHHCCCCCCC---HHHHHHHHCCCHHHHHHHHHHHHHCCCEEECC-CCCCCCEECCCH
Q ss_conf 99855986335---99999981997899999999993259057315-654540002372
Q gi|254780620|r 16 YCAIHNDYPNR---ISQIAEACCISELFLFKILQPLVKAGIVETVR-GRRGGVRLCRPA 70 (144)
Q Consensus 16 ~La~~~~~~~s---~~eIA~~~~i~~~~l~kil~~L~~agli~S~r-G~~GGy~Lak~~ 70 (144)
|+..++ +-++ .-+|.+..|++..+++--+..++++|.+.+.| |+.+-|+|+...
T Consensus 18 ~l~~~G-g~Iw~gsLI~il~~fG~sE~~vRaal~Rm~kaG~l~~er~grks~Y~LSDkg 75 (291)
T COG3327 18 YLGHRG-GWIWIGSLIQILAEFGISETTVRAALSRMVKAGWLVGEREGRKSFYRLSDKG 75 (291)
T ss_pred HHCCCC-CEEEHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCHHEEECCCCCCEEECHHH
T ss_conf 305578-7354878999999719427889999999874220100004663302105889
No 154
>COG4753 Response regulator containing CheY-like receiver domain and AraC-type DNA-binding domain [Signal transduction mechanisms]
Probab=86.23 E-value=1.6 Score=24.14 Aligned_cols=69 Identities=17% Similarity=0.237 Sum_probs=44.2
Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE---ECCCCCCC-CEECCCHHHCCHHHHHHHHC
Q ss_conf 99999985598633599999981997899999999993259057---31565454-00023721260999999971
Q gi|254780620|r 12 RVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVE---TVRGRRGG-VRLCRPADQITILDVVKATE 83 (144)
Q Consensus 12 ~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~---S~rG~~GG-y~Lak~~~~Itl~dI~~aie 83 (144)
.++.|+..|-.++.|.++||+..++||.||.++++.....++-+ =+|=.++= +.| ....++.+|...++
T Consensus 376 ~~l~~I~~h~se~LtL~~la~~f~in~~Ylgqlfk~~~~e~F~~ylnkvRi~~ak~~Ll---~t~~~i~eI~~~vG 448 (475)
T COG4753 376 KVLDYIHKHFSENLTLKDLAKVFHINPVYLGQLFKKETGESFTEYLNKVRIEKAKQLLL---QTNDSIYEIAYKVG 448 (475)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHH---HCCCCHHHHHHHHC
T ss_conf 99999999851788799998773708999999999986141989999999999999999---63772999999977
No 155
>pfam00888 Cullin Cullin family.
Probab=85.85 E-value=3.2 Score=22.36 Aligned_cols=44 Identities=20% Similarity=0.322 Sum_probs=28.2
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCE
Q ss_conf 99999998559863359999998199789999999999325905
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIV 54 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli 54 (144)
+.+++.|..+.....|.++|.+.+++|..-+.+.|+.|..+++.
T Consensus 538 ~Q~~iLLlFN~~~~lT~~eI~~~t~i~~~~L~r~L~sL~~~k~~ 581 (605)
T pfam00888 538 YQMAVLLLFNDQEELTVEELSEATGLSDDLLRRTLQSLLKAKVL 581 (605)
T ss_pred HHHHHHHHCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEE
T ss_conf 99999997489898689999988890999999999999620401
No 156
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family; InterPro: IPR010166 This entry 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, IPR000835 from INTERPRO..
Probab=85.78 E-value=2.1 Score=23.52 Aligned_cols=53 Identities=21% Similarity=0.210 Sum_probs=43.3
Q ss_pred HHHHHHHHHHHHHHCCC---CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECC
Q ss_conf 68999999999985598---633599999981997899999999993259057315
Q gi|254780620|r 6 RTDYGIRVLMYCAIHND---YPNRISQIAEACCISELFLFKILQPLVKAGIVETVR 58 (144)
Q Consensus 6 ~~~yAi~~l~~La~~~~---~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~r 58 (144)
..++++-.+++.....+ +..+.++|.+..+.+++.+-+.++.|.+.|++.=.|
T Consensus 25 ~~e~~~L~~l~~~~~~e~vl~~~~~K~i~~~~~~~~~~~~~~~k~L~~k~~l~K~R 80 (112)
T TIGR01889 25 LEELLILYYLLKLEKNEKVLNKLTLKEIIKEILIKQSKLVKIIKKLSKKGYLSKER 80 (112)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCC
T ss_conf 99999999999986311454323088899875678346789998777504411478
No 157
>pfam06971 Put_DNA-bind_N Putative DNA-binding protein N-terminus. This family represents the N-terminus (approximately 50 residues) of a number of putative bacterial DNA-binding proteins.
Probab=85.77 E-value=1.1 Score=25.10 Aligned_cols=35 Identities=17% Similarity=-0.024 Sum_probs=28.0
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 99999998559863359999998199789999999
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKIL 45 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil 45 (144)
+|+|-.|...+-..+|+++||+..++++..++|=|
T Consensus 14 ~R~L~~L~~~g~~~vSS~eLa~~~gv~~aqiRKDl 48 (49)
T pfam06971 14 YRYLEELLEEGVERVSSKELSEAIGIDAAQIRKDF 48 (49)
T ss_pred HHHHHHHHHCCCCEECHHHHHHHHCCCHHHHHCCC
T ss_conf 99999999859904979999999793999961424
No 158
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=85.76 E-value=2.4 Score=23.11 Aligned_cols=38 Identities=21% Similarity=0.207 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCC
Q ss_conf 33599999981997899999999993259057315654
Q gi|254780620|r 24 PNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRR 61 (144)
Q Consensus 24 ~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~ 61 (144)
-++-++||+..++...-+++||..|...|++...|.+.
T Consensus 32 e~tDeela~~l~i~~~~vrriL~~L~e~~li~~~k~rd 69 (176)
T COG1675 32 ELTDEELAELLGIKKNEVRRILYALYEDGLISYRKKRD 69 (176)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEECC
T ss_conf 76748998886763999999999998579268886014
No 159
>PRK10816 DNA-binding transcriptional regulator PhoP; Provisional
Probab=85.56 E-value=2.3 Score=23.22 Aligned_cols=54 Identities=11% Similarity=0.154 Sum_probs=36.0
Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHC-----CC----HHHHHHHHHHHHH---CCCEEECCCCCCCCEEC
Q ss_conf 999999855986335999999819-----97----8999999999932---59057315654540002
Q gi|254780620|r 12 RVLMYCAIHNDYPNRISQIAEACC-----IS----ELFLFKILQPLVK---AGIVETVRGRRGGVRLC 67 (144)
Q Consensus 12 ~~l~~La~~~~~~~s~~eIA~~~~-----i~----~~~l~kil~~L~~---agli~S~rG~~GGy~La 67 (144)
..|.+|+.|+++.+|-++|.+..- .. ..++.++=++|.. ..+|+++||. ||++-
T Consensus 156 ~LL~~L~~~~~~vvsre~l~~~vw~~~~~~~~~sld~~I~rLRkKl~~~~~~~~I~tvrG~--GY~~~ 221 (223)
T PRK10816 156 TIMETLIRNNGKVVSKDSLMLQLYPDAELRESHTIDVLMGRLRKKIQAQYPQEVITTVRGQ--GYLFE 221 (223)
T ss_pred HHHHHHHHCCCEEECHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEECCC--CEEEE
T ss_conf 9999999879923839999998549987888677999999999974335899818997895--67987
No 160
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=85.46 E-value=2.3 Score=23.29 Aligned_cols=50 Identities=22% Similarity=0.129 Sum_probs=38.4
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEE
Q ss_conf 99999998559863359999998199789999999999325905731565454000
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRL 66 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~L 66 (144)
+|+|-.|...+-..+||++||+..++++..++|=|+.+-.-| +||. ||.-
T Consensus 19 ~r~L~~l~~~g~~~iSS~eLa~~~gi~~~qVRKDls~fG~fG----~~G~--GY~V 68 (211)
T PRK05472 19 YRYLKELLEEGVERVSSKELAEAVGVDSAQIRKDLSYFGELG----KRGV--GYNV 68 (211)
T ss_pred HHHHHHHHHCCCEEECHHHHHHHHCCCHHHHHHHHHHHCCCC----CCCC--CCCH
T ss_conf 999999998598389799999996989999998999864579----9998--8129
No 161
>TIGR00331 hrcA heat-inducible transcription repressor HrcA; InterPro: IPR002571 In response to elevated temperature, both prokaryotic and eukaryotic cells increase expression of a small family of chaperones. The regulatory network that functions to control the transcription of the heat shock genes in bacteria includes unique structural motifs in the promoter region of these genes and the expression of alternate sigma factors. One of the conserved structural motifs, the inverted repeat CIRCE element, is found in the 5' region of many heat shock operons . For Bacillus subtilis three classes of heat shock genes regulated by different mechanisms have been described. Regulation of class I heat shock genes (dnaK and groE operons) involves an inverted repeat (CIRCE element) which most probably serves as an operator for a repressor .; GO: 0006355 regulation of transcription DNA-dependent.
Probab=85.43 E-value=1.3 Score=24.63 Aligned_cols=50 Identities=14% Similarity=0.119 Sum_probs=42.6
Q ss_pred HHHHHHHHHHHCCCCCCCHHHHHHH--HCCCHHHHHHHHHHHHHCCCEEECC
Q ss_conf 9999999998559863359999998--1997899999999993259057315
Q gi|254780620|r 9 YGIRVLMYCAIHNDYPNRISQIAEA--CCISELFLFKILQPLVKAGIVETVR 58 (144)
Q Consensus 9 yAi~~l~~La~~~~~~~s~~eIA~~--~~i~~~~l~kil~~L~~agli~S~r 58 (144)
-=|++++.--...++|+.|+.|++. .++|++.+|..|+.|=.-|||+..=
T Consensus 6 ~iL~~Iv~~Y~~~~~PVGSk~L~~~~~l~~SSATIRN~Ma~LE~~Gfi~k~H 57 (343)
T TIGR00331 6 KILKAIVEEYIKTGEPVGSKTLLEKYNLGLSSATIRNDMADLEELGFIEKPH 57 (343)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCC
T ss_conf 9999999997334896204767756179999703657799987502200474
No 162
>pfam00325 Crp Bacterial regulatory proteins, crp family.
Probab=85.29 E-value=1.1 Score=25.23 Aligned_cols=31 Identities=19% Similarity=0.348 Sum_probs=28.4
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCE
Q ss_conf 3359999998199789999999999325905
Q gi|254780620|r 24 PNRISQIAEACCISELFLFKILQPLVKAGIV 54 (144)
Q Consensus 24 ~~s~~eIA~~~~i~~~~l~kil~~L~~agli 54 (144)
|+|-.+||+-.+.+...+.+++.+|++.|+|
T Consensus 2 pmsrqdIadylGlt~ETVsR~l~~L~~~glI 32 (32)
T pfam00325 2 PMSRQEIADYLGLTRETVSRLLKRLREKGLI 32 (32)
T ss_pred CCCHHHHHHHHCCHHHHHHHHHHHHHHCCCC
T ss_conf 8658899998472599999999999985789
No 163
>PRK10643 DNA-binding transcriptional regulator BasR; Provisional
Probab=85.08 E-value=3.2 Score=22.35 Aligned_cols=61 Identities=20% Similarity=0.260 Sum_probs=41.5
Q ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHCC-----C----HHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHH
Q ss_conf 6899999999998559863359999998199-----7----8999999999932590573156545400023721
Q gi|254780620|r 6 RTDYGIRVLMYCAIHNDYPNRISQIAEACCI-----S----ELFLFKILQPLVKAGIVETVRGRRGGVRLCRPAD 71 (144)
Q Consensus 6 ~~~yAi~~l~~La~~~~~~~s~~eIA~~~~i-----~----~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~ 71 (144)
..|| .+|.+|..++++.+|-++|.+...- + ..|+.++=++|.+ +.|+++||. ||+|.++-+
T Consensus 152 ~~E~--~lL~~L~~~~g~vvsre~L~~~v~~~~~~~~~~~ld~~I~rLRkKl~~-~~I~tvrG~--GY~l~~~~~ 221 (222)
T PRK10643 152 PKEY--ALLSRLMLKAGSPVHREILYNDIYNWDNEPSTNTLEVHIHNLRDKVGK-DRIRTVRGF--GYMLVANEE 221 (222)
T ss_pred HHHH--HHHHHHHHCCCCCCCHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHCCC-CCEEEECCC--CEEEEECCC
T ss_conf 7999--999999967999868999999960878888867699999999976699-857976773--769801788
No 164
>PRK11642 exoribonuclease R; Provisional
Probab=84.94 E-value=3.4 Score=22.26 Aligned_cols=54 Identities=19% Similarity=0.148 Sum_probs=39.7
Q ss_pred HHHHHHHCCCCCCCHHHHHHHHCCCH----HHHHHHHHHHHHCCCEEECCCCCCCCEECCC
Q ss_conf 99999855986335999999819978----9999999999325905731565454000237
Q gi|254780620|r 13 VLMYCAIHNDYPNRISQIAEACCISE----LFLFKILQPLVKAGIVETVRGRRGGVRLCRP 69 (144)
Q Consensus 13 ~l~~La~~~~~~~s~~eIA~~~~i~~----~~l~kil~~L~~agli~S~rG~~GGy~Lak~ 69 (144)
+|-+|..+ ++|++..+||+..++.. .-|.+.|..|.+.|.|... +.|.|.|...
T Consensus 24 il~~l~~~-~~p~~~~el~~~~~l~~~~~~~~L~~~L~~l~~~g~l~~~--r~~~y~~~~~ 81 (813)
T PRK11642 24 ILEHLTKR-EKPASREELAVELNIEGEEQLEALRRRLRAMERDGQLVFT--RRQCYALPER 81 (813)
T ss_pred HHHHHHHC-CCCCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCEEEC--CCCCCCCCCC
T ss_conf 99999968-8989999999981999889999999999999968977874--8972367776
No 165
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=84.81 E-value=1.7 Score=24.02 Aligned_cols=45 Identities=18% Similarity=0.218 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHC
Q ss_conf 33599999981997899999999993259057315654540002372126
Q gi|254780620|r 24 PNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQI 73 (144)
Q Consensus 24 ~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~I 73 (144)
+.+-++||...|+++..+.++|+.|++.| |. ++| +..-..|++.+
T Consensus 173 ~~t~~~lA~~lG~tretvsR~L~~L~~~G-I~-~~~---~~I~I~D~~~L 217 (236)
T PRK09392 173 PYEKRTLASYLGMTPENLSRAFAALASHG-VH-VQG---SAVTITDKAAL 217 (236)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCC-CE-EEC---CEEEECCHHHH
T ss_conf 47899999987898999999999999799-68-969---99999889999
No 166
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=84.74 E-value=2.6 Score=22.94 Aligned_cols=59 Identities=19% Similarity=0.151 Sum_probs=45.0
Q ss_pred CCCHH----HHHHHHCCCHHHHHHHHHHHHHCCCEEECC-CCCCCCEECCCHHHCCHHHHHHHH
Q ss_conf 33599----999981997899999999993259057315-654540002372126099999997
Q gi|254780620|r 24 PNRIS----QIAEACCISELFLFKILQPLVKAGIVETVR-GRRGGVRLCRPADQITILDVVKAT 82 (144)
Q Consensus 24 ~~s~~----eIA~~~~i~~~~l~kil~~L~~agli~S~r-G~~GGy~Lak~~~~Itl~dI~~ai 82 (144)
+.|+. +|.+....++..+.-+++.|.|.|+|.+.| |+..+|+=--.-+++.-......+
T Consensus 20 ~~t~~eI~~~l~~~~ews~sTV~TLl~RL~KKg~l~~~kdgr~~~y~pL~~~~~~~~~~~~~~l 83 (123)
T COG3682 20 PATVREIIEELPADREWSYSTVKTLLNRLVKKGLLTRKKDGRAFRYSPLLTRDQYVAGESQDLL 83 (123)
T ss_pred CCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCHHHHHCCCEEEECCCCCHHHHHHHHHHHHH
T ss_conf 8669999999863236008789999999986430431103872543011478999999999999
No 167
>COG3710 CadC DNA-binding winged-HTH domains [Transcription]
Probab=82.76 E-value=4 Score=21.80 Aligned_cols=66 Identities=14% Similarity=0.119 Sum_probs=47.7
Q ss_pred HHHHHHHHHHHHHCCCCCCCHHHHHHHH----CCCHHHHHHH-------HHHHHH-CCCEEECCCCCCCCEECCCHHHCC
Q ss_conf 8999999999985598633599999981----9978999999-------999932-590573156545400023721260
Q gi|254780620|r 7 TDYGIRVLMYCAIHNDYPNRISQIAEAC----CISELFLFKI-------LQPLVK-AGIVETVRGRRGGVRLCRPADQIT 74 (144)
Q Consensus 7 ~~yAi~~l~~La~~~~~~~s~~eIA~~~----~i~~~~l~ki-------l~~L~~-agli~S~rG~~GGy~Lak~~~~It 74 (144)
+..++++|.+|..+.++.+|=++|-+.. .....-|.+. |..-.. +.+|.+++++ ||++..+...+.
T Consensus 33 ~~~~~~lL~~L~e~~geVvsk~eL~~~VW~~~~v~~~~Ltq~I~~LRr~L~d~~~~~~~I~TvPrr--Gyk~~~~v~~~~ 110 (148)
T COG3710 33 GPRELKLLSLLLERAGEVVSKDELLDAVWPGRIVTVNTLTQAISALRRALRDIGDGHRLIATVPRR--GYKFTADVIIII 110 (148)
T ss_pred CHHHHHHHHHHHHCCCCEECHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCC--CEEECCCEEEEC
T ss_conf 667889999998546860529999998579962644549999999999863468766389983785--469737569951
No 168
>PRK11564 stationary phase inducible protein CsiE; Provisional
Probab=82.54 E-value=4.5 Score=21.50 Aligned_cols=71 Identities=10% Similarity=0.100 Sum_probs=50.8
Q ss_pred CCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH----HCCCEEECCCCCCCCEECCCHHHCCH
Q ss_conf 64568999999999985598633599999981997899999999993----25905731565454000237212609
Q gi|254780620|r 3 LTKRTDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLV----KAGIVETVRGRRGGVRLCRPADQITI 75 (144)
Q Consensus 3 is~~~~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~----~agli~S~rG~~GGy~Lak~~~~Itl 75 (144)
+|..-+ -..++++|.. +++++|...+++..++|++.+.+=+..++ +-.=++=.+-+++||++.-+..++..
T Consensus 11 lS~~ER-~~~ill~Ll~-~~e~vtl~~L~~~l~VSr~Ti~~DLk~l~~~L~~y~~L~L~~~r~~Gy~I~G~E~~kR~ 85 (426)
T PRK11564 11 LSAPQR-RCQILLMLFQ-PGLTVTLETISQLNGVDDDIARQDIAETAREIQRYHHLTLTTGQDGSYRIEGTALDQRL 85 (426)
T ss_pred CCHHHH-HHHHHHHHHC-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCEEEEEECCCEEEEECCHHHHHH
T ss_conf 999999-9999999977-99973499999996998889999999999998300886999817973899736899999
No 169
>smart00351 PAX Paired Box domain.
Probab=82.45 E-value=2.6 Score=22.94 Aligned_cols=47 Identities=26% Similarity=0.350 Sum_probs=38.1
Q ss_pred HHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCC
Q ss_conf 9999985598633599999981997899999999993259057315654540
Q gi|254780620|r 13 VLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGV 64 (144)
Q Consensus 13 ~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy 64 (144)
-++.||..+ ++.-+||..+.+|...+.|||......|-+. .|.-||-
T Consensus 25 kIveLa~~G---~rpcdISr~L~VShGCVSKIL~Ry~etGsi~--Pg~igGs 71 (125)
T smart00351 25 RIVELAQNG---VRPCDISRQLCVSHGCVSKILGRYYETGSIR--PGAIGGS 71 (125)
T ss_pred HHHHHHHCC---CCHHHHHHHHCCCCCHHHHHHHHHHHCCCCC--CCCCCCC
T ss_conf 999999859---9899987564577106999999997138878--9987788
No 170
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=82.35 E-value=1.2 Score=24.81 Aligned_cols=68 Identities=16% Similarity=0.200 Sum_probs=47.1
Q ss_pred CHHHHHHHHHHHHHHH-CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE-ECCCCCCCCEECCCHHHC
Q ss_conf 4568999999999985-598633599999981997899999999993259057-315654540002372126
Q gi|254780620|r 4 TKRTDYGIRVLMYCAI-HNDYPNRISQIAEACCISELFLFKILQPLVKAGIVE-TVRGRRGGVRLCRPADQI 73 (144)
Q Consensus 4 s~~~~yAi~~l~~La~-~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~-S~rG~~GGy~Lak~~~~I 73 (144)
.++++ +-++..+-. ..++.+....|.-..|++.....+++..|.++|++. ..-|+.+.|.|...-.++
T Consensus 12 ~rR~R--~eIi~dIL~~~~~~~~~~Tri~y~aNlny~~~~~yi~~L~~~Gli~~~~~~~~~~y~lT~KG~~f 81 (95)
T COG3432 12 KRRSR--LEIIFDILKAISEGGIGITRIIYGANLNYKRAQKYIEMLVEKGLIIKQDNGRRKVYELTEKGKRF 81 (95)
T ss_pred HCCHH--HHHHHHHHHHHCCCCCCCEEEEEECCCCHHHHHHHHHHHHHCCCEEECCCCCCCEEEECHHHHHH
T ss_conf 31019--99999999984179998624664327677999999999986787786148864458988568999
No 171
>pfam04703 FaeA FaeA-like protein. This family represents a number of fimbrial protein transcription regulators found in Gram-negative bacteria. These proteins are thought to facilitate binding of the leucine-rich regulatory protein to regulatory elements, possibly by inhibiting deoxyadenosine methylation of these elements by deoxyadenosine methylase.
Probab=82.19 E-value=4.2 Score=21.67 Aligned_cols=54 Identities=26% Similarity=0.262 Sum_probs=41.0
Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECC---CCCCCCEE
Q ss_conf 99999985598633599999981997899999999993259057315---65454000
Q gi|254780620|r 12 RVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVR---GRRGGVRL 66 (144)
Q Consensus 12 ~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~r---G~~GGy~L 66 (144)
.+|.|+..- +.|+.+.|||+..+++.=..+--|..|-++|-|+-.. |..|-|+|
T Consensus 4 ~Il~~i~~i-~~p~~T~eIAda~gls~YQaR~YL~~Lek~g~i~rsp~rrG~~tlW~l 60 (61)
T pfam04703 4 SILTFINSI-GAPCKTREIADALGLSAYQARYYLEQLEKEGKIERSPLRRGAPTLWRL 60 (61)
T ss_pred HHHHHHHHC-CCCCCHHHHHHHHCCHHHHHHHHHHHHHHCCCEECCCCCCCCHHHHHC
T ss_conf 899999874-898418899998550799999999999870752305534672146650
No 172
>COG0745 OmpR Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=81.99 E-value=4.8 Score=21.38 Aligned_cols=57 Identities=28% Similarity=0.331 Sum_probs=41.0
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCC---------CHHHHHHHHHHHHHCC----CEEECCCCCCCCEECCC
Q ss_conf 99999998559863359999998199---------7899999999993259----05731565454000237
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCI---------SELFLFKILQPLVKAG----IVETVRGRRGGVRLCRP 69 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i---------~~~~l~kil~~L~~ag----li~S~rG~~GGy~Lak~ 69 (144)
..+|.+|+.++++.+|-++|-+..-- =..|+.++=++|...+ +|+++||. ||+|..+
T Consensus 159 f~lL~~L~~~~g~v~sR~~L~~~vw~~~~~~~~rtvdvhI~rLR~Kl~~~~~~~~~I~TvrG~--GY~l~~~ 228 (229)
T COG0745 159 FELLELLARHPGRVLSREQLLEAVWGYDFEVDSRTVDVHISRLRKKLEKDPGAGRLIRTVRGV--GYRLEEP 228 (229)
T ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCEEHHHHHHHHHHHCCCCCCCCEEEEEECE--EEEEEEC
T ss_conf 999999996699526899999986086668764330599889999733567877729999452--6898408
No 173
>TIGR00373 TIGR00373 conserved hypothetical protein TIGR00373; InterPro: IPR005241 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=81.96 E-value=2.6 Score=22.92 Aligned_cols=82 Identities=20% Similarity=0.166 Sum_probs=56.2
Q ss_pred HHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCC-----CEECCCHHHCC------HHH
Q ss_conf 9999999998559863359999998199789999999999325905731565454-----00023721260------999
Q gi|254780620|r 9 YGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGG-----VRLCRPADQIT------ILD 77 (144)
Q Consensus 9 yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GG-----y~Lak~~~~It------l~d 77 (144)
=|+.+|--|... |.+|-.+||+.+++--..+||+|-+|-.+|++.=+|-+.-- |...-.+++++ +-+
T Consensus 17 e~~~vl~~L~~k--Ge~Tdeeis~elg~klN~vRk~Ly~LYdagladYkR~kD~eT~Wy~YtW~~~~eK~~~v~Krk~~e 94 (168)
T TIGR00373 17 EAIEVLESLLIK--GEVTDEEISKELGIKLNVVRKLLYKLYDAGLADYKRRKDDETNWYEYTWKIELEKVLDVVKRKLEE 94 (168)
T ss_pred CHHHHHHHHCCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHCCEEEEEEECCCCCCCCEEEECCCCCCHHHHHHHHHHHH
T ss_conf 213444222026--874778888883840557889999873030100021368988852365166702147898788999
Q ss_pred HHH----HHC--CCCCCCCCC
Q ss_conf 999----971--876311146
Q gi|254780620|r 78 VVK----ATE--ESFFVAECF 92 (144)
Q Consensus 78 I~~----aie--~~~~~~~C~ 92 (144)
+++ ++| ...-++-|.
T Consensus 95 ~~kkLreklEfE~nn~ff~Cp 115 (168)
T TIGR00373 95 LVKKLREKLEFEKNNMFFVCP 115 (168)
T ss_pred HHHHHHHHHHHHCCCEEEEEC
T ss_conf 999999874231077258713
No 174
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=81.73 E-value=4.7 Score=21.40 Aligned_cols=59 Identities=19% Similarity=0.086 Sum_probs=44.8
Q ss_pred HHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECC
Q ss_conf 9999999999855986335999999819978999999999932590573156545400023
Q gi|254780620|r 8 DYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCR 68 (144)
Q Consensus 8 ~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak 68 (144)
..-.++|-+|+.. +..++.+||+..++++.-+.+.+..|...|+|+..+=..==|.|..
T Consensus 6 ~~E~kIL~~L~~~--~~~~~eeLa~~~g~d~~~V~~ai~~L~~kglI~vee~~~~~~~LTe 64 (501)
T PRK04172 6 PNEKKVLKALAEL--KKATAEELAEKLGLDEEAVMRAAEWLEEKGLVEVEEKVTEFYELTE 64 (501)
T ss_pred HHHHHHHHHHHHC--CCCCHHHHHHHCCCCHHHHHHHHHHHHHCCCEEEEEEEEEEEEECH
T ss_conf 7899999999747--9999999998829999999999998875899799988888999888
No 175
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=80.81 E-value=4.4 Score=21.58 Aligned_cols=13 Identities=15% Similarity=0.064 Sum_probs=7.0
Q ss_pred HHHHHHCCHHHHH
Q ss_conf 9998417999999
Q gi|254780620|r 119 FDVLTQYSIECLV 131 (144)
Q Consensus 119 ~~~L~~~TL~dl~ 131 (144)
..+++..|.+++.
T Consensus 142 L~~~eg~s~~EIA 154 (197)
T PRK09643 142 AVDMQGYSVADTA 154 (197)
T ss_pred HHHHCCCCHHHHH
T ss_conf 9998199999999
No 176
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=79.32 E-value=5.9 Score=20.84 Aligned_cols=44 Identities=11% Similarity=-0.012 Sum_probs=30.1
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH----HHHCCCEEECCCCCCCCEECC
Q ss_conf 6335999999819978999999999----932590573156545400023
Q gi|254780620|r 23 YPNRISQIAEACCISELFLFKILQP----LVKAGIVETVRGRRGGVRLCR 68 (144)
Q Consensus 23 ~~~s~~eIA~~~~i~~~~l~kil~~----L~~agli~S~rG~~GGy~Lak 68 (144)
++.|+.|||+..++|...++.=+.. |...+++...+| .||.|..
T Consensus 16 ~~lt~~eLA~~L~VS~RTIR~DI~~iN~~L~~~~i~~~~~~--~GY~L~i 63 (585)
T PRK09863 16 QDRSGGELAQQLGVSRRTIVRDIAYINFTLNGKAIGSISGS--AKYHLEI 63 (585)
T ss_pred CCCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCEEEEECC--CCEEEEE
T ss_conf 99998999987499711789999999999841851898468--7528886
No 177
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=79.14 E-value=5.8 Score=20.87 Aligned_cols=45 Identities=18% Similarity=0.259 Sum_probs=26.6
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Q ss_conf 999999985598633599999981997899999999993259057
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVE 55 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~ 55 (144)
-.++-|+..|=.+++|.++||+..++|+.|+.+++.+-..-.+.+
T Consensus 194 ~~il~YI~~hY~e~IsL~diA~~~~lS~~y~sr~FKk~tG~T~~~ 238 (302)
T PRK10371 194 SQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQRVMQLTMKQ 238 (302)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCHHH
T ss_conf 999999999828999999999897959999999999998909999
No 178
>TIGR02063 RNase_R ribonuclease R; InterPro: IPR011805 This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in Escherichia coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Not included in this entry are shorter, divergent forms from the Chlamydiae and the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans , .; GO: 0003723 RNA binding, 0004518 nuclease activity.
Probab=79.06 E-value=6 Score=20.79 Aligned_cols=59 Identities=24% Similarity=0.268 Sum_probs=45.2
Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHCCCH----HHHHHHHHHHHHCCC-EEECCCCCCCCEECCCHH
Q ss_conf 999999855986335999999819978----999999999932590-573156545400023721
Q gi|254780620|r 12 RVLMYCAIHNDYPNRISQIAEACCISE----LFLFKILQPLVKAGI-VETVRGRRGGVRLCRPAD 71 (144)
Q Consensus 12 ~~l~~La~~~~~~~s~~eIA~~~~i~~----~~l~kil~~L~~agl-i~S~rG~~GGy~Lak~~~ 71 (144)
.++-+|-.++++|.+.++|++..++.. ..|+|+|..|.+.|+ |... .++|.|.+.....
T Consensus 6 ~i~~~l~~~~~~p~~~~~l~~~~~~~~~~~~~~l~~~L~~L~~~G~i~~~~-a~~~~~~~~~~~~ 69 (755)
T TIGR02063 6 EILELLKSKKGKPISLKELAKAFGLKGAEEKKALRKRLRALEDDGLIVKKN-ARRGLYALPESLK 69 (755)
T ss_pred HHHHHHHCCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCEEEEEE-CCCCEEECCCCCC
T ss_conf 999997236787638899999960569435799999999997679089996-2775241356556
No 179
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=78.92 E-value=6 Score=20.76 Aligned_cols=51 Identities=16% Similarity=0.111 Sum_probs=38.3
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCC
Q ss_conf 99999998559863359999998199789999999999325905731565454000237
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRP 69 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~ 69 (144)
-+++-+|-. .+.++++|||+..++|+..+++=|..|...+.+. ||+.+..+
T Consensus 10 ~~Il~~L~~--~g~v~v~eLa~~~~VS~~TIRRDL~~~~~~~~~~------gG~~~~~~ 60 (252)
T PRK10681 10 GQLLQALKR--SDKLHLKDAAALLGVSEMTIRRDLNAESAPVVLL------GGYIVLEP 60 (252)
T ss_pred HHHHHHHHH--CCCEEHHHHHHHHCCCHHHHHHCHHHHHCCCEEE------EEEEECCC
T ss_conf 999999998--6979999999887979989987888652798896------34887277
No 180
>PRK13503 transcriptional activator RhaS; Provisional
Probab=78.57 E-value=4.5 Score=21.52 Aligned_cols=22 Identities=18% Similarity=0.196 Sum_probs=9.4
Q ss_pred HHHHHHHHHHHH-HHCCHHHHHH
Q ss_conf 999999999998-4179999991
Q gi|254780620|r 111 LRKALNAFFDVL-TQYSIECLVR 132 (144)
Q Consensus 111 ~~~~~~~~~~~L-~~~TL~dl~~ 132 (144)
+..+.+.+.+-+ +.+||+|+++
T Consensus 173 ~~~i~~yI~~hy~~~isl~~lA~ 195 (278)
T PRK13503 173 LNQLLAWLEDHFAEEVNWEAVAD 195 (278)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHH
T ss_conf 99999999997579999999998
No 181
>pfam09012 FeoC FeoC like transcriptional regulator. This family contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependant transcriptional repressor.
Probab=78.52 E-value=5.1 Score=21.18 Aligned_cols=42 Identities=14% Similarity=0.181 Sum_probs=35.6
Q ss_pred HHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCC
Q ss_conf 99855986335999999819978999999999932590573156
Q gi|254780620|r 16 YCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRG 59 (144)
Q Consensus 16 ~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG 59 (144)
|++.+ +.+|..+||.+.++|++-|+-.|..|.+.|-|.-+..
T Consensus 8 ~l~~~--g~~s~~~Ls~~f~~~~~~v~~ML~~wi~kGkv~k~~~ 49 (68)
T pfam09012 8 YLQER--GRASLAELARHFKMSPDAVEAMLEVWIRKGKVRKLED 49 (68)
T ss_pred HHHHH--CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECC
T ss_conf 99991--9847999998979399999999999998797587248
No 182
>cd00131 PAX Paired Box domain
Probab=78.13 E-value=4.2 Score=21.70 Aligned_cols=48 Identities=23% Similarity=0.265 Sum_probs=39.3
Q ss_pred HHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCE
Q ss_conf 99999855986335999999819978999999999932590573156545400
Q gi|254780620|r 13 VLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVR 65 (144)
Q Consensus 13 ~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~ 65 (144)
-++.||.++ +.--+||..+.+|...+.|||......|-+. .|.-||..
T Consensus 25 kIVeLa~~G---~RpcdISR~L~VShGCVSKIL~Ry~eTGsi~--Pg~igGsk 72 (128)
T cd00131 25 RIVELAQSG---IRPCDISRQLRVSHGCVSKILNRYYETGSIR--PGAIGGSK 72 (128)
T ss_pred HHHHHHHCC---CCHHHHHHHHCCCCHHHHHHHHHHHHCCCCC--CCCCCCCC
T ss_conf 999999859---9788888763777216899999887027666--88878988
No 183
>COG1695 Predicted transcriptional regulators [Transcription]
Probab=77.64 E-value=4.2 Score=21.69 Aligned_cols=74 Identities=18% Similarity=0.230 Sum_probs=44.8
Q ss_pred HHHHHHHHHHHHCCCCCC-CHHHHHHHHC----CCHHHHHHHHHHHHHCCCEEECCCCCCC------CEECCCHHHCCHH
Q ss_conf 999999999985598633-5999999819----9789999999999325905731565454------0002372126099
Q gi|254780620|r 8 DYGIRVLMYCAIHNDYPN-RISQIAEACC----ISELFLFKILQPLVKAGIVETVRGRRGG------VRLCRPADQITIL 76 (144)
Q Consensus 8 ~yAi~~l~~La~~~~~~~-s~~eIA~~~~----i~~~~l~kil~~L~~agli~S~rG~~GG------y~Lak~~~~Itl~ 76 (144)
....-+|..|+..+.... -.+++.+..+ +++..+..+|.+|.+.|+|.+.....+| |+|...-. -.|.
T Consensus 9 ~l~~~iL~~L~~~~~~Gyei~~~~~~~~~~~~~~s~gtiYp~L~~Le~~Gli~~~~~~~~~g~~rk~Y~lTe~G~-~~l~ 87 (138)
T COG1695 9 SLELLILSLLSEKPSHGYEIIKELEELSGGLWEPSPGTIYPLLKRLEKEGLIESRWEESGGGPPRKYYRLTEKGK-EELA 87 (138)
T ss_pred HHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCEEEEEEECCCCCCCEEEEECHHHH-HHHH
T ss_conf 389999999702997399999999987289777887635899999998897678974058986401798388899-9999
Q ss_pred HHHHHH
Q ss_conf 999997
Q gi|254780620|r 77 DVVKAT 82 (144)
Q Consensus 77 dI~~ai 82 (144)
+..+..
T Consensus 88 ~~~~~~ 93 (138)
T COG1695 88 ELREEW 93 (138)
T ss_pred HHHHHH
T ss_conf 999988
No 184
>pfam05584 Sulfolobus_pRN Sulfolobus plasmid regulatory protein. This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=77.45 E-value=4.4 Score=21.60 Aligned_cols=50 Identities=20% Similarity=0.216 Sum_probs=40.6
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCC
Q ss_conf 99999998559863359999998199789999999999325905731565454
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGG 63 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GG 63 (144)
-++|+.|+ + +-.|.+++.+..+++..-|-..|..|.+.|+|.-.=++-||
T Consensus 8 ~~Il~~ls--~-~c~tLEeL~e~T~~~k~~llV~Ltrl~k~GiI~RkW~k~~g 57 (72)
T pfam05584 8 ELILIRLS--G-KCATLEELQEKTGADKNELLVTLTRLYKRGIIYRKWRKYGG 57 (72)
T ss_pred HHHHHHHH--C-CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCHHHHHHHHCC
T ss_conf 99999997--2-55779999998588825799999999877750556666225
No 185
>TIGR01016 sucCoAbeta succinyl-CoA synthetase, beta subunit; InterPro: IPR005809 There are four different enzymes that share a similar catalytic mechanism which involves the phosphorylation by ATP (or GTP) of a specific histidine residue in the active site. These enzymes are: ATP citrate-lyase (4.1.3.8 from EC) , the primary enzyme responsible for the synthesis of cytosolic acetyl-CoA in many tissues, catalyzes the formation of acetyl-CoA and oxaloacetate from citrate and CoA with the concomitant hydrolysis of ATP to ADP and phosphate. ATP-citrate lyase is a tetramer of identical subunits; Succinyl-CoA ligase (GDP-forming) (6.2.1.4 from EC) is a mitochondrial enzyme that catalyzes the substrate level phosphorylation step of the tricarboxylic acid cycle: the formation of succinyl-CoA from succinate with a concomitant hydrolysis of GTP to GDP and phosphate. This enzyme is a dimer composed of an alpha and a beta subunits; Succinyl-CoA ligase (ADP-forming) (6.2.1.5 from EC) is a bacterial enzyme that during aerobic metabolism functions in the citric acid cycle, coupling the hydrolysis of succinyl-CoA to the synthesis of ATP. It can also function in the other direction for anabolic purposes. This enzyme is a tetramer composed of two alpha and two beta subunits; and Malate-CoA ligase (6.2.1.9 from EC) (malyl-CoA synthetase) , is a bacterial enzyme that forms malyl-CoA from malate and CoA with the concomitant hydrolysis of ATP to ADP and phosphate. Malate-CoA ligase is composed of two different subunits. This entry corresponds to a conserved region located in the first half of ATP citrate lyase and in the beta subunits of succinyl-CoA ligases and malate-CoA ligase. ; GO: 0003824 catalytic activity, 0008152 metabolic process.
Probab=77.30 E-value=2.4 Score=23.15 Aligned_cols=49 Identities=20% Similarity=0.296 Sum_probs=35.0
Q ss_pred CCHHHHHHHHCCCHH---------HHHHHHHHHH-HCCCEEEC-----CCCCCCCEECCCHHHC
Q ss_conf 359999998199789---------9999999993-25905731-----5654540002372126
Q gi|254780620|r 25 NRISQIAEACCISEL---------FLFKILQPLV-KAGIVETV-----RGRRGGVRLCRPADQI 73 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~---------~l~kil~~L~-~agli~S~-----rG~~GGy~Lak~~~~I 73 (144)
..+++|=.++++|.+ =++.+...|. ..-.|+|+ ||+.||..++++++++
T Consensus 6 YqAK~if~~YGiPvp~g~v~~s~~e~~~~~~~~g~~~~VvKaQVhaGGRGKAGGv~~a~s~ee~ 69 (389)
T TIGR01016 6 YQAKEIFAKYGIPVPEGEVATSVEEVEEIAEELGEGKVVVKAQVHAGGRGKAGGVKVAKSKEEA 69 (389)
T ss_pred HHHHHHHHHCCCCCCCCCEEECHHHHHHHHHHCCCCCEEEEEEEEECCCCCCCCEEEEECHHHH
T ss_conf 5589999847896788600416789999999707997899987732671121576897087999
No 186
>pfam00292 PAX 'Paired box' domain.
Probab=77.06 E-value=4.6 Score=21.49 Aligned_cols=48 Identities=23% Similarity=0.240 Sum_probs=39.3
Q ss_pred HHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCE
Q ss_conf 99999855986335999999819978999999999932590573156545400
Q gi|254780620|r 13 VLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVR 65 (144)
Q Consensus 13 ~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~ 65 (144)
-++.||..+- .--+||..+.+|...+.|||......|-+. .|.-||..
T Consensus 25 kIVeLa~~G~---RpCdISR~L~VShGCVSKIL~Ry~etGsi~--Pg~iGGsk 72 (125)
T pfam00292 25 KIVELAHSGV---RPCDISRQLRVSHGCVSKILGRYQETGSIR--PGVIGGSK 72 (125)
T ss_pred HHHHHHHCCC---CHHHHHHHHCCCCHHHHHHHHHHHHCCCCC--CCCCCCCC
T ss_conf 9999998499---788887762676216899999887227767--88778988
No 187
>PRK10529 DNA-binding transcriptional activator KdpE; Provisional
Probab=76.97 E-value=6.9 Score=20.42 Aligned_cols=58 Identities=16% Similarity=0.146 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHC-----CC----HHHHHHHHHHHHHC----CCEEECCCCCCCCEEC
Q ss_conf 689999999999855986335999999819-----97----89999999999325----9057315654540002
Q gi|254780620|r 6 RTDYGIRVLMYCAIHNDYPNRISQIAEACC-----IS----ELFLFKILQPLVKA----GIVETVRGRRGGVRLC 67 (144)
Q Consensus 6 ~~~yAi~~l~~La~~~~~~~s~~eIA~~~~-----i~----~~~l~kil~~L~~a----gli~S~rG~~GGy~La 67 (144)
..|| .+|-+|+.++++.+|-++|.+..- .. ..|+.++=++|... .+|.++||. ||+|.
T Consensus 154 ~~E~--~lL~~L~~~~g~vvsre~L~~~vw~~~~~~~~~~idv~I~rLRkKl~~~~~~~~~I~TvrG~--GYr~~ 224 (225)
T PRK10529 154 PIEF--RLLAVLLNNAGKVLTQRQLLNQVWGPNAVEHSHYLRIYMGHLRQKLEQDPTRPRHFITETGI--GYRFM 224 (225)
T ss_pred HHHH--HHHHHHHHCCCCEECHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCEEEECCC--CEEEC
T ss_conf 6899--99999997799619699999996499989886879999999999720078999828956781--65665
No 188
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=76.87 E-value=6.5 Score=20.57 Aligned_cols=59 Identities=12% Similarity=0.119 Sum_probs=41.7
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHH
Q ss_conf 999999985598633599999981997899999999993259057315654540002372126099
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITIL 76 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~ 76 (144)
+|..+..+...+ -.|..++|++.+++...+.+-++..++.|+. ....+.|| .|..++-.
T Consensus 9 ~R~~~~~~~~~~-G~S~re~Ak~~gvs~sTvy~wv~r~~e~G~~-l~~~~~~G-----rP~kl~~~ 67 (138)
T COG3415 9 LRERVVDAVVGE-GLSCREAAKRFGVSISTVYRWVRRYRETGLD-LPPKPRKG-----RPRKLSEE 67 (138)
T ss_pred HHHHHHHHHHHC-CCCHHHHHHHHCCCHHHHHHHHHHHCCCCCC-CCCCCCCC-----CCCCCCHH
T ss_conf 999999999976-8549999999692299999999873335331-56766899-----97325889
No 189
>pfam04079 DUF387 Putative transcriptional regulators (Ypuh-like). This family of conserved bacterial proteins are thought to possibly be helix-turn-helix type transcriptional regulators.
Probab=76.59 E-value=5.5 Score=21.02 Aligned_cols=64 Identities=25% Similarity=0.321 Sum_probs=42.3
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCC-----CCCCCEECCCHHHCCHHHHHHHH
Q ss_conf 9999999855986335999999819978999999999932590573156-----54540002372126099999997
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRG-----RRGGVRLCRPADQITILDVVKAT 82 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG-----~~GGy~Lak~~~~Itl~dI~~ai 82 (144)
|-++++.+ ++|+|.++|++..+ +...+++++..|.+. +-+..+| .+|||++.-.|+ ..+++..+
T Consensus 3 IEAiLF~s---~~pls~~~l~~~~~-~~~~i~~~l~~L~~~-y~~~~~gi~i~~~~~gy~~~tk~~---~~~~~~~~ 71 (159)
T pfam04079 3 IEALLFAA---GEPLSLEELAKILG-SREEVREALDELKEE-YEDRDRGLELVEVAGGYRLQTKPE---YAEYVKRL 71 (159)
T ss_pred HHHHHHHC---CCCCCHHHHHHHHC-CHHHHHHHHHHHHHH-HHCCCCCEEEEEECCEEEEEEHHH---HHHHHHHH
T ss_conf 99999973---89979999998849-999999999999999-850898189999899889988599---99999998
No 190
>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=76.46 E-value=7.1 Score=20.34 Aligned_cols=70 Identities=27% Similarity=0.260 Sum_probs=55.6
Q ss_pred HHHHHHHHHHHHHCCCCCCCHHHHHHHH-CCCHHHHHHHHHHHHHCCCEEECC--CCCCCCEECCCHHHCCHHH
Q ss_conf 8999999999985598633599999981-997899999999993259057315--6545400023721260999
Q gi|254780620|r 7 TDYGIRVLMYCAIHNDYPNRISQIAEAC-CISELFLFKILQPLVKAGIVETVR--GRRGGVRLCRPADQITILD 77 (144)
Q Consensus 7 ~~yAi~~l~~La~~~~~~~s~~eIA~~~-~i~~~~l~kil~~L~~agli~S~r--G~~GGy~Lak~~~~Itl~d 77 (144)
.+.+-+++.+++.+.+.++|..+||... ++|...+.+-+..|..+-++...+ +.++..++.+++ .+-+.|
T Consensus 219 ~~~~k~i~~~l~~~~g~~~s~~~l~~~l~~is~~Tv~~yl~~le~~~ll~~v~~~~~~~~~~~~k~~-Kiy~~D 291 (398)
T COG1373 219 ADLMKRILRFLASNIGSPISYSSLARELKGISKDTIRKYLSYLEDAFLLFLVPRYGENLKKRLRKPK-KLYLID 291 (398)
T ss_pred HHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHEEEEEECCCCCCCEEECCCC-CEEEEC
T ss_conf 7999999999875036645699999997234466899999998542378985137775110111347-479966
No 191
>pfam03428 RP-C Replication protein C N-terminal domain. Replication protein C is involved in the early stages of viral DNA replication.
Probab=76.35 E-value=5.8 Score=20.87 Aligned_cols=55 Identities=25% Similarity=0.254 Sum_probs=38.3
Q ss_pred CHHHHHHHH-CCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECC-CHHHCCHHHHHHHHCCC
Q ss_conf 599999981-9978999999999932590573156545400023-72126099999997187
Q gi|254780620|r 26 RISQIAEAC-CISELFLFKILQPLVKAGIVETVRGRRGGVRLCR-PADQITILDVVKATEES 85 (144)
Q Consensus 26 s~~eIA~~~-~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak-~~~~Itl~dI~~aie~~ 85 (144)
|-.+||+.. |+|...|++.+..|+.+|+|.=.-.++| -+.++ +.+ ++|.+|++-+
T Consensus 72 SN~~La~r~~G~s~~tlrrhla~LveaGLi~rrDS~Ng-KRy~rR~~~----G~i~~A~Gfd 128 (177)
T pfam03428 72 SNAQLSLRAHGMSESTLRRHLAALVDAGLIIRRDSPNG-KRYARRGGD----GEIEEAFGFD 128 (177)
T ss_pred CHHHHHHHHCCCCHHHHHHHHHHHHHCCCEEECCCCCC-CCCCEECCC----CCEEEEECCC
T ss_conf 89999999849988999999999998897452369998-501623799----8776344647
No 192
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=76.09 E-value=5.3 Score=21.10 Aligned_cols=56 Identities=14% Similarity=0.105 Sum_probs=40.5
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHC------CCEEECCCCCCCCEECCCHHHCCHHHHHHHH
Q ss_conf 863359999998199789999999999325------9057315654540002372126099999997
Q gi|254780620|r 22 DYPNRISQIAEACCISELFLFKILQPLVKA------GIVETVRGRRGGVRLCRPADQITILDVVKAT 82 (144)
Q Consensus 22 ~~~~s~~eIA~~~~i~~~~l~kil~~L~~a------gli~S~rG~~GGy~Lak~~~~Itl~dI~~ai 82 (144)
+.++|.++|++..++++..++.++..|.+. |+.- .-.+|||+|.-.|+ +.+.++.+
T Consensus 11 ~p~vs~~~L~~~~~~~~~~i~~~l~~L~~~Y~~~~~gi~l--~~~~~gy~l~t~~e---~~~~i~~~ 72 (182)
T PRK00135 11 EEGLSLRQLAEILELEPTEVKQLLEELQEKYEGDDRGLKL--IEFAETYKLVTKEE---NADYLQKL 72 (182)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCEEE--EEECCEEEEEECHH---HHHHHHHH
T ss_conf 9998999999886889899999999999996248973799--99999999998199---99999998
No 193
>PRK10736 hypothetical protein; Provisional
Probab=76.03 E-value=7.3 Score=20.27 Aligned_cols=50 Identities=28% Similarity=0.234 Sum_probs=37.0
Q ss_pred HHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCC-EECCC
Q ss_conf 985598633599999981997899999999993259057315654540-00237
Q gi|254780620|r 17 CAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGV-RLCRP 69 (144)
Q Consensus 17 La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy-~Lak~ 69 (144)
|+.-++++.++.+|+++.++|..-+...|-.|-=+|+|.+..| || ++.|.
T Consensus 304 L~~~g~~~~~vD~La~~tgl~v~~v~~~LleLEL~G~V~~~pG---gY~RlrRa 354 (364)
T PRK10736 304 LANVGDEVTPVDVVAERAGQPVPEVVTQLLELELAGWIAAVPG---GYVRLRRA 354 (364)
T ss_pred HHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCC---CEEEEECC
T ss_conf 9855899989999999979099999999999994891780699---47997547
No 194
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=75.97 E-value=5.8 Score=20.87 Aligned_cols=39 Identities=10% Similarity=0.240 Sum_probs=25.1
Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 999999855986335999999819978999999999932
Q gi|254780620|r 12 RVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVK 50 (144)
Q Consensus 12 ~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~ 50 (144)
+++-+|..|-+++.|.++||+..++|+.++.+.+++-..
T Consensus 220 ~~~~~i~~~l~~~ls~~~lA~~~~~S~R~l~R~Fk~~~G 258 (320)
T PRK09393 220 PLIDWMRAHLAQPHTVASLAARAAMSPRTFLRRFEAATG 258 (320)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHC
T ss_conf 999999961114788999999978798799989978869
No 195
>KOG2165 consensus
Probab=75.93 E-value=7.4 Score=20.25 Aligned_cols=61 Identities=10% Similarity=0.124 Sum_probs=43.2
Q ss_pred HHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHH
Q ss_conf 89999999999855986335999999819978999999999932590573156545400023721260999
Q gi|254780620|r 7 TDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILD 77 (144)
Q Consensus 7 ~~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~d 77 (144)
-.||.-+ ++. +....+|.+++|+..++|++.+++-|.-..+.|++.-..|. .+|...|+-+
T Consensus 602 p~qA~iI--~~F-qek~twt~eelse~l~ip~~~lrrrL~fWi~~GvL~e~~~~-------s~tgt~T~iE 662 (765)
T KOG2165 602 PEQAAII--NLF-QEKNTWTLEELSESLGIPVPALRRRLSFWIQKGVLREEPII-------SDTGTLTVIE 662 (765)
T ss_pred HHHHHHH--HHH-CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEECCCCC-------CCCCEEEECC
T ss_conf 8999999--996-47452439999988689979999999999974822147887-------8876146332
No 196
>PTZ00326 phenylalanyl-tRNA synthetase; Provisional
Probab=75.78 E-value=7.4 Score=20.23 Aligned_cols=63 Identities=11% Similarity=0.052 Sum_probs=47.8
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCC
Q ss_conf 56899999999998559863359999998199789999999999325905731565454000237
Q gi|254780620|r 5 KRTDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRP 69 (144)
Q Consensus 5 ~~~~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~ 69 (144)
++.+-+-.+|-+|... +.+++.++|+..++++.-+.+.+..|...|+|+..+=..==|.|...
T Consensus 3 ~~~~~~~~iL~~L~~~--~~~~s~ela~~~g~~~~~Vvgai~sLeskglV~vee~~~~~~~LTeE 65 (505)
T PTZ00326 3 QKEEELNTLLEALESA--ESVTSLAVAEDLSIDHQDVVGAIKSLEALNYIKTEEIKSNTLKLTKE 65 (505)
T ss_pred CHHHHHHHHHHHHHHC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEEEEEEEEECHH
T ss_conf 4168999999999866--99999999998596999999999999868997999998889998988
No 197
>COG2865 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]
Probab=75.42 E-value=5.4 Score=21.05 Aligned_cols=50 Identities=16% Similarity=0.184 Sum_probs=37.5
Q ss_pred HHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCC
Q ss_conf 999985598633599999981997899999999993259057315654540
Q gi|254780620|r 14 LMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGV 64 (144)
Q Consensus 14 l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy 64 (144)
++.++.. .+++|..++++..+++..-.++.+..|.+.|++...--.+.|+
T Consensus 407 il~~~~e-n~~~T~~~L~~~l~is~~~i~r~i~~Lv~~g~~~~~g~~~~g~ 456 (467)
T COG2865 407 ILELIKE-NGKVTARELREILGISSETIRRRIANLVKRGLLKQLGSSGRGT 456 (467)
T ss_pred HHHHHHH-CCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCHHHHHCCCCCCC
T ss_conf 9999752-6655889999885756456999999984431788747689971
No 198
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor; InterPro: IPR014209 The bacterial core RNA polymerase complex, which consists of five subunits, 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 . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homologue sigma-E (sigma-29, see IPR014200 from INTERPRO), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note: that in Bacillus subtilis (and apparently also in Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=74.67 E-value=2.4 Score=23.13 Aligned_cols=27 Identities=19% Similarity=0.225 Sum_probs=21.4
Q ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 598633599999981997899999999
Q gi|254780620|r 20 HNDYPNRISQIAEACCISELFLFKILQ 46 (144)
Q Consensus 20 ~~~~~~s~~eIA~~~~i~~~~l~kil~ 46 (144)
..+..-|=.|||+.+|||++||++|=.
T Consensus 191 ~~~~~~tQREIA~~LgISRSYVSRIEK 217 (228)
T TIGR02846 191 KDGREKTQREIAKILGISRSYVSRIEK 217 (228)
T ss_pred CCCCCCCHHHHHHHHCCCCHHHHHHHH
T ss_conf 888954178998770865004548889
No 199
>pfam05848 CtsR Firmicute transcriptional repressor of class III stress genes (CtsR). This family consists of several Firmicute transcriptional repressor of class III stress genes (CtsR) proteins. CtsR of L. monocytogenes negatively regulates the clpC, clpP and clpE genes belonging to the CtsR regulon.
Probab=74.06 E-value=1.5 Score=24.40 Aligned_cols=61 Identities=18% Similarity=0.258 Sum_probs=38.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHH---HHHHHCCCEEECCCCCCCCE-ECC---CHHHCCHHHHHHHHCCCC
Q ss_conf 359999998199789999999---99932590573156545400-023---721260999999971876
Q gi|254780620|r 25 NRISQIAEACCISELFLFKIL---QPLVKAGIVETVRGRRGGVR-LCR---PADQITILDVVKATEESF 86 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil---~~L~~agli~S~rG~~GGy~-Lak---~~~~Itl~dI~~aie~~~ 86 (144)
+.=.|||+..+.-|+.+-=|+ -...+.=+|+|.||- |||. ..| +.+.--+.++++.+++.+
T Consensus 25 I~R~eLA~~F~CvPSQINYVl~TRFT~e~GY~VESkRGG-GGyIRI~kv~~~~~~~~~~~l~~~ig~~i 92 (151)
T pfam05848 25 IKRSELADQFNCVPSQINYVINTRFTIERGYIVESKRGG-GGYIRIVKVEFSDDHDLLDQLIQLIGDSI 92 (151)
T ss_pred EEHHHHHHHCCCCHHHCEEEEEEEECCCCCEEEEEECCC-CCEEEEEEECCCCHHHHHHHHHHHHCCCC
T ss_conf 758998987197713512676533426675499863278-86699999525871899999999864636
No 200
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=73.57 E-value=8.5 Score=19.90 Aligned_cols=62 Identities=19% Similarity=0.314 Sum_probs=44.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHHHCC-CCCCCCC
Q ss_conf 359999998199789999999999325905731565454000237212609999999718-7631114
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKATEE-SFFVAEC 91 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~aie~-~~~~~~C 91 (144)
.|+.|+|+..|+|+.-+ .---+.|+|...|. .|||++=-+.+--.|.-|...-+. .+.+.++
T Consensus 1 ytIgevA~~~Gvs~~tl----RyYE~~GLl~P~R~-~~gyR~Y~~~dl~rL~~I~~l~~~lGfsL~eI 63 (96)
T cd04774 1 YKVDEVAKRLGLTKRTL----KYYEEIGLVSPERS-EGRYRLYSEEDLKRLERILRLREVLGFSLQEV 63 (96)
T ss_pred CCHHHHHHHHCCCHHHH----HHHHHCCCCCCCCC-CCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 94889999989799999----99998799899869-99982359999999999999999579989999
No 201
>COG0664 Crp cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
Probab=73.20 E-value=7.3 Score=20.28 Aligned_cols=37 Identities=24% Similarity=0.304 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCC
Q ss_conf 3359999998199789999999999325905731565
Q gi|254780620|r 24 PNRISQIAEACCISELFLFKILQPLVKAGIVETVRGR 60 (144)
Q Consensus 24 ~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~ 60 (144)
+++-.+||...++++..+.+++..|++.|+|...+++
T Consensus 171 ~~~~~~ia~~~g~~~~~vsr~l~~l~~~g~i~~~~~~ 207 (214)
T COG0664 171 PLTHKDLAEYLGLSRETVSRILKELRKDGLISVRGKK 207 (214)
T ss_pred ECCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCE
T ss_conf 1669999988689999999999998868949978975
No 202
>pfam04492 Phage_rep_O Bacteriophage replication protein O. Replication protein O is necessary for the initiation of bacteriophage DNA replication. Protein O interacts with the lambda replication origin, and also with replication protein P to form an oligomer. It is speculated that the N-terminal half interacts with the replication origin while the C terminal half mediates protein-protein interaction.
Probab=73.19 E-value=8.7 Score=19.84 Aligned_cols=33 Identities=30% Similarity=0.249 Sum_probs=30.5
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Q ss_conf 633599999981997899999999993259057
Q gi|254780620|r 23 YPNRISQIAEACCISELFLFKILQPLVKAGIVE 55 (144)
Q Consensus 23 ~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~ 55 (144)
..++.++||+.+++++.++.+-+..|.+.++|.
T Consensus 53 d~I~~sqi~~mtgi~~~~Vs~a~~~Li~~~vi~ 85 (100)
T pfam04492 53 DRVTNEQIAELTGLSRTHVSEAKKSLVKRGIII 85 (100)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCH
T ss_conf 362299999997888545999999999768644
No 203
>pfam10007 DUF2250 Uncharacterized protein conserved in archaea (DUF2250). Members of this family of hypothetical archaeal proteins have no known function.
Probab=73.01 E-value=8.7 Score=19.82 Aligned_cols=52 Identities=21% Similarity=0.200 Sum_probs=42.1
Q ss_pred HHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCC
Q ss_conf 899999999998559863359999998199789999999999325905731565
Q gi|254780620|r 7 TDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGR 60 (144)
Q Consensus 7 ~~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~ 60 (144)
..-++.+|.++...+ +--+..||...++|...+...+..|.+.|+|+-+.|.
T Consensus 7 d~~~l~IL~hl~~a~--~DYak~ia~~t~ipleev~~~l~~L~~~GLlEr~~g~ 58 (93)
T pfam10007 7 DPLMLTILKHLKKAN--VDYAKSIAKNTKIPLEEVRDLLDKLEEMGLLERVTGS 58 (93)
T ss_pred CHHHHHHHHHHHHHC--CCHHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEHHHH
T ss_conf 888899999999848--7499999998189899999999999987680010014
No 204
>COG4463 CtsR Transcriptional repressor of class III stress genes [Transcription]
Probab=72.73 E-value=1.6 Score=24.15 Aligned_cols=63 Identities=16% Similarity=0.188 Sum_probs=36.6
Q ss_pred CCHHHHHHHHHHHHHHHCCCCC--CCHHHHHHHHCCCHH---HHHHHHHHHHHCCCEEECCCCCCCCE-ECC
Q ss_conf 6456899999999998559863--359999998199789---99999999932590573156545400-023
Q gi|254780620|r 3 LTKRTDYGIRVLMYCAIHNDYP--NRISQIAEACCISEL---FLFKILQPLVKAGIVETVRGRRGGVR-LCR 68 (144)
Q Consensus 3 is~~~~yAi~~l~~La~~~~~~--~s~~eIA~~~~i~~~---~l~kil~~L~~agli~S~rG~~GGy~-Lak 68 (144)
+|--.+-=|+-++ +...++. +.-++||+....-|+ |+-|.=-.-.+.=+|+|.||- |||. ..|
T Consensus 4 ~SDiIE~YlK~ll--~es~~~ivEIkRselAd~FqcVPSQINYVIkTRFT~erGY~VESKRGG-GGYIRI~K 72 (153)
T COG4463 4 TSDIIEAYLKELL--EESTEEIVEIKRSELADQFQCVPSQINYVIKTRFTEERGYLVESKRGG-GGYIRIIK 72 (153)
T ss_pred HHHHHHHHHHHHH--HHCCCCHHHHHHHHHHHHCCCCHHHEEEEEEEEEECCCCEEEEEECCC-CCEEEEEE
T ss_conf 5789999999999--855232320149777554251626600455556505565488851378-75699998
No 205
>TIGR02277 PaaX_trns_reg phenylacetic acid degradation operon negative regulatory protein PaaX; InterPro: IPR011965 This transcriptional regulator is always found in association with operons believed to be involved in the degradation of phenylacetic acid . The gene product has been shown to bind to the promoter sites and repress their transcription ..
Probab=72.72 E-value=2.2 Score=23.33 Aligned_cols=50 Identities=24% Similarity=0.304 Sum_probs=44.8
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECC-CCCCCCEECCCHHHCCH
Q ss_conf 599999981997899999999993259057315-65454000237212609
Q gi|254780620|r 26 RISQIAEACCISELFLFKILQPLVKAGIVETVR-GRRGGVRLCRPADQITI 75 (144)
Q Consensus 26 s~~eIA~~~~i~~~~l~kil~~L~~agli~S~r-G~~GGy~Lak~~~~Itl 75 (144)
+.-++-+..|++..+|+=-|..|+++|.+++-| |++==|+|+-....-+-
T Consensus 22 ~Li~~l~~~Gi~E~~VRTAvsRL~a~GWL~~Er~GRrSfY~L~D~G~~~~~ 72 (287)
T TIGR02277 22 SLIELLEGLGINERLVRTAVSRLVAQGWLQSERKGRRSFYRLSDKGRREFA 72 (287)
T ss_pred HHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHH
T ss_conf 699996225888337999999986510001024544145778899999999
No 206
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=72.60 E-value=5.1 Score=21.21 Aligned_cols=32 Identities=19% Similarity=0.217 Sum_probs=27.5
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Q ss_conf 33599999981997899999999993259057
Q gi|254780620|r 24 PNRISQIAEACCISELFLFKILQPLVKAGIVE 55 (144)
Q Consensus 24 ~~s~~eIA~~~~i~~~~l~kil~~L~~agli~ 55 (144)
|+|+++||+..++|+.++.+++......++-+
T Consensus 1 plsl~~lA~~~~~S~~~l~~~f~~~~g~s~~~ 32 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKETGTTPKQ 32 (84)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHCCCHHH
T ss_conf 98999999988909999999999988939999
No 207
>COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]
Probab=72.52 E-value=8.4 Score=19.92 Aligned_cols=41 Identities=12% Similarity=0.228 Sum_probs=31.9
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Q ss_conf 99999998559863359999998199789999999999325
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKA 51 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~a 51 (144)
.+++-.|-.+-++|.|.++||+..++|+..+++.++.-...
T Consensus 223 ~~~i~~me~nle~plsl~~LA~~~~~S~R~leRlF~~~lG~ 263 (328)
T COG4977 223 LRAIELMEANLEEPLSLEELADRAGLSRRQLERLFRAELGV 263 (328)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHCC
T ss_conf 99999999865388689999999687887899999999688
No 208
>pfam04539 Sigma70_r3 Sigma-70 region 3. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but as some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme.
Probab=71.62 E-value=8.8 Score=19.81 Aligned_cols=60 Identities=15% Similarity=0.037 Sum_probs=38.4
Q ss_pred HHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHH
Q ss_conf 999998559863359999998199789999999999325905731565454000237212609999999
Q gi|254780620|r 13 VLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKA 81 (144)
Q Consensus 13 ~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~a 81 (144)
+--.|...-|+.-|.+|||+.+++|..-+.+++..-+..--+..--|..| +-+++|++.-
T Consensus 9 a~~~L~q~lgR~Pt~eEiA~~l~~s~~~v~~~~~~~~~~~SLd~p~~~~~---------~~~l~d~i~D 68 (78)
T pfam04539 9 AQRELEQELGREPTPEEIAEELGISEEKVREVLEAAREPVSLDLPVGEEE---------DGELGDLLED 68 (78)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCEEEECCCCCCC---------CCCHHHHCCC
T ss_conf 99999999888999999999969499999999987589866106768899---------8628662059
No 209
>pfam04182 B-block_TFIIIC B-block binding subunit of TFIIIC. Yeast transcription factor IIIC (TFIIIC) is a multi-subunit 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.
Probab=70.94 E-value=9.7 Score=19.54 Aligned_cols=48 Identities=17% Similarity=0.067 Sum_probs=41.1
Q ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEC
Q ss_conf 999999998559863359999998199789999999999325905731
Q gi|254780620|r 10 GIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETV 57 (144)
Q Consensus 10 Ai~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~ 57 (144)
...+|..+|......+...++++..+..+.-+-..+..|.+.|+|.-.
T Consensus 4 ~~~lL~~Ia~~r~~Gi~q~dL~k~~~~D~rs~~~~~k~L~~~gLI~k~ 51 (73)
T pfam04182 4 QFELLEEIARSRYNGITQSDLAKLTGQDPRSVFYRLKKLEDKGLIVKQ 51 (73)
T ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHCCCEEEE
T ss_conf 899999999517688018999999689964317989999878897855
No 210
>COG5631 Predicted transcription regulator, contains HTH domain (MarR family) [Transcription]
Probab=70.76 E-value=8.8 Score=19.80 Aligned_cols=44 Identities=18% Similarity=0.277 Sum_probs=34.7
Q ss_pred HHHHHCCCCCCCHHHHHHHHCCCHHHH-HHHHHHHHHCCCEEECC
Q ss_conf 999855986335999999819978999-99999993259057315
Q gi|254780620|r 15 MYCAIHNDYPNRISQIAEACCISELFL-FKILQPLVKAGIVETVR 58 (144)
Q Consensus 15 ~~La~~~~~~~s~~eIA~~~~i~~~~l-~kil~~L~~agli~S~r 58 (144)
++.-.|.+++-+..+|+..+++-..++ .--+.+|-+.|+|+.++
T Consensus 89 lH~irhrdR~K~laDic~~ln~eDth~itYslrKL~k~gLit~t~ 133 (199)
T COG5631 89 LHIIRHRDRPKSLADICQMLNREDTHNITYSLRKLLKGGLITRTG 133 (199)
T ss_pred HHHHHHCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCEECCC
T ss_conf 888761574156999999856332104799999998556542378
No 211
>PRK13500 transcriptional activator RhaR; Provisional
Probab=70.39 E-value=9.6 Score=19.56 Aligned_cols=41 Identities=12% Similarity=0.130 Sum_probs=29.3
Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC
Q ss_conf 99999985598633599999981997899999999993259
Q gi|254780620|r 12 RVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAG 52 (144)
Q Consensus 12 ~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~ag 52 (144)
+++.||..+=.++++.+++|+..++|..++.+.+++-....
T Consensus 210 ~ll~~l~~~~~ep~~l~~lA~~~~lS~r~L~R~Fk~~tG~T 250 (312)
T PRK13500 210 KLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMT 250 (312)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCC
T ss_conf 99999998744999899999897889999999999998919
No 212
>PRK13412 fkp bifunctional fucokinase/L-fucose-1-P-guanylyltransferase; Provisional
Probab=69.82 E-value=6.1 Score=20.73 Aligned_cols=38 Identities=11% Similarity=0.146 Sum_probs=14.5
Q ss_pred CCCHHHHHHHHHHHHHCCCEEECCCCCCC---CEECCCHHH
Q ss_conf 99789999999999325905731565454---000237212
Q gi|254780620|r 35 CISELFLFKILQPLVKAGIVETVRGRRGG---VRLCRPADQ 72 (144)
Q Consensus 35 ~i~~~~l~kil~~L~~agli~S~rG~~GG---y~Lak~~~~ 72 (144)
+++++.+.+++..+.---+=.+..|++|| |.++|+|..
T Consensus 900 g~~~~~V~~l~~~i~p~~~G~kL~GAGGGGfl~~~aKdp~~ 940 (974)
T PRK13412 900 GTNPAAVEAIIETIKDYTLGYKLPGAGGGGYLYMVAKDPGA 940 (974)
T ss_pred CCCCHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEECCHHH
T ss_conf 99958999999975223310414556777679999748778
No 213
>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB; InterPro: IPR011879 PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself . It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well.; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0000160 two-component signal transduction system (phosphorelay), 0006817 phosphate transport.
Probab=69.50 E-value=2.7 Score=22.87 Aligned_cols=55 Identities=27% Similarity=0.336 Sum_probs=41.9
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHH------------CCCHHHHHHHHHHHHHCCCEEECCCCCCCCEEC
Q ss_conf 999999985598633599999981------------997899999999993259057315654540002
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEAC------------CISELFLFKILQPLVKAGIVETVRGRRGGVRLC 67 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~------------~i~~~~l~kil~~L~~agli~S~rG~~GGy~La 67 (144)
.|.|-|+..|+++..|=++|=++. .+--.-|+|-|..=..+.+|+++||. ||+|.
T Consensus 160 fRLL~FFM~HPeRV~SReQLLD~VWG~dvyVE~RTVDVHIRRLRKaL~~~g~~~~vqTVRGa--GYrfs 226 (226)
T TIGR02154 160 FRLLHFFMTHPERVYSREQLLDRVWGRDVYVEERTVDVHIRRLRKALEPGGLEDLVQTVRGA--GYRFS 226 (226)
T ss_pred HHHHHHHHHCCCCEEEHHHHHHHHCCCCEEEECCCEEEEECCHHHHCCCCCCCCCEEEECCC--CCCCC
T ss_conf 78899986237734404232011058943251350003220005423878888715651046--62589
No 214
>COG4519 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=69.39 E-value=11 Score=19.33 Aligned_cols=64 Identities=22% Similarity=0.296 Sum_probs=46.3
Q ss_pred CCCCHHHHHHHHHHHHHH--HCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE-----ECCCCCCCCEECC
Q ss_conf 976456899999999998--5598633599999981997899999999993259057-----3156545400023
Q gi|254780620|r 1 MHLTKRTDYGIRVLMYCA--IHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVE-----TVRGRRGGVRLCR 68 (144)
Q Consensus 1 Mkis~~~~yAi~~l~~La--~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~-----S~rG~~GGy~Lak 68 (144)
|-||. -+|=| +|+| ...++..++.+|-...|-|+..+.-++..|-.-|++- ..|-..|+|+|..
T Consensus 1 Melsp--vFaRR--LYla~Li~S~e~~nVP~lm~~TGwPRRT~QDvikAlpglgi~l~FvQ~G~Rnn~GyYql~d 71 (95)
T COG4519 1 MELSP--VFARR--LYLAYLIDSGETANVPELMAATGWPRRTAQDVIKALPGLGIVLEFVQEGARNNQGYYQLRD 71 (95)
T ss_pred CCCCH--HHHHH--HHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHCCCCCEEEEEEECCCCCCCCCEEEEE
T ss_conf 96458--99999--9999999404457708899873896347999998575777088863013205788268630
No 215
>cd02417 Peptidase_C39_likeA A sub-family of peptidase C39 which contains Cyclolysin and Hemolysin processing peptidases. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in this
Probab=69.00 E-value=6.4 Score=20.60 Aligned_cols=51 Identities=14% Similarity=0.124 Sum_probs=41.9
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHH--HHHHHHHHHHHCCCEE
Q ss_conf 56899999999998559863359999998199789--9999999993259057
Q gi|254780620|r 5 KRTDYGIRVLMYCAIHNDYPNRISQIAEACCISEL--FLFKILQPLVKAGIVE 55 (144)
Q Consensus 5 ~~~~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~--~l~kil~~L~~agli~ 55 (144)
++.|.++.+|.+++.+.+..++.++|.+..+++.. -+..+++..++.|+-.
T Consensus 3 ~~~d~GlacLa~va~~~G~~~~~~~Lr~~~~~~~~~~s~~~l~raA~~~Gl~a 55 (121)
T cd02417 3 TKPDSGLLALVLLARYHGIAADPEQLRHEFGLAGEPFNSTELLLAAKSLGLKA 55 (121)
T ss_pred CCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHCCCEE
T ss_conf 76775999999999980898999999997499988989999999999879847
No 216
>KOG3411 consensus
Probab=68.91 E-value=5.8 Score=20.86 Aligned_cols=37 Identities=41% Similarity=0.522 Sum_probs=29.4
Q ss_pred HHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCH
Q ss_conf 981997899999999993259057315654540002372
Q gi|254780620|r 32 EACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPA 70 (144)
Q Consensus 32 ~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~ 70 (144)
...+.+....+|+||.|.+.|+|+ +-++||-+|...-
T Consensus 91 h~~~as~~i~rkvlQ~Le~~~~ve--~hp~gGR~lt~~G 127 (143)
T KOG3411 91 HFCDASGGIARKVLQALEKMGIVE--KHPKGGRRLTEQG 127 (143)
T ss_pred HHHCCCCHHHHHHHHHHHHCCCEE--ECCCCCCEECCCC
T ss_conf 220346389999999998679646--5799762437210
No 217
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=68.85 E-value=11 Score=19.26 Aligned_cols=110 Identities=11% Similarity=0.099 Sum_probs=69.5
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCC--HHHHHHHHCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 5999999819978999999999932590573156545400023721260--99999997187631114688778887656
Q gi|254780620|r 26 RISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQIT--ILDVVKATEESFFVAECFASHKIDCPLVG 103 (144)
Q Consensus 26 s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~It--l~dI~~aie~~~~~~~C~~~~~~~C~~~~ 103 (144)
.+.++|+.+|+||.-+.+.++.|. |...|--.|-|.. ..+++. |-.+-.-++....+-++..+....-+...
T Consensus 2 kT~~vAk~LGVspkTVQRWvKq~n----i~~~rNE~GHy~F--t~e~l~~lLk~~~~q~~qg~~~~~~~~~~~~~~~~~~ 75 (178)
T PRK13182 2 KTPFVAKKLGVSPKTVQRWVKQLN----LPIERNEYGHYIF--TEDDLDQLLKYHRSQIEQGQNMQDTQKPSSNDVEELK 75 (178)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHC----CCCCCCCCCCEEE--CHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
T ss_conf 717889993999299999999958----9955365544332--4989999999999986057545656566676642112
Q ss_pred C-----------C----------CHHHHHHHHHHHHHHHHHHCCHHHHHHCHHHHHHHH
Q ss_conf 6-----------4----------479999999999999984179999991589899952
Q gi|254780620|r 104 S-----------C----------GLTSVLRKALNAFFDVLTQYSIECLVRNRSSIKKIF 141 (144)
Q Consensus 104 ~-----------c----------~~~~~~~~~~~~~~~~L~~~TL~dl~~~~~~~~~l~ 141 (144)
. - .+..-++++++.+.+.-+.+-=-.|+..++.++.++
T Consensus 76 ~~~~~~~q~~~s~~~E~le~~l~~~~~Rl~~LE~qL~qKADDVVSyQLLqHRrEiEEm~ 134 (178)
T PRK13182 76 TQVNTIVQNISSHDFEQLEAQLNTITRRLDELEEQLQQKADDVVSYQLLQHRREMEEML 134 (178)
T ss_pred CCCCHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEHHHHHHHHHHHHHHH
T ss_conf 34311322666540999999999999999999999986423200189998799999999
No 218
>KOG2268 consensus
Probab=68.82 E-value=5.7 Score=20.91 Aligned_cols=77 Identities=21% Similarity=0.188 Sum_probs=57.3
Q ss_pred HHHH--HHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCC-CCCCCEECCCH------HHCCHHHHHHH
Q ss_conf 9999--999855986335999999819978999999999932590573156-54540002372------12609999999
Q gi|254780620|r 11 IRVL--MYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRG-RRGGVRLCRPA------DQITILDVVKA 81 (144)
Q Consensus 11 i~~l--~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG-~~GGy~Lak~~------~~Itl~dI~~a 81 (144)
+|+| +.+...+.+.++..-|+...++-.....|++..|.|..+|.-.|+ ..-||+|.-.. ..++..+++..
T Consensus 16 FRvLtAvEmgmrnHEiVP~~li~~ia~ik~gg~~k~l~dL~KhkLia~~r~~k~dGYRLTy~GyDyLAlktL~~R~~v~s 95 (465)
T KOG2268 16 FRVLTAVEMGMRNHEIVPTPLIASIAGIKGGGVTKVLSDLCKHKLIAYERNKKYDGYRLTYAGYDYLALKTLSNRGSVES 95 (465)
T ss_pred HHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCHHHHHHHHHHCCHHHH
T ss_conf 58999998740367536689999998502675689999999767787641454453476425612999998873320564
Q ss_pred HCCCCC
Q ss_conf 718763
Q gi|254780620|r 82 TEESFF 87 (144)
Q Consensus 82 ie~~~~ 87 (144)
++..+-
T Consensus 96 vGnqIG 101 (465)
T KOG2268 96 VGNQIG 101 (465)
T ss_pred HCCCCC
T ss_conf 333234
No 219
>pfam01399 PCI PCI domain. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15).
Probab=68.63 E-value=11 Score=19.24 Aligned_cols=48 Identities=21% Similarity=0.085 Sum_probs=36.9
Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCC
Q ss_conf 9999998559863359999998199789999999999325905731565
Q gi|254780620|r 12 RVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGR 60 (144)
Q Consensus 12 ~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~ 60 (144)
+++..++. +-..++.++||+..++|...++.++..+-..|.|+..=-.
T Consensus 49 ~~l~~~~~-~y~~i~~~~ia~~l~i~~~~vE~~l~~~I~~g~i~~kID~ 96 (105)
T pfam01399 49 LNLRQLAK-PYSSISLSDLAKLLGLSVDEVEKILSKLIRDGRIRGKIDQ 96 (105)
T ss_pred HHHHHHHH-HHHHCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEEC
T ss_conf 99999976-5754119889988299999999999999977988999958
No 220
>pfam08784 RPA_C Replication protein A C terminal. This domain 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.
Probab=68.11 E-value=11 Score=19.17 Aligned_cols=51 Identities=12% Similarity=0.044 Sum_probs=40.0
Q ss_pred HHHHHHHHHHHHH--CCCCCCCHHHHHHHH-CCCHHHHHHHHHHHHHCCCEEEC
Q ss_conf 8999999999985--598633599999981-99789999999999325905731
Q gi|254780620|r 7 TDYGIRVLMYCAI--HNDYPNRISQIAEAC-CISELFLFKILQPLVKAGIVETV 57 (144)
Q Consensus 7 ~~yAi~~l~~La~--~~~~~~s~~eIA~~~-~i~~~~l~kil~~L~~agli~S~ 57 (144)
+.-+=+++-+|.. +.++-++..+|+.++ ++|..-+++.+..|...|+|=|+
T Consensus 46 s~~~~~V~~~i~~~~~~~eG~h~~~l~~~l~~~~~~~i~~a~d~L~~eG~IYsT 99 (103)
T pfam08784 46 TPLQDQVLNLIKQSCPGEEGVHVDELAAQLNGLPVNDIRQAVDFLSNEGHIYST 99 (103)
T ss_pred CHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHCCEEEEC
T ss_conf 899999999999548898872799999998299999999999999848806642
No 221
>COG3177 Fic family protein [Function unknown]
Probab=68.07 E-value=11 Score=19.17 Aligned_cols=45 Identities=22% Similarity=0.239 Sum_probs=34.7
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCE
Q ss_conf 986335999999819978999999999932590573156545400
Q gi|254780620|r 21 NDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVR 65 (144)
Q Consensus 21 ~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~ 65 (144)
.++..++.+++...++|.+-+.+-++.|.+-|+++.+.+++=+|.
T Consensus 301 ~~~~~t~~~~~~~~~~s~~Ta~r~l~~l~~~g~l~~~~~~~r~~~ 345 (348)
T COG3177 301 QEGYLTAAEIEAILGVSKATATRDLKELLELGILEEVKGRGRSKL 345 (348)
T ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCCCCCEE
T ss_conf 267645999999828988889999999974770566588987101
No 222
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=67.89 E-value=11 Score=19.14 Aligned_cols=70 Identities=26% Similarity=0.269 Sum_probs=52.5
Q ss_pred HHHHHHHHHHHCCCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHCCCEEECC----CCCCCCEECCCHHHCCHHHHHHHHC
Q ss_conf 999999999855986335999999819-97899999999993259057315----6545400023721260999999971
Q gi|254780620|r 9 YGIRVLMYCAIHNDYPNRISQIAEACC-ISELFLFKILQPLVKAGIVETVR----GRRGGVRLCRPADQITILDVVKATE 83 (144)
Q Consensus 9 yAi~~l~~La~~~~~~~s~~eIA~~~~-i~~~~l~kil~~L~~agli~S~r----G~~GGy~Lak~~~~Itl~dI~~aie 83 (144)
+.+.++-.|.. ++....+|-...+ +++..|.+-|+.|.+.|+|.=+- .+.=.|+|..- --+|..|+.++.
T Consensus 24 W~~lIl~~L~~---g~~RF~eL~r~i~~Is~k~Ls~~Lk~Le~~Glv~R~~~~~~PprveY~LT~~--G~~L~~vl~~l~ 98 (120)
T COG1733 24 WTLLILRDLFD---GPKRFNELRRSIGGISPKMLSRRLKELEEDGLVERVVYPEEPPRVEYRLTEK--GRDLLPVLLALA 98 (120)
T ss_pred CHHHHHHHHHC---CCCCHHHHHHHCCCCCHHHHHHHHHHHHHCCCEEEEECCCCCCEEEEEEHHH--HHHHHHHHHHHH
T ss_conf 49999999954---9873999986774548999999999999889989874178995347776343--276999999999
No 223
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that 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. This subgroup lacks one of the c
Probab=67.84 E-value=11 Score=19.14 Aligned_cols=62 Identities=15% Similarity=0.300 Sum_probs=40.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHHH-CCCCCCCCC
Q ss_conf 3599999981997899999999993259057315654540002372126099999997-187631114
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKAT-EESFFVAEC 91 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~ai-e~~~~~~~C 91 (144)
+++.|+|+..|+|+..+ .---+.|+|.+.+-..|||+.=- .+++.-...++.. +-.+.+-+.
T Consensus 1 M~Ige~A~~~gvs~~Tl----RyYe~~GLl~p~~r~~~GyR~Y~-~~~~~~l~~I~~~r~~G~sL~eI 63 (133)
T cd04787 1 MKVKELANAAGVTPDTV----RFYTRIGLLRPTRDPVNGYRLYS-EKDLSRLRFILSARQLGFSLKDI 63 (133)
T ss_pred CCHHHHHHHHCCCHHHH----HHHHHCCCCCCCCCCCCCCEECH-HHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 96899999989789999----99998599988622899945132-99999999999999869999999
No 224
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=67.11 E-value=12 Score=19.05 Aligned_cols=73 Identities=19% Similarity=0.262 Sum_probs=55.5
Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHC-----CHHHHHHHHCCCC
Q ss_conf 99999985598633599999981997899999999993259057315654540002372126-----0999999971876
Q gi|254780620|r 12 RVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQI-----TILDVVKATEESF 86 (144)
Q Consensus 12 ~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~I-----tl~dI~~aie~~~ 86 (144)
.+|+.|. ++|-|.+||-+..+++++-+..-+.+|...|+|.-. ++=|+|+--.+-| .+.+.++++|+..
T Consensus 17 ~lLllL~---egPkti~EI~~~l~vs~~ai~pqiKkL~~~~LV~~~---~~~Y~LS~~G~iiv~km~~ll~tl~v~e~n~ 90 (260)
T COG4742 17 DLLLLLK---EGPKTIEEIKNELNVSSSAILPQIKKLKDKGLVVQE---GDRYSLSSLGKIIVEKMEPLLDTLEVFEENY 90 (260)
T ss_pred HHHHHHH---HCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCEEEC---CCEEEECCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999998---589889999988589938889999987138987851---9998734008999999999999999997314
Q ss_pred CCCC
Q ss_conf 3111
Q gi|254780620|r 87 FVAE 90 (144)
Q Consensus 87 ~~~~ 90 (144)
.+..
T Consensus 91 dyW~ 94 (260)
T COG4742 91 DYWS 94 (260)
T ss_pred HHHH
T ss_conf 6774
No 225
>pfam00376 MerR MerR family regulatory protein.
Probab=66.79 E-value=6.8 Score=20.45 Aligned_cols=37 Identities=27% Similarity=0.317 Sum_probs=28.6
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEE
Q ss_conf 59999998199789999999999325905731565454000
Q gi|254780620|r 26 RISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRL 66 (144)
Q Consensus 26 s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~L 66 (144)
|+.|+|+..++|+..|+. .-+.|++.+.+-..|||++
T Consensus 1 ti~e~A~~~gvs~~tlR~----ye~~Gli~~~~r~~~g~R~ 37 (38)
T pfam00376 1 TIGEVAKLLGVSPRTLRY----YEKIGLLPPPRRTEGGYRR 37 (38)
T ss_pred CHHHHHHHHCCCHHHHHH----HHHCCCCCCCCCCCCCCCC
T ss_conf 989999998879999999----9986898998769998117
No 226
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=66.17 E-value=12 Score=18.94 Aligned_cols=36 Identities=17% Similarity=0.117 Sum_probs=25.5
Q ss_pred HHHHHHHHC-CCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 999999855-986335999999819978999999999
Q gi|254780620|r 12 RVLMYCAIH-NDYPNRISQIAEACCISELFLFKILQP 47 (144)
Q Consensus 12 ~~l~~La~~-~~~~~s~~eIA~~~~i~~~~l~kil~~ 47 (144)
++.-|+..| .+.-.|.+.||+..++|+.||.+++..
T Consensus 202 r~~~~I~~nL~dp~Ls~~~iA~~~giS~R~L~rlF~~ 238 (303)
T PRK09685 202 KAVALIDQSIQEEILRPEWIAGELGISVRSLYRLFAE 238 (303)
T ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 9999999863899989999999979999999999998
No 227
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family.
Probab=65.49 E-value=13 Score=18.86 Aligned_cols=63 Identities=14% Similarity=0.074 Sum_probs=50.8
Q ss_pred HHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECC-CCCCCCEECCCHHHCCHHHHHHHHCCCC
Q ss_conf 99985598633599999981997899999999993259057315-6545400023721260999999971876
Q gi|254780620|r 15 MYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVR-GRRGGVRLCRPADQITILDVVKATEESF 86 (144)
Q Consensus 15 ~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~r-G~~GGy~Lak~~~~Itl~dI~~aie~~~ 86 (144)
-.|+.+-|..-|..|||+..++++.-|+.++..-+..==++..= |.. ++..|+|++..-++..
T Consensus 204 ReL~q~lGR~Ps~~EiAe~lel~~~qvR~~l~~~~~p~SLd~~VrG~e---------~dt~LgdLl~d~~~~~ 267 (336)
T TIGR02997 204 RELSQKLGRRPSEAEIAEALELEPEQVRELLQRARQPVSLDTRVRGDE---------EDTELGDLLEDEDGES 267 (336)
T ss_pred HHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCC---------CCCHHHHHCCCCCCCC
T ss_conf 999998388978689998838898899999997078744577326888---------5422654326888998
No 228
>PRK09775 hypothetical protein; Provisional
Probab=63.98 E-value=14 Score=18.69 Aligned_cols=64 Identities=16% Similarity=0.163 Sum_probs=50.2
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHHH-CCCCC
Q ss_conf 633599999981997899999999993259057315654540002372126099999997-18763
Q gi|254780620|r 23 YPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKAT-EESFF 87 (144)
Q Consensus 23 ~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~ai-e~~~~ 87 (144)
+|.++.+|++++++|.+.+.+.+..|. ..+|+--+|+.=.|.|.++..-.+-.-+|++= +|..+
T Consensus 11 Gp~~a~eLa~~lgvSqpTlSR~l~~l~-~~Vv~~G~aR~trYAl~r~~rg~~~~plyrVD~~G~a~ 75 (443)
T PRK09775 11 GPLSAAELAQRLGISQATLSRLLAAAG-PQVLRFGKARATRYALLRPVRGGEAFPLYRVDEDGRAH 75 (443)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHCC-CCEEEECCCCCCEEEECCCCCCCCCCCEEEECCCCCCC
T ss_conf 993599999986888888999998625-72788545543000012565775656317877888620
No 229
>COG1386 scpB Chromosome segregation and condensation protein B [DNA replication, recombination and repair]
Probab=63.85 E-value=14 Score=18.67 Aligned_cols=56 Identities=21% Similarity=0.213 Sum_probs=37.2
Q ss_pred CCCCCCHHHHHHHHCC-CHHHHHHHHHHHHHCCCEEECCC-----CCCCCEECCCHHHCCHHHHHHHH
Q ss_conf 9863359999998199-78999999999932590573156-----54540002372126099999997
Q gi|254780620|r 21 NDYPNRISQIAEACCI-SELFLFKILQPLVKAGIVETVRG-----RRGGVRLCRPADQITILDVVKAT 82 (144)
Q Consensus 21 ~~~~~s~~eIA~~~~i-~~~~l~kil~~L~~agli~S~rG-----~~GGy~Lak~~~~Itl~dI~~ai 82 (144)
.++|+|.++|++..++ +...+.+++..|...- .-|| .++||++.-.|+ ..|.+..+
T Consensus 20 ~~~pls~~~L~~il~~~~~~~~~~~l~~l~~~y---~~rg~~L~~~~~~~r~~t~~~---~~~~~~~l 81 (184)
T COG1386 20 GGEPLSLKELAEILGIVSADAIIDALAELKEEY---EDRGLELVEVAEGWRLQTKQE---YAEYLEKL 81 (184)
T ss_pred CCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHH---CCCCEEEEEECCCEEEEEHHH---HHHHHHHH
T ss_conf 479978999999868884788999999999862---579804999737156776377---89999998
No 230
>COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]
Probab=63.82 E-value=11 Score=19.31 Aligned_cols=51 Identities=35% Similarity=0.391 Sum_probs=34.7
Q ss_pred CCCCCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHH
Q ss_conf 86335999999819--------------978999999999932590573156545400023721260999
Q gi|254780620|r 22 DYPNRISQIAEACC--------------ISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILD 77 (144)
Q Consensus 22 ~~~~s~~eIA~~~~--------------i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~d 77 (144)
++++.++.++..+| -+.+..++|||.|-++|+|+-++ +|-.|+ |+-=|+.|
T Consensus 65 ~gpvGi~rL~t~YGg~k~rG~rP~~~~~gsgsI~RkilqqLE~~G~V~k~~---~GR~lt--p~GrsllD 129 (147)
T COG2238 65 DGPVGIERLRTAYGGRKNRGSRPEKFRKGSGSIIRKVLQQLEKAGLVEKTP---KGRVLT--PKGRSLLD 129 (147)
T ss_pred CCCHHHHHHHHHHCCCCCCCCCCHHHHCCCCHHHHHHHHHHHHCCCEEECC---CCCEEC--CCCHHHHH
T ss_conf 376019999998786666888943442377369999999999778565268---986508--13065899
No 231
>PRK00696 sucC succinyl-CoA synthetase subunit beta; Provisional
Probab=63.44 E-value=12 Score=19.10 Aligned_cols=25 Identities=32% Similarity=0.666 Sum_probs=20.6
Q ss_pred HHCCCEEECCCCCCCCEECCCHHHC
Q ss_conf 3259057315654540002372126
Q gi|254780620|r 49 VKAGIVETVRGRRGGVRLCRPADQI 73 (144)
Q Consensus 49 ~~agli~S~rG~~GGy~Lak~~~~I 73 (144)
.|+.+...-||+.||..++++|++.
T Consensus 45 vKAQV~aGGRGKaGGVk~~~s~~ea 69 (388)
T PRK00696 45 VKAQVHAGGRGKAGGVKVAKSKEEV 69 (388)
T ss_pred EEEEECCCCCCCCCEEEEECCHHHH
T ss_conf 9980545888868607990899999
No 232
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=63.28 E-value=12 Score=18.98 Aligned_cols=38 Identities=18% Similarity=0.110 Sum_probs=33.4
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECC
Q ss_conf 98633599999981997899999999993259057315
Q gi|254780620|r 21 NDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVR 58 (144)
Q Consensus 21 ~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~r 58 (144)
....+|--.||+.+|++-+..++||..|.+.|+|.-+-
T Consensus 59 k~k~VTPy~La~K~~I~~SvArkvLr~L~~rG~l~lvs 96 (107)
T PRK09334 59 KEKIVTPYTLASKYGIKISVAKKVLRELEKRGVLVLYS 96 (107)
T ss_pred CCCEECHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEE
T ss_conf 48367589999885710899999999999789789981
No 233
>TIGR02545 ATP_syn_fliI flagellar protein export ATPase FliI; InterPro: IPR013379 FliI proteins are involved in bacterial flagellum systems, acting to drive protein export for flagellar biosynthesis. The most closely related proteins are the YscN proteins of bacterial type III secretion systems.; GO: 0016887 ATPase activity, 0001539 ciliary or flagellar motility, 0009296 flagellum biogenesis, 0009288 flagellin-based flagellum.
Probab=62.82 E-value=14 Score=18.56 Aligned_cols=122 Identities=11% Similarity=0.142 Sum_probs=79.5
Q ss_pred HHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCC---CCCCCEECCCHHHC--CHHHHHHHH-CCCCCCC
Q ss_conf 99855986335999999819978999999999932590573156---54540002372126--099999997-1876311
Q gi|254780620|r 16 YCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRG---RRGGVRLCRPADQI--TILDVVKAT-EESFFVA 89 (144)
Q Consensus 16 ~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG---~~GGy~Lak~~~~I--tl~dI~~ai-e~~~~~~ 89 (144)
.+++..|+|=+++ |=||+-..++-+.+=++|++...+| ..|=|.---+-++. .+.|.++.+ ||.+-+.
T Consensus 266 EigLa~GEPP~tk------GYpPSVF~~Lp~L~ERaG~~p~~~~~GsITa~yTVLVeGDD~~ePiAD~~RgiLDGHIvLs 339 (439)
T TIGR02545 266 EIGLAAGEPPTTK------GYPPSVFSELPRLLERAGIVPGAKGGGSITAFYTVLVEGDDMNEPIADAVRGILDGHIVLS 339 (439)
T ss_pred HHHHHCCCCCCCC------CCCCHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEEEEECCCCCCHHHHHHHHHCCCEEEEC
T ss_conf 9998717876667------8970489999999987086469888730568999987368998737877500102207732
Q ss_pred CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHCHHHHHHHHCCC
Q ss_conf 1468877888765664479999999999999984179999991589899952789
Q gi|254780620|r 90 ECFASHKIDCPLVGSCGLTSVLRKALNAFFDVLTQYSIECLVRNRSSIKKIFNAG 144 (144)
Q Consensus 90 ~C~~~~~~~C~~~~~c~~~~~~~~~~~~~~~~L~~~TL~dl~~~~~~~~~l~~~~ 144 (144)
.-..+....-++.-.-.+.+++.++-..-... ....+..|+...+..+.|.+.|
T Consensus 340 R~lA~~G~YPaIDvl~SiSR~m~~i~~~e~~~-~a~~~r~l~a~Y~~~eDLi~iG 393 (439)
T TIGR02545 340 RKLAERGHYPAIDVLRSISRLMPDIVSPEHNK-AARKLRKLLATYKDAEDLIRIG 393 (439)
T ss_pred HHHHHCCCCCCCCCCHHHHHHHHHHCCHHHHH-HHHHHHHHHHHHHHHHHHHHHC
T ss_conf 26764588987572222788777627988999-9999999999888889999817
No 234
>TIGR02018 his_ut_repres histidine utilization repressor; InterPro: IPR010248 This entry represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.; GO: 0003677 DNA binding, 0016564 transcription repressor activity, 0006547 histidine metabolic process, 0045892 negative regulation of transcription DNA-dependent.
Probab=62.69 E-value=13 Score=18.83 Aligned_cols=61 Identities=18% Similarity=0.318 Sum_probs=46.6
Q ss_pred CCCCCCH-HHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECC--CHHHCC--HHHHHHHHC
Q ss_conf 9863359-99999819978999999999932590573156545400023--721260--999999971
Q gi|254780620|r 21 NDYPNRI-SQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCR--PADQIT--ILDVVKATE 83 (144)
Q Consensus 21 ~~~~~s~-~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak--~~~~It--l~dI~~aie 83 (144)
+|..+.+ .||.+.+|+|+=.+-|-|..|.++|+|.=.+|.+ =| -+. +-.+=+ |.+|=.+-+
T Consensus 21 ~g~R~PsE~EL~~~~G~SRMTvnrALreLt~~G~l~R~qg~G-TF-VA~ae~k~~s~qvll~i~nIa~ 86 (234)
T TIGR02018 21 PGHRIPSENELVAQFGVSRMTVNRALRELTDAGLLERRQGVG-TF-VARAEPKAQSAQVLLEIRNIAD 86 (234)
T ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCE-EE-ECCCCCCCCCHHHHHCCCCHHH
T ss_conf 767568779999774872335789999887568188127850-04-4177765310144202566489
No 235
>pfam01638 HxlR HxlR-like helix-turn-helix. HxlR, a member of this family, is a DNA-binding protein that acts as a positive regulator of the formaldehyde-inducible hxlAB operon in Bacillus subtilis.
Probab=62.49 E-value=14 Score=18.53 Aligned_cols=70 Identities=20% Similarity=0.242 Sum_probs=50.0
Q ss_pred HHHHHHHHHHHCCCCCCCHHHHHHHH-CCCHHHHHHHHHHHHHCCCEEEC--C--CCCCCCEECCCHHHCCHHHHHHHHC
Q ss_conf 99999999985598633599999981-99789999999999325905731--5--6545400023721260999999971
Q gi|254780620|r 9 YGIRVLMYCAIHNDYPNRISQIAEAC-CISELFLFKILQPLVKAGIVETV--R--GRRGGVRLCRPADQITILDVVKATE 83 (144)
Q Consensus 9 yAi~~l~~La~~~~~~~s~~eIA~~~-~i~~~~l~kil~~L~~agli~S~--r--G~~GGy~Lak~~~~Itl~dI~~aie 83 (144)
..+.++-.|. . ++..-.+|.+.. ++|+..|.+=|..|..+|+|+-+ . .+.=-|+|... -.++..|+.++.
T Consensus 6 Wt~~Il~~L~--~-g~~rF~el~~~l~gis~~vLs~rLk~L~~~gli~r~~~~~~p~~~eY~LT~~--G~~l~pvl~~l~ 80 (90)
T pfam01638 6 WKLLILRELL--D-GPKRFSELKRALPGISQKMLTQRLRELEQDGIINREVYPEVPPKVEYSLTEK--GRSLEPILQAMC 80 (90)
T ss_pred CHHHHHHHHH--C-CCCCHHHHHHHCCCCCHHHHHHHHHHHHHCCCEEEEECCCCCCCEEEEECCC--HHHHHHHHHHHH
T ss_conf 7999999997--4-9988999997765769899999999999889937645699999368743907--878999999999
No 236
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=62.03 E-value=13 Score=18.76 Aligned_cols=39 Identities=18% Similarity=0.133 Sum_probs=33.9
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCC
Q ss_conf 986335999999819978999999999932590573156
Q gi|254780620|r 21 NDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRG 59 (144)
Q Consensus 21 ~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG 59 (144)
....+|...|+.+.+|+-+..+++|..|...|.|.-+-+
T Consensus 56 ~~r~VTpy~la~r~gI~~SvAr~vLR~LeeeGvv~lvsk 94 (107)
T COG4901 56 RERVVTPYVLASRYGINGSVARIVLRHLEEEGVVQLVSK 94 (107)
T ss_pred CCEEECHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECC
T ss_conf 451554999888855525899999999876774440016
No 237
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family; InterPro: IPR014284 The bacterial core RNA polymerase complex, which consists of five subunits, 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 . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry is found in all varieties of the sigma-70 type sigma factors, including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (IPR000394 from INTERPRO) are included within this entry. ; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=61.53 E-value=15 Score=18.42 Aligned_cols=35 Identities=23% Similarity=0.057 Sum_probs=25.1
Q ss_pred HHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 9999855986335999999819978999999999932
Q gi|254780620|r 14 LMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVK 50 (144)
Q Consensus 14 l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~ 50 (144)
++.|..-. ..|.+|||+.+|+|+.-+++.++.-++
T Consensus 122 ~~~l~~~~--~~s~~eIA~~lg~s~~~v~~~~~ra~~ 156 (162)
T TIGR02937 122 VLVLRYLE--GLSYKEIAEILGISEGTVKSRLKRARK 156 (162)
T ss_pred HHHHHHHH--CCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 99999971--899889999868999999999999999
No 238
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=61.50 E-value=15 Score=18.42 Aligned_cols=58 Identities=12% Similarity=0.094 Sum_probs=42.0
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCC
Q ss_conf 99999998559863359999998199789999999999325905731565454000237
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRP 69 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~ 69 (144)
.|.+..++. .=..+|.+.||+..+++...+++++..+...|.|...=-..-|+.--.+
T Consensus 12 ~~~l~~~~~-~Y~~is~~~la~~l~l~~~~vE~~l~~~I~~~~l~akIDq~~g~v~f~~ 69 (88)
T smart00088 12 LTNLLQLSE-PYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEE 69 (88)
T ss_pred HHHHHHHHH-HHCEEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEECCCCEEEECC
T ss_conf 999999977-6242569999989492999999999999967977999808999898668
No 239
>smart00753 PAM PCI/PINT associated module.
Probab=61.50 E-value=15 Score=18.42 Aligned_cols=58 Identities=12% Similarity=0.094 Sum_probs=42.0
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCC
Q ss_conf 99999998559863359999998199789999999999325905731565454000237
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRP 69 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~ 69 (144)
.|.+..++. .=..+|.+.||+..+++...+++++..+...|.|...=-..-|+.--.+
T Consensus 12 ~~~l~~~~~-~Y~~is~~~la~~l~l~~~~vE~~l~~~I~~~~l~akIDq~~g~v~f~~ 69 (88)
T smart00753 12 LTNLLQLSE-PYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEE 69 (88)
T ss_pred HHHHHHHHH-HHCEEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEECCCCEEEECC
T ss_conf 999999977-6242569999989492999999999999967977999808999898668
No 240
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. 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 su
Probab=61.27 E-value=15 Score=18.39 Aligned_cols=62 Identities=15% Similarity=0.312 Sum_probs=41.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHHH-CCCCCCCCC
Q ss_conf 3599999981997899999999993259057315654540002372126099999997-187631114
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKAT-EESFFVAEC 91 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~ai-e~~~~~~~C 91 (144)
+++.|+|+..|+|..-+ .---+.|++.+.+-..+||+.=- ++++.-...++.. .-.+.+-++
T Consensus 1 M~IgelA~~~gvs~~tl----R~YE~~GLl~p~~r~~nGyR~Y~-~~~i~~l~~I~~~r~lGfsL~eI 63 (131)
T cd04786 1 MKIGELAKRSGMAASRI----RFYEAEGLLSSVERSANGYRDYP-PETVWVLEIISSAQQAGFSLDEI 63 (131)
T ss_pred CCHHHHHHHHCCCHHHH----HHHHHCCCCCCCCCCCCCCEEEC-HHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 97899999988788999----99997799898776999975349-99999999999999969999999
No 241
>COG5111 RPC34 DNA-directed RNA polymerase III, subunit C34 [Transcription]
Probab=61.21 E-value=11 Score=19.25 Aligned_cols=59 Identities=17% Similarity=0.210 Sum_probs=47.3
Q ss_pred CCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCC
Q ss_conf 64568999999999985598633599999981997899999999993259057315654
Q gi|254780620|r 3 LTKRTDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRR 61 (144)
Q Consensus 3 is~~~~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~ 61 (144)
+++-.+|-..+--++...+++.+=.+.|-.+++++...+-|.|..|-...+|+|++-.+
T Consensus 80 ~~tm~~~E~~vYs~i~~SG~EGiW~Ktik~rTNlh~~vV~kcLkSlESkr~vKSvKsvK 138 (301)
T COG5111 80 INTMDDYELTVYSLISQSGGEGIWLKTIKDRTNLHHNVVGKCLKSLESKRIVKSVKSVK 138 (301)
T ss_pred CCCCCHHHHHHHHHHHHCCCCCEEHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 56445589999999986388744133444422673899999998888778898766504
No 242
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=60.46 E-value=16 Score=18.31 Aligned_cols=46 Identities=17% Similarity=0.228 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHHHH-CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Q ss_conf 68999999999985-59863359999998199789999999999325
Q gi|254780620|r 6 RTDYGIRVLMYCAI-HNDYPNRISQIAEACCISELFLFKILQPLVKA 51 (144)
Q Consensus 6 ~~~yAi~~l~~La~-~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~a 51 (144)
..+.-+-+.+|+|- ..+-|.|..|||+..+++..-+.|....|.+.
T Consensus 163 ~~~~i~AAclY~ACR~~~~prtl~Eia~~~~i~~k~i~r~~~~l~~~ 209 (310)
T PRK00423 163 SIEGVVAAALYAACRRCKVPRTLDEIAEVSRVSRKEIGRTYRFLARE 209 (310)
T ss_pred CHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf 47778999999999976999749999999598899999999999998
No 243
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. 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. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=60.06 E-value=16 Score=18.27 Aligned_cols=63 Identities=16% Similarity=0.213 Sum_probs=42.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHHHCCCCCCCCC
Q ss_conf 3599999981997899999999993259057315654540002372126099999997187631114
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKATEESFFVAEC 91 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~aie~~~~~~~C 91 (144)
.|+.|+|+..|+|+..+ .---+.|++.+.|-..+||+.=-+-+=-.+..|...-+-...+.++
T Consensus 1 mtIgelAk~~gvs~~tl----RyYE~~GLl~p~r~~~~gyR~Y~~~~i~~l~~I~~lr~~G~sl~eI 63 (108)
T cd04773 1 MTIGELAHLLGVPPSTL----RHWEKEGLLSPDREPETGYRVYDPSDVRDARLIHLLRRGGYLLEQI 63 (108)
T ss_pred CCHHHHHHHHCCCHHHH----HHHHHCCCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 96899999989799999----9999779829987799985467999999999999999969999999
No 244
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=59.97 E-value=16 Score=18.32 Aligned_cols=72 Identities=24% Similarity=0.260 Sum_probs=48.1
Q ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHH--------------HHHHHHCCCEEECCCCCCCCEECCCHH
Q ss_conf 689999999999855986335999999819978999999--------------999932590573156545400023721
Q gi|254780620|r 6 RTDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKI--------------LQPLVKAGIVETVRGRRGGVRLCRPAD 71 (144)
Q Consensus 6 ~~~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~ki--------------l~~L~~agli~S~rG~~GGy~Lak~~~ 71 (144)
-.||+-++.- |.+. .-+|-++||+.++...+.+.+| |-++-.=-+++...+...+ .-.++-.
T Consensus 77 vedY~e~Ir~--ARE~-~G~SqedLA~ki~ek~svI~~iE~g~~~P~~~~akkLEk~LgIkL~e~~~~~~~~-~~~~~~~ 152 (165)
T COG1813 77 VEDYGERIRE--AREK-RGLSQEDLAAKLKEKVSVIRRIERGEATPNIKVAKKLEKLLGIKLVEKVDEEEEG-PKGKDDD 152 (165)
T ss_pred HHHHHHHHHH--HHHH-CCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHHHHHCCEEEEECCCCCCC-CCCCCCC
T ss_conf 8779999999--9998-2888999999965469999999841367558899999998585522003555446-5667767
Q ss_pred HCCHHHHHHH
Q ss_conf 2609999999
Q gi|254780620|r 72 QITILDVVKA 81 (144)
Q Consensus 72 ~Itl~dI~~a 81 (144)
.+||+||++.
T Consensus 153 ~~TLGdiv~i 162 (165)
T COG1813 153 GLTLGDIVRI 162 (165)
T ss_pred CCCCCCEEEE
T ss_conf 8753244875
No 245
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=59.91 E-value=16 Score=18.25 Aligned_cols=46 Identities=26% Similarity=0.149 Sum_probs=31.3
Q ss_pred CCCCHHHHHHHHHHHHHHHC-CCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 97645689999999999855-9863359999998199789999999999
Q gi|254780620|r 1 MHLTKRTDYGIRVLMYCAIH-NDYPNRISQIAEACCISELFLFKILQPL 48 (144)
Q Consensus 1 Mkis~~~~yAi~~l~~La~~-~~~~~s~~eIA~~~~i~~~~l~kil~~L 48 (144)
|-+|+.-.-+-+ -.|+.+ .--+.|.++||+.+++++..++||++.-
T Consensus 1 MSLn~eq~~~Tk--~elqan~el~~LS~~~iA~~Ln~t~~~lekil~~t 47 (97)
T COG4367 1 MSLNPEQKQRTK--QELQANFELCPLSDEEIATALNWTEVKLEKILQVT 47 (97)
T ss_pred CCCCHHHHHHHH--HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 988989999889--99997544064529999999588799999999885
No 246
>COG1167 ARO8 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]
Probab=59.72 E-value=16 Score=18.23 Aligned_cols=54 Identities=17% Similarity=0.196 Sum_probs=40.7
Q ss_pred HHHHHHHHHHHH-HCCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCC
Q ss_conf 899999999998-5598-63359999998199789999999999325905731565
Q gi|254780620|r 7 TDYGIRVLMYCA-IHND-YPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGR 60 (144)
Q Consensus 7 ~~yAi~~l~~La-~~~~-~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~ 60 (144)
.-..|+-.+.=. ..++ +.-|..++|+..+++...+.+-...|...|+|.|..|.
T Consensus 9 l~~~i~~~I~~g~l~~g~rLPs~R~la~~l~vs~~Tv~~ay~~L~~~G~i~~~~gs 64 (459)
T COG1167 9 LAEQLREAILSGRLKPGDRLPSIRQLAQDLGVSRSTVSRAYEELEARGYIESRPGS 64 (459)
T ss_pred HHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCC
T ss_conf 99999999976987898918766999999487488999999999976785512566
No 247
>PRK06654 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=59.17 E-value=17 Score=18.18 Aligned_cols=109 Identities=13% Similarity=0.010 Sum_probs=64.8
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC-------CC--------EEECCCCCCCCEEC-----CCHHHCCHHHHHHHHCCC
Q ss_conf 59999998199789999999999325-------90--------57315654540002-----372126099999997187
Q gi|254780620|r 26 RISQIAEACCISELFLFKILQPLVKA-------GI--------VETVRGRRGGVRLC-----RPADQITILDVVKATEES 85 (144)
Q Consensus 26 s~~eIA~~~~i~~~~l~kil~~L~~a-------gl--------i~S~rG~~GGy~La-----k~~~~Itl~dI~~aie~~ 85 (144)
.+..=+++.|..|..+.+|+..|..- ++ +.|.+|..+++..- .+|.-+..++.+..+-+.
T Consensus 11 ~~~~~~kr~GllP~li~wIl~~laaiifiv~v~~it~~~vsk~v~s~~g~~~t~~~vs~ey~~~~p~L~~Y~~~~e~r~n 90 (177)
T PRK06654 11 LGASAAKRVGLLPDLIIWILQILAIGIFTVTVMIIVSYFVSKMVVSQSGAPHTFPPFSNEYLEKRPMLIWYESIDEIRGN 90 (177)
T ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEHHHHHHHCCCCCCCCCCCHHHCCCCCHHHHHHHCCHHCCC
T ss_conf 45642002486769999999999999885422567644211567750268888675325550588633554311331045
Q ss_pred ------CCCCCCCCCCCCCCCCCCC---CCHHHHHHHHHHHHHHHHHHCCHHHHHHCHHHHH
Q ss_conf ------6311146887788876566---4479999999999999984179999991589899
Q gi|254780620|r 86 ------FFVAECFASHKIDCPLVGS---CGLTSVLRKALNAFFDVLTQYSIECLVRNRSSIK 138 (144)
Q Consensus 86 ------~~~~~C~~~~~~~C~~~~~---c~~~~~~~~~~~~~~~~L~~~TL~dl~~~~~~~~ 138 (144)
.+++-- -.- ..+.+.. -.+..-.-++.+-+..++.+.|.++| ++++.++
T Consensus 91 TaD~~~at~Vv~-~aL--GY~~n~k~l~~EL~~R~v~lkD~i~~yfs~kT~~EL-rne~qiK 148 (177)
T PRK06654 91 TADAPPKTFVVK-LAL--GYAENNVNILQELGRQKVRLKDIIREYFSQRTGQEI-KNESQIK 148 (177)
T ss_pred CCCCCCCEEEEE-EEE--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHH
T ss_conf 566787218999-874--246788779999976485899999999845109987-5189999
No 248
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family; InterPro: IPR013430 Proteins in this entry form a distinct group of helix-turn-helix proteins, which are strictly bacterial and nearly always shorter than 110 amino acids. They include the characterised member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is encoded by the upstream member of the gene pair.; GO: 0003677 DNA binding.
Probab=58.71 E-value=8.9 Score=19.77 Aligned_cols=22 Identities=23% Similarity=0.253 Sum_probs=20.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 3599999981997899999999
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQ 46 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~ 46 (144)
+|+.++|+.+++|++.+.+|++
T Consensus 21 ~s~~~LA~~LgVsr~~~sriv~ 42 (81)
T TIGR02607 21 LSVRALAKALGVSRSTLSRIVN 42 (81)
T ss_pred HHHHHHHHHCCCCHHHHHHHHH
T ss_conf 0689999870999788888874
No 249
>COG4310 Uncharacterized protein conserved in bacteria with an aminopeptidase-like domain [General function prediction only]
Probab=58.43 E-value=13 Score=18.77 Aligned_cols=44 Identities=25% Similarity=0.320 Sum_probs=32.6
Q ss_pred CHHHHHHHHHHHH--HCCCEEECCCCCCCCEECCCHHHCCHHHHHH
Q ss_conf 7899999999993--2590573156545400023721260999999
Q gi|254780620|r 37 SELFLFKILQPLV--KAGIVETVRGRRGGVRLCRPADQITILDVVK 80 (144)
Q Consensus 37 ~~~~l~kil~~L~--~agli~S~rG~~GGy~Lak~~~~Itl~dI~~ 80 (144)
+-.+|+|-.-.|+ ++|+|-|--|-+||+.+.+.-..=++.|=+-
T Consensus 230 si~wLsrnee~lkhvk~GlVlsClGD~g~~nykrtrrgna~iDki~ 275 (435)
T COG4310 230 SIVWLSRNEECLKHVKHGLVLSCLGDGGGPNYKRTRRGNALIDKIA 275 (435)
T ss_pred HHHHHHCCHHHHHHHHCCEEEEEECCCCCCCCEECCCCCHHHHHHH
T ss_conf 2456752366776543146899852789855111123533789999
No 250
>pfam01090 Ribosomal_S19e Ribosomal protein S19e.
Probab=57.64 E-value=14 Score=18.55 Aligned_cols=50 Identities=34% Similarity=0.397 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHH
Q ss_conf 335999999819--------------978999999999932590573156545400023721260999
Q gi|254780620|r 24 PNRISQIAEACC--------------ISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILD 77 (144)
Q Consensus 24 ~~s~~eIA~~~~--------------i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~d 77 (144)
++-+..++...+ -|-..++++||.|-++|||+-.. +||-.|.. +--+++|
T Consensus 66 piGV~~L~~~YGg~k~rG~~P~h~~~~Sg~iiR~~lQqLE~~glvek~~--~~GR~iT~--~G~~~LD 129 (140)
T pfam01090 66 PVGVGRLRKIYGGRKRRGVRPSHFVKGSGSIIRKALQQLEKAGLVEKDP--KGGRRLTP--QGRSDLD 129 (140)
T ss_pred CCCHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCEEECC--CCCCEECH--HHHHHHH
T ss_conf 9418899999788878998998776676279999999998788877769--99937898--6899999
No 251
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=57.10 E-value=18 Score=17.97 Aligned_cols=40 Identities=18% Similarity=0.224 Sum_probs=36.0
Q ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCC
Q ss_conf 5986335999999819978999999999932590573156
Q gi|254780620|r 20 HNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRG 59 (144)
Q Consensus 20 ~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG 59 (144)
+..+|.|..|+|+..+--++-|.+-|+.|.+-|+|.-.++
T Consensus 74 a~~~P~Si~ElAe~vgRdv~nvhr~Ls~l~~~GlI~fe~~ 113 (144)
T COG4190 74 AQEEPASINELAELVGRDVKNVHRTLSTLADLGLIFFEED 113 (144)
T ss_pred HHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEEECC
T ss_conf 7419513899999867546889899999986482787417
No 252
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147; InterPro: IPR011873 This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterised..
Probab=56.93 E-value=18 Score=17.95 Aligned_cols=59 Identities=19% Similarity=0.127 Sum_probs=44.9
Q ss_pred HHHHHHHHHHCCCCCCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEECCCC-CCCCEECCCHHH
Q ss_conf 9999999985598633599999981--99789999999999325905731565-454000237212
Q gi|254780620|r 10 GIRVLMYCAIHNDYPNRISQIAEAC--CISELFLFKILQPLVKAGIVETVRGR-RGGVRLCRPADQ 72 (144)
Q Consensus 10 Ai~~l~~La~~~~~~~s~~eIA~~~--~i~~~~l~kil~~L~~agli~S~rG~-~GGy~Lak~~~~ 72 (144)
|||-++-+- +..+-...+||..+ -||..-+++-+..|.+.|+|+ +|. .|+|....+.=.
T Consensus 131 viRe~~~~~--~~~~~~~~~la~~~~P~IS~~qvk~sl~LL~~l~li~--K~~q~G~y~~~~~~vs 192 (281)
T TIGR02147 131 VIRELVAVM--PFADDDPEELAKRLKPKISAEQVKESLDLLERLGLIK--KNEQDGFYKQTDKAVS 192 (281)
T ss_pred HHHHHHHHC--CCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCE--EECCCCCEEEECCCEE
T ss_conf 999998754--8999986899987079857899999999986233201--1030587676076066
No 253
>COG2344 AT-rich DNA-binding protein [General function prediction only]
Probab=56.70 E-value=18 Score=17.93 Aligned_cols=42 Identities=14% Similarity=0.046 Sum_probs=32.5
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC
Q ss_conf 999999985598633599999981997899999999993259
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAG 52 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~ag 52 (144)
.|++-.|...+-..+||+|||+..++.+..++|=++..-.-|
T Consensus 19 yR~le~l~a~~v~rvsS~els~~~~vdsatIRrDfSYFG~lG 60 (211)
T COG2344 19 YRVLERLHASGVERVSSKELSEALGVDSATIRRDFSYFGELG 60 (211)
T ss_pred HHHHHHHHHCCCCEECHHHHHHHHCCCHHHHHHHHHHHHHCC
T ss_conf 999999987298012689999986899999863567877527
No 254
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR; InterPro: IPR012712 This Helix-Turn-Helix transcriptional regulator is a member of the MarR family and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.; GO: 0003677 DNA binding, 0016564 transcription repressor activity, 0010124 phenylacetate catabolic process, 0016481 negative regulation of transcription.
Probab=56.53 E-value=15 Score=18.42 Aligned_cols=51 Identities=25% Similarity=0.318 Sum_probs=41.4
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCC
Q ss_conf 99999998559863359999998199789999999999325905731565454
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGG 63 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GG 63 (144)
=|+|-.|+.. +.+-+.++|+..+|=.|-|..|+..|=+.|+|.=.+-.+=|
T Consensus 31 WRilR~L~~~--G~~e~~~LA~~A~iL~PSLTgiL~rLE~~glv~R~k~~~DQ 81 (130)
T TIGR02337 31 WRILRVLAEK--GSMEFTELADRACILRPSLTGILARLEKRGLVVRLKASNDQ 81 (130)
T ss_pred HHHHHHHHCC--CCCCHHHHHHHHCCCCCCHHHHHHHHHHCCCEECCCCCCCC
T ss_conf 9999988338--99486878866414799657899999745870225888774
No 255
>TIGR01764 excise DNA binding domain, excisionase family; InterPro: IPR010093 An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This entry represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This entry identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (IPR000551 from INTERPRO).; GO: 0003677 DNA binding.
Probab=56.41 E-value=11 Score=19.33 Aligned_cols=40 Identities=18% Similarity=0.257 Sum_probs=29.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCC
Q ss_conf 359999998199789999999999325905731565454000237
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRP 69 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~ 69 (144)
.|++|.|+-+|+|.+++.+. .+.|=+.+.|= ++.|++.++
T Consensus 2 lTv~EaA~yLgv~~~t~~~l----~~~g~l~~~~~-G~~~ri~~~ 41 (49)
T TIGR01764 2 LTVEEAAEYLGVSKSTVYRL----IEEGELPAYRV-GRHYRIKRE 41 (49)
T ss_pred CCHHHHHHHCCCCHHHHHHH----HHCCCCCEEEC-CCCEECCHH
T ss_conf 87788997719990578999----97189850006-860202499
No 256
>COG4861 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.49 E-value=10 Score=19.40 Aligned_cols=60 Identities=15% Similarity=0.115 Sum_probs=42.9
Q ss_pred HHHHHHHHHHCCCC-CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHH
Q ss_conf 99999999855986-3359999998199789999999999325905731565454000237212
Q gi|254780620|r 10 GIRVLMYCAIHNDY-PNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQ 72 (144)
Q Consensus 10 Ai~~l~~La~~~~~-~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~ 72 (144)
+.+....|-..+.- .....|||...+++...+.++|-.|+.+|++ +|..-||+|-+-.+=
T Consensus 148 raqv~~ALL~aP~lv~~P~REIAasAgVsvGTa~~t~d~LrE~G~L---~~~~s~rRL~~~d~L 208 (345)
T COG4861 148 RAQVVCALLDAPQLVDAPLREIAASAGVSVGTAKETMDTLRETGFL---EHLGSRRRLVRTDEL 208 (345)
T ss_pred HHHHHHHHHCCHHHHCCHHHHHHHHCCCEECHHHHHHHHHHHCCHH---HCCCCCCEEHHHHHH
T ss_conf 8889999755887754458888764051011088889998860102---126762300307889
No 257
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=54.74 E-value=20 Score=17.73 Aligned_cols=62 Identities=27% Similarity=0.440 Sum_probs=46.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHHH-CCCCCCCCC
Q ss_conf 3599999981997899999999993259057315654540002372126099999997-187631114
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKAT-EESFFVAEC 91 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~ai-e~~~~~~~C 91 (144)
.++.++|+..|+|+.. ++---+.|+|...+-..|||++=.+.+ +....++... +-...+.++
T Consensus 1 ~~I~eva~~~gvs~~t----LRyYe~~GLl~p~~~~~~gyR~Ys~~d-l~~l~~I~~~r~~G~sL~eI 63 (124)
T COG0789 1 YTIGEVAKLTGVSVRT----LRFYERKGLLSPERRDEGGYRYYTPED-LELLQIIKTLRELGFSLAEI 63 (124)
T ss_pred CCHHHHHHHHCCCHHH----HHHHHHHCCCCCCCCCCCCCEECCHHH-HHHHHHHHHHHHCCCCHHHH
T ss_conf 9599999997969999----999999089997635899976319999-99999999999869989999
No 258
>COG0758 Smf Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]
Probab=54.49 E-value=20 Score=17.71 Aligned_cols=43 Identities=23% Similarity=0.268 Sum_probs=27.5
Q ss_pred HHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCC
Q ss_conf 9855986335999999819978999999999932590573156
Q gi|254780620|r 17 CAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRG 59 (144)
Q Consensus 17 La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG 59 (144)
++..+.++++..+|+...+++..-+...|-.|.-+|.|....|
T Consensus 302 ~~~~~~~~~~~d~l~~~~~~~~~~~~~~L~elel~G~i~~~~g 344 (350)
T COG0758 302 LANLGDEPKEIDRLASCTGLTIAQVLAWLLELELEGKVKRLGG 344 (350)
T ss_pred HHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECC
T ss_conf 9872688746999998868889999999999984694786388
No 259
>KOG3233 consensus
Probab=54.44 E-value=5.6 Score=20.95 Aligned_cols=42 Identities=14% Similarity=0.194 Sum_probs=35.7
Q ss_pred HHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCC
Q ss_conf 855986335999999819978999999999932590573156
Q gi|254780620|r 18 AIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRG 59 (144)
Q Consensus 18 a~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG 59 (144)
-..+++.+.+++|-...++|...+.|+|..|....||+|++-
T Consensus 94 e~sg~~GIW~k~ik~ksnLp~~~v~K~LkSLEsKkLIKsVKs 135 (297)
T KOG3233 94 EESGNEGIWSKEIKRKSNLPQTVVNKILKSLESKKLIKSVKS 135 (297)
T ss_pred HHCCCCCEEEEHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 973898356220321158879999999998777789999986
No 260
>pfam05331 DUF742 Protein of unknown function (DUF742). This family consists of several uncharacterized Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins is unknown.
Probab=54.31 E-value=6.9 Score=20.43 Aligned_cols=36 Identities=19% Similarity=0.248 Sum_probs=33.2
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECC
Q ss_conf 633599999981997899999999993259057315
Q gi|254780620|r 23 YPNRISQIAEACCISELFLFKILQPLVKAGIVETVR 58 (144)
Q Consensus 23 ~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~r 58 (144)
++.|+.|||-..++|...++=++..|..+|+|....
T Consensus 54 ~p~SVAEiAA~L~LPl~VvrVLl~DL~~~G~v~v~~ 89 (114)
T pfam05331 54 APLSVAEIAARLDLPVGVVRVLLSDLLDAGLLTVRA 89 (114)
T ss_pred CCCCHHHHHHHHCCCCEEEEEEHHHHHHCCCEEECC
T ss_conf 852099999731898402301587687589768508
No 261
>PRK13239 alkylmercury lyase; Provisional
Probab=54.09 E-value=20 Score=17.67 Aligned_cols=54 Identities=15% Similarity=0.063 Sum_probs=36.3
Q ss_pred HCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEEC--CCHHHCC
Q ss_conf 5598633599999981997899999999993259057315654540002--3721260
Q gi|254780620|r 19 IHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLC--RPADQIT 74 (144)
Q Consensus 19 ~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~La--k~~~~It 74 (144)
...|+|+|.+.||+..+.|...++++|..+.. +.--..|+=.||=|. -.|...+
T Consensus 31 La~G~PVs~~~LA~~~g~~~e~v~~~L~~~~~--teyD~~G~Iig~GLTlrpT~Hrf~ 86 (206)
T PRK13239 31 LAKGRPVSRETLAGALGWPVEEVAAVLEQAPD--TEYDEDGRIIGYGLTLRPTPHRFE 86 (206)
T ss_pred HHCCCCCCHHHHHHHHCCCHHHHHHHHHHCCC--EEECCCCCEEEEECCCCCCCCEEE
T ss_conf 85699999999998869999999999985777--258589858865041166686789
No 262
>PRK09526 lacI lac repressor; Reviewed
Probab=54.04 E-value=14 Score=18.64 Aligned_cols=25 Identities=16% Similarity=0.214 Sum_probs=18.7
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 8633599999981997899999999
Q gi|254780620|r 22 DYPNRISQIAEACCISELFLFKILQ 46 (144)
Q Consensus 22 ~~~~s~~eIA~~~~i~~~~l~kil~ 46 (144)
.+++|.++||+..|+|...|+++|+
T Consensus 3 ~k~~TikDIA~~agVS~sTVSrvLn 27 (342)
T PRK09526 3 SKPVTLYDVARYAGVSYQTVSRVLN 27 (342)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHC
T ss_conf 8997699999998969999999978
No 263
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=53.81 E-value=17 Score=18.04 Aligned_cols=35 Identities=17% Similarity=0.071 Sum_probs=24.3
Q ss_pred HHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Q ss_conf 98559863359999998199789999999999325
Q gi|254780620|r 17 CAIHNDYPNRISQIAEACCISELFLFKILQPLVKA 51 (144)
Q Consensus 17 La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~a 51 (144)
+....+...+.++||+..+++..-+...+......
T Consensus 125 l~~~~~r~pt~~eiA~~l~~s~e~v~~~l~~~~~~ 159 (257)
T PRK08583 125 LTDELQRSPKISEIADRLGVSEEEVLEAMEMGKSY 159 (257)
T ss_pred HHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCC
T ss_conf 99980899879999989595999999999975168
No 264
>pfam12324 HTH_15 Helix-turn-helix domain of alkylmercury lyase. Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This is the N terminal helix-turn-helix domain associated with pfam03243.
Probab=53.40 E-value=21 Score=17.60 Aligned_cols=39 Identities=18% Similarity=0.101 Sum_probs=29.8
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 9999999855986335999999819978999999999932
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVK 50 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~ 50 (144)
++.|+.+-. .|+|+|.+.||...+-|..-++++|..+..
T Consensus 26 ~~~LLr~La-~G~PVt~~~LA~a~g~~~e~V~~~L~~~p~ 64 (77)
T pfam12324 26 FRPLLRMLA-DGRPVTREDLAGATGKPVERVAKVLAQAPS 64 (77)
T ss_pred HHHHHHHHH-CCCCCCHHHHHHHHCCCHHHHHHHHHHCCC
T ss_conf 999999994-799868999998969899999999985889
No 265
>pfam09205 DUF1955 Domain of unknown function (DUF1955). Members of this family are found in hypothetical proteins synthesized by the Archaeal organism Sulfolobus. Their exact function has not, as yet, been determined.
Probab=53.18 E-value=21 Score=17.58 Aligned_cols=52 Identities=21% Similarity=0.187 Sum_probs=32.7
Q ss_pred CCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHH---HHCCCHHHHHHHHHHHHHCCC
Q ss_conf 97645689999999999855986335999999---819978999999999932590
Q gi|254780620|r 1 MHLTKRTDYGIRVLMYCAIHNDYPNRISQIAE---ACCISELFLFKILQPLVKAGI 53 (144)
Q Consensus 1 Mkis~~~~yAi~~l~~La~~~~~~~s~~eIA~---~~~i~~~~l~kil~~L~~agl 53 (144)
|+.++-++|-=.+|-+|..++ +.-+..+|.. ...+||++|-||-..++|-|=
T Consensus 80 ~~~n~~seyvdlALd~lv~q~-kkdqLd~i~~el~neei~~eillkianA~kkig~ 134 (160)
T pfam09205 80 MRANKDSEYVDLALDALVQQG-KKDQLDKILAELFNEEIPPEILLKIANAYKKIGN 134 (160)
T ss_pred HHHCCCHHHHHHHHHHHHHHC-CHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCC
T ss_conf 881741899999999999826-0868999999871479987999999999988533
No 266
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=53.11 E-value=15 Score=18.41 Aligned_cols=25 Identities=20% Similarity=0.077 Sum_probs=20.2
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 8633599999981997899999999
Q gi|254780620|r 22 DYPNRISQIAEACCISELFLFKILQ 46 (144)
Q Consensus 22 ~~~~s~~eIA~~~~i~~~~l~kil~ 46 (144)
.+.+|.++||+..|+|...|+++|+
T Consensus 4 ~kkvTi~dIA~~aGVS~aTVSrvLn 28 (342)
T PRK10014 4 AKKITIHDVALAAGVSVSTVSLVLS 28 (342)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHC
T ss_conf 9988799999998969999999977
No 267
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=52.99 E-value=21 Score=17.56 Aligned_cols=16 Identities=19% Similarity=0.183 Sum_probs=8.7
Q ss_pred CCCHHHHHHHHCCCHH
Q ss_conf 3359999998199789
Q gi|254780620|r 24 PNRISQIAEACCISEL 39 (144)
Q Consensus 24 ~~s~~eIA~~~~i~~~ 39 (144)
.++.++||+..||+++
T Consensus 178 ~~~l~dLA~~lGISks 193 (215)
T COG3413 178 RVSLKDLAKELGISKS 193 (215)
T ss_pred CCCHHHHHHHHCCCHH
T ss_conf 5899999999599888
No 268
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=52.99 E-value=21 Score=17.56 Aligned_cols=46 Identities=28% Similarity=0.276 Sum_probs=36.3
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECC
Q ss_conf 999999985598633599999981997899999999993259057315
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVR 58 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~r 58 (144)
+.++-.+... ...+..+|+...+++...+..-+..|..+|+|...+
T Consensus 28 ~~il~~l~~~--~~~~~~~l~~~~~~~~~~v~~hL~~L~~~glv~~~~ 73 (110)
T COG0640 28 LEILSLLAEG--GELTVGELAEALGLSQSTVSHHLKVLREAGLVELRR 73 (110)
T ss_pred HHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEE
T ss_conf 9999999873--513799999885767889999999998789957886
No 269
>TIGR02403 trehalose_treC alpha,alpha-phosphotrehalase; InterPro: IPR012769 Trehalose is a glucose disaccharide that serves in many biological systems as a compatible solute for protection against hyperosmotic and thermal stress. This family describes trehalose-6-phosphate hydrolase, product of the treC (or treA) gene, which is often found together with a trehalose uptake transporter and a trehalose operon repressor.; GO: 0008788 alphaalpha-phosphotrehalase activity, 0005993 trehalose catabolic process, 0005737 cytoplasm.
Probab=52.73 E-value=3.5 Score=22.13 Aligned_cols=62 Identities=15% Similarity=0.137 Sum_probs=42.7
Q ss_pred CCCCCCCEECCCHHHCCHHHHHHHHCCCCCCCCCCCC-CCCCCCCCCCCCHHHHHHHHHHHHHH-HHHHCCHHHH
Q ss_conf 5654540002372126099999997187631114688-77888765664479999999999999-9841799999
Q gi|254780620|r 58 RGRRGGVRLCRPADQITILDVVKATEESFFVAECFAS-HKIDCPLVGSCGLTSVLRKALNAFFD-VLTQYSIECL 130 (144)
Q Consensus 58 rG~~GGy~Lak~~~~Itl~dI~~aie~~~~~~~C~~~-~~~~C~~~~~c~~~~~~~~~~~~~~~-~L~~~TL~dl 130 (144)
+|.. |||| ||+-.|.-+..+.+|... ...---=...-.+|.+++++.+++.. .-+.+|+.|+
T Consensus 188 KGV~-GFRl----------DVINLIsK~~~f~dd~~~~~DGR~fYTDGP~VH~YL~Em~~~vF~~~~~~~TVGEm 251 (555)
T TIGR02403 188 KGVD-GFRL----------DVINLISKDQFFEDDEIGEGDGRRFYTDGPRVHEYLQEMNQEVFGQDNDIVTVGEM 251 (555)
T ss_pred CCCC-CEEE----------EEEEECCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCC
T ss_conf 6987-1354----------27740347632566677888682221586048899999987605657873686144
No 270
>cd04447 DEP_BRCC3 DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in BBRC3-like proteins. BBRC3, also known as DEPDC1B, is a DEP containing protein of unknown function.
Probab=52.40 E-value=17 Score=18.10 Aligned_cols=28 Identities=21% Similarity=0.513 Sum_probs=25.3
Q ss_pred CCCHHHHHHHHHHHHHCCCEEECCCCCC
Q ss_conf 9978999999999932590573156545
Q gi|254780620|r 35 CISELFLFKILQPLVKAGIVETVRGRRG 62 (144)
Q Consensus 35 ~i~~~~l~kil~~L~~agli~S~rG~~G 62 (144)
.+++.-.-+++++|-++++++.++|+-|
T Consensus 52 ~vtR~q~v~L~q~fl~~~vfE~V~~~~~ 79 (92)
T cd04447 52 EVTRQQTVQLLKKFLKNHVIEDIKGRWG 79 (92)
T ss_pred CCCHHHHHHHHHHHHHCCCEEECCCCCC
T ss_conf 6459999999999997793454666457
No 271
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. 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. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=52.31 E-value=22 Score=17.50 Aligned_cols=61 Identities=23% Similarity=0.326 Sum_probs=40.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHHHCCCCCCC
Q ss_conf 35999999819978999999999932590573156545400023721260999999971876311
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKATEESFFVA 89 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~aie~~~~~~ 89 (144)
.|..++|+..|+|+..| ..--+.|+|.+.+-..|||++=-..+=..|..|-...+....+.
T Consensus 2 ~tIgeva~~~gvs~~tL----Ryye~~gli~p~~~~~~g~R~Ys~~dl~~l~~I~~l~~~G~sl~ 62 (88)
T cd01105 2 IGIGEVSKLTGVSPRQL----RYWEEKGLIKSIRSDGGGQRKYSLADVDRLLVIKELLDEGFTLA 62 (88)
T ss_pred CCHHHHHHHHCCCHHHH----HHHHHCCCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHCCCCHH
T ss_conf 67899999989599999----99999499899876999821479999999999999999799899
No 272
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=50.52 E-value=23 Score=17.33 Aligned_cols=14 Identities=14% Similarity=0.268 Sum_probs=8.0
Q ss_pred CCHHHHHHHHHHHH
Q ss_conf 97899999999993
Q gi|254780620|r 36 ISELFLFKILQPLV 49 (144)
Q Consensus 36 i~~~~l~kil~~L~ 49 (144)
-|..||.+|-..+.
T Consensus 67 ~p~a~L~rIA~Nl~ 80 (178)
T PRK12529 67 QPRAYLARIANCVL 80 (178)
T ss_pred HHHHHHHHHHHHHH
T ss_conf 48999999999999
No 273
>PRK09492 treR trehalose repressor; Provisional
Probab=50.47 E-value=16 Score=18.23 Aligned_cols=24 Identities=17% Similarity=0.188 Sum_probs=17.6
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 633599999981997899999999
Q gi|254780620|r 23 YPNRISQIAEACCISELFLFKILQ 46 (144)
Q Consensus 23 ~~~s~~eIA~~~~i~~~~l~kil~ 46 (144)
+.+|.++||+..|+|...|+++|+
T Consensus 3 kkvTikDIA~~aGVS~aTVSrvLn 26 (315)
T PRK09492 3 NKLTIKDIARLSGVGKSTVSRVLN 26 (315)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHC
T ss_conf 988799999998979999999978
No 274
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=50.42 E-value=23 Score=17.32 Aligned_cols=55 Identities=20% Similarity=0.143 Sum_probs=40.8
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHH
Q ss_conf 9863359999998199789999999999325905731565454000237212609999
Q gi|254780620|r 21 NDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDV 78 (144)
Q Consensus 21 ~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI 78 (144)
+....+..|+++..++++..++--++.|..++++++.+ .||- +.--|.+.|.++-
T Consensus 112 ~nPG~~lsEl~~nl~i~R~TlRyhlriLe~~~li~a~~--~~g~-~~yfpa~~t~~~~ 166 (240)
T COG3398 112 PNPGFSLSELRANLYINRSTLRYHLRILESNPLIEAGR--VGGA-LRYFPADMTYGEA 166 (240)
T ss_pred CCCCCCHHHHHHHCCCCHHHHHHHHHHHHHCCCHHHHC--CCCC-EEECCCCCCCCCC
T ss_conf 58985199999865887599999999997576612212--3785-4772687886630
No 275
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=50.37 E-value=15 Score=18.41 Aligned_cols=50 Identities=14% Similarity=0.213 Sum_probs=36.2
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHHHCCCCCCC
Q ss_conf 986335999999819978999999999932590573156545400023721260999999971876311
Q gi|254780620|r 21 NDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKATEESFFVA 89 (144)
Q Consensus 21 ~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~aie~~~~~~ 89 (144)
.++-.|.+|+|+..|+|.+|+.+|- +|+. +|.=-+|..|-+|++-|....
T Consensus 15 ~ErGmT~~eLAe~AGIS~s~LSqIE------------~Gk~-------NPSL~tLe~IA~AL~VPL~~L 64 (119)
T PRK13890 15 DERHMTKKELSDRSGVSISFLSDLT------------TGKA-------NPSLKVMEDIAQALETPLPLL 64 (119)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHH------------CCCC-------CCCHHHHHHHHHHHCCCHHHH
T ss_conf 9859979999988298899999997------------7998-------987999999999987977998
No 276
>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU; InterPro: IPR014088 Members of this protein family include S-adenosylmethionine-dependent C-20 methyltransferase (BchU), part of the pathway of bacteriochlorophyll c production in photosynthetic green sulphur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produce bacteriochlorophyll d..
Probab=50.34 E-value=23 Score=17.31 Aligned_cols=46 Identities=20% Similarity=0.148 Sum_probs=38.6
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCH
Q ss_conf 8633599999981997899999999993259057315654540002372
Q gi|254780620|r 22 DYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPA 70 (144)
Q Consensus 22 ~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~ 70 (144)
++|-+..++|..++.=|+.|++.|..|++-++|+-.-|+ |+|..=+
T Consensus 21 ~~P~~LA~LA~~T~~VPPRLE~lL~Tl~Q~~~~~~~~~~---W~LT~FA 66 (306)
T TIGR02716 21 EAPKDLADLAALTESVPPRLEKLLITLRQIRLVTLEDDK---WSLTEFA 66 (306)
T ss_pred HCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHEEECCCCC---CCCCHHH
T ss_conf 132468988762389972479999998872100024884---1144454
No 277
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. 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. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe
Probab=50.28 E-value=23 Score=17.31 Aligned_cols=58 Identities=24% Similarity=0.248 Sum_probs=41.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHHH-CCCCCC
Q ss_conf 3599999981997899999999993259057315654540002372126099999997-187631
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKAT-EESFFV 88 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~ai-e~~~~~ 88 (144)
.++.++|+..++++..|+-= -+.|+|...| .|||+|=.+.+--.|.-|-+.+ |-.+.+
T Consensus 2 y~Ig~vA~l~gv~~~TLR~Y----Er~GLi~P~R--~~G~RlYs~~Di~rLrfIkrL~~e~G~nl 60 (120)
T cd04767 2 YPIGVVAELLNIHPETLRIW----ERHGLIKPAR--RNGQRLYSNNDLKRLRFIKKLINEKGLNI 60 (120)
T ss_pred CCHHHHHHHHCCCHHHHHHH----HHCCCCCCCC--CCCCCCCCHHHHHHHHHHHHHHHHCCCCH
T ss_conf 24899999978688999999----9858968888--89822779999999999999999759689
No 278
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=49.34 E-value=24 Score=17.22 Aligned_cols=14 Identities=29% Similarity=0.161 Sum_probs=7.6
Q ss_pred HHHHHHCCHHHHHH
Q ss_conf 99984179999991
Q gi|254780620|r 119 FDVLTQYSIECLVR 132 (144)
Q Consensus 119 ~~~L~~~TL~dl~~ 132 (144)
..++.+.|..++.+
T Consensus 139 l~~~~~~s~~EIA~ 152 (185)
T PRK06811 139 KRYLLGESIEEIAK 152 (185)
T ss_pred HHHHCCCCHHHHHH
T ss_conf 99994999999999
No 279
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; InterPro: IPR014322 The bacterial core RNA polymerase complex, which consists of five subunits, 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 . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:IPR014236 from INTERPRO and SigG:IPR014212 from INTERPRO as well as SigB:IPR014288 from INTERPRO), and the high GC Gram-positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=49.15 E-value=16 Score=18.19 Aligned_cols=67 Identities=16% Similarity=0.148 Sum_probs=46.3
Q ss_pred HHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH--CCCEEECCCCCCCCEECCCHHHCCHHHHHHHHCCCC
Q ss_conf 9999855986335999999819978999999999932--590573156545400023721260999999971876
Q gi|254780620|r 14 LMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVK--AGIVETVRGRRGGVRLCRPADQITILDVVKATEESF 86 (144)
Q Consensus 14 l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~--agli~S~rG~~GGy~Lak~~~~Itl~dI~~aie~~~ 86 (144)
-=.|+..-|+.-|+.|||+.+++++-=+--.|-.-.. +-=|...-+..+ +-+.++|+|.+-.-|+..
T Consensus 97 ~eeL~~~lgR~Pt~~EiAe~L~~s~EEv~~aleA~~~Y~~~Sld~~~~a~~------dg~~~~L~D~lG~~D~~~ 165 (229)
T TIGR02980 97 TEELTQRLGRSPTVAEIAEELGVSEEEVVEALEAGNSYSALSLDATIEADD------DGDPIALLDTLGDEDDAL 165 (229)
T ss_pred HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCCCCCCCC------CCCHHHHHHHHCCCCCHH
T ss_conf 999999828898878999885889999999998654178611200045588------884245664440224326
No 280
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. 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. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=49.02 E-value=23 Score=17.32 Aligned_cols=51 Identities=24% Similarity=0.243 Sum_probs=36.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHH
Q ss_conf 359999998199789999999999325905731565454000237212609999999
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKA 81 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~a 81 (144)
.|+.++|+..|+|+..++- --+.|+|...|- .|||++= +.++|.....+.-
T Consensus 2 YtIgevA~~~Gvs~~tLR~----yE~~GLl~P~R~-~~g~R~Y-s~~di~~l~~I~~ 52 (91)
T cd04766 2 YVISVAAELSGMHPQTLRL----YERLGLLSPSRT-DGGTRRY-SERDIERLRRIQR 52 (91)
T ss_pred CCHHHHHHHHCCCHHHHHH----HHHCCCCCCCCC-CCCCEEC-CHHHHHHHHHHHH
T ss_conf 6589999998929999999----998599798839-9999744-7999999999999
No 281
>pfam03297 Ribosomal_S25 S25 ribosomal protein.
Probab=48.74 E-value=25 Score=17.16 Aligned_cols=41 Identities=15% Similarity=0.116 Sum_probs=35.5
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCC
Q ss_conf 86335999999819978999999999932590573156545
Q gi|254780620|r 22 DYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRG 62 (144)
Q Consensus 22 ~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~G 62 (144)
-..+|...+++++.|+-+..++.|..|...|+|.-+-..++
T Consensus 56 ~KlITpsvvseRlKI~gSLAR~aL~~L~~kGlIk~V~~h~~ 96 (104)
T pfam03297 56 YKLITPSVLSDRLKINGSLARRALRELEEKGLIKPVVKHSA 96 (104)
T ss_pred CEEECHHHHHHHHHCCHHHHHHHHHHHHHCCCEEEEECCCC
T ss_conf 63773999777760218999999999998899887711576
No 282
>pfam08221 HTH_9 RNA polymerase III subunit RPC82 helix-turn-helix domain. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In Saccharomyces cerevisiae, the enzyme is composed of 15 subunits, ranging from 160 to about 10 kDa. This region is a probably DNA-binding helix-turn-helix.
Probab=48.59 E-value=25 Score=17.15 Aligned_cols=48 Identities=15% Similarity=-0.006 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Q ss_conf 68999999999985598633599999981997899999999993259057
Q gi|254780620|r 6 RTDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVE 55 (144)
Q Consensus 6 ~~~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~ 55 (144)
+.+.+=++.-+|-.+ +..|..+|....++|+..+++-|..|.+.++|.
T Consensus 11 fGei~~~V~~~Ll~~--g~~tl~~i~~~t~L~~~~Vk~aL~vLIQhnlV~ 58 (62)
T pfam08221 11 FGEVVAKVVSTLLRK--GRLTLREIVKLTKLSLDQVKKSLVVLIQHNCVQ 58 (62)
T ss_pred CCHHHHHHHHHHHHC--CCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
T ss_conf 373899999999985--881699999782899999999999999997899
No 283
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=48.52 E-value=14 Score=18.56 Aligned_cols=24 Identities=13% Similarity=-0.032 Sum_probs=20.2
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 863359999998199789999999
Q gi|254780620|r 22 DYPNRISQIAEACCISELFLFKIL 45 (144)
Q Consensus 22 ~~~~s~~eIA~~~~i~~~~l~kil 45 (144)
.+..|.+++|++.|+|..+|.||=
T Consensus 18 ~~glTL~eLA~~sGvS~s~LSqIE 41 (185)
T PRK09943 18 QQGLSQRRAAELSGLTHSAISTIE 41 (185)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 859989999988796999999998
No 284
>KOG2167 consensus
Probab=48.33 E-value=25 Score=17.12 Aligned_cols=53 Identities=17% Similarity=0.156 Sum_probs=39.1
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCC
Q ss_conf 99999998559863359999998199789999999999325905731565454
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGG 63 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GG 63 (144)
..+++.|..++++..|.+||-++++|...-|++.++.|.-+..=--++-|+|+
T Consensus 499 fq~~vll~fn~~~~~s~~ei~~~t~i~d~el~rtlqsl~cgr~rvl~~~pkg~ 551 (661)
T KOG2167 499 FQTLVLLMFNEGEGLSYEEIKESTGIEDIELRRTLQSLACGRARVLQKVPKGK 551 (661)
T ss_pred HHHHHHHCCCCCCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCEEEEECCCCC
T ss_conf 87767410478886339999985464079999999997524421344378988
No 285
>pfam07037 DUF1323 Putative transcription regulator (DUF1323). This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. This family appears to have an HTH domain and is therefore likely to act as a transcriptional regulator.
Probab=48.27 E-value=23 Score=17.30 Aligned_cols=37 Identities=22% Similarity=0.224 Sum_probs=29.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECC-CCCCCC
Q ss_conf 3599999981997899999999993259057315-654540
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQPLVKAGIVETVR-GRRGGV 64 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~r-G~~GGy 64 (144)
+|.+|+|+..|.+..-+-| .-++.|+.++.+ |+.||-
T Consensus 1 mT~eELa~~~G~srQtINk---waRkeGW~t~~~~GVQGGk 38 (122)
T pfam07037 1 MTPEELAELTGYSRQTINR---WVRKEGWKTSPKPGVKGGK 38 (122)
T ss_pred CCHHHHHHHHCCHHHHHHH---HHHHCCCCCCCCCCCCCCE
T ss_conf 9878998874712999999---9997387048878865761
No 286
>pfam02980 FokI_C Restriction endonuclease FokI, catalytic domain.
Probab=48.16 E-value=23 Score=17.33 Aligned_cols=54 Identities=22% Similarity=0.076 Sum_probs=33.0
Q ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHHH
Q ss_conf 9999981997899999999993259057315654540002372126099999997
Q gi|254780620|r 28 SQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKAT 82 (144)
Q Consensus 28 ~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~ai 82 (144)
+--++-.+.|..|.+-|-..|++.|+|++..-.- -..+...--+-|++..|+..
T Consensus 72 kiksd~EGtSDKYaR~I~~WL~k~Glv~q~~K~v-t~t~g~r~~~~tig~~Y~IT 125 (142)
T pfam02980 72 KIKSNWEGTSDKYARMIAGWLVKLGLVKQTTKKV-THTLKKRKFEETIGTVYQIT 125 (142)
T ss_pred HHHCCCCCCHHHHHHHHHHHHHHHCHHEECCEEE-EEECCCCCCCCCCCEEEEEE
T ss_conf 7743565561899999999998813013122588-98527632121266468982
No 287
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=48.10 E-value=22 Score=17.44 Aligned_cols=44 Identities=27% Similarity=0.317 Sum_probs=31.9
Q ss_pred CCCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCH
Q ss_conf 335999999819--------------97899999999993259057315654540002372
Q gi|254780620|r 24 PNRISQIAEACC--------------ISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPA 70 (144)
Q Consensus 24 ~~s~~eIA~~~~--------------i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~ 70 (144)
++-+..++...| -|...++++||.|-++|+|+-.+ ||-.|+..-
T Consensus 67 pvGv~~Lr~~YGg~k~rG~~P~h~~~aSg~iiR~~LQqLE~~glvek~~---~GR~iT~~G 124 (150)
T PRK09333 67 PVGVERLRTAYGGRKNRGVKPEHFVKGSGSIIRKALQQLEAAGLVEKTK---KGRVITPKG 124 (150)
T ss_pred CCCHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCEEECC---CCCEECHHH
T ss_conf 9418899999788988998998777775589999999998788857679---986779868
No 288
>pfam00464 SHMT Serine hydroxymethyltransferase.
Probab=47.83 E-value=25 Score=17.08 Aligned_cols=57 Identities=25% Similarity=0.397 Sum_probs=34.7
Q ss_pred HHHHHHHHCC----CHHHHHHHHH------HHHHCCCEEE-----CCCCCCCCEECCCHHHCCHHHHHHHHCCCCC
Q ss_conf 9999998199----7899999999------9932590573-----1565454000237212609999999718763
Q gi|254780620|r 27 ISQIAEACCI----SELFLFKILQ------PLVKAGIVET-----VRGRRGGVRLCRPADQITILDVVKATEESFF 87 (144)
Q Consensus 27 ~~eIA~~~~i----~~~~l~kil~------~L~~agli~S-----~rG~~GGy~Lak~~~~Itl~dI~~aie~~~~ 87 (144)
..+||+..+. --.++.-++. .|.-+.+|.+ .|||.||..|.+++.+ ++.+.++....
T Consensus 180 ~reIad~vgA~l~~D~aH~~GLIA~g~~p~Pl~~ADvvt~tTHKTlrGPrGGiIl~~~~~~----e~~~kId~avF 251 (380)
T pfam00464 180 FREIADEVGAYLMVDMAHIAGLVAAGVIPSPFPYAHVVTTTTHKTLRGPRGGMIFFREILY----ELEKKINSAVF 251 (380)
T ss_pred HHHHHHHCCCEEEEEHHHHHHHHHCCCCCCCCCCCEEEECCCCCCCCCCCCEEEEECCCHH----HHHHHHCCCCC
T ss_conf 9999975098899863777777742437995466657853545667899851798378379----99999714048
No 289
>pfam03965 Pencillinase_R Penicillinase repressor. The penicillinase repressor negatively regulates expression of the penicillinase gene. The N-terminal region of this protein is involved in operator recognition, while the C-terminal is responsible for dimerization of the protein.
Probab=47.71 E-value=26 Score=17.07 Aligned_cols=61 Identities=16% Similarity=0.154 Sum_probs=42.3
Q ss_pred CCCCHHHHHHHHC----CCHHHHHHHHHHHHHCCCEEECC-CCCCCCEECCCHHHCCHHHHHHHHC
Q ss_conf 6335999999819----97899999999993259057315-6545400023721260999999971
Q gi|254780620|r 23 YPNRISQIAEACC----ISELFLFKILQPLVKAGIVETVR-GRRGGVRLCRPADQITILDVVKATE 83 (144)
Q Consensus 23 ~~~s~~eIA~~~~----i~~~~l~kil~~L~~agli~S~r-G~~GGy~Lak~~~~Itl~dI~~aie 83 (144)
++.|+.+|.+... .+++-+..+|..|.+.|+|+..+ |+.-=|.=..+.++..-..+-..++
T Consensus 16 ~~~t~~ei~~~l~~~~~~~~tTv~T~L~rL~~KG~l~~~~~gr~~~Y~p~v~~~~~~~~~~~~~~~ 81 (115)
T pfam03965 16 GPATVKEVVEELPEPRDWAYSTVKTLLTRLVKKGLLSREKDGRAYIYSPLVSREEAVASAVKQLLD 81 (115)
T ss_pred CCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEEEEECCCCEEEEECCCHHHHHHHHHHHHHH
T ss_conf 997799999985145688572899999999977862687339947987468899999999999999
No 290
>COG3711 BglG Transcriptional antiterminator [Transcription]
Probab=47.49 E-value=26 Score=17.05 Aligned_cols=59 Identities=20% Similarity=0.189 Sum_probs=37.6
Q ss_pred HHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHH----HHHHHCCCEEECCCCCCCCEECCCHHHC
Q ss_conf 99998559863359999998199789999999----9993259057315654540002372126
Q gi|254780620|r 14 LMYCAIHNDYPNRISQIAEACCISELFLFKIL----QPLVKAGIVETVRGRRGGVRLCRPADQI 73 (144)
Q Consensus 14 l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil----~~L~~agli~S~rG~~GGy~Lak~~~~I 73 (144)
+++.....+..+++.++|+..++|...++.-+ ..|...|+-...+.+ ||+.+.-++...
T Consensus 9 ~l~~l~~~~~~~~~~~la~~l~vS~Rti~~~i~~In~~l~~~~~~~~~~~~-~~~~~~~~~~~~ 71 (491)
T COG3711 9 LLLLLLLKNPLLTIKELAEQLGVSRRTIRYDIKKINESLEEGGIPIIKRKG-GGYILEEDERAL 71 (491)
T ss_pred HHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCEEEECCC-CEEECCHHHHHH
T ss_conf 999987346886999999996976744988899999888618850244378-726456266778
No 291
>cd00378 SHMT Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl group of N5, N10-methylene tetrahydrofolate to glycine resulting in the formation of serine and tetrahydrofolate. Both eukaryotic and prokaryotic SHMT enzymes form tight obligate homodimers; the mammalian enzyme forms a homotetramer comprising four pyridoxal phosphate-bound active sites.
Probab=47.35 E-value=26 Score=17.03 Aligned_cols=34 Identities=38% Similarity=0.655 Sum_probs=22.0
Q ss_pred HHHHCCCEE-----ECCCCCCCCEECCCHHHCCHHHHHHHHCCCC
Q ss_conf 993259057-----3156545400023721260999999971876
Q gi|254780620|r 47 PLVKAGIVE-----TVRGRRGGVRLCRPADQITILDVVKATEESF 86 (144)
Q Consensus 47 ~L~~agli~-----S~rG~~GGy~Lak~~~~Itl~dI~~aie~~~ 86 (144)
.|.-+.+|. +.|||.||..|.+++ ++.+.++...
T Consensus 211 Pl~~ADvvt~tTHKTlrGPrGGiIl~~~~------~~~~kId~av 249 (402)
T cd00378 211 PLPGADVVTTTTHKTLRGPRGGLILTRKG------ELAKKINSAV 249 (402)
T ss_pred CCCCCEEEECCCCCCCCCCCCEEEEECCH------HHHHHHHHHH
T ss_conf 76876577446434578998408995427------8998854650
No 292
>pfam03551 PadR Transcriptional regulator PadR-like family. Members of this family are transcriptional regulators that appear to be related to the pfam01047 family. This family includes PadR, a protein that is involved in negative regulation of phenolic acid metabolism.
Probab=46.74 E-value=26 Score=16.98 Aligned_cols=36 Identities=36% Similarity=0.460 Sum_probs=27.3
Q ss_pred HHHHHH----HCCCHHHHHHHHHHHHHCCCEEECCCCCCC
Q ss_conf 999998----199789999999999325905731565454
Q gi|254780620|r 28 SQIAEA----CCISELFLFKILQPLVKAGIVETVRGRRGG 63 (144)
Q Consensus 28 ~eIA~~----~~i~~~~l~kil~~L~~agli~S~rG~~GG 63 (144)
+.|.+. ..+++..+..+|.+|.+.|+|++.....+|
T Consensus 22 ~~i~~~~~~~~~~~~g~iY~~L~~Le~~G~i~~~~~~~~~ 61 (81)
T pfam03551 22 KELEELSGGFYRPSEGTLYPILKRLEKEGLVESEWEDSGG 61 (81)
T ss_pred HHHHHHHCCCCCCCCCCHHHHHHHHHHCCCEEEEEEECCC
T ss_conf 9999985991047967699999999988995899754589
No 293
>COG0045 SucC Succinyl-CoA synthetase, beta subunit [Energy production and conversion]
Probab=46.26 E-value=19 Score=17.77 Aligned_cols=26 Identities=35% Similarity=0.629 Sum_probs=22.4
Q ss_pred HHCCCEEECCCCCCCCEECCCHHHCC
Q ss_conf 32590573156545400023721260
Q gi|254780620|r 49 VKAGIVETVRGRRGGVRLCRPADQIT 74 (144)
Q Consensus 49 ~~agli~S~rG~~GGy~Lak~~~~It 74 (144)
+|+.+...-||+.||.++++++++..
T Consensus 45 vKaQV~aGGRGKaGGVk~~~s~~ea~ 70 (387)
T COG0045 45 VKAQVHAGGRGKAGGVKLAKSPEEAK 70 (387)
T ss_pred EEEEEEECCCCCCCCEEEECCHHHHH
T ss_conf 99225305766667668838989999
No 294
>pfam04967 HTH_10 HTH DNA binding domain.
Probab=46.12 E-value=27 Score=16.92 Aligned_cols=25 Identities=20% Similarity=0.129 Sum_probs=20.5
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 6335999999819978999999999
Q gi|254780620|r 23 YPNRISQIAEACCISELFLFKILQP 47 (144)
Q Consensus 23 ~~~s~~eIA~~~~i~~~~l~kil~~ 47 (144)
+.++.++||+..++|++-+...|++
T Consensus 22 R~~~l~elA~~lgis~sT~~~hLr~ 46 (53)
T pfam04967 22 RRVTLKDLAKELGISKSTLSEHLRR 46 (53)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 7688999999969899999999999
No 295
>pfam05491 RuvB_C Holliday junction DNA helicase ruvB C-terminus. The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein. This family consists of the C-terminal region of the RuvB protein which is thought to be helicase DNA-binding domain.
Probab=45.83 E-value=27 Score=16.89 Aligned_cols=50 Identities=22% Similarity=0.253 Sum_probs=37.7
Q ss_pred HHHHHHHHHC-CCCCCCHHHHHHHHCCCHHHHHHHHH-HHHHCCCEE-ECCCC
Q ss_conf 9999999855-98633599999981997899999999-993259057-31565
Q gi|254780620|r 11 IRVLMYCAIH-NDYPNRISQIAEACCISELFLFKILQ-PLVKAGIVE-TVRGR 60 (144)
Q Consensus 11 i~~l~~La~~-~~~~~s~~eIA~~~~i~~~~l~kil~-~L~~agli~-S~rG~ 60 (144)
.+.|-.|..+ +++|+..+.||-..+..+..++-+.- -|-+.|+|+ +-||+
T Consensus 10 ~~yL~~l~~~f~ggPvGl~tla~~l~e~~~TiE~viEPyLi~~G~i~RTprGR 62 (75)
T pfam05491 10 RRYLETLIEKFGGGPVGLDTLAAALGEERDTIEDVIEPYLIQIGFIQRTPRGR 62 (75)
T ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHCCCCHH
T ss_conf 99999999970899712999999986874089998439999954432088548
No 296
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=45.82 E-value=27 Score=16.89 Aligned_cols=14 Identities=7% Similarity=0.218 Sum_probs=6.8
Q ss_pred HHHHHHCCHHHHHH
Q ss_conf 99984179999991
Q gi|254780620|r 119 FDVLTQYSIECLVR 132 (144)
Q Consensus 119 ~~~L~~~TL~dl~~ 132 (144)
..++.+.|.+++.+
T Consensus 147 L~~~egls~~EIA~ 160 (195)
T PRK12532 147 LKEILGFSSDEIQQ 160 (195)
T ss_pred HHHHCCCCHHHHHH
T ss_conf 99981999999999
No 297
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=44.76 E-value=28 Score=16.79 Aligned_cols=36 Identities=11% Similarity=0.024 Sum_probs=25.8
Q ss_pred HHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 999855986335999999819978999999999932
Q gi|254780620|r 15 MYCAIHNDYPNRISQIAEACCISELFLFKILQPLVK 50 (144)
Q Consensus 15 ~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~ 50 (144)
-.|....+...|..+||+..++++.-+..++.....
T Consensus 176 ~~L~~~lGr~Pt~~EIAe~lgi~~e~V~~~l~~~~~ 211 (318)
T PRK07405 176 RQLSQQLGRAATIGELAEELELTPKQVREYLERARQ 211 (318)
T ss_pred HHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHCC
T ss_conf 999987189864899998859999999999998078
No 298
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; InterPro: IPR014331 The bacterial core RNA polymerase complex, which consists of five subunits, 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 . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry of sigma factors are members of the sigma-70 family and are abundantly found in the species Rhodopirellula baltica, and Verrucomicrobium spinosum and to a lesser extent in Gemmata obscuriglobus.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=44.63 E-value=29 Score=16.78 Aligned_cols=37 Identities=19% Similarity=0.155 Sum_probs=29.1
Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 999999855986335999999819978999999999932
Q gi|254780620|r 12 RVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVK 50 (144)
Q Consensus 12 ~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~ 50 (144)
|-|+.+...+| +++++||+.+|.++.-+++-|+.+++
T Consensus 121 R~Ll~~rY~~G--~~~~~~A~~~g~~~~A~~~~L~R~R~ 157 (163)
T TIGR02989 121 RELLQLRYQRG--VSLEALAEQLGRTVNAVYKALSRLRV 157 (163)
T ss_pred HHHHHHHHCCC--CCHHHHHHHHCCHHHHHHHHHHHHHH
T ss_conf 99999982279--78789998847138999999999999
No 299
>pfam04545 Sigma70_r4 Sigma-70, region 4. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.
Probab=43.84 E-value=29 Score=16.71 Aligned_cols=33 Identities=15% Similarity=0.067 Sum_probs=23.9
Q ss_pred HHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 99999855986335999999819978999999999
Q gi|254780620|r 13 VLMYCAIHNDYPNRISQIAEACCISELFLFKILQP 47 (144)
Q Consensus 13 ~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~ 47 (144)
-++.|.... ..|..|||+..|+|...+++++..
T Consensus 11 ~ii~l~y~~--~~t~~EIA~~lgis~~~V~~~~~r 43 (50)
T pfam04545 11 EVLVLRFGE--GLTLEEIGERLGISRERVRQIEKR 43 (50)
T ss_pred HHHHHHCCC--CCHHHHHHHHHCCCHHHHHHHHHH
T ss_conf 999987068--824999999989799999999999
No 300
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=43.55 E-value=30 Score=16.68 Aligned_cols=14 Identities=7% Similarity=-0.014 Sum_probs=6.8
Q ss_pred HHHHHHCCHHHHHH
Q ss_conf 99984179999991
Q gi|254780620|r 119 FDVLTQYSIECLVR 132 (144)
Q Consensus 119 ~~~L~~~TL~dl~~ 132 (144)
...++..|-+++.+
T Consensus 129 L~~~eGlsy~EIAe 142 (168)
T PRK12525 129 MSQLEGLTYVEIGE 142 (168)
T ss_pred HHHHCCCCHHHHHH
T ss_conf 99992999999999
No 301
>COG0478 RIO-like serine/threonine protein kinase fused to N-terminal HTH domain [Signal transduction mechanisms]
Probab=43.33 E-value=30 Score=16.66 Aligned_cols=76 Identities=17% Similarity=0.091 Sum_probs=54.8
Q ss_pred HHHHHHH--HHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHC------CHHHHHHHH
Q ss_conf 9999999--85598633599999981997899999999993259057315654540002372126------099999997
Q gi|254780620|r 11 IRVLMYC--AIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQI------TILDVVKAT 82 (144)
Q Consensus 11 i~~l~~L--a~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~I------tl~dI~~ai 82 (144)
+|+|-.+ ....-+-++...|.+...+++..+..-+.+|.+-++|.=.....=||+|.-..-+. .-.++++++
T Consensus 16 ~rlLraiE~~mR~~e~VP~~~i~~~ar~~~~~~~~~L~~L~~l~lv~r~~~~y~Gy~lT~~GyD~LAL~~l~~r~~ve~i 95 (304)
T COG0478 16 FRLLRAIEGGMRSHEWVPLELIKKRARMDEEELLYRLKRLDKLKLVSRRTISYEGYQLTFSGYDALALHALVKRGIVEAI 95 (304)
T ss_pred HHHHHHHHHCCCCCCCCCHHHHHHHCCCCHHHHHHHHHHHHHCCCEECCCCCCEEEEEEECCHHHHHHHHHHHCCHHHHH
T ss_conf 89999998423224312399998870898789999999887547564257763138987543139999999974718762
Q ss_pred CCCC
Q ss_conf 1876
Q gi|254780620|r 83 EESF 86 (144)
Q Consensus 83 e~~~ 86 (144)
..++
T Consensus 96 G~~I 99 (304)
T COG0478 96 GTKI 99 (304)
T ss_pred CCCC
T ss_conf 3312
No 302
>pfam00165 HTH_AraC Bacterial regulatory helix-turn-helix proteins, AraC family. In the absence of arabinose, the N-terminal arm of AraC binds to the DNA binding domain (pfam00165) and helps to hold the two DNA binding domains in a relative orientation that favours DNA looping. In the presence of arabinose, the arms bind over the arabinose on the dimerization domain, thus freeing the DNA-binding domains. The freed DNA-binding domains are then able to assume a conformation suitable for binding to the adjacent DNA sites that are utilized when AraC activates transcription, and hence AraC ceases looping the DNA when arabinose is added.
Probab=43.29 E-value=26 Score=16.99 Aligned_cols=27 Identities=19% Similarity=0.266 Sum_probs=23.2
Q ss_pred CCCCHHHHHHHHCC-CHHHHHHHHHHHH
Q ss_conf 63359999998199-7899999999993
Q gi|254780620|r 23 YPNRISQIAEACCI-SELFLFKILQPLV 49 (144)
Q Consensus 23 ~~~s~~eIA~~~~i-~~~~l~kil~~L~ 49 (144)
...++.+||...|. ++.|..+++++-.
T Consensus 7 ~~~~i~~IA~~~g~~s~~~f~r~fk~~~ 34 (43)
T pfam00165 7 TNWTIADIAEELGFSSQSYFSRLFKKYT 34 (43)
T ss_pred CCCCHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf 8997999999968997689999999988
No 303
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=43.16 E-value=30 Score=16.64 Aligned_cols=49 Identities=20% Similarity=0.328 Sum_probs=41.2
Q ss_pred CCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCC
Q ss_conf 986335999999819-9789999999999325905731565454000237
Q gi|254780620|r 21 NDYPNRISQIAEACC-ISELFLFKILQPLVKAGIVETVRGRRGGVRLCRP 69 (144)
Q Consensus 21 ~~~~~s~~eIA~~~~-i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~ 69 (144)
.+.+-|..++.+..+ .|+..+.+.+..|.+.|++....+...+++....
T Consensus 22 ~g~~ps~~e~~~~~~~~s~~~~~~~l~~L~~~g~i~~~~~~~r~i~~~~~ 71 (201)
T COG1974 22 TGYPPSIREIGDALGLASPSAIHSHLKALERKGYIRRDPTKARAIRILQL 71 (201)
T ss_pred HCCCCHHHHHHHHHCCCCHHHHHHHHHHHHCCCCEEECCCCCCCEECCCC
T ss_conf 28993089998751789848999999997308858745898743011244
No 304
>PRK12370 invasion protein regulator; Provisional
Probab=43.03 E-value=30 Score=16.63 Aligned_cols=60 Identities=22% Similarity=0.204 Sum_probs=41.8
Q ss_pred HHHHHHHHHHCCCCCCCHHHHHHHH----CCCHHHHH-------HHHHHHHHCCCEEECCCCCCCCEECCCHH
Q ss_conf 9999999985598633599999981----99789999-------99999932590573156545400023721
Q gi|254780620|r 10 GIRVLMYCAIHNDYPNRISQIAEAC----CISELFLF-------KILQPLVKAGIVETVRGRRGGVRLCRPAD 71 (144)
Q Consensus 10 Ai~~l~~La~~~~~~~s~~eIA~~~----~i~~~~l~-------kil~~L~~agli~S~rG~~GGy~Lak~~~ 71 (144)
++-.|++|-.+.|+.+|-.||=+.. -+|..-+. |++..=....||+++.|+ ||++..|..
T Consensus 40 vf~lL~lLvenrdrvVSKdELi~~VW~griVSEstLtsrI~a~RkaLgD~~eqr~IrTv~gk--GyRF~~~V~ 110 (553)
T PRK12370 40 EYAVLVILLEAAGEIVSKNTLLDQVWGDAEVNEESLTRCIYALRRILSEDKEHRYIETLYGQ--GYRFNRPVV 110 (553)
T ss_pred HHHHHHHHHHCCCCEECHHHHHHHHCCCCEECHHHHHHHHHHHHHHHCCCCCCEEEEHHCCC--CEEECCCCC
T ss_conf 99999999847675374999999835996203889999999999985875445024410378--424256402
No 305
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=42.87 E-value=30 Score=16.62 Aligned_cols=28 Identities=18% Similarity=-0.056 Sum_probs=19.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCC
Q ss_conf 3599999981997899999999993259
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQPLVKAG 52 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~~L~~ag 52 (144)
-+.++||+.+++|+.-++.+...+....
T Consensus 149 ~~~~eiA~~l~~~~~~v~~~~~~~~~~~ 176 (289)
T PRK07500 149 EIHREIATALGVSLSDVEMMDARLSGPD 176 (289)
T ss_pred CHHHHHHHHHCCCHHHHHHHHHHHHCCC
T ss_conf 4399999880999999999999973798
No 306
>pfam09681 Phage_rep_org_N N-terminal phage replisome organiser (Phage_rep_org_N). This entry represents the N-terminal domain of a small family of phage proteins. The protein contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The region is N-terminal to the low-complexity region.
Probab=42.82 E-value=30 Score=16.61 Aligned_cols=44 Identities=16% Similarity=0.157 Sum_probs=35.9
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECC
Q ss_conf 6335999999819978999999999932590573156545400023
Q gi|254780620|r 23 YPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCR 68 (144)
Q Consensus 23 ~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak 68 (144)
-|.+.++||...+.|...++.-|+.+.+-|+|+-.- +|=|.+..
T Consensus 52 ipy~~e~LA~~~~~~~~~V~~Al~~f~~~glIe~~e--~g~i~i~~ 95 (121)
T pfam09681 52 IPYTAEMLATIFDRPLNTVRLALKVFEKLGMIEITE--NGVIKIPN 95 (121)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEC--CCEEEEEC
T ss_conf 898799999998888789999999999889789802--99388653
No 307
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; InterPro: IPR014327 The bacterial core RNA polymerase complex, which consists of five subunits, 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 . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This group of sigma factors are members of the sigma-70 family and are found primarily in the genus Bacteroides. This appears to have resulted from a lineage-specific expansion as Bacteroides thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037 (Tannerella forsythensis ATCC 43037), Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currently only two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=42.34 E-value=31 Score=16.57 Aligned_cols=33 Identities=18% Similarity=0.036 Sum_probs=22.2
Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 99999985598633599999981997899999999
Q gi|254780620|r 12 RVLMYCAIHNDYPNRISQIAEACCISELFLFKILQ 46 (144)
Q Consensus 12 ~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~ 46 (144)
|-+--|+...| .|-+|||+.+|||+..|+.-++
T Consensus 125 R~iF~lsr~eg--~s~~EIA~~L~iS~~TVe~hi~ 157 (167)
T TIGR02985 125 REIFILSRFEG--LSNKEIAEELGISVKTVEYHIT 157 (167)
T ss_pred HHHHHHHHHHC--CCHHHHHHHHCCCHHHHHHHHH
T ss_conf 99999988617--9867899884898889999999
No 308
>pfam01418 HTH_6 Helix-turn-helix domain, rpiR family. This domain contains a helix-turn-helix motif. The best characterized member of this family is RpiR, a regulator of the expression of rpiB gene.
Probab=42.15 E-value=31 Score=16.55 Aligned_cols=45 Identities=20% Similarity=0.253 Sum_probs=35.0
Q ss_pred HHHHHHHHHCCCC--CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Q ss_conf 9999999855986--33599999981997899999999993259057
Q gi|254780620|r 11 IRVLMYCAIHNDY--PNRISQIAEACCISELFLFKILQPLVKAGIVE 55 (144)
Q Consensus 11 i~~l~~La~~~~~--~~s~~eIA~~~~i~~~~l~kil~~L~~agli~ 55 (144)
-++.-|+-.|++. ..|+.+||+..++|++-+-|..++|-=.||-+
T Consensus 19 ~~ia~yil~~~~~~~~~si~~lA~~~~vS~atv~Rf~kklG~~Gf~e 65 (106)
T pfam01418 19 KKIADYILASPDNAIHLSIAELAKAAGVSEASVVRFCRKLGFSGFSD 65 (106)
T ss_pred HHHHHHHHHCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHCCCCHHH
T ss_conf 99999999299999883399999896998999999999958998999
No 309
>KOG1511 consensus
Probab=42.15 E-value=31 Score=16.55 Aligned_cols=45 Identities=20% Similarity=0.186 Sum_probs=34.5
Q ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCC-CCEECCCHHHC
Q ss_conf 9999819978999999999932590573156545-40002372126
Q gi|254780620|r 29 QIAEACCISELFLFKILQPLVKAGIVETVRGRRG-GVRLCRPADQI 73 (144)
Q Consensus 29 eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~G-Gy~Lak~~~~I 73 (144)
.+-+..|++.+-+++|.+..++-||..--.|++| |+.+.-=+..+
T Consensus 303 ~LL~alGVsH~~le~v~~~t~k~gi~sKLTGAGgGGc~itlL~~~~ 348 (397)
T KOG1511 303 DLLDALGVSHPSLELVCTTTRKLGIHSKLTGAGGGGCVITLLKPGT 348 (397)
T ss_pred HHHHHHCCCCHHHHHHHHHHHHHCCCEECCCCCCCCEEEEEECCCC
T ss_conf 8898757794889999999998286000123787865999978998
No 310
>pfam10078 DUF2316 Uncharacterized protein conserved in bacteria (DUF2316). Members of this family of hypothetical bacterial proteins have no known function.
Probab=42.14 E-value=31 Score=16.55 Aligned_cols=46 Identities=17% Similarity=-0.009 Sum_probs=30.9
Q ss_pred CCCCHHHHHHHHHHHHHHHC-CCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 97645689999999999855-9863359999998199789999999999
Q gi|254780620|r 1 MHLTKRTDYGIRVLMYCAIH-NDYPNRISQIAEACCISELFLFKILQPL 48 (144)
Q Consensus 1 Mkis~~~~yAi~~l~~La~~-~~~~~s~~eIA~~~~i~~~~l~kil~~L 48 (144)
|-+|..-.-+-+ ..|..+ .-...|.++||+.+++++..+++||+.=
T Consensus 1 MSLn~~Q~~~T~--~ELqeNf~~~~ls~~~iA~dL~~s~~~ve~vL~m~ 47 (89)
T pfam10078 1 MSLNIEEMQATR--KELQANFELSGLTIEQVAKDLNTTPEKVEALLQLK 47 (89)
T ss_pred CCCCHHHHHHHH--HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCC
T ss_conf 998899999999--99999998838989999989499999999999734
No 311
>KOG0538 consensus
Probab=41.46 E-value=21 Score=17.59 Aligned_cols=84 Identities=25% Similarity=0.200 Sum_probs=51.1
Q ss_pred HHHHCCCEEECCCCCCCCEECCCHHHCC-HHHHHHHHCCCCCCCCCCC--C---------CCCCC-----------CCCC
Q ss_conf 9932590573156545400023721260-9999999718763111468--8---------77888-----------7656
Q gi|254780620|r 47 PLVKAGIVETVRGRRGGVRLCRPADQIT-ILDVVKATEESFFVAECFA--S---------HKIDC-----------PLVG 103 (144)
Q Consensus 47 ~L~~agli~S~rG~~GGy~Lak~~~~It-l~dI~~aie~~~~~~~C~~--~---------~~~~C-----------~~~~ 103 (144)
.---+|||-|. +||-+|---|..|+ |-+|++|+++.+..+--.. . -...| ...+
T Consensus 242 e~G~~GIIVSN---HGgRQlD~vpAtI~~L~Evv~aV~~ri~V~lDGGVR~G~DVlKALALGAk~VfiGRP~v~gLA~~G 318 (363)
T KOG0538 242 EAGVAGIIVSN---HGGRQLDYVPATIEALPEVVKAVEGRIPVFLDGGVRRGTDVLKALALGAKGVFIGRPIVWGLAAKG 318 (363)
T ss_pred HHCCCEEEEEC---CCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHCCCCEEEECCCCEEEECCCC
T ss_conf 80886599857---875325766411887999999862854799726733542799998516736885672102000256
Q ss_pred CCCHHHHHHHHHHHHHHHH---HHCCHHHHHHC
Q ss_conf 6447999999999999998---41799999915
Q gi|254780620|r 104 SCGLTSVLRKALNAFFDVL---TQYSIECLVRN 133 (144)
Q Consensus 104 ~c~~~~~~~~~~~~~~~~L---~~~TL~dl~~~ 133 (144)
.-.+..+++-+.+.|.-.| .-.|++++-++
T Consensus 319 e~GV~~vl~iL~~efe~tmaLsGc~sv~ei~~~ 351 (363)
T KOG0538 319 EAGVKKVLDILRDEFELTMALSGCRSVKEITRN 351 (363)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCCHHHCCCC
T ss_conf 032999999999999999998478606540745
No 312
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=41.45 E-value=32 Score=16.48 Aligned_cols=25 Identities=16% Similarity=0.347 Sum_probs=12.1
Q ss_pred CCCCCCEECCCHHHCCHHHHHHHH-CCC
Q ss_conf 654540002372126099999997-187
Q gi|254780620|r 59 GRRGGVRLCRPADQITILDVVKAT-EES 85 (144)
Q Consensus 59 G~~GGy~Lak~~~~Itl~dI~~ai-e~~ 85 (144)
|+. || +.|+.+.-.+.+-++.+ .|.
T Consensus 95 Ga~-g~-l~K~~~~~~l~~aI~~v~~G~ 120 (204)
T PRK09958 95 GAN-GF-VSKKEGMNNIIAAIEAAKNGY 120 (204)
T ss_pred CCC-EE-EECCCCHHHHHHHHHHHHCCC
T ss_conf 863-79-978999999999999997799
No 313
>PRK11778 putative periplasmic protease; Provisional
Probab=41.35 E-value=24 Score=17.24 Aligned_cols=64 Identities=27% Similarity=0.214 Sum_probs=35.1
Q ss_pred HHHHHHHHHHCCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEC--C--CCCCCCEECCCHHHCC
Q ss_conf 9999999985598633-59999998199789999999999325905731--5--6545400023721260
Q gi|254780620|r 10 GIRVLMYCAIHNDYPN-RISQIAEACCISELFLFKILQPLVKAGIVETV--R--GRRGGVRLCRPADQIT 74 (144)
Q Consensus 10 Ai~~l~~La~~~~~~~-s~~eIA~~~~i~~~~l~kil~~L~~agli~S~--r--G~~GGy~Lak~~~~It 74 (144)
-|-+++-.|..+++.+ ..+ =....=-.+-..+--|+.|+.+|+=-++ - .+.|||..|..+++|-
T Consensus 91 eitaiL~~a~~~DeV~~rle-s~GG~v~~yglaasql~rlr~~~i~ltv~vd~VAASGGY~mAc~ADkIv 159 (317)
T PRK11778 91 EITAILAVAKPGDEVLLRLE-SPGGVVHGYGLAASQLQRLRDAGIPLTVCVDKVAASGGYMMACVADKII 159 (317)
T ss_pred HHHHHHHHCCCCCEEEEEEE-CCCCEEEHHHHHHHHHHHHHHCCCCEEEEEEEEECCCCEEEEECCCEEE
T ss_conf 99999974878986999997-8995666057799999999867992899970130243022652188799
No 314
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer 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=41.17 E-value=32 Score=16.46 Aligned_cols=39 Identities=26% Similarity=0.353 Sum_probs=29.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECC
Q ss_conf 35999999819978999999999932590573156545400023
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCR 68 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak 68 (144)
.|..|+|+..|+++.-++ ---+.|++...|.. |||++=.
T Consensus 1 ytI~eva~~~gvs~~tlR----~ye~~gLl~p~R~~-~g~R~Y~ 39 (49)
T cd04761 1 YTIGELAKLTGVSPSTLR----YYERIGLLSPARTE-GGYRLYS 39 (49)
T ss_pred CCHHHHHHHHCCCHHHHH----HHHHCCCCCCCCCC-CCCEEEC
T ss_conf 958899999893999999----99997998988099-9998619
No 315
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=40.22 E-value=33 Score=16.37 Aligned_cols=12 Identities=17% Similarity=0.094 Sum_probs=6.4
Q ss_pred HHHHCCHHHHHH
Q ss_conf 984179999991
Q gi|254780620|r 121 VLTQYSIECLVR 132 (144)
Q Consensus 121 ~L~~~TL~dl~~ 132 (144)
.+++.|.+++.+
T Consensus 167 ~~eg~s~~EIA~ 178 (209)
T PRK08295 167 YLDGKSYQEIAE 178 (209)
T ss_pred HHCCCCHHHHHH
T ss_conf 986999999999
No 316
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=39.92 E-value=28 Score=16.86 Aligned_cols=20 Identities=20% Similarity=0.293 Sum_probs=7.5
Q ss_pred CHHHHHHHHCCCHHHHHHHH
Q ss_conf 59999998199789999999
Q gi|254780620|r 26 RISQIAEACCISELFLFKIL 45 (144)
Q Consensus 26 s~~eIA~~~~i~~~~l~kil 45 (144)
|.++||+..|+|...++++|
T Consensus 3 Ti~DVA~~AGVS~aTVSrvL 22 (346)
T PRK10401 3 TIRDVARQAGVSVATVSRVL 22 (346)
T ss_pred CHHHHHHHHCCCHHHHHHHH
T ss_conf 78999999897999999997
No 317
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=39.81 E-value=34 Score=16.33 Aligned_cols=14 Identities=7% Similarity=0.159 Sum_probs=7.7
Q ss_pred HHHHHHCCHHHHHH
Q ss_conf 99984179999991
Q gi|254780620|r 119 FDVLTQYSIECLVR 132 (144)
Q Consensus 119 ~~~L~~~TL~dl~~ 132 (144)
...+++.|.+++.+
T Consensus 130 L~~~eGls~~EIA~ 143 (172)
T PRK12523 130 YNRLDGMGHAEIAE 143 (172)
T ss_pred HHHHCCCCHHHHHH
T ss_conf 99993999999999
No 318
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=39.78 E-value=34 Score=16.33 Aligned_cols=60 Identities=25% Similarity=0.257 Sum_probs=40.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHHHCCCCCC
Q ss_conf 3599999981997899999999993259057315654540002372126099999997187631
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKATEESFFV 88 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~aie~~~~~ 88 (144)
.|..|+|+..|+++..|+- .=++-|++...|. .|||++=.+.+=-.+.-|-...+....+
T Consensus 1 ysI~eva~~~Gv~~~tLR~---wE~~~~l~~p~R~-~~g~R~Ys~~di~~l~~I~~l~~~G~~i 60 (68)
T cd04763 1 YTIGEVALLTGIKPHVLRA---WEREFGLLKPQRS-DGGHRLFNDADIDRILEIKRWIDNGVQV 60 (68)
T ss_pred CCHHHHHHHHCCCHHHHHH---HHHCCCCCCCCCC-CCCCCCCCHHHHHHHHHHHHHHHCCCCH
T ss_conf 9788999998879457589---8870589998679-9999654999999999999999979989
No 319
>COG0112 GlyA Glycine/serine hydroxymethyltransferase [Amino acid transport and metabolism]
Probab=39.77 E-value=19 Score=17.77 Aligned_cols=55 Identities=27% Similarity=0.469 Sum_probs=35.0
Q ss_pred HHHHHHHHCCC----HHHHHHHH------HHHHHCCCEEE-----CCCCCCCCEECCCHHHCCHHHHHHHHCCCCC
Q ss_conf 99999981997----89999999------99932590573-----1565454000237212609999999718763
Q gi|254780620|r 27 ISQIAEACCIS----ELFLFKIL------QPLVKAGIVET-----VRGRRGGVRLCRPADQITILDVVKATEESFF 87 (144)
Q Consensus 27 ~~eIA~~~~i~----~~~l~kil------~~L~~agli~S-----~rG~~GGy~Lak~~~~Itl~dI~~aie~~~~ 87 (144)
.++||+..|.= -.|+.-++ +.+..|.+|+| .|||.||..|+++ .++.+.++...+
T Consensus 186 ~reIad~VGA~L~~DmAHiaGLVA~G~~p~P~~~AdvVTtTTHKTlrGPrGG~Il~~~------eel~kkin~aVF 255 (413)
T COG0112 186 FREIADEVGAYLMVDMAHVAGLIAGGVHPNPLPHADVVTTTTHKTLRGPRGGIILTND------EELAKKINSAVF 255 (413)
T ss_pred HHHHHHHHCCEEEEHHHHHHHHHHCCCCCCCCCCCCEEECCCCCCCCCCCCEEEEECC------HHHHHHHHHHCC
T ss_conf 9999987193677217788888745667999875526757753477899841798362------999987640007
No 320
>pfam00356 LacI Bacterial regulatory proteins, lacI family.
Probab=39.67 E-value=27 Score=16.92 Aligned_cols=21 Identities=19% Similarity=0.328 Sum_probs=15.8
Q ss_pred CHHHHHHHHCCCHHHHHHHHH
Q ss_conf 599999981997899999999
Q gi|254780620|r 26 RISQIAEACCISELFLFKILQ 46 (144)
Q Consensus 26 s~~eIA~~~~i~~~~l~kil~ 46 (144)
|.++||+..|+|+..+.++|+
T Consensus 1 Ti~DIA~~agVS~~TVSr~ln 21 (46)
T pfam00356 1 TIKDVARLAGVSKATVSRVLN 21 (46)
T ss_pred CHHHHHHHHCCCHHHHHHHHC
T ss_conf 999999998979999999987
No 321
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=39.66 E-value=34 Score=16.32 Aligned_cols=36 Identities=19% Similarity=0.133 Sum_probs=25.7
Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 99999985598633599999981997899999999993
Q gi|254780620|r 12 RVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLV 49 (144)
Q Consensus 12 ~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~ 49 (144)
|.++.|....| .|.+|||+.+|+|...+...+..-.
T Consensus 16 r~vl~l~y~~~--~s~~EIa~~lgis~~tVk~~l~rA~ 51 (55)
T cd06171 16 REVILLRFGEG--LSYEEIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred HHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 89899999809--9999999998959999999999999
No 322
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. 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. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=39.20 E-value=35 Score=16.27 Aligned_cols=53 Identities=19% Similarity=0.264 Sum_probs=39.8
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHHHC
Q ss_conf 5999999819978999999999932590573156545400023721260999999971
Q gi|254780620|r 26 RISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKATE 83 (144)
Q Consensus 26 s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~aie 83 (144)
+..|+|+..|+|+..+ .-.-+.|++...+-..+||++= ..+++.-...++++-
T Consensus 2 ri~ElA~~~Gvs~~ti----R~YE~~GLlpp~~R~~nGYR~Y-~e~~l~~L~~iR~L~ 54 (99)
T cd04772 2 RTVDLARAIGLSPQTV----RNYESLGLIPPAERTANGYRIY-TDKHIAALRAYRALL 54 (99)
T ss_pred CHHHHHHHHCCCHHHH----HHHHHCCCCCCCCCCCCCCCCC-CHHHHHHHHHHHHHH
T ss_conf 7899999989699999----9999969999978699998348-999999999999980
No 323
>pfam05567 Neisseria_PilC Neisseria PilC protein. This family consists of several PilC protein sequences from Neisseria gonorrhoeae and N. meningitidis. PilC is a phase-variable protein associated with pilus-mediated adherence of pathogenic Neisseria to target cells.
Probab=39.17 E-value=20 Score=17.66 Aligned_cols=37 Identities=32% Similarity=0.363 Sum_probs=31.9
Q ss_pred CCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHH
Q ss_conf 9789999999999325905731565454000237212
Q gi|254780620|r 36 ISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQ 72 (144)
Q Consensus 36 i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~ 72 (144)
-+..-|+|.|......||+...-|.+|||.|.+-.++
T Consensus 567 ~~dstLAK~LrafAekgY~gdrYgvdGGfvlR~~~~~ 603 (1039)
T pfam05567 567 NTESTLAKELRAFAEKGYVGDRYGVDGGFVLRRVTDD 603 (1039)
T ss_pred CCCCHHHHHHHHHHHHCCCCCCEEECCCEEEEEECCC
T ss_conf 7811799999999860766663010485589970146
No 324
>pfam09286 Pro-kuma_activ Pro-kumamolisin, activation domain. Members of this family are found in various subtilase propeptides, and adopt a ferredoxin-like fold, with an alpha+beta sandwich. Cleavage of the domain results in activation of the peptide.
Probab=38.94 E-value=35 Score=16.25 Aligned_cols=64 Identities=16% Similarity=0.003 Sum_probs=48.7
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHHHCCCCCCCC
Q ss_conf 863359999998199789999999999325905731565454000237212609999999718763111
Q gi|254780620|r 22 DYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKATEESFFVAE 90 (144)
Q Consensus 22 ~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~aie~~~~~~~ 90 (144)
++-.|.+|+++..+-++..+.+|.+.|+..|+-.... ++|.+.-. +.|+.++=+++.-......
T Consensus 45 g~~Lt~~e~~~~~~ps~~~~~~V~~wL~~~g~~~~~~-~~~~~i~~----~~tv~~~e~~f~t~~~~y~ 108 (141)
T pfam09286 45 GKHLSREEVAALFAPSQETVDAVRAWLESAGITVERA-ANGDWITF----SGTVAQAERLFGTEFHRYE 108 (141)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCEEEE-CCCCEEEE----EEEHHHHHHHHCCEEEEEE
T ss_conf 6668999999887899999999999999869954885-17988999----9799999998688358999
No 325
>PRK09483 response regulator; Provisional
Probab=38.92 E-value=35 Score=16.25 Aligned_cols=26 Identities=15% Similarity=0.319 Sum_probs=14.2
Q ss_pred CCCCCCEECCCHHHCCHHHHHHHH-CCCC
Q ss_conf 654540002372126099999997-1876
Q gi|254780620|r 59 GRRGGVRLCRPADQITILDVVKAT-EESF 86 (144)
Q Consensus 59 G~~GGy~Lak~~~~Itl~dI~~ai-e~~~ 86 (144)
|+.| | +.|+...-.|.+-++++ .|..
T Consensus 97 Ga~g-y-l~K~~~~~~l~~ai~~v~~G~~ 123 (216)
T PRK09483 97 GAAG-Y-LSKGAAPQEVVSAIRSVHSGQR 123 (216)
T ss_pred CCCE-E-EECCCCHHHHHHHHHHHHCCCC
T ss_conf 8878-9-9479999999999999985997
No 326
>pfam08461 HTH_12 Ribonuclease R winged-helix domain. This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaebacteria.
Probab=38.80 E-value=35 Score=16.24 Aligned_cols=52 Identities=29% Similarity=0.250 Sum_probs=38.6
Q ss_pred HHHHHHHCCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHCCCEEECCCCCCCCEEC
Q ss_conf 9999985598633599999981-----997899999999993259057315654540002
Q gi|254780620|r 13 VLMYCAIHNDYPNRISQIAEAC-----CISELFLFKILQPLVKAGIVETVRGRRGGVRLC 67 (144)
Q Consensus 13 ~l~~La~~~~~~~s~~eIA~~~-----~i~~~~l~kil~~L~~agli~S~rG~~GGy~La 67 (144)
||-.|+.+ +.|+++++||+.+ +++..-++--|+.|-..||.+-+ |.. |-.|.
T Consensus 3 ILriL~~~-~~Pigak~ia~~L~~rG~~i~eRaVRYhL~~Lde~GlT~k~-g~~-Gr~iT 59 (66)
T pfam08461 3 ILRILAES-DKPIGAKIIAEELNLRGYDIGERAVRYHLRILDERGLTRRV-GYA-GREIT 59 (66)
T ss_pred HHHHHHHC-CCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCHHHH-CCC-CCEEC
T ss_conf 89999985-99864999999999828584089999999999886345762-788-75625
No 327
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=38.78 E-value=35 Score=16.23 Aligned_cols=52 Identities=19% Similarity=0.160 Sum_probs=33.0
Q ss_pred HHHHHHHHHCCCCCCC-HHHHHHH----HCCCHHHHHHHHHHHHHCCCEEECCCCCC
Q ss_conf 9999999855986335-9999998----19978999999999932590573156545
Q gi|254780620|r 11 IRVLMYCAIHNDYPNR-ISQIAEA----CCISELFLFKILQPLVKAGIVETVRGRRG 62 (144)
Q Consensus 11 i~~l~~La~~~~~~~s-~~eIA~~----~~i~~~~l~kil~~L~~agli~S~rG~~G 62 (144)
+-+|..|+..+.-..- .+.|.+. ..+++..+..+|++|.++|+|+|..+...
T Consensus 7 l~iL~~L~~~~~hGYei~k~i~~~~~~~~~~~~gtlYp~L~rLe~~glI~~~~~~~~ 63 (100)
T TIGR03433 7 LLILRTLALGPLHGYGIAQRIQQRSEDVLQVEEGSLYPALHRLEKRGWIAAEWGESE 63 (100)
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCEEEEEEECC
T ss_conf 999999824997799999999997499706787728999999998898488851057
No 328
>pfam00984 UDPG_MGDP_dh UDP-glucose/GDP-mannose dehydrogenase family, central domain. The UDP-glucose/GDP-mannose dehydrogenaseses are a small group of enzymes which possesses the ability to catalyse the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate.
Probab=38.54 E-value=23 Score=17.34 Aligned_cols=47 Identities=15% Similarity=0.075 Sum_probs=31.9
Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCC-CCCEECCCHHHC
Q ss_conf 99999981997899999999993259057315654-540002372126
Q gi|254780620|r 27 ISQIAEACCISELFLFKILQPLVKAGIVETVRGRR-GGVRLCRPADQI 73 (144)
Q Consensus 27 ~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~-GGy~Lak~~~~I 73 (144)
..+|+++.+++..-+.+.+..=.+-|---...|++ ||..|-||+..+
T Consensus 25 l~~l~~~~g~d~~~v~~~~~~d~ri~~~~~~pg~G~GG~ClpkD~~al 72 (96)
T pfam00984 25 LANICEAVGADVSEVARAAGLDPRIGRKFLNPGPGFGGSCFPKDPRAL 72 (96)
T ss_pred HHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCEEECCHHHHHHH
T ss_conf 999999949978882054101664466668899985114625419999
No 329
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; 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 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=37.88 E-value=36 Score=16.15 Aligned_cols=62 Identities=18% Similarity=0.180 Sum_probs=41.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHHHCCCCCCCC
Q ss_conf 359999998199789999999999325905731565454000237212609999999718763111
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKATEESFFVAE 90 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~aie~~~~~~~ 90 (144)
.|+.|+|+..|+|+.-+ .-=-+.|++.+.+-..+||++=.+.+--.|.-|..+-+-...+-+
T Consensus 1 ytIgelA~~~gvs~~tl----RyYe~~GLl~~~~r~~~gyR~Y~~~~v~rl~~I~~lr~lG~sL~e 62 (113)
T cd01109 1 YTIKEVAEKTGLSADTL----RYYEKEGLLPPVKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKD 62 (113)
T ss_pred CCHHHHHHHHCCCHHHH----HHHHHCCCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHCCCCHHH
T ss_conf 97889999989599999----999983897998408998862349898999979759987998999
No 330
>pfam08100 dimerization dimerization domain. This domain is found at the N-terminus of a variety of plant O-methyltransferases. It has been shown to mediate dimerization of these proteins.
Probab=37.80 E-value=37 Score=16.14 Aligned_cols=32 Identities=25% Similarity=0.298 Sum_probs=23.8
Q ss_pred HHHCCCCCCCHHHHHHHHC-CC---HHHHHHHHHHHH
Q ss_conf 9855986335999999819-97---899999999993
Q gi|254780620|r 17 CAIHNDYPNRISQIAEACC-IS---ELFLFKILQPLV 49 (144)
Q Consensus 17 La~~~~~~~s~~eIA~~~~-i~---~~~l~kil~~L~ 49 (144)
++.+ |++.|..||+.... .+ +.++.++|+.|.
T Consensus 15 I~~~-G~~~s~seias~Lp~~~p~~~~~l~RimRlLA 50 (50)
T pfam08100 15 IAKH-GKPLSPSELASKLPTVNPEAPVMLDRLLRLLA 50 (50)
T ss_pred HHHC-CCCCCHHHHHHHCCCCCCCCHHHHHHHHHHHC
T ss_conf 9886-89689999998678889861579999998759
No 331
>pfam08442 ATP-grasp_2 ATP-grasp domain.
Probab=37.44 E-value=12 Score=19.03 Aligned_cols=26 Identities=35% Similarity=0.677 Sum_probs=21.5
Q ss_pred HHCCCEEECCCCCCCCEECCCHHHCC
Q ss_conf 32590573156545400023721260
Q gi|254780620|r 49 VKAGIVETVRGRRGGVRLCRPADQIT 74 (144)
Q Consensus 49 ~~agli~S~rG~~GGy~Lak~~~~It 74 (144)
.|+.+...-||+.||..++++|++..
T Consensus 44 vKaQv~aGGRGKaGGVk~~~~~~ea~ 69 (202)
T pfam08442 44 VKAQVLAGGRGKAGGVKLAKSPEEAK 69 (202)
T ss_pred EEEEECCCCCCCCCEEEEECCHHHHH
T ss_conf 98742358887677389978999999
No 332
>COG2005 ModE N-terminal domain of molybdenum-binding protein [General function prediction only]
Probab=37.31 E-value=37 Score=16.10 Aligned_cols=47 Identities=32% Similarity=0.379 Sum_probs=32.3
Q ss_pred CHHHHHHHHCCCHHHHHHH---HHHHHHCCCEEECCCCC--CCCEECCCHHH
Q ss_conf 5999999819978999999---99993259057315654--54000237212
Q gi|254780620|r 26 RISQIAEACCISELFLFKI---LQPLVKAGIVETVRGRR--GGVRLCRPADQ 72 (144)
Q Consensus 26 s~~eIA~~~~i~~~~l~ki---l~~L~~agli~S~rG~~--GGy~Lak~~~~ 72 (144)
|+..=|+..++|+.+.--. |..+-...+|++.||.. ||-.|..-.+.
T Consensus 33 SIs~AAk~~GiSYk~AW~~i~~~n~~~~~plVe~~rGGk~gGga~LT~~g~~ 84 (130)
T COG2005 33 SISAAAKAAGISYKSAWDYIKALNRLLGEPLVERRRGGKGGGGAVLTDFGER 84 (130)
T ss_pred CHHHHHHHCCCCHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCHHHHHHHH
T ss_conf 8999999849977999999999999838870663357788885113799999
No 333
>PRK09430 djlA Dna-J like membrane chaperone protein; Provisional
Probab=37.09 E-value=38 Score=16.08 Aligned_cols=72 Identities=15% Similarity=0.135 Sum_probs=41.5
Q ss_pred HHHHHHHHHHCCCCCCC-----HHHHHHHHCCCHHHHHHHHHHHHHCCCEEE--CCCCCCCCEECCCHHHCCHHHHHHHH
Q ss_conf 99999999855986335-----999999819978999999999932590573--15654540002372126099999997
Q gi|254780620|r 10 GIRVLMYCAIHNDYPNR-----ISQIAEACCISELFLFKILQPLVKAGIVET--VRGRRGGVRLCRPADQITILDVVKAT 82 (144)
Q Consensus 10 Ai~~l~~La~~~~~~~s-----~~eIA~~~~i~~~~l~kil~~L~~agli~S--~rG~~GGy~Lak~~~~Itl~dI~~ai 82 (144)
-|.+|..+|...|.... ..+||+..++|+.-.++|++.....-=..+ .+...+|+. .++..-++.|-|+++
T Consensus 131 lL~~L~~iA~ADG~l~~~E~~~L~~Ia~~lg~s~~~f~~i~a~~~a~~~f~~~~~~~~~~~~~--~~~~~~~l~~~Y~iL 208 (269)
T PRK09430 131 FLEIQIQAAFADGSLHPNERQVLYVIAEELGFSRFQFDQLLRMMQAEFQFGQGGYQQQSGGWQ--QASSGPTLEDAYKVL 208 (269)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC--CCCCCCCCCCCHHHH
T ss_conf 999999999855899999999999999993989999999999999887530122001233335--678887766738996
Q ss_pred C
Q ss_conf 1
Q gi|254780620|r 83 E 83 (144)
Q Consensus 83 e 83 (144)
+
T Consensus 209 g 209 (269)
T PRK09430 209 G 209 (269)
T ss_pred C
T ss_conf 9
No 334
>cd04446 DEP_DEPDC4 DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in DEPDC4-like proteins. DEPDC4 is a DEP domain containing protein of unknown function.
Probab=37.05 E-value=37 Score=16.08 Aligned_cols=29 Identities=14% Similarity=0.126 Sum_probs=25.4
Q ss_pred CCCHHHHHHHHHHHHHCCCEEECCCCCCC
Q ss_conf 99789999999999325905731565454
Q gi|254780620|r 35 CISELFLFKILQPLVKAGIVETVRGRRGG 63 (144)
Q Consensus 35 ~i~~~~l~kil~~L~~agli~S~rG~~GG 63 (144)
.+|+.-..+++|+|-++++++.+.|+-|+
T Consensus 51 dVtR~q~v~Lcq~fl~~~VfE~v~~k~~~ 79 (95)
T cd04446 51 DVPRAKAVRLCQALMDCRVFEAVGTKVFK 79 (95)
T ss_pred CCCHHHHHHHHHHHHHCCCEECCCCCCCC
T ss_conf 87899999999999976920011331045
No 335
>PRK05949 RNA polymerase sigma factor; Validated
Probab=36.93 E-value=38 Score=16.06 Aligned_cols=35 Identities=11% Similarity=-0.050 Sum_probs=24.7
Q ss_pred HHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 99855986335999999819978999999999932
Q gi|254780620|r 16 YCAIHNDYPNRISQIAEACCISELFLFKILQPLVK 50 (144)
Q Consensus 16 ~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~ 50 (144)
.+...-+...+..|||+..++++..+..++.....
T Consensus 186 ~l~~~lgr~pt~~EiA~~l~i~~~~v~~~l~~~~~ 220 (327)
T PRK05949 186 ELSQKLGRSATPAEIAKALELEPSQIREYLSMARQ 220 (327)
T ss_pred HHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCC
T ss_conf 99998188998899998949999999999984188
No 336
>PRK13824 replication initiation protein RepC; Provisional
Probab=36.83 E-value=38 Score=16.05 Aligned_cols=49 Identities=20% Similarity=0.175 Sum_probs=35.0
Q ss_pred HHHHHHHHHH-HHCC------C-CCC---CHHHHHHHH-CCCHHHHHHHHHHHHHCCCEEE
Q ss_conf 9999999999-8559------8-633---599999981-9978999999999932590573
Q gi|254780620|r 8 DYGIRVLMYC-AIHN------D-YPN---RISQIAEAC-CISELFLFKILQPLVKAGIVET 56 (144)
Q Consensus 8 ~yAi~~l~~L-a~~~------~-~~~---s~~eIA~~~-~i~~~~l~kil~~L~~agli~S 56 (144)
+-++++|-.| +.++ + +++ |-..|+.+. |++...|++-+..|+.+|+|.=
T Consensus 55 dr~laVL~aLlsf~p~~~l~~~~~liVfpSN~~L~~R~~Gm~~sTlRRhLa~LveaGLI~r 115 (404)
T PRK13824 55 DRALAVLNALLSFYPETELSEEAGLVVFPSNAQLSLRAHGMAGATLRRHLAALVEAGLIIR 115 (404)
T ss_pred HHHHHHHHHHHCCCCCCCCCCCCCCEECCCHHHHHHHHCCCCHHHHHHHHHHHHHCCCEEE
T ss_conf 7689999999811884557889876322289999998759987899999999997695561
No 337
>COG0616 SppA Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=36.42 E-value=17 Score=18.09 Aligned_cols=35 Identities=29% Similarity=0.455 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHCC-CEEECCC--CCCCCEECCCHHHCC
Q ss_conf 9999999993259-0573156--545400023721260
Q gi|254780620|r 40 FLFKILQPLVKAG-IVETVRG--RRGGVRLCRPADQIT 74 (144)
Q Consensus 40 ~l~kil~~L~~ag-li~S~rG--~~GGy~Lak~~~~It 74 (144)
.+.+-++.|++.+ ++-++.+ ..|||.++..+++|-
T Consensus 117 ~i~~~l~~l~~~~PV~v~v~~~AASGGY~IA~aAd~I~ 154 (317)
T COG0616 117 LIARALKRLRAKKPVVVSVGGYAASGGYYIALAADKIV 154 (317)
T ss_pred HHHHHHHHHHHCCCEEEEECCCCCCHHHHHHHCCCEEE
T ss_conf 99999998753298999988732028999984078798
No 338
>PRK07239 bifunctional uroporphyrinogen-III synthetase/response regulator domain protein; Validated
Probab=36.24 E-value=39 Score=15.99 Aligned_cols=57 Identities=21% Similarity=0.127 Sum_probs=22.3
Q ss_pred HHHHHHCCCCCCCHHHHHHHH---CCCHHHHHHHHHHHHH----CCCEEECCCCCCCCEECCCHHH
Q ss_conf 999985598633599999981---9978999999999932----5905731565454000237212
Q gi|254780620|r 14 LMYCAIHNDYPNRISQIAEAC---CISELFLFKILQPLVK----AGIVETVRGRRGGVRLCRPADQ 72 (144)
Q Consensus 14 l~~La~~~~~~~s~~eIA~~~---~i~~~~l~kil~~L~~----agli~S~rG~~GGy~Lak~~~~ 72 (144)
|-.|+.++|..+|=.++...+ +....-++.-+..|+. .++|+++=.+ ||+|+.+|.+
T Consensus 315 lr~La~~pG~VvsR~~ll~~lpg~~~d~Have~av~RLR~alg~~~~v~TVvKR--GYRLa~~~~~ 378 (381)
T PRK07239 315 LRALAARPGRVVSRADLLRALPGGGTDEHAVETAVARLRTALGDPKLVQTVVKR--GYRLAVDPRD 378 (381)
T ss_pred HHHHHHCCCCEECHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEECC--CEEECCCCCC
T ss_conf 999973899667399999748899987068999999999855998616887224--2453337766
No 339
>TIGR01743 purR_Bsub pur operon repressor; InterPro: IPR010078 This entry represents the pur operon repressor PurR of low-GC Gram-positive bacteria. This homodimeric repressor contains a large region homologous to phosphoribosyltransferases and is inhibited by 5-phosphoribosyl 1-pyrophosphate.; GO: 0003677 DNA binding, 0016564 transcription repressor activity, 0016481 negative regulation of transcription, 0045982 negative regulation of purine base metabolic process.
Probab=36.02 E-value=39 Score=15.97 Aligned_cols=71 Identities=15% Similarity=0.242 Sum_probs=49.2
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHH-------HHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHHH
Q ss_conf 99999998559863359999998199789-------9999999993259057315654540002372126099999997
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCISEL-------FLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKAT 82 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i~~~-------~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~ai 82 (144)
.-+.-||-.||.+.++...=+++++...+ .+++++.+.. -|=|.++.|++||.+-.=.-.+-.--+-++-+
T Consensus 8 v~l~~~L~~nP~kLi~L~~F~d~y~~AKSsiSEDi~I~~~~le~~~-~G~~~T~~GAaGGv~YiP~~~~~~~~~fv~~l 85 (269)
T TIGR01743 8 VVLTKYLIENPNKLISLNKFSDKYESAKSSISEDIVIIKEVLEKFD-IGKLETVPGAAGGVKYIPEVSEKEAKEFVEEL 85 (269)
T ss_pred HHHHHHHHHCCEEECCCHHHHHHHHHHHCCHHHHHHHHHHHHHHCC-CCEEEEECCCCCCEEEECCCCCHHHHHHHHHH
T ss_conf 7767777427801027005787764211110144899999850068-86478614788970584564604568899999
No 340
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=35.84 E-value=39 Score=15.96 Aligned_cols=29 Identities=17% Similarity=0.158 Sum_probs=15.1
Q ss_pred CCCCCCCEECCCHHHCCHHHHHHHH-CCCCCC
Q ss_conf 5654540002372126099999997-187631
Q gi|254780620|r 58 RGRRGGVRLCRPADQITILDVVKAT-EESFFV 88 (144)
Q Consensus 58 rG~~GGy~Lak~~~~Itl~dI~~ai-e~~~~~ 88 (144)
.|+. ||.+...+. -.|.+.++++ .|...+
T Consensus 101 ~Ga~-Gyl~K~~~~-~~L~~AI~~v~~G~~~~ 130 (216)
T PRK10840 101 LDIE-GIVLKQGAP-TDLPKALAALQKGKKFT 130 (216)
T ss_pred CCCC-EEEECCCCH-HHHHHHHHHHHCCCCCC
T ss_conf 8974-899878999-99999999998799439
No 341
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares 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=35.61 E-value=40 Score=15.93 Aligned_cols=63 Identities=16% Similarity=0.131 Sum_probs=41.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECC-CCCCCCEECCCHHHCCHHHHHHHHCCCCCCCCC
Q ss_conf 3599999981997899999999993259057315-654540002372126099999997187631114
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQPLVKAGIVETVR-GRRGGVRLCRPADQITILDVVKATEESFFVAEC 91 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~r-G~~GGy~Lak~~~~Itl~dI~~aie~~~~~~~C 91 (144)
.|+.|+|+..|+|+..+ .-=-+.|+|...+ +..+||+.=.+-+--.+..|...-+-.+.+-+.
T Consensus 1 ~tIgevAk~~gvs~~Tl----RyYE~~GLl~P~~~~~~ngyR~Y~~~~i~~l~~I~~lr~~G~sL~eI 64 (108)
T cd01107 1 FTIGEFAKLSNLSIKAL----RYYDKIGLLKPAYVDPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEI 64 (108)
T ss_pred CCHHHHHHHHCCCHHHH----HHHHHCCCCCCCEECCCCCCEEECHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 97899999989599999----99998599885415699984437788989999999999979999999
No 342
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. 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=35.35 E-value=40 Score=15.91 Aligned_cols=63 Identities=19% Similarity=0.160 Sum_probs=42.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHHHCCCCCCCCC
Q ss_conf 3599999981997899999999993259057315654540002372126099999997187631114
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKATEESFFVAEC 91 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~aie~~~~~~~C 91 (144)
.|+.++|+..|+|+.-+ .---+.|++...+-..+||+.=.+-+-..|..|..+=+-.+++-++
T Consensus 1 ~tIge~Ak~~gvs~~tl----RyYe~~GLl~p~~~~~ngyR~Y~~~~~~~l~~I~~lr~~G~~L~eI 63 (96)
T cd04768 1 LTIGEFAKLAGVSIRTL----RHYDDIGLFKPAKIAENGYRYYSYAQLYQLQFILFLRELGFSLAEI 63 (96)
T ss_pred CCHHHHHHHHCCCHHHH----HHHHHCCCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 97899999988699999----9998439979872499998517999999999999999979999999
No 343
>TIGR02663 nifX nitrogen fixation protein NifX; InterPro: IPR013480 NifX is involved in the biosynthesis of the iron-molybdenum cofactor (FeMo-Co) found in the dinitrogenase enzyme of the nitrogenase complex in nitrogen-fixing bacteria. This complex catalyses the reduction of atmospheric dinitrogen to ammonia. The role of NifX in cofactor biosynthesis is not fully understood, though it appears to be associated with mature FeMo-Co and may be involved in the addition of heterometal and/or homocitrate .; GO: 0051540 metal cluster binding, 0009399 nitrogen fixation, 0051188 cofactor biosynthetic process.
Probab=35.32 E-value=17 Score=18.18 Aligned_cols=24 Identities=29% Similarity=0.319 Sum_probs=14.1
Q ss_pred CCCCCHHHHHHHH-----CCCHHHHHHHH
Q ss_conf 8633599999981-----99789999999
Q gi|254780620|r 22 DYPNRISQIAEAC-----CISELFLFKIL 45 (144)
Q Consensus 22 ~~~~s~~eIA~~~-----~i~~~~l~kil 45 (144)
.++.|.+++=+++ |.|||+|+|+|
T Consensus 97 ~~pesI~~~l~~l~~mL~G~PPPWLRK~L 125 (125)
T TIGR02663 97 NEPESISEVLEKLQKMLKGNPPPWLRKAL 125 (125)
T ss_pred CCCCCHHHHHHHHHHHHCCCCCCHHCCCC
T ss_conf 88726688999999873388671110039
No 344
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=35.09 E-value=37 Score=16.14 Aligned_cols=20 Identities=15% Similarity=0.262 Sum_probs=9.0
Q ss_pred CHHHHHHHHCCCHHHHHHHH
Q ss_conf 59999998199789999999
Q gi|254780620|r 26 RISQIAEACCISELFLFKIL 45 (144)
Q Consensus 26 s~~eIA~~~~i~~~~l~kil 45 (144)
|.++||+..|+|..-++++|
T Consensus 3 TIkDIA~~AGVS~sTVSrvL 22 (342)
T PRK10727 3 TIKDVARLAGVSVATVSRVI 22 (342)
T ss_pred CHHHHHHHHCCCHHHHHHHH
T ss_conf 88999999796999999997
No 345
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two 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 two conserved cysteines that define a monovalent copper ion 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=35.05 E-value=41 Score=15.88 Aligned_cols=60 Identities=15% Similarity=0.201 Sum_probs=36.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHHHCCCCCC
Q ss_conf 3599999981997899999999993259057315654540002372126099999997187631
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKATEESFFV 88 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~aie~~~~~ 88 (144)
.++.++|+..|+|+..+ ..--+.|++...+-..+||+.=-+.+--.|.-|..+-+-.+.+
T Consensus 1 M~Ige~Ak~~gvs~~tl----RyYe~~GLl~p~~r~~~gyR~Y~~~~~~~l~~I~~~r~~G~sL 60 (127)
T cd01108 1 MNIGEAAKLTGLSAKMI----RYYEEIGLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSL 60 (127)
T ss_pred CCHHHHHHHHCCCHHHH----HHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCH
T ss_conf 97899999989599999----9999858989865199998425199999999999999879989
No 346
>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=34.95 E-value=41 Score=15.87 Aligned_cols=61 Identities=25% Similarity=0.316 Sum_probs=37.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE-CCCCCCCCEECCCHHHCCHHHHHHHHCCCCCCCC
Q ss_conf 35999999819978999999999932590573-1565454000237212609999999718763111
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQPLVKAGIVET-VRGRRGGVRLCRPADQITILDVVKATEESFFVAE 90 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~~L~~agli~S-~rG~~GGy~Lak~~~~Itl~dI~~aie~~~~~~~ 90 (144)
.++.|+|+..|+|+.-+ ..--+.|++.. .|.. |||+.=-+-+--.|.-|..+-+-.+.+.+
T Consensus 1 m~Ige~A~~~gvs~~tl----R~Ye~~GLl~~~~R~~-~gyR~Y~~~~l~~l~~I~~lr~~G~sL~e 62 (123)
T cd04770 1 MKIGELAKAAGVSPDTI----RYYERIGLLPPPQRSE-NGYRLYGEADLARLRFIRRAQALGFSLAE 62 (123)
T ss_pred CCHHHHHHHHCCCHHHH----HHHHHCCCCCCCEECC-CCCEEEHHHHHHHHHHHHHHHHCCCCHHH
T ss_conf 96899999989599999----9999818987514679-99562137787889999999986999999
No 347
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=34.49 E-value=41 Score=15.83 Aligned_cols=14 Identities=7% Similarity=0.117 Sum_probs=6.9
Q ss_pred HHHHHHCCHHHHHH
Q ss_conf 99984179999991
Q gi|254780620|r 119 FDVLTQYSIECLVR 132 (144)
Q Consensus 119 ~~~L~~~TL~dl~~ 132 (144)
..++.+.|.+++.+
T Consensus 142 Lr~~~~ls~~EIA~ 155 (191)
T PRK12520 142 MREWLELETEEICK 155 (191)
T ss_pred HHHHHCCCHHHHHH
T ss_conf 99993899999999
No 348
>pfam00382 TFIIB Transcription factor TFIIB repeat.
Probab=34.25 E-value=39 Score=16.00 Aligned_cols=25 Identities=16% Similarity=0.307 Sum_probs=9.8
Q ss_pred HHHHHHH-CCCCCCCHHHHHHHHCCC
Q ss_conf 9999985-598633599999981997
Q gi|254780620|r 13 VLMYCAI-HNDYPNRISQIAEACCIS 37 (144)
Q Consensus 13 ~l~~La~-~~~~~~s~~eIA~~~~i~ 37 (144)
+.+|+|- ..+.+.|.+|||+..+++
T Consensus 42 A~iY~Acr~~~~~rt~~eia~v~~vs 67 (71)
T pfam00382 42 ACLYIACRLEEVKRTLKEISSVAQVS 67 (71)
T ss_pred HHHHHHHHHCCCCCCHHHHHHHHCCC
T ss_conf 99999999808998999999996898
No 349
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=34.19 E-value=42 Score=15.80 Aligned_cols=83 Identities=17% Similarity=0.148 Sum_probs=49.8
Q ss_pred CCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHHH
Q ss_conf 64568999999999985598633599999981997899999999993259057315654540002372126099999997
Q gi|254780620|r 3 LTKRTDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKAT 82 (144)
Q Consensus 3 is~~~~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~ai 82 (144)
+++.+-|.+-++ +-.++.+-.+-++|.+.++++..++..+|+.|..+.++.= ++. =.+..|-..-.+-+=+...
T Consensus 603 is~~s~~q~~vf--ll~n~~e~lt~eei~e~T~l~~~dl~~~L~sl~~ak~~~l--~~~--~~~~~p~~~fy~ne~f~~~ 676 (773)
T COG5647 603 ISTFSVYQLLVF--LLFNDHEELTFEEILELTKLSTDDLKRVLQSLSCAKLVVL--LKD--DKLVSPNTKFYVNENFSSK 676 (773)
T ss_pred HHHHHHHHHHHH--HHHCCCCCEEHHHHHHHCCCCHHHHHHHHHHHHHHHEEEE--CCC--CCCCCCCCEEEECCCCCCC
T ss_conf 237999999999--9816764221999974248885669999999874211233--366--5668988637871443354
Q ss_pred CCCCCCCCC
Q ss_conf 187631114
Q gi|254780620|r 83 EESFFVAEC 91 (144)
Q Consensus 83 e~~~~~~~C 91 (144)
-..+.++-|
T Consensus 677 ~~rIki~~~ 685 (773)
T COG5647 677 LERIKINYI 685 (773)
T ss_pred CCEEEECCC
T ss_conf 502430100
No 350
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=34.00 E-value=42 Score=15.78 Aligned_cols=27 Identities=19% Similarity=0.256 Sum_probs=12.9
Q ss_pred CCCCCCCEECCCHHHCCHHHHHHHH-CCCC
Q ss_conf 5654540002372126099999997-1876
Q gi|254780620|r 58 RGRRGGVRLCRPADQITILDVVKAT-EESF 86 (144)
Q Consensus 58 rG~~GGy~Lak~~~~Itl~dI~~ai-e~~~ 86 (144)
.|+.| | +.|+.+.=.+.+-++.+ .|..
T Consensus 98 ~Ga~g-~-l~K~~~~~~l~~ai~~v~~G~~ 125 (210)
T PRK09935 98 AGANG-F-VSKRKDLNDIYNAVQMILSGYS 125 (210)
T ss_pred CCCCE-E-EECCCCHHHHHHHHHHHHCCCC
T ss_conf 68776-8-8678999999999999985995
No 351
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=33.70 E-value=43 Score=15.75 Aligned_cols=14 Identities=14% Similarity=0.052 Sum_probs=7.5
Q ss_pred HHHHHHCCHHHHHH
Q ss_conf 99984179999991
Q gi|254780620|r 119 FDVLTQYSIECLVR 132 (144)
Q Consensus 119 ~~~L~~~TL~dl~~ 132 (144)
..++++.|..++.+
T Consensus 142 l~~~e~~s~~EIA~ 155 (189)
T PRK12515 142 LVYYHEKSVEEVGE 155 (189)
T ss_pred HHHHCCCCHHHHHH
T ss_conf 99984999999999
No 352
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=33.64 E-value=39 Score=15.97 Aligned_cols=23 Identities=13% Similarity=0.105 Sum_probs=17.4
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 33599999981997899999999
Q gi|254780620|r 24 PNRISQIAEACCISELFLFKILQ 46 (144)
Q Consensus 24 ~~s~~eIA~~~~i~~~~l~kil~ 46 (144)
.+|.++||+..|+|...++++|+
T Consensus 9 MaTikDIA~~aGVS~sTVSrvLn 31 (341)
T PRK11041 9 MATMKDVALKAGVSTATVSRALM 31 (341)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHC
T ss_conf 88899999997979999999978
No 353
>pfam07638 Sigma70_ECF ECF sigma factor. These proteins are probably RNA polymerase sigma factors belonging to the extra-cytoplasmic function (ECF) subfamily and show sequence similarity to pfam04542 and pfam04545.
Probab=33.56 E-value=43 Score=15.73 Aligned_cols=14 Identities=7% Similarity=0.140 Sum_probs=7.1
Q ss_pred HHHHHHCCHHHHHH
Q ss_conf 99984179999991
Q gi|254780620|r 119 FDVLTQYSIECLVR 132 (144)
Q Consensus 119 ~~~L~~~TL~dl~~ 132 (144)
..++++.|.+++..
T Consensus 146 L~~~eglS~~EIAe 159 (185)
T pfam07638 146 LRFFAGLSNDEIAE 159 (185)
T ss_pred HHHHCCCCHHHHHH
T ss_conf 89975999999999
No 354
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=33.52 E-value=43 Score=15.73 Aligned_cols=99 Identities=19% Similarity=0.163 Sum_probs=55.4
Q ss_pred HHHHHHHHCCCC--CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHHHCCCCCCC
Q ss_conf 999999855986--335999999819978999999999932590573156545400023721260999999971876311
Q gi|254780620|r 12 RVLMYCAIHNDY--PNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKATEESFFVA 89 (144)
Q Consensus 12 ~~l~~La~~~~~--~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~aie~~~~~~ 89 (144)
++--|+-.+++. ..|+.+||+..++|++-+-|..++|-=.||=+=+ +.|+....+= +...+.
T Consensus 22 ~iA~yil~~~~~~~~~si~elA~~a~VS~aTv~Rf~~kLGf~Gf~efk------~~l~~~l~~~----------~~~~~~ 85 (281)
T COG1737 22 KIADYILANPDEVALLSIAELAERAGVSPATVVRFARKLGFEGFSEFK------LALAQELAEG----------RAQLLR 85 (281)
T ss_pred HHHHHHHHCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHCCCCCHHHHH------HHHHHHHHHC----------CCCCCC
T ss_conf 999999939678856149999988199888999999985999889999------9999997633----------331000
Q ss_pred CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHH
Q ss_conf 1468877888765664479999999999999984179999991
Q gi|254780620|r 90 ECFASHKIDCPLVGSCGLTSVLRKALNAFFDVLTQYSIECLVR 132 (144)
Q Consensus 90 ~C~~~~~~~C~~~~~c~~~~~~~~~~~~~~~~L~~~TL~dl~~ 132 (144)
. ... +....-....++....+.+...++...-+++-+
T Consensus 86 ~-~~~-----~~~~~~~~~~~~~~~~~~l~~t~~~l~~~~l~~ 122 (281)
T COG1737 86 E-IAE-----DDGPESILEKLLAANIAALERTLNLLDEEALER 122 (281)
T ss_pred C-CCC-----CCCHHHHHHHHHHHHHHHHHHHHHHCCHHHHHH
T ss_conf 0-245-----675468999999999999999985368999999
No 355
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer 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=33.30 E-value=43 Score=15.71 Aligned_cols=62 Identities=19% Similarity=0.181 Sum_probs=40.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHHHCCCCCCCCC
Q ss_conf 3599999981997899999999993259057315654540002372126099999997187631114
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKATEESFFVAEC 91 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~aie~~~~~~~C 91 (144)
.|+.++|+..|+|+..|+ .--+.|+|...|.. |||+.=-+-+=..|..|...-+-...+.+.
T Consensus 1 ysI~eva~~~gvs~~tlR----~Ye~~GLl~p~r~~-~g~R~Y~~~~i~~l~~I~~lr~~G~sl~~I 62 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLR----YYEEKGLLPPERSE-NGYRLYSEEDLERLRLIRRLRELGLSLKEI 62 (100)
T ss_pred CCHHHHHHHHCCCHHHHH----HHHHCCCCCCCCCC-CCCCCCCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 978899999895999999----99876999988358-997425699999999999999979999999
No 356
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=33.09 E-value=39 Score=15.97 Aligned_cols=21 Identities=19% Similarity=0.328 Sum_probs=16.7
Q ss_pred CHHHHHHHHCCCHHHHHHHHH
Q ss_conf 599999981997899999999
Q gi|254780620|r 26 RISQIAEACCISELFLFKILQ 46 (144)
Q Consensus 26 s~~eIA~~~~i~~~~l~kil~ 46 (144)
|.++||+..|+|..-+.++|+
T Consensus 2 Ti~dvA~~aGVS~sTVSr~ln 22 (70)
T smart00354 2 TIKDVARLAGVSKATVSRVLN 22 (70)
T ss_pred CHHHHHHHHCCCHHHHHHHHC
T ss_conf 899999998959999999977
No 357
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=32.84 E-value=44 Score=15.66 Aligned_cols=13 Identities=8% Similarity=-0.018 Sum_probs=5.8
Q ss_pred HHHHHHCCHHHHH
Q ss_conf 9998417999999
Q gi|254780620|r 119 FDVLTQYSIECLV 131 (144)
Q Consensus 119 ~~~L~~~TL~dl~ 131 (144)
...+...|.+++.
T Consensus 130 L~~~egls~~EIA 142 (190)
T PRK12516 130 LIGASGFAYEEAA 142 (190)
T ss_pred HHHHCCCCHHHHH
T ss_conf 8998299999999
No 358
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=32.76 E-value=44 Score=15.66 Aligned_cols=26 Identities=19% Similarity=0.314 Sum_probs=10.9
Q ss_pred CCCCCCCEECCCHHHCCHHHHHHHH-CCC
Q ss_conf 5654540002372126099999997-187
Q gi|254780620|r 58 RGRRGGVRLCRPADQITILDVVKAT-EES 85 (144)
Q Consensus 58 rG~~GGy~Lak~~~~Itl~dI~~ai-e~~ 85 (144)
-|+.| |.+.. .+.=.+..-++.+ .|.
T Consensus 95 ~Ga~g-yl~K~-~~~~~l~~ai~~v~~G~ 121 (211)
T COG2197 95 AGADG-YLLKD-ASPEELVEAIRAVAAGG 121 (211)
T ss_pred CCCCE-EEECC-CCHHHHHHHHHHHHCCC
T ss_conf 79969-98679-99999999999997588
No 359
>COG2169 Ada Adenosine deaminase [Nucleotide transport and metabolism]
Probab=32.76 E-value=44 Score=15.66 Aligned_cols=49 Identities=10% Similarity=0.096 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Q ss_conf 68999999999985598633599999981997899999999993259057
Q gi|254780620|r 6 RTDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVE 55 (144)
Q Consensus 6 ~~~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~ 55 (144)
.++-.-.++-+|..+ .++.+.++++...+.++.|+.+++++-..-..++
T Consensus 80 ~~~~V~~a~~~ie~~-~~~~~le~la~~lg~sp~~~~R~FK~~~G~Tp~~ 128 (187)
T COG2169 80 RSGLVATACRLIEQN-PEKRWLEELADELGVSPSTLHRLFKAITGMTPKE 128 (187)
T ss_pred CCHHHHHHHHHHHCC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCHHH
T ss_conf 327999999999818-8746389999996789599999999983899999
No 360
>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=32.71 E-value=44 Score=15.65 Aligned_cols=62 Identities=19% Similarity=0.211 Sum_probs=43.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHHHCCCCCCCCC
Q ss_conf 3599999981997899999999993259057315654540002372126099999997187631114
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKATEESFFVAEC 91 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~aie~~~~~~~C 91 (144)
.++.|+|+..|+|+.- +.---+.|++.+.|.. +||+.=-+.+=-.|..|..+-+-..++-++
T Consensus 2 ~~Ige~a~~~gis~~t----lRyYe~~GLl~~~r~~-~gyR~Y~~~~i~~l~~I~~lr~~G~sL~eI 63 (102)
T cd04775 2 YTIGQMSRKFGVSRST----LLYYESIGLIPSARSE-ANYRLYSEADLSRLEKIVFLQAGGLPLEEI 63 (102)
T ss_pred CCHHHHHHHHCCCHHH----HHHHHHCCCCCCCCCC-CCCEECCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 8789999998949999----9999987999987399-999637899999999999999969999999
No 361
>pfam09397 Ftsk_gamma Ftsk gamma domain. 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=32.54 E-value=45 Score=15.63 Aligned_cols=39 Identities=15% Similarity=0.172 Sum_probs=34.6
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCC
Q ss_conf 863359999998199789999999999325905731565
Q gi|254780620|r 22 DYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGR 60 (144)
Q Consensus 22 ~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~ 60 (144)
.+..|+.-|-.+.+|-++...+|+-.|-..|+|....|.
T Consensus 19 ~~~~S~S~lQR~~~IGynRAariid~LE~~GiVsp~~g~ 57 (67)
T pfam09397 19 TQKASTSLLQRRLRIGYNRAARLIEQMEEEGIVGPANGS 57 (67)
T ss_pred HCCCCHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf 186348999999710506999999999998488887789
No 362
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=32.40 E-value=45 Score=15.62 Aligned_cols=13 Identities=15% Similarity=0.092 Sum_probs=6.8
Q ss_pred HHHHHCCHHHHHH
Q ss_conf 9984179999991
Q gi|254780620|r 120 DVLTQYSIECLVR 132 (144)
Q Consensus 120 ~~L~~~TL~dl~~ 132 (144)
..+++.|.+++.+
T Consensus 117 ~~~egls~~EIA~ 129 (159)
T PRK12527 117 RKLEGLSHQQIAE 129 (159)
T ss_pred HHHCCCCHHHHHH
T ss_conf 9873979999999
No 363
>COG4800 Predicted transcriptional regulator with an HTH domain [Transcription]
Probab=32.29 E-value=45 Score=15.61 Aligned_cols=23 Identities=30% Similarity=0.267 Sum_probs=19.8
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 33599999981997899999999
Q gi|254780620|r 24 PNRISQIAEACCISELFLFKILQ 46 (144)
Q Consensus 24 ~~s~~eIA~~~~i~~~~l~kil~ 46 (144)
-.+..|-|++.|+|++.|.||++
T Consensus 29 glt~~eFak~anIP~StLYKil~ 51 (170)
T COG4800 29 GLTPSEFAKRANIPLSTLYKILK 51 (170)
T ss_pred CCCHHHHHHHCCCCHHHHHHHHH
T ss_conf 99989998870998999999981
No 364
>pfam06413 Neugrin Neugrin. This family consists of several mouse and human neugrin proteins. Neugrin and m-neugrin are mainly expressed in neurons in the nervous system, and are thought to play an important role in the process of neuronal differentiation.
Probab=32.19 E-value=45 Score=15.60 Aligned_cols=51 Identities=20% Similarity=0.195 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHH----------------HHHHCCCEEECC
Q ss_conf 999999999985598633599999981997899999999----------------993259057315
Q gi|254780620|r 8 DYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQ----------------PLVKAGIVETVR 58 (144)
Q Consensus 8 ~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~----------------~L~~agli~S~r 58 (144)
.-|+.-+-||..+.-+.+|+..+|+...+++.-+++||. .|+++|++.+..
T Consensus 13 ~da~e~IR~Lh~~~Pe~~t~~~LAe~F~VSpeaIrRILKSKw~Pt~e~klKQD~kv~kk~G~~~~~~ 79 (225)
T pfam06413 13 WEAIEQIRYLKQEFPEEWTVPRLAEGFDVSTDVIRRVLKSKFVPTLERKLKQDQKVLKKAGLARQIL 79 (225)
T ss_pred HHHHHHHHHHHHHCCHHCCHHHHHHHCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCHHHHH
T ss_conf 9999999999873840115899986078899999999971578868887542289998525200022
No 365
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=31.92 E-value=43 Score=15.72 Aligned_cols=19 Identities=5% Similarity=-0.039 Sum_probs=7.8
Q ss_pred CCHHHHHHHHHHHHHCCCE
Q ss_conf 9789999999999325905
Q gi|254780620|r 36 ISELFLFKILQPLVKAGIV 54 (144)
Q Consensus 36 i~~~~l~kil~~L~~agli 54 (144)
+++..-+||++...+-||.
T Consensus 28 Vs~~Tr~rV~~aa~eLgY~ 46 (335)
T PRK10703 28 VAEETRNAVWAAIKELHYS 46 (335)
T ss_pred CCHHHHHHHHHHHHHHCCC
T ss_conf 8999999999999982999
No 366
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=31.90 E-value=40 Score=15.94 Aligned_cols=19 Identities=16% Similarity=0.134 Sum_probs=8.8
Q ss_pred CCHHHHHHHHHHHHHCCCE
Q ss_conf 9789999999999325905
Q gi|254780620|r 36 ISELFLFKILQPLVKAGIV 54 (144)
Q Consensus 36 i~~~~l~kil~~L~~agli 54 (144)
+++..-+||++.-.+-||.
T Consensus 30 Vs~~Tr~rV~~aa~eLgY~ 48 (330)
T PRK11303 30 ISDKTVEKVMAVVREHNYH 48 (330)
T ss_pred CCHHHHHHHHHHHHHHCCC
T ss_conf 6999999999999996899
No 367
>pfam08281 Sigma70_r4_2 Sigma-70, region 4. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif.
Probab=31.76 E-value=46 Score=15.56 Aligned_cols=37 Identities=24% Similarity=0.087 Sum_probs=25.4
Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 999999855986335999999819978999999999932
Q gi|254780620|r 12 RVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVK 50 (144)
Q Consensus 12 ~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~ 50 (144)
|.++.|..-.| .|.+|||+..|+|+.-+..-+..=++
T Consensus 16 r~~~~l~~~~~--~s~~eIA~~lg~s~~tVk~~l~RA~~ 52 (54)
T pfam08281 16 REVFLLRYLEG--LSYAEIAELLGISEGTVKSRLSRARK 52 (54)
T ss_pred HHHHHHHHHHC--CCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 98968799878--59999999989499999999999997
No 368
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=31.59 E-value=46 Score=15.54 Aligned_cols=37 Identities=30% Similarity=0.293 Sum_probs=29.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEE
Q ss_conf 359999998199789999999999325905731565454000
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRL 66 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~L 66 (144)
.+..|.|+..|+|+.-|+ .-.+.|.|.+.|=+ ||+++
T Consensus 1 lt~~e~A~~lgVs~~Tlr----rW~~~G~i~~~rt~-~GhRr 37 (49)
T cd04762 1 LTTKEAAELLGVSPSTLR----RWVKEGKLKAIRTP-GGHRR 37 (49)
T ss_pred CCHHHHHHHHCCCHHHHH----HHHHCCCCCEEECC-CCCEE
T ss_conf 988999999798999999----99987994315889-98776
No 369
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=31.50 E-value=46 Score=15.53 Aligned_cols=12 Identities=8% Similarity=0.069 Sum_probs=6.1
Q ss_pred HHHHCCHHHHHH
Q ss_conf 984179999991
Q gi|254780620|r 121 VLTQYSIECLVR 132 (144)
Q Consensus 121 ~L~~~TL~dl~~ 132 (144)
++++.+..++.+
T Consensus 138 ~~~g~s~~eIA~ 149 (180)
T PRK11924 138 YVEGLSYQEIAD 149 (180)
T ss_pred HHHCCCHHHHHH
T ss_conf 996859999999
No 370
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They 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=31.19 E-value=47 Score=15.50 Aligned_cols=63 Identities=21% Similarity=0.274 Sum_probs=40.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHHHCCCCCCCCC
Q ss_conf 3599999981997899999999993259057315654540002372126099999997187631114
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKATEESFFVAEC 91 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~aie~~~~~~~C 91 (144)
.++.|+|+..|+|...+ .---+.|++...+-..+||+.=-+-+--.|..|...-+-...+.+.
T Consensus 1 y~Ige~Ak~~gvs~~tl----RyYe~~GLl~p~~r~~~gyR~Y~~~~i~~l~~I~~lr~~G~sl~eI 63 (96)
T cd04788 1 WKIGELARRTGLSVRTL----HHYDHIGLLSPSQRTEGGHRLYDRADIRRLHQIIALRRLGFSLREI 63 (96)
T ss_pred CCHHHHHHHHCCCHHHH----HHHHHCCCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 94889999989599999----9999739989888799988218999999999999999979999999
No 371
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=30.92 E-value=36 Score=16.15 Aligned_cols=11 Identities=18% Similarity=0.434 Sum_probs=4.6
Q ss_pred CCCCCCEECCCHH
Q ss_conf 6545400023721
Q gi|254780620|r 59 GRRGGVRLCRPAD 71 (144)
Q Consensus 59 G~~GGy~Lak~~~ 71 (144)
|+.| | |.|+.+
T Consensus 97 GA~g-y-l~K~~~ 107 (202)
T PRK09390 97 GAID-F-IEKPFE 107 (202)
T ss_pred CCHH-H-CCCCCC
T ss_conf 9464-4-559999
No 372
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=30.81 E-value=48 Score=15.46 Aligned_cols=14 Identities=7% Similarity=0.133 Sum_probs=7.3
Q ss_pred HHHHHHCCHHHHHH
Q ss_conf 99984179999991
Q gi|254780620|r 119 FDVLTQYSIECLVR 132 (144)
Q Consensus 119 ~~~L~~~TL~dl~~ 132 (144)
...+++.|.+++.+
T Consensus 130 L~~~egls~~EIA~ 143 (172)
T PRK09651 130 LSQLDGLTYSEIAH 143 (172)
T ss_pred HHHHCCCCHHHHHH
T ss_conf 99883999999999
No 373
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=30.68 E-value=48 Score=15.45 Aligned_cols=14 Identities=14% Similarity=-0.043 Sum_probs=7.7
Q ss_pred HHHHHHCCHHHHHH
Q ss_conf 99984179999991
Q gi|254780620|r 119 FDVLTQYSIECLVR 132 (144)
Q Consensus 119 ~~~L~~~TL~dl~~ 132 (144)
..++.+.|.+++.+
T Consensus 139 L~~~~g~s~~EIA~ 152 (186)
T PRK05602 139 LQYYQGLSNIEAAR 152 (186)
T ss_pred HHHHCCCCHHHHHH
T ss_conf 99863899999999
No 374
>pfam07106 TBPIP Tat binding protein 1(TBP-1)-interacting protein (TBPIP). This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation.
Probab=30.61 E-value=48 Score=15.44 Aligned_cols=113 Identities=12% Similarity=0.091 Sum_probs=65.0
Q ss_pred HHHHHHHCCCCCCCHHHHHHHHC--CCHHHHHHHHHHHHHCCCEEECC-CCCCCCEECCCHHHCCHHHHHHHHCCCCCCC
Q ss_conf 99999855986335999999819--97899999999993259057315-6545400023721260999999971876311
Q gi|254780620|r 13 VLMYCAIHNDYPNRISQIAEACC--ISELFLFKILQPLVKAGIVETVR-GRRGGVRLCRPADQITILDVVKATEESFFVA 89 (144)
Q Consensus 13 ~l~~La~~~~~~~s~~eIA~~~~--i~~~~l~kil~~L~~agli~S~r-G~~GGy~Lak~~~~Itl~dI~~aie~~~~~~ 89 (144)
++-||-. .++|.|+.+|+..++ ++.+.+.|+|-.|+..|-|...- |+.==|....+.-+..=-+-+.+++..+.-
T Consensus 6 Vl~yl~~-qNRPys~~dv~~nL~~~~~K~~vqK~Ld~L~~~gki~~K~~GKqkiY~~~Q~~~~~~~~eel~~~d~~i~~- 83 (169)
T pfam07106 6 ILKYLNE-QNRPYSVQDVVDNLQNGLGKTAVQKALDELVDEGKIICKEYGKQKIYLCNQDQFELPSDEELNKLDMEIEE- 83 (169)
T ss_pred HHHHHHH-HCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHCCCEEEEECCCEEEEEECCCCCCCCCHHHHHHHHHHHHH-
T ss_conf 9999998-38998499999988162449999999999997697135435764577346201356998899876999999-
Q ss_pred CCCCCCCCCCCCCCC-CCHHHHHHHHHHHHHHHHHHCCHHHHHHCHHHHH
Q ss_conf 146887788876566-4479999999999999984179999991589899
Q gi|254780620|r 90 ECFASHKIDCPLVGS-CGLTSVLRKALNAFFDVLTQYSIECLVRNRSSIK 138 (144)
Q Consensus 90 ~C~~~~~~~C~~~~~-c~~~~~~~~~~~~~~~~L~~~TL~dl~~~~~~~~ 138 (144)
.... -.+..-...+...+.......|..++......++
T Consensus 84 -----------L~~~l~~l~~~~~~l~~el~~L~s~~t~eel~~~i~~L~ 122 (169)
T pfam07106 84 -----------LREEVQLLKQDCSTLEIELKSLTSDLTTEELQEEIQELK 122 (169)
T ss_pred -----------HHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf -----------999999999999999999999875899999999999999
No 375
>PRK10403 transcriptional regulator NarP; Provisional
Probab=30.58 E-value=48 Score=15.44 Aligned_cols=27 Identities=22% Similarity=0.345 Sum_probs=11.9
Q ss_pred CCCCCCCEECCCHHHCCHHHHHHHH-CCCC
Q ss_conf 5654540002372126099999997-1876
Q gi|254780620|r 58 RGRRGGVRLCRPADQITILDVVKAT-EESF 86 (144)
Q Consensus 58 rG~~GGy~Lak~~~~Itl~dI~~ai-e~~~ 86 (144)
.|.. ||. .|+.+.-.+.+.++.+ .|..
T Consensus 101 ~Ga~-gyl-~K~~~~~~l~~ai~~v~~G~~ 128 (215)
T PRK10403 101 AGAD-GYL-LKDSDPEVLLEAIRAGAKGSK 128 (215)
T ss_pred CCCC-EEE-ECCCCHHHHHHHHHHHHCCCC
T ss_conf 6876-688-489999999999999984998
No 376
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, 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 domain
Probab=30.20 E-value=49 Score=15.40 Aligned_cols=63 Identities=16% Similarity=0.141 Sum_probs=43.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHHHCCCCCCCCC
Q ss_conf 3599999981997899999999993259057315654540002372126099999997187631114
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKATEESFFVAEC 91 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~aie~~~~~~~C 91 (144)
.++.++|+..|+|+.. +.---+.|+|...+-..+||++=-+.+-..|.-|...=+-...+-+|
T Consensus 2 ~tI~e~Ak~~gvs~~T----LRyYe~~GLl~P~~r~~nGYR~Ys~~dl~rL~~I~~lr~lG~sL~eI 64 (172)
T cd04790 2 LTISQLARQFGLSRST----LLYYERIGLLSPSARSESNYRLYGERDLERLEQICAYRSAGVSLEDI 64 (172)
T ss_pred CCHHHHHHHHCCCHHH----HHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 9789999998949889----99999887989988499987077999999999999999879999999
No 377
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=30.18 E-value=49 Score=15.40 Aligned_cols=24 Identities=25% Similarity=0.185 Sum_probs=15.8
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 599999981997899999999993
Q gi|254780620|r 26 RISQIAEACCISELFLFKILQPLV 49 (144)
Q Consensus 26 s~~eIA~~~~i~~~~l~kil~~L~ 49 (144)
+.++||+.+++++.-+..+.+.+.
T Consensus 153 ~~~eiA~~l~~~~~~v~~~~~~l~ 176 (284)
T PRK06596 153 EVEMIAEELGVSEEEVREMESRLS 176 (284)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHC
T ss_conf 299999997919999999999853
No 378
>PRK10130 transcriptional regulator EutR; Provisional
Probab=29.42 E-value=50 Score=15.32 Aligned_cols=26 Identities=12% Similarity=0.207 Sum_probs=13.9
Q ss_pred HHHHHHHHHHHHHHHH-HCCHHHHHHC
Q ss_conf 9999999999999984-1799999915
Q gi|254780620|r 108 TSVLRKALNAFFDVLT-QYSIECLVRN 133 (144)
Q Consensus 108 ~~~~~~~~~~~~~~L~-~~TL~dl~~~ 133 (144)
+.+...+.+.+.+..+ .+|+.||.+.
T Consensus 239 r~Iv~ra~~~i~~~~~~pltv~~lc~~ 265 (350)
T PRK10130 239 RRLLSRAREYVLENMSEPVTVLDLCNQ 265 (350)
T ss_pred HHHHHHHHHHHHHCCCCCCCHHHHHHH
T ss_conf 999999999998486799999999988
No 379
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=29.40 E-value=51 Score=15.32 Aligned_cols=29 Identities=17% Similarity=0.056 Sum_probs=22.6
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 98633599999981997899999999993
Q gi|254780620|r 21 NDYPNRISQIAEACCISELFLFKILQPLV 49 (144)
Q Consensus 21 ~~~~~s~~eIA~~~~i~~~~l~kil~~L~ 49 (144)
-|...+.+|||+..++++.-+..++..-.
T Consensus 182 lGR~Pt~eEIA~~lgi~~~~v~~~l~~~~ 210 (320)
T PRK07921 182 LGREATDEELAEESGIPEEKINDLLEHSR 210 (320)
T ss_pred HCCCCCHHHHHHHCCCCHHHHHHHHHHCC
T ss_conf 38999899999881999999999999728
No 380
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=29.30 E-value=51 Score=15.31 Aligned_cols=35 Identities=29% Similarity=0.189 Sum_probs=23.0
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHH----HHHHHHH
Q ss_conf 99999998559863359999998199789999----9999993
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLF----KILQPLV 49 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~----kil~~L~ 49 (144)
..+|.+++. | .|.++||+..++++.-++ +++++|.
T Consensus 6 ~~il~~~~~--G--~s~~eIA~~L~is~~TV~~~~~~i~~Kl~ 44 (57)
T cd06170 6 REVLRLLAE--G--KTNKEIADILGISEKTVKTHLRNIMRKLG 44 (57)
T ss_pred HHHHHHHHC--C--CCHHHHHHHHCCCHHHHHHHHHHHHHHHC
T ss_conf 999999980--7--99999999989789999999999999868
No 381
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), 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=29.30 E-value=51 Score=15.31 Aligned_cols=62 Identities=11% Similarity=0.196 Sum_probs=44.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHHHC--CCCCCCCC
Q ss_conf 35999999819978999999999932590573156545400023721260999999971--87631114
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKATE--ESFFVAEC 91 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~aie--~~~~~~~C 91 (144)
+++.|+|+..|+|... +.---+.|++...+-..+||++ =+.+++.-...++... -...+.++
T Consensus 1 M~IgelA~~tGvs~~T----IRyYe~~GLL~p~~R~~~g~r~-Y~~~~v~rL~~Ir~l~~~lG~sL~eI 64 (95)
T cd04780 1 MRMSELSKRSGVSVAT----IKYYLREGLLPEGRRLAPNQAE-YSEAHVERLRLIRALQQEGGLPISQI 64 (95)
T ss_pred CCHHHHHHHHCCCHHH----HHHHHHCCCCCCCCCCCCCCEE-CCHHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 9789999998978999----9999997899987769998715-49999999999999999369999999
No 382
>pfam02796 HTH_7 Helix-turn-helix domain of resolvase.
Probab=28.93 E-value=37 Score=16.10 Aligned_cols=23 Identities=30% Similarity=0.336 Sum_probs=20.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 35999999819978999999999
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQP 47 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~~ 47 (144)
.+..+||+..++++..+.+++..
T Consensus 22 ~~i~~IA~~~~vsrsTvYRyl~~ 44 (45)
T pfam02796 22 ISIKQIAKIFGISRSTVYRYLAA 44 (45)
T ss_pred CCHHHHHHHHCCHHHHHHHHCCC
T ss_conf 94999999986008888764458
No 383
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=28.91 E-value=52 Score=15.27 Aligned_cols=57 Identities=18% Similarity=0.128 Sum_probs=33.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHHH
Q ss_conf 3599999981997899999999993259057315654540002372126099999997
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKAT 82 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~ai 82 (144)
.+..+|+...+++.+-+.+++..|+++|+--|.-.-... .+.-++.--.++||++..
T Consensus 317 y~l~~i~~~~k~~~P~~~~~i~aL~~~Gy~asrtH~~p~-~iKTdAp~~~i~~i~r~~ 373 (376)
T PRK04338 317 YDLHELAKKLKLSVPPLDEVLEALREAGFEASRTHFSPT-GFKTDAPLDEIKEIIKSL 373 (376)
T ss_pred EEHHHHHHHCCCCCCCHHHHHHHHHHCCCEEEECCCCCC-CEECCCCHHHHHHHHHHH
T ss_conf 868999986499999999999999977988996678999-880479999999999985
No 384
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=28.87 E-value=52 Score=15.26 Aligned_cols=44 Identities=23% Similarity=0.332 Sum_probs=34.6
Q ss_pred HHHHHHHHCCCC--CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Q ss_conf 999999855986--33599999981997899999999993259057
Q gi|254780620|r 12 RVLMYCAIHNDY--PNRISQIAEACCISELFLFKILQPLVKAGIVE 55 (144)
Q Consensus 12 ~~l~~La~~~~~--~~s~~eIA~~~~i~~~~l~kil~~L~~agli~ 55 (144)
++.-|+-.|++. ..|+.|||+..++|++-+-|..++|-=.||-+
T Consensus 33 ~IA~yIL~~~~~v~~~si~eLA~~~~vS~aTVvRf~kkLGf~Gf~e 78 (293)
T PRK11337 33 RVVDWLLKPGNLSCATALKDVAEALAVSEAMIVKVAKLLGFSGFRN 78 (293)
T ss_pred HHHHHHHCCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHCCCCHHH
T ss_conf 9999998298999766699999895998889999999957897899
No 385
>PTZ00095 40S ribosomal protein S19; Provisional
Probab=28.86 E-value=52 Score=15.26 Aligned_cols=44 Identities=30% Similarity=0.292 Sum_probs=29.9
Q ss_pred CCCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEECCCCCCCCEECC
Q ss_conf 335999999819--------------978999999999932590573156545400023
Q gi|254780620|r 24 PNRISQIAEACC--------------ISELFLFKILQPLVKAGIVETVRGRRGGVRLCR 68 (144)
Q Consensus 24 ~~s~~eIA~~~~--------------i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak 68 (144)
++-+..+...++ -|...++++||.|-++|+|+-.. .+||-+|+.
T Consensus 91 pvGV~~Lrk~YGg~krrG~~P~h~~~aSg~IiR~~LQqLE~~glVek~~-~~~GR~iT~ 148 (169)
T PTZ00095 91 DVGYGGLRKRFSSKKRRGSAPNHTVRASGKILRWICQQLEKLGLVEQGP-KKSGRRLTR 148 (169)
T ss_pred CCCHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCEEECC-CCCCCEECH
T ss_conf 9628899999788878988987777665389999999998788876468-999888787
No 386
>pfam10668 Phage_terminase Phage terminase small subunit. This family of small highly conserved proteins come from a subset of Firmicute species. Its putative function is as a phage terminase small subunit.
Probab=28.86 E-value=52 Score=15.26 Aligned_cols=32 Identities=22% Similarity=0.200 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 999999999985598633599999981997899999
Q gi|254780620|r 8 DYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFK 43 (144)
Q Consensus 8 ~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~k 43 (144)
|-|.. +|+- .++..+..+||+.+++|+..+++
T Consensus 10 DkA~e--iy~~--s~G~~~l~~IA~~L~vs~~~Irk 41 (60)
T pfam10668 10 DKAKE--MWKE--SGGTMKLKDIANKLNVSESQIRK 41 (60)
T ss_pred HHHHH--HHHH--CCCCEEHHHHHHHHCCCHHHHHH
T ss_conf 89999--9998--28964499999996879888760
No 387
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=28.75 E-value=52 Score=15.26 Aligned_cols=10 Identities=30% Similarity=0.152 Sum_probs=3.1
Q ss_pred HHHHHHHCCC
Q ss_conf 9999932590
Q gi|254780620|r 44 ILQPLVKAGI 53 (144)
Q Consensus 44 il~~L~~agl 53 (144)
|++.-.+-||
T Consensus 38 V~~aa~elgY 47 (327)
T PRK10339 38 ILEIAEKLEY 47 (327)
T ss_pred HHHHHHHHCC
T ss_conf 9999999689
No 388
>TIGR02392 rpoH_proteo alternative sigma factor RpoH; InterPro: IPR012759 The bacterial core RNA polymerase complex, which consists of five subunits, 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 . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents the proteobacterial clade of sigma factors called RpoH. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0008270 zinc ion binding, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent, 0009408 response to heat.
Probab=28.61 E-value=52 Score=15.23 Aligned_cols=23 Identities=17% Similarity=0.140 Sum_probs=18.2
Q ss_pred CC-CCCHHHHHHHHCCCHHHHHHH
Q ss_conf 86-335999999819978999999
Q gi|254780620|r 22 DY-PNRISQIAEACCISELFLFKI 44 (144)
Q Consensus 22 ~~-~~s~~eIA~~~~i~~~~l~ki 44 (144)
+. +.|..+||..+|||.-.++||
T Consensus 242 d~~~~TL~~LA~eygvSaERiRQi 265 (279)
T TIGR02392 242 DDGKLTLHELAAEYGVSAERIRQI 265 (279)
T ss_pred CCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 889964789998848746679999
No 389
>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=28.06 E-value=53 Score=15.18 Aligned_cols=62 Identities=27% Similarity=0.352 Sum_probs=40.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHHHCCCCCCCCC
Q ss_conf 3599999981997899999999993259057315654540002372126099999997187631114
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKATEESFFVAEC 91 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~aie~~~~~~~C 91 (144)
.++.|+|+..|+|+.-+ .-=-+.|+|.+.|.. +||+.=.+-+=-.+.-|-.+-.-...+.++
T Consensus 2 ~~Ige~A~~~gvs~~Tl----RyYe~~GLl~~~R~~-ngyR~Y~~~~l~~l~~I~~lr~~G~sL~eI 63 (102)
T cd04789 2 YTISELAEKAGISRSTL----LYYEKLGLITGTRNA-NGYRLYPDSDLQRLLLIQQLQAGGLSLKEC 63 (102)
T ss_pred CCHHHHHHHHCCCHHHH----HHHHHCCCCCCCCCC-CCCCCCCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 80999999989799999----999986998988199-999506999999999999999979989999
No 390
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=27.66 E-value=54 Score=15.13 Aligned_cols=45 Identities=20% Similarity=0.175 Sum_probs=34.4
Q ss_pred HHHHHHHHHCCCC--CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Q ss_conf 9999999855986--33599999981997899999999993259057
Q gi|254780620|r 11 IRVLMYCAIHNDY--PNRISQIAEACCISELFLFKILQPLVKAGIVE 55 (144)
Q Consensus 11 i~~l~~La~~~~~--~~s~~eIA~~~~i~~~~l~kil~~L~~agli~ 55 (144)
-++.-|+-.|++. ..|+.+||+..++|++-+-|..++|-=.||-+
T Consensus 19 k~IA~yIl~n~~~v~~~si~eLA~~~~vS~aTVvRf~kkLGf~Gf~e 65 (282)
T PRK11557 19 RKLADYLLLQPDTARHLSSQQLANEAGVSQSSVVKFAQKLGYKGFPA 65 (282)
T ss_pred HHHHHHHHCCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHCCCCHHH
T ss_conf 99999998098999765699999896999889999999938998999
No 391
>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=27.41 E-value=55 Score=15.11 Aligned_cols=39 Identities=18% Similarity=0.175 Sum_probs=34.4
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCC
Q ss_conf 863359999998199789999999999325905731565
Q gi|254780620|r 22 DYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGR 60 (144)
Q Consensus 22 ~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~ 60 (144)
.+..|++-|-.+.+|.++...+|+-.|-..|+|....|.
T Consensus 17 ~~~~S~S~lQR~l~IGynRAariid~lE~~GiVsp~~g~ 55 (63)
T smart00843 17 TQKASTSLLQRRLRIGYNRAARLIDQLEEEGIVGPANGS 55 (63)
T ss_pred HCCCCHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf 086248999999720506999999999998587887799
No 392
>PRK10651 transcriptional regulator NarL; Provisional
Probab=27.39 E-value=55 Score=15.10 Aligned_cols=28 Identities=18% Similarity=0.368 Sum_probs=11.5
Q ss_pred CCCCCCCEECCCHHHCCHHHHHHHH-CCCCC
Q ss_conf 5654540002372126099999997-18763
Q gi|254780620|r 58 RGRRGGVRLCRPADQITILDVVKAT-EESFF 87 (144)
Q Consensus 58 rG~~GGy~Lak~~~~Itl~dI~~ai-e~~~~ 87 (144)
.|+. || +.|+.+.-.|.+.++.+ .|...
T Consensus 101 ~Ga~-gy-l~K~~~~~~L~~ai~~v~~g~~~ 129 (216)
T PRK10651 101 RGAD-GY-LLKDMEPEDLLKALHQAAAGEMV 129 (216)
T ss_pred CCCC-EE-EECCCCHHHHHHHHHHHHCCCCC
T ss_conf 6987-89-83789999999999999859971
No 393
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=27.02 E-value=38 Score=16.05 Aligned_cols=27 Identities=15% Similarity=0.247 Sum_probs=10.8
Q ss_pred CCCCCCCEECCCHHHCCHHHHHHHH-CCCC
Q ss_conf 5654540002372126099999997-1876
Q gi|254780620|r 58 RGRRGGVRLCRPADQITILDVVKAT-EESF 86 (144)
Q Consensus 58 rG~~GGy~Lak~~~~Itl~dI~~ai-e~~~ 86 (144)
.|+.| |.+ |+...=.+.+-++++ .|..
T Consensus 93 ~Ga~g-~l~-K~~~~~el~~aI~~v~~G~~ 120 (196)
T PRK10360 93 AGARG-FLS-KRCSPDELIAAVHTVATGGC 120 (196)
T ss_pred CCCCE-EEE-CCCCHHHHHHHHHHHHCCCC
T ss_conf 59988-997-78999999999999986995
No 394
>PRK07075 isochorismate-pyruvate lyase; Reviewed
Probab=27.00 E-value=56 Score=15.06 Aligned_cols=27 Identities=19% Similarity=0.171 Sum_probs=20.9
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCC
Q ss_conf 599999981997899999999993259
Q gi|254780620|r 26 RISQIAEACCISELFLFKILQPLVKAG 52 (144)
Q Consensus 26 s~~eIA~~~~i~~~~l~kil~~L~~ag 52 (144)
+..+.|+..|+||.++++|...|...-
T Consensus 60 ~~r~~A~~~Gl~pd~vE~l~r~li~~~ 86 (101)
T PRK07075 60 ERRRWAEQAGLDADFVEKLFAQLIHWY 86 (101)
T ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHH
T ss_conf 999999985969999999999999999
No 395
>pfam02005 TRM N2,N2-dimethylguanosine tRNA methyltransferase. This enzyme EC:2.1.1.32 used S-AdoMet to methylate tRNA. The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs. The enzyme is found in both eukaryotes and archaebacteria
Probab=26.62 E-value=57 Score=15.02 Aligned_cols=22 Identities=18% Similarity=0.240 Sum_probs=11.7
Q ss_pred HCCCHHHHHHHHHHHHHCCCEE
Q ss_conf 1997899999999993259057
Q gi|254780620|r 34 CCISELFLFKILQPLVKAGIVE 55 (144)
Q Consensus 34 ~~i~~~~l~kil~~L~~agli~ 55 (144)
.|.|.+||.-.++.+++.|++-
T Consensus 129 fGSp~pfldsAi~av~~~GlL~ 150 (375)
T pfam02005 129 FGSPAPFLDSAVQSVKRGGLLC 150 (375)
T ss_pred CCCCCHHHHHHHHHHCCCCEEE
T ss_conf 9992177999999831598899
No 396
>pfam00538 Linker_histone linker histone H1 and H5 family. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures Histone H1 is replaced by histone H5 in some cell types.
Probab=26.61 E-value=57 Score=15.02 Aligned_cols=44 Identities=25% Similarity=0.363 Sum_probs=32.0
Q ss_pred CCHHH----HHHHH--CCCH----HHHHHHHHHHHHCCCEEECC--CCCCCCEECC
Q ss_conf 35999----99981--9978----99999999993259057315--6545400023
Q gi|254780620|r 25 NRISQ----IAEAC--CISE----LFLFKILQPLVKAGIVETVR--GRRGGVRLCR 68 (144)
Q Consensus 25 ~s~~e----IA~~~--~i~~----~~l~kil~~L~~agli~S~r--G~~GGy~Lak 68 (144)
.|... |.... +.++ .+|.+-|..++..|-+.=++ |+.|=|.|++
T Consensus 22 SS~~AI~KyI~~~y~~~~~~~~~~~~l~~aLk~~v~~G~lvq~KG~GasGsfkl~k 77 (77)
T pfam00538 22 SSVQAIKKYIEANYKVDINASNLAPLLKLALKKGVKSGKLVQVKGTGASGSFKLAK 77 (77)
T ss_pred CCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCEECCC
T ss_conf 65999999999768788877779999999999887649788531557863044288
No 397
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=26.45 E-value=57 Score=15.00 Aligned_cols=14 Identities=14% Similarity=0.173 Sum_probs=7.6
Q ss_pred HHHHHHCCHHHHHH
Q ss_conf 99984179999991
Q gi|254780620|r 119 FDVLTQYSIECLVR 132 (144)
Q Consensus 119 ~~~L~~~TL~dl~~ 132 (144)
...+++.|.+++.+
T Consensus 134 L~~~eg~s~~EIAe 147 (183)
T PRK07037 134 MVRLRGETLQDIAR 147 (183)
T ss_pred HHHHCCCCHHHHHH
T ss_conf 89873989999999
No 398
>pfam07381 DUF1495 Winged helix DNA-binding domain (DUF1495). This family consists of several hypothetical archaeal proteins of around 110 residues in length. The structure of this domain possesses a winged helix DNA-binding domain suggesting these proteins are bacterial transcription factors.
Probab=26.29 E-value=57 Score=14.98 Aligned_cols=63 Identities=19% Similarity=0.326 Sum_probs=46.0
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHH----------HHHHCCCEEECCCCCCC--CEEC
Q ss_conf 568999999999985598633599999981997899999999----------99325905731565454--0002
Q gi|254780620|r 5 KRTDYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQ----------PLVKAGIVETVRGRRGG--VRLC 67 (144)
Q Consensus 5 ~~~~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~----------~L~~agli~S~rG~~GG--y~La 67 (144)
.+++.--.++.||......+.-.+|||...+..|..+.--|. .|..-|+|+..-+..|. |.|.
T Consensus 6 ~rS~lR~kIl~yL~~iyp~~~y~~eIsr~v~s~psNv~GaL~G~G~RY~~e~SLi~lGLV~~~~~~~g~k~Y~lT 80 (90)
T pfam07381 6 NKSEVRRKILVYLYSIYPEPTYLSEISRRVRSDPSNVLGALEGMGKRYNGESSLIELGLVTVREGNPGTKVYKLT 80 (90)
T ss_pred HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCHHHHHHCCCCCCCCCHHHHHHCCCEEEEECCCCEEEEEEC
T ss_conf 888999999999997188757899998885679213257750356454631435761766677326871588737
No 399
>PRK13558 bacterio-opsin activator; Provisional
Probab=26.13 E-value=58 Score=14.97 Aligned_cols=36 Identities=11% Similarity=0.031 Sum_probs=16.7
Q ss_pred HCCCEEECCCCCCCCEECC-CHHHCCHHHHHHHHCCC
Q ss_conf 2590573156545400023-72126099999997187
Q gi|254780620|r 50 KAGIVETVRGRRGGVRLCR-PADQITILDVVKATEES 85 (144)
Q Consensus 50 ~agli~S~rG~~GGy~Lak-~~~~Itl~dI~~aie~~ 85 (144)
..+.|.|..=-.|+..|.- =|..-.+..+++.+...
T Consensus 552 ~G~~vrs~ta~~g~~~lvvevp~~advR~vve~l~~~ 588 (674)
T PRK13558 552 CGSRVIRMHADRTTLELDVRVGTEGAARRVLSTLRDK 588 (674)
T ss_pred CCCEEEEEEECCCCEEEEEECCCCCCHHHHHHHHHHH
T ss_conf 6976889998489379999878865389999999853
No 400
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family; InterPro: IPR011517 The bacterial core RNA polymerase complex, which consists of five subunits, 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 . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents a group of sigma factors that are able to regulate extra cellular function (ECF) . Eubacteria display considerable genetic diversity between ECF-sigma factors, but all retain two features: the ability to respond to extra-cytoplasmic functions; and regulation by anti-sigma and anti-anti-sigma factors . This family show sequence similarity to IPR007627 from INTERPRO and IPR007630 from INTERPRO.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=26.13 E-value=58 Score=14.97 Aligned_cols=20 Identities=20% Similarity=0.051 Sum_probs=12.6
Q ss_pred CCHHHHHHHHCCCHHHHHHH
Q ss_conf 35999999819978999999
Q gi|254780620|r 25 NRISQIAEACCISELFLFKI 44 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~ki 44 (144)
.+.+|||+.+++|++.|+|=
T Consensus 162 l~~~E~A~~L~~S~~Tv~Rd 181 (194)
T TIGR02999 162 LTVEEIAELLGVSVRTVERD 181 (194)
T ss_pred CCHHHHHHHHCCCHHHHHHH
T ss_conf 89899999868888789987
No 401
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. 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. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=25.98 E-value=58 Score=14.95 Aligned_cols=60 Identities=28% Similarity=0.264 Sum_probs=39.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHHH-CCCCCCC
Q ss_conf 3599999981997899999999993259057315654540002372126099999997-1876311
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKAT-EESFFVA 89 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~ai-e~~~~~~ 89 (144)
.++.++|+..|+++..|+.- -+-|+|...|- .|||++=.+-+=-.|.-|.+.+ +....+.
T Consensus 2 Y~IgevA~l~Gv~~~tLR~y----Er~gli~P~Rt-~gG~R~Ys~~Dl~~L~~I~~L~~~~G~~l~ 62 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVY----DRLGLVSPART-NGGGRRYSNNDLELLRQVQRLSQDEGFNLA 62 (98)
T ss_pred CCHHHHHHHHCCCHHHHHHH----HHCCCCCCCCC-CCCCCCCCHHHHHHHHHHHHHHHHCCCCHH
T ss_conf 35899999979899999999----99389786618-999943499999999999999995898899
No 402
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=25.75 E-value=59 Score=14.92 Aligned_cols=26 Identities=8% Similarity=0.028 Sum_probs=11.0
Q ss_pred HHHHHHHHHHHHCCCCCCCHHHHHHH
Q ss_conf 99999999998559863359999998
Q gi|254780620|r 8 DYGIRVLMYCAIHNDYPNRISQIAEA 33 (144)
Q Consensus 8 ~yAi~~l~~La~~~~~~~s~~eIA~~ 33 (144)
+|.=+.+.|+...-+.+-.+++|++.
T Consensus 18 ~~~~~L~~~~~r~~g~~~~AEDivQd 43 (167)
T PRK12528 18 AHHHWLTGWLRRRLGCPQSAADLAQD 43 (167)
T ss_pred HHHHHHHHHHHHHHCCHHHHHHHHHH
T ss_conf 99999999999993988579999999
No 403
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. 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 predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. 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=25.70 E-value=59 Score=14.92 Aligned_cols=61 Identities=15% Similarity=0.151 Sum_probs=40.3
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHHHCCCCCCCC
Q ss_conf 59999998199789999999999325905731565454000237212609999999718763111
Q gi|254780620|r 26 RISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKATEESFFVAE 90 (144)
Q Consensus 26 s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~aie~~~~~~~ 90 (144)
.+.|+|+..|+|+..+ ..--+.|++.+.+-..|||+.=.+.+--.|.-|..+-+-.+.+-+
T Consensus 2 ~Ige~a~~~gvs~~tl----RyYE~~GLl~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~~GfsL~e 62 (127)
T cd04784 2 KIGELAKKTGCSVETI----RYYEKEGLLPAPARSANNYRLYDEEHLERLLFIRRCRSLDMSLDE 62 (127)
T ss_pred CHHHHHHHHCCCHHHH----HHHHHCCCCCCCEECCCCCEECCHHHHHHHHHHHHHHHCCCCHHH
T ss_conf 6899999989499999----999985898875347999543639999999999999864987999
No 404
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. 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, an
Probab=25.57 E-value=59 Score=14.90 Aligned_cols=62 Identities=16% Similarity=0.197 Sum_probs=39.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHHHCCCCCCCCC
Q ss_conf 3599999981997899999999993259057315654540002372126099999997187631114
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKATEESFFVAEC 91 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~aie~~~~~~~C 91 (144)
+|+.|+|+..|+|...+ ..=-+.|++.+.+. .|||+.=.+.+--.|.-|..+=+-.+.+.++
T Consensus 1 mtIgelA~~~gvs~~Ti----RyYE~~GLl~~~~r-~~gyR~Y~~~~l~rl~~I~~~r~lGfsL~EI 62 (120)
T cd04781 1 LDIAEVARQSGLPASTL----RYYEEKGLIASIGR-RGLRRQYDPQVLDRLALIALGRAAGFSLDEI 62 (120)
T ss_pred CCHHHHHHHHCCCHHHH----HHHHHCCCCCCCCC-CCCCCCCCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 96899999988688989----89996498065446-9984158899999999999999959999999
No 405
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They 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=25.55 E-value=59 Score=14.90 Aligned_cols=63 Identities=17% Similarity=0.129 Sum_probs=41.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHHHCCCCCCCCC
Q ss_conf 3599999981997899999999993259057315654540002372126099999997187631114
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKATEESFFVAEC 91 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~aie~~~~~~~C 91 (144)
.++.++|+..|+|+..+ .-=-+.|++...+-..+||+.=..-+--.|..|..+=+-.+++-++
T Consensus 1 y~Ige~Ak~~gvs~~TL----RyYe~~GLl~p~~~~~ngYR~Y~~~~~~~l~~I~~~r~lG~sL~eI 63 (97)
T cd04782 1 FTTGEFAKLCGISKQTL----FHYDKIGLFKPEIVKENGYRYYTLEQFEQLDIILLLKELGISLKEI 63 (97)
T ss_pred CCHHHHHHHHCCCHHHH----HHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 97899999989699999----9999669989861399998427999999999999999969999999
No 406
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=25.46 E-value=60 Score=14.89 Aligned_cols=31 Identities=10% Similarity=-0.076 Sum_probs=22.5
Q ss_pred HHHCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 9855986335999999819978999999999
Q gi|254780620|r 17 CAIHNDYPNRISQIAEACCISELFLFKILQP 47 (144)
Q Consensus 17 La~~~~~~~s~~eIA~~~~i~~~~l~kil~~ 47 (144)
+...-|..-|..|||+.++++..-+..++..
T Consensus 108 l~~~lgr~Pt~~EiA~~l~is~~~v~~~~~~ 138 (229)
T PRK12427 108 IAKRLGHEPNFEEISAELNLTADEYQEYLLL 138 (229)
T ss_pred HHHHHCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 9998588999999998919999999999998
No 407
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=25.33 E-value=60 Score=14.88 Aligned_cols=50 Identities=22% Similarity=0.206 Sum_probs=37.5
Q ss_pred HCCCCCCCHHHHHHHHCCC-----HHHHHHHHHHHHHCCCEEECC---CCCCCCEECC
Q ss_conf 5598633599999981997-----899999999993259057315---6545400023
Q gi|254780620|r 19 IHNDYPNRISQIAEACCIS-----ELFLFKILQPLVKAGIVETVR---GRRGGVRLCR 68 (144)
Q Consensus 19 ~~~~~~~s~~eIA~~~~i~-----~~~l~kil~~L~~agli~S~r---G~~GGy~Lak 68 (144)
.+.++|.++.+|.+..+.. ..+|+.|-..|++.|..--++ =++=||....
T Consensus 13 ~e~~eplt~~ei~~~~~~~~~~~v~~~L~hiak~lkr~g~~Llv~Pa~CkkCGfef~~ 70 (97)
T COG3357 13 LESDEPLTVAEIFELLNGEKEKEVYDHLEHIAKSLKRKGKRLLVRPARCKKCGFEFRD 70 (97)
T ss_pred HCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCEEEECCHHHCCCCCCCCC
T ss_conf 8079951399999997687348899999999999974786688547322226862365
No 408
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=25.30 E-value=60 Score=14.87 Aligned_cols=14 Identities=14% Similarity=0.123 Sum_probs=7.5
Q ss_pred HHHHHHCCHHHHHH
Q ss_conf 99984179999991
Q gi|254780620|r 119 FDVLTQYSIECLVR 132 (144)
Q Consensus 119 ~~~L~~~TL~dl~~ 132 (144)
..++.+.|..++.+
T Consensus 138 l~~~~~~s~~EIA~ 151 (177)
T PRK09415 138 LFYYEELSIKEIAT 151 (177)
T ss_pred HHHHCCCCHHHHHH
T ss_conf 99980998999999
No 409
>cd02421 Peptidase_C39_likeD A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in this sub-family.
Probab=25.28 E-value=60 Score=14.87 Aligned_cols=61 Identities=20% Similarity=0.200 Sum_probs=41.8
Q ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHH--HHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCC
Q ss_conf 6899999999998559863359999998199789--99999999932590573156545400023721260
Q gi|254780620|r 6 RTDYGIRVLMYCAIHNDYPNRISQIAEACCISEL--FLFKILQPLVKAGIVETVRGRRGGVRLCRPADQIT 74 (144)
Q Consensus 6 ~~~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~--~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~It 74 (144)
+-|.-+.+|++++.+.+.++|.+.|.....+... -.........++|+-... ..++.++|+
T Consensus 4 ~~D~LL~cL~~l~r~~g~~~s~~~L~~glpl~~~~ls~~~~~rAA~~~Gl~a~~--------v~~~l~~l~ 66 (124)
T cd02421 4 RDDPLLDCLVLLARQFGKPASRDSLVAGLPLDDGRLSPALFPRAAARAGLSARV--------VRRPLDAIP 66 (124)
T ss_pred CCCHHHHHHHHHHHHHCCCCCHHHHHHCCCCCCCCCCHHHHHHHHHHCCCEEEE--------EECCHHHCC
T ss_conf 588799999999999589999999984499877885999999999987983256--------426886857
No 410
>pfam04645 DUF603 Protein of unknown function, DUF603. This family includes several uncharacterized proteins from Borrelia species.
Probab=25.28 E-value=60 Score=14.87 Aligned_cols=37 Identities=16% Similarity=0.194 Sum_probs=27.7
Q ss_pred HHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC
Q ss_conf 9985598633599999981997899999999993259
Q gi|254780620|r 16 YCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAG 52 (144)
Q Consensus 16 ~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~ag 52 (144)
|.+...++..+-.+||+.+|+++.+|.|.=++--..+
T Consensus 11 Yv~yF~eG~L~D~eIA~~LGVsr~nV~kmRqKwes~~ 47 (181)
T pfam04645 11 YVAYFKEGSLSDAEIAKELGVSRVNVWRMRQKWESGE 47 (181)
T ss_pred HHHHHHCCCCCHHHHHHHHCCHHHHHHHHHHHHHHCC
T ss_conf 9999961787579999997830999999999998127
No 411
>TIGR03026 NDP-sugDHase nucleotide sugar dehydrogenase. All of these enzymes contain three Pfam domains, pfam03721, pfam00984, and pfam03720 for the N-terminal, central, and C-terminal regions respectively.
Probab=25.14 E-value=55 Score=15.11 Aligned_cols=45 Identities=18% Similarity=0.107 Sum_probs=23.1
Q ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCC-CCCEECCCHHH
Q ss_conf 9999981997899999999993259057315654-54000237212
Q gi|254780620|r 28 SQIAEACCISELFLFKILQPLVKAGIVETVRGRR-GGVRLCRPADQ 72 (144)
Q Consensus 28 ~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~-GGy~Lak~~~~ 72 (144)
..+|+..|+...-+.+.+..=.+-|.---..|++ ||+.|-|||..
T Consensus 226 a~lce~~gid~~eV~~a~~~d~rig~~~~~PG~G~GG~ClpkD~~~ 271 (411)
T TIGR03026 226 ARICEALGIDVYEVIEAAGTDPRIGFNFLNPGPGVGGHCIPKDPLA 271 (411)
T ss_pred HHHHHHHCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHH
T ss_conf 9999985689999997617899877778899799998755303999
No 412
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=25.12 E-value=60 Score=14.85 Aligned_cols=41 Identities=17% Similarity=0.231 Sum_probs=31.1
Q ss_pred HHHHHHHCCCCCCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEE
Q ss_conf 9999985598633599999981---9978999999999932590573
Q gi|254780620|r 13 VLMYCAIHNDYPNRISQIAEAC---CISELFLFKILQPLVKAGIVET 56 (144)
Q Consensus 13 ~l~~La~~~~~~~s~~eIA~~~---~i~~~~l~kil~~L~~agli~S 56 (144)
||-||+. ++.|..||.+.+ +.++..+..++..|...|||.=
T Consensus 36 Al~~Ls~---r~rs~~El~~kL~~k~~~~~~I~~vi~~L~~~gyidD 79 (184)
T PRK00117 36 ALRLLSR---RERSEKELRDKLAKKEISEEVIEEVLDRLKEEGLLDD 79 (184)
T ss_pred HHHHCCC---CHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCC
T ss_conf 9998033---5146999999998869999999999999998699894
No 413
>PRK13749 transcriptional regulator MerD; Provisional
Probab=25.05 E-value=61 Score=14.85 Aligned_cols=43 Identities=21% Similarity=0.297 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCH
Q ss_conf 33599999981997899999999993259057315654540002372
Q gi|254780620|r 24 PNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPA 70 (144)
Q Consensus 24 ~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~ 70 (144)
..|+.++|+..|+|...+ ..-.+-|++....-..|||++=-+.
T Consensus 3 aytIg~LA~~aGVsv~tI----R~Y~~~GLL~p~~Rt~gGyRlyd~~ 45 (121)
T PRK13749 3 AYTVSRLALDAGVSVHIV----RDYLLRGLLRPVACTTGGYGLFDDA 45 (121)
T ss_pred CCCHHHHHHHHCCCHHHH----HHHHHCCCCCCCCCCCCCCCCCCHH
T ss_conf 420999999959973554----8898768989988899884367899
No 414
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=24.96 E-value=61 Score=14.84 Aligned_cols=43 Identities=16% Similarity=0.146 Sum_probs=33.7
Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCE
Q ss_conf 9999998559863359999998199789999999999325905
Q gi|254780620|r 12 RVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIV 54 (144)
Q Consensus 12 ~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli 54 (144)
++.-++..+...+.+..++|...++++.++.+.+.......+.
T Consensus 24 ~~~~~i~~~~~~~~~l~~la~~~g~S~~~l~r~f~~~~g~s~~ 66 (127)
T COG2207 24 RALDYIEENLAEPLTLEDLARRLGMSRRTLSRLFKKETGTSPS 66 (127)
T ss_pred HHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCHH
T ss_conf 9999998641379999999999798999999999999797999
No 415
>pfam07900 DUF1670 Protein of unknown function (DUF1670). The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=24.95 E-value=61 Score=14.84 Aligned_cols=50 Identities=14% Similarity=0.050 Sum_probs=40.6
Q ss_pred HHHHHHHH---HCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEECCCC
Q ss_conf 99999998---559863359999998199789999999999325-905731565
Q gi|254780620|r 11 IRVLMYCA---IHNDYPNRISQIAEACCISELFLFKILQPLVKA-GIVETVRGR 60 (144)
Q Consensus 11 i~~l~~La---~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~a-gli~S~rG~ 60 (144)
-+.++-+. -..|+..|..++|.-+++|++.+++-+..+.+. |.|--+||-
T Consensus 89 ~~~i~Ri~~EA~~QgglLT~~Dla~LL~~S~~TI~~~ik~ye~~~g~vvPtRG~ 142 (220)
T pfam07900 89 EKKIVRIFNEAYEQGALLTHADIAILLGVSTTTISRHVKEYEERTGEVVPTRGI 142 (220)
T ss_pred HHHHHHHHHHHHHCCCEEEHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf 999999999999738851176699998898889999999999970966357872
No 416
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=24.86 E-value=61 Score=14.82 Aligned_cols=14 Identities=21% Similarity=0.328 Sum_probs=7.5
Q ss_pred HHHHHHCCHHHHHH
Q ss_conf 99984179999991
Q gi|254780620|r 119 FDVLTQYSIECLVR 132 (144)
Q Consensus 119 ~~~L~~~TL~dl~~ 132 (144)
..++.+.|.+++.+
T Consensus 139 L~~~eg~s~~EIA~ 152 (188)
T PRK12517 139 LQVIGGFSGEEIAE 152 (188)
T ss_pred HHHHCCCCHHHHHH
T ss_conf 99983999999999
No 417
>pfam03979 Sigma70_r1_1 Sigma-70 factor, region 1.1. Region 1.1 modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase. Region 1.1 is also involved in promoter binding.
Probab=24.26 E-value=63 Score=14.76 Aligned_cols=48 Identities=17% Similarity=0.077 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHHHCCCCCCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEE
Q ss_conf 8999999999985598633599999981---997899999999993259057
Q gi|254780620|r 7 TDYGIRVLMYCAIHNDYPNRISQIAEAC---CISELFLFKILQPLVKAGIVE 55 (144)
Q Consensus 7 ~~yAi~~l~~La~~~~~~~s~~eIA~~~---~i~~~~l~kil~~L~~agli~ 55 (144)
..-+|+-|+-++... +.+|-.+|.+.+ .+++..+..|+..|...||--
T Consensus 5 ~~~~ik~LI~~GK~~-GylTy~eIn~~Lp~~~~~~d~ie~i~~~L~~~gI~V 55 (79)
T pfam03979 5 SQAQVKKLIEQGKKR-GYLTYDEINEALPPDDVDSEQIDDIISMLEDMGIEV 55 (79)
T ss_pred HHHHHHHHHHHHHHC-CEEEHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEE
T ss_conf 799999999987645-836399999768876799999999999999889968
No 418
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=24.03 E-value=63 Score=14.73 Aligned_cols=22 Identities=23% Similarity=0.102 Sum_probs=19.7
Q ss_pred CCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 3359999998199789999999
Q gi|254780620|r 24 PNRISQIAEACCISELFLFKIL 45 (144)
Q Consensus 24 ~~s~~eIA~~~~i~~~~l~kil 45 (144)
-+|-+++|+..|+++.++.++.
T Consensus 10 glsq~~lA~~~gis~~~is~~E 31 (56)
T smart00530 10 GLTQEELAEKLGVSRSTLSRIE 31 (56)
T ss_pred CCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9999999999895999999999
No 419
>PRK05927 hypothetical protein; Provisional
Probab=23.66 E-value=65 Score=14.69 Aligned_cols=75 Identities=21% Similarity=0.170 Sum_probs=44.2
Q ss_pred HHHHHHHHHHHHHHC-CC---CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCC-------EECCCHHHCC
Q ss_conf 689999999999855-98---633599999981997899999999993259057315654540-------0023721260
Q gi|254780620|r 6 RTDYGIRVLMYCAIH-ND---YPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGV-------RLCRPADQIT 74 (144)
Q Consensus 6 ~~~yAi~~l~~La~~-~~---~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy-------~Lak~~~~It 74 (144)
..||-...+-.+-.. ++ ...|..||.....++.--++.+|..|+.|| +.|.+| ||- +-.-.|.+++
T Consensus 107 ~~eyy~~l~r~ik~~~P~i~ihafs~~Ei~~~a~~~g~s~~e~L~~Lk~AG-L~slPG--gGAEIl~d~VR~~I~p~K~s 183 (350)
T PRK05927 107 GIDYLEELVRITVQEFPSLHPHFFSAVEIAHAAQVSGISTEQALQRLWDAG-QRTIPG--GGAEILSERVRKIISPKKMG 183 (350)
T ss_pred CHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHCC-CCCCCC--CCCCCCCHHHHHHCCCCCCC
T ss_conf 869999999999974888665669999999999885999999999999737-676899--87501687777514888889
Q ss_pred HHHHHHHHC
Q ss_conf 999999971
Q gi|254780620|r 75 ILDVVKATE 83 (144)
Q Consensus 75 l~dI~~aie 83 (144)
-.+=+++++
T Consensus 184 ~~~Wl~i~~ 192 (350)
T PRK05927 184 PDGWINFHK 192 (350)
T ss_pred HHHHHHHHH
T ss_conf 999999999
No 420
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=23.61 E-value=46 Score=15.54 Aligned_cols=21 Identities=19% Similarity=0.053 Sum_probs=11.1
Q ss_pred HCCCHHHHHHHHHHHHHCCCE
Q ss_conf 199789999999999325905
Q gi|254780620|r 34 CCISELFLFKILQPLVKAGIV 54 (144)
Q Consensus 34 ~~i~~~~l~kil~~L~~agli 54 (144)
-++++..-++|++...+-||.
T Consensus 22 ~~Vs~~tr~~I~~~~~elgY~ 42 (52)
T cd01392 22 PRVSEETRERVLAAAEELGYR 42 (52)
T ss_pred CCCCHHHHHHHHHHHHHHCCC
T ss_conf 989999999999999998889
No 421
>PRK11064 wecC UDP-N-acetyl-D-mannosamine dehydrogenase; Provisional
Probab=23.47 E-value=61 Score=14.85 Aligned_cols=43 Identities=19% Similarity=0.218 Sum_probs=26.5
Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCC-CCCCEECCCHH
Q ss_conf 9999998199789999999999325905731565-45400023721
Q gi|254780620|r 27 ISQIAEACCISELFLFKILQPLVKAGIVETVRGR-RGGVRLCRPAD 71 (144)
Q Consensus 27 ~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~-~GGy~Lak~~~ 71 (144)
...+|+..|+...-+.+....=.+-+++. .|+ -||+.|-|||-
T Consensus 229 la~lce~~gid~~evi~~~~~~~r~~~l~--pG~G~GG~ClpkD~~ 272 (415)
T PRK11064 229 LSLICDDQGINVWELIRLANRHPRVNILQ--PGPGVGGHCIAVDPW 272 (415)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCCCCCCCC--CCCCCCCCCCCCCHH
T ss_conf 99999980999999999728898877788--999887748674869
No 422
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=23.42 E-value=65 Score=14.66 Aligned_cols=30 Identities=13% Similarity=-0.058 Sum_probs=22.2
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Q ss_conf 863359999998199789999999999325
Q gi|254780620|r 22 DYPNRISQIAEACCISELFLFKILQPLVKA 51 (144)
Q Consensus 22 ~~~~s~~eIA~~~~i~~~~l~kil~~L~~a 51 (144)
+...+..+||+.++++..-+..++......
T Consensus 109 ~r~pt~~eia~~l~~s~e~v~~~~~~~~~~ 138 (234)
T PRK06986 109 GREPTDTEVAEKLGLSLEEYREMLLDTNIS 138 (234)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHCCC
T ss_conf 879989999989594999999999985057
No 423
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=23.28 E-value=66 Score=14.64 Aligned_cols=44 Identities=16% Similarity=0.170 Sum_probs=34.3
Q ss_pred HHHHHHHHCCCC--CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Q ss_conf 999999855986--33599999981997899999999993259057
Q gi|254780620|r 12 RVLMYCAIHNDY--PNRISQIAEACCISELFLFKILQPLVKAGIVE 55 (144)
Q Consensus 12 ~~l~~La~~~~~--~~s~~eIA~~~~i~~~~l~kil~~L~~agli~ 55 (144)
++.-|+-.|++. ..|+.+||+..++|++-+-+..++|-=.||-+
T Consensus 20 ~iA~yIl~n~~~v~~~si~eLA~~~~vS~aTV~Rf~kkLGf~Gf~e 65 (284)
T PRK11302 20 KVAEVILASPQTAIHSSIATLAKMANVSEPTVNRFCRSLDTKGFPD 65 (284)
T ss_pred HHHHHHHCCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHCCCCHHH
T ss_conf 9999998098999766699999896998889999999957897899
No 424
>KOG2908 consensus
Probab=23.24 E-value=66 Score=14.64 Aligned_cols=46 Identities=17% Similarity=0.209 Sum_probs=33.6
Q ss_pred HHHHHHHHHHC---CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Q ss_conf 99999999855---98633599999981997899999999993259057
Q gi|254780620|r 10 GIRVLMYCAIH---NDYPNRISQIAEACCISELFLFKILQPLVKAGIVE 55 (144)
Q Consensus 10 Ai~~l~~La~~---~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~ 55 (144)
-+.+|+.+... ..+.+|.++||+.+.+|..-++-++-+--.-|+|+
T Consensus 277 ~LmaLiEi~F~rpa~~R~lsf~~Ia~~tkip~~eVE~LVMKAlslgLik 325 (380)
T KOG2908 277 RLLALIEITFSRPANERTLSFKEIAEATKIPNKEVELLVMKALSLGLIK 325 (380)
T ss_pred HHHHHHHHHHCCCCHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
T ss_conf 9999999995274031100199999995797887999999997115101
No 425
>pfam08535 KorB KorB domain. This family consists of several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon. This domain includes the DNA-binding HTH motif.
Probab=22.92 E-value=67 Score=14.60 Aligned_cols=52 Identities=19% Similarity=0.305 Sum_probs=34.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEC--CCCCCCCEECCCHHHCCHHHHHHHHCC
Q ss_conf 359999998199789999999999325905731--565454000237212609999999718
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQPLVKAGIVETV--RGRRGGVRLCRPADQITILDVVKATEE 84 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~--rG~~GGy~Lak~~~~Itl~dI~~aie~ 84 (144)
.+-.+||+.+|-|+.|+.+.++.+.--..|... -|+ .+|++ +|+++.++.+.
T Consensus 4 ~kk~~IAk~LGks~s~VS~hlaL~d~Pd~l~~l~~~g~------~~dv~--~l~eL~~~~~k 57 (93)
T pfam08535 4 VKQAEIAKKLGKSKSFVSQHLALLDMPDCIREAYDSGR------CSDIR--ALYELRRAARK 57 (93)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHCCC------CCCHH--HHHHHHHHHHH
T ss_conf 77999999978898899999998348699999987477------68799--99999999997
No 426
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=22.54 E-value=68 Score=14.55 Aligned_cols=43 Identities=16% Similarity=0.131 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCC
Q ss_conf 99999999998559863359999998199789999999999325905731565
Q gi|254780620|r 8 DYGIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIVETVRGR 60 (144)
Q Consensus 8 ~yAi~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~ 60 (144)
==|||+++..-.-.. ..|-.++|+-+|++++-|.+ |+.+.||.
T Consensus 7 lPaiRa~lA~~L~ee-G~Sq~~iA~LLGltqaAVS~---------Yls~krg~ 49 (119)
T COG2522 7 LPAIRALLAKELIEE-GLSQYRIAKLLGLTQAAVSQ---------YLSGKRGS 49 (119)
T ss_pred HHHHHHHHHHHHHHC-CCCHHHHHHHHCCCHHHHHH---------HHCCCCCH
T ss_conf 798999999999995-88699999996888999999---------97367736
No 427
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=22.51 E-value=68 Score=14.55 Aligned_cols=23 Identities=17% Similarity=0.091 Sum_probs=20.3
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 33599999981997899999999
Q gi|254780620|r 24 PNRISQIAEACCISELFLFKILQ 46 (144)
Q Consensus 24 ~~s~~eIA~~~~i~~~~l~kil~ 46 (144)
-.|..++|+..|+++.++.++.+
T Consensus 12 ~ls~~~lA~~~gis~~~l~~~e~ 34 (58)
T cd00093 12 GLTQEELAEKLGVSRSTISRIEN 34 (58)
T ss_pred CCCHHHHHHHCCCCHHHHHHHHC
T ss_conf 99999995714999999999987
No 428
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. 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. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=22.43 E-value=68 Score=14.54 Aligned_cols=61 Identities=20% Similarity=0.291 Sum_probs=41.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHHHCCCCCCCCC
Q ss_conf 3599999981997899999999993259057315654540002372126099999997187631114
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKATEESFFVAEC 91 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~aie~~~~~~~C 91 (144)
.|+.++|+..|+|+.-+ .-=-+.|++...| .|||++=.+.+--.|.-|..+-+-...+-++
T Consensus 1 ytIge~A~~~gvs~~tl----RyYe~~GLl~p~r--~~g~R~Y~~~~~~~l~~I~~~r~~G~sL~eI 61 (118)
T cd04776 1 YTISELAREFDVTPRTL----RFYEDKGLLSPER--RGQTRVYSRRDRARLKLILRGKRLGFSLEEI 61 (118)
T ss_pred CCHHHHHHHHCCCHHHH----HHHHHCCCCCCCC--CCCCCCCCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 95889999989799999----9999869987555--7986860899999999999999829989999
No 429
>PRK08184 enoyl-CoA hydratase; Provisional
Probab=22.26 E-value=22 Score=17.45 Aligned_cols=43 Identities=19% Similarity=0.204 Sum_probs=25.6
Q ss_pred HCCCHHHHHHHHHHHHHCCCEEECCC--CCCCCEECCCHHHCCHHH
Q ss_conf 19978999999999932590573156--545400023721260999
Q gi|254780620|r 34 CCISELFLFKILQPLVKAGIVETVRG--RRGGVRLCRPADQITILD 77 (144)
Q Consensus 34 ~~i~~~~l~kil~~L~~agli~S~rG--~~GGy~Lak~~~~Itl~d 77 (144)
.|-.+..++-- +.-....+|..+.| ++|||.|+-.-++|-|-|
T Consensus 116 TNETRn~~Eds-s~~sg~~fiaavnG~~AGGGYELALAcd~I~LvD 160 (558)
T PRK08184 116 TNETRNGIEDS-SRHSGLKFLAAVNGTCAGGGYELALACDEIILVD 160 (558)
T ss_pred CCHHHHHHHHH-HHCCCCEEEEEECCCCCCCCEEEEHHCCEEEEEC
T ss_conf 44001214444-3235847875433533478421102156689970
No 430
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=22.12 E-value=69 Score=14.50 Aligned_cols=29 Identities=7% Similarity=0.170 Sum_probs=14.0
Q ss_pred CCCCCCCEECCCHHHCCHHHHHHHH-CCCCCC
Q ss_conf 5654540002372126099999997-187631
Q gi|254780620|r 58 RGRRGGVRLCRPADQITILDVVKAT-EESFFV 88 (144)
Q Consensus 58 rG~~GGy~Lak~~~~Itl~dI~~ai-e~~~~~ 88 (144)
.|.. ||.|...+.+ .|.+-++++ .|...+
T Consensus 102 aGa~-GyllK~~~~~-~Li~aIr~v~~G~~~l 131 (216)
T PRK10100 102 PHIN-GVFYAMEDQE-RVVNGLQGVLRGECYF 131 (216)
T ss_pred CCCC-EEEECCCCHH-HHHHHHHHHHCCCCCC
T ss_conf 5876-6766899999-9999999998799723
No 431
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative; InterPro: IPR004458 Archaeal transcription initiation factor 2 is, like its eukaryotic homologue, a heterotrimeric protein with alpha, beta and gamma subunits . It is thought play an essential role in the recognition of the correct codon for the start of translation, similar to the role of eukaryotic transcription initiation factor. The eukaryotic factor forms a ternary complex with the methionine initiator tRNA and GTP, which binds to the 40S ribosomal subunit as part of the 43S preinitiation complex . The beta and gamma subunits are responsible for recruiting the initiator tRNA and GTP, while the alpha subunit is involved in the regulation of the translation initiation process. The beta subunit has also been shown to interact with other transcription factors. All three subunits of the archaeal and eukaryotic factors are well conserved among the diverse species of eukaryotes and archaea, but do not occur in prokaryotes. The archaeal beta subunit has an unfolded N-terminal domain, a mixed alpha/beta core domain and a C-terminal zinc finger . The N-terminal region is thought to interact with the gamma subunit, while the central and C-terminal domains are thought to provide RNA-binding sites.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation.
Probab=22.08 E-value=69 Score=14.50 Aligned_cols=58 Identities=29% Similarity=0.311 Sum_probs=41.4
Q ss_pred CHHHHHHHHCCCHHHHHH-HHHHHHHCCCEEECCCCCCC-CEECCCHHHCCHHHHHHHHCC-CCCCCCCC
Q ss_conf 599999981997899999-99999325905731565454-000237212609999999718-76311146
Q gi|254780620|r 26 RISQIAEACCISELFLFK-ILQPLVKAGIVETVRGRRGG-VRLCRPADQITILDVVKATEE-SFFVAECF 92 (144)
Q Consensus 26 s~~eIA~~~~i~~~~l~k-il~~L~~agli~S~rG~~GG-y~Lak~~~~Itl~dI~~aie~-~~~~~~C~ 92 (144)
--.+||+.+|=++.|+.| ++..|--||.++ || ..| ...+|=..+=+-||+ --.++-|.
T Consensus 42 NFre~AkalNRde~hl~KyllkelGtAGnle------gGRliL---Qgkft~~ll~~ri~Dyvr~yViCr 102 (134)
T TIGR00311 42 NFREIAKALNRDEDHLLKYLLKELGTAGNLE------GGRLIL---QGKFTESLLKKRIDDYVRKYVICR 102 (134)
T ss_pred HHHHHHHHHCCCHHHHHHHHHHHCCCCCCCC------CCEEEE---CCCCCHHHHHHHHHHHHHCEEEEC
T ss_conf 1899988738998899999998607876346------760232---132587887757756763234321
No 432
>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=22.03 E-value=70 Score=14.49 Aligned_cols=62 Identities=24% Similarity=0.354 Sum_probs=39.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHH-HHCCCCCCCCC
Q ss_conf 35999999819978999999999932590573156545400023721260999999-97187631114
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVK-ATEESFFVAEC 91 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~-aie~~~~~~~C 91 (144)
.|+.++|+..|+|+.-+ ..=-+.|++.+..-..|||++= +++++.-...++ +-+-.+.+-++
T Consensus 1 m~IgevA~~~gvs~~Tl----RyYE~~GLl~~~~R~~~gyR~Y-~~~~l~rL~~I~~~r~~G~sL~eI 63 (126)
T cd04783 1 LTIGELAKAAGVNVETI----RYYQRRGLLPEPPRPEGGYRRY-PEETVTRLRFIKRAQELGFTLDEI 63 (126)
T ss_pred CCHHHHHHHHCCCHHHH----HHHHHCCCCCCCCCCCCCCCCC-CHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 97899999989398999----9999869988763189996017-799999999999999879989999
No 433
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=21.90 E-value=70 Score=14.48 Aligned_cols=13 Identities=0% Similarity=-0.000 Sum_probs=6.0
Q ss_pred HHHHHHCCHHHHH
Q ss_conf 9998417999999
Q gi|254780620|r 119 FDVLTQYSIECLV 131 (144)
Q Consensus 119 ~~~L~~~TL~dl~ 131 (144)
..++...|.+++.
T Consensus 117 L~~~egls~~EIA 129 (161)
T PRK09047 117 LRYWEDMDVAETA 129 (161)
T ss_pred HHHHHCCCHHHHH
T ss_conf 9999877999999
No 434
>pfam08888 HopJ HopJ type III effector protein. Pathovars of Pseudomonas syringae interact with their plant hosts via the action of Hrp outer protein (Hop) effector proteins, injected into plant cells by the type III secretion system. The proteins in this family are called HopJ after the original member HopPmaJ.
Probab=21.90 E-value=55 Score=15.11 Aligned_cols=77 Identities=14% Similarity=0.201 Sum_probs=44.4
Q ss_pred EECCCHHHCCHHHHHHHHCCCCCCCCCC-CC---CCCCCCCCCCCCHHHHHH--H-HHHHHHHHHHHCCHHHHHHCH---
Q ss_conf 0023721260999999971876311146-88---778887656644799999--9-999999998417999999158---
Q gi|254780620|r 65 RLCRPADQITILDVVKATEESFFVAECF-AS---HKIDCPLVGSCGLTSVLR--K-ALNAFFDVLTQYSIECLVRNR--- 134 (144)
Q Consensus 65 ~Lak~~~~Itl~dI~~aie~~~~~~~C~-~~---~~~~C~~~~~c~~~~~~~--~-~~~~~~~~L~~~TL~dl~~~~--- 134 (144)
.|+..|++|...|++..||..-.+..+. .+ .+......++|.+-.+-. . -++.....+.+.-=.|++.++
T Consensus 8 ~L~~~p~~i~F~d~~a~Id~~Y~ftptaF~NG~~~N~ageN~GScKif~fa~l~~Ls~~~TL~~Fg~~Yr~dVl~~P~g~ 87 (110)
T pfam08888 8 KLSSQPEEIEFEDTMAVIEEHYDFTPTAFTNGDLVNEAGENEGSCKIFAFAQLNGLSEEETLACFGEHYREDVLANPEGT 87 (110)
T ss_pred HHHCCCCEEEHHHHHHHHHHHCCCCCCCCCCCCEECCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf 99679873148999999997076666552377610447677631799899999189989999999999999986199998
Q ss_pred --HHHHHHH
Q ss_conf --9899952
Q gi|254780620|r 135 --SSIKKIF 141 (144)
Q Consensus 135 --~~~~~l~ 141 (144)
.++|..+
T Consensus 88 dH~NIR~Fm 96 (110)
T pfam08888 88 DHQNIRNFM 96 (110)
T ss_pred CHHHHHHHH
T ss_conf 538899999
No 435
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=21.90 E-value=70 Score=14.48 Aligned_cols=35 Identities=29% Similarity=0.129 Sum_probs=23.1
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 999999985598633599999981997899999999993
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLV 49 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~ 49 (144)
..++.+++. | .|.++||+..++++..++.-+..+.
T Consensus 9 ~~il~~l~~--G--~s~~eIA~~L~is~~TV~~~~~~i~ 43 (58)
T smart00421 9 REVLRLLAE--G--LTNKEIAERLGISEKTVKTHLSNIM 43 (58)
T ss_pred HHHHHHHHH--C--CCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 999999981--7--9999999898978989999999999
No 436
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=21.86 E-value=70 Score=14.47 Aligned_cols=53 Identities=21% Similarity=0.305 Sum_probs=34.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHHH
Q ss_conf 3599999981997899999999993259057315654540002372126099999997
Q gi|254780620|r 25 NRISQIAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKAT 82 (144)
Q Consensus 25 ~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~ai 82 (144)
.|+.|+|+..|+|+..+ .---+.|++...+-..+||+.= ++++|.....++..
T Consensus 1 ytI~e~a~~~gvs~~tl----R~ye~~Gll~p~~r~~~g~R~Y-~~~di~~l~~I~~l 53 (70)
T smart00422 1 YTIGEVAKLAGVSVRTL----RYYERIGLLPPPIRTEGGYRLY-SDEDLERLRFIKRL 53 (70)
T ss_pred CCHHHHHHHHCCCHHHH----HHHHHCCCCCCCCCCCCCCEEC-CHHHHHHHHHHHHH
T ss_conf 97889999989699999----9999858989984489997443-99999999999999
No 437
>pfam04552 Sigma54_DBD Sigma-54, DNA binding domain. This DNA binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore this region contains a putative helix-turn-helix motif. At the C-terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins.
Probab=21.80 E-value=70 Score=14.47 Aligned_cols=33 Identities=24% Similarity=0.282 Sum_probs=26.1
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCC
Q ss_conf 6335999999819978999999999932590573156
Q gi|254780620|r 23 YPNRISQIAEACCISELFLFKILQPLVKAGIVETVRG 59 (144)
Q Consensus 23 ~~~s~~eIA~~~~i~~~~l~kil~~L~~agli~S~rG 59 (144)
.|.+.++||+.++++.+.+.++++ ..++..-+|
T Consensus 48 ~PLtlk~iA~~l~lh~STVSRav~----~Kyi~tp~G 80 (160)
T pfam04552 48 RPLTLREVAEALGMHESTVSRATT----NKYLATPRG 80 (160)
T ss_pred CCCCHHHHHHHCCCCCCHHHHHHH----HHHHHCCCC
T ss_conf 576199999880998106999996----139767995
No 438
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=21.70 E-value=71 Score=14.45 Aligned_cols=12 Identities=0% Similarity=-0.003 Sum_probs=5.6
Q ss_pred HHHHHCCHHHHH
Q ss_conf 998417999999
Q gi|254780620|r 120 DVLTQYSIECLV 131 (144)
Q Consensus 120 ~~L~~~TL~dl~ 131 (144)
.++++.+.+++.
T Consensus 161 r~~eglS~~EIA 172 (207)
T PRK12544 161 REFIELETPEIC 172 (207)
T ss_pred HHHCCCCHHHHH
T ss_conf 998199999999
No 439
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=21.64 E-value=71 Score=14.45 Aligned_cols=40 Identities=18% Similarity=-0.129 Sum_probs=27.3
Q ss_pred HHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCE
Q ss_conf 9998559863359999998199789999999999325905
Q gi|254780620|r 15 MYCAIHNDYPNRISQIAEACCISELFLFKILQPLVKAGIV 54 (144)
Q Consensus 15 ~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli 54 (144)
-.+....+..-|.++||+.+++++.-+..++........+
T Consensus 120 ~~l~~~~gr~pt~~EiA~~l~is~~~v~~~~~~~~~~~~~ 159 (256)
T PRK07408 120 QELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRMPL 159 (256)
T ss_pred HHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCE
T ss_conf 9999987899989999989596999999999987278873
No 440
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=21.51 E-value=71 Score=14.43 Aligned_cols=29 Identities=10% Similarity=0.150 Sum_probs=16.8
Q ss_pred HHHHHHHHHCCC----EEECCCCC---CCCEECCCH
Q ss_conf 999999932590----57315654---540002372
Q gi|254780620|r 42 FKILQPLVKAGI----VETVRGRR---GGVRLCRPA 70 (144)
Q Consensus 42 ~kil~~L~~agl----i~S~rG~~---GGy~Lak~~ 70 (144)
..++..-+..|+ -.+.+++. |...|++..
T Consensus 104 ~~~~~eA~~~Gl~~G~t~p~~~~~g~~g~lSla~~~ 139 (240)
T PRK10188 104 QALWDAARAHGLRRGVTQCLMLPNRALGFLSFSRSS 139 (240)
T ss_pred HHHHHHHHHCCCCCCEEEEEECCCCCEEEEEEECCC
T ss_conf 999999998298676178887279983899985478
No 441
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=21.50 E-value=71 Score=14.43 Aligned_cols=13 Identities=8% Similarity=0.008 Sum_probs=6.4
Q ss_pred HHHHHHCCHHHHH
Q ss_conf 9998417999999
Q gi|254780620|r 119 FDVLTQYSIECLV 131 (144)
Q Consensus 119 ~~~L~~~TL~dl~ 131 (144)
..++.+.|.+++.
T Consensus 147 L~~~eg~s~~EIA 159 (196)
T PRK12524 147 LRHIEGLSNPEIA 159 (196)
T ss_pred HHHHCCCCHHHHH
T ss_conf 9998089999999
No 442
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=21.48 E-value=71 Score=14.43 Aligned_cols=33 Identities=18% Similarity=-0.004 Sum_probs=23.8
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCE
Q ss_conf 863359999998199789999999999325905
Q gi|254780620|r 22 DYPNRISQIAEACCISELFLFKILQPLVKAGIV 54 (144)
Q Consensus 22 ~~~~s~~eIA~~~~i~~~~l~kil~~L~~agli 54 (144)
+...|..+||+..+++..-+...+..-..+-.+
T Consensus 124 gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~ 156 (257)
T PRK05911 124 GKEPTDGELCEYLNISQQELSGWFSSARPALIL 156 (257)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCEE
T ss_conf 889999999988397999999999853552223
No 443
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=21.45 E-value=72 Score=14.42 Aligned_cols=47 Identities=21% Similarity=0.215 Sum_probs=23.8
Q ss_pred HHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEECCCHHHCCHHHHHHHH
Q ss_conf 99981997899999999993259057315654540002372126099999997
Q gi|254780620|r 30 IAEACCISELFLFKILQPLVKAGIVETVRGRRGGVRLCRPADQITILDVVKAT 82 (144)
Q Consensus 30 IA~~~~i~~~~l~kil~~L~~agli~S~rG~~GGy~Lak~~~~Itl~dI~~ai 82 (144)
++......++-+.+.+..+++...|-..+= =+|+++..+ +.++++.+
T Consensus 41 ~SG~~~~~r~~l~~ll~~~~~gD~lvV~~L----DRLgRs~~d--~l~~l~~l 87 (200)
T PRK13413 41 ISGTKSYKDRQLGKLLKRVRKGDILIVSEL----SRLGRNLFE--IMEILNIC 87 (200)
T ss_pred CCCCCCCCCHHHHHHHHHCCCCCEEEEEEC----CHHHCCHHH--HHHHHHHH
T ss_conf 657877767699999986659998999767----374288999--99999999
No 444
>TIGR02207 lipid_A_htrB lipid A biosynthesis lauroyl (or palmitoleoyl) acyltransferase; InterPro: IPR011920 Bacterial lipopolysachharides (LPS) are glycolipids that make up the outer monolayer of the outer membranes of most Gram-negative bacteria. Though LPS moleculesare variable, they all show the same general features: an outer polysaccharide which is attached to the lipid component, termed lipid A . The polysaccharide component consists of a variable repeat-structure polysaccharide known as the O-antigen, and a highly conserved short core oligosaccharide which connects the O-antigen to lipid A. Lipid A is a glucosamine-based phospholipid that makes up the membrane anchor region of LPS . The structure of lipid A is relatively invariant between species, presumably reflecting its fundamental role in membrane integrity. Recognition of lipid A by the innate immune system can lead to a response even at picomolar levels. In some genera, such as Neisseria and Haemophilus, lipooligosaccharides (LOS) are the predominant glycolipids . These are analogous to LPS except that they lack O-antigens, with the LOS oligosaccharide structures limited to 10 saccharide units. This entry represents a narrow clade of acyltransferases, nearly all of which transfer a lauroyl group to KDO2-lipid IV-A, a lipid A precursor; these proteins are termed lipid A biosynthesis lauroyl acyltransferase, HtrB. An exception is a closely related paralog of Escherichia coli HtrB, LpxP, which acts in cold shock conditions by transferring a palmitoleoyl rather than lauroyl group to the lipid A precursor. Members of this family are homologous to the family of acyltransferases responsible for the next step in lipid A biosynthesis .; GO: 0016747 transferase activity transferring groups other than amino-acyl groups, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane.
Probab=21.43 E-value=48 Score=15.44 Aligned_cols=32 Identities=31% Similarity=0.348 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHCCCEE--ECCCCCC-CCEECCCH
Q ss_conf 99999999993259057--3156545-40002372
Q gi|254780620|r 39 LFLFKILQPLVKAGIVE--TVRGRRG-GVRLCRPA 70 (144)
Q Consensus 39 ~~l~kil~~L~~agli~--S~rG~~G-Gy~Lak~~ 70 (144)
..=.-+|.++.++-+|- .+|..+| ||+|.-.|
T Consensus 222 ttGT~~L~~~~~~~v~Pf~~~R~~dg~gY~L~I~P 256 (308)
T TIGR02207 222 TTGTSVLARLSKCAVVPFTPVRKEDGSGYRLIIDP 256 (308)
T ss_pred HHHHHHHHHHCCCEECCCEEEECCCCCEEEEEEEC
T ss_conf 99999999716972603222346799602788726
No 445
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=21.40 E-value=72 Score=14.42 Aligned_cols=45 Identities=9% Similarity=0.099 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHCCCCCCCHHHHHHHHC---CCHHHHHHHHHHHHHCCC
Q ss_conf 9999999999855986335999999819---978999999999932590
Q gi|254780620|r 8 DYGIRVLMYCAIHNDYPNRISQIAEACC---ISELFLFKILQPLVKAGI 53 (144)
Q Consensus 8 ~yAi~~l~~La~~~~~~~s~~eIA~~~~---i~~~~l~kil~~L~~agl 53 (144)
.-+|+.|+-++... +.+|-.||.+.+- .++..+..|+..|...||
T Consensus 10 ~~~ik~LI~~GKe~-GyLTy~EInd~LP~d~~~~eqId~ii~~L~~~GI 57 (620)
T PRK05658 10 QSALKLLIKRGKER-GYLTYAELNDHLPEDIVDSEQIEDIISMINDMGI 57 (620)
T ss_pred HHHHHHHHHHHHHC-CCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHCCC
T ss_conf 89999999985416-8265999997689989998999999999997797
No 446
>pfam09639 YjcQ YjcQ protein. YjcQ is a protein of approx. 100 residues containing four alpha helices and three beta strands. It is expressed in bacteria and also in viruses. It appears to be under the regulation of SigD RNA polymerase which is responsible for the expression of many genes encoding cell-surface proteins related to flagellar assembly, motility, chemotaxis and autolysis in the late exponential growth phase. The exact function of YjcQ is unknown. However, it is thought to be a prophage head protein in viruses.
Probab=21.31 E-value=72 Score=14.40 Aligned_cols=24 Identities=21% Similarity=0.175 Sum_probs=20.7
Q ss_pred HCCCHHHHHHHHHHHHHCCCEEEC
Q ss_conf 199789999999999325905731
Q gi|254780620|r 34 CCISELFLFKILQPLVKAGIVETV 57 (144)
Q Consensus 34 ~~i~~~~l~kil~~L~~agli~S~ 57 (144)
.+++..+..+++..|+.+|+|..+
T Consensus 20 ~~i~~~~f~~il~~L~d~GyI~Gv 43 (88)
T pfam09639 20 PDITDDQFSDALEMLRDEGYIKGV 43 (88)
T ss_pred CCCCHHHHHHHHHHHHHCCCCCCE
T ss_conf 996689999999999977983316
No 447
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=21.21 E-value=72 Score=14.39 Aligned_cols=12 Identities=17% Similarity=0.069 Sum_probs=5.9
Q ss_pred HHHHHCCHHHHH
Q ss_conf 998417999999
Q gi|254780620|r 120 DVLTQYSIECLV 131 (144)
Q Consensus 120 ~~L~~~TL~dl~ 131 (144)
.++.+.|.+++.
T Consensus 118 ~~~eg~s~~EIA 129 (181)
T PRK09637 118 TELEGLSQKEIA 129 (181)
T ss_pred HHHCCCCHHHHH
T ss_conf 988599999999
No 448
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit; InterPro: IPR002023 Respiratory-chain NADH dehydrogenase (ubiquinone) (1.6.5.3 from EC) , (also known as complex I or NADH-ubiquinone oxidoreductase) is an oligomeric enzymatic complex located in the inner mitochondrial membrane which also seems to exist in the chloroplast and in cyanobacteria (as a NADH-plastoquinone oxidoreductase). Among the 25 to 30 polypeptide subunits of this bioenergetic enzyme complex there is one with a molecular weight of 24 kDa (in mammals), which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 2Fe-2S iron-sulphur cluster. The 24 kDa subunit is nuclear encoded, as a precursor form with a transit peptide in mammals and in Neurospora crassa. There is a highly conserved region located in the central section of this subunit that contains two conserved cysteines, that are probably involved in the binding of the 2Fe-2S centre. The 24 kDa subunit is highly similar to , : Subunit E of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoE) Subunit NQO2 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase ; GO: 0016491 oxidoreductase activity, 0051287 NAD binding, 0006118 electron transport.
Probab=21.14 E-value=73 Score=14.38 Aligned_cols=39 Identities=15% Similarity=0.140 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHHCC-CCCCC---HHHHHHHHCCCHHHHHHHH
Q ss_conf 899999999998559-86335---9999998199789999999
Q gi|254780620|r 7 TDYGIRVLMYCAIHN-DYPNR---ISQIAEACCISELFLFKIL 45 (144)
Q Consensus 7 ~~yAi~~l~~La~~~-~~~~s---~~eIA~~~~i~~~~l~kil 45 (144)
-+-||--++.+|+.. .+-++ .+.||+.+++|+..++-|.
T Consensus 16 ~RSA~~~~L~~aQ~~n~Gwv~~~~i~~vA~~L~~~~~~V~eVA 58 (153)
T TIGR01958 16 KRSAILPALRIAQKQNKGWVSPEAIEAVAEMLGIPPVWVYEVA 58 (153)
T ss_pred HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCHHHEEEEE
T ss_conf 6899999999998740786488999999998688701302131
No 449
>COG3811 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.90 E-value=64 Score=14.69 Aligned_cols=63 Identities=14% Similarity=0.268 Sum_probs=34.7
Q ss_pred CCCCHHHHHHHHHHHHHHHCCCCC----CCHHHHHHHHCCCH------HHHHHHHHHHHHCCCEEECCCCCCCCEECCC
Q ss_conf 976456899999999998559863----35999999819978------9999999999325905731565454000237
Q gi|254780620|r 1 MHLTKRTDYGIRVLMYCAIHNDYP----NRISQIAEACCISE------LFLFKILQPLVKAGIVETVRGRRGGVRLCRP 69 (144)
Q Consensus 1 Mkis~~~~yAi~~l~~La~~~~~~----~s~~eIA~~~~i~~------~~l~kil~~L~~agli~S~rG~~GGy~Lak~ 69 (144)
|.+|+-..--+| .||+ +|.. --+..|+...+.++ .----++++|++.++|.|..|. -|+..+.
T Consensus 1 mniSk~eQRtLH---~LAq-GGrIe~~rd~~grI~~v~C~tRdGw~l~dctlavF~kLKrK~li~S~~G~--PYRIt~~ 73 (85)
T COG3811 1 MNISKPEQRTLH---ALAQ-GGRIEIERDASGRITSVECYTRDGWLLPDCTLAVFRKLKRKKLIKSSQGG--PYRITRR 73 (85)
T ss_pred CCCCHHHHHHHH---HHHC-CCEEEEEECCCCCEEEEEEECCCCCCCCCCCHHHHHHHHHCCCEECCCCC--CEEEEHH
T ss_conf 974508889999---9964-88389986478868889986236600578519999998750334326899--5686276
No 450
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=20.89 E-value=74 Score=14.35 Aligned_cols=12 Identities=8% Similarity=0.307 Sum_probs=4.7
Q ss_pred HHHHHCCHHHHH
Q ss_conf 998417999999
Q gi|254780620|r 120 DVLTQYSIECLV 131 (144)
Q Consensus 120 ~~L~~~TL~dl~ 131 (144)
.++...+.+++.
T Consensus 151 r~~egls~~EIA 162 (201)
T PRK12545 151 REFLDFEIDDIC 162 (201)
T ss_pred HHHHCCCHHHHH
T ss_conf 999289899999
No 451
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=20.87 E-value=74 Score=14.35 Aligned_cols=12 Identities=17% Similarity=0.146 Sum_probs=6.3
Q ss_pred HHHHCCHHHHHH
Q ss_conf 984179999991
Q gi|254780620|r 121 VLTQYSIECLVR 132 (144)
Q Consensus 121 ~L~~~TL~dl~~ 132 (144)
++.+.|.+++.+
T Consensus 150 ~~~~~s~~EIA~ 161 (192)
T PRK09652 150 EIEGLSYEEIAE 161 (192)
T ss_pred HHCCCCHHHHHH
T ss_conf 972999999999
No 452
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=20.81 E-value=74 Score=14.34 Aligned_cols=37 Identities=16% Similarity=-0.037 Sum_probs=26.8
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 9999999855986335999999819978999999999
Q gi|254780620|r 11 IRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQP 47 (144)
Q Consensus 11 i~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~ 47 (144)
.++-..+....+...|.++||+..++++.-+.++++.
T Consensus 179 ~ra~~~l~~~~gr~pt~eEIA~~lg~~~~~v~~~l~~ 215 (328)
T PRK05657 179 LRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLAL 215 (328)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 9999999998489998999999969599999999974
No 453
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=20.75 E-value=74 Score=14.33 Aligned_cols=22 Identities=14% Similarity=0.155 Sum_probs=19.3
Q ss_pred CCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 6335999999819978999999
Q gi|254780620|r 23 YPNRISQIAEACCISELFLFKI 44 (144)
Q Consensus 23 ~~~s~~eIA~~~~i~~~~l~ki 44 (144)
..+|-+++|+..+++..|+.+|
T Consensus 14 ~glTQ~~LA~~aGvs~~~Is~i 35 (58)
T TIGR03070 14 LGLTQADLADLAGVGLRFIRDI 35 (58)
T ss_pred CCCCHHHHHHHHCCCHHHHHHH
T ss_conf 4998999998819989999999
No 454
>pfam05043 Mga Mga helix-turn-helix domain. M regulator protein trans-acting positive regulator (Mga) is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions. This domain is found in the centre of the Mga proteins. This family also contains a number of bacterial RofA transcriptional regulators that seem to be largely restricted to streptococci. These proteins have been shown to regulate the expression of important bacterial adhesins. This is presumably a DNA-binding domain.
Probab=20.73 E-value=74 Score=14.33 Aligned_cols=39 Identities=23% Similarity=0.358 Sum_probs=30.0
Q ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 99999999855986335999999819978999999999932
Q gi|254780620|r 10 GIRVLMYCAIHNDYPNRISQIAEACCISELFLFKILQPLVK 50 (144)
Q Consensus 10 Ai~~l~~La~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~ 50 (144)
..++|-++-.+ +..+..++|+...+|.+.+.|.+..+.+
T Consensus 18 ~f~il~~lf~~--~~~s~~~~a~~l~iS~sTl~R~ik~l~~ 56 (87)
T pfam05043 18 KFQLLKFLFFH--EFFSLTSLAQKLFISESTLYRLIKKLNK 56 (87)
T ss_pred HHHHHHHHHCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 99999999818--9998999999978899999999999999
No 455
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=20.71 E-value=74 Score=14.33 Aligned_cols=33 Identities=9% Similarity=-0.101 Sum_probs=23.1
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCC
Q ss_conf 986335999999819978999999999932590
Q gi|254780620|r 21 NDYPNRISQIAEACCISELFLFKILQPLVKAGI 53 (144)
Q Consensus 21 ~~~~~s~~eIA~~~~i~~~~l~kil~~L~~agl 53 (144)
.+...+.++||+.++++..-+.+++........
T Consensus 139 ~gr~Pt~~EiA~~lg~~~~~v~~~l~~~~~~~~ 171 (263)
T PRK07122 139 LGRAPTASELAAELGMDREEVVEGLVAGSSYNT 171 (263)
T ss_pred HCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCC
T ss_conf 688999999998969399999999987335898
Done!