Query gi|254781218|ref|YP_003065631.1| hypothetical protein CLIBASIA_05625 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 205
No_of_seqs 204 out of 5029
Neff 6.4
Searched_HMMs 39220
Date Mon May 30 08:13:12 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254781218.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK09706 transcriptional repre 99.7 6.5E-17 1.6E-21 124.3 10.5 69 30-98 4-72 (135)
2 PRK09706 transcriptional repre 99.7 3E-17 7.8E-22 126.3 8.2 72 110-181 2-73 (135)
3 PHA01976 helix-turn-helix prot 99.7 4.8E-17 1.2E-21 125.1 8.4 63 31-93 2-64 (67)
4 PHA01976 helix-turn-helix prot 99.6 2.5E-15 6.3E-20 114.5 8.3 63 113-175 2-64 (67)
5 PRK09943 DNA-binding transcrip 99.6 1E-14 2.7E-19 110.7 8.1 70 27-96 3-72 (185)
6 PRK09943 DNA-binding transcrip 99.5 6.9E-14 1.8E-18 105.6 8.6 67 112-178 6-72 (185)
7 PRK08154 anaerobic benzoate ca 99.4 5.2E-12 1.3E-16 94.0 9.7 151 23-177 20-186 (304)
8 TIGR03070 couple_hipB transcri 99.4 1.7E-12 4.2E-17 97.1 7.1 58 30-87 1-58 (58)
9 pfam01381 HTH_3 Helix-turn-hel 99.4 1.7E-12 4.3E-17 97.1 7.0 55 36-90 1-55 (55)
10 smart00530 HTH_XRE Helix-turn- 99.4 2E-12 5.2E-17 96.5 7.1 56 35-90 1-56 (56)
11 smart00530 HTH_XRE Helix-turn- 99.3 8.8E-12 2.2E-16 92.6 7.0 56 117-172 1-56 (56)
12 COG1476 Predicted transcriptio 99.3 1.3E-11 3.3E-16 91.6 7.7 61 34-94 4-64 (68)
13 pfam01381 HTH_3 Helix-turn-hel 99.3 1.1E-11 2.7E-16 92.1 6.8 55 118-172 1-55 (55)
14 PRK13890 conjugal transfer pro 99.3 2E-11 5.1E-16 90.4 8.1 66 32-97 6-71 (119)
15 cd00093 HTH_XRE Helix-turn-hel 99.2 3.8E-11 9.7E-16 88.7 7.2 58 33-90 1-58 (58)
16 COG1476 Predicted transcriptio 99.2 1.2E-10 3.1E-15 85.6 7.2 61 116-176 4-64 (68)
17 TIGR03070 couple_hipB transcri 99.1 1.5E-10 3.9E-15 84.9 7.0 57 113-169 2-58 (58)
18 PRK13890 conjugal transfer pro 99.1 2.6E-10 6.6E-15 83.5 8.1 62 114-175 6-67 (119)
19 cd00093 HTH_XRE Helix-turn-hel 99.1 1.7E-10 4.2E-15 84.7 6.9 58 115-172 1-58 (58)
20 PRK08154 anaerobic benzoate ca 99.1 7.6E-10 1.9E-14 80.7 8.8 72 112-183 27-98 (304)
21 PRK09726 DNA-binding transcrip 99.1 5.1E-10 1.3E-14 81.7 7.0 64 25-88 6-69 (88)
22 COG1813 Predicted transcriptio 99.0 2.2E-09 5.5E-14 77.8 7.7 64 114-177 80-143 (165)
23 PRK06424 transcription factor; 99.0 2.8E-09 7.2E-14 77.1 8.2 57 113-169 84-140 (144)
24 PRK08359 transcription factor; 98.9 4.9E-09 1.3E-13 75.6 7.6 56 114-169 84-139 (175)
25 COG3620 Predicted transcriptio 98.9 7.9E-09 2E-13 74.4 8.2 101 34-145 8-118 (187)
26 COG1813 Predicted transcriptio 98.9 7E-09 1.8E-13 74.7 6.5 74 24-97 72-145 (165)
27 PRK09726 DNA-binding transcrip 98.8 1.1E-08 2.7E-13 73.5 6.8 65 107-171 6-70 (88)
28 PRK06424 transcription factor; 98.8 1.8E-08 4.7E-13 72.1 7.0 67 21-87 74-140 (144)
29 PRK08359 transcription factor; 98.8 2.3E-08 5.9E-13 71.5 6.6 66 27-92 79-144 (175)
30 PRK04140 hypothetical protein; 98.7 4.9E-08 1.3E-12 69.4 7.2 136 33-173 127-279 (319)
31 PRK04140 hypothetical protein; 98.7 7E-08 1.8E-12 68.5 7.0 56 114-169 126-181 (319)
32 PRK13355 bifunctional HTH-doma 98.7 9.6E-08 2.5E-12 67.6 7.2 67 31-97 5-76 (518)
33 PRK13355 bifunctional HTH-doma 98.5 4E-07 1E-11 63.8 7.9 67 113-179 5-76 (518)
34 TIGR02607 antidote_HigA addict 98.5 4.7E-07 1.2E-11 63.4 6.2 55 38-92 14-68 (81)
35 pfam07022 Phage_CI_repr Bacter 98.4 1E-06 2.7E-11 61.2 7.3 62 117-179 2-64 (65)
36 COG2944 Predicted transcriptio 98.4 7.9E-07 2E-11 62.0 6.2 48 115-162 46-93 (104)
37 COG1395 Predicted transcriptio 98.4 9.9E-07 2.5E-11 61.4 6.6 55 33-87 127-181 (313)
38 KOG3398 consensus 98.4 6.1E-07 1.6E-11 62.7 5.5 108 46-172 23-132 (135)
39 COG1395 Predicted transcriptio 98.4 1.2E-06 3.1E-11 60.8 6.5 63 114-176 126-192 (313)
40 TIGR00270 TIGR00270 conserved 98.3 9E-07 2.3E-11 61.7 5.6 74 26-99 78-151 (169)
41 COG3620 Predicted transcriptio 98.3 1.4E-06 3.5E-11 60.5 6.5 60 116-175 8-73 (187)
42 TIGR02607 antidote_HigA addict 98.3 1.6E-06 4E-11 60.2 6.3 62 112-173 5-67 (81)
43 KOG3398 consensus 98.3 1.2E-06 3E-11 60.9 5.2 77 11-89 55-131 (135)
44 COG2944 Predicted transcriptio 98.3 1.4E-06 3.7E-11 60.4 5.5 43 33-75 46-88 (104)
45 COG1709 Predicted transcriptio 98.3 7.6E-07 1.9E-11 62.1 3.7 75 17-93 14-89 (241)
46 COG1709 Predicted transcriptio 98.2 1.9E-06 4.8E-11 59.7 4.7 53 113-165 27-80 (241)
47 COG3093 VapI Plasmid maintenan 98.2 5.9E-06 1.5E-10 56.6 6.7 52 42-93 21-72 (104)
48 PRK10072 putative transcriptio 98.2 5.9E-06 1.5E-10 56.6 6.4 54 117-171 37-90 (96)
49 COG3093 VapI Plasmid maintenan 98.2 1E-05 2.6E-10 55.1 7.5 64 111-174 7-71 (104)
50 COG1396 HipB Predicted transcr 98.1 2.1E-05 5.5E-10 53.1 8.3 65 32-96 2-67 (120)
51 COG1426 Predicted transcriptio 98.1 1.5E-05 3.7E-10 54.2 6.7 64 30-93 2-71 (284)
52 pfam07022 Phage_CI_repr Bacter 98.0 3.4E-05 8.6E-10 51.9 7.1 59 36-95 3-62 (65)
53 TIGR00270 TIGR00270 conserved 97.9 1.4E-05 3.6E-10 54.3 4.9 71 106-176 76-146 (169)
54 PRK10856 hypothetical protein; 97.9 4.9E-05 1.3E-09 50.9 7.6 64 30-93 13-82 (332)
55 COG1396 HipB Predicted transcr 97.9 0.00011 2.8E-09 48.8 9.2 63 114-176 2-65 (120)
56 TIGR02612 mob_myst_A mobile my 97.9 2.9E-05 7.5E-10 52.3 5.3 56 36-91 30-87 (150)
57 PRK10072 putative transcriptio 97.9 4.4E-05 1.1E-09 51.2 6.1 49 35-84 37-85 (96)
58 TIGR02612 mob_myst_A mobile my 97.8 1.6E-05 4E-10 54.0 3.6 78 117-199 29-108 (150)
59 COG1426 Predicted transcriptio 97.8 9.3E-05 2.4E-09 49.2 7.5 65 113-177 3-73 (284)
60 PRK10856 hypothetical protein; 97.7 0.00019 4.8E-09 47.3 7.3 67 110-176 11-83 (332)
61 COG3655 Predicted transcriptio 97.6 0.00015 3.7E-09 48.0 5.9 61 33-93 4-65 (73)
62 COG3655 Predicted transcriptio 97.5 0.00034 8.5E-09 45.8 6.1 62 114-175 3-65 (73)
63 TIGR02885 spore_sigF RNA polym 97.4 0.00037 9.5E-09 45.5 5.4 123 17-148 67-221 (231)
64 TIGR02684 dnstrm_HI1420 probab 97.3 0.00065 1.6E-08 44.0 6.2 59 110-170 31-89 (91)
65 COG5499 Predicted transcriptio 97.3 0.00062 1.6E-08 44.1 5.8 57 116-173 63-119 (120)
66 COG5499 Predicted transcriptio 97.2 0.00077 2E-08 43.5 5.7 73 18-91 44-119 (120)
67 pfam08667 BetR BetR domain. Th 97.2 0.0026 6.6E-08 40.3 8.3 64 110-173 2-69 (146)
68 COG4800 Predicted transcriptio 97.2 0.0019 4.7E-08 41.2 7.3 59 24-83 9-67 (170)
69 COG4800 Predicted transcriptio 96.8 0.008 2E-07 37.3 7.6 54 111-165 14-67 (170)
70 PRK05932 RNA polymerase factor 96.7 0.0025 6.3E-08 40.4 4.5 36 126-161 349-384 (461)
71 COG2522 Predicted transcriptio 96.7 0.0075 1.9E-07 37.4 6.8 58 31-89 9-68 (119)
72 pfam04552 Sigma54_DBD Sigma-54 96.7 0.0045 1.2E-07 38.8 5.5 136 6-157 13-157 (160)
73 PHA00542 putative Cro-like pro 96.6 0.0065 1.6E-07 37.8 6.0 57 27-83 14-71 (82)
74 PRK07408 RNA polymerase sigma 96.6 0.06 1.5E-06 31.9 11.0 137 21-165 104-251 (256)
75 TIGR02684 dnstrm_HI1420 probab 96.5 0.0042 1.1E-07 39.0 4.4 54 32-87 35-88 (91)
76 COG2522 Predicted transcriptio 96.3 0.013 3.3E-07 35.9 6.2 40 114-153 10-49 (119)
77 PRK02866 cyanate hydratase; Va 96.3 0.097 2.5E-06 30.6 10.8 62 30-91 4-65 (147)
78 PRK02866 cyanate hydratase; Va 96.2 0.038 9.6E-07 33.1 8.1 64 110-173 2-65 (147)
79 PRK07122 RNA polymerase sigma 96.2 0.095 2.4E-06 30.6 10.1 131 17-149 113-253 (263)
80 PRK12469 RNA polymerase factor 96.1 0.0062 1.6E-07 38.0 3.7 40 125-164 362-401 (475)
81 COG1508 RpoN DNA-directed RNA 96.1 0.069 1.8E-06 31.5 8.9 102 45-159 331-441 (444)
82 KOG3802 consensus 96.0 0.055 1.4E-06 32.1 8.2 126 26-170 205-336 (398)
83 TIGR02846 spore_sigmaK RNA pol 96.0 0.003 7.7E-08 39.9 1.7 25 42-66 193-217 (228)
84 pfam08667 BetR BetR domain. Th 96.0 0.055 1.4E-06 32.1 8.1 63 30-92 4-70 (146)
85 COG1191 FliA DNA-directed RNA 95.9 0.084 2.1E-06 30.9 8.6 43 116-165 202-244 (247)
86 pfam07900 DUF1670 Protein of u 95.8 0.02 5.1E-07 34.8 5.2 94 44-148 105-219 (220)
87 TIGR02980 SigBFG RNA polymeras 95.8 0.0082 2.1E-07 37.2 3.2 118 15-148 58-218 (229)
88 PRK05911 RNA polymerase sigma 95.8 0.12 3.1E-06 29.9 8.9 125 25-149 105-244 (257)
89 smart00352 POU Found in Pit-Oc 95.7 0.022 5.6E-07 34.6 5.0 53 29-83 9-67 (75)
90 PRK06288 RNA polymerase sigma 95.7 0.16 4E-06 29.3 9.3 125 25-149 109-247 (261)
91 PHA00542 putative Cro-like pro 95.5 0.038 9.8E-07 33.0 5.6 49 117-165 22-71 (82)
92 PRK08558 adenine phosphoribosy 95.5 0.075 1.9E-06 31.2 7.0 56 30-85 5-64 (238)
93 PRK12427 flagellar biosynthesi 95.4 0.21 5.5E-06 28.4 11.8 113 26-149 95-220 (229)
94 pfam00157 Pou Pou domain - N-t 95.4 0.021 5.4E-07 34.6 4.1 53 29-83 9-67 (75)
95 COG5606 Uncharacterized conser 95.4 0.025 6.3E-07 34.2 4.4 61 28-88 25-86 (91)
96 PRK03975 tfx putative transcri 95.2 0.034 8.7E-07 33.4 4.4 32 37-69 13-44 (139)
97 PRK08583 RNA polymerase sigma 95.0 0.3 7.6E-06 27.6 10.2 127 20-149 106-244 (257)
98 PRK06986 fliA flagellar biosyn 94.9 0.16 4E-06 29.3 7.3 127 25-165 90-231 (234)
99 pfam04814 HNF-1_N Hepatocyte n 94.9 0.11 2.8E-06 30.2 6.4 54 108-161 110-163 (177)
100 TIGR02980 SigBFG RNA polymeras 94.8 0.015 3.8E-07 35.6 1.7 31 36-66 188-218 (229)
101 PRK09526 lacI lac repressor; R 94.7 0.058 1.5E-06 32.0 4.5 48 41-88 2-52 (342)
102 PRK07670 RNA polymerase sigma 94.7 0.28 7.2E-06 27.7 8.1 117 32-149 107-236 (250)
103 COG3636 Predicted transcriptio 94.6 0.16 4.1E-06 29.2 6.7 56 112-169 37-92 (100)
104 PRK09492 treR trehalose repres 94.6 0.09 2.3E-06 30.8 5.4 48 42-89 2-52 (315)
105 PRK10014 DNA-binding transcrip 94.6 0.075 1.9E-06 31.3 5.0 48 41-88 3-53 (342)
106 COG2390 DeoR Transcriptional r 94.6 0.091 2.3E-06 30.7 5.3 71 23-93 5-88 (321)
107 TIGR01321 TrpR trp operon repr 94.5 0.071 1.8E-06 31.4 4.6 57 17-76 30-88 (95)
108 TIGR00721 tfx DNA-binding prot 94.5 0.027 6.9E-07 34.0 2.4 28 42-69 19-46 (142)
109 PRK10014 DNA-binding transcrip 94.4 0.091 2.3E-06 30.7 5.1 36 125-160 5-40 (342)
110 PRK09492 treR trehalose repres 94.3 0.12 3.1E-06 30.0 5.5 45 126-170 4-51 (315)
111 TIGR02395 rpoN_sigma RNA polym 94.2 0.02 5E-07 34.9 1.2 104 40-156 361-474 (477)
112 pfam01710 Transposase_14 Trans 94.1 0.34 8.8E-06 27.2 7.5 90 28-148 3-93 (120)
113 PRK09526 lacI lac repressor; R 94.0 0.13 3.3E-06 29.8 5.1 37 125-161 4-40 (342)
114 PRK08558 adenine phosphoribosy 94.0 0.31 7.9E-06 27.4 7.0 43 125-167 22-64 (238)
115 TIGR02885 spore_sigF RNA polym 94.0 0.02 5E-07 34.9 0.9 28 39-66 194-221 (231)
116 pfam05339 DUF739 Protein of un 93.9 0.24 6E-06 28.2 6.3 57 116-172 6-62 (69)
117 COG5606 Uncharacterized conser 93.9 0.11 2.8E-06 30.2 4.6 61 110-170 25-86 (91)
118 COG2973 TrpR Trp operon repres 93.9 0.29 7.3E-06 27.7 6.7 64 17-83 34-99 (103)
119 PRK11303 DNA-binding transcrip 93.6 0.17 4.4E-06 29.0 5.2 46 45-90 1-52 (330)
120 COG3636 Predicted transcriptio 93.5 0.46 1.2E-05 26.4 7.2 54 32-87 39-92 (100)
121 pfam00356 LacI Bacterial regul 93.5 0.19 4.8E-06 28.8 5.3 35 128-162 1-35 (46)
122 PRK05901 RNA polymerase sigma 93.5 0.61 1.6E-05 25.6 8.2 129 19-149 235-378 (398)
123 COG1191 FliA DNA-directed RNA 93.4 0.12 3.1E-06 30.0 4.1 15 127-141 127-141 (247)
124 smart00352 POU Found in Pit-Oc 93.1 0.15 3.9E-06 29.3 4.2 52 112-165 10-67 (75)
125 TIGR00673 cynS cyanate hydrata 93.1 0.7 1.8E-05 25.2 9.2 106 27-135 9-114 (156)
126 pfam00356 LacI Bacterial regul 93.1 0.26 6.7E-06 27.9 5.4 37 46-82 1-37 (46)
127 PRK07405 RNA polymerase sigma 93.0 0.73 1.9E-05 25.1 9.2 107 43-149 55-208 (318)
128 PRK10401 DNA-binding transcrip 92.8 0.28 7.2E-06 27.7 5.3 44 45-88 2-48 (346)
129 smart00354 HTH_LACI helix_turn 92.8 0.27 7E-06 27.8 5.2 27 46-72 2-28 (70)
130 KOG1168 consensus 92.8 0.065 1.6E-06 31.7 2.0 128 23-168 210-349 (385)
131 PRK05657 RNA polymerase sigma 92.8 0.78 2E-05 25.0 10.4 125 43-173 191-328 (328)
132 COG1356 tfx Transcriptional re 92.7 0.072 1.8E-06 31.4 2.1 47 41-88 20-69 (143)
133 smart00354 HTH_LACI helix_turn 92.7 0.32 8.2E-06 27.3 5.4 45 128-172 2-49 (70)
134 pfam04814 HNF-1_N Hepatocyte n 92.6 0.7 1.8E-05 25.2 7.1 67 5-71 84-155 (177)
135 PRK10727 DNA-binding transcrip 92.6 0.31 7.9E-06 27.5 5.2 44 45-88 2-48 (342)
136 PRK09210 RNA polymerase sigma 92.5 0.86 2.2E-05 24.7 8.6 130 18-149 205-349 (368)
137 pfam02376 CUT CUT domain. The 92.4 0.3 7.6E-06 27.6 4.9 40 109-148 3-43 (81)
138 PRK11041 DNA-binding transcrip 92.3 0.36 9.1E-06 27.1 5.3 46 44-89 9-57 (341)
139 PRK10703 DNA-binding transcrip 92.2 0.36 9.2E-06 27.0 5.2 44 46-89 3-49 (335)
140 PRK08099 nicotinamide-nucleoti 92.0 0.59 1.5E-05 25.7 6.1 55 35-89 6-61 (411)
141 PRK01381 Trp operon repressor; 91.9 0.38 9.8E-06 26.9 5.1 64 17-83 29-94 (99)
142 COG1609 PurR Transcriptional r 91.9 0.44 1.1E-05 26.5 5.3 43 45-87 1-46 (333)
143 cd04762 HTH_MerR-trunc Helix-T 91.8 0.19 4.8E-06 28.8 3.4 28 127-154 1-28 (49)
144 PRK10339 DNA-binding transcrip 91.7 0.51 1.3E-05 26.1 5.5 42 45-86 2-48 (327)
145 cd04780 HTH_MerR-like_sg5 Heli 91.6 0.15 3.9E-06 29.4 2.7 69 45-138 1-70 (95)
146 PRK10703 DNA-binding transcrip 91.4 0.54 1.4E-05 25.9 5.4 12 35-46 35-46 (335)
147 pfam08965 DUF1870 Domain of un 91.2 0.6 1.5E-05 25.7 5.5 47 35-81 4-52 (117)
148 COG1609 PurR Transcriptional r 91.2 0.53 1.3E-05 26.0 5.2 46 127-172 1-49 (333)
149 pfam00157 Pou Pou domain - N-t 91.2 0.35 9E-06 27.1 4.2 51 113-165 11-67 (75)
150 KOG3802 consensus 91.1 0.25 6.4E-06 28.0 3.5 59 110-173 207-271 (398)
151 PRK07500 rpoH2 RNA polymerase 91.1 0.22 5.7E-06 28.3 3.1 113 46-165 150-277 (289)
152 PRK05572 sporulation sigma fac 91.0 1.2 3.1E-05 23.8 9.9 121 22-149 108-240 (251)
153 cd04774 HTH_YfmP Helix-Turn-He 90.6 1.3 3.4E-05 23.5 8.2 70 45-140 1-71 (96)
154 pfam01371 Trp_repressor Trp re 90.6 0.55 1.4E-05 25.9 4.8 38 29-66 32-71 (88)
155 smart00342 HTH_ARAC helix_turn 90.5 1.2 3.1E-05 23.8 6.5 69 44-145 1-70 (84)
156 COG4197 Uncharacterized protei 90.4 0.31 8E-06 27.4 3.4 44 129-172 15-60 (96)
157 PRK10344 DNA-binding transcrip 90.2 1.2 3E-05 23.9 6.2 54 117-173 12-65 (90)
158 pfam08535 KorB KorB domain. Th 89.9 0.92 2.4E-05 24.5 5.5 44 43-87 2-59 (93)
159 PHA00675 hypothetical protein 89.5 0.6 1.5E-05 25.7 4.3 35 114-148 27-61 (78)
160 TIGR02846 spore_sigmaK RNA pol 89.5 0.2 5.2E-06 28.6 1.9 23 126-148 195-217 (228)
161 PRK10423 transcriptional repre 89.5 0.8 2E-05 24.9 4.9 42 48-89 2-46 (327)
162 COG3423 Nlp Predicted transcri 89.5 1.6 4E-05 23.1 6.4 56 117-175 12-67 (82)
163 cd01392 HTH_LacI Helix-turn-he 89.5 0.73 1.9E-05 25.1 4.7 34 131-164 2-35 (52)
164 PRK03975 tfx putative transcri 89.3 0.39 1E-05 26.8 3.2 28 123-150 16-43 (139)
165 pfam02001 DUF134 Protein of un 89.2 0.37 9.3E-06 27.0 3.0 38 121-165 47-84 (100)
166 PRK07598 RNA polymerase sigma 89.1 1.7 4.5E-05 22.8 9.7 23 70-92 177-202 (410)
167 cd04789 HTH_Cfa Helix-Turn-Hel 89.1 1.6 4.1E-05 23.1 6.1 27 45-71 2-29 (102)
168 PRK07921 RNA polymerase sigma 89.0 1.8 4.6E-05 22.7 8.2 22 127-148 279-300 (320)
169 PHA00675 hypothetical protein 89.0 0.7 1.8E-05 25.3 4.3 35 30-64 25-59 (78)
170 COG4197 Uncharacterized protei 89.0 0.45 1.1E-05 26.5 3.3 47 46-92 14-62 (96)
171 cd01110 HTH_SoxR Helix-Turn-He 88.9 1.6 4E-05 23.1 6.1 28 44-71 1-29 (139)
172 pfam04545 Sigma70_r4 Sigma-70, 88.9 0.54 1.4E-05 26.0 3.6 28 38-65 14-41 (50)
173 PRK12427 flagellar biosynthesi 88.9 0.62 1.6E-05 25.6 3.9 20 127-146 116-135 (229)
174 PRK08215 sporulation sigma fac 88.7 1.9 4.8E-05 22.6 10.4 30 120-149 219-248 (257)
175 pfam02001 DUF134 Protein of un 88.6 0.56 1.4E-05 25.9 3.5 27 40-66 48-74 (100)
176 COG4565 CitB Response regulato 88.4 2 5E-05 22.5 7.7 24 124-147 171-194 (224)
177 TIGR02392 rpoH_proteo alternat 88.3 0.82 2.1E-05 24.8 4.2 127 19-149 111-268 (279)
178 cd04781 HTH_MerR-like_sg6 Heli 88.2 1.6 4.1E-05 23.0 5.7 27 45-71 1-28 (120)
179 PRK10227 DNA-binding transcrip 88.1 2.1 5.3E-05 22.4 7.3 46 45-90 1-63 (135)
180 PRK09744 DNA-binding transcrip 88.0 0.86 2.2E-05 24.7 4.2 35 128-165 12-46 (75)
181 TIGR02835 spore_sigmaE RNA pol 87.9 0.29 7.4E-06 27.6 1.7 24 126-149 198-221 (234)
182 TIGR02850 spore_sigG RNA polym 87.9 0.9 2.3E-05 24.6 4.3 32 118-149 214-245 (254)
183 PRK09514 zntR zinc-responsive 87.8 0.87 2.2E-05 24.7 4.1 28 45-72 2-30 (140)
184 PRK08301 sporulation sigma fac 87.7 0.79 2E-05 24.9 3.8 26 124-149 201-226 (239)
185 TIGR02959 SigZ RNA polymerase 87.6 0.45 1.2E-05 26.4 2.6 30 121-150 111-141 (170)
186 PRK06596 RNA polymerase factor 87.6 2.2 5.6E-05 22.2 7.7 112 36-149 139-271 (284)
187 PRK12529 RNA polymerase sigma 87.5 0.79 2E-05 24.9 3.7 29 120-148 137-165 (178)
188 PRK06759 RNA polymerase factor 87.2 0.98 2.5E-05 24.4 4.1 33 117-149 113-145 (154)
189 PRK13752 putative transcriptio 87.0 2.4 6.1E-05 22.0 6.0 30 43-72 6-36 (144)
190 PRK05949 RNA polymerase sigma 86.9 2.4 6.2E-05 21.9 10.2 109 43-151 64-219 (327)
191 cd04782 HTH_BltR Helix-Turn-He 86.8 2.4 6.2E-05 21.9 6.2 28 45-72 1-29 (97)
192 pfam05269 Phage_CII Bacterioph 86.7 0.48 1.2E-05 26.3 2.3 44 43-88 22-65 (91)
193 cd00569 HTH_Hin_like Helix-tur 86.5 1.2 3.1E-05 23.8 4.2 25 122-146 17-41 (42)
194 COG1513 CynS Cyanate lyase [In 86.4 2.6 6.6E-05 21.8 10.1 103 29-134 6-108 (151)
195 TIGR02937 sigma70-ECF RNA poly 86.3 1 2.7E-05 24.2 3.8 32 117-148 121-152 (162)
196 PRK09863 putative frv operon r 86.0 2.7 6.9E-05 21.6 8.0 98 39-148 12-114 (585)
197 TIGR00721 tfx DNA-binding prot 85.7 0.66 1.7E-05 25.4 2.6 38 122-166 17-54 (142)
198 cd04764 HTH_MlrA-like_sg1 Heli 85.5 0.6 1.5E-05 25.7 2.3 66 45-137 1-67 (67)
199 PRK04217 hypothetical protein; 85.5 1.1 2.7E-05 24.1 3.5 38 121-165 53-90 (110)
200 COG1974 LexA SOS-response tran 85.2 1.3 3.4E-05 23.5 4.0 48 39-87 7-54 (201)
201 cd04767 HTH_HspR-like_MBC Heli 85.1 3 7.6E-05 21.4 5.7 74 45-149 2-76 (120)
202 PRK12523 RNA polymerase sigma 84.7 1.3 3.4E-05 23.6 3.8 29 120-148 129-157 (172)
203 cd04766 HTH_HspR Helix-Turn-He 84.7 3.1 7.9E-05 21.3 6.0 69 45-139 2-71 (91)
204 KOG1168 consensus 84.6 0.55 1.4E-05 25.9 1.8 38 112-149 220-266 (385)
205 pfam01047 MarR MarR family. Th 84.5 1.3 3.3E-05 23.6 3.6 27 38-64 11-37 (59)
206 PRK00423 tfb transcription ini 84.5 3.2 8.1E-05 21.2 9.9 102 43-145 181-295 (310)
207 COG2842 Uncharacterized ATPase 84.2 2.7 6.9E-05 21.6 5.2 54 32-86 7-61 (297)
208 PRK12528 RNA polymerase sigma 84.1 2.1 5.3E-05 22.3 4.5 31 118-148 127-157 (167)
209 pfam02787 CPSase_L_D3 Carbamoy 83.9 1.4 3.6E-05 23.4 3.6 52 122-173 67-119 (122)
210 TIGR01764 excise DNA binding d 83.9 1 2.6E-05 24.3 2.9 31 127-157 2-32 (49)
211 PHA01083 hypothetical protein 83.7 2.4 6E-05 22.0 4.7 63 36-98 5-69 (153)
212 pfam05930 Phage_AlpA Prophage 83.6 1.5 3.8E-05 23.3 3.6 32 127-158 4-35 (51)
213 smart00419 HTH_CRP helix_turn_ 83.4 1.1 2.9E-05 24.0 2.9 20 45-64 9-28 (48)
214 COG1342 Predicted DNA-binding 83.4 1.3 3.3E-05 23.6 3.2 38 121-165 44-81 (99)
215 TIGR02999 Sig-70_X6 RNA polyme 82.9 1.8 4.5E-05 22.8 3.8 32 116-147 151-183 (194)
216 pfam07037 DUF1323 Putative tra 82.5 1.1 2.8E-05 24.1 2.6 22 45-66 1-22 (122)
217 COG2512 Predicted membrane-ass 82.5 1.6 4.2E-05 23.0 3.5 33 116-148 199-232 (258)
218 PRK08311 putative RNA polymera 82.0 4 0.0001 20.6 5.4 99 59-168 120-221 (237)
219 PRK07773 replicative DNA helic 82.0 3.4 8.7E-05 21.0 5.0 53 111-166 709-761 (868)
220 cd04773 HTH_TioE_rpt2 Second H 81.9 1.8 4.7E-05 22.7 3.5 28 45-72 1-29 (108)
221 PRK12525 RNA polymerase sigma 81.8 2.1 5.3E-05 22.4 3.8 28 120-147 128-155 (168)
222 pfam00376 MerR MerR family reg 81.7 1.8 4.6E-05 22.7 3.5 27 128-154 1-27 (38)
223 PRK09954 hypothetical protein; 81.6 1.9 4.9E-05 22.6 3.5 28 36-63 9-36 (362)
224 cd04761 HTH_MerR-SF Helix-Turn 81.4 1.9 4.9E-05 22.6 3.5 28 127-154 1-28 (49)
225 smart00422 HTH_MERR helix_turn 81.4 2 5E-05 22.5 3.6 68 45-138 1-69 (70)
226 PRK07406 RNA polymerase sigma 81.2 4.3 0.00011 20.4 9.9 108 44-151 122-276 (385)
227 TIGR02405 trehalos_R_Ecol treh 81.0 0.71 1.8E-05 25.2 1.2 31 45-75 2-32 (311)
228 cd06571 Bac_DnaA_C C-terminal 80.9 4.3 0.00011 20.4 7.5 61 74-145 3-64 (90)
229 TIGR02997 Sig70-cyanoRpoD RNA 80.7 4.4 0.00011 20.3 7.4 141 37-178 55-266 (336)
230 TIGR02941 Sigma_B RNA polymera 80.6 0.75 1.9E-05 25.1 1.2 136 10-148 79-244 (256)
231 PRK03573 transcriptional regul 80.3 2.4 6.1E-05 21.9 3.7 29 36-64 37-66 (144)
232 KOG2252 consensus 80.3 2.8 7.1E-05 21.6 4.0 119 28-173 327-469 (558)
233 pfam08279 HTH_11 HTH domain. T 80.2 2.6 6.7E-05 21.7 3.9 20 127-146 16-35 (55)
234 cd04765 HTH_MlrA-like_sg2 Heli 80.2 4.6 0.00012 20.2 5.3 67 45-137 1-69 (99)
235 TIGR02147 Fsuc_second hypothet 80.1 1.5 3.9E-05 23.2 2.6 43 44-86 27-71 (281)
236 cd04768 HTH_BmrR-like Helix-Tu 80.1 2.4 6E-05 22.0 3.6 28 45-72 1-29 (96)
237 PRK11512 DNA-binding transcrip 79.7 2.8 7.2E-05 21.5 3.9 29 36-64 46-74 (144)
238 PRK10046 dpiA two-component re 79.6 4.8 0.00012 20.1 5.4 24 124-147 175-198 (225)
239 cd06171 Sigma70_r4 Sigma70, re 79.6 2.9 7.4E-05 21.5 3.9 27 120-146 20-46 (55)
240 cd00092 HTH_CRP helix_turn_hel 79.2 4.9 0.00013 20.0 5.1 23 125-147 24-46 (67)
241 cd04763 HTH_MlrA-like Helix-Tu 79.2 2.3 5.9E-05 22.1 3.3 64 46-136 2-67 (68)
242 COG0568 RpoD DNA-directed RNA 78.8 5.1 0.00013 19.9 6.8 103 43-149 204-322 (342)
243 cd01107 HTH_BmrR Helix-Turn-He 78.7 2.7 6.8E-05 21.7 3.5 29 45-73 1-30 (108)
244 PRK10430 DNA-binding transcrip 78.7 5.1 0.00013 19.9 5.3 32 116-147 165-199 (239)
245 smart00347 HTH_MARR helix_turn 78.5 3.2 8.3E-05 21.1 3.9 29 37-65 17-45 (101)
246 pfam07638 Sigma70_ECF ECF sigm 78.4 3.5 8.9E-05 20.9 4.0 29 118-146 143-171 (185)
247 cd04787 HTH_HMRTR_unk Helix-Tu 78.4 2.8 7.2E-05 21.5 3.6 28 45-72 1-29 (133)
248 COG3415 Transposase and inacti 78.1 5.3 0.00014 19.8 5.1 40 30-69 7-46 (138)
249 cd01108 HTH_CueR Helix-Turn-He 77.9 3 7.6E-05 21.4 3.6 28 45-72 1-29 (127)
250 cd04783 HTH_MerR1 Helix-Turn-H 77.8 2.9 7.5E-05 21.4 3.5 28 45-72 1-29 (126)
251 COG0789 SoxR Predicted transcr 77.8 2.9 7.4E-05 21.4 3.5 28 45-72 1-29 (124)
252 PRK11511 DNA-binding transcrip 77.7 5.5 0.00014 19.7 9.0 84 42-172 23-107 (127)
253 pfam04218 CENP-B_N CENP-B N-te 77.7 4.5 0.00011 20.3 4.4 35 116-150 11-46 (53)
254 cd04770 HTH_HMRTR Helix-Turn-H 77.6 2.8 7.2E-05 21.5 3.4 27 45-71 1-28 (123)
255 cd00592 HTH_MerR-like Helix-Tu 77.6 3.1 7.9E-05 21.3 3.6 67 45-138 1-68 (100)
256 COG1318 Predicted transcriptio 77.5 4.8 0.00012 20.1 4.5 31 122-152 57-87 (182)
257 PRK06930 positive control sigm 77.3 4.7 0.00012 20.2 4.4 43 120-169 124-166 (170)
258 PRK13413 mpi multiple promoter 77.2 3.1 8E-05 21.2 3.5 29 122-150 168-196 (200)
259 pfam05225 HTH_psq helix-turn-h 77.0 5.7 0.00015 19.6 4.9 39 113-152 4-42 (45)
260 PRK10572 DNA-binding transcrip 76.9 5.8 0.00015 19.6 9.6 33 124-156 197-229 (290)
261 pfam07471 Phage_Nu1 Phage DNA 76.8 2.6 6.7E-05 21.7 3.0 24 43-66 1-24 (164)
262 PRK09651 RNA polymerase sigma 76.8 3.6 9.2E-05 20.9 3.7 29 119-147 128-156 (172)
263 PRK11753 cAMP-regulatory prote 76.7 5.8 0.00015 19.6 5.3 23 126-148 168-190 (211)
264 PRK09646 RNA polymerase sigma 76.6 5.9 0.00015 19.6 6.1 42 120-168 152-193 (194)
265 cd01104 HTH_MlrA-CarA Helix-Tu 76.4 3.2 8.2E-05 21.2 3.4 65 45-136 1-67 (68)
266 TIGR02479 FliA_WhiG RNA polyme 76.2 6 0.00015 19.5 9.8 117 25-147 78-215 (227)
267 pfam02796 HTH_7 Helix-turn-hel 76.2 3.2 8.1E-05 21.2 3.3 28 122-149 17-44 (45)
268 pfam04967 HTH_10 HTH DNA bindi 76.2 2.8 7.2E-05 21.5 3.0 23 125-147 22-44 (53)
269 cd04785 HTH_CadR-PbrR-like Hel 76.1 3.5 9E-05 20.9 3.5 28 45-72 1-29 (126)
270 cd04769 HTH_MerR2 Helix-Turn-H 76.1 3.3 8.5E-05 21.1 3.4 66 45-137 1-67 (116)
271 TIGR00160 MGSA methylglyoxal s 75.7 1.6 4.1E-05 23.0 1.7 25 69-93 89-120 (143)
272 PRK12527 RNA polymerase sigma 75.6 3.6 9.3E-05 20.8 3.5 29 118-146 113-141 (159)
273 pfam01527 Transposase_8 Transp 75.5 5.6 0.00014 19.7 4.4 27 123-149 20-46 (75)
274 cd04772 HTH_TioE_rpt1 First He 75.2 3.9 1E-04 20.6 3.6 21 46-66 2-22 (99)
275 pfam02954 HTH_8 Bacterial regu 75.0 5.7 0.00015 19.6 4.4 31 116-146 8-38 (42)
276 PRK05803 sporulation sigma fac 74.6 4.8 0.00012 20.1 3.9 26 124-149 192-217 (228)
277 cd01282 HTH_MerR-like_sg3 Heli 74.6 4.2 0.00011 20.5 3.6 67 45-138 1-68 (112)
278 PRK07037 extracytoplasmic-func 74.6 6.3 0.00016 19.4 4.5 29 120-148 133-161 (183)
279 PRK11161 fumarate/nitrate redu 74.3 6.7 0.00017 19.2 5.1 24 125-148 183-206 (235)
280 cd01105 HTH_GlnR-like Helix-Tu 74.2 4.2 0.00011 20.5 3.5 67 45-137 2-69 (88)
281 TIGR02044 CueR Cu(I)-responsiv 74.2 6.8 0.00017 19.2 5.7 78 47-124 3-101 (127)
282 cd04786 HTH_MerR-like_sg7 Heli 74.1 4.4 0.00011 20.4 3.6 28 45-72 1-29 (131)
283 cd01109 HTH_YyaN Helix-Turn-He 73.8 3.9 0.0001 20.6 3.3 27 45-71 1-28 (113)
284 cd01106 HTH_TipAL-Mta Helix-Tu 73.4 4.6 0.00012 20.2 3.6 28 45-72 1-29 (103)
285 PRK11179 DNA-binding transcrip 73.4 5.2 0.00013 19.9 3.8 27 36-62 15-41 (153)
286 COG3311 AlpA Predicted transcr 73.3 4.3 0.00011 20.4 3.4 34 125-158 12-45 (70)
287 cd01279 HTH_HspR-like Helix-Tu 73.2 7.2 0.00018 19.0 5.0 71 45-141 2-73 (98)
288 PRK11169 leucine-responsive tr 72.9 5.4 0.00014 19.8 3.8 27 36-62 20-46 (164)
289 PRK09775 hypothetical protein; 72.7 5.2 0.00013 19.9 3.7 31 35-65 3-33 (443)
290 cd04784 HTH_CadR-PbrR Helix-Tu 72.5 4.9 0.00012 20.0 3.5 28 45-72 1-29 (127)
291 cd04775 HTH_Cfa-like Helix-Tur 71.9 5.3 0.00013 19.8 3.6 25 45-69 2-27 (102)
292 COG1522 Lrp Transcriptional re 71.7 5.9 0.00015 19.6 3.8 28 36-63 14-41 (154)
293 PRK13918 CRP/FNR family transc 71.4 4 0.0001 20.6 2.9 41 126-166 145-198 (201)
294 PRK13749 transcriptional regul 70.9 6.8 0.00017 19.2 4.0 48 43-90 2-66 (121)
295 PRK09391 fixK transcriptional 70.7 4.3 0.00011 20.4 2.9 24 124-147 171-194 (224)
296 TIGR02985 Sig70_bacteroi1 RNA 70.5 6.7 0.00017 19.2 3.8 27 120-146 129-155 (167)
297 smart00344 HTH_ASNC helix_turn 70.5 6.8 0.00017 19.2 3.9 27 36-62 9-35 (108)
298 pfam08281 Sigma70_r4_2 Sigma-7 70.2 8.3 0.00021 18.6 4.3 29 118-146 18-46 (54)
299 PRK13503 transcriptional activ 69.8 8.6 0.00022 18.5 8.5 41 117-157 176-218 (278)
300 pfam08299 Bac_DnaA_C domain. 69.7 8.6 0.00022 18.5 7.2 61 74-145 4-65 (70)
301 PHA00361 cI Repressor 69.5 2.3 5.9E-05 22.0 1.3 19 78-96 1-19 (165)
302 cd04790 HTH_Cfa-like_unk Helix 69.0 6.5 0.00017 19.3 3.5 47 45-91 2-65 (172)
303 TIGR02417 fruct_sucro_rep D-fr 68.9 4 0.0001 20.6 2.4 48 46-93 1-54 (335)
304 COG2452 Predicted site-specifi 68.4 6.3 0.00016 19.4 3.3 23 44-66 1-23 (193)
305 TIGR02051 MerR Hg(II)-responsi 68.3 1.6 4E-05 23.1 0.2 21 48-68 3-24 (126)
306 cd06170 LuxR_C_like C-terminal 68.1 6.1 0.00015 19.5 3.2 23 124-146 13-35 (57)
307 pfam07750 GcrA GcrA cell cycle 67.8 5.3 0.00013 19.8 2.9 28 34-61 6-36 (162)
308 COG3413 Predicted DNA binding 67.3 5.8 0.00015 19.6 3.0 69 73-148 125-200 (215)
309 pfam09048 Cro Cro. Members of 67.1 8.4 0.00021 18.6 3.8 30 38-69 7-36 (58)
310 cd04776 HTH_GnyR Helix-Turn-He 67.0 7.5 0.00019 18.9 3.5 64 45-138 1-67 (118)
311 pfam10668 Phage_terminase Phag 66.7 4.2 0.00011 20.5 2.2 21 127-147 23-43 (60)
312 TIGR03001 Sig-70_gmx1 RNA poly 66.5 4.3 0.00011 20.4 2.2 29 121-149 177-205 (249)
313 pfam00196 GerE Bacterial regul 65.8 7.1 0.00018 19.0 3.2 23 124-146 16-38 (58)
314 PRK09637 RNA polymerase sigma 65.8 8 0.0002 18.7 3.4 42 118-166 114-155 (181)
315 PRK12516 RNA polymerase sigma 65.6 7.4 0.00019 18.9 3.3 44 118-168 127-170 (190)
316 PRK13182 racA polar chromosome 65.5 5.8 0.00015 19.6 2.7 23 45-67 1-23 (178)
317 PRK13919 putative RNA polymera 65.4 10 0.00027 18.0 4.6 28 120-147 146-173 (187)
318 cd01111 HTH_MerD Helix-Turn-He 65.3 7.5 0.00019 18.9 3.2 28 45-72 1-29 (107)
319 PRK11557 putative DNA-binding 65.0 11 0.00027 18.0 4.0 58 26-83 15-74 (282)
320 pfam01418 HTH_6 Helix-turn-hel 64.9 6.6 0.00017 19.2 2.9 56 29-84 18-75 (106)
321 cd04788 HTH_NolA-AlbR Helix-Tu 64.4 9.2 0.00023 18.4 3.5 28 45-72 1-29 (96)
322 PRK11922 RNA polymerase sigma 64.2 8.9 0.00023 18.4 3.4 29 120-148 159-187 (231)
323 PRK12541 RNA polymerase sigma 64.0 8.3 0.00021 18.6 3.2 28 119-146 121-148 (161)
324 PRK09392 ftrB transcriptional 63.9 7.2 0.00018 19.0 2.9 23 125-147 172-194 (236)
325 smart00421 HTH_LUXR helix_turn 63.9 8 0.0002 18.7 3.2 24 123-146 15-38 (58)
326 COG5484 Uncharacterized conser 63.4 6.5 0.00017 19.3 2.6 27 42-68 17-43 (279)
327 cd04777 HTH_MerR-like_sg1 Heli 63.4 7.3 0.00018 19.0 2.9 64 45-138 1-67 (107)
328 PRK12539 RNA polymerase sigma 63.0 11 0.00028 17.9 3.7 27 120-146 141-167 (184)
329 COG2826 Tra8 Transposase and i 62.5 8.2 0.00021 18.7 3.0 34 35-69 15-49 (318)
330 PRK12532 RNA polymerase sigma 62.3 9.4 0.00024 18.3 3.3 27 120-146 146-172 (195)
331 PRK12517 RNA polymerase sigma 61.7 11 0.00027 18.0 3.4 29 119-147 137-165 (188)
332 pfam09339 HTH_IclR IclR helix- 61.5 7.1 0.00018 19.0 2.5 26 123-148 15-40 (52)
333 smart00420 HTH_DEOR helix_turn 61.5 11 0.00027 18.0 3.4 28 118-145 6-33 (53)
334 PRK12526 RNA polymerase sigma 61.4 11 0.00027 17.9 3.4 28 120-147 163-190 (206)
335 pfam04760 IF2_N Translation in 60.9 13 0.00032 17.5 5.4 42 126-167 3-51 (52)
336 PRK12524 RNA polymerase sigma 60.8 11 0.00028 17.9 3.4 51 119-176 145-195 (196)
337 PRK12543 RNA polymerase sigma 60.3 12 0.00029 17.7 3.4 30 118-147 137-166 (190)
338 PRK10360 DNA-binding transcrip 60.3 11 0.00028 17.9 3.3 27 122-148 148-174 (196)
339 PRK12547 RNA polymerase sigma 60.2 11 0.00027 18.0 3.3 30 118-147 120-149 (164)
340 PRK09647 RNA polymerase sigma 59.7 11 0.00027 17.9 3.2 28 120-147 167-194 (222)
341 PRK09935 transcriptional regul 59.7 11 0.00028 17.9 3.3 33 116-148 152-186 (210)
342 TIGR01529 argR_whole arginine 59.3 13 0.00033 17.4 3.6 32 34-65 5-43 (155)
343 PRK12542 RNA polymerase sigma 59.2 11 0.00029 17.8 3.2 41 118-165 130-170 (185)
344 TIGR02233 Myxo_sigma_rel Myxoc 59.1 6.8 0.00017 19.2 2.1 32 120-151 34-65 (106)
345 PRK12536 RNA polymerase sigma 58.9 12 0.00029 17.7 3.3 28 120-147 136-163 (178)
346 PRK09644 RNA polymerase sigma 58.9 11 0.00027 18.0 3.1 29 118-146 116-144 (165)
347 PRK09047 RNA polymerase factor 58.5 11 0.00028 17.9 3.1 27 120-146 116-142 (161)
348 TIGR02047 CadR-PbrR Cd(II)/Pb( 58.3 5.4 0.00014 19.8 1.5 25 48-72 4-28 (127)
349 PRK12546 RNA polymerase sigma 58.2 12 0.0003 17.7 3.2 42 120-168 123-164 (188)
350 PRK12519 RNA polymerase sigma 57.9 13 0.00034 17.4 3.4 28 120-147 151-178 (194)
351 PRK09978 DNA-binding transcrip 57.9 14 0.00036 17.2 6.9 24 42-65 156-179 (274)
352 PRK11302 DNA-binding transcrip 57.9 14 0.00036 17.2 3.9 58 27-84 16-75 (284)
353 smart00418 HTH_ARSR helix_turn 57.8 13 0.00034 17.3 3.4 23 124-146 8-30 (66)
354 TIGR02329 propionate_PrpR prop 57.8 13 0.00032 17.5 3.3 36 113-148 622-657 (658)
355 cd04779 HTH_MerR-like_sg4 Heli 57.7 14 0.00036 17.2 3.5 27 46-72 2-29 (134)
356 PRK10403 transcriptional regul 57.6 12 0.00032 17.5 3.2 36 122-168 164-199 (215)
357 PHA01082 putative transcriptio 57.6 6.4 0.00016 19.3 1.7 40 42-81 28-68 (133)
358 PRK09958 DNA-binding transcrip 57.4 13 0.00033 17.4 3.3 27 122-148 154-180 (204)
359 PRK11924 RNA polymerase sigma 57.4 15 0.00037 17.1 4.4 30 118-147 133-162 (180)
360 COG3888 Predicted transcriptio 57.2 13 0.00033 17.5 3.2 28 36-63 10-39 (321)
361 pfam06056 Terminase_5 Putative 56.7 11 0.00028 17.9 2.8 29 124-152 11-39 (58)
362 PRK12544 RNA polymerase sigma 56.7 13 0.00034 17.3 3.3 28 120-147 159-186 (207)
363 PRK05602 RNA polymerase sigma 56.7 15 0.00038 17.0 3.9 29 119-147 137-165 (186)
364 PRK09645 RNA polymerase sigma 56.3 15 0.00039 17.0 3.8 47 118-168 124-170 (171)
365 COG1737 RpiR Transcriptional r 56.3 12 0.0003 17.7 2.9 57 29-85 20-78 (281)
366 COG3355 Predicted transcriptio 56.3 15 0.00039 17.0 3.6 23 41-63 39-61 (126)
367 PRK08295 RNA polymerase factor 56.2 15 0.00039 17.0 4.5 26 122-147 166-191 (209)
368 COG2197 CitB Response regulato 55.7 14 0.00036 17.2 3.2 27 122-148 159-185 (211)
369 PRK13502 transcriptional activ 55.6 16 0.0004 16.9 8.3 28 124-151 190-217 (282)
370 PRK12540 RNA polymerase sigma 55.6 14 0.00036 17.2 3.2 42 120-168 121-162 (181)
371 PRK12530 RNA polymerase sigma 55.5 15 0.00037 17.1 3.3 27 120-146 146-172 (191)
372 PRK10840 transcriptional regul 55.3 15 0.00037 17.1 3.3 47 122-168 161-211 (216)
373 PRK09483 response regulator; P 55.0 15 0.00038 17.0 3.3 51 122-172 159-214 (216)
374 PRK10783 mltD membrane-bound l 54.3 16 0.00042 16.8 7.7 54 123-176 348-431 (449)
375 COG1497 Predicted transcriptio 54.3 13 0.00034 17.3 3.0 26 40-65 21-46 (260)
376 pfam08220 HTH_DeoR DeoR-like h 53.9 17 0.00042 16.8 3.4 29 117-145 5-33 (57)
377 PRK12538 RNA polymerase sigma 53.9 17 0.00042 16.8 3.4 29 119-147 180-208 (233)
378 PRK12512 RNA polymerase sigma 53.8 16 0.00042 16.8 3.3 30 118-147 139-168 (184)
379 TIGR02899 spore_safA spore coa 53.5 8.1 0.00021 18.7 1.7 20 74-93 5-24 (44)
380 PRK11923 algU RNA polymerase s 53.4 17 0.00043 16.7 3.4 27 120-146 148-174 (193)
381 PRK12522 RNA polymerase sigma 53.4 16 0.00041 16.8 3.3 28 119-146 128-155 (173)
382 PRK09640 RNA polymerase sigma 53.0 17 0.00042 16.8 3.3 30 117-146 141-170 (188)
383 PRK12514 RNA polymerase sigma 53.0 16 0.00042 16.8 3.2 28 120-147 139-166 (179)
384 pfam11268 DUF3071 Protein of u 53.0 17 0.00044 16.7 3.5 28 120-147 62-89 (169)
385 PRK09638 RNA polymerase sigma 52.8 17 0.00044 16.7 4.1 29 119-147 136-164 (177)
386 pfam07278 DUF1441 Protein of u 52.8 17 0.00044 16.6 3.4 25 45-69 2-26 (152)
387 COG1595 RpoE DNA-directed RNA 52.7 17 0.00044 16.6 3.8 29 120-148 137-165 (182)
388 COG0856 Orotate phosphoribosyl 52.6 14 0.00035 17.3 2.8 55 30-93 2-62 (203)
389 PRK12537 RNA polymerase sigma 52.5 17 0.00045 16.6 4.0 28 120-147 145-172 (184)
390 PRK03902 manganese transport t 52.4 18 0.00045 16.6 9.9 121 22-172 3-127 (142)
391 smart00346 HTH_ICLR helix_turn 52.1 13 0.00032 17.5 2.5 24 124-147 18-41 (91)
392 PRK12535 RNA polymerase sigma 51.9 18 0.00045 16.6 3.3 28 120-147 142-169 (195)
393 PRK09649 RNA polymerase sigma 51.7 18 0.00045 16.6 3.2 28 120-147 140-167 (185)
394 cd00090 HTH_ARSR Arsenical Res 51.4 18 0.00046 16.5 3.9 28 118-146 13-40 (78)
395 TIGR00491 aIF-2 translation in 51.4 4.6 0.00012 20.2 0.2 47 32-84 415-461 (1145)
396 TIGR01817 nifA Nif-specific re 51.3 18 0.00047 16.5 3.6 30 116-145 533-562 (574)
397 PRK10371 DNA-binding transcrip 51.2 18 0.00047 16.5 9.1 42 114-155 193-236 (302)
398 PRK11337 DNA-binding transcrip 51.2 18 0.00047 16.5 4.6 59 27-85 29-89 (293)
399 PRK09641 RNA polymerase sigma 51.0 18 0.00047 16.5 4.1 27 120-146 146-172 (187)
400 KOG3647 consensus 50.8 19 0.00047 16.5 4.8 136 25-173 48-195 (338)
401 PRK10651 transcriptional regul 50.3 19 0.00048 16.4 3.3 25 123-147 167-191 (216)
402 PRK10219 DNA-binding transcrip 50.3 19 0.00048 16.4 11.0 81 32-145 7-90 (107)
403 PRK12545 RNA polymerase sigma 50.1 19 0.00049 16.4 3.2 30 118-147 147-176 (201)
404 pfam02042 RWP-RK RWP-RK domain 50.0 19 0.00049 16.4 4.5 33 118-150 7-39 (52)
405 PRK12515 RNA polymerase sigma 49.9 19 0.00049 16.4 3.7 48 120-171 141-188 (189)
406 PRK12511 RNA polymerase sigma 49.8 10 0.00025 18.1 1.7 26 121-146 122-147 (182)
407 TIGR02043 ZntR Zn(II)-responsi 49.7 7.7 0.0002 18.8 1.1 27 47-73 4-31 (132)
408 COG1654 BirA Biotin operon rep 49.6 19 0.0005 16.3 4.1 19 45-63 20-38 (79)
409 PRK12531 RNA polymerase sigma 49.3 20 0.0005 16.3 4.1 30 118-147 149-178 (194)
410 PRK09834 DNA-binding transcrip 49.1 15 0.00039 17.0 2.6 25 40-64 22-46 (264)
411 PRK09643 RNA polymerase sigma 48.9 20 0.00051 16.3 3.4 30 118-147 139-168 (197)
412 TIGR01369 CPSaseII_lrg carbamo 48.2 7.5 0.00019 18.9 0.9 117 58-174 416-557 (1089)
413 pfam00325 Crp Bacterial regula 48.1 16 0.0004 16.9 2.5 22 126-147 2-23 (32)
414 PRK11608 pspF phage shock prot 47.7 21 0.00053 16.2 4.5 94 55-148 208-321 (325)
415 PRK04182 cytidylate kinase; Pr 47.7 21 0.00053 16.2 4.1 113 19-137 7-124 (178)
416 smart00760 Bac_DnaA_C Bacteria 46.7 22 0.00055 16.1 6.5 53 74-137 4-56 (60)
417 PRK10163 DNA-binding transcrip 46.3 22 0.00056 16.0 3.0 25 41-65 37-61 (271)
418 PRK01905 DNA-binding protein F 46.1 22 0.00056 16.0 3.9 32 116-147 40-71 (77)
419 COG4189 Predicted transcriptio 46.0 22 0.00056 16.0 4.9 25 120-144 31-55 (308)
420 pfam00440 TetR_N Bacterial reg 45.8 22 0.00057 16.0 3.8 33 118-150 8-40 (47)
421 PRK11569 transcriptional repre 45.5 22 0.00057 16.0 2.9 24 41-64 40-63 (274)
422 pfam09572 RE_XamI XamI restric 44.7 23 0.00059 15.9 4.8 74 20-96 6-92 (251)
423 TIGR03454 partition_RepB plasm 44.6 23 0.00059 15.9 3.3 57 119-175 170-227 (325)
424 PRK10141 DNA-binding transcrip 44.1 24 0.0006 15.8 3.7 21 126-146 28-48 (106)
425 PRK09652 RNA polymerase sigma 43.9 24 0.00061 15.8 4.5 27 120-146 147-173 (192)
426 PRK06811 RNA polymerase factor 43.6 24 0.00061 15.8 4.1 27 120-146 138-164 (185)
427 PRK12534 RNA polymerase sigma 43.5 24 0.00062 15.8 4.1 29 118-146 145-173 (187)
428 PRK12518 RNA polymerase sigma 42.7 25 0.00063 15.7 4.1 29 119-147 129-157 (175)
429 pfam01022 HTH_5 Bacterial regu 42.6 25 0.00064 15.7 4.1 26 122-147 11-36 (47)
430 COG2963 Transposase and inacti 42.6 25 0.00064 15.7 3.3 40 25-64 5-45 (116)
431 PRK09642 RNA polymerase sigma 42.5 25 0.00064 15.7 3.2 27 120-146 116-142 (160)
432 pfam02540 NAD_synthase NAD syn 42.4 25 0.00064 15.6 7.6 32 116-147 199-230 (243)
433 TIGR01950 SoxR redox-sensitive 42.1 12 0.00032 17.5 1.2 25 45-69 2-27 (142)
434 PRK09393 ftrA transcriptional 42.0 26 0.00065 15.6 10.9 31 122-152 228-258 (320)
435 TIGR02702 SufR_cyano iron-sulf 41.7 25 0.00063 15.7 2.7 27 37-63 8-34 (215)
436 pfam06413 Neugrin Neugrin. Thi 40.9 27 0.00068 15.5 5.3 45 34-78 17-63 (225)
437 pfam04645 DUF603 Protein of un 40.0 27 0.0007 15.4 3.5 30 43-72 17-51 (181)
438 pfam04458 DUF505 Protein of un 39.9 27 0.0007 15.4 3.5 47 32-83 105-152 (591)
439 COG1321 TroR Mn-dependent tran 39.9 28 0.0007 15.4 4.4 115 23-167 6-122 (154)
440 smart00497 IENR1 Intron encode 39.6 20 0.0005 16.3 1.9 24 128-151 19-42 (53)
441 TIGR02812 fadR_gamma fatty aci 39.6 12 0.00031 17.6 0.9 116 48-191 34-163 (275)
442 PRK09648 RNA polymerase sigma 39.3 28 0.00072 15.4 3.3 27 120-146 147-173 (187)
443 PRK12513 RNA polymerase sigma 39.3 28 0.00072 15.4 4.6 28 120-147 149-176 (194)
444 PRK10365 transcriptional regul 38.8 29 0.00073 15.3 4.1 32 116-147 408-439 (441)
445 PRK09409 insertion element IS2 38.5 29 0.00074 15.3 3.5 26 41-66 8-33 (301)
446 TIGR02983 SigE-fam_strep RNA p 38.3 15 0.00039 17.0 1.2 59 88-146 81-149 (165)
447 TIGR02960 SigX5 RNA polymerase 38.3 29 0.00074 15.3 2.7 24 121-144 154-177 (329)
448 PRK10906 DNA-binding transcrip 37.8 30 0.00076 15.2 3.0 28 36-63 11-38 (252)
449 COG1510 Predicted transcriptio 37.6 22 0.00056 16.0 1.9 33 32-64 28-61 (177)
450 pfam04297 UPF0122 Putative hel 37.4 30 0.00077 15.2 2.6 22 42-63 31-52 (101)
451 PRK13509 transcriptional repre 37.4 30 0.00077 15.2 3.1 29 36-64 11-39 (251)
452 PRK09802 DNA-binding transcrip 37.0 31 0.00078 15.1 3.0 28 36-63 23-50 (269)
453 PRK12533 RNA polymerase sigma 36.7 31 0.00079 15.1 3.3 28 120-147 147-174 (217)
454 PRK11388 DNA-binding transcrip 36.3 31 0.0008 15.1 4.4 32 116-147 594-625 (639)
455 COG1414 IclR Transcriptional r 35.8 32 0.00081 15.0 3.6 22 43-64 18-39 (246)
456 cd07377 WHTH_GntR Winged helix 35.7 32 0.00082 15.0 3.3 17 46-62 27-43 (66)
457 PRK09639 RNA polymerase sigma 35.7 32 0.00082 15.0 4.9 24 124-147 125-148 (166)
458 PRK13501 transcriptional activ 35.5 32 0.00082 15.0 7.0 31 125-155 191-221 (290)
459 pfam07453 NUMOD1 NUMOD1 domain 35.5 24 0.00061 15.8 1.8 19 128-146 18-36 (37)
460 pfam05732 RepL Firmicute plasm 34.5 31 0.00079 15.1 2.3 46 127-178 76-126 (165)
461 PRK00430 fis DNA-binding prote 34.4 34 0.00086 14.9 3.9 61 75-146 31-91 (98)
462 COG0656 ARA1 Aldo/keto reducta 34.3 34 0.00086 14.9 3.2 59 129-187 175-238 (280)
463 PRK10923 glnG nitrogen regulat 34.1 34 0.00087 14.8 4.2 33 116-148 432-464 (469)
464 pfam02084 Bindin Bindin. 34.0 34 0.00086 14.9 2.4 52 62-127 90-141 (239)
465 PRK00118 putative DNA-binding 33.9 34 0.00087 14.8 2.8 23 41-63 30-52 (105)
466 PRK09480 slmA nucleoid occlusi 33.9 34 0.00087 14.8 2.6 30 41-70 27-56 (194)
467 PRK10681 DNA-binding transcrip 33.5 35 0.00089 14.8 4.3 30 34-63 11-40 (252)
468 KOG0774 consensus 33.3 17 0.00043 16.7 0.8 23 130-152 222-244 (334)
469 PRK09940 transcriptional regul 33.1 35 0.0009 14.7 8.7 37 114-150 135-174 (253)
470 PRK09415 RNA polymerase factor 32.9 36 0.00091 14.7 5.7 27 120-146 137-163 (177)
471 PRK05234 mgsA methylglyoxal sy 32.9 36 0.00091 14.7 2.8 45 54-98 62-128 (146)
472 PRK04280 arginine repressor; P 32.9 33 0.00085 14.9 2.2 29 36-64 10-44 (149)
473 COG1339 Transcriptional regula 32.7 36 0.00091 14.7 3.4 26 39-65 15-40 (214)
474 PRK13500 transcriptional activ 31.9 37 0.00094 14.6 7.0 42 114-155 208-251 (312)
475 PRK10402 DNA-binding transcrip 31.8 37 0.00095 14.6 2.8 39 127-165 157-208 (213)
476 TIGR00651 pta phosphate acetyl 31.5 38 0.00096 14.6 2.5 34 21-54 55-88 (322)
477 PRK09390 fixJ response regulat 31.5 38 0.00096 14.6 3.2 33 116-148 144-178 (202)
478 PRK12681 cysB transcriptional 31.4 38 0.00096 14.6 4.1 29 35-63 5-35 (324)
479 COG1725 Predicted transcriptio 31.0 38 0.00098 14.5 2.6 36 28-63 12-54 (125)
480 COG1349 GlpR Transcriptional r 30.8 39 0.00098 14.5 4.3 31 33-63 8-38 (253)
481 COG1124 DppF ABC-type dipeptid 30.7 39 0.00099 14.5 3.3 49 48-97 122-170 (252)
482 pfam01325 Fe_dep_repress Iron 30.1 40 0.001 14.4 3.7 22 43-64 19-40 (58)
483 PRK10434 srlR DNA-bindng trans 30.1 40 0.001 14.4 3.3 28 36-63 11-38 (256)
484 PRK05294 carB carbamoyl phosph 29.7 40 0.001 14.4 4.1 107 64-174 419-540 (1063)
485 PRK13980 NAD synthetase; Provi 29.5 40 0.001 14.4 7.6 71 75-146 167-238 (264)
486 pfam08822 DUF1804 Protein of u 29.4 41 0.001 14.4 4.7 118 29-160 4-127 (165)
487 COG3829 RocR Transcriptional r 29.4 41 0.001 14.4 4.1 34 116-149 523-556 (560)
488 cd00086 homeodomain Homeodomai 29.4 41 0.001 14.4 2.5 17 131-147 32-48 (59)
489 PRK11361 acetoacetate metaboli 29.4 41 0.001 14.4 4.1 31 117-147 421-451 (457)
490 cd04778 HTH_MerR-like_sg2 Heli 29.4 41 0.001 14.4 2.8 28 45-72 2-30 (219)
491 COG2378 Predicted transcriptio 29.3 41 0.001 14.3 3.3 34 31-64 9-42 (311)
492 PHA02519 plasmid partition pro 28.9 42 0.0011 14.3 5.4 64 23-86 8-97 (387)
493 COG1582 FlgEa Uncharacterized 28.8 28 0.00072 15.3 1.3 46 1-46 12-61 (67)
494 pfam05043 Mga Mga helix-turn-h 28.6 42 0.0011 14.3 3.7 46 116-169 20-65 (87)
495 TIGR01132 pgm phosphoglucomuta 28.5 32 0.00082 15.0 1.5 27 10-36 224-255 (553)
496 pfam00165 HTH_AraC Bacterial r 28.5 42 0.0011 14.3 2.8 36 42-77 6-42 (43)
497 cd01422 MGS Methylglyoxal synt 28.3 38 0.00098 14.5 1.9 18 70-87 87-104 (115)
498 PRK04435 hypothetical protein; 28.2 33 0.00085 14.9 1.6 28 119-146 26-53 (146)
499 pfam04936 DUF658 Protein of un 28.2 43 0.0011 14.2 2.7 27 128-154 16-42 (134)
500 pfam01316 Arg_repressor Argini 28.1 36 0.00093 14.7 1.7 18 46-63 21-43 (70)
No 1
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=99.72 E-value=6.5e-17 Score=124.32 Aligned_cols=69 Identities=17% Similarity=0.256 Sum_probs=64.3
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCC
Q ss_conf 999999999999859988999998489999999887799888999999999982899999614532210
Q gi|254781218|r 30 KDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDR 98 (205)
Q Consensus 30 ~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~ 98 (205)
+-||+||+.+|+.+||||.+||+.+|||+++||+||+|...|+.+.|.+||++|+||++|||.|+.-..
T Consensus 4 ~tiG~Ri~~~R~~~glTQ~eLA~~~Gvs~~tVs~wE~g~~~P~~~~L~~LA~~L~vs~~wLL~G~~d~~ 72 (135)
T PRK09706 4 ETLGQRIRYRRKQLKLSQRALAKAVGVSHVSISQWERDETEPAGKNLFALAQALQCSPTWLLFGDEDKQ 72 (135)
T ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHCCCCCCCC
T ss_conf 309999999999859999999999698899999998289888999999999998909999848887789
No 2
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=99.71 E-value=3e-17 Score=126.34 Aligned_cols=72 Identities=28% Similarity=0.445 Sum_probs=66.5
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCH
Q ss_conf 467779999999997298389999997799999999741488999899999999828999995247210254
Q gi|254781218|r 110 DPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIYFGDEVIVP 181 (205)
Q Consensus 110 d~~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~~G~e~~~~ 181 (205)
+...+|.||+.+|+.+||||.+||+.+|+++++|++||+|.+.|+.+.+.+||++|||+++|||+|++...|
T Consensus 2 ~~~tiG~Ri~~~R~~~glTQ~eLA~~~Gvs~~tVs~wE~g~~~P~~~~L~~LA~~L~vs~~wLL~G~~d~~~ 73 (135)
T PRK09706 2 KNETLGQRIRYRRKQLKLSQRALAKAVGVSHVSISQWERDETEPAGKNLFALAQALQCSPTWLLFGDEDKQP 73 (135)
T ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHCCCCCCCCC
T ss_conf 713099999999998599999999996988999999982898889999999999989099998488877899
No 3
>PHA01976 helix-turn-helix protein
Probab=99.70 E-value=4.8e-17 Score=125.10 Aligned_cols=63 Identities=17% Similarity=0.276 Sum_probs=58.9
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCC
Q ss_conf 999999999998599889999984899999998877998889999999999828999996145
Q gi|254781218|r 31 DVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDG 93 (205)
Q Consensus 31 ~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~g 93 (205)
.+|.||+.+|+.+||||+|||+++||++++|++||+|.+.|+++.|+.||++|+||+|||++.
T Consensus 2 ~F~~RL~~lR~~~g~sQ~eLA~~lGVs~~~is~wE~g~~~P~~d~L~~la~~~~VS~D~LlGr 64 (67)
T PHA01976 2 SFAIQLIKARNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTLDWLCGR 64 (67)
T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCC
T ss_conf 789999999998699999999994998999999987898999899999999979789999267
No 4
>PHA01976 helix-turn-helix protein
Probab=99.61 E-value=2.5e-15 Score=114.53 Aligned_cols=63 Identities=19% Similarity=0.398 Sum_probs=60.5
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCC
Q ss_conf 779999999997298389999997799999999741488999899999999828999995247
Q gi|254781218|r 113 AIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIYFG 175 (205)
Q Consensus 113 ~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~~G 175 (205)
.+|.||+++|+.+||||.|||+.+||++++|++||+|++.|+++.|.+||.+||||+|||+..
T Consensus 2 ~F~~RL~~lR~~~g~sQ~eLA~~lGVs~~~is~wE~g~~~P~~d~L~~la~~~~VS~D~LlGr 64 (67)
T PHA01976 2 SFAIQLIKARNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTLDWLCGR 64 (67)
T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCC
T ss_conf 789999999998699999999994998999999987898999899999999979789999267
No 5
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=99.57 E-value=1e-14 Score=110.69 Aligned_cols=70 Identities=20% Similarity=0.196 Sum_probs=64.2
Q ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCC
Q ss_conf 9999999999999998599889999984899999998877998889999999999828999996145322
Q gi|254781218|r 27 QYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVI 96 (205)
Q Consensus 27 ~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~ 96 (205)
+..-.||.|||.+|+++|||+++||++.|+|.++||++|||...||+.+|.+||++|+|++.+||..+..
T Consensus 3 d~~~~iG~rIr~lR~~~glTL~eLA~~sGvS~s~LSqIErg~~~PSl~tL~kIa~aL~v~l~~lf~~~~~ 72 (185)
T PRK09943 3 DEGLAPGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFFSEPEK 72 (185)
T ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCC
T ss_conf 4032488999999998599899999887969999999987999999999999999849999998277455
No 6
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=99.51 E-value=6.9e-14 Score=105.61 Aligned_cols=67 Identities=31% Similarity=0.430 Sum_probs=63.5
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCC
Q ss_conf 7779999999997298389999997799999999741488999899999999828999995247210
Q gi|254781218|r 112 YAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIYFGDEV 178 (205)
Q Consensus 112 ~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~~G~e~ 178 (205)
.+||.|||.+|+.+|||+.+||+..|+|++++|++|+|+..|++.+|.+||++|||++.+||.+.+.
T Consensus 6 ~~iG~rIr~lR~~~glTL~eLA~~sGvS~s~LSqIErg~~~PSl~tL~kIa~aL~v~l~~lf~~~~~ 72 (185)
T PRK09943 6 LAPGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFFSEPEK 72 (185)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCC
T ss_conf 2488999999998599899999887969999999987999999999999999849999998277455
No 7
>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed
Probab=99.37 E-value=5.2e-12 Score=94.03 Aligned_cols=151 Identities=19% Similarity=0.214 Sum_probs=110.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCC-
Q ss_conf 6689999999999999999859988999998489999999887799888999999999982899999614532210000-
Q gi|254781218|r 23 PEIRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYE- 101 (205)
Q Consensus 23 ~~~~~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~- 101 (205)
.+.-.|...+|.|+|.+|+.+|||+++||+..|||..++.++|.|..+|||-.|.++|.+|+|++.+|+.......+.-
T Consensus 20 ~~~~~~l~~lg~rvr~~R~~rg~sr~~la~~sgvS~r~la~lE~G~gN~si~~L~~iA~Al~~~l~~l~~~~~~~~~~~~ 99 (304)
T PRK08154 20 AEEDPFLAALGERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCPLADLLGDEDTSSPDWP 99 (304)
T ss_pred CCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCHHHH
T ss_conf 43366999999999999997599899999872998999998825888851999999999959989998178888881289
Q ss_pred CCCCH-HHHHHHHHHHHHHHHHHHCC----C-------CHHHHHHHHCCCHHHHHHHHCCC-CCCCHHHHHHHHHHHCCC
Q ss_conf 23213-45546777999999999729----8-------38999999779999999974148-899989999999982899
Q gi|254781218|r 102 DVTNK-KRLDPYAIGARLKSIRKDKG----M-------SQIEFGKLLGMPNSTLSNYEQGR-TIPEIKPARKIKQVTKKH 168 (205)
Q Consensus 102 ~~~~~-~~~d~~~iG~rLk~lR~~~g----l-------sq~elA~~lgis~~tis~~E~g~-~~Ps~~~l~kIa~~lgvs 168 (205)
.+.+. ...+ ...++++|...+ . ..--|--+.|.-++|+.+..... ..|-++.=..|.+..|++
T Consensus 100 ~~~~~l~~~~----~~~~~~~~~~l~~~~~~~~~~~~~~rIaLIGlmGaGKSTvGr~LA~~Lg~pFvDlD~~IEk~aG~s 175 (304)
T PRK08154 100 LIRELLEQAT----PAQLARARDALSGMLGTGGGAARRPRIALIGLRGAGKSTLGRMLAARLGVPFVELNREIEREAGLS 175 (304)
T ss_pred HHHHHHHCCC----HHHHHHHHHHHHHHHCCCCCCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCEEECHHHHHHHHCCC
T ss_conf 9999985189----999999999987630237666777847988999998889999999995989778779999992999
Q ss_pred HHHHHC--CCC
Q ss_conf 999524--721
Q gi|254781218|r 169 LDWIYF--GDE 177 (205)
Q Consensus 169 ~d~L~~--G~e 177 (205)
+..+|. |++
T Consensus 176 I~eIFa~~GE~ 186 (304)
T PRK08154 176 VSEIFALYGQE 186 (304)
T ss_pred HHHHHHHHCHH
T ss_conf 99999986889
No 8
>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=99.37 E-value=1.7e-12 Score=97.08 Aligned_cols=58 Identities=21% Similarity=0.189 Sum_probs=55.1
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf 9999999999998599889999984899999998877998889999999999828999
Q gi|254781218|r 30 KDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISF 87 (205)
Q Consensus 30 ~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~ 87 (205)
++||..||..|+.+||||.+||+.+|+|+++|+++|+|..+|+++.+.+||++|++++
T Consensus 1 ~~lG~~Ir~~Rk~~glTQ~~LA~~aGvs~~~Is~iE~G~~~~~l~~l~~i~~aLGi~l 58 (58)
T TIGR03070 1 KQIGALVRARRKALGLTQADLADLAGVGLRFIRDIEKGKPTVRLDKVLRVLEALGLEL 58 (58)
T ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCC
T ss_conf 9588999999999499899999881998999999978999888999999999808989
No 9
>pfam01381 HTH_3 Helix-turn-helix. This large family of DNA binding helix-turn helix proteins includes Cro and CI.
Probab=99.36 E-value=1.7e-12 Score=97.06 Aligned_cols=55 Identities=24% Similarity=0.290 Sum_probs=46.0
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHH
Q ss_conf 9999998599889999984899999998877998889999999999828999996
Q gi|254781218|r 36 IKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWI 90 (205)
Q Consensus 36 ik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~L 90 (205)
||.+|+.+|+||++||+.+|+++++|++||+|...|+++.+.+||++|+|+++||
T Consensus 1 ir~~R~~~g~tq~~lA~~~gis~~~is~~E~g~~~p~~~~l~~ia~~l~v~~~~l 55 (55)
T pfam01381 1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55 (55)
T ss_pred CHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHC
T ss_conf 9898978299899999998969999999987999999999999999978979879
No 10
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=99.36 E-value=2e-12 Score=96.52 Aligned_cols=56 Identities=27% Similarity=0.332 Sum_probs=44.0
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHH
Q ss_conf 99999998599889999984899999998877998889999999999828999996
Q gi|254781218|r 35 RIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWI 90 (205)
Q Consensus 35 rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~L 90 (205)
|||.+|+.+||||++||+.+|+++++|++||+|...|+++.+.+||++|+|+++||
T Consensus 1 rlr~~R~~~glsq~~lA~~~gis~~~is~~E~g~~~p~~~~l~~ia~~l~~~~~~l 56 (56)
T smart00530 1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56 (56)
T ss_pred CHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHC
T ss_conf 98999977299999999998959999999997998999999999999988889879
No 11
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=99.29 E-value=8.8e-12 Score=92.61 Aligned_cols=56 Identities=36% Similarity=0.602 Sum_probs=54.7
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHH
Q ss_conf 99999997298389999997799999999741488999899999999828999995
Q gi|254781218|r 117 RLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWI 172 (205)
Q Consensus 117 rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L 172 (205)
||+++|+.+||||.+||+.+|++++++++||+|.+.|+.+.+.+||++||++++||
T Consensus 1 rlr~~R~~~glsq~~lA~~~gis~~~is~~E~g~~~p~~~~l~~ia~~l~~~~~~l 56 (56)
T smart00530 1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56 (56)
T ss_pred CHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHC
T ss_conf 98999977299999999998959999999997998999999999999988889879
No 12
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=99.28 E-value=1.3e-11 Score=91.60 Aligned_cols=61 Identities=21% Similarity=0.291 Sum_probs=51.7
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCC
Q ss_conf 9999999985998899999848999999988779988899999999998289999961453
Q gi|254781218|r 34 TRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGE 94 (205)
Q Consensus 34 ~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge 94 (205)
.|+|.+|...|+||++||+.+|||+++|..||+|+..||+....+||..|+++++.+|.-+
T Consensus 4 nk~k~~R~~~~ltQ~elA~~vgVsRQTi~~iEkgky~Psl~La~kia~~f~~~iedIF~~~ 64 (68)
T COG1476 4 NKLKELRAELGLTQEELAKLVGVSRQTIIAIEKGKYNPSLELALKIARVFGKTIEDIFQLE 64 (68)
T ss_pred HHHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf 5999999982858999999919579999999917988309999999999399799998652
No 13
>pfam01381 HTH_3 Helix-turn-helix. This large family of DNA binding helix-turn helix proteins includes Cro and CI.
Probab=99.27 E-value=1.1e-11 Score=92.10 Aligned_cols=55 Identities=33% Similarity=0.550 Sum_probs=53.7
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHH
Q ss_conf 9999997298389999997799999999741488999899999999828999995
Q gi|254781218|r 118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWI 172 (205)
Q Consensus 118 Lk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L 172 (205)
||++|+.+||||.+||+.+|++++++++||+|.+.|+.+.+.+||++||++++||
T Consensus 1 ir~~R~~~g~tq~~lA~~~gis~~~is~~E~g~~~p~~~~l~~ia~~l~v~~~~l 55 (55)
T pfam01381 1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55 (55)
T ss_pred CHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHC
T ss_conf 9898978299899999998969999999987999999999999999978979879
No 14
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=99.27 E-value=2e-11 Score=90.42 Aligned_cols=66 Identities=14% Similarity=0.154 Sum_probs=59.5
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCC
Q ss_conf 999999999985998899999848999999988779988899999999998289999961453221
Q gi|254781218|r 32 VGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVID 97 (205)
Q Consensus 32 iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~ 97 (205)
+=.+|+.+|.++|+||.+||++.|+|.+++|.+|+|+.+||+++|..||++++|++.+|+...+.|
T Consensus 6 fftNv~RLr~ErGmT~~eLAe~AGIS~s~LSqIE~Gk~NPSL~tLe~IA~AL~VPL~~Lle~~dld 71 (119)
T PRK13890 6 FFTNVLRLLDERHMTKKELSDRSGVSISFLSDLTTGKANPSLKVMEDIAQALETPLPLLLESTDLD 71 (119)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHCCCC
T ss_conf 588799999985997999998829889999999779989879999999999879779987623589
No 15
>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=99.22 E-value=3.8e-11 Score=88.68 Aligned_cols=58 Identities=29% Similarity=0.377 Sum_probs=46.0
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHH
Q ss_conf 9999999998599889999984899999998877998889999999999828999996
Q gi|254781218|r 33 GTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWI 90 (205)
Q Consensus 33 G~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~L 90 (205)
|.+|+.+|+.+|+||.+||+.+|+++++|++||+|...|+++.+.+||+.|+|+++|+
T Consensus 1 g~~l~~~r~~~~ls~~~lA~~~gis~~~l~~~e~g~~~p~~~~l~~la~~~~~~~~~l 58 (58)
T cd00093 1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58 (58)
T ss_pred CHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHC
T ss_conf 9899999997599999995714999999999987998999999999999938989879
No 16
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=99.15 E-value=1.2e-10 Score=85.58 Aligned_cols=61 Identities=31% Similarity=0.498 Sum_probs=58.8
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCC
Q ss_conf 9999999972983899999977999999997414889998999999998289999952472
Q gi|254781218|r 116 ARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIYFGD 176 (205)
Q Consensus 116 ~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~~G~ 176 (205)
.|++.+|...||||.+||+.+|++++||..||+|+..|++....+||+.|+++++.+|+-+
T Consensus 4 nk~k~~R~~~~ltQ~elA~~vgVsRQTi~~iEkgky~Psl~La~kia~~f~~~iedIF~~~ 64 (68)
T COG1476 4 NKLKELRAELGLTQEELAKLVGVSRQTIIAIEKGKYNPSLELALKIARVFGKTIEDIFQLE 64 (68)
T ss_pred HHHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf 5999999982858999999919579999999917988309999999999399799998652
No 17
>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=99.13 E-value=1.5e-10 Score=84.93 Aligned_cols=57 Identities=21% Similarity=0.378 Sum_probs=55.1
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf 779999999997298389999997799999999741488999899999999828999
Q gi|254781218|r 113 AIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHL 169 (205)
Q Consensus 113 ~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~ 169 (205)
.+|..||+.|+.+||||.+||+..|+++++++++|+|+..|+++.+.+|+.+||+++
T Consensus 2 ~lG~~Ir~~Rk~~glTQ~~LA~~aGvs~~~Is~iE~G~~~~~l~~l~~i~~aLGi~l 58 (58)
T TIGR03070 2 QIGALVRARRKALGLTQADLADLAGVGLRFIRDIEKGKPTVRLDKVLRVLEALGLEL 58 (58)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCC
T ss_conf 588999999999499899999881998999999978999888999999999808989
No 18
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=99.13 E-value=2.6e-10 Score=83.54 Aligned_cols=62 Identities=19% Similarity=0.267 Sum_probs=58.7
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCC
Q ss_conf 79999999997298389999997799999999741488999899999999828999995247
Q gi|254781218|r 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIYFG 175 (205)
Q Consensus 114 iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~~G 175 (205)
+...++.+|+++|||+.|||+..|+|.+.+|++|+|+..|++.++.+||++|+|++.+|+--
T Consensus 6 fftNv~RLr~ErGmT~~eLAe~AGIS~s~LSqIE~Gk~NPSL~tLe~IA~AL~VPL~~Lle~ 67 (119)
T PRK13890 6 FFTNVLRLLDERHMTKKELSDRSGVSISFLSDLTTGKANPSLKVMEDIAQALETPLPLLLES 67 (119)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHH
T ss_conf 58879999998599799999882988999999977998987999999999987977998762
No 19
>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=99.12 E-value=1.7e-10 Score=84.72 Aligned_cols=58 Identities=36% Similarity=0.606 Sum_probs=56.3
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHH
Q ss_conf 9999999997298389999997799999999741488999899999999828999995
Q gi|254781218|r 115 GARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWI 172 (205)
Q Consensus 115 G~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L 172 (205)
|.+|+.+|+.+|+||.+||+.+|++++++++||+|...|+.+.+.+||++||++++||
T Consensus 1 g~~l~~~r~~~~ls~~~lA~~~gis~~~l~~~e~g~~~p~~~~l~~la~~~~~~~~~l 58 (58)
T cd00093 1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58 (58)
T ss_pred CHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHC
T ss_conf 9899999997599999995714999999999987998999999999999938989879
No 20
>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed
Probab=99.08 E-value=7.6e-10 Score=80.65 Aligned_cols=72 Identities=21% Similarity=0.317 Sum_probs=66.5
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCHHH
Q ss_conf 777999999999729838999999779999999974148899989999999982899999524721025456
Q gi|254781218|r 112 YAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIYFGDEVIVPKS 183 (205)
Q Consensus 112 ~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~~G~e~~~~~~ 183 (205)
..+|.|+|.+|..+|||++++|+..|+|..++.+.|.|...|++..|.+||.+|+|++.+|+.......|+.
T Consensus 27 ~~lg~rvr~~R~~rg~sr~~la~~sgvS~r~la~lE~G~gN~si~~L~~iA~Al~~~l~~l~~~~~~~~~~~ 98 (304)
T PRK08154 27 AALGERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCPLADLLGDEDTSSPDW 98 (304)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCHHH
T ss_conf 999999999999759989999987299899999882588885199999999995998999817888888128
No 21
>PRK09726 DNA-binding transcriptional regulator HipB; Provisional
Probab=99.06 E-value=5.1e-10 Score=81.70 Aligned_cols=64 Identities=20% Similarity=0.192 Sum_probs=57.4
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHH
Q ss_conf 8999999999999999985998899999848999999988779988899999999998289999
Q gi|254781218|r 25 IRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFD 88 (205)
Q Consensus 25 ~~~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d 88 (205)
+....+.+|..||..|+.+||||.++|+.+|+.+++||++|+|-..+++++|.+|+.+|++.+.
T Consensus 6 ki~sp~qLa~~Lr~~Rk~~gLsQ~~lA~~vGi~Q~TiS~~E~~p~~~~leTLFkiL~aL~Lel~ 69 (88)
T PRK09726 6 KIYSPTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMT 69 (88)
T ss_pred CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHCCCEEE
T ss_conf 0289999999999999985987999999819749999999759987869999999996787688
No 22
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=98.98 E-value=2.2e-09 Score=77.84 Aligned_cols=64 Identities=27% Similarity=0.385 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCC
Q ss_conf 7999999999729838999999779999999974148899989999999982899999524721
Q gi|254781218|r 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIYFGDE 177 (205)
Q Consensus 114 iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~~G~e 177 (205)
+|.+|+..|+.+||||++||+.+++..+.+.+||+|+..|+.+.+.+|.++||+.+.|..-+++
T Consensus 80 Y~e~Ir~ARE~~G~SqedLA~ki~ek~svI~~iE~g~~~P~~~~akkLEk~LgIkL~e~~~~~~ 143 (165)
T COG1813 80 YGERIREAREKRGLSQEDLAAKLKEKVSVIRRIERGEATPNIKVAKKLEKLLGIKLVEKVDEEE 143 (165)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHHHHHCCEEEEECCCCC
T ss_conf 9999999999828889999999654699999998413675588999999985855220035554
No 23
>PRK06424 transcription factor; Provisional
Probab=98.98 E-value=2.8e-09 Score=77.13 Aligned_cols=57 Identities=25% Similarity=0.390 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf 779999999997298389999997799999999741488999899999999828999
Q gi|254781218|r 113 AIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHL 169 (205)
Q Consensus 113 ~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~ 169 (205)
.+|.+||.+|+.+||||.|||..++...+.|.++|+|...|+.+.+.+|-++|||++
T Consensus 84 Dy~~~Ir~ARE~~GlsqeeLA~ki~ek~svI~kiE~G~l~P~~~~~kKLEk~L~I~L 140 (144)
T PRK06424 84 DYAELVKNARERLSMSQADLAAKIFERKNVIASIERGDLLPDIKTARKLEKILGITL 140 (144)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCEE
T ss_conf 799999999998499999999996544999999983898999899999999849676
No 24
>PRK08359 transcription factor; Validated
Probab=98.92 E-value=4.9e-09 Score=75.63 Aligned_cols=56 Identities=25% Similarity=0.401 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf 79999999997298389999997799999999741488999899999999828999
Q gi|254781218|r 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHL 169 (205)
Q Consensus 114 iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~ 169 (205)
+|.+|+.+|+.+||||+|||..++...+.|.++|+|...|+.+.+.+|-++|||++
T Consensus 84 Y~~~Ir~ARE~~GlSqeeLA~ki~ek~nvI~kiE~G~l~P~~~~akKLEk~L~IkL 139 (175)
T PRK08359 84 YAERVYEAIRKSGLSYEELSHKVGLSVNDLRRIAHGEYTPTIEEARKLERFFKIKL 139 (175)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCEEE
T ss_conf 99999999998599999999997222999999983887999899999999849068
No 25
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=98.90 E-value=7.9e-09 Score=74.36 Aligned_cols=101 Identities=21% Similarity=0.289 Sum_probs=74.5
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHC------CCHHHHHCCCCCCCCCCCCCCHH
Q ss_conf 999999998599889999984899999998877998889999999999828------99999614532210000232134
Q gi|254781218|r 34 TRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYE------ISFDWIYDGEVIDRRYEDVTNKK 107 (205)
Q Consensus 34 ~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~------vs~d~Ll~ge~~~~~~~~~~~~~ 107 (205)
+-||..|+..|+||++||..+|+||+.|.++|.|...|.+.++.+|-++|. +..+-++.......+.+|-
T Consensus 8 edlrk~Rk~LGitQ~dLA~~aGVSQ~~IArlE~G~vdPrlSt~k~Il~aL~e~e~~~ita~~iM~spvv~v~pdDs---- 83 (187)
T COG3620 8 EDLRKRRKELGITQKDLARRAGVSQPYIARLEAGKVDPRLSTVKRILEALEEAEKTRITAKTIMHSPVVSVSPDDS---- 83 (187)
T ss_pred HHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCEEEHHHHCCCCEEEECCHHH----
T ss_conf 9999999875977899998708648889998638879308999999999998546667576653587058772466----
Q ss_pred HHHHHHHHHHHHHHHHHCCCCHHHHHHH---HC-CCHHHHHH
Q ss_conf 5546777999999999729838999999---77-99999999
Q gi|254781218|r 108 RLDPYAIGARLKSIRKDKGMSQIEFGKL---LG-MPNSTLSN 145 (205)
Q Consensus 108 ~~d~~~iG~rLk~lR~~~glsq~elA~~---lg-is~~tis~ 145 (205)
+ ...-.++..+|+||--+-+. +| |+...+.+
T Consensus 84 ------i-~~vv~lM~~~g~SQlPVi~~~k~VGsItE~~iv~ 118 (187)
T COG3620 84 ------I-SDVVNLMRDKGISQLPVIEEDKVVGSITENDIVR 118 (187)
T ss_pred ------H-HHHHHHHHHCCCCCCCEEECCEEEEEECHHHHHH
T ss_conf ------9-9999999975975275410886453314989999
No 26
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=98.85 E-value=7e-09 Score=74.67 Aligned_cols=74 Identities=23% Similarity=0.281 Sum_probs=68.8
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCC
Q ss_conf 68999999999999999985998899999848999999988779988899999999998289999961453221
Q gi|254781218|r 24 EIRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVID 97 (205)
Q Consensus 24 ~~~~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~ 97 (205)
+..+.-.+.|++|+..|+++||+|++||++++++.+.|.+||+|...|+++.+-+|.+.|+|.+.|...++...
T Consensus 72 ~~~elvedY~e~Ir~ARE~~G~SqedLA~ki~ek~svI~~iE~g~~~P~~~~akkLEk~LgIkL~e~~~~~~~~ 145 (165)
T COG1813 72 ELPELVEDYGERIREAREKRGLSQEDLAAKLKEKVSVIRRIERGEATPNIKVAKKLEKLLGIKLVEKVDEEEEG 145 (165)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHHHHHCCEEEEECCCCCCC
T ss_conf 17888877999999999982888999999965469999999841367558899999998585522003555446
No 27
>PRK09726 DNA-binding transcriptional regulator HipB; Provisional
Probab=98.83 E-value=1.1e-08 Score=73.55 Aligned_cols=65 Identities=25% Similarity=0.380 Sum_probs=60.0
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHH
Q ss_conf 45546777999999999729838999999779999999974148899989999999982899999
Q gi|254781218|r 107 KRLDPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDW 171 (205)
Q Consensus 107 ~~~d~~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~ 171 (205)
++.+|..+|..||.+|+.+|+||.++|+.+|+.+++||++|++-..+++++|++|..+||+.+.-
T Consensus 6 ki~sp~qLa~~Lr~~Rk~~gLsQ~~lA~~vGi~Q~TiS~~E~~p~~~~leTLFkiL~aL~Lel~i 70 (88)
T PRK09726 6 KIYSPTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMTL 70 (88)
T ss_pred CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHCCCEEEE
T ss_conf 02899999999999999859879999998197499999997599878699999999967876887
No 28
>PRK06424 transcription factor; Provisional
Probab=98.79 E-value=1.8e-08 Score=72.09 Aligned_cols=67 Identities=18% Similarity=0.169 Sum_probs=61.1
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf 1566899999999999999998599889999984899999998877998889999999999828999
Q gi|254781218|r 21 ITPEIRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISF 87 (205)
Q Consensus 21 ~~~~~~~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~ 87 (205)
+.-+..+.-.+.|.+||..|+.+||||++||.+++...+.|.++|+|...|++++..+|-++|+|++
T Consensus 74 ~~~~~~elveDy~~~Ir~ARE~~GlsqeeLA~ki~ek~svI~kiE~G~l~P~~~~~kKLEk~L~I~L 140 (144)
T PRK06424 74 ASDEDLDIVEDYAELVKNARERLSMSQADLAAKIFERKNVIASIERGDLLPDIKTARKLEKILGITL 140 (144)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCEE
T ss_conf 3034566887799999999998499999999996544999999983898999899999999849676
No 29
>PRK08359 transcription factor; Validated
Probab=98.76 E-value=2.3e-08 Score=71.46 Aligned_cols=66 Identities=12% Similarity=0.121 Sum_probs=60.7
Q ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHC
Q ss_conf 999999999999999859988999998489999999887799888999999999982899999614
Q gi|254781218|r 27 QYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYD 92 (205)
Q Consensus 27 ~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ 92 (205)
+.-.+.|++||..|+.+||||++||.++++..+.|.++|+|...|++++.-+|-++|+|++-.-..
T Consensus 79 ElveDY~~~Ir~ARE~~GlSqeeLA~ki~ek~nvI~kiE~G~l~P~~~~akKLEk~L~IkL~E~~e 144 (175)
T PRK08359 79 DIVEDYAERVYEAIRKSGLSYEELSHKVGLSVNDLRRIAHGEYTPTIEEARKLERFFKIKLIERVE 144 (175)
T ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCEEEEEECC
T ss_conf 777569999999999859999999999722299999998388799989999999984906885146
No 30
>PRK04140 hypothetical protein; Provisional
Probab=98.71 E-value=4.9e-08 Score=69.45 Aligned_cols=136 Identities=16% Similarity=0.193 Sum_probs=83.5
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHH---HHCCCCCCCCCCCCCCHHHH
Q ss_conf 999999999859988999998489999999887799888999999999982899999---61453221000023213455
Q gi|254781218|r 33 GTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDW---IYDGEVIDRRYEDVTNKKRL 109 (205)
Q Consensus 33 G~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~---Ll~ge~~~~~~~~~~~~~~~ 109 (205)
|+.+|.+|+.+|||..+||..+|||+.+|++||+|...+|++++++|.+.|+.++-. +|.+..-...........
T Consensus 127 g~~Lr~~Re~~g~SlG~LA~~LGVSRrtv~~YE~g~~~~sievA~kLeeif~~~i~~~Idil~~~~~~~~~~~~~~~~-- 204 (319)
T PRK04140 127 GDLLRELREKLGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDEPLTKPIDILDSAERVEDDEKTLEEP-- 204 (319)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC--
T ss_conf 799999999819888899998498699999997068866499999999983873235520223201254334576787--
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCC-------C-------CCCHHHHHHHHHHHCCCHHHHH
Q ss_conf 46777999999999729838999999779999999974148-------8-------9998999999998289999952
Q gi|254781218|r 110 DPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGR-------T-------IPEIKPARKIKQVTKKHLDWIY 173 (205)
Q Consensus 110 d~~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~-------~-------~Ps~~~l~kIa~~lgvs~d~L~ 173 (205)
.....-.++-......|+.-... -.-|-..++.-+... . .-....+..|+++++...=++.
T Consensus 205 ~~~~~e~~i~~~L~~iG~~v~~~---~kAPFdavs~~e~~~~~lLTgi~~~~~~~~~rrA~~~~~is~v~~s~sv~I~ 279 (319)
T PRK04140 205 EDDPFEKEVIEILSRLGFDVLPT---KKAPFDAVAEDEKDENSLLTGISEFRTEETKRRARIVSSISEVTNSESVFIL 279 (319)
T ss_pred CCCHHHHHHHHHHHHCCCEEEEE---CCCCHHHHHHCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEE
T ss_conf 65415679999999649646773---2597777510235564467545333328899999999999998668539998
No 31
>PRK04140 hypothetical protein; Provisional
Probab=98.68 E-value=7e-08 Score=68.52 Aligned_cols=56 Identities=30% Similarity=0.464 Sum_probs=53.1
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf 79999999997298389999997799999999741488999899999999828999
Q gi|254781218|r 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHL 169 (205)
Q Consensus 114 iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~ 169 (205)
=|.+||..|+++|||..+||+.+|+|+.|+++||+|...++++.+.+|.++||..+
T Consensus 126 dg~~Lr~~Re~~g~SlG~LA~~LGVSRrtv~~YE~g~~~~sievA~kLeeif~~~i 181 (319)
T PRK04140 126 DGDLLRELREKLGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDEPL 181 (319)
T ss_pred CHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHHHHHCCCC
T ss_conf 47999999998198888999984986999999970688664999999999838732
No 32
>PRK13355 bifunctional HTH-domain containing protein/aminotransferase; Provisional
Probab=98.65 E-value=9.6e-08 Score=67.65 Aligned_cols=67 Identities=16% Similarity=0.280 Sum_probs=60.3
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHH-----CCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCC
Q ss_conf 999999999998599889999984-----8999999988779988899999999998289999961453221
Q gi|254781218|r 31 DVGTRIKDIRKANNKTQKEMAIGA-----NQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVID 97 (205)
Q Consensus 31 ~iG~rik~lR~~~gltQ~elA~~~-----gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~ 97 (205)
-.++|++.+++.+|++|.+|+..+ -+.+++||+|++|+..|.-+.+--||..++|+.+||++|+...
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 76 (518)
T PRK13355 5 TQAERLVQLMNSRGLKQEDLVHAAEARGVKVGKSHISQYVRGKTGPRSDKLPFLASELGVSEGWLLGGESES 76 (518)
T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHCCCCCCC
T ss_conf 089999999987699689999999981755047888777338864421179999999688978860799765
No 33
>PRK13355 bifunctional HTH-domain containing protein/aminotransferase; Provisional
Probab=98.55 E-value=4e-07 Score=63.84 Aligned_cols=67 Identities=19% Similarity=0.311 Sum_probs=60.7
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHH---C--CCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCC
Q ss_conf 779999999997298389999997---7--999999997414889998999999998289999952472102
Q gi|254781218|r 113 AIGARLKSIRKDKGMSQIEFGKLL---G--MPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIYFGDEVI 179 (205)
Q Consensus 113 ~iG~rLk~lR~~~glsq~elA~~l---g--is~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~~G~e~~ 179 (205)
..++||+++|+.+||+|.+|+... | +.++.+|+|++|++.|.-+.+..+|.+|+|+.+||+.|+...
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 76 (518)
T PRK13355 5 TQAERLVQLMNSRGLKQEDLVHAAEARGVKVGKSHISQYVRGKTGPRSDKLPFLASELGVSEGWLLGGESES 76 (518)
T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHCCCCCCC
T ss_conf 089999999987699689999999981755047888777338864421179999999688978860799765
No 34
>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=98.45 E-value=4.7e-07 Score=63.38 Aligned_cols=55 Identities=15% Similarity=0.135 Sum_probs=32.3
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHC
Q ss_conf 9999859988999998489999999887799888999999999982899999614
Q gi|254781218|r 38 DIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYD 92 (205)
Q Consensus 38 ~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ 92 (205)
+.-+-.|+|+.+||+++|||+++||++=||++.+|.++.++||++|+.|.++-|+
T Consensus 14 EfL~PLg~s~~~LA~~LgVsr~~~sriv~~~~~iT~dmALRL~~~lG~sp~~WLn 68 (81)
T TIGR02607 14 EFLEPLGLSVRALAKALGVSRSTLSRIVNGRRGITADMALRLAKALGTSPEFWLN 68 (81)
T ss_pred HHHHCCCHHHHHHHHHCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHCCCHHHHHH
T ss_conf 7521047068999987099978888887448998888999999973898768998
No 35
>pfam07022 Phage_CI_repr Bacteriophage CI repressor helix-turn-helix domain. This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic.
Probab=98.42 E-value=1e-06 Score=61.25 Aligned_cols=62 Identities=24% Similarity=0.366 Sum_probs=51.3
Q ss_pred HHHHHHHHCCCC-HHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCC
Q ss_conf 999999972983-899999977999999997414889998999999998289999952472102
Q gi|254781218|r 117 RLKSIRKDKGMS-QIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIYFGDEVI 179 (205)
Q Consensus 117 rLk~lR~~~gls-q~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~~G~e~~ 179 (205)
.|..+.+..|.+ +.|||+.+||++++++.|-...+. +.+.+.+++..+|+++|||++|+..+
T Consensus 2 vi~Rl~~a~G~~t~~eLA~~LgI~~stis~w~~R~~~-P~e~iv~~~~~tGvsl~WL~~G~G~~ 64 (65)
T pfam07022 2 VIERLMKAYGFKSRSELADHLGVSKSTLSTWYKRDSF-PAEWVIRCALETGVSLDWLATGDGEL 64 (65)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCC-CHHHHHHHHHHHCCCHHHHHCCCCCC
T ss_conf 8999999968886999999969888889999986999-89999999999882999997089999
No 36
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=98.39 E-value=7.9e-07 Score=62.01 Aligned_cols=48 Identities=33% Similarity=0.557 Sum_probs=41.1
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHH
Q ss_conf 999999999729838999999779999999974148899989999999
Q gi|254781218|r 115 GARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIK 162 (205)
Q Consensus 115 G~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa 162 (205)
+..|+.+|+..||||.+||..+|++.+|+++||+|+..|+-..+.-+.
T Consensus 46 ~~eIk~iRe~~~lSq~vFA~~L~vs~~Tv~~WEqGr~kPsg~AlkLL~ 93 (104)
T COG2944 46 PTEIKAIREKLGLSQPVFARYLGVSVSTVRKWEQGRKKPSGAALKLLR 93 (104)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHCCCCCCCCHHHHHHH
T ss_conf 899999999828889999999888799999998178589979999999
No 37
>COG1395 Predicted transcriptional regulator [Transcription]
Probab=98.39 E-value=9.9e-07 Score=61.39 Aligned_cols=55 Identities=18% Similarity=0.310 Sum_probs=49.7
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf 9999999998599889999984899999998877998889999999999828999
Q gi|254781218|r 33 GTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISF 87 (205)
Q Consensus 33 G~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~ 87 (205)
|+++|..|+++|+|..+||.-+|+|+.+|++||+|...||++...+|-+.|+..+
T Consensus 127 ge~Lre~Ree~glSlG~lA~~lgVSRktV~~YE~G~~~~sleva~kLeei~g~~i 181 (313)
T COG1395 127 GEKLREKREEMGLSLGDLATMLGVSRKTVYKYEKGLSDASLEVALKLEEIFGEDI 181 (313)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHCCCCCCCCHHHHHHHHHHHCCHH
T ss_conf 2999999998086787889883846888987624777732999999999856222
No 38
>KOG3398 consensus
Probab=98.39 E-value=6.1e-07 Score=62.70 Aligned_cols=108 Identities=22% Similarity=0.291 Sum_probs=78.7
Q ss_pred CHHHHHHHHCCCHHHHHHHHCCCCC--CCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 8899999848999999988779988--89999999999828999996145322100002321345546777999999999
Q gi|254781218|r 46 TQKEMAIGANQLESAVNLFENGMCS--TSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRK 123 (205)
Q Consensus 46 tQ~elA~~~gis~~~is~~E~G~~~--psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~ 123 (205)
.+-.-|...|+...+.-+|-.|... |+-..+.+ +++|.-+.... .-+..+|.-|.+.|.
T Consensus 23 ~~vnaa~r~g~~v~t~~k~~~g~nkq~~~~~~t~k------------lD~etE~~~~~-------~v~~~Vg~aIq~aR~ 83 (135)
T KOG3398 23 KAVNAARRAGVDVETVKKFPAGLNKQHPSTQSTAK------------LDRETEELGHD-------RVPLEVGKAIQQARA 83 (135)
T ss_pred HHHHHHHHHCCCHHHHHHHCCCCCCCCCCCCCHHH------------CCCCCCCCCCC-------CCCHHHHHHHHHHHH
T ss_conf 99999997264024354220345566865421120------------24665323523-------014789999999888
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHH
Q ss_conf 7298389999997799999999741488999899999999828999995
Q gi|254781218|r 124 DKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWI 172 (205)
Q Consensus 124 ~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L 172 (205)
.+||||++||..++-.++.+..||+|+..|.-..|.++.++|||.++|=
T Consensus 84 ~KgmsqkDLA~kInekpqVv~dyEsGrAIpNqqil~kmEraLgvKlrgk 132 (135)
T KOG3398 84 QKGMSQKDLAQKINEKPQVIQDYESGRAIPNQQILSKMERALGVKLRGK 132 (135)
T ss_pred HCCCCHHHHHHHHCCCCHHHHHHHCCCCCCHHHHHHHHHHHHCEECCCC
T ss_conf 6375488999996028613655750356741999999999853112465
No 39
>COG1395 Predicted transcriptional regulator [Transcription]
Probab=98.36 E-value=1.2e-06 Score=60.83 Aligned_cols=63 Identities=22% Similarity=0.438 Sum_probs=57.6
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCC----CHHHHHCCC
Q ss_conf 799999999972983899999977999999997414889998999999998289----999952472
Q gi|254781218|r 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKK----HLDWIYFGD 176 (205)
Q Consensus 114 iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgv----s~d~L~~G~ 176 (205)
-|.+||+.|.++|+|..++|..+|+|+.++++||+|.+.|+++.+.++-.+||. ++|||-.-+
T Consensus 126 dge~Lre~Ree~glSlG~lA~~lgVSRktV~~YE~G~~~~sleva~kLeei~g~~iv~~Idi~~~~~ 192 (313)
T COG1395 126 DGEKLREKREEMGLSLGDLATMLGVSRKTVYKYEKGLSDASLEVALKLEEIFGEDIVKPIDILKIPE 192 (313)
T ss_pred CHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHCCCCCCCCHHHHHHHHHHHCCHHHCCEECCCCCC
T ss_conf 4299999999808678788988384688898762477773299999999985622203200113667
No 40
>TIGR00270 TIGR00270 conserved hypothetical protein TIGR00270; InterPro: IPR004451 This family of conserved hypothetical proteins includes proteins of unknown function from archaebacteria..
Probab=98.35 E-value=9e-07 Score=61.66 Aligned_cols=74 Identities=15% Similarity=0.169 Sum_probs=63.9
Q ss_pred HHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCC
Q ss_conf 99999999999999998599889999984899999998877998889999999999828999996145322100
Q gi|254781218|r 26 RQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRR 99 (205)
Q Consensus 26 ~~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~ 99 (205)
.+..++.|.=||.-|+.+||||++||++++.-.|.|.++|+-...|..+.+-.|=+.|+|++-+-+..+...+.
T Consensus 78 ~elvEdyg~iIR~eREKRgwS~E~LAkki~eK~S~i~kiE~~e~eP~~k~~~kLEkllkIkL~E~~~e~~~eks 151 (169)
T TIGR00270 78 EELVEDYGRIIREEREKRGWSREELAKKIKEKASVIKKIEREELEPEEKVVKKLEKLLKIKLLEKVEEEKLEKS 151 (169)
T ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCCCCEECC
T ss_conf 66664322542200014687878999987410678888754037988899999888835010023571000015
No 41
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=98.34 E-value=1.4e-06 Score=60.54 Aligned_cols=60 Identities=18% Similarity=0.372 Sum_probs=52.8
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHC------CCHHHHHCC
Q ss_conf 999999997298389999997799999999741488999899999999828------999995247
Q gi|254781218|r 116 ARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTK------KHLDWIYFG 175 (205)
Q Consensus 116 ~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lg------vs~d~L~~G 175 (205)
+-||..|+..|+||++||+..|+|+..+.++|.|+..|.++++.+|-++|. ++-+-++.-
T Consensus 8 edlrk~Rk~LGitQ~dLA~~aGVSQ~~IArlE~G~vdPrlSt~k~Il~aL~e~e~~~ita~~iM~s 73 (187)
T COG3620 8 EDLRKRRKELGITQKDLARRAGVSQPYIARLEAGKVDPRLSTVKRILEALEEAEKTRITAKTIMHS 73 (187)
T ss_pred HHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCEEEHHHHCCC
T ss_conf 999999987597789999870864888999863887930899999999999854666757665358
No 42
>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=98.32 E-value=1.6e-06 Score=60.18 Aligned_cols=62 Identities=23% Similarity=0.217 Sum_probs=56.7
Q ss_pred HHHHHHHH-HHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHH
Q ss_conf 77799999-999972983899999977999999997414889998999999998289999952
Q gi|254781218|r 112 YAIGARLK-SIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIY 173 (205)
Q Consensus 112 ~~iG~rLk-~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~ 173 (205)
--.|+.|+ ++.+..|||+.+||+.+|||+++++++.+|++-.+.+.+.+||++||.|++|-+
T Consensus 5 ~HPGE~L~eEfL~PLg~s~~~LA~~LgVsr~~~sriv~~~~~iT~dmALRL~~~lG~sp~~WL 67 (81)
T TIGR02607 5 AHPGEILLEEFLEPLGLSVRALAKALGVSRSTLSRIVNGRRGITADMALRLAKALGTSPEFWL 67 (81)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHCCCHHHHH
T ss_conf 788413287752104706899998709997888888744899888899999997389876899
No 43
>KOG3398 consensus
Probab=98.29 E-value=1.2e-06 Score=60.91 Aligned_cols=77 Identities=16% Similarity=0.184 Sum_probs=65.1
Q ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHH
Q ss_conf 6543331000156689999999999999999859988999998489999999887799888999999999982899999
Q gi|254781218|r 11 LKSLQEYTLIITPEIRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDW 89 (205)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~ 89 (205)
.+.+-+.|-+..++ -...++|.-|...|.++||||++||.+++-.++.|..||+|+.-|.-.+|-++-.+|+|-++|
T Consensus 55 t~klD~etE~~~~~--~v~~~Vg~aIq~aR~~KgmsqkDLA~kInekpqVv~dyEsGrAIpNqqil~kmEraLgvKlrg 131 (135)
T KOG3398 55 TAKLDRETEELGHD--RVPLEVGKAIQQARAQKGMSQKDLAQKINEKPQVIQDYESGRAIPNQQILSKMERALGVKLRG 131 (135)
T ss_pred HHHCCCCCCCCCCC--CCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHCCCCCCHHHHHHHHHHHHCEECCC
T ss_conf 12024665323523--014789999999888637548899999602861365575035674199999999985311246
No 44
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=98.29 E-value=1.4e-06 Score=60.40 Aligned_cols=43 Identities=28% Similarity=0.122 Sum_probs=40.3
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHH
Q ss_conf 9999999998599889999984899999998877998889999
Q gi|254781218|r 33 GTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRY 75 (205)
Q Consensus 33 G~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~ 75 (205)
|..|+.+|+..|+||.+||..+|+|.+++++||.|...|+---
T Consensus 46 ~~eIk~iRe~~~lSq~vFA~~L~vs~~Tv~~WEqGr~kPsg~A 88 (104)
T COG2944 46 PTEIKAIREKLGLSQPVFARYLGVSVSTVRKWEQGRKKPSGAA 88 (104)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHCCCCCCCCHH
T ss_conf 8999999998288899999998887999999981785899799
No 45
>COG1709 Predicted transcriptional regulator [Transcription]
Probab=98.27 E-value=7.6e-07 Score=62.12 Aligned_cols=75 Identities=21% Similarity=0.237 Sum_probs=59.5
Q ss_pred HHHCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCC-CCHHHHHHHHHHHCCCHHHHHCC
Q ss_conf 100015668999999999999999985998899999848999999988779988-89999999999828999996145
Q gi|254781218|r 17 YTLIITPEIRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCS-TSIRYALYLRNEYEISFDWIYDG 93 (205)
Q Consensus 17 ~~~~~~~~~~~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~-psi~~l~~la~~~~vs~d~Ll~g 93 (205)
.+.-|.+|+ -+.++.|+-+|++|+.-+.||.+||..+|+|+|.||.||.|++. |.+..+.++.++| +++|.==+|
T Consensus 14 va~rIaGdI-vlS~~pge~lrKWR~~F~iSQ~elA~~l~vSpSVISDYE~GRRk~Pg~~~vkk~V~AL-IeID~eRGg 89 (241)
T COG1709 14 LAKRIAGDI-VLSEDPGETLRKWREIFNVSQTELARELGVSPSVISDYESGRRKSPGIAFVKKFVEAL-IEIDEERGG 89 (241)
T ss_pred HHHHHHCCE-EECCCHHHHHHHHHHHCCCCHHHHHHHHCCCCCEEEHHHCCCCCCCCHHHHHHHHHHH-HHHHHHHCC
T ss_conf 988820427-8607825899999998182499999872899100312112575686178999999999-866686156
No 46
>COG1709 Predicted transcriptional regulator [Transcription]
Probab=98.21 E-value=1.9e-06 Score=59.67 Aligned_cols=53 Identities=32% Similarity=0.465 Sum_probs=50.4
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCC-CCHHHHHHHHHHH
Q ss_conf 7799999999972983899999977999999997414889-9989999999982
Q gi|254781218|r 113 AIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTI-PEIKPARKIKQVT 165 (205)
Q Consensus 113 ~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~-Ps~~~l~kIa~~l 165 (205)
..|+-||.+|...+.||.|+|..+|++++.+|.||.|++. |....+.++-.+|
T Consensus 27 ~pge~lrKWR~~F~iSQ~elA~~l~vSpSVISDYE~GRRk~Pg~~~vkk~V~AL 80 (241)
T COG1709 27 DPGETLRKWREIFNVSQTELARELGVSPSVISDYESGRRKSPGIAFVKKFVEAL 80 (241)
T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHCCCCCEEEHHHCCCCCCCCHHHHHHHHHHH
T ss_conf 825899999998182499999872899100312112575686178999999999
No 47
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=98.18 E-value=5.9e-06 Score=56.61 Aligned_cols=52 Identities=19% Similarity=0.161 Sum_probs=36.0
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCC
Q ss_conf 8599889999984899999998877998889999999999828999996145
Q gi|254781218|r 42 ANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDG 93 (205)
Q Consensus 42 ~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~g 93 (205)
-.||||.+||+.+||++.+||++=||++..+.++.++|+++|+.|.+.-++-
T Consensus 21 p~glt~~~lA~~lgV~r~~is~ling~~~iT~dmAlrL~k~fGtspefWlNl 72 (104)
T COG3093 21 PLGLTQTELAEALGVTRNTISELINGRRAITADMALRLAKVFGTSPEFWLNL 72 (104)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHH
T ss_conf 2169899999993998999999983776789999999999929989999999
No 48
>PRK10072 putative transcriptional regulator; Provisional
Probab=98.16 E-value=5.9e-06 Score=56.61 Aligned_cols=54 Identities=17% Similarity=0.410 Sum_probs=44.3
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHH
Q ss_conf 9999999729838999999779999999974148899989999999982899999
Q gi|254781218|r 117 RLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDW 171 (205)
Q Consensus 117 rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~ 171 (205)
-++++|+..|++|.+||+.+|+|.+++..||.+++.|+-..+.-++ +..-++..
T Consensus 37 dvkaIR~~tgl~q~eFA~~lGvSv~tvksWEq~Rr~Ptg~a~klL~-li~~nP~l 90 (96)
T PRK10072 37 EFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVKPSSAELKLMR-LIQANPAL 90 (96)
T ss_pred CHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHH-HHHHCHHH
T ss_conf 3999998809999999999777799999999678789839999999-99879799
No 49
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=98.15 E-value=1e-05 Score=55.10 Aligned_cols=64 Identities=22% Similarity=0.314 Sum_probs=57.9
Q ss_pred HHHHHHHHHH-HHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHC
Q ss_conf 6777999999-999729838999999779999999974148899989999999982899999524
Q gi|254781218|r 111 PYAIGARLKS-IRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIYF 174 (205)
Q Consensus 111 ~~~iG~rLk~-lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~~ 174 (205)
|.-.|+-|+. +.+-.|+|+.++|+.+|+++.+++.+.+|++..+.+.+.+|+++||+++++.+.
T Consensus 7 P~~PGEiL~eeflep~glt~~~lA~~lgV~r~~is~ling~~~iT~dmAlrL~k~fGtspefWlN 71 (104)
T COG3093 7 PAHPGEILREEFLEPLGLTQTELAEALGVTRNTISELINGRRAITADMALRLAKVFGTSPEFWLN 71 (104)
T ss_pred CCCCHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHH
T ss_conf 99941889999845216989999999399899999998377678999999999992998999999
No 50
>COG1396 HipB Predicted transcriptional regulators [Transcription]
Probab=98.10 E-value=2.1e-05 Score=53.14 Aligned_cols=65 Identities=26% Similarity=0.363 Sum_probs=59.4
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCC-CCCHHHHHHHHHHHCCCHHHHHCCCCC
Q ss_conf 99999999998599889999984899999998877998-889999999999828999996145322
Q gi|254781218|r 32 VGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMC-STSIRYALYLRNEYEISFDWIYDGEVI 96 (205)
Q Consensus 32 iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~-~psi~~l~~la~~~~vs~d~Ll~ge~~ 96 (205)
+|.+++.+|+..|+||+++|..+|++..+++.||+|.. .|++..+..++..|++...+++.....
T Consensus 2 ~~~~~~~~r~~~~~s~~~~a~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 67 (120)
T COG1396 2 IGERLKELRKKKGLSQEELAERLGVSRSTISRIERGRSESPSLELLARLAAALGVSLDELLEEEEE 67 (120)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHH
T ss_conf 789999999986999999998939889999999807877846999999999969789988400222
No 51
>COG1426 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]
Probab=98.05 E-value=1.5e-05 Score=54.16 Aligned_cols=64 Identities=16% Similarity=0.208 Sum_probs=56.9
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCH------HHHHHHHHHHCCCHHHHHCC
Q ss_conf 99999999999985998899999848999999988779988899------99999999828999996145
Q gi|254781218|r 30 KDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSI------RYALYLRNEYEISFDWIYDG 93 (205)
Q Consensus 30 ~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi------~~l~~la~~~~vs~d~Ll~g 93 (205)
+.+|+++|..|+.+|||++++|.+++|..+++-.+|+|...--. .++...|++++++.|.|+..
T Consensus 2 ~~~Ge~Lr~~Re~~gLsL~dva~~t~I~~~~L~aiEeg~~~~lp~~~y~rG~ir~YA~~l~ld~~~l~~~ 71 (284)
T COG1426 2 KTLGERLRQAREEKGLSLEDVAARTKIRKSYLRALEEGNFDKLPGPVYIRGYIRSYAKFLGLDEDELLQA 71 (284)
T ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHH
T ss_conf 6778999999998499999999885775999999866770106415767899999999968998999998
No 52
>pfam07022 Phage_CI_repr Bacteriophage CI repressor helix-turn-helix domain. This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic.
Probab=97.96 E-value=3.4e-05 Score=51.92 Aligned_cols=59 Identities=19% Similarity=0.249 Sum_probs=49.7
Q ss_pred HHHHHHHCCC-CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCC
Q ss_conf 9999998599-88999998489999999887799888999999999982899999614532
Q gi|254781218|r 36 IKDIRKANNK-TQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEV 95 (205)
Q Consensus 36 ik~lR~~~gl-tQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~ 95 (205)
|..+-+..|. ||.|||..+||++++||.|-..-.. +.+.+++++...+||+|||+.|+-
T Consensus 3 i~Rl~~a~G~~t~~eLA~~LgI~~stis~w~~R~~~-P~e~iv~~~~~tGvsl~WL~~G~G 62 (65)
T pfam07022 3 IERLMKAYGFKSRSELADHLGVSKSTLSTWYKRDSF-PAEWVIRCALETGVSLDWLATGDG 62 (65)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCC-CHHHHHHHHHHHCCCHHHHHCCCC
T ss_conf 999999968886999999969888889999986999-899999999998829999970899
No 53
>TIGR00270 TIGR00270 conserved hypothetical protein TIGR00270; InterPro: IPR004451 This family of conserved hypothetical proteins includes proteins of unknown function from archaebacteria..
Probab=97.95 E-value=1.4e-05 Score=54.28 Aligned_cols=71 Identities=20% Similarity=0.165 Sum_probs=62.3
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCC
Q ss_conf 34554677799999999972983899999977999999997414889998999999998289999952472
Q gi|254781218|r 106 KKRLDPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIYFGD 176 (205)
Q Consensus 106 ~~~~d~~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~~G~ 176 (205)
...+-...+|.-||..|+.+|||++|||+.+..-.+++.++|+....|....+.+|-+.|++++-.=+..+
T Consensus 76 t~~elvEdyg~iIR~eREKRgwS~E~LAkki~eK~S~i~kiE~~e~eP~~k~~~kLEkllkIkL~E~~~e~ 146 (169)
T TIGR00270 76 TVEELVEDYGRIIREEREKRGWSREELAKKIKEKASVIKKIEREELEPEEKVVKKLEKLLKIKLLEKVEEE 146 (169)
T ss_pred HHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCCC
T ss_conf 35666643225422000146878789999874106788887540379888999998888350100235710
No 54
>PRK10856 hypothetical protein; Provisional
Probab=97.94 E-value=4.9e-05 Score=50.92 Aligned_cols=64 Identities=17% Similarity=0.120 Sum_probs=56.5
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCC------CHHHHHHHHHHHCCCHHHHHCC
Q ss_conf 999999999999859988999998489999999887799888------9999999999828999996145
Q gi|254781218|r 30 KDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCST------SIRYALYLRNEYEISFDWIYDG 93 (205)
Q Consensus 30 ~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~p------si~~l~~la~~~~vs~d~Ll~g 93 (205)
.-+|.+||..|+++|||++++|.+++++.+.|-.+|+|.... ---++...|+.++++.+.|+..
T Consensus 13 ~t~G~~Lr~ARE~~GlSi~dvA~~LkL~~~~ieALE~dd~~~Lp~~tF~RGylRsYAr~LglD~~~ll~~ 82 (332)
T PRK10856 13 LTTGVRLRQAREQLGLSQQAVAERLCLKVSTVRDIEEDKAPADLASTFLRGYIRSYARLVHIPEEELLPG 82 (332)
T ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCHHCCCCHHHHHHHHHHHHHHHCCCHHHHHHH
T ss_conf 6887999999998599999999870898999999857822108703647999999999978897996542
No 55
>COG1396 HipB Predicted transcriptional regulators [Transcription]
Probab=97.92 E-value=0.00011 Score=48.78 Aligned_cols=63 Identities=37% Similarity=0.560 Sum_probs=59.5
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCC-CCCHHHHHHHHHHHCCCHHHHHCCC
Q ss_conf 79999999997298389999997799999999741488-9998999999998289999952472
Q gi|254781218|r 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRT-IPEIKPARKIKQVTKKHLDWIYFGD 176 (205)
Q Consensus 114 iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~-~Ps~~~l~kIa~~lgvs~d~L~~G~ 176 (205)
+|.+++.+|+..|++|.++|..+|++..+++.||+|.. .|....+..++..+++...+++...
T Consensus 2 ~~~~~~~~r~~~~~s~~~~a~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 (120)
T COG1396 2 IGERLKELRKKKGLSQEELAERLGVSRSTISRIERGRSESPSLELLARLAAALGVSLDELLEEE 65 (120)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHH
T ss_conf 7899999999869999999989398899999998078778469999999999697899884002
No 56
>TIGR02612 mob_myst_A mobile mystery protein A; InterPro: IPR013435 Proteins in this entry are more often encoded within mobilisation-related contexts than not. This includes a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and plasmids in Agrobacterium tumefaciens and Coxiella burnetii. They are found together with mobile mystery protein B, a member of the Fic protein family (IPR003812 from INTERPRO). Mobile mystery protein A is encoded by the upstream member of the gene pair and contains a helix-turn-helix domain..
Probab=97.86 E-value=2.9e-05 Score=52.30 Aligned_cols=56 Identities=14% Similarity=0.221 Sum_probs=31.8
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCC--CCCCHHHHHHHHHHHCCCHHHHH
Q ss_conf 999999859988999998489999999887799--88899999999998289999961
Q gi|254781218|r 36 IKDIRKANNKTQKEMAIGANQLESAVNLFENGM--CSTSIRYALYLRNEYEISFDWIY 91 (205)
Q Consensus 36 ik~lR~~~gltQ~elA~~~gis~~~is~~E~G~--~~psi~~l~~la~~~~vs~d~Ll 91 (205)
||.+|+..|||-.+||..+||+++.|..+|+.. ...+++.|-.-|+++||.+=|-|
T Consensus 30 vR~~R~ALGms~~QLA~RlGV~p~Rv~~~E~~E~~G~VTL~tlr~aAEAl~C~FVYaf 87 (150)
T TIGR02612 30 VRAIRKALGMSGAQLAARLGVTPQRVEAIEKSELSGAVTLKTLRKAAEALDCTFVYAF 87 (150)
T ss_pred HHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCEEEEEC
T ss_conf 6889877251578876652897377999888875553558889999998598443401
No 57
>PRK10072 putative transcriptional regulator; Provisional
Probab=97.85 E-value=4.4e-05 Score=51.23 Aligned_cols=49 Identities=14% Similarity=0.063 Sum_probs=40.8
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHC
Q ss_conf 99999998599889999984899999998877998889999999999828
Q gi|254781218|r 35 RIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYE 84 (205)
Q Consensus 35 rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~ 84 (205)
-++.+|+..|++|.+||..+|+|.++|-.||.|++.|+-.-+ +|-....
T Consensus 37 dvkaIR~~tgl~q~eFA~~lGvSv~tvksWEq~Rr~Ptg~a~-klL~li~ 85 (96)
T PRK10072 37 EFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVKPSSAEL-KLMRLIQ 85 (96)
T ss_pred CHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHHH-HHHHHHH
T ss_conf 399999880999999999977779999999967878983999-9999998
No 58
>TIGR02612 mob_myst_A mobile mystery protein A; InterPro: IPR013435 Proteins in this entry are more often encoded within mobilisation-related contexts than not. This includes a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and plasmids in Agrobacterium tumefaciens and Coxiella burnetii. They are found together with mobile mystery protein B, a member of the Fic protein family (IPR003812 from INTERPRO). Mobile mystery protein A is encoded by the upstream member of the gene pair and contains a helix-turn-helix domain..
Probab=97.84 E-value=1.6e-05 Score=53.95 Aligned_cols=78 Identities=21% Similarity=0.282 Sum_probs=61.2
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCC--CCCHHHHHHHHHHHCCCHHHHHCCCCCCCHHHHHHHHHHHHHH
Q ss_conf 99999997298389999997799999999741488--9998999999998289999952472102545677754235678
Q gi|254781218|r 117 RLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRT--IPEIKPARKIKQVTKKHLDWIYFGDEVIVPKSIKRAKGNQSSK 194 (205)
Q Consensus 117 rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~--~Ps~~~l~kIa~~lgvs~d~L~~G~e~~~~~~~~~~~~~~~~~ 194 (205)
=||.+|+.+|||-.+||..+||.++.|..+|...- ..++.++.+-|+++||..=|=|=- +.++...-.++..+
T Consensus 29 WvR~~R~ALGms~~QLA~RlGV~p~Rv~~~E~~E~~G~VTL~tlr~aAEAl~C~FVYafVP-----~~sLE~t~~~QArK 103 (150)
T TIGR02612 29 WVRAIRKALGMSGAQLAARLGVTPQRVEAIEKSELSGAVTLKTLRKAAEALDCTFVYAFVP-----KTSLEATVRAQARK 103 (150)
T ss_pred CHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCEEEEECCC-----CCCHHHHHHHHHHH
T ss_conf 1688987725157887665289737799988887555355888999999859844340188-----60278999999999
Q ss_pred HHHHH
Q ss_conf 77654
Q gi|254781218|r 195 KSKKD 199 (205)
Q Consensus 195 ~sk~d 199 (205)
.++..
T Consensus 104 vA~~~ 108 (150)
T TIGR02612 104 VAKEI 108 (150)
T ss_pred HHHHH
T ss_conf 99999
No 59
>COG1426 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]
Probab=97.83 E-value=9.3e-05 Score=49.21 Aligned_cols=65 Identities=23% Similarity=0.250 Sum_probs=56.3
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCC--CCH----HHHHHHHHHHCCCHHHHHCCCC
Q ss_conf 7799999999972983899999977999999997414889--998----9999999982899999524721
Q gi|254781218|r 113 AIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTI--PEI----KPARKIKQVTKKHLDWIYFGDE 177 (205)
Q Consensus 113 ~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~--Ps~----~~l~kIa~~lgvs~d~L~~G~e 177 (205)
.+|++||+.|+.+|||+.|++..++|.++.+..+|+|.-. |.. ..++..|+++|++.|-|+-.-+
T Consensus 3 ~~Ge~Lr~~Re~~gLsL~dva~~t~I~~~~L~aiEeg~~~~lp~~~y~rG~ir~YA~~l~ld~~~l~~~~~ 73 (284)
T COG1426 3 TLGERLRQAREEKGLSLEDVAARTKIRKSYLRALEEGNFDKLPGPVYIRGYIRSYAKFLGLDEDELLQAFE 73 (284)
T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHH
T ss_conf 77899999999849999999988577599999986677010641576789999999996899899999864
No 60
>PRK10856 hypothetical protein; Provisional
Probab=97.70 E-value=0.00019 Score=47.33 Aligned_cols=67 Identities=19% Similarity=0.226 Sum_probs=57.4
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCC--CC----HHHHHHHHHHHCCCHHHHHCCC
Q ss_conf 4677799999999972983899999977999999997414889--99----8999999998289999952472
Q gi|254781218|r 110 DPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTI--PE----IKPARKIKQVTKKHLDWIYFGD 176 (205)
Q Consensus 110 d~~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~--Ps----~~~l~kIa~~lgvs~d~L~~G~ 176 (205)
+...+|.+||+.|+.+|||+.|+|+.+.++...+..+|+|... |. -..++..|+.||++.+-|+..-
T Consensus 11 ~~~t~G~~Lr~ARE~~GlSi~dvA~~LkL~~~~ieALE~dd~~~Lp~~tF~RGylRsYAr~LglD~~~ll~~~ 83 (332)
T PRK10856 11 EALTTGVRLRQAREQLGLSQQAVAERLCLKVSTVRDIEEDKAPADLASTFLRGYIRSYARLVHIPEEELLPGL 83 (332)
T ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCHHCCCCHHHHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf 6568879999999985999999998708989999998578221087036479999999999788979965421
No 61
>COG3655 Predicted transcriptional regulator [Transcription]
Probab=97.63 E-value=0.00015 Score=47.98 Aligned_cols=61 Identities=13% Similarity=0.076 Sum_probs=36.1
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCC-CCCCHHHHHHHHHHHCCCHHHHHCC
Q ss_conf 999999999859988999998489999999887799-8889999999999828999996145
Q gi|254781218|r 33 GTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGM-CSTSIRYALYLRNEYEISFDWIYDG 93 (205)
Q Consensus 33 G~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~-~~psi~~l~~la~~~~vs~d~Ll~g 93 (205)
..++..+.-.+++++.+||+.+|+|.+++|.+.+|+ ...++++|-+||.+++|.+..|+.-
T Consensus 4 ~~~l~~~l~~r~~~~~eLa~~igis~~~ls~l~~gk~k~I~~~tL~~iC~~LeCqpgDiley 65 (73)
T COG3655 4 AVRLDVMLADRKISLKELAEAIGISEANLSKLKTGKVKAIRLSTLEKICKALECQPGDILEY 65 (73)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCEEEHHHHHHHHHHCCCCHHHEEEE
T ss_conf 37679999997501778999984369899999728866044899999999838984054577
No 62
>COG3655 Predicted transcriptional regulator [Transcription]
Probab=97.47 E-value=0.00034 Score=45.77 Aligned_cols=62 Identities=21% Similarity=0.267 Sum_probs=56.0
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCC-CCHHHHHHHHHHHCCCHHHHHCC
Q ss_conf 799999999972983899999977999999997414889-99899999999828999995247
Q gi|254781218|r 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTI-PEIKPARKIKQVTKKHLDWIYFG 175 (205)
Q Consensus 114 iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~-Ps~~~l~kIa~~lgvs~d~L~~G 175 (205)
+..++..++.+++++..|+|+.+|++..+++...+|+.. .+.++|.+||++|++.+.-|+--
T Consensus 3 i~~~l~~~l~~r~~~~~eLa~~igis~~~ls~l~~gk~k~I~~~tL~~iC~~LeCqpgDiley 65 (73)
T COG3655 3 IAVRLDVMLADRKISLKELAEAIGISEANLSKLKTGKVKAIRLSTLEKICKALECQPGDILEY 65 (73)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCEEEHHHHHHHHHHCCCCHHHEEEE
T ss_conf 137679999997501778999984369899999728866044899999999838984054577
No 63
>TIGR02885 spore_sigF RNA polymerase sigma-F factor; InterPro: IPR014236 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 , . Members of this entry represent RNA polymerase sigma factor F. Within the Firmicutes, Sigma-F is specifically, and universally, a component of the endospore formation program, and is expressed in the forespore to turn on the expression of dozens of genes. It is closely related to sigma-G, which is also expressed in the forespore.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=97.38 E-value=0.00037 Score=45.49 Aligned_cols=123 Identities=20% Similarity=0.254 Sum_probs=78.7
Q ss_pred HHHCCC-HHHHH------------HHHHHHHHHHHHHHHC------CCCHHHHHHHHCCCHHH-HHHHHCCCCCCCHHHH
Q ss_conf 100015-66899------------9999999999999985------99889999984899999-9988779988899999
Q gi|254781218|r 17 YTLIIT-PEIRQ------------YWKDVGTRIKDIRKAN------NKTQKEMAIGANQLESA-VNLFENGMCSTSIRYA 76 (205)
Q Consensus 17 ~~~~~~-~~~~~------------~~~~iG~rik~lR~~~------gltQ~elA~~~gis~~~-is~~E~G~~~psi~~l 76 (205)
|||||= +|++= ..|++|.+|++-|+.. .=|-.|||+.+|+++-. |...|.+...-++.-.
T Consensus 67 YAVPmI~GEIkRFLRDDG~ikVSRSlK~la~k~~~~kE~L~~~l~R~PTi~Elae~lg~~~EEiv~A~Es~~~~~sly~t 146 (231)
T TIGR02885 67 YAVPMIMGEIKRFLRDDGIIKVSRSLKELARKIRYEKEELTKKLGREPTINELAEALGVSPEEIVMALESARSLQSLYDT 146 (231)
T ss_pred CCCCHHHHHHHHHHCCCCCEEEEHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHCCE
T ss_conf 12220221222310268855751527899999987799999983899888999887587887866442025761011001
Q ss_pred HHHHHHHCCCHHHHHCCCCCCCCCCCC--CCHHHHHHHHHHHHHHH----------HHHHCCCCHHHHHHHHCCCHHHHH
Q ss_conf 999998289999961453221000023--21345546777999999----------999729838999999779999999
Q gi|254781218|r 77 LYLRNEYEISFDWIYDGEVIDRRYEDV--TNKKRLDPYAIGARLKS----------IRKDKGMSQIEFGKLLGMPNSTLS 144 (205)
Q Consensus 77 ~~la~~~~vs~d~Ll~ge~~~~~~~~~--~~~~~~d~~~iG~rLk~----------lR~~~glsq~elA~~lgis~~tis 144 (205)
+ +.=+=++=+|++ .. .|. ......+..++-+-|.+ +|=-+..||.|+|+.+|||+-.+|
T Consensus 147 v---h~dDGdPi~LlD-----~i-~d~~~~~~~~~~ki~Lke~i~~Ld~rer~ii~LRYFKDkTQ~eVA~~LGISQVQVS 217 (231)
T TIGR02885 147 V---HEDDGDPILLLD-----QI-ADKGSEDSDLLEKIALKEAISKLDERERQIIMLRYFKDKTQTEVAKMLGISQVQVS 217 (231)
T ss_pred E---ECCCCCHHHHHH-----HH-CCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHCCCCCCHHH
T ss_conf 1---417946446766-----52-12577136899989999998612522678977410140017999977185700122
Q ss_pred HHHC
Q ss_conf 9741
Q gi|254781218|r 145 NYEQ 148 (205)
Q Consensus 145 ~~E~ 148 (205)
++|+
T Consensus 218 RlEk 221 (231)
T TIGR02885 218 RLEK 221 (231)
T ss_pred HHHH
T ss_conf 7899
No 64
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein; InterPro: IPR014057 Members of this strictly bacterial protein family are small, at roughly 100 amino acids. The gene is almost invariably the downstream member of a gene pair. It is a predicted DNA-binding protein from a clade within the helix-turn-helix family IPR001387 from INTERPRO. These gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module..
Probab=97.34 E-value=0.00065 Score=44.01 Aligned_cols=59 Identities=27% Similarity=0.390 Sum_probs=53.4
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHH
Q ss_conf 4677799999999972983899999977999999997414889998999999998289999
Q gi|254781218|r 110 DPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLD 170 (205)
Q Consensus 110 d~~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d 170 (205)
||.-|-.-|=.+=+.+|||| +|+.+|+++.++.+=.+++..|+.+++.++.++||+.+.
T Consensus 31 Dp~~~~~ALG~iArArGMtq--lA~~tGlsREsLYkALs~~GnP~f~T~lkV~~ALG~~L~ 89 (91)
T TIGR02684 31 DPALIAAALGVIARARGMTQ--LAKKTGLSRESLYKALSGGGNPTFDTILKVTKALGLKLT 89 (91)
T ss_pred CHHHHHHHHHHHHHHCCHHH--HHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHCCCEEE
T ss_conf 98899999889986516578--999828767887887356889566888999984086020
No 65
>COG5499 Predicted transcription regulator containing HTH domain [Transcription]
Probab=97.30 E-value=0.00062 Score=44.11 Aligned_cols=57 Identities=18% Similarity=0.298 Sum_probs=49.3
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHH
Q ss_conf 9999999972983899999977999999997414889998999999998289999952
Q gi|254781218|r 116 ARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIY 173 (205)
Q Consensus 116 ~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~ 173 (205)
+-|+.++...|+|+.+||..+| |++.+|++.+|++.-+++.++++.+-||++.|-|+
T Consensus 63 e~I~t~Md~~glt~~dLa~~iG-Sks~vS~iL~~rraLTle~ikkL~q~~gIpa~~lI 119 (120)
T COG5499 63 EVIRTLMDQYGLTLADLANEIG-SKSRVSNILSGRRALTLEHIKKLHQRFGIPADVLI 119 (120)
T ss_pred HHHHHHHHHHCCCHHHHHHHHC-CHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHC
T ss_conf 9999999993871888899867-61889999732067669999999998695888753
No 66
>COG5499 Predicted transcription regulator containing HTH domain [Transcription]
Probab=97.25 E-value=0.00077 Score=43.54 Aligned_cols=73 Identities=19% Similarity=0.165 Sum_probs=60.5
Q ss_pred HHCCCHHHHHHHHHH---HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHH
Q ss_conf 000156689999999---99999999985998899999848999999988779988899999999998289999961
Q gi|254781218|r 18 TLIITPEIRQYWKDV---GTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIY 91 (205)
Q Consensus 18 ~~~~~~~~~~~~~~i---G~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll 91 (205)
+++-.+|.++|...- =+-|+.+..+.|+|+.+||..+| |.+.+|++-+|++..++++..+|...|+|+.|-|+
T Consensus 44 tl~eAyE~kh~~i~aP~pve~I~t~Md~~glt~~dLa~~iG-Sks~vS~iL~~rraLTle~ikkL~q~~gIpa~~lI 119 (120)
T COG5499 44 TLIEAYEFKHYPIAAPDPVEVIRTLMDQYGLTLADLANEIG-SKSRVSNILSGRRALTLEHIKKLHQRFGIPADVLI 119 (120)
T ss_pred HHHHHHHHHHCHHHCCCHHHHHHHHHHHHCCCHHHHHHHHC-CHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHC
T ss_conf 99860665514031688889999999993871888899867-61889999732067669999999998695888753
No 67
>pfam08667 BetR BetR domain. This family includes an N-terminal helix-turn-helix domain.
Probab=97.23 E-value=0.0026 Score=40.29 Aligned_cols=64 Identities=14% Similarity=0.212 Sum_probs=54.7
Q ss_pred HHHHHHHHHHHHHHHCCCCHH----HHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHH
Q ss_conf 467779999999997298389----9999977999999997414889998999999998289999952
Q gi|254781218|r 110 DPYAIGARLKSIRKDKGMSQI----EFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIY 173 (205)
Q Consensus 110 d~~~iG~rLk~lR~~~glsq~----elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~ 173 (205)
|...+..|+|++....|+... .+++.||+|.+...+-.+|.+-=.+..+.+||+.||+++..||
T Consensus 2 ~~~~ia~rvr~lL~r~GI~kRqh~s~is~iL~LSfS~a~RKLkG~spW~l~Ql~kVA~~fg~~~a~L~ 69 (146)
T pfam08667 2 DDLIVAERVRKLLTRTGIAERQHNTTIANILGLSFSQAYRKLKGSIPWNLAQLQKVAQYFGVPAAILL 69 (146)
T ss_pred CCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHH
T ss_conf 01899999999998639975677889999978748988787358997449999999999597999992
No 68
>COG4800 Predicted transcriptional regulator with an HTH domain [Transcription]
Probab=97.20 E-value=0.0019 Score=41.17 Aligned_cols=59 Identities=17% Similarity=0.085 Sum_probs=49.6
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 689999999999999999859988999998489999999887799888999999999982
Q gi|254781218|r 24 EIRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEY 83 (205)
Q Consensus 24 ~~~~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~ 83 (205)
++.+..+++|.-++.+-.++|||..+||+..|+..|++.++-+| +.|.+++|.+|.+..
T Consensus 9 ~~ies~E~F~~~l~~~l~Elglt~~eFak~anIP~StLYKil~G-~dpr~~tl~~I~kti 67 (170)
T COG4800 9 ECIESGEDFGSCLQKLLDELGLTPSEFAKRANIPLSTLYKILKG-SDPRYDTLTRIFKTI 67 (170)
T ss_pred HHHHCHHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHC-CCCCHHHHHHHHHHH
T ss_conf 99964007999999999981999899988709989999999817-996577899999999
No 69
>COG4800 Predicted transcriptional regulator with an HTH domain [Transcription]
Probab=96.80 E-value=0.008 Score=37.26 Aligned_cols=54 Identities=24% Similarity=0.354 Sum_probs=50.3
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 6777999999999729838999999779999999974148899989999999982
Q gi|254781218|r 111 PYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVT 165 (205)
Q Consensus 111 ~~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~l 165 (205)
...+|+-++.+..++||+..|||+..|++.+|+.++..| +.|..+++.+|-+..
T Consensus 14 ~E~F~~~l~~~l~Elglt~~eFak~anIP~StLYKil~G-~dpr~~tl~~I~kti 67 (170)
T COG4800 14 GEDFGSCLQKLLDELGLTPSEFAKRANIPLSTLYKILKG-SDPRYDTLTRIFKTI 67 (170)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHC-CCCCHHHHHHHHHHH
T ss_conf 007999999999981999899988709989999999817-996577899999999
No 70
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=96.71 E-value=0.0025 Score=40.40 Aligned_cols=36 Identities=17% Similarity=0.238 Sum_probs=24.5
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHH
Q ss_conf 983899999977999999997414889998999999
Q gi|254781218|r 126 GMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKI 161 (205)
Q Consensus 126 glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kI 161 (205)
-|+++++|+.+|++.+|||+.-+|+..-+..-++.+
T Consensus 349 PL~lkdiA~~lglheSTVSRav~~Kyi~tp~G~~~l 384 (461)
T PRK05932 349 PLVLKDIAEALGMHESTISRATTNKYMATPRGIFEL 384 (461)
T ss_pred CCCHHHHHHHCCCCHHHHHHHHHCCEECCCCCEEEH
T ss_conf 763999998739981258898716611489744669
No 71
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=96.69 E-value=0.0075 Score=37.44 Aligned_cols=58 Identities=12% Similarity=0.046 Sum_probs=36.4
Q ss_pred HHHHHH-HHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCC-CCHHHHHHHHHHHCCCHHH
Q ss_conf 999999-9999985998899999848999999988779988-8999999999982899999
Q gi|254781218|r 31 DVGTRI-KDIRKANNKTQKEMAIGANQLESAVNLFENGMCS-TSIRYALYLRNEYEISFDW 89 (205)
Q Consensus 31 ~iG~ri-k~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~-psi~~l~~la~~~~vs~d~ 89 (205)
-|-..+ +.+|.. |+||.+.|+.+|+||++||+|=+|.+. ..++.+..+.+....-+..
T Consensus 9 aiRa~lA~~L~ee-G~Sq~~iA~LLGltqaAVS~Yls~krg~~~~~~~~e~~e~i~~l~~~ 68 (119)
T COG2522 9 AIRALLAKELIEE-GLSQYRIAKLLGLTQAAVSQYLSGKRGSARLEDIGETDEEIRSLVAE 68 (119)
T ss_pred HHHHHHHHHHHHC-CCCHHHHHHHHCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 8999999999995-88699999996888999999973677368899999899999999999
No 72
>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=96.65 E-value=0.0045 Score=38.79 Aligned_cols=136 Identities=21% Similarity=0.175 Sum_probs=84.4
Q ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCC
Q ss_conf 77766654333100015668999999999999999985998899999848999999988779988899999999998289
Q gi|254781218|r 6 FLETSLKSLQEYTLIITPEIRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEI 85 (205)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~v 85 (205)
++-.+++-++.--+.++..+-++.++.=.. .-..-+-||.+++|+.+|++.||||+.-+|+.--+..-++.|...|.-
T Consensus 13 ~li~~i~~R~~Tl~~V~~~Iv~~Q~~Ff~~--g~~~l~PLtlk~iA~~l~lh~STVSRav~~Kyi~tp~Gi~~lk~fFs~ 90 (160)
T pfam04552 13 WLIRSLEQRAETLLKVAREIVRRQEDFLEK--GPEALRPLTLREVAEALGMHESTVSRATTNKYLATPRGLFELKYFFSS 90 (160)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--CCCCCCCCCHHHHHHHCCCCCCHHHHHHHHHHHHCCCCEEEHHHHHHC
T ss_conf 999999999999999999999997999847--853575761999998809981069999961397679951659998501
Q ss_pred CHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH----CCCCHHHHHHHHC-----CCHHHHHHHHCCCCCCCHH
Q ss_conf 999961453221000023213455467779999999997----2983899999977-----9999999974148899989
Q gi|254781218|r 86 SFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRKD----KGMSQIEFGKLLG-----MPNSTLSNYEQGRTIPEIK 156 (205)
Q Consensus 86 s~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~~----~glsq~elA~~lg-----is~~tis~~E~g~~~Ps~~ 156 (205)
.+. ..... ..+...|-.+|+++-.. +-+|-.++++.+. |++.|+.+|-..-..|+..
T Consensus 91 ~~~--------~~~~~------~~S~~~ik~~I~~lI~~Ed~~~PlSD~~I~~~L~~~Gi~IaRRTVaKYR~~L~Ip~s~ 156 (160)
T pfam04552 91 AVS--------TSGGG------EASATAIRALIKKLIAAEDPKKPLSDDKIVELLKEQGIDIARRTVAKYREALNIPSSS 156 (160)
T ss_pred CCC--------CCCCC------CHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCCEEHHHHHHHHHHCCCCCHH
T ss_conf 367--------88863------0229999999999998247899999999999999779952146199999883999665
Q ss_pred H
Q ss_conf 9
Q gi|254781218|r 157 P 157 (205)
Q Consensus 157 ~ 157 (205)
.
T Consensus 157 ~ 157 (160)
T pfam04552 157 Q 157 (160)
T ss_pred H
T ss_conf 3
No 73
>PHA00542 putative Cro-like protein
Probab=96.61 E-value=0.0065 Score=37.83 Aligned_cols=57 Identities=9% Similarity=-0.004 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCC-CCCCHHHHHHHHHHH
Q ss_conf 999999999999999859988999998489999999887799-888999999999982
Q gi|254781218|r 27 QYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGM-CSTSIRYALYLRNEY 83 (205)
Q Consensus 27 ~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~-~~psi~~l~~la~~~ 83 (205)
..++.--..|-..-...||||.+++...||+++.||++-.|+ ..|.+.++.+|.+.|
T Consensus 14 ~~y~k~P~E~V~aLi~~G~tQ~qI~~~tgv~QpsisRilsGk~kDpR~s~v~~L~~L~ 71 (82)
T PHA00542 14 AAYTQRPDELVCALIRAGWSQEQIADATDVSQPTICRIYSGRHKDPRYSVVEKLRHLV 71 (82)
T ss_pred HHHHCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHCCCCCCCCCHHHHHHHHHH
T ss_conf 7653298999999998225699999860877036899980887897206999999998
No 74
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=96.60 E-value=0.06 Score=31.85 Aligned_cols=137 Identities=12% Similarity=0.091 Sum_probs=67.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHH---CCCCCCCHHHHHHHHHHHCCCHHHHHCCCC
Q ss_conf 156689999999999999999859--988999998489999999887---799888999999999982899999614532
Q gi|254781218|r 21 ITPEIRQYWKDVGTRIKDIRKANN--KTQKEMAIGANQLESAVNLFE---NGMCSTSIRYALYLRNEYEISFDWIYDGEV 95 (205)
Q Consensus 21 ~~~~~~~~~~~iG~rik~lR~~~g--ltQ~elA~~~gis~~~is~~E---~G~~~psi~~l~~la~~~~vs~d~Ll~ge~ 95 (205)
++..+.+....+-.-.+.++...| -|-+++|+.+|++...+..+. .+....|++..+.=-..-.+++..++.++.
T Consensus 104 iP~~~~~~~~ki~~~~~~l~~~~gr~pt~~EiA~~l~is~~~v~~~~~~~~~~~~~SLd~~~~~~~d~~~~l~d~l~d~~ 183 (256)
T PRK07408 104 IPRRWLELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRMPLSLDAPVSQDEDGSTSLGDLLPDPR 183 (256)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCEECCCCCCCCCCCCCHHHHHCCCCC
T ss_conf 36999999999999999999987899989999989596999999999987278873056647799987611777558999
Q ss_pred CCCCCCCCCCHHHHHHH---HHHHHHH---HHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 21000023213455467---7799999---9999729838999999779999999974148899989999999982
Q gi|254781218|r 96 IDRRYEDVTNKKRLDPY---AIGARLK---SIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVT 165 (205)
Q Consensus 96 ~~~~~~~~~~~~~~d~~---~iG~rLk---~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~l 165 (205)
.+. ..........-.. .+..|=+ .+|-..++|+.|.|+.+|||+..+++++. ..+.++-+.|
T Consensus 184 ~~~-~~~~~e~~~~L~~~l~~L~eREr~Il~~ry~~~~tl~EIa~~lgvS~~rVsqi~~-------~AL~kLR~~L 251 (256)
T PRK07408 184 YRS-FQLAQEDRIRLQQALAQLEERTREVLEFVFLHDLTQKEAAERLGISPVTVSRRVK-------KGLQQLKKLL 251 (256)
T ss_pred CCH-HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH-------HHHHHHHHHH
T ss_conf 753-8899999999999985699999999999963799899999897989999999999-------9999999972
No 75
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein; InterPro: IPR014057 Members of this strictly bacterial protein family are small, at roughly 100 amino acids. The gene is almost invariably the downstream member of a gene pair. It is a predicted DNA-binding protein from a clade within the helix-turn-helix family IPR001387 from INTERPRO. These gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module..
Probab=96.50 E-value=0.0042 Score=39.00 Aligned_cols=54 Identities=13% Similarity=0.129 Sum_probs=47.2
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf 99999999998599889999984899999998877998889999999999828999
Q gi|254781218|r 32 VGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISF 87 (205)
Q Consensus 32 iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~ 87 (205)
|-.=|=.+=+.+|||| +|++.|+++-++.+==++..+|+++++++++++|||.+
T Consensus 35 ~~~ALG~iArArGMtq--lA~~tGlsREsLYkALs~~GnP~f~T~lkV~~ALG~~L 88 (91)
T TIGR02684 35 IAAALGVIARARGMTQ--LAKKTGLSRESLYKALSGGGNPTFDTILKVTKALGLKL 88 (91)
T ss_pred HHHHHHHHHHHCCHHH--HHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHCCCEE
T ss_conf 9999889986516578--99982876788788735688956688899998408602
No 76
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=96.35 E-value=0.013 Score=35.94 Aligned_cols=40 Identities=33% Similarity=0.478 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCC
Q ss_conf 7999999999729838999999779999999974148899
Q gi|254781218|r 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIP 153 (205)
Q Consensus 114 iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~P 153 (205)
|-..|......+|+||.+.|+++|+++..+|+|-.|++.|
T Consensus 10 iRa~lA~~L~eeG~Sq~~iA~LLGltqaAVS~Yls~krg~ 49 (119)
T COG2522 10 IRALLAKELIEEGLSQYRIAKLLGLTQAAVSQYLSGKRGS 49 (119)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCH
T ss_conf 9999999999958869999999688899999997367736
No 77
>PRK02866 cyanate hydratase; Validated
Probab=96.26 E-value=0.097 Score=30.58 Aligned_cols=62 Identities=15% Similarity=0.040 Sum_probs=56.8
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHH
Q ss_conf 99999999999985998899999848999999988779988899999999998289999961
Q gi|254781218|r 30 KDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIY 91 (205)
Q Consensus 30 ~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll 91 (205)
.++-++|-..+..+|||-+++|+.+|.|.-.+...=-|+...+-+..-+++..|+.+-+..-
T Consensus 4 ~~lte~i~~aK~~kgltw~~ia~~~G~s~v~~aaa~lGQ~~~~~e~A~~l~~~L~L~~~~~~ 65 (147)
T PRK02866 4 EELTEKILAAKKEKGLTWADIAEAIGLSEVWVTAALLGQMTLPAEEAEKVAELLGLDEDAVA 65 (147)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHHHHCCCCHHHHH
T ss_conf 99999999999984998999998949899999999846778999999999997499999999
No 78
>PRK02866 cyanate hydratase; Validated
Probab=96.23 E-value=0.038 Score=33.09 Aligned_cols=64 Identities=13% Similarity=0.223 Sum_probs=58.2
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHH
Q ss_conf 4677799999999972983899999977999999997414889998999999998289999952
Q gi|254781218|r 110 DPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIY 173 (205)
Q Consensus 110 d~~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~ 173 (205)
+...+-++|-..+..+|+|-.++|+.+|.+.-.+....-|....+.+.+.+++++|+.+-+-.-
T Consensus 2 ~r~~lte~i~~aK~~kgltw~~ia~~~G~s~v~~aaa~lGQ~~~~~e~A~~l~~~L~L~~~~~~ 65 (147)
T PRK02866 2 KREELTEKILAAKKEKGLTWADIAEAIGLSEVWVTAALLGQMTLPAEEAEKVAELLGLDEDAVA 65 (147)
T ss_pred CHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHHHHCCCCHHHHH
T ss_conf 8899999999999984998999998949899999999846778999999999997499999999
No 79
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=96.21 E-value=0.095 Score=30.61 Aligned_cols=131 Identities=13% Similarity=0.132 Sum_probs=62.9
Q ss_pred HHHCCCHHHHHHHHHHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHH---CCCCCCCHHHHHHHHHHHCCCHHHHH
Q ss_conf 100015668999999999999999985--9988999998489999999887---79988899999999998289999961
Q gi|254781218|r 17 YTLIITPEIRQYWKDVGTRIKDIRKAN--NKTQKEMAIGANQLESAVNLFE---NGMCSTSIRYALYLRNEYEISFDWIY 91 (205)
Q Consensus 17 ~~~~~~~~~~~~~~~iG~rik~lR~~~--gltQ~elA~~~gis~~~is~~E---~G~~~psi~~l~~la~~~~vs~d~Ll 91 (205)
.++-++...++....|..-...+.... .-|-.++|+.+|++...|...- +.....|++....-.......+...+
T Consensus 113 ~~IRlP~~~~~~~~ki~~~~~~l~~~~gr~Pt~~EiA~~lg~~~~~v~~~l~~~~~~~~~SlD~~~~~~~~~~~~l~d~~ 192 (263)
T PRK07122 113 WSVKVPRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSSYNTLSIDSGGGSGDDDARAIADTL 192 (263)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHC
T ss_conf 75465799999989999999999998688999999998969399999999987335898778788888886520354641
Q ss_pred CCCCCCCCCCCCCCHHHHHH--HHHH---HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf 45322100002321345546--7779---9999999972983899999977999999997414
Q gi|254781218|r 92 DGEVIDRRYEDVTNKKRLDP--YAIG---ARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQG 149 (205)
Q Consensus 92 ~ge~~~~~~~~~~~~~~~d~--~~iG---~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g 149 (205)
... +.....+.....+.. ..+- ..|=.+|=..++|+.|.|+.+|||+..++++++.
T Consensus 193 ~d~--~~~~e~~~~~~~L~~~l~~L~eREr~Vi~lry~e~~Tl~EIa~~lGiSreRVrQIe~~ 253 (263)
T PRK07122 193 GDV--DAGLDHIENREALRPLLAALPERERTVLVLRFFESMTQTQIAERVGISQMHVSRLLAK 253 (263)
T ss_pred CCC--CHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 697--6428999999999999975999999999999569998999999989799999999999
No 80
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=96.14 E-value=0.0062 Score=37.95 Aligned_cols=40 Identities=18% Similarity=0.223 Sum_probs=28.4
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHH
Q ss_conf 2983899999977999999997414889998999999998
Q gi|254781218|r 125 KGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQV 164 (205)
Q Consensus 125 ~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~ 164 (205)
+-|+++++|+.+|++.+|||+.-+|+..-+..-++.+...
T Consensus 362 kPL~lkdiA~~lglheSTVSRav~~Kyi~tp~Gi~~lk~F 401 (475)
T PRK12469 362 KPLVLRDVAEELGLHESTVSRATGNKYMATPRGTFEFKHF 401 (475)
T ss_pred CCCCHHHHHHHHCCCCCHHHHHHCCCEECCCCCEEEHHHH
T ss_conf 6734999999819982037688627502379854669986
No 81
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=96.11 E-value=0.069 Score=31.47 Aligned_cols=102 Identities=20% Similarity=0.207 Sum_probs=69.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH-
Q ss_conf 9889999984899999998877998889999999999828999996145322100002321345546777999999999-
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRK- 123 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~- 123 (205)
|+.+++|..+|++.|||||.=+++.--+..-+..|...|-..+..=-+|+..+ ..+|-++|+++-.
T Consensus 331 L~LrdvA~~i~~HESTISRai~nKy~~tprG~feLk~FFs~~i~s~~gg~~~S-------------~~~Ik~~Ik~lI~~ 397 (444)
T COG1508 331 LVLRDVADEIGMHESTISRAITNKYLATPRGLFELKYFFSSSLASSEGGEASS-------------TEAIKALIKKLIEA 397 (444)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCEEEHHHHHHHHCCCCCCCCCCC-------------HHHHHHHHHHHHHH
T ss_conf 31999998837128889999825410488633448988777416788876444-------------89999999998753
Q ss_pred ---HCCCCHHHHHHHH-----CCCHHHHHHHHCCCCCCCHHHHH
Q ss_conf ---7298389999997-----79999999974148899989999
Q gi|254781218|r 124 ---DKGMSQIEFGKLL-----GMPNSTLSNYEQGRTIPEIKPAR 159 (205)
Q Consensus 124 ---~~glsq~elA~~l-----gis~~tis~~E~g~~~Ps~~~l~ 159 (205)
.+-+|-..+++++ .|++.|+.+|-..-++|+...-+
T Consensus 398 E~~~~pLSD~kIa~lLkekGi~iARRTVAKYRe~L~I~sS~~Rk 441 (444)
T COG1508 398 EDKKKPLSDSKIAELLKEKGIDVARRTVAKYREELNIPSSSQRK 441 (444)
T ss_pred CCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCHHHHH
T ss_conf 16778887899999999719842588599999880899565540
No 82
>KOG3802 consensus
Probab=96.05 E-value=0.055 Score=32.07 Aligned_cols=126 Identities=17% Similarity=0.193 Sum_probs=75.6
Q ss_pred HHHHHHHHHHHHHHHHHCCCCHHHHHHHHC------CCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCC
Q ss_conf 999999999999999985998899999848------99999998877998889999999999828999996145322100
Q gi|254781218|r 26 RQYWKDVGTRIKDIRKANNKTQKEMAIGAN------QLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRR 99 (205)
Q Consensus 26 ~~~~~~iG~rik~lR~~~gltQ~elA~~~g------is~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~ 99 (205)
.+-.+.+++.+|..|...|+||.+++.++| .|+.+|+|+|.= ..|...+.+|--.|+ -||=.-|.....
T Consensus 205 leELEqFAK~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEAL--qLSFKNMCKLKPLL~---KWLeEAes~~~~ 279 (398)
T KOG3802 205 LEELEQFAKTFKQRRIKLGFTQADVGLALGALYGNVFSQTTICRFEAL--QLSFKNMCKLKPLLE---KWLEEAESREST 279 (398)
T ss_pred HHHHHHHHHHHHHHEECCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHH--CCCHHHHHHHHHHHH---HHHHHHHCCCCC
T ss_conf 999999999987650003644267888987650764430266676762--547787766379999---999998603345
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHH
Q ss_conf 00232134554677799999999972983899999977999999997414889998999999998289999
Q gi|254781218|r 100 YEDVTNKKRLDPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLD 170 (205)
Q Consensus 100 ~~~~~~~~~~d~~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d 170 (205)
.....-. .|+.-- |+++.-|=.|... +..+.+.--..-.|+.+.+-.||+-|+..-|
T Consensus 280 -~~~~~~e-----~i~a~~---RkRKKRTSie~~v-----r~aLE~~F~~npKPt~qEIt~iA~~L~leKE 336 (398)
T KOG3802 280 -GSPNSIE-----KIGAQS---RKRKKRTSIEVNV-----RGALEKHFLKNPKPTSQEITHIAESLQLEKE 336 (398)
T ss_pred -CCCCCHH-----HHHCCC---CCCCCCCCEEHHH-----HHHHHHHHHHCCCCCHHHHHHHHHHHCCCCC
T ss_conf -7777788-----861343---3344345210889-----9999999986889988999999998466643
No 83
>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=96.05 E-value=0.003 Score=39.89 Aligned_cols=25 Identities=32% Similarity=0.239 Sum_probs=18.5
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 8599889999984899999998877
Q gi|254781218|r 42 ANNKTQKEMAIGANQLESAVNLFEN 66 (205)
Q Consensus 42 ~~gltQ~elA~~~gis~~~is~~E~ 66 (205)
...-||.|.|+.+|||+|+|||||+
T Consensus 193 ~~~~tQREIA~~LgISRSYVSRIEK 217 (228)
T TIGR02846 193 GREKTQREIAKILGISRSYVSRIEK 217 (228)
T ss_pred CCCCCHHHHHHHHCCCCHHHHHHHH
T ss_conf 8954178998770865004548889
No 84
>pfam08667 BetR BetR domain. This family includes an N-terminal helix-turn-helix domain.
Probab=96.03 E-value=0.055 Score=32.08 Aligned_cols=63 Identities=8% Similarity=-0.028 Sum_probs=58.0
Q ss_pred HHHHHHHHHHHHHCCCCHH----HHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHC
Q ss_conf 9999999999998599889----99998489999999887799888999999999982899999614
Q gi|254781218|r 30 KDVGTRIKDIRKANNKTQK----EMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYD 92 (205)
Q Consensus 30 ~~iG~rik~lR~~~gltQ~----elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ 92 (205)
.-|.+|+|++-...|+.-. .++..+|+|.|...+==+|...=.++.+.+++.+|++++..||+
T Consensus 4 ~~ia~rvr~lL~r~GI~kRqh~s~is~iL~LSfS~a~RKLkG~spW~l~Ql~kVA~~fg~~~a~L~~ 70 (146)
T pfam08667 4 LIVAERVRKLLTRTGIAERQHNTTIANILGLSFSQAYRKLKGSIPWNLAQLQKVAQYFGVPAAILLI 70 (146)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHC
T ss_conf 8999999999986399756778899999787489887873589974499999999995979999927
No 85
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=95.90 E-value=0.084 Score=30.95 Aligned_cols=43 Identities=21% Similarity=0.392 Sum_probs=32.7
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 99999999729838999999779999999974148899989999999982
Q gi|254781218|r 116 ARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVT 165 (205)
Q Consensus 116 ~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~l 165 (205)
+.+-.+|-..++||+|.|+.+|||.+.+|+++. ..+.+|-+.|
T Consensus 202 k~Vl~l~y~eelt~kEI~~~LgISes~VSql~k-------kai~kLr~~l 244 (247)
T COG1191 202 KLVLVLRYKEELTQKEIAEVLGISESRVSRLHK-------KAIKKLRKEL 244 (247)
T ss_pred HHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHH-------HHHHHHHHHH
T ss_conf 999999997015799999994914989999999-------9999999986
No 86
>pfam07900 DUF1670 Protein of unknown function (DUF1670). The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=95.83 E-value=0.02 Score=34.81 Aligned_cols=94 Identities=18% Similarity=0.273 Sum_probs=62.9
Q ss_pred CCCHHHHHHHHCCCHHHHHHH------HCCCCCC----------CHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHH
Q ss_conf 998899999848999999988------7799888----------999999999982899999614532210000232134
Q gi|254781218|r 44 NKTQKEMAIGANQLESAVNLF------ENGMCST----------SIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKK 107 (205)
Q Consensus 44 gltQ~elA~~~gis~~~is~~------E~G~~~p----------si~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~ 107 (205)
=|||+++|..+++|..+|+++ |+|..-| ++.+=-.+++.| +.| ...+++....
T Consensus 105 lLT~~Dla~LL~~S~~TI~~~ik~ye~~~g~vvPtRG~i~DiGp~vTHK~iiv~~~-------lkg----~~t~eiaR~t 173 (220)
T pfam07900 105 LLTHADIAILLGVSTTTISRHVKEYEERTGEVVPTRGIIKDIGPSVTHKRKIVELY-------LKG----YQTSEIARLT 173 (220)
T ss_pred EEEHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHH-------HCC----CCHHHHHHHH
T ss_conf 51176699998898889999999999970966357872034587620689999999-------826----8888999985
Q ss_pred HHHHHHHHHHHHHH-----HHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 55467779999999-----997298389999997799999999741
Q gi|254781218|r 108 RLDPYAIGARLKSI-----RKDKGMSQIEFGKLLGMPNSTLSNYEQ 148 (205)
Q Consensus 108 ~~d~~~iG~rLk~l-----R~~~glsq~elA~~lgis~~tis~~E~ 148 (205)
.+++.+|-.-|+.. -..+||+-.+.|-.+|+|...+..|+.
T Consensus 174 ~HS~~AvdRYi~df~rV~~l~~kg~~~~ei~~~tG~s~~lv~eY~~ 219 (220)
T pfam07900 174 NHSPESIDRYIKDFTRVEKLTEKGMSEEEIRYITGISERLVEEYVE 219 (220)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 3798999999987689999998678799999997765899999972
No 87
>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=95.83 E-value=0.0082 Score=37.19 Aligned_cols=118 Identities=22% Similarity=0.329 Sum_probs=72.6
Q ss_pred HHHHHCCC-HHHHHHHHH------HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf 33100015-668999999------99999999998599889999984899999998877998889999999999828999
Q gi|254781218|r 15 QEYTLIIT-PEIRQYWKD------VGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISF 87 (205)
Q Consensus 15 ~~~~~~~~-~~~~~~~~~------iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~ 87 (205)
--|+|||= +|++=|-.+ |--|+|+++-+-+-..++|+..+|= .|++ -.||+.++||.
T Consensus 58 ~tyAVPtI~GEIkR~fRD~~W~vrVPRrlkEl~~~~~~a~eeL~~~lgR-------------~Pt~---~EiAe~L~~s~ 121 (229)
T TIGR02980 58 STYAVPTIMGEIKRFFRDDTWAVRVPRRLKELRLKINKATEELTQRLGR-------------SPTV---AEIAEELGVSE 121 (229)
T ss_pred CCCCCCCEEEEEEEEEECCCCEEECCHHHHHHHHHHHHHHHHHHHHHCC-------------CCCH---HHHHHHHCCCH
T ss_conf 6410460233231334248732660513898899999999999998288-------------9887---89998858899
Q ss_pred HHHHCC----CC-----CCCCC---CCCCCHHHHHH--------------HHHHHHHH----------HHHHHCCCCHHH
Q ss_conf 996145----32-----21000---02321345546--------------77799999----------999972983899
Q gi|254781218|r 88 DWIYDG----EV-----IDRRY---EDVTNKKRLDP--------------YAIGARLK----------SIRKDKGMSQIE 131 (205)
Q Consensus 88 d~Ll~g----e~-----~~~~~---~~~~~~~~~d~--------------~~iG~rLk----------~lR~~~glsq~e 131 (205)
++.+-+ .. +|... .|-...+.+|. .++=.-|. .+|=-.+|||.|
T Consensus 122 EEv~~aleA~~~Y~~~Sld~~~~a~~dg~~~~L~D~lG~~D~~~e~~~~~~aLk~~l~~LpeRER~il~lRFf~~~TQ~e 201 (229)
T TIGR02980 122 EEVVEALEAGNSYSALSLDATIEADDDGDPIALLDTLGDEDDALETVEDRLALKPLLAALPERERRILLLRFFEDKTQSE 201 (229)
T ss_pred HHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCHHHCEEEEEEEECCCCHHH
T ss_conf 99999998654178611200045588884245664440224326789999999999850790270761000106977899
Q ss_pred HHHHHCCCHHHHHHHHC
Q ss_conf 99997799999999741
Q gi|254781218|r 132 FGKLLGMPNSTLSNYEQ 148 (205)
Q Consensus 132 lA~~lgis~~tis~~E~ 148 (205)
.|+.+|||+..+|++++
T Consensus 202 iA~~lGiSQMhVSRl~~ 218 (229)
T TIGR02980 202 IAERLGISQMHVSRLLR 218 (229)
T ss_pred HHHHCCCCHHHHHHHHH
T ss_conf 99781843678899999
No 88
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=95.76 E-value=0.12 Score=29.95 Aligned_cols=125 Identities=15% Similarity=0.175 Sum_probs=64.6
Q ss_pred HHHHHHHHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHCCCCCC---CHHHHHHH--HHHHCCCHHHHHCCCCCC
Q ss_conf 8999999999999999985--9988999998489999999887799888---99999999--998289999961453221
Q gi|254781218|r 25 IRQYWKDVGTRIKDIRKAN--NKTQKEMAIGANQLESAVNLFENGMCST---SIRYALYL--RNEYEISFDWIYDGEVID 97 (205)
Q Consensus 25 ~~~~~~~iG~rik~lR~~~--gltQ~elA~~~gis~~~is~~E~G~~~p---si~~l~~l--a~~~~vs~d~Ll~ge~~~ 97 (205)
+.+....+-.-.+.++... .-|-.++|+.+|++...+..+....... |++.-... -..-++++...+.++..+
T Consensus 105 ~~~~~~ki~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~d~~~~~~l~d~i~d~~~~ 184 (257)
T PRK05911 105 VHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPSQSDDEAGLALEERIADERAE 184 (257)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCEECCCCCCCCCCCCCCCCCHHHHCCCCCCC
T ss_conf 99999999999999999868899999999883979999999998535522230578888788887653077746798889
Q ss_pred CCCCCCCCHHHH--HHHH---HH---HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf 000023213455--4677---79---9999999972983899999977999999997414
Q gi|254781218|r 98 RRYEDVTNKKRL--DPYA---IG---ARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQG 149 (205)
Q Consensus 98 ~~~~~~~~~~~~--d~~~---iG---~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g 149 (205)
.....+...... ...+ +- ..|-.+|-..++|++|.|+.+|+|+..+++++..
T Consensus 185 ~~~~~~~~~~~~~~L~~al~~L~erEr~Ii~lry~e~~Tl~EIg~~lgvS~eRVrQi~~~ 244 (257)
T PRK05911 185 TGYDVVDKKEFSSILANAILALEEKERKVMALYYYEELVLKEIGKILGVSESRVSQIHSK 244 (257)
T ss_pred CHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 989999999999999999865899999999987489878999998979889999999999
No 89
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=95.72 E-value=0.022 Score=34.57 Aligned_cols=53 Identities=15% Similarity=0.108 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHC------CCHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 999999999999985998899999848------9999999887799888999999999982
Q gi|254781218|r 29 WKDVGTRIKDIRKANNKTQKEMAIGAN------QLESAVNLFENGMCSTSIRYALYLRNEY 83 (205)
Q Consensus 29 ~~~iG~rik~lR~~~gltQ~elA~~~g------is~~~is~~E~G~~~psi~~l~~la~~~ 83 (205)
.+.+...+|..|...|+||.++|.++| .|+++|+++|+=. .|...+.+|--.+
T Consensus 9 le~Fa~~fk~rRi~LG~TQ~dVG~aL~~l~g~~~SQttIcRFE~l~--LS~kn~~kLkPiL 67 (75)
T smart00352 9 LEAFAKTFKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEALQ--LSFKNMCKLKPLL 67 (75)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHCC--CCHHHHHHHHHHH
T ss_conf 9999999999898737759999999998618643146888988605--4798899889999
No 90
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=95.69 E-value=0.16 Score=29.28 Aligned_cols=125 Identities=17% Similarity=0.155 Sum_probs=60.3
Q ss_pred HHHHHHHHHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHCC---CCCCCHHHHHHHHHH-HCCCHHHHHCCCCCCC
Q ss_conf 899999999999999998--5998899999848999999988779---988899999999998-2899999614532210
Q gi|254781218|r 25 IRQYWKDVGTRIKDIRKA--NNKTQKEMAIGANQLESAVNLFENG---MCSTSIRYALYLRNE-YEISFDWIYDGEVIDR 98 (205)
Q Consensus 25 ~~~~~~~iG~rik~lR~~--~gltQ~elA~~~gis~~~is~~E~G---~~~psi~~l~~la~~-~~vs~d~Ll~ge~~~~ 98 (205)
+.+....+...++.+... +.-|.+++|+.+|++...+..+... ....|++..+..... =++++-..+.++....
T Consensus 109 ~~~~~~ki~~~~~~l~~~~gr~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~~~~d~l~d~~~~~ 188 (261)
T PRK06288 109 VRQKARQVERAIAMLEAKLGRTPTDDEIAKELGISLEEYHSLLSKVSGTSVVSLNDLLFLGDENDEVSLMDTLEDPAAMN 188 (261)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCC
T ss_conf 99999999999999999868999878888781999999999999972699747677765799986430878705889899
Q ss_pred CCCCCCCHHHH--HHHH---H---HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf 00023213455--4677---7---99999999972983899999977999999997414
Q gi|254781218|r 99 RYEDVTNKKRL--DPYA---I---GARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQG 149 (205)
Q Consensus 99 ~~~~~~~~~~~--d~~~---i---G~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g 149 (205)
+.......... ...+ + -..|=.+|-..++|+.+.|+.+|||+..++++|..
T Consensus 189 p~~~~e~~~~~~~l~~~l~~L~erEr~Il~lry~e~~Tl~eIa~~lgiS~eRVrQie~~ 247 (261)
T PRK06288 189 PDEIIEKEEIKRVIVEAINTLPEREKKVITLYYYEDLTLKEIGEVLGVTESRISQIHTK 247 (261)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 99999999999999999870899999999998079988999999979789999999999
No 91
>PHA00542 putative Cro-like protein
Probab=95.52 E-value=0.038 Score=33.05 Aligned_cols=49 Identities=18% Similarity=0.251 Sum_probs=41.9
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCC-CCCHHHHHHHHHHH
Q ss_conf 99999997298389999997799999999741488-99989999999982
Q gi|254781218|r 117 RLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRT-IPEIKPARKIKQVT 165 (205)
Q Consensus 117 rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~-~Ps~~~l~kIa~~l 165 (205)
.|-......|++|.+.++.+|+++.+++++..|+. .|.+..+.++...+
T Consensus 22 E~V~aLi~~G~tQ~qI~~~tgv~QpsisRilsGk~kDpR~s~v~~L~~L~ 71 (82)
T PHA00542 22 ELVCALIRAGWSQEQIADATDVSQPTICRIYSGRHKDPRYSVVEKLRHLV 71 (82)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHCCCCCCCCCHHHHHHHHHH
T ss_conf 99999998225699999860877036899980887897206999999998
No 92
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=95.46 E-value=0.075 Score=31.24 Aligned_cols=56 Identities=16% Similarity=0.179 Sum_probs=43.3
Q ss_pred HHHHHHHHHH---HHH-CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCC
Q ss_conf 9999999999---998-5998899999848999999988779988899999999998289
Q gi|254781218|r 30 KDVGTRIKDI---RKA-NNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEI 85 (205)
Q Consensus 30 ~~iG~rik~l---R~~-~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~v 85 (205)
+.+..|++-. |.- .-+|-+||++.+|+..+.++||-||..-||.+....|-+.++-
T Consensus 5 e~~~~~L~av~~LR~lK~~~tykELs~~~gip~s~L~RYv~g~vlPs~e~A~~i~~~l~~ 64 (238)
T PRK08558 5 EKLRLQLDAVRYLRSLKKTYTYEELSSILGLPESVLSRYVNGHVLPSVERAREIVEKLKP 64 (238)
T ss_pred HHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHH
T ss_conf 899999999999999850268999998879799998505348878758999999998421
No 93
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=95.43 E-value=0.21 Score=28.43 Aligned_cols=113 Identities=14% Similarity=0.111 Sum_probs=62.5
Q ss_pred HHHHHHHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCC
Q ss_conf 999999999999999985--998899999848999999988779988899999999998289999961453221000023
Q gi|254781218|r 26 RQYWKDVGTRIKDIRKAN--NKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDV 103 (205)
Q Consensus 26 ~~~~~~iG~rik~lR~~~--gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~ 103 (205)
++..+.+..-.+.++... .=|-.++|+.+|++...+..+...... ..-+|+|..+.++.........
T Consensus 95 r~~~~ki~~a~~~l~~~lgr~Pt~~EiA~~l~is~~~v~~~~~~~~~-----------~~~~sld~~~~~e~~~~~~~~~ 163 (229)
T PRK12427 95 RQKTHKTNEAIRQIAKRLGHEPNFEEISAELNLTADEYQEYLLLENA-----------GAMESLDEILALEAHNDILQSR 163 (229)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCC-----------CCCCCCCCCCCCCCCCCCCCCC
T ss_conf 99999999999999998588999999998919999999999998736-----------6875723344578876545676
Q ss_pred C-CHHHH----HHHH---HHHH---HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf 2-13455----4677---7999---99999972983899999977999999997414
Q gi|254781218|r 104 T-NKKRL----DPYA---IGAR---LKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQG 149 (205)
Q Consensus 104 ~-~~~~~----d~~~---iG~r---Lk~lR~~~glsq~elA~~lgis~~tis~~E~g 149 (205)
. ..... ...+ +.+| +=.++=..++|++|.|+.+|+|.+.++++++.
T Consensus 164 ~~~e~~~~~~~L~~al~~L~erEr~Vi~l~y~e~ltlkEIa~~LgvS~~RVsQi~~k 220 (229)
T PRK12427 164 DLEENIIIEDNLKQAISQLDEREQMILHLYYQQELSMKEIAQVLDLTEARICQLNKK 220 (229)
T ss_pred CHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 646789999999999971999999999998058998999999979889999999999
No 94
>pfam00157 Pou Pou domain - N-terminal to homeobox domain.
Probab=95.43 E-value=0.021 Score=34.65 Aligned_cols=53 Identities=15% Similarity=0.142 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHCC------CHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 9999999999999859988999998489------999999887799888999999999982
Q gi|254781218|r 29 WKDVGTRIKDIRKANNKTQKEMAIGANQ------LESAVNLFENGMCSTSIRYALYLRNEY 83 (205)
Q Consensus 29 ~~~iG~rik~lR~~~gltQ~elA~~~gi------s~~~is~~E~G~~~psi~~l~~la~~~ 83 (205)
.+......|..|...|+||.+++.++|. |+++|+++|+=. .|.....+|--.+
T Consensus 9 le~Fa~~fk~rRi~LG~TQ~dVg~al~~l~G~~~SQttIcRFE~l~--Ls~kn~~kLkP~L 67 (75)
T pfam00157 9 LEQFAKEFKQRRIKLGYTQADVGLALGALYGPVFSQTTICRFEALQ--LSFKNMCKLKPLL 67 (75)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHCC--CCHHHHHHHHHHH
T ss_conf 9999999999898737759999999998708654235888888504--4799899889999
No 95
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=95.42 E-value=0.025 Score=34.24 Aligned_cols=61 Identities=15% Similarity=0.035 Sum_probs=44.5
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCC-CCCCHHHHHHHHHHHCCCHH
Q ss_conf 99999999999999859988999998489999999887799-88899999999998289999
Q gi|254781218|r 28 YWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGM-CSTSIRYALYLRNEYEISFD 88 (205)
Q Consensus 28 ~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~-~~psi~~l~~la~~~~vs~d 88 (205)
..-.++..|+.+-++++++|++.|+.+||+++.+|.+-+|+ ...+++-|+....+.+-.++
T Consensus 25 ir~~l~~~i~~~i~q~~l~Q~qiae~lgV~qprvS~l~~gk~~~fs~dkLvtml~~~g~ei~ 86 (91)
T COG5606 25 IRSALMMAIKQWIEQAALSQAQIAELLGVTQPRVSDLARGKIQDFSIDKLVTMLARAGQEID 86 (91)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCHHHHHHHHHHHHHHHCCCCCC
T ss_conf 99999999999999978779999998388873188998361457669999999997598552
No 96
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=95.16 E-value=0.034 Score=33.37 Aligned_cols=32 Identities=19% Similarity=0.177 Sum_probs=26.8
Q ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCC
Q ss_conf 999998599889999984899999998877998
Q gi|254781218|r 37 KDIRKANNKTQKEMAIGANQLESAVNLFENGMC 69 (205)
Q Consensus 37 k~lR~~~gltQ~elA~~~gis~~~is~~E~G~~ 69 (205)
=.+| .+|+||.+.|..+|.|++.||.+|+.-+
T Consensus 13 L~lR-~~G~tQ~eIA~~lgTSraNvs~iEk~A~ 44 (139)
T PRK03975 13 LRLR-KRGLTQQEIADILGTSRANISIIEKRAR 44 (139)
T ss_pred HHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 9999-8289799999997732889999999999
No 97
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=94.96 E-value=0.3 Score=27.56 Aligned_cols=127 Identities=15% Similarity=0.144 Sum_probs=59.5
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHH-CCCC--CCCHHHHHHHH-HHHCCCHHHHHCC
Q ss_conf 015668999999999999999985--9988999998489999999887-7998--88999999999-9828999996145
Q gi|254781218|r 20 IITPEIRQYWKDVGTRIKDIRKAN--NKTQKEMAIGANQLESAVNLFE-NGMC--STSIRYALYLR-NEYEISFDWIYDG 93 (205)
Q Consensus 20 ~~~~~~~~~~~~iG~rik~lR~~~--gltQ~elA~~~gis~~~is~~E-~G~~--~psi~~l~~la-~~~~vs~d~Ll~g 93 (205)
-++..+.+....|-.-...+.... .-|-+++|+.+|++...|...- .+.. ..|++..+.-. +...+++...+..
T Consensus 106 r~P~~~~~~~~ki~~~~~~l~~~~~r~pt~~eiA~~l~~s~e~v~~~l~~~~~~~~~Sld~~~~~d~d~~~~~~~d~~~~ 185 (257)
T PRK08583 106 HVPRRIKELGPKIKKAVDELTDELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSDGSTVTLLDIVGQ 185 (257)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHCCCC
T ss_conf 35499999988899999999998089987999998959599999999997516897027888877888771204330489
Q ss_pred CCCCCCCCCCCCHHHHHHHH---HHHHHH---HHHHHCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf 32210000232134554677---799999---999972983899999977999999997414
Q gi|254781218|r 94 EVIDRRYEDVTNKKRLDPYA---IGARLK---SIRKDKGMSQIEFGKLLGMPNSTLSNYEQG 149 (205)
Q Consensus 94 e~~~~~~~~~~~~~~~d~~~---iG~rLk---~lR~~~glsq~elA~~lgis~~tis~~E~g 149 (205)
. +..+... ........+ +..|=+ .+|-..++|+.+.|+.+|||+..++++++.
T Consensus 186 ~--e~~~e~~-e~~~~l~~~l~~L~erEr~Ii~lry~~~~t~~eIa~~lGiS~eRVrQi~~~ 244 (257)
T PRK08583 186 Q--EDGYELT-EQRMILEKILPVLSDREKSIIQCTFIENLSQKETGERLGISQMHVSRLQRQ 244 (257)
T ss_pred C--CCHHHHH-HHHHHHHHHHHCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 6--6247899-999999999954999999999999579999999999989699999999999
No 98
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=94.95 E-value=0.16 Score=29.29 Aligned_cols=127 Identities=14% Similarity=0.163 Sum_probs=60.6
Q ss_pred HHHHHHHHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHCCCCC---CCHHHHHHHHHHHCCCHHHHHCCCCC--C
Q ss_conf 8999999999999999985--998899999848999999988779988---89999999999828999996145322--1
Q gi|254781218|r 25 IRQYWKDVGTRIKDIRKAN--NKTQKEMAIGANQLESAVNLFENGMCS---TSIRYALYLRNEYEISFDWIYDGEVI--D 97 (205)
Q Consensus 25 ~~~~~~~iG~rik~lR~~~--gltQ~elA~~~gis~~~is~~E~G~~~---psi~~l~~la~~~~vs~d~Ll~ge~~--~ 97 (205)
+.+..+.|...++.+.... .-|.+++|+.+|++...|...-..... .|++.. ..+-+.+...... +
T Consensus 90 ~~~~~~~i~~~~~~l~~~~~r~pt~~eia~~l~~s~e~v~~~~~~~~~~~~~sld~~-------~~~~~~~~~~~~~~~~ 162 (234)
T PRK06986 90 VRRNAREVADAIRELEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDDL-------GESGELLTDEDQSEHE 162 (234)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCC-------CCCCCCCCCCCCCCCC
T ss_conf 999999999999999998787998999998959499999999998505778687767-------7664311122245789
Q ss_pred CCCCCCCCHHHHHH--H---HHH---HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 00002321345546--7---779---99999999729838999999779999999974148899989999999982
Q gi|254781218|r 98 RRYEDVTNKKRLDP--Y---AIG---ARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVT 165 (205)
Q Consensus 98 ~~~~~~~~~~~~d~--~---~iG---~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~l 165 (205)
.+..++........ . .+- ..|-.+|-..++|+.|.|+.+|+|+..++++|+. .+.++-+.|
T Consensus 163 ~~~~~~~~~~~~~~l~~~l~~L~~rEr~Ii~l~y~~~~tl~eIa~~lgiS~eRVrQie~~-------AL~kLR~~L 231 (234)
T PRK06986 163 DPLQQLEDEELREALVEAIEKLPEREQLVLSLYYDEELNLKEIGAVLGVSESRVSQIHSQ-------AIKRLRARL 231 (234)
T ss_pred CHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH-------HHHHHHHHH
T ss_conf 999999999999999999980999999999987389989999999979789999999999-------999999987
No 99
>pfam04814 HNF-1_N Hepatocyte nuclear factor 1 (HNF-1), N terminus. This family consists of the N terminus of homeobox-containing transcription factor HNF-1. This region contains a dimerization sequence and an acidic region that may be involved in transcription activation. Mutations and the common Ala/Val 98 polymorphism in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3).
Probab=94.92 E-value=0.11 Score=30.25 Aligned_cols=54 Identities=22% Similarity=0.260 Sum_probs=44.0
Q ss_pred HHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHH
Q ss_conf 554677799999999972983899999977999999997414889998999999
Q gi|254781218|r 108 RLDPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKI 161 (205)
Q Consensus 108 ~~d~~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kI 161 (205)
..|+-.+.+-||..+..++++|.++++.+|++++.+|+|.|-..-.....-..+
T Consensus 110 ~~d~~~v~~~Ik~~m~~h~ipQ~~vv~~TGlnQS~lSq~LnkGt~Mk~~kr~al 163 (177)
T pfam04814 110 REDPWRVAKMIKSYMQQHNIPQREVVDATGLNQSHLSQHLNKGTPMKTQKRAAL 163 (177)
T ss_pred HHCHHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHCCCCCHHHHHHHH
T ss_conf 728499999999999876884667876106559999999966884078999999
No 100
>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=94.79 E-value=0.015 Score=35.60 Aligned_cols=31 Identities=26% Similarity=0.137 Sum_probs=23.1
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 9999998599889999984899999998877
Q gi|254781218|r 36 IKDIRKANNKTQKEMAIGANQLESAVNLFEN 66 (205)
Q Consensus 36 ik~lR~~~gltQ~elA~~~gis~~~is~~E~ 66 (205)
|=.+|=-.++||.|+|+.+||||=+|||+|+
T Consensus 188 il~lRFf~~~TQ~eiA~~lGiSQMhVSRl~~ 218 (229)
T TIGR02980 188 ILLLRFFEDKTQSEIAERLGISQMHVSRLLR 218 (229)
T ss_pred EEEEEEECCCCHHHHHHHCCCCHHHHHHHHH
T ss_conf 6100010697789999781843678899999
No 101
>PRK09526 lacI lac repressor; Reviewed
Probab=94.69 E-value=0.058 Score=31.97 Aligned_cols=48 Identities=17% Similarity=-0.032 Sum_probs=37.6
Q ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHH---HHHHHCCCHH
Q ss_conf 98599889999984899999998877998889999999---9998289999
Q gi|254781218|r 41 KANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALY---LRNEYEISFD 88 (205)
Q Consensus 41 ~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~---la~~~~vs~d 88 (205)
+++..|-+++|+.+|+|.+|||++=||....|-++-.+ .++.++-.++
T Consensus 2 ~~k~~TikDIA~~agVS~sTVSrvLn~~~~vs~~tr~rV~~~a~elgY~pn 52 (342)
T PRK09526 2 KSKPVTLYDVARYAGVSYQTVSRVLNQASHVSAKTREKVEAAMAELNYVPN 52 (342)
T ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCC
T ss_conf 989976999999989699999999789799999999999999998399978
No 102
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=94.68 E-value=0.28 Score=27.70 Aligned_cols=117 Identities=16% Similarity=0.151 Sum_probs=54.4
Q ss_pred HHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHCCCCC---CCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCH
Q ss_conf 99999999998--5998899999848999999988779988---899999999998289999961453221000023213
Q gi|254781218|r 32 VGTRIKDIRKA--NNKTQKEMAIGANQLESAVNLFENGMCS---TSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNK 106 (205)
Q Consensus 32 iG~rik~lR~~--~gltQ~elA~~~gis~~~is~~E~G~~~---psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~ 106 (205)
|-.-++.+... +.-|-+++|+.+|+++..|..+-+.... .|++....- ..-+.++...+.++....+.......
T Consensus 107 i~~~~~~l~~~~gr~ps~~eia~~lg~s~~~v~~~~~~~~~~~~~Sld~~~~~-~~~~~~~~~~~~d~~~~~pe~~~~~~ 185 (250)
T PRK07670 107 VEAAIEKLEQRYMRNVTPSEVAAELGMSEEEVVTTMNEGFFANLLSIDEKLHD-QDDGENVQVMIRDDKAVTPEEKLVKE 185 (250)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCCC-CCCCCHHHHHHHCCCCCCHHHHHHHH
T ss_conf 99999999998389998889987719999999999998754798036777778-88850477888524679999999999
Q ss_pred HHHHH--H---HHHHH---HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf 45546--7---77999---99999972983899999977999999997414
Q gi|254781218|r 107 KRLDP--Y---AIGAR---LKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQG 149 (205)
Q Consensus 107 ~~~d~--~---~iG~r---Lk~lR~~~glsq~elA~~lgis~~tis~~E~g 149 (205)
..... . .+-.| |=.+|-..++|+.+.|+.+|||+..+++++..
T Consensus 186 ~~~~~L~~~l~~L~~rEr~Vl~l~y~e~~Tl~eIa~~lgvS~erVrQi~~~ 236 (250)
T PRK07670 186 ELIEQLAEKIKELNEKEQLVISLFYKEELTLTEIGQVLNLSTSRISQIHSK 236 (250)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 999999999855899999999997489868999999989799999999999
No 103
>COG3636 Predicted transcriptional regulator [Transcription]
Probab=94.63 E-value=0.16 Score=29.23 Aligned_cols=56 Identities=20% Similarity=0.229 Sum_probs=45.0
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf 7779999999997298389999997799999999741488999899999999828999
Q gi|254781218|r 112 YAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHL 169 (205)
Q Consensus 112 ~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~ 169 (205)
.-|..-+-.+-..+||+| +|+..|+++..+.+-.+....|++.++-++.+++|.-+
T Consensus 37 a~i~~alg~var~~GMsq--vA~~aGlsRe~LYkaLS~~GNPtf~Til~V~kAlG~rl 92 (100)
T COG3636 37 ALIAAALGVVARSRGMSQ--VARKAGLSREGLYKALSPGGNPTFDTILAVLKALGLRL 92 (100)
T ss_pred HHHHHHHHHHHHHCCHHH--HHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHCCCEE
T ss_conf 999999999998657899--99994966999999847899975899999999808654
No 104
>PRK09492 treR trehalose repressor; Provisional
Probab=94.61 E-value=0.09 Score=30.77 Aligned_cols=48 Identities=23% Similarity=0.004 Sum_probs=37.4
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHH---HHHHHHHCCCHHH
Q ss_conf 85998899999848999999988779988899999---9999982899999
Q gi|254781218|r 42 ANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYA---LYLRNEYEISFDW 89 (205)
Q Consensus 42 ~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l---~~la~~~~vs~d~ 89 (205)
.+.+|.+++|+.+|+|.+|||++=||....|-++- .+.++.++-.++-
T Consensus 2 ~kkvTikDIA~~aGVS~aTVSrvLn~~~~vs~eTr~rV~~~a~elgY~Pn~ 52 (315)
T PRK09492 2 QNKLTIKDIARLSGVGKSTVSRVLNNEPKVSPRTRERVEAVINQHGFSPSK 52 (315)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCH
T ss_conf 898879999999897999999997898999999999999999996998077
No 105
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=94.60 E-value=0.075 Score=31.27 Aligned_cols=48 Identities=21% Similarity=0.115 Sum_probs=37.8
Q ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHH---HHHHHHHCCCHH
Q ss_conf 985998899999848999999988779988899999---999998289999
Q gi|254781218|r 41 KANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYA---LYLRNEYEISFD 88 (205)
Q Consensus 41 ~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l---~~la~~~~vs~d 88 (205)
+.+.+|.+++|+.+|||.+|||++=||....|-++- .+.++.++-.++
T Consensus 3 ~~kkvTi~dIA~~aGVS~aTVSrvLn~~~~Vs~eTr~rV~~aa~elgY~pn 53 (342)
T PRK10014 3 TAKKITIHDVALAAGVSVSTVSLVLSGKGRISTATGERVNQAIEELGFVRN 53 (342)
T ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCC
T ss_conf 999887999999989699999999779899999999999999999489978
No 106
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=94.55 E-value=0.091 Score=30.74 Aligned_cols=71 Identities=14% Similarity=0.157 Sum_probs=51.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH-----HCCCC--------CCCHHHHHHHHHHHCCCHHH
Q ss_conf 668999999999999999985998899999848999999988-----77998--------88999999999982899999
Q gi|254781218|r 23 PEIRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLF-----ENGMC--------STSIRYALYLRNEYEISFDW 89 (205)
Q Consensus 23 ~~~~~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~-----E~G~~--------~psi~~l~~la~~~~vs~d~ 89 (205)
++......+.-.++..+.-..|+||.|+|+++|+|+.+++++ +.|.. ..+.+.--.|.+.|++.--+
T Consensus 5 ~~~~~~~~~l~~~~A~lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I~i~~~~~~~~~Le~~L~~~fgL~~a~ 84 (321)
T COG2390 5 PDMLMEEERLLARAAWLYYVEGLTQSEIAERLGISRATVSRLLAKAREEGIVKISINSPVEGCLELEQQLKERFGLKEAI 84 (321)
T ss_pred CCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEEEECCCCCCHHHHHHHHHHHCCCCEEE
T ss_conf 30012689999999999984688799999883988999999999999879389996798765399999999965997699
Q ss_pred HHCC
Q ss_conf 6145
Q gi|254781218|r 90 IYDG 93 (205)
Q Consensus 90 Ll~g 93 (205)
...+
T Consensus 85 VVp~ 88 (321)
T COG2390 85 VVPS 88 (321)
T ss_pred EECC
T ss_conf 9748
No 107
>TIGR01321 TrpR trp operon repressor; InterPro: IPR013335 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan . The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit. This entry represents Trp repressors found in proteobacterial and chlamydial species.; GO: 0016564 transcription repressor activity, 0006355 regulation of transcription DNA-dependent.
Probab=94.46 E-value=0.071 Score=31.40 Aligned_cols=57 Identities=16% Similarity=0.253 Sum_probs=42.5
Q ss_pred HHHCCCHHHHHHHHHHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHH
Q ss_conf 100015668999999999999999985--998899999848999999988779988899999
Q gi|254781218|r 17 YTLIITPEIRQYWKDVGTRIKDIRKAN--NKTQKEMAIGANQLESAVNLFENGMCSTSIRYA 76 (205)
Q Consensus 17 ~~~~~~~~~~~~~~~iG~rik~lR~~~--gltQ~elA~~~gis~~~is~~E~G~~~psi~~l 76 (205)
+++..+++ -.++||.|++-++.-. ++||.|++.++|+|-.+|.|==|.....+.+.-
T Consensus 30 L~L~Lt~~---Er~dl~~R~~I~~~LL~~~~~QREi~~~lG~SiA~ITRGSn~Lk~~D~~~~ 88 (95)
T TIGR01321 30 LELLLTAD---EREDLGSRVRIVEELLEGEMSQREIAEKLGVSIATITRGSNALKALDPEFK 88 (95)
T ss_pred HHHHCCHH---HHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCHHHH
T ss_conf 99736863---799998799999999614897478888637616678787887516987889
No 108
>TIGR00721 tfx DNA-binding protein, Tfx family; InterPro: IPR004645 This is a family of Tfx DNA-binding proteins, which is restricted to the archaea. Homology among the members is strongest in the helix-turn-helix-containing N-terminal region. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.; GO: 0003677 DNA binding.
Probab=94.45 E-value=0.027 Score=33.99 Aligned_cols=28 Identities=21% Similarity=0.190 Sum_probs=24.8
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHHCCCC
Q ss_conf 8599889999984899999998877998
Q gi|254781218|r 42 ANNKTQKEMAIGANQLESAVNLFENGMC 69 (205)
Q Consensus 42 ~~gltQ~elA~~~gis~~~is~~E~G~~ 69 (205)
.+||+|++.|+.++.|++.||.+|+--.
T Consensus 19 ~kGl~Q~eIAk~LkTtRaNvS~iEkrA~ 46 (142)
T TIGR00721 19 EKGLKQKEIAKILKTTRANVSIIEKRAL 46 (142)
T ss_pred HCCCCHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf 3388878898772672013789888744
No 109
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=94.42 E-value=0.091 Score=30.73 Aligned_cols=36 Identities=17% Similarity=0.144 Sum_probs=14.8
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHH
Q ss_conf 298389999997799999999741488999899999
Q gi|254781218|r 125 KGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARK 160 (205)
Q Consensus 125 ~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~k 160 (205)
+.+|..|+|+.+|+|..|+|+..||....+.++..+
T Consensus 5 kkvTi~dIA~~aGVS~aTVSrvLn~~~~Vs~eTr~r 40 (342)
T PRK10014 5 KKITIHDVALAAGVSVSTVSLVLSGKGRISTATGER 40 (342)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHH
T ss_conf 988799999998969999999977989999999999
No 110
>PRK09492 treR trehalose repressor; Provisional
Probab=94.32 E-value=0.12 Score=29.98 Aligned_cols=45 Identities=11% Similarity=0.110 Sum_probs=23.2
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHH---HHHHCCCHH
Q ss_conf 983899999977999999997414889998999999---998289999
Q gi|254781218|r 126 GMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKI---KQVTKKHLD 170 (205)
Q Consensus 126 glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kI---a~~lgvs~d 170 (205)
.+|.+|+|+.+|+|..|+|+..||....+.++-++| ++.||..++
T Consensus 4 kvTikDIA~~aGVS~aTVSrvLn~~~~vs~eTr~rV~~~a~elgY~Pn 51 (315)
T PRK09492 4 KLTIKDIARLSGVGKSTVSRVLNNEPKVSPRTRERVEAVINQHGFSPS 51 (315)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCC
T ss_conf 887999999989799999999789899999999999999999699807
No 111
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor; InterPro: IPR000394 Sigma factors are bacterial transcription initiation factors that promote the attachment of the core RNA polymerase to specific initiation sites and are then released. They alter the specificity of promoter recognition. 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. The sigma-70 family has many different sigma factors (see the relevant entry IPR000943 from INTERPRO). The sigma-54 family consists exclusively of sigma-54 factor , required for the transcription of promoters that have a characteristic -24 and -12 consensus recognition element but which are devoid of the typical -10, -35 sequences recognized by the major sigma factors. The sigma-54 factor is also characterised by its interaction with ATP-dependent positive regulatory proteins that bind to upstream activating sequences. Structurally sigma-54 factors consist of three distinct regions: A relatively well conserved N-terminal glutamine-rich region of about 50 residues that contains a potential leucine zipper motif. A region of variable length which is not well conserved. A well conserved C-terminal region of about 350 residues that contains a second potential leucine zipper, a potential DNA-binding 'helix-turn-helix' motif and a perfectly conserved octapeptide whose function is not known. ; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0003899 DNA-directed RNA polymerase activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=94.19 E-value=0.02 Score=34.85 Aligned_cols=104 Identities=20% Similarity=0.174 Sum_probs=72.5
Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf 99859988999998489999999887799888999999999982899999614532210000232134554677799999
Q gi|254781218|r 40 RKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLK 119 (205)
Q Consensus 40 R~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk 119 (205)
+.-+=||.+++|..+|++.|||||.=+|+.--+-.-++.|-..|-=.+..=-.+ ...+..+|=..|+
T Consensus 361 ~~LkPL~L~~vA~el~~heSTiSRai~~KYl~T~~G~f~Lk~FFS~~v~~~~~~-------------~~~S~~~ik~~~~ 427 (477)
T TIGR02395 361 AALKPLTLREVAEELGLHESTISRAINNKYLQTPRGVFELKYFFSSGVSTESAE-------------GEASSTAIKALIK 427 (477)
T ss_pred HCCCCCCHHHHHHHHCCCCCCEEEEECCCEEECCCCCHHHHHHCCHHHCCCCCC-------------HHHHHHHHHHHHH
T ss_conf 006886389999885889872463317735760764033654312012034565-------------0346999999999
Q ss_pred HH----HHHCCCCHHHHHHHHC------CCHHHHHHHHCCCCCCCHH
Q ss_conf 99----9972983899999977------9999999974148899989
Q gi|254781218|r 120 SI----RKDKGMSQIEFGKLLG------MPNSTLSNYEQGRTIPEIK 156 (205)
Q Consensus 120 ~l----R~~~glsq~elA~~lg------is~~tis~~E~g~~~Ps~~ 156 (205)
++ .+.+-||=.++|+.+. |++.||.+|=.--.+|+-.
T Consensus 428 ~lI~~E~k~kPLSD~~i~~~L~e~G~i~~ARRTVaKYRe~L~ipss~ 474 (477)
T TIGR02395 428 ELIAAEDKRKPLSDQKIAELLKEKGGIKIARRTVAKYREELGIPSSS 474 (477)
T ss_pred HHHHCCCCCCCCCHHHHHHHHHHCCCEEEEEECHHHHHHHCCCCCCC
T ss_conf 99970178999766899999986298589960228989634889723
No 112
>pfam01710 Transposase_14 Transposase. Transposase proteins are necessary for efficient DNA transposition. This family includes insertion sequences from Synechocystis PCC 6803 three of which are characterized as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily.
Probab=94.10 E-value=0.34 Score=27.17 Aligned_cols=90 Identities=12% Similarity=0.116 Sum_probs=58.3
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHH
Q ss_conf 99999999999999859988999998489999999887799888999999999982899999614532210000232134
Q gi|254781218|r 28 YWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKK 107 (205)
Q Consensus 28 ~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~ 107 (205)
|..++=+|+=...+ .|.|-.+.|...+||.++|.+|-+....-+ ....+ ....
T Consensus 3 YS~DlR~rVl~~ve-~G~S~~eaA~~F~Is~~Tv~rWlkr~~~~~----------------------~~~~~----r~~~ 55 (120)
T pfam01710 3 YSLDLRKKVIDYIE-SGGSITEASKVFQIGRATIYRWLKREKLGA----------------------LKVEP----RGRH 55 (120)
T ss_pred CCHHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHCHHCCC----------------------CCCCC----CCCC
T ss_conf 76899999999998-699999999993702999999985500147----------------------78888----8988
Q ss_pred HHHHHHHHHHHH-HHHHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 554677799999-99997298389999997799999999741
Q gi|254781218|r 108 RLDPYAIGARLK-SIRKDKGMSQIEFGKLLGMPNSTLSNYEQ 148 (205)
Q Consensus 108 ~~d~~~iG~rLk-~lR~~~glsq~elA~~lgis~~tis~~E~ 148 (205)
++|. +.|+ .+...-++++.|.|+.+||++++|++...
T Consensus 56 Kid~----~~L~~~V~~~pD~tl~E~A~~~gVs~~tI~~aLk 93 (120)
T pfam01710 56 KIDR----DALKNDVKDNPDAYLKERAKKFGVTPSSIHYALK 93 (120)
T ss_pred CCCH----HHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHH
T ss_conf 7789----9999999988672099999983987999999999
No 113
>PRK09526 lacI lac repressor; Reviewed
Probab=93.98 E-value=0.13 Score=29.83 Aligned_cols=37 Identities=16% Similarity=0.208 Sum_probs=16.9
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHH
Q ss_conf 2983899999977999999997414889998999999
Q gi|254781218|r 125 KGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKI 161 (205)
Q Consensus 125 ~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kI 161 (205)
+..|.+|.|+.+|+|.+|+|+..||....+.++-.+|
T Consensus 4 k~~TikDIA~~agVS~sTVSrvLn~~~~vs~~tr~rV 40 (342)
T PRK09526 4 KPVTLYDVARYAGVSYQTVSRVLNQASHVSAKTREKV 40 (342)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHH
T ss_conf 9976999999989699999999789799999999999
No 114
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=93.98 E-value=0.31 Score=27.45 Aligned_cols=43 Identities=35% Similarity=0.607 Sum_probs=38.7
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCC
Q ss_conf 2983899999977999999997414889998999999998289
Q gi|254781218|r 125 KGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKK 167 (205)
Q Consensus 125 ~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgv 167 (205)
.-+|-+||++.+|++.+.+++|-||+..|+.+.+..|-..++-
T Consensus 22 ~~~tykELs~~~gip~s~L~RYv~g~vlPs~e~A~~i~~~l~~ 64 (238)
T PRK08558 22 KTYTYEELSSILGLPESVLSRYVNGHVLPSVERAREIVEKLKP 64 (238)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHH
T ss_conf 0268999998879799998505348878758999999998421
No 115
>TIGR02885 spore_sigF RNA polymerase sigma-F factor; InterPro: IPR014236 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 , . Members of this entry represent RNA polymerase sigma factor F. Within the Firmicutes, Sigma-F is specifically, and universally, a component of the endospore formation program, and is expressed in the forespore to turn on the expression of dozens of genes. It is closely related to sigma-G, which is also expressed in the forespore.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=93.95 E-value=0.02 Score=34.86 Aligned_cols=28 Identities=29% Similarity=0.249 Sum_probs=16.6
Q ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 9998599889999984899999998877
Q gi|254781218|r 39 IRKANNKTQKEMAIGANQLESAVNLFEN 66 (205)
Q Consensus 39 lR~~~gltQ~elA~~~gis~~~is~~E~ 66 (205)
+|=-+..||.|+|..+||||=+|||+|+
T Consensus 194 LRYFKDkTQ~eVA~~LGISQVQVSRlEk 221 (231)
T TIGR02885 194 LRYFKDKTQTEVAKMLGISQVQVSRLEK 221 (231)
T ss_pred EECCCCCHHHHHHHHCCCCCCHHHHHHH
T ss_conf 4101400179999771857001227899
No 116
>pfam05339 DUF739 Protein of unknown function (DUF739). This family contains several bacteriophage proteins. Some of the proteins in this family have been labeled putative cro repressor proteins.
Probab=93.87 E-value=0.24 Score=28.17 Aligned_cols=57 Identities=21% Similarity=0.150 Sum_probs=46.5
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHH
Q ss_conf 999999997298389999997799999999741488999899999999828999995
Q gi|254781218|r 116 ARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWI 172 (205)
Q Consensus 116 ~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L 172 (205)
.+||....++--+|..||..+|++..+++.-.+++..=....+.+.++.||++.|-+
T Consensus 6 ~kLrgrI~Ek~gtq~~Fa~~lg~se~tlslkln~~v~w~q~ei~kai~lL~i~~d~i 62 (69)
T pfam05339 6 SKLKGRILEKYGTQYNFASAIGLSERSLSLKLNDKVIWVANEIEKAIDLLGIPKDDI 62 (69)
T ss_pred HHHCCHHHHHHCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHH
T ss_conf 886032889956798999995811768889876867753999999999968998887
No 117
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=93.87 E-value=0.11 Score=30.22 Aligned_cols=61 Identities=18% Similarity=0.242 Sum_probs=50.4
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCC-CCCCHHHHHHHHHHHCCCHH
Q ss_conf 46777999999999729838999999779999999974148-89998999999998289999
Q gi|254781218|r 110 DPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGR-TIPEIKPARKIKQVTKKHLD 170 (205)
Q Consensus 110 d~~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~-~~Ps~~~l~kIa~~lgvs~d 170 (205)
...+++.-|+.+.+..+|+|.+.|+.+|++++.+|..-+|+ ...++..|.-.....|..++
T Consensus 25 ir~~l~~~i~~~i~q~~l~Q~qiae~lgV~qprvS~l~~gk~~~fs~dkLvtml~~~g~ei~ 86 (91)
T COG5606 25 IRSALMMAIKQWIEQAALSQAQIAELLGVTQPRVSDLARGKIQDFSIDKLVTMLARAGQEID 86 (91)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCHHHHHHHHHHHHHHHCCCCCC
T ss_conf 99999999999999978779999998388873188998361457669999999997598552
No 118
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=93.85 E-value=0.29 Score=27.67 Aligned_cols=64 Identities=19% Similarity=0.298 Sum_probs=46.4
Q ss_pred HHHCCCHHHHHHHHHHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 100015668999999999999999985--9988999998489999999887799888999999999982
Q gi|254781218|r 17 YTLIITPEIRQYWKDVGTRIKDIRKAN--NKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEY 83 (205)
Q Consensus 17 ~~~~~~~~~~~~~~~iG~rik~lR~~~--gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~ 83 (205)
+++.++|+ -++.+|.|++.+++-. .++|.|++.++|++-.+|.|=-|.....+.+.--.+.+.+
T Consensus 34 L~llLTpd---EReal~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITRGSN~LK~~~~~~k~~L~~~l 99 (103)
T COG2973 34 LTLLLTPD---EREALGTRVRIVEELLRGELSQREIAQKLGVSIATITRGSNSLKTADPEFKQWLEKVL 99 (103)
T ss_pred HHHHCCHH---HHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHCCCHHHHCCCCHHHHHHHHHHH
T ss_conf 99976876---8999999999999999563539999998586256550444442359878999999973
No 119
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=93.63 E-value=0.17 Score=29.00 Aligned_cols=46 Identities=15% Similarity=0.090 Sum_probs=35.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHHCCCCC---CC---HHHHHHHHHHHCCCHHHH
Q ss_conf 98899999848999999988779988---89---999999999828999996
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFENGMCS---TS---IRYALYLRNEYEISFDWI 90 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E~G~~~---ps---i~~l~~la~~~~vs~d~L 90 (205)
+|-+++|+++|||.+|||+.=||... .| -+...+.++.++-.++..
T Consensus 1 vTikDVA~~AGVS~aTVSrvLNg~~~~~~Vs~~Tr~rV~~aa~eLgY~Pn~~ 52 (330)
T PRK11303 1 MKLDEIARLAGVSRTTASYVINGKAKQYRISDKTVEKVMAVVREHNYHPNAV 52 (330)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHCCCCCHH
T ss_conf 9789999997979989988838999888769999999999999968994888
No 120
>COG3636 Predicted transcriptional regulator [Transcription]
Probab=93.53 E-value=0.46 Score=26.40 Aligned_cols=54 Identities=7% Similarity=0.042 Sum_probs=45.5
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf 99999999998599889999984899999998877998889999999999828999
Q gi|254781218|r 32 VGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISF 87 (205)
Q Consensus 32 iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~ 87 (205)
|..-+-.+-..+|+|| +|++.|+++..+.+-=+...+|+++++.++++++++-+
T Consensus 39 i~~alg~var~~GMsq--vA~~aGlsRe~LYkaLS~~GNPtf~Til~V~kAlG~rl 92 (100)
T COG3636 39 IAAALGVVARSRGMSQ--VARKAGLSREGLYKALSPGGNPTFDTILAVLKALGLRL 92 (100)
T ss_pred HHHHHHHHHHHCCHHH--HHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHCCCEE
T ss_conf 9999999998657899--99994966999999847899975899999999808654
No 121
>pfam00356 LacI Bacterial regulatory proteins, lacI family.
Probab=93.52 E-value=0.19 Score=28.78 Aligned_cols=35 Identities=14% Similarity=0.209 Sum_probs=18.0
Q ss_pred CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHH
Q ss_conf 38999999779999999974148899989999999
Q gi|254781218|r 128 SQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIK 162 (205)
Q Consensus 128 sq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa 162 (205)
|..|+|+..|+|..|+|+..||....+.++-.+|-
T Consensus 1 Ti~DIA~~agVS~~TVSr~ln~~~~vs~~tr~rI~ 35 (46)
T pfam00356 1 TIKDVARLAGVSKATVSRVLNNPERVSEETREKVE 35 (46)
T ss_pred CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHH
T ss_conf 99999999897999999998797989999999999
No 122
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=93.49 E-value=0.61 Score=25.64 Aligned_cols=129 Identities=13% Similarity=0.165 Sum_probs=56.7
Q ss_pred HCCCHHHHHHHHHHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHCCCCC-CCHHHHHHHHHHHCCCHHHHHCCCC
Q ss_conf 0015668999999999999999985--998899999848999999988779988-8999999999982899999614532
Q gi|254781218|r 19 LIITPEIRQYWKDVGTRIKDIRKAN--NKTQKEMAIGANQLESAVNLFENGMCS-TSIRYALYLRNEYEISFDWIYDGEV 95 (205)
Q Consensus 19 ~~~~~~~~~~~~~iG~rik~lR~~~--gltQ~elA~~~gis~~~is~~E~G~~~-psi~~l~~la~~~~vs~d~Ll~ge~ 95 (205)
+-++.-+.+....+..-.+.+.... .-|-+++|+.+|++...|..+..-... .|++.- +...-+.++..++.++.
T Consensus 235 IRiP~h~~e~~~k~~r~~~~l~~~~gr~Pt~eEiA~~lg~~~~~v~~~~~~~~~~~SLd~~--vg~d~~~~l~d~i~D~~ 312 (398)
T PRK05901 235 IRIPVHMVETINKLGRIERELLQELGREPTPEELAEEMDFTPEKVREIQKYAREPISLDKT--IGDEGDSQFGDFIEDSE 312 (398)
T ss_pred EECCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCC--CCCCCCCCHHHHCCCCC
T ss_conf 5233239999999999999999984899999999988199999999999972898556787--78998651866416999
Q ss_pred CCCCCCCCCC---HHHHHH--HHHHHHHHHH-HHH------CCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf 2100002321---345546--7779999999-997------2983899999977999999997414
Q gi|254781218|r 96 IDRRYEDVTN---KKRLDP--YAIGARLKSI-RKD------KGMSQIEFGKLLGMPNSTLSNYEQG 149 (205)
Q Consensus 96 ~~~~~~~~~~---~~~~d~--~~iG~rLk~l-R~~------~glsq~elA~~lgis~~tis~~E~g 149 (205)
...+...... ...+.. ..+..|=+.+ +.. ..+|..++|+.+|+|+..+.++|..
T Consensus 313 ~~~p~~~~~~~~l~~~l~~~L~~L~~REr~Ii~~RyGL~~~~~~TL~eIg~~lgvSrERVRQIE~k 378 (398)
T PRK05901 313 AVSPVDAVSFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESK 378 (398)
T ss_pred CCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 999999999999999999998389999999999975899989603999998979699999999999
No 123
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=93.38 E-value=0.12 Score=29.97 Aligned_cols=15 Identities=20% Similarity=0.317 Sum_probs=5.8
Q ss_pred CCHHHHHHHHCCCHH
Q ss_conf 838999999779999
Q gi|254781218|r 127 MSQIEFGKLLGMPNS 141 (205)
Q Consensus 127 lsq~elA~~lgis~~ 141 (205)
-|-.|+|+.+|++..
T Consensus 127 pt~~EIA~~L~i~~e 141 (247)
T COG1191 127 PTDEEIAEELGIDKE 141 (247)
T ss_pred CCHHHHHHHHCCCHH
T ss_conf 868999989698999
No 124
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=93.08 E-value=0.15 Score=29.34 Aligned_cols=52 Identities=25% Similarity=0.362 Sum_probs=41.0
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHC------CCHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 77799999999972983899999977------9999999974148899989999999982
Q gi|254781218|r 112 YAIGARLKSIRKDKGMSQIEFGKLLG------MPNSTLSNYEQGRTIPEIKPARKIKQVT 165 (205)
Q Consensus 112 ~~iG~rLk~lR~~~glsq~elA~~lg------is~~tis~~E~g~~~Ps~~~l~kIa~~l 165 (205)
..+....|+.|...|+||.+++..+| .|+++|+++|+=. .+...+.++.-+|
T Consensus 10 e~Fa~~fk~rRi~LG~TQ~dVG~aL~~l~g~~~SQttIcRFE~l~--LS~kn~~kLkPiL 67 (75)
T smart00352 10 EAFAKTFKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEALQ--LSFKNMCKLKPLL 67 (75)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHCC--CCHHHHHHHHHHH
T ss_conf 999999999898737759999999998618643146888988605--4798899889999
No 125
>TIGR00673 cynS cyanate hydratase; InterPro: IPR008076 Cyanase, an enzyme found in bacteria and plants, catalyses the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide, allowing the host organisms to overcome the toxicity of environmental cyanate . The cyanate lyase monomer is composed of two domains: an N-terminal domain that shows structural similarity to the DNA-binding alpha-helix bundle motif, and a C-terminal domain that has an 'open fold' that shows no structural similarity to other proteins . The enzyme is active as a homodecamer of 17kDa subunits, and displays half-site binding of substrates or substrate analogues. The dimer structure reveals the C-terminal domains to be intertwined; the decamer is formed from a pentamer of these dimers. The active site of the enzyme is located between dimers and comprises residues from four adjacent subunits of the homodecamer. Synonym(s): cyanase lyase, cyanase hydrolase ; GO: 0016836 hydro-lyase activity, 0008152 metabolic process.
Probab=93.08 E-value=0.7 Score=25.25 Aligned_cols=106 Identities=14% Similarity=0.083 Sum_probs=81.3
Q ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCH
Q ss_conf 99999999999999985998899999848999999988779988899999999998289999961453221000023213
Q gi|254781218|r 27 QYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNK 106 (205)
Q Consensus 27 ~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~ 106 (205)
+-.-+|...|=...+.+|||-++++..+|.++-.|...=-|....+.+-...+++.|+.+=|.+.--...+.. ..+...
T Consensus 9 nirldl~~~lle~Kk~kgltfad~~~~lG~~ev~~aa~~ygqa~a~~dea~~v~~~L~L~ed~~~eL~~aP~r-~~~~pv 87 (156)
T TIGR00673 9 NIRLDLAKKLLEAKKKKGLTFADVEDKLGKAEVYVAAVLYGQAAADADEAKKVAELLDLEEDEVAELKDAPLR-EGLDPV 87 (156)
T ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHHHHCCCCHHHHHHHHCCCCC-CCCCCC
T ss_conf 2577789999998873599789986531875999999998420688889999998709981134665406666-888898
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCHHHHHHH
Q ss_conf 45546777999999999729838999999
Q gi|254781218|r 107 KRLDPYAIGARLKSIRKDKGMSQIEFGKL 135 (205)
Q Consensus 107 ~~~d~~~iG~rLk~lR~~~glsq~elA~~ 135 (205)
-..||.. .|+=++..-.|++.++++..
T Consensus 88 ~PTDP~~--YRfYE~~~vYG~~lK~v~HE 114 (156)
T TIGR00673 88 VPTDPLV--YRFYEVLQVYGTALKEVVHE 114 (156)
T ss_pred CCCCCHH--HHHHHHHHHHCHHHHHHHHH
T ss_conf 9677606--77788888716036776422
No 126
>pfam00356 LacI Bacterial regulatory proteins, lacI family.
Probab=93.07 E-value=0.26 Score=27.89 Aligned_cols=37 Identities=19% Similarity=-0.014 Sum_probs=30.6
Q ss_pred CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHH
Q ss_conf 8899999848999999988779988899999999998
Q gi|254781218|r 46 TQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNE 82 (205)
Q Consensus 46 tQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~ 82 (205)
|-+++|+.+|+|.++||++=||....+-++-.++-.+
T Consensus 1 Ti~DIA~~agVS~~TVSr~ln~~~~vs~~tr~rI~~~ 37 (46)
T pfam00356 1 TIKDVARLAGVSKATVSRVLNNPERVSEETREKVEAA 37 (46)
T ss_pred CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHH
T ss_conf 9999999989799999999879798999999999999
No 127
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=92.97 E-value=0.73 Score=25.15 Aligned_cols=107 Identities=16% Similarity=0.263 Sum_probs=55.2
Q ss_pred CCCCHHHHHHHHCCCHHHHHH-HHCCC------CCCCHHHHHHHHHHH---CCCHHHHHCC---------CCCC----CC
Q ss_conf 599889999984899999998-87799------888999999999982---8999996145---------3221----00
Q gi|254781218|r 43 NNKTQKEMAIGANQLESAVNL-FENGM------CSTSIRYALYLRNEY---EISFDWIYDG---------EVID----RR 99 (205)
Q Consensus 43 ~gltQ~elA~~~gis~~~is~-~E~G~------~~psi~~l~~la~~~---~vs~d~Ll~g---------e~~~----~~ 99 (205)
+.-|..+.|.++|++...+-+ ++.|. ....+..++.||+-| +++++.|+.. +-+| .+
T Consensus 55 ~~~~~~~~a~a~~~~~~~l~~~~~~g~~A~~~lv~~NLRLVv~iAk~y~~~gl~~~DLIQEGniGLi~AvekFDp~rG~r 134 (318)
T PRK07405 55 REPSDLEWAKAAKLSEEELRRAIAEGEAAKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYR 134 (318)
T ss_pred CCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCE
T ss_conf 78746788876045689999987627999999999819999999986657997988999986899999999709765980
Q ss_pred CC---------------CCCCHHHHHHHHHHHHHHHHH-------HH--CCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf 00---------------232134554677799999999-------97--2983899999977999999997414
Q gi|254781218|r 100 YE---------------DVTNKKRLDPYAIGARLKSIR-------KD--KGMSQIEFGKLLGMPNSTLSNYEQG 149 (205)
Q Consensus 100 ~~---------------~~~~~~~~d~~~iG~rLk~lR-------~~--~glsq~elA~~lgis~~tis~~E~g 149 (205)
|+ .........|..+..++..++ .. +.-|..++|+.+|++...+..+..-
T Consensus 135 FSTYA~wWIrq~I~r~i~~~~r~IRlP~~~~~~~~ki~~~~~~L~~~lGr~Pt~~EIAe~lgi~~e~V~~~l~~ 208 (318)
T PRK07405 135 FSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLER 208 (318)
T ss_pred EEEEHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 22200999999999999976985168778999999999999999987189864899998859999999999998
No 128
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=92.84 E-value=0.28 Score=27.68 Aligned_cols=44 Identities=16% Similarity=-0.043 Sum_probs=34.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHH---HHHHHHCCCHH
Q ss_conf 988999998489999999887799888999999---99998289999
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFENGMCSTSIRYAL---YLRNEYEISFD 88 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E~G~~~psi~~l~---~la~~~~vs~d 88 (205)
.|-+++|+.+|||.+|||+.=||....+-++-- ..++.++-.++
T Consensus 2 vTi~DVA~~AGVS~aTVSrvLn~~~~Vs~eTr~rV~~aa~eLgY~Pn 48 (346)
T PRK10401 2 ITIRDVARQAGVSVATVSRVLNNSALVSPDTREAVMKAVSELGYRPN 48 (346)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCC
T ss_conf 97899999989799999999779499999999999999999499848
No 129
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=92.84 E-value=0.27 Score=27.78 Aligned_cols=27 Identities=30% Similarity=0.168 Sum_probs=15.5
Q ss_pred CHHHHHHHHCCCHHHHHHHHCCCCCCC
Q ss_conf 889999984899999998877998889
Q gi|254781218|r 46 TQKEMAIGANQLESAVNLFENGMCSTS 72 (205)
Q Consensus 46 tQ~elA~~~gis~~~is~~E~G~~~ps 72 (205)
|.+|+|+.+|+|.+++|++=||....+
T Consensus 2 Ti~dvA~~aGVS~sTVSr~ln~~~~Vs 28 (70)
T smart00354 2 TIKDVARLAGVSKATVSRVLNGNGRVS 28 (70)
T ss_pred CHHHHHHHHCCCHHHHHHHHCCCCCCC
T ss_conf 899999998959999999977999899
No 130
>KOG1168 consensus
Probab=92.77 E-value=0.065 Score=31.65 Aligned_cols=128 Identities=16% Similarity=0.180 Sum_probs=68.8
Q ss_pred HHHHH---HHHHHHHHHHHHHHHCCCCHHHHHHHH---------CCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHH
Q ss_conf 66899---999999999999998599889999984---------899999998877998889999999999828999996
Q gi|254781218|r 23 PEIRQ---YWKDVGTRIKDIRKANNKTQKEMAIGA---------NQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWI 90 (205)
Q Consensus 23 ~~~~~---~~~~iG~rik~lR~~~gltQ~elA~~~---------gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~L 90 (205)
+++.. -.+.+++|.|+.|...|.||.++++++ .+|+++|-++|+=.- |-..++.|--.+. .||
T Consensus 210 sD~dtDPReLEaFAErFKQRRIKLGVTQADVG~ALAnLKiPGVGsLSQSTICRFESLTL--SHNNMiALKPILq---aWL 284 (385)
T KOG1168 210 SDMDTDPRELEAFAERFKQRRIKLGVTQADVGKALANLKIPGVGSLSQSTICRFESLTL--SHNNMIALKPILQ---AWL 284 (385)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCEEEEEEECC--CCCCCHHHHHHHH---HHH
T ss_conf 55678889999999998754543064277778898727688755323121332100002--4576310668999---999
Q ss_pred HCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCC
Q ss_conf 145322100002321345546777999999999729838999999779999999974148899989999999982899
Q gi|254781218|r 91 YDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKH 168 (205)
Q Consensus 91 l~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs 168 (205)
=..|..-+.-..++.-..+ +.-|++= |+.-.+ .---+.++-.|-.-.-.|+-+.+..||+-|+..
T Consensus 285 EeAE~a~keK~~~pd~~~l--~~~~ekK---RKRTSI--------AAPEKRsLEayFavQPRPS~EkIAaIAekLDLK 349 (385)
T KOG1168 285 EEAEAAMKEKDTKPDINEL--LPGGEKK---RKRTSI--------AAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLK 349 (385)
T ss_pred HHHHHHHHHHCCCCCHHHC--CCCCCCC---CCCCCC--------CCCCCCCHHHHHCCCCCCCHHHHHHHHHHHHHH
T ss_conf 9999998742358862321--6763111---102332--------484201288885448998600789999863211
No 131
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=92.77 E-value=0.78 Score=24.97 Aligned_cols=125 Identities=13% Similarity=0.140 Sum_probs=66.3
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHCCC-CCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCC---HHHHHH--HHHHH
Q ss_conf 59988999998489999999887799-8889999999999828999996145322100002321---345546--77799
Q gi|254781218|r 43 NNKTQKEMAIGANQLESAVNLFENGM-CSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTN---KKRLDP--YAIGA 116 (205)
Q Consensus 43 ~gltQ~elA~~~gis~~~is~~E~G~-~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~---~~~~d~--~~iG~ 116 (205)
+.-|-+++|+.+|++...|..+-.-. ...|++.-+ ..-=+.++-.++.++....+...... ...+.. ..+..
T Consensus 191 r~pt~eEIA~~lg~~~~~v~~~l~~~~~~~SLD~pv--~~d~~~tl~d~l~D~~~~~pd~~~~~~~l~~~l~~~L~~L~~ 268 (328)
T PRK05657 191 HEPSAEEIAELLDKPVDDVSRMLALNERITSLDAPL--GGDPEKSLLDILADDQENGPEDTTQDDDLKQSIVKWLFELND 268 (328)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCC--CCCCCCHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCH
T ss_conf 999899999996959999999997458763444535--899851178886277899999999999999999999806999
Q ss_pred HHHHHHH-------HCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHH
Q ss_conf 9999999-------72983899999977999999997414889998999999998289999952
Q gi|254781218|r 117 RLKSIRK-------DKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIY 173 (205)
Q Consensus 117 rLk~lR~-------~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~ 173 (205)
|=+.+.. ...+|+.++|+.+|+|+..+.++|+. -+..|.+..+.-|++.|.||
T Consensus 269 REr~II~~RfGL~~~e~~TL~EIg~~lgvSRERVRQIE~~----AL~KLR~~l~~~~l~~~~~~ 328 (328)
T PRK05657 269 KQREVIERRFGLNGYEAATLEEVAREIGLTRERVRQIQVE----ALRRLREILQTQGLSKDALF 328 (328)
T ss_pred HHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHHHCCCCHHHCC
T ss_conf 9999999980889989605999998969799999999999----99998799998699734249
No 132
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=92.68 E-value=0.072 Score=31.38 Aligned_cols=47 Identities=19% Similarity=0.191 Sum_probs=32.3
Q ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHH---HHHHHHHHHCCCHH
Q ss_conf 9859988999998489999999887799888999---99999998289999
Q gi|254781218|r 41 KANNKTQKEMAIGANQLESAVNLFENGMCSTSIR---YALYLRNEYEISFD 88 (205)
Q Consensus 41 ~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~---~l~~la~~~~vs~d 88 (205)
..+||||++.|..++.++..||.+|+.-.. .|+ .-+.|.+.++-++.
T Consensus 20 RekG~tQ~eIA~~L~TTraNvSaIEkrA~e-nIekarnTL~l~~~i~spv~ 69 (143)
T COG1356 20 REKGLTQSEIARILKTTRANVSAIEKRALE-NIEKARNTLLLWEQINSPVS 69 (143)
T ss_pred HHCCCCHHHHHHHHCCCCCCHHHHHHHHHH-HHHHHHHHHHHHHHHCCCEE
T ss_conf 640564899999975451017999999999-89999889999998469758
No 133
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=92.66 E-value=0.32 Score=27.35 Aligned_cols=45 Identities=13% Similarity=0.150 Sum_probs=36.1
Q ss_pred CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHH---HHHHCCCHHHH
Q ss_conf 3899999977999999997414889998999999---99828999995
Q gi|254781218|r 128 SQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKI---KQVTKKHLDWI 172 (205)
Q Consensus 128 sq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kI---a~~lgvs~d~L 172 (205)
|..|+|+..|+|..|+|+..||....+.++-.+| ++.+|..++..
T Consensus 2 Ti~dvA~~aGVS~sTVSr~ln~~~~Vs~~tr~rV~~~a~~lgY~pn~~ 49 (70)
T smart00354 2 TIKDVARLAGVSKATVSRVLNGNGRVSEETREKVLAAMEELGYIPNRV 49 (70)
T ss_pred CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCHH
T ss_conf 899999998959999999977999899999999999999978998999
No 134
>pfam04814 HNF-1_N Hepatocyte nuclear factor 1 (HNF-1), N terminus. This family consists of the N terminus of homeobox-containing transcription factor HNF-1. This region contains a dimerization sequence and an acidic region that may be involved in transcription activation. Mutations and the common Ala/Val 98 polymorphism in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3).
Probab=92.59 E-value=0.7 Score=25.25 Aligned_cols=67 Identities=19% Similarity=0.173 Sum_probs=46.1
Q ss_pred HHHHHHHHHH-HHHHHCCCHHHHHHHH----HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCC
Q ss_conf 7777666543-3310001566899999----99999999999859988999998489999999887799888
Q gi|254781218|r 5 PFLETSLKSL-QEYTLIITPEIRQYWK----DVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCST 71 (205)
Q Consensus 5 ~~~~~~~~~~-~~~~~~~~~~~~~~~~----~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~p 71 (205)
|=++.+++.+ +|.+.....++.++.. .+.+-||..-.++++.|.+++...|+++|+||.+-|--..+
T Consensus 84 pPi~kele~l~~EEaa~qra~Ve~ll~~d~~~v~~~Ik~~m~~h~ipQ~~vv~~TGlnQS~lSq~LnkGt~M 155 (177)
T pfam04814 84 PPILKELERLSPEEAAHQRAEVDRLLREDPWRVAKMIKSYMQQHNIPQREVVDATGLNQSHLSQHLNKGTPM 155 (177)
T ss_pred CCCCHHHHCCCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHCCCCC
T ss_conf 876603222582588888999999997284999999999998768846678761065599999999668840
No 135
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=92.58 E-value=0.31 Score=27.45 Aligned_cols=44 Identities=16% Similarity=-0.062 Sum_probs=35.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHH---HHHHHHHHCCCHH
Q ss_conf 9889999984899999998877998889999---9999998289999
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFENGMCSTSIRY---ALYLRNEYEISFD 88 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E~G~~~psi~~---l~~la~~~~vs~d 88 (205)
-|-+++|+.+|||.+|||+.=||....+-++ ....++.++-.++
T Consensus 2 aTIkDIA~~AGVS~sTVSrvLN~~~~Vs~~Tr~rV~~aa~eLgY~Pn 48 (342)
T PRK10727 2 ATIKDVARLAGVSVATVSRVINNSPKASEASRLAVHSAMESLSYHPN 48 (342)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCC
T ss_conf 98899999979699999999779799999999999999999399858
No 136
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=92.45 E-value=0.86 Score=24.72 Aligned_cols=130 Identities=14% Similarity=0.148 Sum_probs=55.9
Q ss_pred HHCCCHHHHHHHHHHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHCCCCC-CCHHHHHHHHHHHCCCHHHHHCCC
Q ss_conf 00015668999999999999999985--998899999848999999988779988-899999999998289999961453
Q gi|254781218|r 18 TLIITPEIRQYWKDVGTRIKDIRKAN--NKTQKEMAIGANQLESAVNLFENGMCS-TSIRYALYLRNEYEISFDWIYDGE 94 (205)
Q Consensus 18 ~~~~~~~~~~~~~~iG~rik~lR~~~--gltQ~elA~~~gis~~~is~~E~G~~~-psi~~l~~la~~~~vs~d~Ll~ge 94 (205)
++-++..+.+....+-.--+.+.... .-|.+++|+.+|++...|..+.+-... .|++.- +...-+.++..++..+
T Consensus 205 ~IRiPvh~~e~~~kl~r~~r~L~q~lGrePt~eEIA~~lgi~~e~V~~i~~~~~~~~SLd~p--vg~e~~s~l~d~i~D~ 282 (368)
T PRK09210 205 TIRIPVHMVETINKLIRVQRQLLQELGRDPTPEEIAEEMDMPPEKVREILKIAQEPVSLETP--IGEEDDSHLGDFIEDQ 282 (368)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCC--CCCCCCCHHHHHHCCC
T ss_conf 51354249999999999999999983899988999989499899999999853888566886--7887755287552489
Q ss_pred CCCCCCCCCCC---HHHHHH--HHHHHHHHHH-HHHCC------CCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf 22100002321---345546--7779999999-99729------83899999977999999997414
Q gi|254781218|r 95 VIDRRYEDVTN---KKRLDP--YAIGARLKSI-RKDKG------MSQIEFGKLLGMPNSTLSNYEQG 149 (205)
Q Consensus 95 ~~~~~~~~~~~---~~~~d~--~~iG~rLk~l-R~~~g------lsq~elA~~lgis~~tis~~E~g 149 (205)
....+...... +..+.. ..+..|=+.+ +...| +|..++|+.+|+|+..+.++|..
T Consensus 283 ~~~~p~e~~~~~~l~~~l~~~L~~L~~REr~Il~~RfGL~~~~~~TLeEIg~~lgvSRERVRQIE~k 349 (368)
T PRK09210 283 DATSPADHAAYELLKEQLEEVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAK 349 (368)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 9999899999999999999998179999999999975999689614999998969798999999999
No 137
>pfam02376 CUT CUT domain. The CUT domain is a DNA-binding motif which can bind independently or in cooperation with the homeodomain, often found downstream of the CUT domain. Multiple copies of the CUT domain can exist in one protein .
Probab=92.36 E-value=0.3 Score=27.56 Aligned_cols=40 Identities=30% Similarity=0.422 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHH-CCCHHHHHHHHC
Q ss_conf 5467779999999997298389999997-799999999741
Q gi|254781218|r 109 LDPYAIGARLKSIRKDKGMSQIEFGKLL-GMPNSTLSNYEQ 148 (205)
Q Consensus 109 ~d~~~iG~rLk~lR~~~glsq~elA~~l-gis~~tis~~E~ 148 (205)
+|...|..+|++..+.++++|.-||+.+ |.++.++|...+
T Consensus 3 ldT~~i~~~i~~eL~~~~I~Q~~Fa~~vL~rsQGtlSdLL~ 43 (81)
T pfam02376 3 LDTAEIARRIKEELKRANISQALFAEVVLGRSQGSLSDLLR 43 (81)
T ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHHHH
T ss_conf 88999999999999994976999999997318378999881
No 138
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=92.30 E-value=0.36 Score=27.07 Aligned_cols=46 Identities=17% Similarity=-0.086 Sum_probs=36.5
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHH---HHHHCCCHHH
Q ss_conf 998899999848999999988779988899999999---9982899999
Q gi|254781218|r 44 NKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYL---RNEYEISFDW 89 (205)
Q Consensus 44 gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~l---a~~~~vs~d~ 89 (205)
.-|-+++|+.+|||.+|||+.=||....|-++-.++ ++.++-.++.
T Consensus 9 MaTikDIA~~aGVS~sTVSrvLn~~~~Vs~~Tr~rV~~aa~eLgY~pn~ 57 (341)
T PRK11041 9 MATMKDVALKAGVSTATVSRALMNPEKVSQSTRNRVEQAVLEVGYSPQS 57 (341)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCH
T ss_conf 8889999999797999999997898999999999999999981998388
No 139
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=92.24 E-value=0.36 Score=27.04 Aligned_cols=44 Identities=18% Similarity=-0.032 Sum_probs=34.6
Q ss_pred CHHHHHHHHCCCHHHHHHHHCCCCCCCHHH---HHHHHHHHCCCHHH
Q ss_conf 889999984899999998877998889999---99999982899999
Q gi|254781218|r 46 TQKEMAIGANQLESAVNLFENGMCSTSIRY---ALYLRNEYEISFDW 89 (205)
Q Consensus 46 tQ~elA~~~gis~~~is~~E~G~~~psi~~---l~~la~~~~vs~d~ 89 (205)
|-+++|+.+|||.+|||+.=||....|-++ ....++.++=.++.
T Consensus 3 TikDIA~~AGVS~aTVSrvLn~~~~Vs~~Tr~rV~~aa~eLgY~pn~ 49 (335)
T PRK10703 3 TIKDVAKRAGVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPSA 49 (335)
T ss_pred CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCH
T ss_conf 88999999798999999996896998999999999999982999787
No 140
>PRK08099 nicotinamide-nucleotide adenylyltransferase; Provisional
Probab=92.02 E-value=0.59 Score=25.73 Aligned_cols=55 Identities=16% Similarity=0.068 Sum_probs=49.8
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCC-CCCCHHHHHHHHHHHCCCHHH
Q ss_conf 9999999859988999998489999999887799-888999999999982899999
Q gi|254781218|r 35 RIKDIRKANNKTQKEMAIGANQLESAVNLFENGM-CSTSIRYALYLRNEYEISFDW 89 (205)
Q Consensus 35 rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~-~~psi~~l~~la~~~~vs~d~ 89 (205)
-++..|++.|++..++|...|+++.+.+..-+|+ .+||...|..|.+.+++.+.-
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 61 (411)
T PRK08099 6 YLKTAIKQQGCTLQQVADASGMTKGYLSQLLNAKIKSPSAQKLEALHRFLGLEFPR 61 (411)
T ss_pred HHHHHHHHHCCCHHHHHHHHCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCHH
T ss_conf 99999998488298876542340999999862524894378999999995886402
No 141
>PRK01381 Trp operon repressor; Provisional
Probab=91.93 E-value=0.38 Score=26.88 Aligned_cols=64 Identities=17% Similarity=0.276 Sum_probs=44.7
Q ss_pred HHHCCCHHHHHHHHHHHHHHHHHHH-HCC-CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 1000156689999999999999999-859-988999998489999999887799888999999999982
Q gi|254781218|r 17 YTLIITPEIRQYWKDVGTRIKDIRK-ANN-KTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEY 83 (205)
Q Consensus 17 ~~~~~~~~~~~~~~~iG~rik~lR~-~~g-ltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~ 83 (205)
+++.++|+ -.+.||.|++.++. .+| ++|.++|+.+|++-.+|.|=-|-....+.+.-..|.+.+
T Consensus 29 l~~lLTp~---Er~al~~R~~I~~~Ll~ge~sQReIa~~lgvsiAtITRGSn~LK~~~~~~k~~l~~~l 94 (99)
T PRK01381 29 LTLLLTPD---EREALGTRVRIVEELLRGELSQREIKQELGVGIATITRGSNSLKTAPPEFKEWLEQLL 94 (99)
T ss_pred HHHHCCHH---HHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCEECCCCHHHHHCCCHHHHHHHHHHH
T ss_conf 99978999---9999999999999999487649999998497402000026988539999999999986
No 142
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=91.89 E-value=0.44 Score=26.51 Aligned_cols=43 Identities=21% Similarity=0.002 Sum_probs=33.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHH---HHHHCCCH
Q ss_conf 98899999848999999988779988899999999---99828999
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFENGMCSTSIRYALYL---RNEYEISF 87 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~l---a~~~~vs~ 87 (205)
.|.+++|+.+|||.+|+|+.-||....|-++--++ ++.++--+
T Consensus 1 ~TikDVA~~AGVS~sTVSrvln~~~~Vs~eTr~rV~~a~~elgY~p 46 (333)
T COG1609 1 ATIKDVAKLAGVSKATVSRVLNGSPYVSEETREKVLAAIKELGYRP 46 (333)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCC
T ss_conf 9689999996899989889877999879999999999999978998
No 143
>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=91.83 E-value=0.19 Score=28.81 Aligned_cols=28 Identities=25% Similarity=0.405 Sum_probs=20.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHCCCCCCC
Q ss_conf 8389999997799999999741488999
Q gi|254781218|r 127 MSQIEFGKLLGMPNSTLSNYEQGRTIPE 154 (205)
Q Consensus 127 lsq~elA~~lgis~~tis~~E~g~~~Ps 154 (205)
|+..|+|+.+|+++.|+.+|+.....|.
T Consensus 1 lt~~e~A~~lgVs~~TlrrW~~~G~i~~ 28 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKEGKLKA 28 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCE
T ss_conf 9889999997989999999998799431
No 144
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=91.73 E-value=0.51 Score=26.11 Aligned_cols=42 Identities=21% Similarity=0.124 Sum_probs=33.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHCCCC--CCC---HHHHHHHHHHHCCC
Q ss_conf 9889999984899999998877998--889---99999999982899
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFENGMC--STS---IRYALYLRNEYEIS 86 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E~G~~--~ps---i~~l~~la~~~~vs 86 (205)
-|-+++|+.+|||.+|||++=||.. ..+ -+...+.++.++-.
T Consensus 2 aTikDVA~~AGVS~sTVSrvLn~~~~~~V~~~Tr~rV~~aa~elgY~ 48 (327)
T PRK10339 2 ATLKDIAIEAGVSLATVSRVLNDDPTLNVKEETKHRILEIAEKLEYK 48 (327)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCC
T ss_conf 96899999978889999999589899996899999999999996899
No 145
>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=91.60 E-value=0.15 Score=29.36 Aligned_cols=69 Identities=10% Similarity=0.267 Sum_probs=41.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHC-CCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9889999984899999998877-998889999999999828999996145322100002321345546777999999999
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFEN-GMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRK 123 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E~-G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~ 123 (205)
|+-.|||++.|++..+|-.||+ |.-.|+-..--. | ..|. ...... + .-|+.++.
T Consensus 1 M~IgelA~~tGvs~~TIRyYe~~GLL~p~~R~~~g----~--------------r~Y~----~~~v~r--L-~~Ir~l~~ 55 (95)
T cd04780 1 MRMSELSKRSGVSVATIKYYLREGLLPEGRRLAPN----Q--------------AEYS----EAHVER--L-RLIRALQQ 55 (95)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCC----C--------------EECC----HHHHHH--H-HHHHHHHH
T ss_conf 97899999989789999999997899987769998----7--------------1549----999999--9-99999999
Q ss_pred HCCCCHHHHHHHHCC
Q ss_conf 729838999999779
Q gi|254781218|r 124 DKGMSQIEFGKLLGM 138 (205)
Q Consensus 124 ~~glsq~elA~~lgi 138 (205)
..||+..+..+.++.
T Consensus 56 ~lG~sL~eIr~lL~~ 70 (95)
T cd04780 56 EGGLPISQIKEVLDA 70 (95)
T ss_pred HCCCCHHHHHHHHHC
T ss_conf 369999999999843
No 146
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=91.42 E-value=0.54 Score=25.95 Aligned_cols=12 Identities=8% Similarity=-0.100 Sum_probs=3.8
Q ss_pred HHHHHHHHCCCC
Q ss_conf 999999985998
Q gi|254781218|r 35 RIKDIRKANNKT 46 (205)
Q Consensus 35 rik~lR~~~glt 46 (205)
||+..=++.|+.
T Consensus 35 rV~~aa~eLgY~ 46 (335)
T PRK10703 35 AVWAAIKELHYS 46 (335)
T ss_pred HHHHHHHHHCCC
T ss_conf 999999982999
No 147
>pfam08965 DUF1870 Domain of unknown function (DUF1870). This domain is found in a set of hypothetical bacterial proteins.
Probab=91.25 E-value=0.6 Score=25.66 Aligned_cols=47 Identities=19% Similarity=0.065 Sum_probs=33.3
Q ss_pred HHHHHHHHCCCCHHHHHHHHC--CCHHHHHHHHCCCCCCCHHHHHHHHH
Q ss_conf 999999985998899999848--99999998877998889999999999
Q gi|254781218|r 35 RIKDIRKANNKTQKEMAIGAN--QLESAVNLFENGMCSTSIRYALYLRN 81 (205)
Q Consensus 35 rik~lR~~~gltQ~elA~~~g--is~~~is~~E~G~~~psi~~l~~la~ 81 (205)
.+..+|+..-||-.|-|..++ ++..+-.+||+|...++.++.-++..
T Consensus 4 ELQAlR~if~mti~EaA~~I~~~~~s~~Wq~WE~G~~~IP~~i~~~~~~ 52 (117)
T pfam08965 4 ELQALRKILFLTIVEAAELIGQSVSSRTWQRWEKGDIAIPDEVEAKLRK 52 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHH
T ss_conf 8999999999649999999946888899999975898899999999999
No 148
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=91.23 E-value=0.53 Score=26.02 Aligned_cols=46 Identities=15% Similarity=0.162 Sum_probs=35.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHH---HHHHCCCHHHH
Q ss_conf 83899999977999999997414889998999999---99828999995
Q gi|254781218|r 127 MSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKI---KQVTKKHLDWI 172 (205)
Q Consensus 127 lsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kI---a~~lgvs~d~L 172 (205)
.|.+|+|+..|+|++|+|+..||....+-++-++| ++.||..++..
T Consensus 1 ~TikDVA~~AGVS~sTVSrvln~~~~Vs~eTr~rV~~a~~elgY~pn~~ 49 (333)
T COG1609 1 ATIKDVAKLAGVSKATVSRVLNGSPYVSEETREKVLAAIKELGYRPNAV 49 (333)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCHH
T ss_conf 9689999996899989889877999879999999999999978998989
No 149
>pfam00157 Pou Pou domain - N-terminal to homeobox domain.
Probab=91.16 E-value=0.35 Score=27.09 Aligned_cols=51 Identities=24% Similarity=0.361 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHC------CCHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 7799999999972983899999977------9999999974148899989999999982
Q gi|254781218|r 113 AIGARLKSIRKDKGMSQIEFGKLLG------MPNSTLSNYEQGRTIPEIKPARKIKQVT 165 (205)
Q Consensus 113 ~iG~rLk~lR~~~glsq~elA~~lg------is~~tis~~E~g~~~Ps~~~l~kIa~~l 165 (205)
.+....|+.|...|+||.+++..+| .|+++|+++|+=. .+...+.++--+|
T Consensus 11 ~Fa~~fk~rRi~LG~TQ~dVg~al~~l~G~~~SQttIcRFE~l~--Ls~kn~~kLkP~L 67 (75)
T pfam00157 11 QFAKEFKQRRIKLGYTQADVGLALGALYGPVFSQTTICRFEALQ--LSFKNMCKLKPLL 67 (75)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHCC--CCHHHHHHHHHHH
T ss_conf 99999999898737759999999998708654235888888504--4799899889999
No 150
>KOG3802 consensus
Probab=91.15 E-value=0.25 Score=28.00 Aligned_cols=59 Identities=22% Similarity=0.397 Sum_probs=46.5
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHC------CCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHH
Q ss_conf 4677799999999972983899999977------999999997414889998999999998289999952
Q gi|254781218|r 110 DPYAIGARLKSIRKDKGMSQIEFGKLLG------MPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIY 173 (205)
Q Consensus 110 d~~~iG~rLk~lR~~~glsq~elA~~lg------is~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~ 173 (205)
+-..+++-.|+.|...|+||.|++-.+| .|+.||+|+|.=. .+...+-||.=+|. .||=
T Consensus 207 ELEqFAK~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEALq--LSFKNMCKLKPLL~---KWLe 271 (398)
T KOG3802 207 ELEQFAKTFKQRRIKLGFTQADVGLALGALYGNVFSQTTICRFEALQ--LSFKNMCKLKPLLE---KWLE 271 (398)
T ss_pred HHHHHHHHHHHHEECCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHC--CCHHHHHHHHHHHH---HHHH
T ss_conf 99999999876500036442678889876507644302666767625--47787766379999---9999
No 151
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=91.05 E-value=0.22 Score=28.33 Aligned_cols=113 Identities=16% Similarity=0.240 Sum_probs=53.0
Q ss_pred CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCC---HHHHHCCCCCCC-CCCCC---CCHHHHHHHH---HH
Q ss_conf 88999998489999999887799888999999999982899---999614532210-00023---2134554677---79
Q gi|254781218|r 46 TQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEIS---FDWIYDGEVIDR-RYEDV---TNKKRLDPYA---IG 115 (205)
Q Consensus 46 tQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs---~d~Ll~ge~~~~-~~~~~---~~~~~~d~~~---iG 115 (205)
+.+++|+.+|++...|..++.....+++..-..+...=+-+ +|.+.+....+. ..... .........+ +-
T Consensus 150 ~~~eiA~~l~~~~~~v~~~~~~~~~~~~SL~~~~~~d~~~~~~~~d~l~d~~~~p~~~~e~~~~~~~~~~~L~~~l~~L~ 229 (289)
T PRK07500 150 IHREIATALGVSLSDVEMMDARLSGPDSSLNAPQSEEDEGRSERMDFLVDDSPLPDEIVESSIDGERRRQWLTQALQTLN 229 (289)
T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 39999988099999999999997379866668067877774015554046889838999999999999999999985499
Q ss_pred HHHHH---HH--HHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 99999---99--9729838999999779999999974148899989999999982
Q gi|254781218|r 116 ARLKS---IR--KDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVT 165 (205)
Q Consensus 116 ~rLk~---lR--~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~l 165 (205)
.|=+. +| ...++|+.|+|+.+|+|+..++++|+ ..+.+|-+.|
T Consensus 230 eREr~Ii~~r~~~~e~~TL~EIg~~lgvSreRVRQIe~-------kAL~KLR~~L 277 (289)
T PRK07500 230 ERELFIIRERRLREDGATLEALGEELGISKERVRQIEA-------RALEKLRRAL 277 (289)
T ss_pred HHHHHHHHHHCCCCCCCCHHHHHHHHCCCHHHHHHHHH-------HHHHHHHHHH
T ss_conf 99999999976689985899999997979999999999-------9999999999
No 152
>PRK05572 sporulation sigma factor SigF; Validated
Probab=91.02 E-value=1.2 Score=23.75 Aligned_cols=121 Identities=18% Similarity=0.166 Sum_probs=56.4
Q ss_pred CHHHHHHHHHHHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCC
Q ss_conf 566899999999999999998--599889999984899999998877998889999999999828999996145322100
Q gi|254781218|r 22 TPEIRQYWKDVGTRIKDIRKA--NNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRR 99 (205)
Q Consensus 22 ~~~~~~~~~~iG~rik~lR~~--~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~ 99 (205)
+..+.+....+..-...+... +.-|-.++|+.+|++...|...-.....+. .+......=+-+...+++. ..+
T Consensus 108 p~~~~~~~~ki~~~~~~l~~~~~r~ps~~eia~~lg~~~~~v~~~~~~~~~~~--sl~~~~~~~d~~~~~l~d~-~~~-- 182 (251)
T PRK05572 108 SRSLKELANKIRKDKEELSKELGRAPTIEELAEYLGVTPEEVVLAQEASRSPQ--SIHETVHENDGDPITLLDQ-IAD-- 182 (251)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCC--CCCCCCCCCCCCHHHHHHH-CCC--
T ss_conf 68899999889999999999878899899999997939999999998817987--5346666789971566541-268--
Q ss_pred CCCCCCHHHHHHHH-------HHHH---HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf 00232134554677-------7999---99999972983899999977999999997414
Q gi|254781218|r 100 YEDVTNKKRLDPYA-------IGAR---LKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQG 149 (205)
Q Consensus 100 ~~~~~~~~~~d~~~-------iG~r---Lk~lR~~~glsq~elA~~lgis~~tis~~E~g 149 (205)
+.......+... +-.| |=.+|-..++|+.|.|+.+|+|+..++++++.
T Consensus 183 --~~~~~~~~~~~~L~~~l~~L~~rEr~Vi~~ry~~~~tl~EIa~~lgiS~eRVrQI~~~ 240 (251)
T PRK05572 183 --QSEEDDWFDKIALKEAIRELDERERLIIYLRYFKDKTQSEVAKRLGISQVQVSRLEKK 240 (251)
T ss_pred --CCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf --7346899999999999972899999999998178988999999979799999999999
No 153
>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=90.63 E-value=1.3 Score=23.53 Aligned_cols=70 Identities=23% Similarity=0.333 Sum_probs=43.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHH-CCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 988999998489999999887-7998889999999999828999996145322100002321345546777999999999
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFE-NGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRK 123 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E-~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~ 123 (205)
+|-.++|+.+|+|.++|-.|| .|.-.|. .. .+.|.+ |+ ...+. -=.+|..++.
T Consensus 1 ytIgevA~~~Gvs~~tlRyYE~~GLl~P~-R~----~~gyR~--------------Y~----~~dl~---rL~~I~~l~~ 54 (96)
T cd04774 1 YKVDEVAKRLGLTKRTLKYYEEIGLVSPE-RS----EGRYRL--------------YS----EEDLK---RLERILRLRE 54 (96)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCC-CC----CCCCCC--------------CC----HHHHH---HHHHHHHHHH
T ss_conf 94889999989799999999987998998-69----999823--------------59----99999---9999999999
Q ss_pred HCCCCHHHHHHHHCCCH
Q ss_conf 72983899999977999
Q gi|254781218|r 124 DKGMSQIEFGKLLGMPN 140 (205)
Q Consensus 124 ~~glsq~elA~~lgis~ 140 (205)
..|+|..+..+.+..+.
T Consensus 55 ~lGfsL~eIk~lL~~~~ 71 (96)
T cd04774 55 VLGFSLQEVTHFLERPL 71 (96)
T ss_pred HCCCCHHHHHHHHCCCC
T ss_conf 57998999999981988
No 154
>pfam01371 Trp_repressor Trp repressor protein. This protein binds to tryptophan and represses transcription of the Trp operon.
Probab=90.58 E-value=0.55 Score=25.92 Aligned_cols=38 Identities=13% Similarity=0.136 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHH--HHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 999999999999--98599889999984899999998877
Q gi|254781218|r 29 WKDVGTRIKDIR--KANNKTQKEMAIGANQLESAVNLFEN 66 (205)
Q Consensus 29 ~~~iG~rik~lR--~~~gltQ~elA~~~gis~~~is~~E~ 66 (205)
.+.+++|++-.+ -..+.||.++|+.+|+|-.+|+|.-+
T Consensus 32 ~~ala~R~~va~~LL~~~~syreI~~~~g~S~aTItRvsr 71 (88)
T pfam01371 32 REALAQRLRIAKELLRGELSQREIAQELGASIATITRGSN 71 (88)
T ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9999999999999997899899999985985231478899
No 155
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=90.52 E-value=1.2 Score=23.76 Aligned_cols=69 Identities=14% Similarity=0.140 Sum_probs=40.8
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99889999984899999998877998889999999999828999996145322100002321345546777999999999
Q gi|254781218|r 44 NKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRK 123 (205)
Q Consensus 44 gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~ 123 (205)
.||.+++|..+|+|++++++.=+ +.+++++..++.. ..+ ...+.+..
T Consensus 1 plsl~~lA~~~~~S~~~l~~~f~--------------~~~g~s~~~~i~~------------------~Rl-~~a~~~L~ 47 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFK--------------KETGTTPKQYLRD------------------RRL-ERARRLLR 47 (84)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHH--------------HHHCCCHHHHHHH------------------HHH-HHHHHHHH
T ss_conf 98999999988909999999999--------------9889399999999------------------999-99999998
Q ss_pred HCCCCHHHHHHHHCC-CHHHHHH
Q ss_conf 729838999999779-9999999
Q gi|254781218|r 124 DKGMSQIEFGKLLGM-PNSTLSN 145 (205)
Q Consensus 124 ~~glsq~elA~~lgi-s~~tis~ 145 (205)
.-+++..++|..+|. +.+.+.+
T Consensus 48 ~~~~~i~~ia~~~Gy~~~s~f~r 70 (84)
T smart00342 48 DTDLSVTEIALRVGFSSQSYFSR 70 (84)
T ss_pred CCCCHHHHHHHHCCCCCHHHHHH
T ss_conf 57634999988819999999999
No 156
>COG4197 Uncharacterized protein conserved in bacteria, prophage-related [Function unknown]
Probab=90.41 E-value=0.31 Score=27.43 Aligned_cols=44 Identities=20% Similarity=0.327 Sum_probs=22.6
Q ss_pred HHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHC--CCHHHH
Q ss_conf 89999997799999999741488999899999999828--999995
Q gi|254781218|r 129 QIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTK--KHLDWI 172 (205)
Q Consensus 129 q~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lg--vs~d~L 172 (205)
|..||.++|+++.++++|-+|.+.......-.|.++.+ |+...|
T Consensus 15 q~a~a~LLgvsp~~vnQw~~g~r~~~a~r~~aIerAt~g~Vs~~el 60 (96)
T COG4197 15 QKALARLLGVSPPSVNQWIKGRRQVAAERALAIERATSGQVSREEL 60 (96)
T ss_pred HHHHHHHHCCCCHHHHHHHHHEEECCCCCCHHHHHHHCCCCCHHHH
T ss_conf 8999999726814788776520104755332899985377159997
No 157
>PRK10344 DNA-binding transcriptional regulator Nlp; Provisional
Probab=90.23 E-value=1.2 Score=23.89 Aligned_cols=54 Identities=22% Similarity=0.128 Sum_probs=34.8
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHH
Q ss_conf 999999972983899999977999999997414889998999999998289999952
Q gi|254781218|r 117 RLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIY 173 (205)
Q Consensus 117 rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~ 173 (205)
.|......+|.|...++...|++.+|+.+- -..|-..--.-||+++||.+..+-
T Consensus 12 DIiAAL~KrG~sLa~Lsr~aGls~sTL~nA---L~rpwPKgE~iIA~aLGv~P~eIW 65 (90)
T PRK10344 12 DIIAGLRKKGTSMAAESRRNGLSSSTLANA---LSRPWPKGEMIIAKALGTDPWVIW 65 (90)
T ss_pred HHHHHHHHCCCCHHHHHHHCCCCHHHHHHH---HCCCCCHHHHHHHHHHCCCHHHCC
T ss_conf 999999986886999999909986889998---748995679999999787988809
No 158
>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=89.94 E-value=0.92 Score=24.52 Aligned_cols=44 Identities=25% Similarity=0.227 Sum_probs=29.2
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHH--------------CCCCCCCHHHHHHHHHHHCCCH
Q ss_conf 59988999998489999999887--------------7998889999999999828999
Q gi|254781218|r 43 NNKTQKEMAIGANQLESAVNLFE--------------NGMCSTSIRYALYLRNEYEISF 87 (205)
Q Consensus 43 ~gltQ~elA~~~gis~~~is~~E--------------~G~~~psi~~l~~la~~~~vs~ 87 (205)
.|++|.++|+.+|-+.+.||++- +|.. -+++.|..|...+.-.+
T Consensus 2 ~G~kk~~IAk~LGks~s~VS~hlaL~d~Pd~l~~l~~~g~~-~dv~~l~eL~~~~~k~p 59 (93)
T pfam08535 2 KGVKQAEIAKKLGKSKSFVSQHLALLDMPDCIREAYDSGRC-SDIRALYELRRAARKHP 59 (93)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHCCCC-CCHHHHHHHHHHHHHCH
T ss_conf 98779999999788988999999983486999999874776-87999999999999799
No 159
>PHA00675 hypothetical protein
Probab=89.53 E-value=0.6 Score=25.65 Aligned_cols=35 Identities=11% Similarity=0.216 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 79999999997298389999997799999999741
Q gi|254781218|r 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQ 148 (205)
Q Consensus 114 iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~ 148 (205)
.-.+||.+|+..||+-..||...+++++++.++.+
T Consensus 27 ~Vd~IR~LrE~~gl~Yg~La~~f~~pkgtIAkICq 61 (78)
T PHA00675 27 EVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICR 61 (78)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 99999999987284389999997275689999988
No 160
>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=89.53 E-value=0.2 Score=28.57 Aligned_cols=23 Identities=35% Similarity=0.486 Sum_probs=21.5
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 98389999997799999999741
Q gi|254781218|r 126 GMSQIEFGKLLGMPNSTLSNYEQ 148 (205)
Q Consensus 126 glsq~elA~~lgis~~tis~~E~ 148 (205)
..||.|.|..+|||++.+|++|.
T Consensus 195 ~~tQREIA~~LgISRSYVSRIEK 217 (228)
T TIGR02846 195 EKTQREIAKILGISRSYVSRIEK 217 (228)
T ss_pred CCCHHHHHHHHCCCCHHHHHHHH
T ss_conf 54178998770865004548889
No 161
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=89.52 E-value=0.8 Score=24.89 Aligned_cols=42 Identities=19% Similarity=-0.092 Sum_probs=32.9
Q ss_pred HHHHHHHCCCHHHHHHHHCCCCCCCHHH---HHHHHHHHCCCHHH
Q ss_conf 9999984899999998877998889999---99999982899999
Q gi|254781218|r 48 KEMAIGANQLESAVNLFENGMCSTSIRY---ALYLRNEYEISFDW 89 (205)
Q Consensus 48 ~elA~~~gis~~~is~~E~G~~~psi~~---l~~la~~~~vs~d~ 89 (205)
+++|+.+|||.+|||+.=||....|-++ ....++.++=.++.
T Consensus 2 kDIA~~AGVS~sTVSrvLn~~~~Vs~~tr~rV~~aa~elgY~pn~ 46 (327)
T PRK10423 2 KDVARLAGVSTSTVSHVINKDRFVSEAITAKVEAAIKELNYAPSA 46 (327)
T ss_pred HHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCH
T ss_conf 689878698999999997895999999999999999982998688
No 162
>COG3423 Nlp Predicted transcriptional regulator [Transcription]
Probab=89.48 E-value=1.6 Score=23.06 Aligned_cols=56 Identities=25% Similarity=0.255 Sum_probs=38.3
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCC
Q ss_conf 99999997298389999997799999999741488999899999999828999995247
Q gi|254781218|r 117 RLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIYFG 175 (205)
Q Consensus 117 rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~~G 175 (205)
-|....+.+|.|...++...|++.+|+..-.. +.-|.. -.-||.++||++..+--+
T Consensus 12 dI~A~Lkk~G~Sl~~LS~~agls~~tL~n~L~-rp~pkg--EriIA~algv~P~eIWp~ 67 (82)
T COG3423 12 DIIAALKKKGTSLAALSREAGLSSSTLANALD-RPWPKG--ERIIADALGVPPEEIWPS 67 (82)
T ss_pred HHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHC-CCCCHH--HHHHHHHHCCCHHHHCCH
T ss_conf 99999998564299999880878789999874-788718--899999958988881834
No 163
>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=89.48 E-value=0.73 Score=25.14 Aligned_cols=34 Identities=12% Similarity=0.227 Sum_probs=18.4
Q ss_pred HHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHH
Q ss_conf 9999977999999997414889998999999998
Q gi|254781218|r 131 EFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQV 164 (205)
Q Consensus 131 elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~ 164 (205)
|+|+.+|+|..|+|+..|+....+.++..+|-++
T Consensus 2 diA~~~gvS~~TVSr~ln~~~~Vs~~tr~~I~~~ 35 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKPRVSEETRERVLAA 35 (52)
T ss_pred HHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHH
T ss_conf 2888878599999999879898999999999999
No 164
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=89.32 E-value=0.39 Score=26.82 Aligned_cols=28 Identities=25% Similarity=0.516 Sum_probs=25.2
Q ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHCCC
Q ss_conf 9729838999999779999999974148
Q gi|254781218|r 123 KDKGMSQIEFGKLLGMPNSTLSNYEQGR 150 (205)
Q Consensus 123 ~~~glsq~elA~~lgis~~tis~~E~g~ 150 (205)
..+||+|.|.|+.+|.|+..+|-+|..-
T Consensus 16 R~~G~tQ~eIA~~lgTSraNvs~iEk~A 43 (139)
T PRK03975 16 RKRGLTQQEIADILGTSRANISIIEKRA 43 (139)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 9828979999999773288999999999
No 165
>pfam02001 DUF134 Protein of unknown function DUF134. This family of archaeal proteins has no known function.
Probab=89.19 E-value=0.37 Score=27.00 Aligned_cols=38 Identities=21% Similarity=0.267 Sum_probs=22.6
Q ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 999729838999999779999999974148899989999999982
Q gi|254781218|r 121 IRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVT 165 (205)
Q Consensus 121 lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~l 165 (205)
+..-.||+|.|-|+..|||+.|++++-.. .-.|||++|
T Consensus 47 L~D~egl~QeeaA~~MgVSR~Tf~ril~~-------ARkKvA~aL 84 (100)
T pfam02001 47 LVDYEDYTQEEAAKLMGISRRTVWRLLTS-------ARKKIADAL 84 (100)
T ss_pred HHHHCCCCHHHHHHHCCCCHHHHHHHHHH-------HHHHHHHHH
T ss_conf 87360798999998849769999999999-------999999998
No 166
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=89.15 E-value=1.7 Score=22.80 Aligned_cols=23 Identities=9% Similarity=0.258 Sum_probs=15.0
Q ss_pred CCCHHHHHHHHHHH---CCCHHHHHC
Q ss_conf 88999999999982---899999614
Q gi|254781218|r 70 STSIRYALYLRNEY---EISFDWIYD 92 (205)
Q Consensus 70 ~psi~~l~~la~~~---~vs~d~Ll~ 92 (205)
...+..++.||+-| ++++..|+-
T Consensus 177 ~aNLRLVVsIAkkY~~rGl~l~DLIQ 202 (410)
T PRK07598 177 KANLRLVVSVAKKYQNRGLELLDLVQ 202 (410)
T ss_pred HHHHHHHHHHHHHCCCCCCCHHHHHH
T ss_conf 99899999999865789989899998
No 167
>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=89.06 E-value=1.6 Score=23.05 Aligned_cols=27 Identities=26% Similarity=0.234 Sum_probs=21.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHH-CCCCCC
Q ss_conf 988999998489999999887-799888
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFE-NGMCST 71 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E-~G~~~p 71 (205)
+|-.|+|+..|+|.++|-.|| .|.-.|
T Consensus 2 ~~Ige~A~~~gvs~~TlRyYe~~GLl~~ 29 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEKLGLITG 29 (102)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCC
T ss_conf 8099999998979999999998699898
No 168
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=89.02 E-value=1.8 Score=22.75 Aligned_cols=22 Identities=23% Similarity=0.451 Sum_probs=12.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 8389999997799999999741
Q gi|254781218|r 127 MSQIEFGKLLGMPNSTLSNYEQ 148 (205)
Q Consensus 127 lsq~elA~~lgis~~tis~~E~ 148 (205)
+|..|+|+.+|||+..+.++|+
T Consensus 279 ~TL~EIg~~lgvSrERVRQIE~ 300 (320)
T PRK07921 279 RTLDQIGKLFGLSRERVRQIER 300 (320)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
T ss_conf 4799999897969999999999
No 169
>PHA00675 hypothetical protein
Probab=89.00 E-value=0.7 Score=25.27 Aligned_cols=35 Identities=14% Similarity=0.168 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 99999999999985998899999848999999988
Q gi|254781218|r 30 KDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLF 64 (205)
Q Consensus 30 ~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~ 64 (205)
-..=++||++|+..||+-..||...+++.++|.+|
T Consensus 25 d~~Vd~IR~LrE~~gl~Yg~La~~f~~pkgtIAkI 59 (78)
T PHA00675 25 DAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKI 59 (78)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 89999999999872843899999972756899999
No 170
>COG4197 Uncharacterized protein conserved in bacteria, prophage-related [Function unknown]
Probab=88.95 E-value=0.45 Score=26.46 Aligned_cols=47 Identities=19% Similarity=0.114 Sum_probs=42.0
Q ss_pred CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHC--CCHHHHHC
Q ss_conf 889999984899999998877998889999999999828--99999614
Q gi|254781218|r 46 TQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYE--ISFDWIYD 92 (205)
Q Consensus 46 tQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~--vs~d~Ll~ 92 (205)
.|+.+|..+|+++.++|.|-+|.+..+.+....|..+-+ |+-..|-.
T Consensus 14 ~q~a~a~LLgvsp~~vnQw~~g~r~~~a~r~~aIerAt~g~Vs~~elrp 62 (96)
T COG4197 14 GQKALARLLGVSPPSVNQWIKGRRQVAAERALAIERATSGQVSREELRP 62 (96)
T ss_pred CHHHHHHHHCCCCHHHHHHHHHEEECCCCCCHHHHHHHCCCCCHHHHCC
T ss_conf 3899999972681478877652010475533289998537715999766
No 171
>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.
Probab=88.95 E-value=1.6 Score=23.07 Aligned_cols=28 Identities=21% Similarity=0.348 Sum_probs=22.8
Q ss_pred CCCHHHHHHHHCCCHHHHHHHH-CCCCCC
Q ss_conf 9988999998489999999887-799888
Q gi|254781218|r 44 NKTQKEMAIGANQLESAVNLFE-NGMCST 71 (205)
Q Consensus 44 gltQ~elA~~~gis~~~is~~E-~G~~~p 71 (205)
.||-.++|+..|+|.++|-.|| .|.-.|
T Consensus 1 ~mtIgelA~~~gvs~~tiRyYE~~GLl~p 29 (139)
T cd01110 1 ELSVGEVAKRSGVAVSALHFYEQKGLIAS 29 (139)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHCCCCCC
T ss_conf 99789999998878899999998788466
No 172
>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=88.90 E-value=0.54 Score=25.96 Aligned_cols=28 Identities=18% Similarity=0.096 Sum_probs=14.7
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 9999859988999998489999999887
Q gi|254781218|r 38 DIRKANNKTQKEMAIGANQLESAVNLFE 65 (205)
Q Consensus 38 ~lR~~~gltQ~elA~~~gis~~~is~~E 65 (205)
.+|-..|+|+.|+|+.+|+|+++|++.+
T Consensus 14 ~l~y~~~~t~~EIA~~lgis~~~V~~~~ 41 (50)
T pfam04545 14 VLRFGEGLTLEEIGERLGISRERVRQIE 41 (50)
T ss_pred HHHCCCCCHHHHHHHHHCCCHHHHHHHH
T ss_conf 9870688249999999897999999999
No 173
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=88.88 E-value=0.62 Score=25.58 Aligned_cols=20 Identities=15% Similarity=0.190 Sum_probs=9.8
Q ss_pred CCHHHHHHHHCCCHHHHHHH
Q ss_conf 83899999977999999997
Q gi|254781218|r 127 MSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 127 lsq~elA~~lgis~~tis~~ 146 (205)
=|..|+|+.+|++...+..+
T Consensus 116 Pt~~EiA~~l~is~~~v~~~ 135 (229)
T PRK12427 116 PNFEEISAELNLTADEYQEY 135 (229)
T ss_pred CCHHHHHHHHCCCHHHHHHH
T ss_conf 99999998919999999999
No 174
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=88.68 E-value=1.9 Score=22.60 Aligned_cols=30 Identities=23% Similarity=0.444 Sum_probs=25.4
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf 999972983899999977999999997414
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNYEQG 149 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~E~g 149 (205)
..|-..|+|+.|+|+.+|+|+..++++|+.
T Consensus 219 ~~ry~~~~Tl~eIa~~lGvSreRVrQie~~ 248 (257)
T PRK08215 219 NLRFFQGKTQMEVADEIGISQAQVSRLEKA 248 (257)
T ss_pred HHHHCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 999479998999999989699999999999
No 175
>pfam02001 DUF134 Protein of unknown function DUF134. This family of archaeal proteins has no known function.
Probab=88.60 E-value=0.56 Score=25.88 Aligned_cols=27 Identities=19% Similarity=-0.043 Sum_probs=23.4
Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 998599889999984899999998877
Q gi|254781218|r 40 RKANNKTQKEMAIGANQLESAVNLFEN 66 (205)
Q Consensus 40 R~~~gltQ~elA~~~gis~~~is~~E~ 66 (205)
-.-.||+|+|-|.++|||++|++++=.
T Consensus 48 ~D~egl~QeeaA~~MgVSR~Tf~ril~ 74 (100)
T pfam02001 48 VDYEDYTQEEAAKLMGISRRTVWRLLT 74 (100)
T ss_pred HHHCCCCHHHHHHHCCCCHHHHHHHHH
T ss_conf 736079899999884976999999999
No 176
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=88.43 E-value=2 Score=22.50 Aligned_cols=24 Identities=25% Similarity=0.451 Sum_probs=21.1
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 729838999999779999999974
Q gi|254781218|r 124 DKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 124 ~~glsq~elA~~lgis~~tis~~E 147 (205)
...+|..|+|+.+|+|+.|..+|.
T Consensus 171 ~~~~Taeela~~~giSRvTaRRYL 194 (224)
T COG4565 171 DQELTAEELAQALGISRVTARRYL 194 (224)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 776479999988372199999999
No 177
>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=88.29 E-value=0.82 Score=24.83 Aligned_cols=127 Identities=12% Similarity=0.174 Sum_probs=80.0
Q ss_pred HCCCHHHHHHHHHHHHHHHHHHH---HC--C-CCHH---HHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHH-C----
Q ss_conf 00156689999999999999999---85--9-9889---99998489999999887799888999999999982-8----
Q gi|254781218|r 19 LIITPEIRQYWKDVGTRIKDIRK---AN--N-KTQK---EMAIGANQLESAVNLFENGMCSTSIRYALYLRNEY-E---- 84 (205)
Q Consensus 19 ~~~~~~~~~~~~~iG~rik~lR~---~~--g-ltQ~---elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~-~---- 84 (205)
|.|+.+.-|-- +==+||.-++ .. | ++++ .+|..+||+..-|...|+-.+.+++..=...-+.= +
T Consensus 111 VKvATTkaQrK--LFFNLRk~K~ki~~l~~gw~~~~e~~~~A~~L~V~~~eV~eMe~RlsG~D~~L~~~~~~~~~~~~~~ 188 (279)
T TIGR02392 111 VKVATTKAQRK--LFFNLRKMKKKITRLQDGWLNPEEVEAIAEELGVSEEEVLEMESRLSGRDISLNASIDDDEDDGGSD 188 (279)
T ss_pred HHHHCCHHHHH--HHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCH
T ss_conf 88852776788--8765888999863101579898999999976389888998875145537733478876553456311
Q ss_pred -CCHHHHHCC-C-CCCCCCCCCCCHHHHHHHHHHH----------HH---HHHHHHC-CCCHHHHHHHHCCCHHHHHHHH
Q ss_conf -999996145-3-2210000232134554677799----------99---9999972-9838999999779999999974
Q gi|254781218|r 85 -ISFDWIYDG-E-VIDRRYEDVTNKKRLDPYAIGA----------RL---KSIRKDK-GMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 85 -vs~d~Ll~g-e-~~~~~~~~~~~~~~~d~~~iG~----------rL---k~lR~~~-glsq~elA~~lgis~~tis~~E 147 (205)
-+++||-+. . ..........+.. .-...+.. +| |.+. +. +.|..+||...|||..-|.++|
T Consensus 189 ~~~~~yL~D~~~~~~~~~l~~~~~~~-~~~~~L~~AL~~Ld~RsR~I~~~RwL~-d~~~~TL~~LA~eygvSaERiRQiE 266 (279)
T TIGR02392 189 FAPIAYLADKATSDPEATLEEEQWEE-LQTQKLANALESLDARSRRIIEARWLD-DDGKLTLHELAAEYGVSAERIRQIE 266 (279)
T ss_pred HHHHHHHCCCCCCCHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHCCC-CCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 45788630477778889999989999-999999999885228879999873027-8899647899988487466799999
Q ss_pred CC
Q ss_conf 14
Q gi|254781218|r 148 QG 149 (205)
Q Consensus 148 ~g 149 (205)
..
T Consensus 267 ~~ 268 (279)
T TIGR02392 267 KN 268 (279)
T ss_pred HH
T ss_conf 99
No 178
>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=88.17 E-value=1.6 Score=23.00 Aligned_cols=27 Identities=19% Similarity=0.282 Sum_probs=22.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHH-CCCCCC
Q ss_conf 988999998489999999887-799888
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFE-NGMCST 71 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E-~G~~~p 71 (205)
||-.|||+..|+|.+||-.|| .|.-.|
T Consensus 1 mtIgelA~~~gvs~~TiRyYE~~GLl~~ 28 (120)
T cd04781 1 LDIAEVARQSGLPASTLRYYEEKGLIAS 28 (120)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCC
T ss_conf 9689999998868898989996498065
No 179
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=88.08 E-value=2.1 Score=22.36 Aligned_cols=46 Identities=13% Similarity=0.213 Sum_probs=31.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHH-CCCCCCCHH----------------HHHHHHHHHCCCHHHH
Q ss_conf 988999998489999999887-799888999----------------9999999828999996
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFE-NGMCSTSIR----------------YALYLRNEYEISFDWI 90 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E-~G~~~psi~----------------~l~~la~~~~vs~d~L 90 (205)
|+-.+||++.|++..+|-.|| .|.-.|+.. .+++-|+.++.|++.+
T Consensus 1 M~IgelAk~tGv~~~TIRyYE~~GLl~~~~R~~~GyR~Y~~~~l~rL~fI~~ar~lGfsL~EI 63 (135)
T PRK10227 1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEES 63 (135)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 968999999896999999999838977343289992177899999999999998879999999
No 180
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=88.03 E-value=0.86 Score=24.70 Aligned_cols=35 Identities=14% Similarity=0.438 Sum_probs=21.6
Q ss_pred CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 38999999779999999974148899989999999982
Q gi|254781218|r 128 SQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVT 165 (205)
Q Consensus 128 sq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~l 165 (205)
++..+|+.+||+++.+++| |...|.... .+|.++.
T Consensus 12 sk~klA~aLgIs~~aVsqW--ge~IPE~rA-y~le~iT 46 (75)
T PRK09744 12 SKTKLANAAGVRLASVAAW--GELVPEGRA-MRLQEAS 46 (75)
T ss_pred CHHHHHHHHCCCHHHHHHH--HHHCCHHHH-HHHHHHH
T ss_conf 2999999949987999887--401606889-9999985
No 181
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor; InterPro: IPR014200 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 , . Members of this entry represent the endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. In Bacillus subtilis, sigma-29 is synthesized as a precursor (P31), specifically in the mother cell compartment, and is activated by a cleavage that removes the N-terminal 29 amino acids .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=87.94 E-value=0.29 Score=27.64 Aligned_cols=24 Identities=33% Similarity=0.452 Sum_probs=19.7
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf 983899999977999999997414
Q gi|254781218|r 126 GMSQIEFGKLLGMPNSTLSNYEQG 149 (205)
Q Consensus 126 glsq~elA~~lgis~~tis~~E~g 149 (205)
.-+|+++|+++|++++.+++.|..
T Consensus 198 e~tqk~vad~lGisqsyisrlek~ 221 (234)
T TIGR02835 198 EKTQKEVADLLGISQSYISRLEKR 221 (234)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 146788898862468999999999
No 182
>TIGR02850 spore_sigG RNA polymerase sigma-G factor; InterPro: IPR014212 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 , . Members of this entry comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also designated stage III sporulation protein G (SpoIIIG). Members of this entry are closely related to sigma-F (SpoIIAC), another sporulation sigma factor.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=87.90 E-value=0.9 Score=24.58 Aligned_cols=32 Identities=22% Similarity=0.420 Sum_probs=27.8
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf 99999972983899999977999999997414
Q gi|254781218|r 118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQG 149 (205)
Q Consensus 118 Lk~lR~~~glsq~elA~~lgis~~tis~~E~g 149 (205)
|-..|--.|-||-|+|+.+|+++..+++.|..
T Consensus 214 il~~rff~G~tqmeva~eiGisqaqvsrlek~ 245 (254)
T TIGR02850 214 ILKLRFFEGKTQMEVAEEIGISQAQVSRLEKA 245 (254)
T ss_pred HHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHH
T ss_conf 77755314631334565403016888888899
No 183
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=87.78 E-value=0.87 Score=24.69 Aligned_cols=28 Identities=18% Similarity=0.252 Sum_probs=23.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHH-CCCCCCC
Q ss_conf 988999998489999999887-7998889
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFE-NGMCSTS 72 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E-~G~~~ps 72 (205)
++-.+||+..|++..+|-.|| .|.-.|.
T Consensus 2 ~~Ige~A~~~gvs~~tiRyYE~~GLl~~~ 30 (140)
T PRK09514 2 YRIGELAKLCEVTPDTLRFYEKQGLMDPS 30 (140)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCC
T ss_conf 86999999989689999999986999865
No 184
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=87.67 E-value=0.79 Score=24.94 Aligned_cols=26 Identities=27% Similarity=0.419 Sum_probs=22.4
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf 72983899999977999999997414
Q gi|254781218|r 124 DKGMSQIEFGKLLGMPNSTLSNYEQG 149 (205)
Q Consensus 124 ~~glsq~elA~~lgis~~tis~~E~g 149 (205)
...+|+.|.|+.+|+|+..++++|.-
T Consensus 201 ~~~~Tl~EIa~~lgISrerVrQIe~~ 226 (239)
T PRK08301 201 GEEKTQKEVADMLGISQSYISRLEKR 226 (239)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 98406999999989789999999999
No 185
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family; InterPro: IPR014304 This entry is a group of RNA polymerase sigma factors where one of the members is designated as SigZ in Bacillus subtilis . This group has a very sporadic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member Dechloromonas aromatica (strain RCB), that appears to have two of these sigma factors. A member of which appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri (strain ATCC 700601 / ES114), where a second one is chromosomally encoded..
Probab=87.64 E-value=0.45 Score=26.43 Aligned_cols=30 Identities=33% Similarity=0.490 Sum_probs=16.1
Q ss_pred HHHHCCCCHHHHHHHHCCCHHHH-HHHHCCC
Q ss_conf 99972983899999977999999-9974148
Q gi|254781218|r 121 IRKDKGMSQIEFGKLLGMPNSTL-SNYEQGR 150 (205)
Q Consensus 121 lR~~~glsq~elA~~lgis~~ti-s~~E~g~ 150 (205)
+-+-.|+||+++|+.+|+|.+.. |+.-+|+
T Consensus 111 L~el~G~sQ~e~A~kLGlSlSGaKSRVQRGR 141 (170)
T TIGR02959 111 LTELEGLSQKEIAEKLGLSLSGAKSRVQRGR 141 (170)
T ss_pred HHHCCCCCHHHHHHHCCCCCCCHHHHHHHHH
T ss_conf 8750799827998761753351567889999
No 186
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=87.62 E-value=2.2 Score=22.19 Aligned_cols=112 Identities=14% Similarity=0.163 Sum_probs=50.9
Q ss_pred HHHHHHHC----CCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCC---CHHHHHCCCCCCCCCCCCCCHH-
Q ss_conf 99999985----998899999848999999988779988899999999998289---9999614532210000232134-
Q gi|254781218|r 36 IKDIRKAN----NKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEI---SFDWIYDGEVIDRRYEDVTNKK- 107 (205)
Q Consensus 36 ik~lR~~~----gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~v---s~d~Ll~ge~~~~~~~~~~~~~- 107 (205)
++.++... .-+.+++|+.+|++...|..++.-....++..-..+...=+- ..|+|-+. ..+ +.....+..
T Consensus 139 lr~~~~~~~~~~~~~~~eiA~~l~~~~~~v~~~~~~l~~~~~SLd~~~~~~~~~~~~~~d~l~d~-~~~-~~~~~~~~~~ 216 (284)
T PRK06596 139 LRKAKKRLGWLNPEEVEMIAEELGVSEEEVREMESRLSGQDASLDAPIDDDDGESGAPQDYLEDK-SSD-PAAVLEEDNW 216 (284)
T ss_pred HHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHCCC-CCC-HHHHHHHHHH
T ss_conf 99999987145986299999997919999999999853798202378888877754246651467-898-6789999999
Q ss_pred ------HHHH--HHHHHHHHHH---HH--HCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf ------5546--7779999999---99--72983899999977999999997414
Q gi|254781218|r 108 ------RLDP--YAIGARLKSI---RK--DKGMSQIEFGKLLGMPNSTLSNYEQG 149 (205)
Q Consensus 108 ------~~d~--~~iG~rLk~l---R~--~~glsq~elA~~lgis~~tis~~E~g 149 (205)
.+.. ..+..|=+.+ |- ..++|+.|+|+.+|+|+..++++|+.
T Consensus 217 ~~~~~~~L~~al~~L~~REr~Il~~Ry~~d~~~TL~EIg~~lgiSrERVRQIe~k 271 (284)
T PRK06596 217 EDQRRELLADALETLDERSRDIIEARWLDDDKSTLQELAAEYGVSAERIRQIEKN 271 (284)
T ss_pred HHHHHHHHHHHHHHCCHHHHHHHHHHCCCCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 9999999999986099999999999767999948999999979799999999999
No 187
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=87.47 E-value=0.79 Score=24.95 Aligned_cols=29 Identities=21% Similarity=0.327 Sum_probs=25.1
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 99997298389999997799999999741
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNYEQ 148 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~E~ 148 (205)
-++.-.|||+.|.|+.+|||.+|+.++..
T Consensus 137 ~L~r~eGls~~EIAe~LgiS~~tV~~~l~ 165 (178)
T PRK12529 137 LMATLDGMKQKDIAQALDIALPTVKKYIH 165 (178)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 79988299999999998959999999999
No 188
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=87.16 E-value=0.98 Score=24.35 Aligned_cols=33 Identities=12% Similarity=-0.158 Sum_probs=27.4
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf 999999972983899999977999999997414
Q gi|254781218|r 117 RLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQG 149 (205)
Q Consensus 117 rLk~lR~~~glsq~elA~~lgis~~tis~~E~g 149 (205)
.+-.++--.|+|+.|.|+.+|+|..++..|.+.
T Consensus 113 ~ii~~~~~~g~t~~EIA~~~gis~~~Vk~~~r~ 145 (154)
T PRK06759 113 YIIFERFFVGKTMGEIALETEMTYYQVRWIYRQ 145 (154)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 999999996998999999989899999999999
No 189
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=86.98 E-value=2.4 Score=21.97 Aligned_cols=30 Identities=17% Similarity=0.234 Sum_probs=24.5
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHC-CCCCCC
Q ss_conf 599889999984899999998877-998889
Q gi|254781218|r 43 NNKTQKEMAIGANQLESAVNLFEN-GMCSTS 72 (205)
Q Consensus 43 ~gltQ~elA~~~gis~~~is~~E~-G~~~ps 72 (205)
.+++-.+||+..|++..+|-.||+ |.-.|+
T Consensus 6 ~~m~IgelAk~~gvs~~tIRyYE~~GLl~~~ 36 (144)
T PRK13752 6 ENLTIGVFAKAAGVNVETIRFYQRKGLLPEP 36 (144)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHCCCCCCC
T ss_conf 2382999999978984566798725997987
No 190
>PRK05949 RNA polymerase sigma factor; Validated
Probab=86.88 E-value=2.4 Score=21.93 Aligned_cols=109 Identities=18% Similarity=0.280 Sum_probs=59.3
Q ss_pred CCCCHHHHHHHHCCCHHH-HHHHHCCC------CCCCHHHHHHHHHHH---CCCHHHHHCC---------CCCC----CC
Q ss_conf 599889999984899999-99887799------888999999999982---8999996145---------3221----00
Q gi|254781218|r 43 NNKTQKEMAIGANQLESA-VNLFENGM------CSTSIRYALYLRNEY---EISFDWIYDG---------EVID----RR 99 (205)
Q Consensus 43 ~gltQ~elA~~~gis~~~-is~~E~G~------~~psi~~l~~la~~~---~vs~d~Ll~g---------e~~~----~~ 99 (205)
+.-|-.+.|.++|++... -..++.|. ....+..++.||+-| +++++.|+-. +-+| .+
T Consensus 64 ~~~~~~ewa~~~~~~~~~l~~~~~~g~~A~~~LI~sNLRLVvsIAkrY~~~Gl~~~DLIQEGniGLirAvekFDp~rG~R 143 (327)
T PRK05949 64 REPSLPEWADAVNLSETELKQALKQGKRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYK 143 (327)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCE
T ss_conf 89756889987266789999998758999999999819999999986436998989999985899999999809655971
Q ss_pred CC---------------CCCCHHHHHHHHHHHHHHHHHH---------HCCCCHHHHHHHHCCCHHHHHHHHCCCC
Q ss_conf 00---------------2321345546777999999999---------7298389999997799999999741488
Q gi|254781218|r 100 YE---------------DVTNKKRLDPYAIGARLKSIRK---------DKGMSQIEFGKLLGMPNSTLSNYEQGRT 151 (205)
Q Consensus 100 ~~---------------~~~~~~~~d~~~iG~rLk~lR~---------~~glsq~elA~~lgis~~tis~~E~g~~ 151 (205)
|+ .........|..+..++..+++ .+.-+..|+|+.+|++...+..+..-..
T Consensus 144 FSTYA~wWIRq~I~r~i~~~~r~IRlP~~~~~~~~ki~~~~~~l~~~lgr~pt~~EiA~~l~i~~~~v~~~l~~~~ 219 (327)
T PRK05949 144 FSTYAYWWIRQAITRAIAQQARTIRLPIHITEKLNKIKKTQRELSQKLGRSATPAEIAKALELEPSQIREYLSMAR 219 (327)
T ss_pred EEEEHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCC
T ss_conf 3420099998999999998288744637899999999999999999818899889999894999999999998418
No 191
>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=86.84 E-value=2.4 Score=21.92 Aligned_cols=28 Identities=14% Similarity=0.108 Sum_probs=20.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHH-CCCCCCC
Q ss_conf 988999998489999999887-7998889
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFE-NGMCSTS 72 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E-~G~~~ps 72 (205)
+|-.+||+..|||..++-.|| .|.-.|.
T Consensus 1 y~Ige~Ak~~gvs~~TLRyYe~~GLl~p~ 29 (97)
T cd04782 1 FTTGEFAKLCGISKQTLFHYDKIGLFKPE 29 (97)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCC
T ss_conf 97899999989699999999966998986
No 192
>pfam05269 Phage_CII Bacteriophage CII protein. This family consists of several phage CII regulatory proteins. CII plays a key role in the lysis-lysogeny decision in bacteriophage lambda and related phages.
Probab=86.70 E-value=0.48 Score=26.28 Aligned_cols=44 Identities=14% Similarity=0.105 Sum_probs=27.9
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHH
Q ss_conf 5998899999848999999988779988899999999998289999
Q gi|254781218|r 43 NNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFD 88 (205)
Q Consensus 43 ~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d 88 (205)
.-++|..+|+.+|+..+.||+|-.+.. |-..+|+.+-+ |+|.-|
T Consensus 22 a~~gq~~~A~~~Gv~es~ISRwK~~~~-~~~smllAvLE-~Gv~dd 65 (91)
T pfam05269 22 AMLGQRKTAEAVGVDESQISRWKRDWI-PKFSMLLAVLE-WGVVDD 65 (91)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHH-HHHHHHHHHHH-HCCCCH
T ss_conf 998436689996888998634443069-99999999999-555654
No 193
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=86.48 E-value=1.2 Score=23.80 Aligned_cols=25 Identities=36% Similarity=0.440 Sum_probs=16.5
Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 9972983899999977999999997
Q gi|254781218|r 122 RKDKGMSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 122 R~~~glsq~elA~~lgis~~tis~~ 146 (205)
+...|.+..++|..+|||++|+.+|
T Consensus 17 l~~~G~~~~~iA~~~GVsr~Tiyr~ 41 (42)
T cd00569 17 LLAAGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred HHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 9997898999999979799999865
No 194
>COG1513 CynS Cyanate lyase [Inorganic ion transport and metabolism]
Probab=86.38 E-value=2.6 Score=21.77 Aligned_cols=103 Identities=16% Similarity=0.036 Sum_probs=76.9
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHH
Q ss_conf 99999999999998599889999984899999998877998889999999999828999996145322100002321345
Q gi|254781218|r 29 WKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKR 108 (205)
Q Consensus 29 ~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~ 108 (205)
.-++.+.+-...+.+|||-++++..+|.+.-.+...=-|....+.+....+++.++.+-|.+.--...+.+.. +...-.
T Consensus 6 i~~l~~~ll~~Kk~kgLsfaDl~~~lG~~ev~vaa~~ygq~~~~~~ear~v~e~L~L~~~~v~~L~~~p~rg~-l~~~~P 84 (151)
T COG1513 6 ILDLADALLLAKKKKGLSFADLADGLGLAEVFVAAALYGQAALPADEARAVGEALDLDEDAILLLQMIPLRGC-LGPVIP 84 (151)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHHCCCCCCC-CCCCCC
T ss_conf 8999999999787549969999755083399999999762028999999999981998788998421675677-899899
Q ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHH
Q ss_conf 54677799999999972983899999
Q gi|254781218|r 109 LDPYAIGARLKSIRKDKGMSQIEFGK 134 (205)
Q Consensus 109 ~d~~~iG~rLk~lR~~~glsq~elA~ 134 (205)
.||. -.|.-++..-.|.+.+++..
T Consensus 85 TDP~--iYRfYE~~qvYG~~lK~lih 108 (151)
T COG1513 85 TDPL--IYRFYEMLQVYGTTLKALIH 108 (151)
T ss_pred CCHH--HHHHHHHHHHHCHHHHHHHH
T ss_conf 9718--99999999997645999999
No 195
>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=86.26 E-value=1 Score=24.18 Aligned_cols=32 Identities=22% Similarity=0.372 Sum_probs=26.0
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 99999997298389999997799999999741
Q gi|254781218|r 117 RLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQ 148 (205)
Q Consensus 117 rLk~lR~~~glsq~elA~~lgis~~tis~~E~ 148 (205)
.+=.++--.|+|+.|.|+.+|+|..++.....
T Consensus 121 ~~~~l~~~~~~s~~eIA~~lg~s~~~v~~~~~ 152 (162)
T TIGR02937 121 EVLVLRYLEGLSYKEIAEILGISEGTVKSRLK 152 (162)
T ss_pred HHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 99999997189988999986899999999999
No 196
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=85.96 E-value=2.7 Score=21.63 Aligned_cols=98 Identities=11% Similarity=0.014 Sum_probs=49.6
Q ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCC-C----HHHHHCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf 99985998899999848999999988779988899999999998289-9----999614532210000232134554677
Q gi|254781218|r 39 IRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEI-S----FDWIYDGEVIDRRYEDVTNKKRLDPYA 113 (205)
Q Consensus 39 lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~v-s----~d~Ll~ge~~~~~~~~~~~~~~~d~~~ 113 (205)
+-.+..+|+.+||+.+|||..||-+- |..+-..-+...+ + --|.+.-.. +..+....+... ..
T Consensus 12 lL~~~~lt~~eLA~~L~VS~RTIR~D--------I~~iN~~L~~~~i~~~~~~~GY~L~i~d-~~~~~~ll~~~~---~~ 79 (585)
T PRK09863 12 LLEQQDRSGGELAQQLGVSRRTIVRD--------IAYINFTLNGKAIGSISGSAKYHLEILN-RRSLFQLLQKSD---NE 79 (585)
T ss_pred HHHCCCCCHHHHHHHCCCCCHHHHHH--------HHHHHHHHHHCCEEEEECCCCEEEEECC-HHHHHHHHHCCH---HH
T ss_conf 99759999899998749971178999--------9999999841851898468752888678-788987754355---57
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 79999999997298389999997799999999741
Q gi|254781218|r 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQ 148 (205)
Q Consensus 114 iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~ 148 (205)
.-.-+..+.....++..|||+.+-+|++|+.+...
T Consensus 80 ~~~il~~lL~~~~i~l~dLAd~lfVSrsTi~~dl~ 114 (585)
T PRK09863 80 DRLLLLNLLLNTFTPMGQLASALFLSRTWVAERLP 114 (585)
T ss_pred HHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 89999998626898899999985839999999999
No 197
>TIGR00721 tfx DNA-binding protein, Tfx family; InterPro: IPR004645 This is a family of Tfx DNA-binding proteins, which is restricted to the archaea. Homology among the members is strongest in the helix-turn-helix-containing N-terminal region. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.; GO: 0003677 DNA binding.
Probab=85.69 E-value=0.66 Score=25.41 Aligned_cols=38 Identities=24% Similarity=0.384 Sum_probs=30.3
Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHC
Q ss_conf 997298389999997799999999741488999899999999828
Q gi|254781218|r 122 RKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTK 166 (205)
Q Consensus 122 R~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lg 166 (205)
...+||+|.+.|..|+.+++-+|-+|.-- ++.|.++.+
T Consensus 17 lR~kGl~Q~eIAk~LkTtRaNvS~iEkrA-------~EnIeKa~N 54 (142)
T TIGR00721 17 LREKGLKQKEIAKILKTTRANVSIIEKRA-------LENIEKAKN 54 (142)
T ss_pred HHHCCCCHHHHHHHHCCCCHHHHHHHHHH-------HHHHHHHHH
T ss_conf 86338887889877267201378988874-------432377663
No 198
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). 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. 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 in the N-terminal domains of typical MerR-like proteins.
Probab=85.52 E-value=0.6 Score=25.66 Aligned_cols=66 Identities=21% Similarity=0.293 Sum_probs=39.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHCC-CCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 98899999848999999988779-98889999999999828999996145322100002321345546777999999999
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFENG-MCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRK 123 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E~G-~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~ 123 (205)
.|-.|+|+.+|++..++-.||+. .-.|+ .. .+.+ ..|+ ...+. .-..|+.+|
T Consensus 1 YtI~eva~~~Gv~~~tLRyyEk~~~l~~~-R~----~~G~--------------R~Ys----~~di~---~l~~I~~l~- 53 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEKEFNLYIP-RT----ENGR--------------RYYT----DEDIE---LLKKIKTLL- 53 (67)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCC-CC----CCCC--------------CCCC----HHHHH---HHHHHHHHH-
T ss_conf 97899999988687899999873799999-69----9989--------------5239----99999---999999999-
Q ss_pred HCCCCHHHHHHHHC
Q ss_conf 72983899999977
Q gi|254781218|r 124 DKGMSQIEFGKLLG 137 (205)
Q Consensus 124 ~~glsq~elA~~lg 137 (205)
..|+|.++..+.++
T Consensus 54 ~~G~sl~~Ik~~LN 67 (67)
T cd04764 54 EKGLSIKEIKEILN 67 (67)
T ss_pred HCCCCHHHHHHHHC
T ss_conf 96998999999859
No 199
>PRK04217 hypothetical protein; Provisional
Probab=85.47 E-value=1.1 Score=24.14 Aligned_cols=38 Identities=24% Similarity=0.349 Sum_probs=24.8
Q ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 999729838999999779999999974148899989999999982
Q gi|254781218|r 121 IRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVT 165 (205)
Q Consensus 121 lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~l 165 (205)
+..-.||+|.|-|+..|||+.|+.++... .-.+||.+|
T Consensus 53 L~D~egl~qeeaA~~M~VSR~Tf~ril~~-------AR~KvA~aL 90 (110)
T PRK04217 53 LVDYEGLTQEEAGKRMGVSRGTVWRALTS-------ARKKVAQML 90 (110)
T ss_pred HHHHCCCCHHHHHHHCCCCHHHHHHHHHH-------HHHHHHHHH
T ss_conf 87360798999998849769999999999-------999999998
No 200
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=85.20 E-value=1.3 Score=23.50 Aligned_cols=48 Identities=6% Similarity=-0.132 Sum_probs=36.2
Q ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf 9998599889999984899999998877998889999999999828999
Q gi|254781218|r 39 IRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISF 87 (205)
Q Consensus 39 lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~ 87 (205)
.++..+++++++++..|.++ ++..|.++...+|...+-...+.++..-
T Consensus 7 rq~el~~~~~~~~~~~g~~p-s~~e~~~~~~~~s~~~~~~~l~~L~~~g 54 (201)
T COG1974 7 RQKELLDFIRSLIKETGYPP-SIREIGDALGLASPSAIHSHLKALERKG 54 (201)
T ss_pred HHHHHHHHHHHHHHHHCCCC-HHHHHHHHHCCCCHHHHHHHHHHHHCCC
T ss_conf 89998999999999728993-0899987517898489999999973088
No 201
>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=85.06 E-value=3 Score=21.38 Aligned_cols=74 Identities=19% Similarity=0.282 Sum_probs=46.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHH-CCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 988999998489999999887-7998889999999999828999996145322100002321345546777999999999
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFE-NGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRK 123 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E-~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~ 123 (205)
.+-.++|+.+|+++.++-.|| .|...|.-+ +.+ +.|+ ...++ .+ ..|+.+.+
T Consensus 2 y~Ig~vA~l~gv~~~TLR~YEr~GLi~P~R~------~G~--------------RlYs----~~Di~--rL-rfIkrL~~ 54 (120)
T cd04767 2 YPIGVVAELLNIHPETLRIWERHGLIKPARR------NGQ--------------RLYS----NNDLK--RL-RFIKKLIN 54 (120)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCC------CCC--------------CCCC----HHHHH--HH-HHHHHHHH
T ss_conf 2489999997868899999998589688888------982--------------2779----99999--99-99999999
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf 72983899999977999999997414
Q gi|254781218|r 124 DKGMSQIEFGKLLGMPNSTLSNYEQG 149 (205)
Q Consensus 124 ~~glsq~elA~~lgis~~tis~~E~g 149 (205)
+.|++..+....+.+ +..|++-
T Consensus 55 e~G~nlagI~~iLsl----~~c~~~~ 76 (120)
T cd04767 55 EKGLNIAGVKQILSM----YPCWSIR 76 (120)
T ss_pred HCCCCHHHHHHHHHC----CCCHHHH
T ss_conf 759689999999806----3231232
No 202
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=84.73 E-value=1.3 Score=23.55 Aligned_cols=29 Identities=24% Similarity=0.369 Sum_probs=25.4
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 99997298389999997799999999741
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNYEQ 148 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~E~ 148 (205)
.++...|+|+.|.|+.+|||.+++..+-.
T Consensus 129 ~L~~~eGls~~EIA~~LgiS~~tVk~~l~ 157 (172)
T PRK12523 129 LYNRLDGMGHAEIAERLGVSVSRVRQYLA 157 (172)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 99999399999999998939999999999
No 203
>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=84.70 E-value=3.1 Score=21.27 Aligned_cols=69 Identities=20% Similarity=0.294 Sum_probs=39.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHC-CCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9889999984899999998877-998889999999999828999996145322100002321345546777999999999
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFEN-GMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRK 123 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E~-G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~ 123 (205)
+|-.++|+.+|+++.++-.||. |.-.|.-. . +| -..|+ ..| ...-..|+.+.+
T Consensus 2 YtIgevA~~~Gvs~~tLR~yE~~GLl~P~R~-----~-----------~g---~R~Ys------~~d-i~~l~~I~~L~~ 55 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYERLGLLSPSRT-----D-----------GG---TRRYS------ERD-IERLRRIQRLTQ 55 (91)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCC-----C-----------CC---CEECC------HHH-HHHHHHHHHHHH
T ss_conf 6589999998929999999998599798839-----9-----------99---97447------999-999999999999
Q ss_pred HCCCCHHHHHHHHCCC
Q ss_conf 7298389999997799
Q gi|254781218|r 124 DKGMSQIEFGKLLGMP 139 (205)
Q Consensus 124 ~~glsq~elA~~lgis 139 (205)
..|++..+....+...
T Consensus 56 ~~G~sl~~I~~~L~l~ 71 (91)
T cd04766 56 ELGVNLAGVKRILELE 71 (91)
T ss_pred HCCCCHHHHHHHHHHH
T ss_conf 8699899999999808
No 204
>KOG1168 consensus
Probab=84.65 E-value=0.55 Score=25.89 Aligned_cols=38 Identities=34% Similarity=0.525 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHH--------C-CCHHHHHHHHCC
Q ss_conf 7779999999997298389999997--------7-999999997414
Q gi|254781218|r 112 YAIGARLKSIRKDKGMSQIEFGKLL--------G-MPNSTLSNYEQG 149 (205)
Q Consensus 112 ~~iG~rLk~lR~~~glsq~elA~~l--------g-is~~tis~~E~g 149 (205)
.++++|.|+.|.+.|.||.|++..+ | ++++||.++|+=
T Consensus 220 EaFAErFKQRRIKLGVTQADVG~ALAnLKiPGVGsLSQSTICRFESL 266 (385)
T KOG1168 220 EAFAERFKQRRIKLGVTQADVGKALANLKIPGVGSLSQSTICRFESL 266 (385)
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCEEEEEEE
T ss_conf 99999987545430642777788987276887553231213321000
No 205
>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=84.48 E-value=1.3 Score=23.59 Aligned_cols=27 Identities=19% Similarity=0.000 Sum_probs=12.6
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 999985998899999848999999988
Q gi|254781218|r 38 DIRKANNKTQKEMAIGANQLESAVNLF 64 (205)
Q Consensus 38 ~lR~~~gltQ~elA~~~gis~~~is~~ 64 (205)
.+...-+++|.+||+.+++++++++++
T Consensus 11 ~l~~~~~~s~~~la~~~~~~~~~vs~~ 37 (59)
T pfam01047 11 ILYEHGPLTVSELAEKLGVDRSTVTRV 37 (59)
T ss_pred HHHHCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999469929999999988586549999
No 206
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=84.47 E-value=3.2 Score=21.21 Aligned_cols=102 Identities=16% Similarity=0.131 Sum_probs=52.4
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHC------C----CCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHH
Q ss_conf 599889999984899999998877------9----988899999999998289999961453221000023213455467
Q gi|254781218|r 43 NNKTQKEMAIGANQLESAVNLFEN------G----MCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPY 112 (205)
Q Consensus 43 ~gltQ~elA~~~gis~~~is~~E~------G----~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~ 112 (205)
.-.|.+|+|...+++...|++.-+ + ...| .+++.++|..|+++-+..-.-..+-....+..-.....|.
T Consensus 181 ~prtl~Eia~~~~i~~k~i~r~~~~l~~~l~~~~~~~~p-~~~i~Rf~s~L~l~~~v~~~a~~i~~~~~~~~i~~Gr~P~ 259 (310)
T PRK00423 181 VPRTLDEIAEVSRVSRKEIGRTYRFLARELNLKLPPTDP-IDYVPRFASELKLSGEVQKKAIEILRKAKERGLTSGKGPT 259 (310)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCCH-HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCCHH
T ss_conf 997499999995988999999999999984678888899-9999999988699989999999999999972776795868
Q ss_pred HH---HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 77---9999999997298389999997799999999
Q gi|254781218|r 113 AI---GARLKSIRKDKGMSQIEFGKLLGMPNSTLSN 145 (205)
Q Consensus 113 ~i---G~rLk~lR~~~glsq~elA~~lgis~~tis~ 145 (205)
.+ .--|.......+.||.++|+.+|++..|+.+
T Consensus 260 siaAaaIyla~~~~~~~~t~~~Ia~v~~vsevTIr~ 295 (310)
T PRK00423 260 GLAAAAIYIASLLEGERRTQREVAEVAGVTEVTVRN 295 (310)
T ss_pred HHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHH
T ss_conf 999999999999948898999999896988999999
No 207
>COG2842 Uncharacterized ATPase, putative transposase [General function prediction only]
Probab=84.24 E-value=2.7 Score=21.63 Aligned_cols=54 Identities=17% Similarity=0.127 Sum_probs=41.6
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHH-HHHHHHCCC
Q ss_conf 9999999999859988999998489999999887799888999999-999982899
Q gi|254781218|r 32 VGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYAL-YLRNEYEIS 86 (205)
Q Consensus 32 iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~-~la~~~~vs 86 (205)
.=+.+|+.-+..+++|+.+|..+|+++.++|+|=|| ..+.....- +|+..++-.
T Consensus 7 ~~k~~k~f~e~~~~~q~~~a~gi~~~~~~vsk~L~g-~~g~~~~~~a~ia~~le~~ 61 (297)
T COG2842 7 EIKKLKEFAEFSGMCQKYLARGIGTSAPALSKYLNG-YKGDYATNEAKIAAFLEKK 61 (297)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCC-CCCHHHHHHHHHHHHHCCC
T ss_conf 999999999861666999998736684457878437-6741777899999997277
No 208
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=84.08 E-value=2.1 Score=22.32 Aligned_cols=31 Identities=19% Similarity=0.246 Sum_probs=26.0
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 9999997298389999997799999999741
Q gi|254781218|r 118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQ 148 (205)
Q Consensus 118 Lk~lR~~~glsq~elA~~lgis~~tis~~E~ 148 (205)
+=.++...|+|++|.|+.+|||.+|+.++..
T Consensus 127 vf~L~r~~gls~~EIA~~LgiS~~tVk~~l~ 157 (167)
T PRK12528 127 AFLLAQVDGLGYGEIATELGISLATVKRYLN 157 (167)
T ss_pred HHHHHHHHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9999998298999999997979999999999
No 209
>pfam02787 CPSase_L_D3 Carbamoyl-phosphate synthetase large chain, oligomerisation domain. Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain.
Probab=83.89 E-value=1.4 Score=23.36 Aligned_cols=52 Identities=19% Similarity=0.284 Sum_probs=30.8
Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHCCC-CCCCHHHHHHHHHHHCCCHHHHH
Q ss_conf 99729838999999779999999974148-89998999999998289999952
Q gi|254781218|r 122 RKDKGMSQIEFGKLLGMPNSTLSNYEQGR-TIPEIKPARKIKQVTKKHLDWIY 173 (205)
Q Consensus 122 R~~~glsq~elA~~lgis~~tis~~E~g~-~~Ps~~~l~kIa~~lgvs~d~L~ 173 (205)
-+..|+|-.++|..+|++...+..+-... ..|....+.--|-.|.-...|++
T Consensus 67 aK~~GFSD~~IA~l~~~~e~~Ir~~R~~~~i~P~yk~VDTcAaEF~a~TpY~Y 119 (122)
T pfam02787 67 AKKLGFSDAQIAKLLGVTEEEVRKLRKELGIRPVYKMVDTCAAEFEAKTPYYY 119 (122)
T ss_pred HHHHCCCHHHHHHHHCCCHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCC
T ss_conf 99949998999988398699999999987991226210385205577998555
No 210
>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=83.88 E-value=1 Score=24.25 Aligned_cols=31 Identities=19% Similarity=0.314 Sum_probs=24.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHH
Q ss_conf 8389999997799999999741488999899
Q gi|254781218|r 127 MSQIEFGKLLGMPNSTLSNYEQGRTIPEIKP 157 (205)
Q Consensus 127 lsq~elA~~lgis~~tis~~E~g~~~Ps~~~ 157 (205)
||-+|.|+.+|++++|+.+|-..+..|....
T Consensus 2 lTv~EaA~yLgv~~~t~~~l~~~g~l~~~~~ 32 (49)
T TIGR01764 2 LTVEEAAEYLGVSKSTVYRLIEEGELPAYRV 32 (49)
T ss_pred CCHHHHHHHCCCCHHHHHHHHHCCCCCEEEC
T ss_conf 8778899771999057899997189850006
No 211
>PHA01083 hypothetical protein
Probab=83.66 E-value=2.4 Score=21.99 Aligned_cols=63 Identities=22% Similarity=0.220 Sum_probs=50.1
Q ss_pred HHHHHHHCCCCH-HHHHHHHCCCHHHHHHHHCCCC-CCCHHHHHHHHHHHCCCHHHHHCCCCCCC
Q ss_conf 999999859988-9999984899999998877998-88999999999982899999614532210
Q gi|254781218|r 36 IKDIRKANNKTQ-KEMAIGANQLESAVNLFENGMC-STSIRYALYLRNEYEISFDWIYDGEVIDR 98 (205)
Q Consensus 36 ik~lR~~~gltQ-~elA~~~gis~~~is~~E~G~~-~psi~~l~~la~~~~vs~d~Ll~ge~~~~ 98 (205)
+....+.++..| +++|..+|++++.||.+-+|.+ ..+-+..+-||+.-+++.+--+-|-.-|+
T Consensus 5 ldAYK~aknYvQdKQIAhDlg~~pq~iS~~RkG~R~Ylsd~eAifLAe~~GiD~E~aLlG~hADr 69 (153)
T PHA01083 5 LDAYKKAKNYVQYKQIAHDLGVSPQKISKMRTGVRTYISDEEAIFLAESAGIDPEIALLGCHADR 69 (153)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCHHHHCCHHHHHHHHHHCCCCHHHHHHHHHHCC
T ss_conf 99999999888899999980999899999981237643538899989870998888899854112
No 212
>pfam05930 Phage_AlpA Prophage CP4-57 regulatory protein (AlpA). This family consists of several short bacterial and phage proteins which are related to the E. coli protein AlpA. AlpA suppress two phenotypes of a delta lon protease mutant, overproduction of capsular polysaccharide and sensitivity to UV light. Several of the sequences in this family are thought to be DNA-binding proteins.
Probab=83.57 E-value=1.5 Score=23.27 Aligned_cols=32 Identities=19% Similarity=0.242 Sum_probs=25.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHH
Q ss_conf 83899999977999999997414889998999
Q gi|254781218|r 127 MSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPA 158 (205)
Q Consensus 127 lsq~elA~~lgis~~tis~~E~g~~~Ps~~~l 158 (205)
+...|+++.+|++++|+.++++....|..-.+
T Consensus 4 lr~~eV~~~~glsrstiyr~i~~G~FP~pikl 35 (51)
T pfam05930 4 LRLKEVEQLTGLSRSTIYRLIKDGEFPKPIKL 35 (51)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCEEE
T ss_conf 37999999989899999999987999998760
No 213
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=83.37 E-value=1.1 Score=23.97 Aligned_cols=20 Identities=20% Similarity=0.039 Sum_probs=9.9
Q ss_pred CCHHHHHHHHCCCHHHHHHH
Q ss_conf 98899999848999999988
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLF 64 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~ 64 (205)
+||+++|..+|+++.++|+.
T Consensus 9 lt~~~iA~~lG~tretvsR~ 28 (48)
T smart00419 9 LTRQEIAELLGLTRETVSRT 28 (48)
T ss_pred CCHHHHHHHHCCCHHHHHHH
T ss_conf 79999999979979999999
No 214
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=83.36 E-value=1.3 Score=23.59 Aligned_cols=38 Identities=16% Similarity=0.245 Sum_probs=26.1
Q ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 999729838999999779999999974148899989999999982
Q gi|254781218|r 121 IRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVT 165 (205)
Q Consensus 121 lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~l 165 (205)
+....||+|.|.|...|||++|+.+..+ ....|+|.+|
T Consensus 44 LvD~~~l~QeeAA~rMgISr~Tfwr~l~-------sAR~KvA~aL 81 (99)
T COG1342 44 LVDYEGLTQEEAALRMGISRQTFWRLLT-------SARKKVADAL 81 (99)
T ss_pred HHHHHHCCHHHHHHHHCCCHHHHHHHHH-------HHHHHHHHHH
T ss_conf 8868610578999984642999999999-------9999999998
No 215
>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=82.90 E-value=1.8 Score=22.79 Aligned_cols=32 Identities=25% Similarity=0.406 Sum_probs=28.6
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHH-HH
Q ss_conf 999999997298389999997799999999-74
Q gi|254781218|r 116 ARLKSIRKDKGMSQIEFGKLLGMPNSTLSN-YE 147 (205)
Q Consensus 116 ~rLk~lR~~~glsq~elA~~lgis~~tis~-~E 147 (205)
.+|=++|---||+..|.|+.+|||..|+.+ |.
T Consensus 151 a~~veLr~F~Gl~~~E~A~~L~~S~~Tv~Rdw~ 183 (194)
T TIGR02999 151 AEVVELRFFAGLTVEEIAELLGVSVRTVERDWR 183 (194)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 998853110488989999986888878998799
No 216
>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=82.46 E-value=1.1 Score=24.08 Aligned_cols=22 Identities=18% Similarity=0.137 Sum_probs=19.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 9889999984899999998877
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFEN 66 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E~ 66 (205)
||-+|||...|.|+++|++|-+
T Consensus 1 mT~eELa~~~G~srQtINkwaR 22 (122)
T pfam07037 1 MTPEELAELTGYSRQTINRWVR 22 (122)
T ss_pred CCHHHHHHHHCCHHHHHHHHHH
T ss_conf 9878998874712999999999
No 217
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=82.45 E-value=1.6 Score=22.98 Aligned_cols=33 Identities=30% Similarity=0.486 Sum_probs=28.8
Q ss_pred HHHHHHHHHCC-CCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 99999999729-8389999997799999999741
Q gi|254781218|r 116 ARLKSIRKDKG-MSQIEFGKLLGMPNSTLSNYEQ 148 (205)
Q Consensus 116 ~rLk~lR~~~g-lsq~elA~~lgis~~tis~~E~ 148 (205)
+-|+-+|..-| ++|.|+.+.+|.|+.|+++.-+
T Consensus 199 ~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~ 232 (258)
T COG2512 199 EILDLIRERGGRITQAELRRALGLSKTTVSRILR 232 (258)
T ss_pred HHHHHHHHHCCEEEHHHHHHHHCCCHHHHHHHHH
T ss_conf 9999999858978699988860997677999999
No 218
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=82.04 E-value=4 Score=20.60 Aligned_cols=99 Identities=16% Similarity=0.112 Sum_probs=62.6
Q ss_pred HHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHH---HHHHHHHHHHCCCCHHHHHHH
Q ss_conf 99998877998889999999999828999996145322100002321345546777---999999999729838999999
Q gi|254781218|r 59 SAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAI---GARLKSIRKDKGMSQIEFGKL 135 (205)
Q Consensus 59 ~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~i---G~rLk~lR~~~glsq~elA~~ 135 (205)
..-..+|+..+.--|..+.+.-..|+||++.|...-+. ..|...........+ ..-+..+.+.+.|..++++..
T Consensus 120 ~~~~~~e~~~~~eEI~~f~~~L~eygIsf~dLv~~sPK---H~DtR~~~i~iA~~i~~~~~l~~~l~~kK~LPikeL~~~ 196 (237)
T PRK08311 120 EYEEEIENEERREEILEFQKELKEFGITFEDLVEESPK---HRDTRENAIKIAKTIAENEELLEKLKRKKKLPLKELEKR 196 (237)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHCCCC---CHHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCHHHHHHH
T ss_conf 99999988999999999999999939759999772999---878999999999998649999999999288879999988
Q ss_pred HCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCC
Q ss_conf 779999999974148899989999999982899
Q gi|254781218|r 136 LGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKH 168 (205)
Q Consensus 136 lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs 168 (205)
+++++.|+-++ + ..+..++-+|.-.
T Consensus 197 ~~VsrKtlER~---R-----KYIIAv~lIl~~d 221 (237)
T PRK08311 197 VKVSRKTLERN---R-----KYIIAVAIILAGD 221 (237)
T ss_pred CCCCHHHHHHH---H-----HHHHHHHHHHHCC
T ss_conf 59889999742---3-----9999999999199
No 219
>PRK07773 replicative DNA helicase; Validated
Probab=82.00 E-value=3.4 Score=21.01 Aligned_cols=53 Identities=11% Similarity=0.217 Sum_probs=44.1
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHC
Q ss_conf 67779999999997298389999997799999999741488999899999999828
Q gi|254781218|r 111 PYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTK 166 (205)
Q Consensus 111 ~~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lg 166 (205)
|..+-..++..+.+.|+|..+|++.+|+.....+.| +..|+-..+.++|.+++
T Consensus 709 P~evw~~Vr~a~~~~g~t~r~~~~~~g~~~~g~~~~---k~~~SR~Rl~~~A~~l~ 761 (868)
T PRK07773 709 PKKVWKQVRPRLQAKQMTTRQLHEPIGTSYCGSTLW---KHSPSRERAHRVAARIQ 761 (868)
T ss_pred CHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCCHHH---CCCCCHHHHHHHHHHHC
T ss_conf 589999999999860654899998725454640132---03422778999998747
No 220
>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=81.95 E-value=1.8 Score=22.69 Aligned_cols=28 Identities=25% Similarity=0.204 Sum_probs=22.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHH-CCCCCCC
Q ss_conf 988999998489999999887-7998889
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFE-NGMCSTS 72 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E-~G~~~ps 72 (205)
||-.|+|+.+|+|.++|-.|| .|.-.|.
T Consensus 1 mtIgelAk~~gvs~~tlRyYE~~GLl~p~ 29 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEKEGLLSPD 29 (108)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCC
T ss_conf 96899999989799999999977982998
No 221
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=81.83 E-value=2.1 Score=22.36 Aligned_cols=28 Identities=25% Similarity=0.502 Sum_probs=23.9
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 9999729838999999779999999974
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~E 147 (205)
-++...|+|..|.|+.+|||.+|+.+..
T Consensus 128 lL~~~eGlsy~EIAe~LgIS~~tV~~~l 155 (168)
T PRK12525 128 LMSQLEGLTYVEIGERLGVSLSRIHQYM 155 (168)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9999929999999999897999999999
No 222
>pfam00376 MerR MerR family regulatory protein.
Probab=81.75 E-value=1.8 Score=22.70 Aligned_cols=27 Identities=37% Similarity=0.481 Sum_probs=19.1
Q ss_pred CHHHHHHHHCCCHHHHHHHHCCCCCCC
Q ss_conf 389999997799999999741488999
Q gi|254781218|r 128 SQIEFGKLLGMPNSTLSNYEQGRTIPE 154 (205)
Q Consensus 128 sq~elA~~lgis~~tis~~E~g~~~Ps 154 (205)
|..|+|+++|++..++..||.-.-.|+
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~Gli~~ 27 (38)
T pfam00376 1 TIGEVAKLLGVSPRTLRYYEKIGLLPP 27 (38)
T ss_pred CHHHHHHHHCCCHHHHHHHHHCCCCCC
T ss_conf 989999998879999999998689899
No 223
>PRK09954 hypothetical protein; Provisional
Probab=81.56 E-value=1.9 Score=22.56 Aligned_cols=28 Identities=21% Similarity=0.069 Sum_probs=24.6
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 9999998599889999984899999998
Q gi|254781218|r 36 IKDIRKANNKTQKEMAIGANQLESAVNL 63 (205)
Q Consensus 36 ik~lR~~~gltQ~elA~~~gis~~~is~ 63 (205)
++.+|+.=-++|.|||..+|+|+++|.-
T Consensus 9 l~~i~~~p~i~q~ela~~lgisrs~va~ 36 (362)
T PRK09954 9 LAILRRNPLIQQNEIADILQISRSRVAA 36 (362)
T ss_pred HHHHHHCCCCCHHHHHHHHCCCHHHHHH
T ss_conf 9999878995899999997987999999
No 224
>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=81.43 E-value=1.9 Score=22.57 Aligned_cols=28 Identities=32% Similarity=0.364 Sum_probs=18.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHCCCCCCC
Q ss_conf 8389999997799999999741488999
Q gi|254781218|r 127 MSQIEFGKLLGMPNSTLSNYEQGRTIPE 154 (205)
Q Consensus 127 lsq~elA~~lgis~~tis~~E~g~~~Ps 154 (205)
++..|+|+.+|++..++..||.-.-.|+
T Consensus 1 ytI~eva~~~gvs~~tlR~ye~~gLl~p 28 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERIGLLSP 28 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCC
T ss_conf 9588999998939999999999799898
No 225
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=81.38 E-value=2 Score=22.47 Aligned_cols=68 Identities=24% Similarity=0.219 Sum_probs=40.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHH-CCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 988999998489999999887-7998889999999999828999996145322100002321345546777999999999
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFE-NGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRK 123 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E-~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~ 123 (205)
+|-.|+|+.+|++.++|-.|| .|.-.|+...- + ...+- ...| ...-..|+.+|
T Consensus 1 ytI~e~a~~~gvs~~tlR~ye~~Gll~p~~r~~----~---------------g~R~Y-----~~~d-i~~l~~I~~lr- 54 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRTE----G---------------GYRLY-----SDED-LERLRFIKRLK- 54 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCC----C---------------CCEEC-----CHHH-HHHHHHHHHHH-
T ss_conf 978899999896999999999858989984489----9---------------97443-----9999-99999999999-
Q ss_pred HCCCCHHHHHHHHCC
Q ss_conf 729838999999779
Q gi|254781218|r 124 DKGMSQIEFGKLLGM 138 (205)
Q Consensus 124 ~~glsq~elA~~lgi 138 (205)
..|++..+..+.+.+
T Consensus 55 ~~G~~l~~Ik~~l~l 69 (70)
T smart00422 55 ELGFSLEEIKELLEL 69 (70)
T ss_pred HCCCCHHHHHHHHHC
T ss_conf 978999999999962
No 226
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=81.16 E-value=4.3 Score=20.41 Aligned_cols=108 Identities=14% Similarity=0.160 Sum_probs=59.7
Q ss_pred CCCHHHHHHHHCCCHHHHHHHH-CCC------CCCCHHHHHHHHHHH---CCCHHHHHCC---------CCCC----CCC
Q ss_conf 9988999998489999999887-799------888999999999982---8999996145---------3221----000
Q gi|254781218|r 44 NKTQKEMAIGANQLESAVNLFE-NGM------CSTSIRYALYLRNEY---EISFDWIYDG---------EVID----RRY 100 (205)
Q Consensus 44 gltQ~elA~~~gis~~~is~~E-~G~------~~psi~~l~~la~~~---~vs~d~Ll~g---------e~~~----~~~ 100 (205)
--|..+.|+.+|++...+.+.- .|. ....+..++.||+-| +++++.|+-. +-+| .+|
T Consensus 122 ~p~~~ewa~~~~~~~~~l~~~~~~g~~Ar~~LI~aNLRLVVsIAkkY~~rGl~l~DLIQEGniGLirAvEKFDp~rG~RF 201 (385)
T PRK07406 122 FPSVEEWAELVDMPLPKFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKF 201 (385)
T ss_pred CCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCE
T ss_conf 54279999880888899999998799999999999899999999865689989889999858999999998196548822
Q ss_pred C---------------CCCCHHHHHHHHHHHHHHHHHH-------H--CCCCHHHHHHHHCCCHHHHHHHHCCCC
Q ss_conf 0---------------2321345546777999999999-------7--298389999997799999999741488
Q gi|254781218|r 101 E---------------DVTNKKRLDPYAIGARLKSIRK-------D--KGMSQIEFGKLLGMPNSTLSNYEQGRT 151 (205)
Q Consensus 101 ~---------------~~~~~~~~d~~~iG~rLk~lR~-------~--~glsq~elA~~lgis~~tis~~E~g~~ 151 (205)
+ .........|..+...+..+++ . +.-|..++|+.+|++...+..+.+...
T Consensus 202 STYA~WWIRqaI~RaI~~~sr~IRlP~h~~e~l~ki~k~~~~L~~~lGr~Pt~eEIA~~l~i~~e~v~~~~~~~~ 276 (385)
T PRK07406 202 STYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQ 276 (385)
T ss_pred EEHHHHHHHHHHHHHHHHCCCEECCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHCC
T ss_conf 110299999999999997386120208999999999999999998708998699999993999999999998548
No 227
>TIGR02405 trehalos_R_Ecol trehalose operon repressor; InterPro: IPR012771 Trehalose is a non-reducing disaccharide which can be used as both a carbon source and an osmoprotectant in bacteria. Trehalose uptake into the cytoplasm occurs via a trehalose-specific phosphotransferase system which phosphorylates trehalase to trehalose-6-phosphate (Tre6P) during transport into the cytoplasm, and a hydrolase which hydrolyses Tre6P to glucose and glucose-6-phophate. This entry represents LacI-type TreR, a transcriptional repressor of trehalose uptake found mainly within the gamma-proteobacteria. It does not include the GntR-type TreR's such as those found in Bacillus species. It is capable of binding both the inducer Tre6P and trehalose. Binding of trehalose does not affect the repressor's affinity for its DNA binding site, while binding Tre6P substantially reduces its affinity. The repression activity of TreR is therefore regulated by the ratio of trehalose to Tre6P within the cell . The protein is composed of two domains, an N-terminal DNA-binding helix-turn-helix domain, and a C-terminal effector-binding domain which is homologous to that of LacI. The effector-binding domain is composed of two subdomains, both of which form an alpha-beta-alpha sandwhich, with the effector binding site located at the interface of these subdomains . Tre6P and trehalose bind competitively to this site, with the affinty for trehalose substantially lower than that for Tre6P.; GO: 0003677 DNA binding, 0016566 specific transcriptional repressor activity, 0005991 trehalose metabolic process, 0016481 negative regulation of transcription.
Probab=81.05 E-value=0.71 Score=25.22 Aligned_cols=31 Identities=29% Similarity=0.109 Sum_probs=15.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHH
Q ss_conf 9889999984899999998877998889999
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFENGMCSTSIRY 75 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E~G~~~psi~~ 75 (205)
||-++.|+..||+.|||||.=|+...-++++
T Consensus 2 LTIkDIArLagVgKSTVSRVLnNe~~V~~~t 32 (311)
T TIGR02405 2 LTIKDIARLAGVGKSTVSRVLNNESKVSIET 32 (311)
T ss_pred CHHHHHHHHHCCCCEEEEEEEECCCCCCCHH
T ss_conf 6177769770886202331561688887203
No 228
>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.
Probab=80.94 E-value=4.3 Score=20.36 Aligned_cols=61 Identities=20% Similarity=0.154 Sum_probs=41.8
Q ss_pred HHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHC-CCHHHHHH
Q ss_conf 9999999982899999614532210000232134554677799999999972983899999977-99999999
Q gi|254781218|r 74 RYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRKDKGMSQIEFGKLLG-MPNSTLSN 145 (205)
Q Consensus 74 ~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~~~glsq~elA~~lg-is~~tis~ 145 (205)
..+-.+|++|+|+.+.|++..-. +....+..++ +--+|+..|+|..+.|..+| -+++|+..
T Consensus 3 ~I~~~Va~~~~v~~~~i~~~~R~---------~~~~~aR~ia--~yL~r~~~~~s~~~Ig~~fg~rdHsTV~~ 64 (90)
T cd06571 3 LIIEAVAEYFGISVEDLRSKSRK---------KEIALARQIA--MYLARELTGLSLPEIGRAFGGRDHSTVLH 64 (90)
T ss_pred HHHHHHHHHHCCCHHHHHCCCCC---------CHHHHHHHHH--HHHHHHHHCCCHHHHHHHHCCCCHHHHHH
T ss_conf 89999999979989998469887---------1378999999--99999997889999999958997149999
No 229
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family.
Probab=80.67 E-value=4.4 Score=20.31 Aligned_cols=141 Identities=13% Similarity=0.201 Sum_probs=100.0
Q ss_pred HHHHHH--CCCCHHHHHHHHCCCHHHHH-HHH--------------------CCC------CCCCHHHHHHHHHHH---C
Q ss_conf 999998--59988999998489999999-887--------------------799------888999999999982---8
Q gi|254781218|r 37 KDIRKA--NNKTQKEMAIGANQLESAVN-LFE--------------------NGM------CSTSIRYALYLRNEY---E 84 (205)
Q Consensus 37 k~lR~~--~gltQ~elA~~~gis~~~is-~~E--------------------~G~------~~psi~~l~~la~~~---~ 84 (205)
..++.. +..|.+++|+.+|+|...+. .+. .|. ....+..++.||+-| |
T Consensus 55 ~~l~~~~g~~ps~~ewA~~~~~~~~~l~~~l~G~~aWA~~a~l~leLk~~~r~G~RAK~kMi~ANLRLVVSvAKKYq~Rg 134 (336)
T TIGR02997 55 EELEEQLGREPSKEEWAAALGLSEAELRQRLRGLQAWAEAAQLELELKLVLRQGQRAKEKMIKANLRLVVSVAKKYQNRG 134 (336)
T ss_pred HHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCC
T ss_conf 99998508999878999871899889999987657889984225899999997899999998760226889999851368
Q ss_pred CCHHHHH---------CCCCCC----CCCC---------------CCCCHHHHHHHHHHHHHHHHHHH---------CCC
Q ss_conf 9999961---------453221----0000---------------23213455467779999999997---------298
Q gi|254781218|r 85 ISFDWIY---------DGEVID----RRYE---------------DVTNKKRLDPYAIGARLKSIRKD---------KGM 127 (205)
Q Consensus 85 vs~d~Ll---------~ge~~~----~~~~---------------~~~~~~~~d~~~iG~rLk~lR~~---------~gl 127 (205)
+.+=.|+ .-|-+| ++|| ....+++-.|.-|-++|..+++. +-=
T Consensus 135 lElLDLIQEG~lGL~RAVEKFDPtrGYKFSTYAYWWIRQ~ITRAIA~qSRTIRLPiH~~EKLnkiKK~qReL~q~lGR~P 214 (336)
T TIGR02997 135 LELLDLIQEGTLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLNKIKKVQRELSQKLGRRP 214 (336)
T ss_pred CCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 83356887634312211233577778863301246875688999843688324741076666899899899999838897
Q ss_pred CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHH-HHHHCCCHHHHHCC-CCC
Q ss_conf 3899999977999999997414889998999999-99828999995247-210
Q gi|254781218|r 128 SQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKI-KQVTKKHLDWIYFG-DEV 178 (205)
Q Consensus 128 sq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kI-a~~lgvs~d~L~~G-~e~ 178 (205)
|..|+|+.++++...+..+-.-... +++.=.++ -+-=++.+-.|+-. +..
T Consensus 215 s~~EiAe~lel~~~qvR~~l~~~~~-p~SLd~~VrG~e~dt~LgdLl~d~~~~ 266 (336)
T TIGR02997 215 SEAEIAEALELEPEQVRELLQRARQ-PVSLDTRVRGDEEDTELGDLLEDEDGE 266 (336)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHCC-CCCCCCCCCCCCCCCHHHHHCCCCCCC
T ss_conf 8689998838898899999997078-744577326888542265432688899
No 230
>TIGR02941 Sigma_B RNA polymerase sigma-B factor; InterPro: IPR014288 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 sigma factor, sigmaB. It is restricted to certain species within the order Bacillales including Staphylococcus aureus , Listeria monocytogenes and Bacillus cereus (strain ATCC 14579 / DSM 31) ..
Probab=80.56 E-value=0.75 Score=25.07 Aligned_cols=136 Identities=19% Similarity=0.210 Sum_probs=62.9
Q ss_pred HHHHHHHHHHCCC-HHHHHHHHH-------------HHHHHHHHHHHC------CCCHHHHHHHHCCCHHHHH-HHHCCC
Q ss_conf 6654333100015-668999999-------------999999999985------9988999998489999999-887799
Q gi|254781218|r 10 SLKSLQEYTLIIT-PEIRQYWKD-------------VGTRIKDIRKAN------NKTQKEMAIGANQLESAVN-LFENGM 68 (205)
Q Consensus 10 ~~~~~~~~~~~~~-~~~~~~~~~-------------iG~rik~lR~~~------gltQ~elA~~~gis~~~is-~~E~G~ 68 (205)
=..+---|++|.- +|++-|.++ ||-|||..=... -=+-.|.|..+|+|.--|- -.|-|.
T Consensus 79 ~g~~FE~FaiPTiiGEIKrylRDKTWsvHVPRRIKelGpkIkk~~dELT~~lqrSP~i~EIA~~lg~SEEEVLE~Me~g~ 158 (256)
T TIGR02941 79 YGKAFEAFAIPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELTDELQRSPKIAEIADRLGVSEEEVLEIMEMGQ 158 (256)
T ss_pred CCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCHHCCCCCCHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHCCC
T ss_conf 04565662366100101121115643001574110037720145566444421487065464121774888987761477
Q ss_pred --CCCCHHHHHHHHHH-HCCCHHHHHCCCCCCCCCCCCCCHHHHHHH---HHHHH---HHHHHHHCCCCHHHHHHHHCCC
Q ss_conf --88899999999998-289999961453221000023213455467---77999---9999997298389999997799
Q gi|254781218|r 69 --CSTSIRYALYLRNE-YEISFDWIYDGEVIDRRYEDVTNKKRLDPY---AIGAR---LKSIRKDKGMSQIEFGKLLGMP 139 (205)
Q Consensus 69 --~~psi~~l~~la~~-~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~---~iG~r---Lk~lR~~~glsq~elA~~lgis 139 (205)
+..|++..+.=+.= =-|.+=.+++- .....|..++.-+... .+..| |=+.-=..||+|+|-++.+|||
T Consensus 159 sY~alSvD~~iEadsDGStVa~ld~vG~---~edgYd~tE~Rm~LekIlpiLserE~~ii~c~f~enlsQKeTGErlGiS 235 (256)
T TIGR02941 159 SYKALSVDDKIEADSDGSTVALLDLVGE---VEDGYDQTEKRMVLEKILPILSEREKEIIECTFIENLSQKETGERLGIS 235 (256)
T ss_pred CCCEEECCCCCCCCCCCCCCHHHHHHCC---CCCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCCCHHHHHCCHH
T ss_conf 7433322530003688851111112167---6665457888888887410005445676665531478730023222403
Q ss_pred HHHHHHHHC
Q ss_conf 999999741
Q gi|254781218|r 140 NSTLSNYEQ 148 (205)
Q Consensus 140 ~~tis~~E~ 148 (205)
+..+|++-+
T Consensus 236 QMHVSRl~R 244 (256)
T TIGR02941 236 QMHVSRLQR 244 (256)
T ss_pred HHHHHHHHH
T ss_conf 556778889
No 231
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=80.30 E-value=2.4 Score=21.94 Aligned_cols=29 Identities=10% Similarity=0.180 Sum_probs=22.2
Q ss_pred HHHHHH-HCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 999999-85998899999848999999988
Q gi|254781218|r 36 IKDIRK-ANNKTQKEMAIGANQLESAVNLF 64 (205)
Q Consensus 36 ik~lR~-~~gltQ~elA~~~gis~~~is~~ 64 (205)
+..+.. .-|+||.+||..+|+.++++++.
T Consensus 37 L~~L~~~~~g~tq~eLa~~l~v~~~t~tr~ 66 (144)
T PRK03573 37 LHNIHQLPPDQSQIQLAKAIGIEQPSLVRT 66 (144)
T ss_pred HHHHHHCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999997398989999999979878369999
No 232
>KOG2252 consensus
Probab=80.25 E-value=2.8 Score=21.57 Aligned_cols=119 Identities=15% Similarity=0.105 Sum_probs=70.4
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHH-CCCHHHHHHHHCCCCC-----CCHHHHHHHHHHHCCCHHHHHCCCCCCCCCC
Q ss_conf 999999999999998599889999984-8999999988779988-----8999999999982899999614532210000
Q gi|254781218|r 28 YWKDVGTRIKDIRKANNKTQKEMAIGA-NQLESAVNLFENGMCS-----TSIRYALYLRNEYEISFDWIYDGEVIDRRYE 101 (205)
Q Consensus 28 ~~~~iG~rik~lR~~~gltQ~elA~~~-gis~~~is~~E~G~~~-----psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~ 101 (205)
.-++|..||+..-+..++.|.=||+.+ |.|+.++|..=+.-.. .--++..+.++-|+ ..+.
T Consensus 327 dTkeia~rI~~eLk~~sIpQaiFAervLcRSQGTLSDLLrnPKPW~klKsGRetFrRM~~WL~-eP~~------------ 393 (558)
T KOG2252 327 DTKEIAQRIKAELKRYSIPQAIFAERVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMANWLE-EPEF------------ 393 (558)
T ss_pred CHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCHHHHHHHCCCCHHHHCCCCHHHHHHHHHHC-CHHH------------
T ss_conf 189999999999864577378888888612522299996389952544032099999998742-7877------------
Q ss_pred CCCCHHHHHHHHHHHH-HHHHHHHC-----C-------CCHHHH-HHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCC
Q ss_conf 2321345546777999-99999972-----9-------838999-99977999999997414889998999999998289
Q gi|254781218|r 102 DVTNKKRLDPYAIGAR-LKSIRKDK-----G-------MSQIEF-GKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKK 167 (205)
Q Consensus 102 ~~~~~~~~d~~~iG~r-Lk~lR~~~-----g-------lsq~el-A~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgv 167 (205)
.| ++.+|++. + ..++.- .-.+.+-+.|+..+-...-.|+-+..+.|+.-|+.
T Consensus 394 --------------~r~m~~L~~~a~kRke~ep~~d~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L 459 (558)
T KOG2252 394 --------------QRLMSALRKKACKRKEQEPTDDKMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNL 459 (558)
T ss_pred --------------HHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEECHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCC
T ss_conf --------------899998778876401268873335667886156458899999999861789879999999998587
Q ss_pred CH----HHHH
Q ss_conf 99----9952
Q gi|254781218|r 168 HL----DWIY 173 (205)
Q Consensus 168 s~----d~L~ 173 (205)
.+ +||+
T Consensus 460 ~~sTV~NfFm 469 (558)
T KOG2252 460 ELSTVINFFM 469 (558)
T ss_pred CHHHHHHHHH
T ss_conf 6888999877
No 233
>pfam08279 HTH_11 HTH domain. This family includes helix-turn-helix domains in a wide variety of proteins.
Probab=80.24 E-value=2.6 Score=21.71 Aligned_cols=20 Identities=25% Similarity=0.373 Sum_probs=10.4
Q ss_pred CCHHHHHHHHCCCHHHHHHH
Q ss_conf 83899999977999999997
Q gi|254781218|r 127 MSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 127 lsq~elA~~lgis~~tis~~ 146 (205)
+|-.++|+.+|+|..|+.+.
T Consensus 16 vt~~~La~~l~VSr~TV~rd 35 (55)
T pfam08279 16 ISGQELAEKLGVSRRTIRRD 35 (55)
T ss_pred CCHHHHHHHHCCCHHHHHHH
T ss_conf 18999999969889999999
No 234
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), 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. 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.
Probab=80.18 E-value=4.6 Score=20.21 Aligned_cols=67 Identities=16% Similarity=0.047 Sum_probs=39.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHC--CCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 9889999984899999998877--99888999999999982899999614532210000232134554677799999999
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFEN--GMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIR 122 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E~--G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR 122 (205)
.|-.|+|+.+|++++++-.||. |...|.-. +.--+.|+ ..| ...-..|+.+.
T Consensus 1 ysIgEva~~~gv~~~tLRywE~~~~~~~P~r~-------------------~~g~R~Ys------~~d-i~~l~~Ik~Ll 54 (99)
T cd04765 1 FSIGEVAEILGLPPHVLRYWETEFPQLKPVKR-------------------AGGRRYYR------PKD-VELLLLIKHLL 54 (99)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCC-------------------CCCCCCCC------HHH-HHHHHHHHHHH
T ss_conf 97889999989499999999987477488758-------------------99885068------999-99999999999
Q ss_pred HHCCCCHHHHHHHHC
Q ss_conf 972983899999977
Q gi|254781218|r 123 KDKGMSQIEFGKLLG 137 (205)
Q Consensus 123 ~~~glsq~elA~~lg 137 (205)
++.|+|....-+.+.
T Consensus 55 ~~~G~ti~~~k~~L~ 69 (99)
T cd04765 55 YEKGYTIEGAKQALK 69 (99)
T ss_pred HHCCCCHHHHHHHHH
T ss_conf 987987999999998
No 235
>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=80.13 E-value=1.5 Score=23.19 Aligned_cols=43 Identities=12% Similarity=0.015 Sum_probs=38.8
Q ss_pred CCCHHHHHHHHCCCH--HHHHHHHCCCCCCCHHHHHHHHHHHCCC
Q ss_conf 998899999848999--9999887799888999999999982899
Q gi|254781218|r 44 NKTQKEMAIGANQLE--SAVNLFENGMCSTSIRYALYLRNEYEIS 86 (205)
Q Consensus 44 gltQ~elA~~~gis~--~~is~~E~G~~~psi~~l~~la~~~~vs 86 (205)
-.|-..+|+++|.|. +.++++=.|+...+...+.+++.+|+.+
T Consensus 27 ~FS~R~fa~KaGfsS~r~~~~~~~~GK~~Lt~~~i~k~~~~l~Ld 71 (281)
T TIGR02147 27 AFSWRSFAEKAGFSSKRSYLKRIIKGKKNLTKRMIPKFAEALGLD 71 (281)
T ss_pred HHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 330899998648898777888998666753000357666552467
No 236
>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=80.06 E-value=2.4 Score=21.99 Aligned_cols=28 Identities=18% Similarity=0.127 Sum_probs=21.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHH-CCCCCCC
Q ss_conf 988999998489999999887-7998889
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFE-NGMCSTS 72 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E-~G~~~ps 72 (205)
+|-.++|+.+|+|..+|-.|| .|.-.|.
T Consensus 1 ~tIge~Ak~~gvs~~tlRyYe~~GLl~p~ 29 (96)
T cd04768 1 LTIGEFAKLAGVSIRTLRHYDDIGLFKPA 29 (96)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCC
T ss_conf 97899999988699999999843997987
No 237
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=79.74 E-value=2.8 Score=21.52 Aligned_cols=29 Identities=21% Similarity=0.022 Sum_probs=19.7
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 99999985998899999848999999988
Q gi|254781218|r 36 IKDIRKANNKTQKEMAIGANQLESAVNLF 64 (205)
Q Consensus 36 ik~lR~~~gltQ~elA~~~gis~~~is~~ 64 (205)
+..++..-++||.+||+.++++++++++.
T Consensus 46 L~~L~~~~~~t~~eLa~~l~id~~tvt~~ 74 (144)
T PRK11512 46 LCSIRCAACITPVELKKVLSVDLGALTRM 74 (144)
T ss_pred HHHHHHCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 99999869979999999978888789999
No 238
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=79.58 E-value=4.8 Score=20.09 Aligned_cols=24 Identities=13% Similarity=0.134 Sum_probs=21.2
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 729838999999779999999974
Q gi|254781218|r 124 DKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 124 ~~glsq~elA~~lgis~~tis~~E 147 (205)
..++|..|+|+.+|+|+.|..+|.
T Consensus 175 ~~~~ta~eva~~~giSrvTaRRYL 198 (225)
T PRK10046 175 GVQHTAETVAQALTISRTTARRYL 198 (225)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 998689999998585199999999
No 239
>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=79.56 E-value=2.9 Score=21.46 Aligned_cols=27 Identities=30% Similarity=0.479 Sum_probs=14.5
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 999972983899999977999999997
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~ 146 (205)
.++-..|+|..|.|+.+|++.+++..+
T Consensus 20 ~l~y~~~~s~~EIa~~lgis~~tVk~~ 46 (55)
T cd06171 20 LLRFGEGLSYEEIAEILGISRSTVRQR 46 (55)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999980999999999989599999999
No 240
>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=79.20 E-value=4.9 Score=20.02 Aligned_cols=23 Identities=22% Similarity=0.319 Sum_probs=13.9
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 29838999999779999999974
Q gi|254781218|r 125 KGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 125 ~glsq~elA~~lgis~~tis~~E 147 (205)
..||+.|+|+.+|++..|+|+..
T Consensus 24 l~ltr~eiA~~lG~t~eTVsR~l 46 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTL 46 (67)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 17799999999789099999999
No 241
>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=79.18 E-value=2.3 Score=22.07 Aligned_cols=64 Identities=22% Similarity=0.227 Sum_probs=37.1
Q ss_pred CHHHHHHHHCCCHHHHHHHHC--CCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 889999984899999998877--998889999999999828999996145322100002321345546777999999999
Q gi|254781218|r 46 TQKEMAIGANQLESAVNLFEN--GMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRK 123 (205)
Q Consensus 46 tQ~elA~~~gis~~~is~~E~--G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~ 123 (205)
|-.++|+.+||++.++-.||+ |...|. .. +.--..|+ ..| ...-..|+.++
T Consensus 2 sI~eva~~~Gv~~~tLR~wE~~~~l~~p~-R~------------------~~g~R~Ys------~~d-i~~l~~I~~l~- 54 (68)
T cd04763 2 TIGEVALLTGIKPHVLRAWEREFGLLKPQ-RS------------------DGGHRLFN------DAD-IDRILEIKRWI- 54 (68)
T ss_pred CHHHHHHHHCCCHHHHHHHHHCCCCCCCC-CC------------------CCCCCCCC------HHH-HHHHHHHHHHH-
T ss_conf 78899999887945758988705899986-79------------------99996549------999-99999999999-
Q ss_pred HCCCCHHHHHHHH
Q ss_conf 7298389999997
Q gi|254781218|r 124 DKGMSQIEFGKLL 136 (205)
Q Consensus 124 ~~glsq~elA~~l 136 (205)
+.|++.++.++.+
T Consensus 55 ~~G~~i~~i~~lL 67 (68)
T cd04763 55 DNGVQVSKVKKLL 67 (68)
T ss_pred HCCCCHHHHHHHH
T ss_conf 9799899999972
No 242
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=78.77 E-value=5.1 Score=19.93 Aligned_cols=103 Identities=15% Similarity=0.210 Sum_probs=48.9
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH-HHHHCCCC-----------CCCCCCCCCCHHHHH
Q ss_conf 599889999984899999998877998889999999999828999-99614532-----------210000232134554
Q gi|254781218|r 43 NNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISF-DWIYDGEV-----------IDRRYEDVTNKKRLD 110 (205)
Q Consensus 43 ~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~-d~Ll~ge~-----------~~~~~~~~~~~~~~d 110 (205)
+.=+-+++|+.+|++...|-.+++-... +++.=..+..--+-.+ |||-+... ......++-..+ ++
T Consensus 204 r~p~~eeia~~l~~~~~~V~~m~~~~~~-~~SLd~~ig~ded~~l~d~leD~~~~~p~~~~~~~~~~~~~~~~L~~~-Lt 281 (342)
T COG0568 204 REPTPEEIAEELGVSPDKVREMLKRASE-PISLDTPIGDDEDSELGDFLEDDKSVSPEDAVERESLKEDLNEVLAEA-LT 281 (342)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHCCC-CCCCCCCCCCCCCCHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHC-CC
T ss_conf 8997999999959999999999986536-767678488885207888764268789899999888999999998715-99
Q ss_pred HHHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf 6777999999999----72983899999977999999997414
Q gi|254781218|r 111 PYAIGARLKSIRK----DKGMSQIEFGKLLGMPNSTLSNYEQG 149 (205)
Q Consensus 111 ~~~iG~rLk~lR~----~~glsq~elA~~lgis~~tis~~E~g 149 (205)
+.. .++-..|- ....|..++|+..|+++..+.++|+.
T Consensus 282 ~rE--~~Vi~~R~gl~~~~~~TLeevg~~~~vsrERvRQIE~k 322 (342)
T COG0568 282 ERE--RRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEAK 322 (342)
T ss_pred HHH--HHHHHHHHCCCCCCCCHHHHHHHHHCCCHHHHHHHHHH
T ss_conf 999--99999995567999551999998959869999999999
No 243
>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=78.68 E-value=2.7 Score=21.66 Aligned_cols=29 Identities=21% Similarity=0.162 Sum_probs=22.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHH-CCCCCCCH
Q ss_conf 988999998489999999887-79988899
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFE-NGMCSTSI 73 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E-~G~~~psi 73 (205)
+|-.++|+.+|||.++|-.|| .|.-.|..
T Consensus 1 ~tIgevAk~~gvs~~TlRyYE~~GLl~P~~ 30 (108)
T cd01107 1 FTIGEFAKLSNLSIKALRYYDKIGLLKPAY 30 (108)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCE
T ss_conf 978999999895999999999859988541
No 244
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=78.68 E-value=5.1 Score=19.92 Aligned_cols=32 Identities=16% Similarity=0.201 Sum_probs=24.0
Q ss_pred HHHHH-HHHHC--CCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 99999-99972--9838999999779999999974
Q gi|254781218|r 116 ARLKS-IRKDK--GMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 116 ~rLk~-lR~~~--glsq~elA~~lgis~~tis~~E 147 (205)
.+|.+ ++... .+|..|+|+.+|+|+.|..+|.
T Consensus 165 ~~i~~~l~~~~~~~~sa~eva~~~giSRvTaRRYL 199 (239)
T PRK10430 165 RTLCQWIDAHQDYEFSTDELANEVNISRVSCRKYL 199 (239)
T ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 99999998279998469999988585298899999
No 245
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=78.47 E-value=3.2 Score=21.15 Aligned_cols=29 Identities=14% Similarity=0.016 Sum_probs=19.7
Q ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 99999859988999998489999999887
Q gi|254781218|r 37 KDIRKANNKTQKEMAIGANQLESAVNLFE 65 (205)
Q Consensus 37 k~lR~~~gltQ~elA~~~gis~~~is~~E 65 (205)
..+...-++||.++|..++++++++|+.=
T Consensus 17 ~~l~~~~~~t~~~la~~l~~~~~~vs~~v 45 (101)
T smart00347 17 RILYEEGPLSVSELAKRLGVSPSTVTRVL 45 (101)
T ss_pred HHHHHCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 99997699799999999896887999999
No 246
>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=78.40 E-value=3.5 Score=20.95 Aligned_cols=29 Identities=28% Similarity=0.359 Sum_probs=25.1
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 99999972983899999977999999997
Q gi|254781218|r 118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 118 Lk~lR~~~glsq~elA~~lgis~~tis~~ 146 (205)
+=.++...|||..|.|+.+|||..|+...
T Consensus 143 v~~L~~~eglS~~EIAe~Lgis~~TVk~r 171 (185)
T pfam07638 143 LVELRFFAGLSNDEIAERLGVSERTVERN 171 (185)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 98889975999999999979699899999
No 247
>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=78.40 E-value=2.8 Score=21.52 Aligned_cols=28 Identities=21% Similarity=0.296 Sum_probs=22.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHH-CCCCCCC
Q ss_conf 988999998489999999887-7998889
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFE-NGMCSTS 72 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E-~G~~~ps 72 (205)
|+-.|||+..|+|..+|-.|| .|.-.|.
T Consensus 1 M~Ige~A~~~gvs~~TlRyYe~~GLl~p~ 29 (133)
T cd04787 1 MKVKELANAAGVTPDTVRFYTRIGLLRPT 29 (133)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCC
T ss_conf 96899999989789999999985999886
No 248
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=78.08 E-value=5.3 Score=19.81 Aligned_cols=40 Identities=18% Similarity=0.079 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCC
Q ss_conf 9999999999998599889999984899999998877998
Q gi|254781218|r 30 KDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMC 69 (205)
Q Consensus 30 ~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~ 69 (205)
.+.=.++-..=...|+|..++|+.+|+|.++|-+|-+-..
T Consensus 7 ~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~ 46 (138)
T COG3415 7 NDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYR 46 (138)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHC
T ss_conf 8999999999997685499999996922999999998733
No 249
>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=77.91 E-value=3 Score=21.38 Aligned_cols=28 Identities=14% Similarity=0.122 Sum_probs=22.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHH-CCCCCCC
Q ss_conf 988999998489999999887-7998889
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFE-NGMCSTS 72 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E-~G~~~ps 72 (205)
||-.++|+..|+|..+|-.|| .|.-.|.
T Consensus 1 M~Ige~Ak~~gvs~~tlRyYe~~GLl~p~ 29 (127)
T cd01108 1 MNIGEAAKLTGLSAKMIRYYEEIGLIPPP 29 (127)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCC
T ss_conf 97899999989599999999985898986
No 250
>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=77.84 E-value=2.9 Score=21.43 Aligned_cols=28 Identities=18% Similarity=0.251 Sum_probs=22.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHH-CCCCCCC
Q ss_conf 988999998489999999887-7998889
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFE-NGMCSTS 72 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E-~G~~~ps 72 (205)
||-.+||+..|+|..+|-.|| .|.-.|+
T Consensus 1 m~IgevA~~~gvs~~TlRyYE~~GLl~~~ 29 (126)
T cd04783 1 LTIGELAKAAGVNVETIRYYQRRGLLPEP 29 (126)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCC
T ss_conf 97899999989398999999986998876
No 251
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=77.80 E-value=2.9 Score=21.44 Aligned_cols=28 Identities=21% Similarity=0.221 Sum_probs=23.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHH-CCCCCCC
Q ss_conf 988999998489999999887-7998889
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFE-NGMCSTS 72 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E-~G~~~ps 72 (205)
+|-.++|+..|||..++-.|| .|.-.|.
T Consensus 1 ~~I~eva~~~gvs~~tLRyYe~~GLl~p~ 29 (124)
T COG0789 1 YTIGEVAKLTGVSVRTLRFYERKGLLSPE 29 (124)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHCCCCCC
T ss_conf 95999999979699999999990899976
No 252
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=77.71 E-value=5.5 Score=19.74 Aligned_cols=84 Identities=7% Similarity=0.000 Sum_probs=50.7
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 85998899999848999999988779988899999999998289999961453221000023213455467779999999
Q gi|254781218|r 42 ANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSI 121 (205)
Q Consensus 42 ~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~l 121 (205)
...+|.++||+.+|+|++++++.=+.. +|+++-.-+.. ..+ .+-+.+
T Consensus 23 ~~~lsl~~lA~~~~~S~~~l~r~Fk~~--------------~G~s~~~Yi~~------------------~Rl-~~A~~l 69 (127)
T PRK11511 23 ESPLSLEKVSERSGYSKWHLQRMFKKE--------------TGHSLGQYIRS------------------RKM-TEIAQK 69 (127)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHH--------------HCCCHHHHHHH------------------HHH-HHHHHH
T ss_conf 899999999999895999999999999--------------89199999999------------------999-999999
Q ss_pred HHHCCCCHHHHHHHHCCC-HHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHH
Q ss_conf 997298389999997799-999999741488999899999999828999995
Q gi|254781218|r 122 RKDKGMSQIEFGKLLGMP-NSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWI 172 (205)
Q Consensus 122 R~~~glsq~elA~~lgis-~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L 172 (205)
...-+++..+.|..+|.+ .+.+++ ...+.+|++|...
T Consensus 70 L~~t~~~I~~IA~~~Gf~~~~~F~r--------------~Fkk~~G~tP~~y 107 (127)
T PRK11511 70 LKESNEPILYLAERYGFESQQTLTR--------------TFKNYFDVPPHKY 107 (127)
T ss_pred HHHCCCCHHHHHHHHCCCCHHHHHH--------------HHHHHHCCCHHHH
T ss_conf 9985998999999968998899999--------------9999889099999
No 253
>pfam04218 CENP-B_N CENP-B N-terminal DNA-binding domain. Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure.
Probab=77.66 E-value=4.5 Score=20.28 Aligned_cols=35 Identities=23% Similarity=0.504 Sum_probs=27.2
Q ss_pred HHHHHH-HHHCCCCHHHHHHHHCCCHHHHHHHHCCC
Q ss_conf 999999-99729838999999779999999974148
Q gi|254781218|r 116 ARLKSI-RKDKGMSQIEFGKLLGMPNSTLSNYEQGR 150 (205)
Q Consensus 116 ~rLk~l-R~~~glsq~elA~~lgis~~tis~~E~g~ 150 (205)
+++.-+ |.+.|.|..++|...|+..+|++.|...+
T Consensus 11 eKi~iI~~~e~G~s~~~lar~~gi~~STl~~I~Knk 46 (53)
T pfam04218 11 EKIEVIQRSEEGESKASLARRFNVPRSTLRDILKNK 46 (53)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 999999999858968899999698797999999809
No 254
>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=77.64 E-value=2.8 Score=21.51 Aligned_cols=27 Identities=19% Similarity=0.292 Sum_probs=21.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHC-CCCCC
Q ss_conf 9889999984899999998877-99888
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFEN-GMCST 71 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E~-G~~~p 71 (205)
||-.+||+..|+|.++|-.||. |.-.|
T Consensus 1 m~Ige~A~~~gvs~~tlR~Ye~~GLl~~ 28 (123)
T cd04770 1 MKIGELAKAAGVSPDTIRYYERIGLLPP 28 (123)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCC
T ss_conf 9689999998959999999998189875
No 255
>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=77.56 E-value=3.1 Score=21.26 Aligned_cols=67 Identities=22% Similarity=0.274 Sum_probs=38.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHH-CCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 988999998489999999887-7998889999999999828999996145322100002321345546777999999999
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFE-NGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRK 123 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E-~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~ 123 (205)
+|-.+||+.+|+|.++|-.|| .|.-.|.-.. +.+ ..|. ... ...-..|+.+|
T Consensus 1 ysI~eva~~~gvs~~tlR~Ye~~GLl~p~r~~-----~g~--------------R~Y~----~~~---i~~l~~I~~lr- 53 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYEEKGLLPPERSE-----NGY--------------RLYS----EED---LERLRLIRRLR- 53 (100)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCC-----CCC--------------CCCC----HHH---HHHHHHHHHHH-
T ss_conf 97889999989599999999876999988358-----997--------------4256----999---99999999999-
Q ss_pred HCCCCHHHHHHHHCC
Q ss_conf 729838999999779
Q gi|254781218|r 124 DKGMSQIEFGKLLGM 138 (205)
Q Consensus 124 ~~glsq~elA~~lgi 138 (205)
..|++..+..+.+..
T Consensus 54 ~~G~sl~~I~~~l~~ 68 (100)
T cd00592 54 ELGLSLKEIRELLDA 68 (100)
T ss_pred HCCCCHHHHHHHHHC
T ss_conf 979999999999835
No 256
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=77.51 E-value=4.8 Score=20.08 Aligned_cols=31 Identities=32% Similarity=0.432 Sum_probs=18.6
Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHCCCCC
Q ss_conf 9972983899999977999999997414889
Q gi|254781218|r 122 RKDKGMSQIEFGKLLGMPNSTLSNYEQGRTI 152 (205)
Q Consensus 122 R~~~glsq~elA~~lgis~~tis~~E~g~~~ 152 (205)
|...|++..+.|+.+|.+.+|+.++-.|...
T Consensus 57 rekag~Ti~EIAeelG~TeqTir~hlkgetk 87 (182)
T COG1318 57 REKAGMTISEIAEELGRTEQTVRNHLKGETK 87 (182)
T ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHHCCHH
T ss_conf 9870374999999968779999999751403
No 257
>PRK06930 positive control sigma-like factor; Validated
Probab=77.32 E-value=4.7 Score=20.17 Aligned_cols=43 Identities=21% Similarity=0.356 Sum_probs=32.5
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf 99997298389999997799999999741488999899999999828999
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHL 169 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~ 169 (205)
-+....|+|+.|.|+.+||+.+|+..+-. ....+|++-++.++
T Consensus 124 ll~~~~glsy~EIA~~L~Is~~tV~~~l~-------RA~~Ki~~~~~~~L 166 (170)
T PRK06930 124 LMHRGYGLSYSEIAAYLNIKKSTVQSMIE-------RAEKKIAKQINESL 166 (170)
T ss_pred HHHHHHCCCHHHHHHHHCCCHHHHHHHHH-------HHHHHHHHHHCCCC
T ss_conf 88976188899999997988999999999-------99999999854053
No 258
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=77.17 E-value=3.1 Score=21.23 Aligned_cols=29 Identities=24% Similarity=0.358 Sum_probs=24.4
Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHCCC
Q ss_conf 99729838999999779999999974148
Q gi|254781218|r 122 RKDKGMSQIEFGKLLGMPNSTLSNYEQGR 150 (205)
Q Consensus 122 R~~~glsq~elA~~lgis~~tis~~E~g~ 150 (205)
....|+|..++|+.+|+|++|+.+|-.-.
T Consensus 168 ~~~~g~s~~~iak~~gvsrsTvyR~lK~~ 196 (200)
T PRK13413 168 ELKKGTTKSEIAKKLKVSRTTLARFLKTM 196 (200)
T ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 99888999999999892999999999744
No 259
>pfam05225 HTH_psq helix-turn-helix, Psq domain. This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster. In pipsqueak this domain binds to GAGA sequence.
Probab=76.97 E-value=5.7 Score=19.61 Aligned_cols=39 Identities=28% Similarity=0.414 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCC
Q ss_conf 7799999999972983899999977999999997414889
Q gi|254781218|r 113 AIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTI 152 (205)
Q Consensus 113 ~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~ 152 (205)
.+..-|..+|... ||+...|..-||+++|+.+..+|...
T Consensus 4 ~l~~Al~av~~g~-~S~~kAa~~ygIP~sTL~~r~~g~~~ 42 (45)
T pfam05225 4 DLAEALEAVRNGK-MSLRKAARKYGIPRSTLWRRLRGKYS 42 (45)
T ss_pred HHHHHHHHHHCCC-CCHHHHHHHHCCCHHHHHHHHCCCCC
T ss_conf 9999999999199-67999999978985899999756343
No 260
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=76.90 E-value=5.8 Score=19.60 Aligned_cols=33 Identities=9% Similarity=-0.004 Sum_probs=24.5
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHH
Q ss_conf 729838999999779999999974148899989
Q gi|254781218|r 124 DKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIK 156 (205)
Q Consensus 124 ~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~ 156 (205)
...+|..++|+.+|+|++.+++.-....--++.
T Consensus 197 ~~~isl~~lA~~~~lS~s~l~rlFk~~~G~sp~ 229 (290)
T PRK10572 197 ASEFDIESVAQHVCLSPSRLSHLFRQQLGISVL 229 (290)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCHH
T ss_conf 799999999989697999999999986498999
No 261
>pfam07471 Phage_Nu1 Phage DNA packaging protein Nu1. Terminase, the DNA packaging enzyme of bacteriophage lambda, is a heteromultimer composed of subunits Nu1 and A. The smaller Nu1 terminase subunit has a low-affinity ATPase stimulated by non-specific DNA.
Probab=76.76 E-value=2.6 Score=21.71 Aligned_cols=24 Identities=8% Similarity=0.039 Sum_probs=21.6
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 599889999984899999998877
Q gi|254781218|r 43 NNKTQKEMAIGANQLESAVNLFEN 66 (205)
Q Consensus 43 ~gltQ~elA~~~gis~~~is~~E~ 66 (205)
..++.++||+.+|||..+|.+|-.
T Consensus 1 ~~vnk~elA~~~gVS~~tv~~W~~ 24 (164)
T pfam07471 1 MEVNKKQLAEIFGVSIRTIDNWQS 24 (164)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 967899999996988889999998
No 262
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=76.75 E-value=3.6 Score=20.86 Aligned_cols=29 Identities=21% Similarity=0.327 Sum_probs=25.0
Q ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 99999729838999999779999999974
Q gi|254781218|r 119 KSIRKDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 119 k~lR~~~glsq~elA~~lgis~~tis~~E 147 (205)
=.++...|+|..|.|+.+|||.+|+..+-
T Consensus 128 ~~L~~~egls~~EIA~~lgiS~~tVk~~l 156 (172)
T PRK09651 128 FLLSQLDGLTYSEIAHKLGVSISSVKKYV 156 (172)
T ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 99998839999999999893999999999
No 263
>PRK11753 cAMP-regulatory protein; Provisional
Probab=76.72 E-value=5.8 Score=19.57 Aligned_cols=23 Identities=13% Similarity=0.394 Sum_probs=20.2
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 98389999997799999999741
Q gi|254781218|r 126 GMSQIEFGKLLGMPNSTLSNYEQ 148 (205)
Q Consensus 126 glsq~elA~~lgis~~tis~~E~ 148 (205)
.+||.|+|..+|+++.++++..+
T Consensus 168 ~lt~~eLA~~lG~sretvsR~L~ 190 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGRVLK 190 (211)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 46999999886998999999999
No 264
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=76.64 E-value=5.9 Score=19.56 Aligned_cols=42 Identities=14% Similarity=0.198 Sum_probs=34.3
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCC
Q ss_conf 9999729838999999779999999974148899989999999982899
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKH 168 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs 168 (205)
.++...|+|..|.|+.+|++..|+...- -..+.+|.+.||||
T Consensus 152 ~L~~~~g~s~~EIA~~Lgis~~TVk~rl-------~rA~~~LR~~LG~~ 193 (194)
T PRK09646 152 TLAYYGGLTYREVAERLAVPLGTVKTRM-------RDGLRRLRDCLGVS 193 (194)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHH-------HHHHHHHHHHHCCC
T ss_conf 9999939999999999891999999999-------99999999983789
No 265
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), 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- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=76.42 E-value=3.2 Score=21.15 Aligned_cols=65 Identities=14% Similarity=0.112 Sum_probs=34.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHC--CCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 9889999984899999998877--99888999999999982899999614532210000232134554677799999999
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFEN--GMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIR 122 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E~--G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR 122 (205)
.|-.++|+.+|+++.++-.||+ |.-.|.-. +..-+.|++ . ....-..|+.++
T Consensus 1 YtI~eva~~~gv~~~tLR~wE~~~~l~~p~R~-------------------~~g~R~Ys~----~---dv~~l~~I~~l~ 54 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWERRYGLPAPQRT-------------------DGGHRLYSE----A---DVARLRLIRRLT 54 (68)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCC-------------------CCCCEECCH----H---HHHHHHHHHHHH
T ss_conf 97899999988298999999985799999749-------------------999850499----9---999999999999
Q ss_pred HHCCCCHHHHHHHH
Q ss_conf 97298389999997
Q gi|254781218|r 123 KDKGMSQIEFGKLL 136 (205)
Q Consensus 123 ~~~glsq~elA~~l 136 (205)
+.|++..+.+++.
T Consensus 55 -~~G~~l~~I~~l~ 67 (68)
T cd01104 55 -SEGVRISQAAALA 67 (68)
T ss_pred -HCCCCHHHHHHHH
T ss_conf -9789999999870
No 266
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family; InterPro: IPR012845 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 , . Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0045449 regulation of transcription.
Probab=76.25 E-value=6 Score=19.49 Aligned_cols=117 Identities=17% Similarity=0.153 Sum_probs=70.3
Q ss_pred HHHHHHHHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHH-----CCCHHHHHCCCCCC
Q ss_conf 8999999999999999985--9988999998489999999887799888999999999982-----89999961453221
Q gi|254781218|r 25 IRQYWKDVGTRIKDIRKAN--NKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEY-----EISFDWIYDGEVID 97 (205)
Q Consensus 25 ~~~~~~~iG~rik~lR~~~--gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~-----~vs~d~Ll~ge~~~ 97 (205)
.++--++|..=++.+.... .=|-+|+|+.+|++..-|.++.+....-.+-.|=.+-.-. ..++..++..+...
T Consensus 78 ~R~~~~~~~~a~~~Le~~LgR~P~~~EiA~~Lg~~~~e~~~~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (227)
T TIGR02479 78 LRQKARKLEEAIEELEARLGREPTEEEIAEELGMDLKEVRQALNEINAESLVSLDELLESGDDGGAEGSLIDLIEDDKSE 157 (227)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHEECCCCCC
T ss_conf 89998689999999999869898888999983999989999999988998764899984146322345323100143576
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHH--------------HCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 00002321345546777999999999--------------729838999999779999999974
Q gi|254781218|r 98 RRYEDVTNKKRLDPYAIGARLKSIRK--------------DKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 98 ~~~~~~~~~~~~d~~~iG~rLk~lR~--------------~~glsq~elA~~lgis~~tis~~E 147 (205)
.+...+....+-..|.++.+ ..+|+.+|.|+.+|+|.+-||++-
T Consensus 158 ------~P~~~~~~~~L~~~l~~ai~~L~eRE~LVl~LYY~eELnLKEIg~VL~lsESRvSQiH 215 (227)
T TIGR02479 158 ------DPEEELEREELREALAEAIEKLSEREKLVLSLYYYEELNLKEIGEVLGLSESRVSQIH 215 (227)
T ss_pred ------CHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf ------8135899999999999997406855788888864127668899988378705799999
No 267
>pfam02796 HTH_7 Helix-turn-helix domain of resolvase.
Probab=76.24 E-value=3.2 Score=21.22 Aligned_cols=28 Identities=25% Similarity=0.455 Sum_probs=21.3
Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf 9972983899999977999999997414
Q gi|254781218|r 122 RKDKGMSQIEFGKLLGMPNSTLSNYEQG 149 (205)
Q Consensus 122 R~~~glsq~elA~~lgis~~tis~~E~g 149 (205)
+-+.|++..++|+..||+++|+.+|.++
T Consensus 17 L~~~G~~i~~IA~~~~vsrsTvYRyl~~ 44 (45)
T pfam02796 17 LLEEGISIKQIAKIFGISRSTVYRYLAA 44 (45)
T ss_pred HHHCCCCHHHHHHHHCCHHHHHHHHCCC
T ss_conf 9987994999999986008888764458
No 268
>pfam04967 HTH_10 HTH DNA binding domain.
Probab=76.18 E-value=2.8 Score=21.52 Aligned_cols=23 Identities=30% Similarity=0.404 Sum_probs=13.9
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 29838999999779999999974
Q gi|254781218|r 125 KGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 125 ~glsq~elA~~lgis~~tis~~E 147 (205)
++.+..|+|+.+||+++|++...
T Consensus 22 R~~~l~elA~~lgis~sT~~~hL 44 (53)
T pfam04967 22 RRVTLKDLAKELGISKSTLSEHL 44 (53)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 76889999999698999999999
No 269
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR 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 comprise 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=76.10 E-value=3.5 Score=20.91 Aligned_cols=28 Identities=14% Similarity=0.182 Sum_probs=22.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHH-CCCCCCC
Q ss_conf 988999998489999999887-7998889
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFE-NGMCSTS 72 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E-~G~~~ps 72 (205)
||-.+||+..|+|..+|-.|| .|.-.|+
T Consensus 1 m~IgelA~~~gvs~~tlRyYE~~GLl~~~ 29 (126)
T cd04785 1 LSIGELARRTGVNVETIRYYESIGLLPEP 29 (126)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCC
T ss_conf 96899999989499999999984998987
No 270
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. 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 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=76.07 E-value=3.3 Score=21.08 Aligned_cols=66 Identities=18% Similarity=0.225 Sum_probs=38.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHH-CCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 988999998489999999887-7998889999999999828999996145322100002321345546777999999999
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFE-NGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRK 123 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E-~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~ 123 (205)
|.-.|+|+..|+|..+|-.|| .|.-.|.-.. -. -..|+ ... ..--..|+.+|.
T Consensus 1 M~IgevAk~~gvs~~TlRyYE~~GLl~~~~r~-~~-yR~Y~---------------------~~~---l~~l~~I~~~r~ 54 (116)
T cd04769 1 MYIGELAQQTGVTIKAIRLYEEKGLLPSPKRS-GN-YRVYD---------------------AQH---VECLRFIKEARQ 54 (116)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCC-CC-CCCCC---------------------HHH---HHHHHHHHHHHH
T ss_conf 96899999989699999999986999987577-77-33228---------------------999---999999999999
Q ss_pred HCCCCHHHHHHHHC
Q ss_conf 72983899999977
Q gi|254781218|r 124 DKGMSQIEFGKLLG 137 (205)
Q Consensus 124 ~~glsq~elA~~lg 137 (205)
.|+|..|+.+.+.
T Consensus 55 -~GfsL~eI~~ll~ 67 (116)
T cd04769 55 -LGFTLAELKAIFA 67 (116)
T ss_pred -CCCCHHHHHHHHH
T ss_conf -7999999999996
No 271
>TIGR00160 MGSA methylglyoxal synthase; InterPro: IPR004363 Methylglyoxal synthase (MGS) catalyzes the conversion of dihydroxyacetone phosphate to methylglyoxal and phosphate: Glycerone phosphate = methylglyoxal + phosphate It provides bacteria with an alternative to triosephosphate isomerase for metabolizing dihydroxyacetone phosphate. MGS is a small protein of about 13 to 17 kDa. An aspartate residue is involved in the catalytic mechanism. Methylglyoxal synthase contains a domain shared by other enzymes. Other proteins containing this domain include purine biosynthesis protein PurH and carbamoyl phosphate synthetase.; GO: 0008929 methylglyoxal synthase activity, 0019242 methylglyoxal biosynthetic process, 0005737 cytoplasm.
Probab=75.72 E-value=1.6 Score=23.01 Aligned_cols=25 Identities=20% Similarity=0.364 Sum_probs=19.7
Q ss_pred CCCCHHHHHHHHHHHCCCH-------HHHHCC
Q ss_conf 8889999999999828999-------996145
Q gi|254781218|r 69 CSTSIRYALYLRNEYEISF-------DWIYDG 93 (205)
Q Consensus 69 ~~psi~~l~~la~~~~vs~-------d~Ll~g 93 (205)
.+|+++.|++||.+|+|++ |-|+.+
T Consensus 89 HEPDV~ALlRLc~V~nIPlAtN~~TA~~li~~ 120 (143)
T TIGR00160 89 HEPDVKALLRLCDVYNIPLATNVATADILIKS 120 (143)
T ss_pred CCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHC
T ss_conf 88007889878645025034405667887730
No 272
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=75.63 E-value=3.6 Score=20.84 Aligned_cols=29 Identities=24% Similarity=0.336 Sum_probs=24.5
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 99999972983899999977999999997
Q gi|254781218|r 118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 118 Lk~lR~~~glsq~elA~~lgis~~tis~~ 146 (205)
+=.++...|+|..|.|+.+|||.+|+...
T Consensus 113 v~~L~~~egls~~EIA~~lgis~~tVk~~ 141 (159)
T PRK12527 113 SFLLRKLEGLSHQQIAEHLGISRSLVEKH 141 (159)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 99889873979999999989199999999
No 273
>pfam01527 Transposase_8 Transposase. Transposase proteins are necessary for efficient DNA transposition. This family consists of various E. coli insertion elements and other bacterial transposases some of which are members of the IS3 family.
Probab=75.54 E-value=5.6 Score=19.68 Aligned_cols=27 Identities=22% Similarity=0.347 Sum_probs=19.0
Q ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf 972983899999977999999997414
Q gi|254781218|r 123 KDKGMSQIEFGKLLGMPNSTLSNYEQG 149 (205)
Q Consensus 123 ~~~glsq~elA~~lgis~~tis~~E~g 149 (205)
..-|.|..++|..+||+.+++.+|-+-
T Consensus 20 ~~~g~sv~~var~~gi~~~~l~~W~k~ 46 (75)
T pfam01527 20 LEPGASVSELAREHGVSPATLYKWRKK 46 (75)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 809984999999989599999999999
No 274
>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=75.24 E-value=3.9 Score=20.64 Aligned_cols=21 Identities=14% Similarity=0.170 Sum_probs=12.3
Q ss_pred CHHHHHHHHCCCHHHHHHHHC
Q ss_conf 889999984899999998877
Q gi|254781218|r 46 TQKEMAIGANQLESAVNLFEN 66 (205)
Q Consensus 46 tQ~elA~~~gis~~~is~~E~ 66 (205)
+-.|+|+..|+|.++|-.||.
T Consensus 2 ri~ElA~~~Gvs~~tiR~YE~ 22 (99)
T cd04772 2 RTVDLARAIGLSPQTVRNYES 22 (99)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
T ss_conf 789999998969999999999
No 275
>pfam02954 HTH_8 Bacterial regulatory protein, Fis family.
Probab=75.01 E-value=5.7 Score=19.64 Aligned_cols=31 Identities=19% Similarity=0.293 Sum_probs=23.5
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 9999999972983899999977999999997
Q gi|254781218|r 116 ARLKSIRKDKGMSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 116 ~rLk~lR~~~glsq~elA~~lgis~~tis~~ 146 (205)
..|.+..+..+..+.+.|+.+||+++++.+-
T Consensus 8 ~~I~~aL~~~~gn~~~aA~~LGisr~tL~~k 38 (42)
T pfam02954 8 ELIEAALERTGGNKSKAARLLGISRRTLYRK 38 (42)
T ss_pred HHHHHHHHHHCCCHHHHHHHHCCCHHHHHHH
T ss_conf 9999999994997999999979699999999
No 276
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=74.62 E-value=4.8 Score=20.10 Aligned_cols=26 Identities=35% Similarity=0.408 Sum_probs=21.5
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf 72983899999977999999997414
Q gi|254781218|r 124 DKGMSQIEFGKLLGMPNSTLSNYEQG 149 (205)
Q Consensus 124 ~~glsq~elA~~lgis~~tis~~E~g 149 (205)
...+|+.|.|+.+|+|+..++++|..
T Consensus 192 ~~~~Tl~eIg~~lgiSrERVRQIe~~ 217 (228)
T PRK05803 192 GKEKTQREIAKALGISRSYVSRIEKK 217 (228)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 99715999999989799999999999
No 277
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). 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=74.61 E-value=4.2 Score=20.46 Aligned_cols=67 Identities=15% Similarity=0.240 Sum_probs=39.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHH-CCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 988999998489999999887-7998889999999999828999996145322100002321345546777999999999
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFE-NGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRK 123 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E-~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~ 123 (205)
|+-.+||+..|+|..+|-.|| .|.-.|. .-.+.|.+ |. ...+ .--..|+.+|
T Consensus 1 M~Ige~a~~~gvs~~tlRyYe~~GLl~p~-----r~~~gyR~--------------Y~----~~~~---~~l~~I~~lr- 53 (112)
T cd01282 1 MRIGELAARTGVSVRSLRYYEEQGLLVPE-----RSANGYRD--------------YD----EAAV---DRVRQIRRLL- 53 (112)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCC-----CCCCCCEE--------------CC----HHHH---HHHHHHHHHH-
T ss_conf 96899999989799999999984899998-----08998700--------------59----9999---9999999999-
Q ss_pred HCCCCHHHHHHHHCC
Q ss_conf 729838999999779
Q gi|254781218|r 124 DKGMSQIEFGKLLGM 138 (205)
Q Consensus 124 ~~glsq~elA~~lgi 138 (205)
..|||..|..+.+.+
T Consensus 54 ~~G~sl~eI~~~l~~ 68 (112)
T cd01282 54 AAGLTLEEIREFLPC 68 (112)
T ss_pred HCCCCHHHHHHHHHH
T ss_conf 969999999999987
No 278
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=74.60 E-value=6.3 Score=19.38 Aligned_cols=29 Identities=7% Similarity=0.166 Sum_probs=25.0
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 99997298389999997799999999741
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNYEQ 148 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~E~ 148 (205)
.++...|+|+.|.|+.+|||..|+..+-.
T Consensus 133 ~L~~~eg~s~~EIAe~LgiS~~tVk~~l~ 161 (183)
T PRK07037 133 EMVRLRGETLQDIARELNVSQTLVNFMIR 161 (183)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 98987398999999998929999999999
No 279
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=74.30 E-value=6.7 Score=19.18 Aligned_cols=24 Identities=25% Similarity=0.365 Sum_probs=20.5
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 298389999997799999999741
Q gi|254781218|r 125 KGMSQIEFGKLLGMPNSTLSNYEQ 148 (205)
Q Consensus 125 ~glsq~elA~~lgis~~tis~~E~ 148 (205)
..|||.|+|+++|+++.|+++..+
T Consensus 183 l~lt~~dLA~~lG~trEtVsR~L~ 206 (235)
T PRK11161 183 LTMTRGDIGNYLGLTVETISRLLG 206 (235)
T ss_pred ECCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 237899999887898999999999
No 280
>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=74.23 E-value=4.2 Score=20.46 Aligned_cols=67 Identities=12% Similarity=0.017 Sum_probs=41.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHH-CCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 988999998489999999887-7998889999999999828999996145322100002321345546777999999999
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFE-NGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRK 123 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E-~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~ 123 (205)
+|-.++|+.+|++.++|-.|| .|...|....- ..... +.. +....-..|+.++
T Consensus 2 ~tIgeva~~~gvs~~tLRyye~~gli~p~~~~~-------------------~g~R~-----Ys~-~dl~~l~~I~~l~- 55 (88)
T cd01105 2 IGIGEVSKLTGVSPRQLRYWEEKGLIKSIRSDG-------------------GGQRK-----YSL-ADVDRLLVIKELL- 55 (88)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCC-------------------CCCEE-----CCH-HHHHHHHHHHHHH-
T ss_conf 678999999895999999999949989987699-------------------98214-----799-9999999999999-
Q ss_pred HCCCCHHHHHHHHC
Q ss_conf 72983899999977
Q gi|254781218|r 124 DKGMSQIEFGKLLG 137 (205)
Q Consensus 124 ~~glsq~elA~~lg 137 (205)
+.|++..+.++.+.
T Consensus 56 ~~G~sl~~i~~~L~ 69 (88)
T cd01105 56 DEGFTLAAAVEKLR 69 (88)
T ss_pred HCCCCHHHHHHHHH
T ss_conf 97998999999999
No 281
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator; InterPro: IPR011789 This entry represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system . This protein is a member of the MerR family of transcriptional activators and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue .; GO: 0003677 DNA binding, 0005507 copper ion binding, 0016563 transcription activator activity, 0045941 positive regulation of transcription.
Probab=74.22 E-value=6.8 Score=19.17 Aligned_cols=78 Identities=10% Similarity=0.126 Sum_probs=51.8
Q ss_pred HHHHHHHHCCCHHHHHHHH-CCCCCCCHH----------------HHHHHHHHHCCCHHHHHCC----CCCCCCCCCCCC
Q ss_conf 8999998489999999887-799888999----------------9999999828999996145----322100002321
Q gi|254781218|r 47 QKEMAIGANQLESAVNLFE-NGMCSTSIR----------------YALYLRNEYEISFDWIYDG----EVIDRRYEDVTN 105 (205)
Q Consensus 47 Q~elA~~~gis~~~is~~E-~G~~~psi~----------------~l~~la~~~~vs~d~Ll~g----e~~~~~~~~~~~ 105 (205)
--++|+..|+|-.+|--|| .|...|++. .|+.=|+.+|-|++++=.- ....+...||+.
T Consensus 3 Ig~~AK~tglssK~IR~YE~kGLi~Pp~Rse~GYR~Y~~~h~~~L~li~raR~~GFSLeEc~~ll~L~ndp~R~SAdVK~ 82 (127)
T TIGR02044 3 IGQVAKLTGLSSKSIRYYEEKGLIPPPLRSEGGYRTYTDKHVDELRLISRARSVGFSLEECKELLSLWNDPNRTSADVKA 82 (127)
T ss_pred HHHHHCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHH
T ss_conf 67775014772688988776326799886888885638767888899999987189889999998752288898878899
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q ss_conf 3455467779999999997
Q gi|254781218|r 106 KKRLDPYAIGARLKSIRKD 124 (205)
Q Consensus 106 ~~~~d~~~iG~rLk~lR~~ 124 (205)
.+.-.-..|-.+|.++...
T Consensus 83 rtl~k~~E~~~kI~eL~~m 101 (127)
T TIGR02044 83 RTLEKVAELERKISELQEM 101 (127)
T ss_pred HHHHHHHHHHHHHHHHHHH
T ss_conf 9998899999999999889
No 282
>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=74.13 E-value=4.4 Score=20.36 Aligned_cols=28 Identities=21% Similarity=0.334 Sum_probs=22.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHH-CCCCCCC
Q ss_conf 988999998489999999887-7998889
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFE-NGMCSTS 72 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E-~G~~~ps 72 (205)
|+-.+||+..|+|.++|-.|| .|.-.|+
T Consensus 1 M~IgelA~~~gvs~~tlR~YE~~GLl~p~ 29 (131)
T cd04786 1 MKIGELAKRSGMAASRIRFYEAEGLLSSV 29 (131)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCC
T ss_conf 97899999988788999999977998987
No 283
>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=73.82 E-value=3.9 Score=20.62 Aligned_cols=27 Identities=22% Similarity=0.298 Sum_probs=21.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHH-CCCCCC
Q ss_conf 988999998489999999887-799888
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFE-NGMCST 71 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E-~G~~~p 71 (205)
.|-.|||+..|+|.++|-.|| -|.-.|
T Consensus 1 ytIgelA~~~gvs~~tlRyYe~~GLl~~ 28 (113)
T cd01109 1 YTIKEVAEKTGLSADTLRYYEKEGLLPP 28 (113)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCC
T ss_conf 9788999998959999999998389799
No 284
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=73.38 E-value=4.6 Score=20.21 Aligned_cols=28 Identities=18% Similarity=0.158 Sum_probs=21.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHH-CCCCCCC
Q ss_conf 988999998489999999887-7998889
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFE-NGMCSTS 72 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E-~G~~~ps 72 (205)
+|-.++|+.+|+|.+++-.|| .|.-.|.
T Consensus 1 ytIge~a~~~gvs~~tlRyYe~~GLl~p~ 29 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPS 29 (103)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCC
T ss_conf 97889999989699999999853897886
No 285
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=73.37 E-value=5.2 Score=19.88 Aligned_cols=27 Identities=7% Similarity=0.111 Sum_probs=18.3
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHH
Q ss_conf 999999859988999998489999999
Q gi|254781218|r 36 IKDIRKANNKTQKEMAIGANQLESAVN 62 (205)
Q Consensus 36 ik~lR~~~gltQ~elA~~~gis~~~is 62 (205)
|+.|.+.-.+|-.++|+++|+|++++.
T Consensus 15 L~~Lq~d~R~s~~eiA~~lglS~stv~ 41 (153)
T PRK11179 15 LEALMENARTPYAELAKQFGVSPGTIH 41 (153)
T ss_pred HHHHHHCCCCCHHHHHHHHCCCHHHHH
T ss_conf 999998489999999999892999999
No 286
>COG3311 AlpA Predicted transcriptional regulator [Transcription]
Probab=73.33 E-value=4.3 Score=20.39 Aligned_cols=34 Identities=21% Similarity=0.249 Sum_probs=27.7
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHH
Q ss_conf 2983899999977999999997414889998999
Q gi|254781218|r 125 KGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPA 158 (205)
Q Consensus 125 ~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l 158 (205)
+-+...|+++.+|++++|+.++.+.+..|..-.+
T Consensus 12 r~lrl~ev~~~~GlSrstiYr~i~~~~FPkpvkl 45 (70)
T COG3311 12 RLLRLPEVAQLTGLSRSTIYRLIKDGTFPKPVKL 45 (70)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHCCCCCCCCEEC
T ss_conf 1520899999977668999999804779998622
No 287
>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=73.23 E-value=7.2 Score=19.02 Aligned_cols=71 Identities=14% Similarity=0.271 Sum_probs=41.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHHC-CCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9889999984899999998877-998889999999999828999996145322100002321345546777999999999
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFEN-GMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRK 123 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E~-G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~ 123 (205)
++-.++|+.+|++++++-.||+ |...|.- -.|- -..|+ ..| ...-..|+.+.+
T Consensus 2 Y~IgevA~l~Gv~~~tLR~yEr~gli~P~R-----------------t~gG--~R~Ys------~~D-l~~L~~I~~L~~ 55 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVYDRLGLVSPAR-----------------TNGG--GRRYS------NND-LELLRQVQRLSQ 55 (98)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCC-----------------CCCC--CCCCC------HHH-HHHHHHHHHHHH
T ss_conf 358999999798999999999938978661-----------------8999--94349------999-999999999999
Q ss_pred HCCCCHHHHHHHHCCCHH
Q ss_conf 729838999999779999
Q gi|254781218|r 124 DKGMSQIEFGKLLGMPNS 141 (205)
Q Consensus 124 ~~glsq~elA~~lgis~~ 141 (205)
..|++....-..+.+..+
T Consensus 56 ~~G~~l~gik~iL~l~~q 73 (98)
T cd01279 56 DEGFNLAGIKRIIELYPQ 73 (98)
T ss_pred HCCCCHHHHHHHHHHHHH
T ss_conf 589889999999998999
No 288
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=72.91 E-value=5.4 Score=19.77 Aligned_cols=27 Identities=7% Similarity=0.151 Sum_probs=14.5
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHH
Q ss_conf 999999859988999998489999999
Q gi|254781218|r 36 IKDIRKANNKTQKEMAIGANQLESAVN 62 (205)
Q Consensus 36 ik~lR~~~gltQ~elA~~~gis~~~is 62 (205)
|+.|++.-.+|..++|+++|+|++++.
T Consensus 20 L~~Lq~daR~s~~eLA~~vglS~stv~ 46 (164)
T PRK11169 20 LNELQKDGRISNVELSKRVGLSPTPCL 46 (164)
T ss_pred HHHHHHCCCCCHHHHHHHHCCCHHHHH
T ss_conf 999998489999999999892999999
No 289
>PRK09775 hypothetical protein; Provisional
Probab=72.69 E-value=5.2 Score=19.88 Aligned_cols=31 Identities=6% Similarity=0.019 Sum_probs=27.1
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 9999999859988999998489999999887
Q gi|254781218|r 35 RIKDIRKANNKTQKEMAIGANQLESAVNLFE 65 (205)
Q Consensus 35 rik~lR~~~gltQ~elA~~~gis~~~is~~E 65 (205)
-|+.++.+--++-.+|+..+|||+.|+|+-=
T Consensus 3 ~l~~Ll~~Gp~~a~eLa~~lgvSqpTlSR~l 33 (443)
T PRK09775 3 LLTTLLLQGPLSAAELAQRLGISQATLSRLL 33 (443)
T ss_pred HHHHHHHCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 6899997399359999998688888899999
No 290
>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=72.49 E-value=4.9 Score=20.04 Aligned_cols=28 Identities=14% Similarity=0.228 Sum_probs=21.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHH-CCCCCCC
Q ss_conf 988999998489999999887-7998889
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFE-NGMCSTS 72 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E-~G~~~ps 72 (205)
|.-.+||+..|+|..+|-.|| .|.-.|+
T Consensus 1 M~Ige~a~~~gvs~~tlRyYE~~GLl~~~ 29 (127)
T cd04784 1 MKIGELAKKTGCSVETIRYYEKEGLLPAP 29 (127)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCC
T ss_conf 96899999989499999999985898875
No 291
>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=71.87 E-value=5.3 Score=19.84 Aligned_cols=25 Identities=20% Similarity=0.158 Sum_probs=20.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHH-CCCC
Q ss_conf 988999998489999999887-7998
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFE-NGMC 69 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E-~G~~ 69 (205)
+|-.++|+..|+|.++|-.|| .|.-
T Consensus 2 ~~Ige~a~~~gis~~tlRyYe~~GLl 27 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYESIGLI 27 (102)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCC
T ss_conf 87899999989499999999987999
No 292
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=71.71 E-value=5.9 Score=19.55 Aligned_cols=28 Identities=14% Similarity=0.107 Sum_probs=20.8
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 9999998599889999984899999998
Q gi|254781218|r 36 IKDIRKANNKTQKEMAIGANQLESAVNL 63 (205)
Q Consensus 36 ik~lR~~~gltQ~elA~~~gis~~~is~ 63 (205)
++.+++....++.++|+.+|+|++++.+
T Consensus 14 L~~L~~d~r~~~~eia~~lglS~~~v~~ 41 (154)
T COG1522 14 LRLLQEDARISNAELAERVGLSPSTVLR 41 (154)
T ss_pred HHHHHHCCCCCHHHHHHHHCCCHHHHHH
T ss_conf 9999972765799999997979899999
No 293
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=71.42 E-value=4 Score=20.60 Aligned_cols=41 Identities=10% Similarity=0.147 Sum_probs=31.1
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHCC-------------CCCCCHHHHHHHHHHHC
Q ss_conf 983899999977999999997414-------------88999899999999828
Q gi|254781218|r 126 GMSQIEFGKLLGMPNSTLSNYEQG-------------RTIPEIKPARKIKQVTK 166 (205)
Q Consensus 126 glsq~elA~~lgis~~tis~~E~g-------------~~~Ps~~~l~kIa~~lg 166 (205)
.+|++|+|.++|.++.|+++..+. -...+.+.|.+||+.=|
T Consensus 145 ~lT~~eLA~~iGttREtVsR~L~~l~~~GlI~~~~~~I~I~D~~~L~~lAe~~g 198 (201)
T PRK13918 145 YATHDELAAAVGSVRETVTKVVGELSREGVIRSGYGKIQLLDLKALKELAESRG 198 (201)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCEEEEECHHHHHHHHHHCC
T ss_conf 579999998859868999999999998898896799899928999999987447
No 294
>PRK13749 transcriptional regulator MerD; Provisional
Probab=70.91 E-value=6.8 Score=19.16 Aligned_cols=48 Identities=19% Similarity=0.117 Sum_probs=32.3
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHH-CCCCCCCHH----------------HHHHHHHHHCCCHHHH
Q ss_conf 59988999998489999999887-799888999----------------9999999828999996
Q gi|254781218|r 43 NNKTQKEMAIGANQLESAVNLFE-NGMCSTSIR----------------YALYLRNEYEISFDWI 90 (205)
Q Consensus 43 ~gltQ~elA~~~gis~~~is~~E-~G~~~psi~----------------~l~~la~~~~vs~d~L 90 (205)
..+|-.+||+..|+|..+|-.|| .|.-.|+-. ..++-|..+++++|.|
T Consensus 2 ~aytIg~LA~~aGVsv~tIR~Y~~~GLL~p~~Rt~gGyRlyd~~~l~RL~FIR~a~elGf~LdeI 66 (121)
T PRK13749 2 NAYTVSRLALDAGVSVHIVRDYLLRGLLRPVACTTGGYGLFDDAALQRLCFVRAAFEAGIGLDAL 66 (121)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCHHHH
T ss_conf 84209999999599735548898768989988899884367899999999999999908989999
No 295
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=70.74 E-value=4.3 Score=20.39 Aligned_cols=24 Identities=25% Similarity=0.266 Sum_probs=20.6
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 729838999999779999999974
Q gi|254781218|r 124 DKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 124 ~~glsq~elA~~lgis~~tis~~E 147 (205)
...+|+.|+|.++|+++.++++..
T Consensus 171 ~l~lT~~dLA~~lG~trETVsR~L 194 (224)
T PRK09391 171 ALPMSRRDIADYLGLTIETVSRAL 194 (224)
T ss_pred ECCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 715799999988799799999999
No 296
>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=70.49 E-value=6.7 Score=19.21 Aligned_cols=27 Identities=22% Similarity=0.325 Sum_probs=21.5
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 999972983899999977999999997
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~ 146 (205)
.+-...|||-+|.|+.+|||..||-..
T Consensus 129 ~lsr~eg~s~~EIA~~L~iS~~TVe~h 155 (167)
T TIGR02985 129 ILSRFEGLSNKEIAEELGISVKTVEYH 155 (167)
T ss_pred HHHHHHCCCHHHHHHHHCCCHHHHHHH
T ss_conf 998861798678998848988899999
No 297
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=70.47 E-value=6.8 Score=19.17 Aligned_cols=27 Identities=19% Similarity=0.256 Sum_probs=16.5
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHH
Q ss_conf 999999859988999998489999999
Q gi|254781218|r 36 IKDIRKANNKTQKEMAIGANQLESAVN 62 (205)
Q Consensus 36 ik~lR~~~gltQ~elA~~~gis~~~is 62 (205)
|+.+++.-.+|-.++|+.+|+|++++.
T Consensus 9 l~~L~~n~R~s~~~iA~~lg~S~~tv~ 35 (108)
T smart00344 9 LEELQKDARISLAELAKKVGLSPSTVH 35 (108)
T ss_pred HHHHHHCCCCCHHHHHHHHCCCHHHHH
T ss_conf 999998289999999999893999999
No 298
>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=70.21 E-value=8.3 Score=18.63 Aligned_cols=29 Identities=28% Similarity=0.423 Sum_probs=17.1
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 99999972983899999977999999997
Q gi|254781218|r 118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 118 Lk~lR~~~glsq~elA~~lgis~~tis~~ 146 (205)
+=.++.-.|+|..|.|+.+|++.+++..+
T Consensus 18 ~~~l~~~~~~s~~eIA~~lg~s~~tVk~~ 46 (54)
T pfam08281 18 VFLLRYLEGLSYAEIAELLGISEGTVKSR 46 (54)
T ss_pred HHHHHHHHCCCHHHHHHHHCCCHHHHHHH
T ss_conf 96879987859999999989499999999
No 299
>PRK13503 transcriptional activator RhaS; Provisional
Probab=69.81 E-value=8.6 Score=18.54 Aligned_cols=41 Identities=10% Similarity=-0.003 Sum_probs=28.5
Q ss_pred HHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHH
Q ss_conf 99999997--298389999997799999999741488999899
Q gi|254781218|r 117 RLKSIRKD--KGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKP 157 (205)
Q Consensus 117 rLk~lR~~--~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~ 157 (205)
-+.-+... ..++..++|+.+|+++..++++-+...--+...
T Consensus 176 i~~yI~~hy~~~isl~~lA~~~~lS~~~l~r~FK~~tG~t~~~ 218 (278)
T PRK13503 176 LLAWLEDHFAEEVNWEAVADQFSLSLRTLHRQLKQQTGLTPQR 218 (278)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCHHH
T ss_conf 9999999757999999999897959999999999988938999
No 300
>pfam08299 Bac_DnaA_C domain.
Probab=69.74 E-value=8.6 Score=18.53 Aligned_cols=61 Identities=15% Similarity=0.230 Sum_probs=41.2
Q ss_pred HHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHC-CCHHHHHH
Q ss_conf 9999999982899999614532210000232134554677799999999972983899999977-99999999
Q gi|254781218|r 74 RYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRKDKGMSQIEFGKLLG-MPNSTLSN 145 (205)
Q Consensus 74 ~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~~~glsq~elA~~lg-is~~tis~ 145 (205)
+.+-.+|+.|+|+.+.|....- .+....+..++- --+|+..++|..+.+..+| -+++|+..
T Consensus 4 ~I~~~Va~~f~v~~~~i~s~~R---------~~~i~~aR~iam--yL~r~~t~~s~~~IG~~fg~RdHsTVi~ 65 (70)
T pfam08299 4 NIQEIVAEYYNITVEDLLSKSR---------TRSVVRARQIAM--YLLRELTNLSLPEIGEIFGGRDHTTVLH 65 (70)
T ss_pred HHHHHHHHHHCCCHHHHHCCCC---------CCHHHHHHHHHH--HHHHHHHCCCHHHHHHHHCCCCCHHHHH
T ss_conf 9999999882996999837898---------811578999999--9999986799999999938997379999
No 301
>PHA00361 cI Repressor
Probab=69.46 E-value=2.3 Score=22.03 Aligned_cols=19 Identities=16% Similarity=0.144 Sum_probs=16.5
Q ss_pred HHHHHHCCCHHHHHCCCCC
Q ss_conf 9999828999996145322
Q gi|254781218|r 78 YLRNEYEISFDWIYDGEVI 96 (205)
Q Consensus 78 ~la~~~~vs~d~Ll~ge~~ 96 (205)
+||++|+|+++||+.|...
T Consensus 1 ~lA~~Lg~s~~~Ll~g~~~ 19 (165)
T PHA00361 1 KLAKALGTSVDDLLQEDLS 19 (165)
T ss_pred CHHHHHCCCHHHHHCCCCC
T ss_conf 9568669899998557556
No 302
>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=69.00 E-value=6.5 Score=19.27 Aligned_cols=47 Identities=21% Similarity=0.155 Sum_probs=35.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHH-CCCCCCCHH----------------HHHHHHHHHCCCHHHHH
Q ss_conf 988999998489999999887-799888999----------------99999998289999961
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFE-NGMCSTSIR----------------YALYLRNEYEISFDWIY 91 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E-~G~~~psi~----------------~l~~la~~~~vs~d~Ll 91 (205)
+|-.++|+.+|+|..++-.|| .|.-.|+-. ..+...+.+|+|++.+-
T Consensus 2 ~tI~e~Ak~~gvs~~TLRyYe~~GLl~P~~r~~nGYR~Ys~~dl~rL~~I~~lr~lG~sL~eIk 65 (172)
T cd04790 2 LTISQLARQFGLSRSTLLYYERIGLLSPSARSESNYRLYGERDLERLEQICAYRSAGVSLEDIR 65 (172)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHH
T ss_conf 9789999998949889999998879899884999870779999999999999998799999999
No 303
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor; InterPro: IPR012781 Members of this family belong the lacI helix-turn-helix family of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterised members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.; GO: 0003677 DNA binding, 0006355 regulation of transcription DNA-dependent, 0009750 response to fructose stimulus, 0045449 regulation of transcription.
Probab=68.86 E-value=4 Score=20.56 Aligned_cols=48 Identities=13% Similarity=0.079 Sum_probs=36.6
Q ss_pred CHHHHHHHHCCCHHHHHHHHCCCC------CCCHHHHHHHHHHHCCCHHHHHCC
Q ss_conf 889999984899999998877998------889999999999828999996145
Q gi|254781218|r 46 TQKEMAIGANQLESAVNLFENGMC------STSIRYALYLRNEYEISFDWIYDG 93 (205)
Q Consensus 46 tQ~elA~~~gis~~~is~~E~G~~------~psi~~l~~la~~~~vs~d~Ll~g 93 (205)
|..|.|+.+|||..|.|.+=||+. .-+.+.+..+++.++=.++---.|
T Consensus 1 tL~dIA~LAGVS~TTASyViNGka~~~Ris~~T~erV~Avv~e~~Y~Pn~~A~s 54 (335)
T TIGR02417 1 TLDDIAKLAGVSKTTASYVINGKAKEYRISEETVERVMAVVEEQGYKPNVAAAS 54 (335)
T ss_pred CCHHHHHHCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHH
T ss_conf 900576660823232212000431110136787889999898737857755420
No 304
>COG2452 Predicted site-specific integrase-resolvase [DNA replication, recombination, and repair]
Probab=68.37 E-value=6.3 Score=19.38 Aligned_cols=23 Identities=13% Similarity=-0.172 Sum_probs=20.1
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 99889999984899999998877
Q gi|254781218|r 44 NKTQKEMAIGANQLESAVNLFEN 66 (205)
Q Consensus 44 gltQ~elA~~~gis~~~is~~E~ 66 (205)
.|+-++.|+.+||+..++-+|=+
T Consensus 1 ~m~~~e~~~~lgis~~Tl~rw~r 23 (193)
T COG2452 1 LLRPKEACQLLGISYSTLLRWIR 23 (193)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 98889999983947999999987
No 305
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator; InterPro: IPR011794 This entry represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon . This protein is a member of the MerR family of transcriptional activators and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix .; GO: 0003677 DNA binding, 0045340 mercury ion binding, 0045449 regulation of transcription, 0046689 response to mercury ion.
Probab=68.30 E-value=1.6 Score=23.12 Aligned_cols=21 Identities=24% Similarity=0.408 Sum_probs=14.4
Q ss_pred HHHHHHHCCCHHHHHHHH-CCC
Q ss_conf 999998489999999887-799
Q gi|254781218|r 48 KEMAIGANQLESAVNLFE-NGM 68 (205)
Q Consensus 48 ~elA~~~gis~~~is~~E-~G~ 68 (205)
.+||+++||..-||-.|| +|.
T Consensus 3 g~LA~~~GVNvETiRyYeRkGL 24 (126)
T TIGR02051 3 GELAKAAGVNVETIRYYERKGL 24 (126)
T ss_pred HHHHHHCCCCEEEEEHHHHCCC
T ss_conf 1136666897012210010077
No 306
>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=68.12 E-value=6.1 Score=19.46 Aligned_cols=23 Identities=22% Similarity=0.462 Sum_probs=11.5
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 72983899999977999999997
Q gi|254781218|r 124 DKGMSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 124 ~~glsq~elA~~lgis~~tis~~ 146 (205)
..|++-.|.|+.+|++..|+..+
T Consensus 13 ~~G~s~~eIA~~L~is~~TV~~~ 35 (57)
T cd06170 13 AEGKTNKEIADILGISEKTVKTH 35 (57)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 80799999999989789999999
No 307
>pfam07750 GcrA GcrA cell cycle regulator. GcrA is a master cell cycle regulator that, together with CtrA (see pfam00072 and pfam00486), is involved in controlling cell cycle progression and asymmetric polar morphogenesis. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery.
Probab=67.80 E-value=5.3 Score=19.83 Aligned_cols=28 Identities=18% Similarity=0.246 Sum_probs=21.8
Q ss_pred HHHHHHHHH--CCCCHHHHHHHHC-CCHHHH
Q ss_conf 999999998--5998899999848-999999
Q gi|254781218|r 34 TRIKDIRKA--NNKTQKEMAIGAN-QLESAV 61 (205)
Q Consensus 34 ~rik~lR~~--~gltQ~elA~~~g-is~~~i 61 (205)
+||..|++. .|+|..++|+.+| ||+++|
T Consensus 6 Erve~LkkLW~eGlSaSqIA~~LGgvTRNAV 36 (162)
T pfam07750 6 ERVELLKKLWLEGLSASQIAAQLGGVSRNAV 36 (162)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCCCCCE
T ss_conf 9999999999853659999999765540000
No 308
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=67.35 E-value=5.8 Score=19.59 Aligned_cols=69 Identities=17% Similarity=0.102 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHCCCHHHHH-CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHH------HHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 9999999998289999961-4532210000232134554677799999999------97298389999997799999999
Q gi|254781218|r 73 IRYALYLRNEYEISFDWIY-DGEVIDRRYEDVTNKKRLDPYAIGARLKSIR------KDKGMSQIEFGKLLGMPNSTLSN 145 (205)
Q Consensus 73 i~~l~~la~~~~vs~d~Ll-~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR------~~~glsq~elA~~lgis~~tis~ 145 (205)
...+..+++.+.....+.. ..........+.+.++.. -|+.+- --+..+..|+|+.+||+++|++.
T Consensus 125 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~LTdrQ~~-------vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~e 197 (215)
T COG3413 125 KDELRDLLEILNFEDKEEVIESAFVEIGKNDLTDRQLE-------VLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSE 197 (215)
T ss_pred HHHHHHHHHHHCCCCHHEECCCCCCCCCCCCCCHHHHH-------HHHHHHHCCCCCCCCCCCHHHHHHHHCCCHHHHHH
T ss_conf 78999999884323101021344234564469999999-------99999985898887658999999995998889999
Q ss_pred HHC
Q ss_conf 741
Q gi|254781218|r 146 YEQ 148 (205)
Q Consensus 146 ~E~ 148 (205)
+.+
T Consensus 198 hLR 200 (215)
T COG3413 198 HLR 200 (215)
T ss_pred HHH
T ss_conf 999
No 309
>pfam09048 Cro Cro. Members of this family are involved in the repression of transcription by binding as a homodimer to palindromic DNA operator sites in phage lambda: they repress genes expressed in early phage development and are necessary for the late stage of lytic growth. These proteins have a secondary structure consisting of three alpha-helices and three beta-sheets, and dimerize through interactions between the two antiparallel beta-strands.
Probab=67.15 E-value=8.4 Score=18.59 Aligned_cols=30 Identities=17% Similarity=0.013 Sum_probs=17.7
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCC
Q ss_conf 99998599889999984899999998877998
Q gi|254781218|r 38 DIRKANNKTQKEMAIGANQLESAVNLFENGMC 69 (205)
Q Consensus 38 ~lR~~~gltQ~elA~~~gis~~~is~~E~G~~ 69 (205)
+.-+..| |...|+.+|+.+++||+-=+-.+
T Consensus 7 dyv~~~G--Q~kaA~~lGV~Q~AISKAlragR 36 (58)
T pfam09048 7 DYVEEHG--QAKAAKDLGVNQSAISKALRAGR 36 (58)
T ss_pred HHHHHHC--HHHHHHHCCCCHHHHHHHHHCCC
T ss_conf 9999976--59899982975899999996488
No 310
>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=67.00 E-value=7.5 Score=18.89 Aligned_cols=64 Identities=31% Similarity=0.370 Sum_probs=39.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHH-CCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH--
Q ss_conf 988999998489999999887-79988899999999998289999961453221000023213455467779999999--
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFE-NGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSI-- 121 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E-~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~l-- 121 (205)
+|-.++|+..|+|..+|-.|| .|.-.|.-+ +.+ ..|. +..+ .+|+.+
T Consensus 1 ytIge~A~~~gvs~~tlRyYe~~GLl~p~r~------~g~--------------R~Y~---------~~~~-~~l~~I~~ 50 (118)
T cd04776 1 YTISELAREFDVTPRTLRFYEDKGLLSPERR------GQT--------------RVYS---------RRDR-ARLKLILR 50 (118)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCC------CCC--------------CCCC---------HHHH-HHHHHHHH
T ss_conf 9588999998979999999998699875557------986--------------8608---------9999-99999999
Q ss_pred HHHCCCCHHHHHHHHCC
Q ss_conf 99729838999999779
Q gi|254781218|r 122 RKDKGMSQIEFGKLLGM 138 (205)
Q Consensus 122 R~~~glsq~elA~~lgi 138 (205)
-+..|+|..|..+.+.+
T Consensus 51 ~r~~G~sL~eI~~~L~l 67 (118)
T cd04776 51 GKRLGFSLEEIRELLDL 67 (118)
T ss_pred HHHCCCCHHHHHHHHHH
T ss_conf 99829989999999964
No 311
>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=66.69 E-value=4.2 Score=20.45 Aligned_cols=21 Identities=14% Similarity=0.347 Sum_probs=11.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHH
Q ss_conf 838999999779999999974
Q gi|254781218|r 127 MSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 127 lsq~elA~~lgis~~tis~~E 147 (205)
++..+.|+.||++.++|++|-
T Consensus 23 ~~l~~IA~~L~vs~~~IrkWK 43 (60)
T pfam10668 23 MKLKDIANKLNVSESQIRKWK 43 (60)
T ss_pred EEHHHHHHHHCCCHHHHHHCC
T ss_conf 449999999687988876031
No 312
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1; InterPro: IPR011745 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 describes sigma-70 factors in Myxococcus xanthus DK 1622 and in other members of the Mycococcales. Each of the six members in M. xanthusis is encoded near a gene for a predicted serine/threonine kinase. Members of this family show sequence similarity to members of Pfam family IPR007630 from INTERPRO (region 4 of sigma-70 like sigma-factors), a helix-turn-helix family in which trusted and noise cutoffs deliberately are set artificially high and which therefore has many false negatives.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=66.48 E-value=4.3 Score=20.41 Aligned_cols=29 Identities=21% Similarity=0.305 Sum_probs=20.1
Q ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf 99972983899999977999999997414
Q gi|254781218|r 121 IRKDKGMSQIEFGKLLGMPNSTLSNYEQG 149 (205)
Q Consensus 121 lR~~~glsq~elA~~lgis~~tis~~E~g 149 (205)
+.--.|+|..++|.+-+++++|+|+|-..
T Consensus 177 LHfv~~Ls~~r~g~my~~~~STvsR~~~~ 205 (249)
T TIGR03001 177 LHFVEGLSMDRLGAMYQVHRSTVSRWVAQ 205 (249)
T ss_pred HHHHCCCCHHHHHHHHCCCCHHHHHHHHH
T ss_conf 68820332999987745775078999999
No 313
>pfam00196 GerE Bacterial regulatory proteins, luxR family.
Probab=65.78 E-value=7.1 Score=19.03 Aligned_cols=23 Identities=26% Similarity=0.410 Sum_probs=12.0
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 72983899999977999999997
Q gi|254781218|r 124 DKGMSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 124 ~~glsq~elA~~lgis~~tis~~ 146 (205)
..|++-.|.|+.+|++..|+..+
T Consensus 16 ~~G~s~~eIA~~L~is~~TV~~h 38 (58)
T pfam00196 16 AAGKSNKEIADILGISEKTVKVH 38 (58)
T ss_pred HHCCCHHHHHHHHCCCHHHHHHH
T ss_conf 80799999999978889999999
No 314
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=65.78 E-value=8 Score=18.73 Aligned_cols=42 Identities=24% Similarity=0.285 Sum_probs=29.7
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHC
Q ss_conf 9999997298389999997799999999741488999899999999828
Q gi|254781218|r 118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTK 166 (205)
Q Consensus 118 Lk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lg 166 (205)
+=.++...|+|..|.|+.+|+|.+|+...-. ....+|.+.|.
T Consensus 114 v~~L~~~eg~s~~EIA~~L~is~~tVksrl~-------RAr~~Lr~~LE 155 (181)
T PRK09637 114 ALRLTELEGLSQKEIAEKLGLSLSGAKSRVQ-------RGRVKLKELLE 155 (181)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH-------HHHHHHHHHHH
T ss_conf 9799988599999999998949999999999-------99999999997
No 315
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=65.57 E-value=7.4 Score=18.92 Aligned_cols=44 Identities=9% Similarity=0.171 Sum_probs=30.6
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCC
Q ss_conf 999999729838999999779999999974148899989999999982899
Q gi|254781218|r 118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKH 168 (205)
Q Consensus 118 Lk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs 168 (205)
+=.++...|+|.+|.|+.+|||..|+...-. ....++.+.|++.
T Consensus 127 vl~L~~~egls~~EIAe~Lgis~~TVksrl~-------RAr~~Lr~~L~~~ 170 (190)
T PRK12516 127 AIILIGASGFAYEEAAEICGCAVGTIKSRVS-------RARARLQEILQIE 170 (190)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH-------HHHHHHHHHHHHC
T ss_conf 9998998299999999998949999999999-------9999999999845
No 316
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=65.48 E-value=5.8 Score=19.59 Aligned_cols=23 Identities=9% Similarity=-0.081 Sum_probs=19.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf 98899999848999999988779
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFENG 67 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E~G 67 (205)
|...++|+++|||+.+|.||-+-
T Consensus 1 mkT~~vAk~LGVspkTVQRWvKq 23 (178)
T PRK13182 1 MKTPFVAKKLGVSPKTVQRWVKQ 23 (178)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 97178899939992999999999
No 317
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=65.45 E-value=10 Score=18.00 Aligned_cols=28 Identities=29% Similarity=0.507 Sum_probs=24.2
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 9999729838999999779999999974
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~E 147 (205)
.++...|+|..|.|+.+||+..|+..+-
T Consensus 146 ~L~~~~g~s~~EIA~~L~is~~TVk~~l 173 (187)
T PRK13919 146 EVLYYQGYTHREAARLLGLPLGTLKTWA 173 (187)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9999859999999999893999999999
No 318
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which 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 N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=65.27 E-value=7.5 Score=18.90 Aligned_cols=28 Identities=14% Similarity=0.154 Sum_probs=21.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHH-CCCCCCC
Q ss_conf 988999998489999999887-7998889
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFE-NGMCSTS 72 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E-~G~~~ps 72 (205)
+|-.++|+..|+|..+|-.|| .|.-.|.
T Consensus 1 ytIgelA~~~Gvs~~TiRyYe~~GLl~~~ 29 (107)
T cd01111 1 YSISQLALDAGVSVHIVRDYLLRGLLHPV 29 (107)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCC
T ss_conf 95889999978894899899987898998
No 319
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=64.98 E-value=11 Score=17.96 Aligned_cols=58 Identities=14% Similarity=0.045 Sum_probs=40.0
Q ss_pred HHHHHHHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHH-HHHHHH
Q ss_conf 999999999999999-9859988999998489999999887799888999999-999982
Q gi|254781218|r 26 RQYWKDVGTRIKDIR-KANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYAL-YLRNEY 83 (205)
Q Consensus 26 ~~~~~~iG~rik~lR-~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~-~la~~~ 83 (205)
....+.|++-|-.-. +...+|-.+||+.+|+|+++|.|+=+-...-...-+. .|+..+
T Consensus 15 t~~Ek~IA~yIl~n~~~v~~~si~eLA~~~~vS~aTVvRf~kkLGf~Gf~efK~~l~~~~ 74 (282)
T PRK11557 15 AQSDRKLADYLLLQPDTARHLSSQQLANEAGVSQSSVVKFAQKLGYKGFPALKLALSEAL 74 (282)
T ss_pred CHHHHHHHHHHHCCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf 999999999998098999765699999896999889999999938998999999999998
No 320
>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=64.94 E-value=6.6 Score=19.25 Aligned_cols=56 Identities=20% Similarity=0.127 Sum_probs=28.2
Q ss_pred HHHHHHHHHHH-HHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCH-HHHHHHHHHHC
Q ss_conf 99999999999-9985998899999848999999988779988899-99999999828
Q gi|254781218|r 29 WKDVGTRIKDI-RKANNKTQKEMAIGANQLESAVNLFENGMCSTSI-RYALYLRNEYE 84 (205)
Q Consensus 29 ~~~iG~rik~l-R~~~gltQ~elA~~~gis~~~is~~E~G~~~psi-~~l~~la~~~~ 84 (205)
.+.|++-|-.- .....+|-.+||+++|+|+++|.|+=+-...-.. ++=+.|+..+.
T Consensus 18 e~~ia~yil~~~~~~~~~si~~lA~~~~vS~atv~Rf~kklG~~Gf~efk~~La~~~~ 75 (106)
T pfam01418 18 EKKIADYILASPDNAIHLSIAELAKAAGVSEASVVRFCRKLGFSGFSDLKVALAGELA 75 (106)
T ss_pred HHHHHHHHHHCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHC
T ss_conf 9999999992999998833999998969989999999999589989999999999865
No 321
>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=64.43 E-value=9.2 Score=18.36 Aligned_cols=28 Identities=18% Similarity=0.160 Sum_probs=21.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHH-CCCCCCC
Q ss_conf 988999998489999999887-7998889
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFE-NGMCSTS 72 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E-~G~~~ps 72 (205)
++-.+||+..|||..+|-.|| .|.-.|.
T Consensus 1 y~Ige~Ak~~gvs~~tlRyYe~~GLl~p~ 29 (96)
T cd04788 1 WKIGELARRTGLSVRTLHHYDHIGLLSPS 29 (96)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCC
T ss_conf 94889999989599999999973998988
No 322
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=64.25 E-value=8.9 Score=18.44 Aligned_cols=29 Identities=24% Similarity=0.334 Sum_probs=24.8
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 99997298389999997799999999741
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNYEQ 148 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~E~ 148 (205)
.++...|||..|.|+.+|+|..|+...-.
T Consensus 159 ~L~~~eglS~~EIA~~Lgis~~TVKsrL~ 187 (231)
T PRK11922 159 VLRVVEELSVEETAQALGLPEETVKTRLH 187 (231)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 99999399999999998939999999999
No 323
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=63.98 E-value=8.3 Score=18.64 Aligned_cols=28 Identities=18% Similarity=0.213 Sum_probs=23.8
Q ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 9999972983899999977999999997
Q gi|254781218|r 119 KSIRKDKGMSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 119 k~lR~~~glsq~elA~~lgis~~tis~~ 146 (205)
=.+|.-.|+|..|.|+.+|+|.+++...
T Consensus 121 ~~L~~~~g~s~~EIA~~lgis~~tVk~~ 148 (161)
T PRK12541 121 LLLRDYYGFSYKEIAEMTGLSLAKVKIE 148 (161)
T ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 9989974999999999989399999999
No 324
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=63.91 E-value=7.2 Score=19.01 Aligned_cols=23 Identities=22% Similarity=0.192 Sum_probs=19.7
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 29838999999779999999974
Q gi|254781218|r 125 KGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 125 ~glsq~elA~~lgis~~tis~~E 147 (205)
..+++.++|..+|+++.|+++..
T Consensus 172 l~~t~~~lA~~lG~tretvsR~L 194 (236)
T PRK09392 172 LPYEKRTLASYLGMTPENLSRAF 194 (236)
T ss_pred ECCCHHHHHHHHCCCHHHHHHHH
T ss_conf 34789999998789899999999
No 325
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=63.85 E-value=8 Score=18.71 Aligned_cols=24 Identities=21% Similarity=0.412 Sum_probs=13.3
Q ss_pred HHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 972983899999977999999997
Q gi|254781218|r 123 KDKGMSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 123 ~~~glsq~elA~~lgis~~tis~~ 146 (205)
-..|++..+.|+.+|++..|+..+
T Consensus 15 l~~G~s~~eIA~~L~is~~TV~~~ 38 (58)
T smart00421 15 LAEGLTNKEIAERLGISEKTVKTH 38 (58)
T ss_pred HHHCCCHHHHHHHHCCCHHHHHHH
T ss_conf 981799999998989789899999
No 326
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=63.41 E-value=6.5 Score=19.27 Aligned_cols=27 Identities=7% Similarity=0.047 Sum_probs=22.8
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHHCCC
Q ss_conf 859988999998489999999887799
Q gi|254781218|r 42 ANNKTQKEMAIGANQLESAVNLFENGM 68 (205)
Q Consensus 42 ~~gltQ~elA~~~gis~~~is~~E~G~ 68 (205)
-.|+..+++|+++||++.+|-.|-+-.
T Consensus 17 l~gmk~~dIAeklGvspntiksWKrr~ 43 (279)
T COG5484 17 LKGMKLKDIAEKLGVSPNTIKSWKRRD 43 (279)
T ss_pred HHHCCHHHHHHHHCCCHHHHHHHHHHC
T ss_conf 843419999999689868888778740
No 327
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=63.39 E-value=7.3 Score=18.99 Aligned_cols=64 Identities=20% Similarity=0.254 Sum_probs=38.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHH-CCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH--
Q ss_conf 988999998489999999887-79988899999999998289999961453221000023213455467779999999--
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFE-NGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSI-- 121 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E-~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~l-- 121 (205)
|+-.+||+..|||..||-.|| .|.-.|.-. +. -+.++. . .+ .+|+-+
T Consensus 1 m~Ige~Ak~~~vs~~TlRyYe~~GLl~P~~~------~g-----~r~Y~~-------~-----------d~-~~L~~I~~ 50 (107)
T cd04777 1 MKIGKFAKKNNITIDTVRHYIDLGLLIPEKK------GG-----QYFFDE-------K-----------CQ-DDLEFILE 50 (107)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCC------CC-----CCCCCH-------H-----------HH-HHHHHHHH
T ss_conf 9689999996998988899998588688768------99-----466199-------9-----------99-99999999
Q ss_pred HHHCCCCHHHHHHHHCC
Q ss_conf 99729838999999779
Q gi|254781218|r 122 RKDKGMSQIEFGKLLGM 138 (205)
Q Consensus 122 R~~~glsq~elA~~lgi 138 (205)
-+..|+|..|..+.+.+
T Consensus 51 ~k~lgfsL~eIk~ll~l 67 (107)
T cd04777 51 LKGLGFSLIEIQKIFSY 67 (107)
T ss_pred HHHCCCCHHHHHHHHHH
T ss_conf 98889989999999962
No 328
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=63.05 E-value=11 Score=17.86 Aligned_cols=27 Identities=26% Similarity=0.209 Sum_probs=23.7
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 999972983899999977999999997
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~ 146 (205)
.++...|+|..|.|+.+|+|..++...
T Consensus 141 ~L~~~eg~s~~EIA~~lgis~~tVks~ 167 (184)
T PRK12539 141 QAVKLDGLSVAEAATRSGMSESAVKVS 167 (184)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999994999999999989199999999
No 329
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=62.49 E-value=8.2 Score=18.67 Aligned_cols=34 Identities=15% Similarity=0.113 Sum_probs=26.3
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH-CCCC
Q ss_conf 9999999859988999998489999999887-7998
Q gi|254781218|r 35 RIKDIRKANNKTQKEMAIGANQLESAVNLFE-NGMC 69 (205)
Q Consensus 35 rik~lR~~~gltQ~elA~~~gis~~~is~~E-~G~~ 69 (205)
+|..++ ..|+|-.++|..+|-.+||||+== +|..
T Consensus 15 ~I~~l~-~~~~S~reIA~~LgRh~sTIsRElkRn~~ 49 (318)
T COG2826 15 EIERLL-KAKMSIREIAKQLNRHHSTISRELKRNRT 49 (318)
T ss_pred HHHHHH-HCCCCHHHHHHHHCCCCCHHHHHHHCCCC
T ss_conf 999999-85998999999857686204279866875
No 330
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=62.32 E-value=9.4 Score=18.30 Aligned_cols=27 Identities=19% Similarity=0.345 Sum_probs=21.1
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 999972983899999977999999997
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~ 146 (205)
.+|...|+|..|.|+.+|+|.+++...
T Consensus 146 ~L~~~egls~~EIA~~lgis~~tVks~ 172 (195)
T PRK12532 146 TLKEILGFSSDEIQQMCGISTSNYHTI 172 (195)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999981999999999989599999999
No 331
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=61.67 E-value=11 Score=17.99 Aligned_cols=29 Identities=17% Similarity=0.184 Sum_probs=24.1
Q ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 99999729838999999779999999974
Q gi|254781218|r 119 KSIRKDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 119 k~lR~~~glsq~elA~~lgis~~tis~~E 147 (205)
=.++.-.|+|..|.|+.+|||..|+...-
T Consensus 137 i~L~~~eg~s~~EIA~~Lgis~~tVksrl 165 (188)
T PRK12517 137 LLLQVIGGFSGEEIAEILDLNKNTVMTRL 165 (188)
T ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 99999839999999999893999999999
No 332
>pfam09339 HTH_IclR IclR helix-turn-helix domain.
Probab=61.49 E-value=7.1 Score=19.04 Aligned_cols=26 Identities=31% Similarity=0.422 Sum_probs=19.2
Q ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 97298389999997799999999741
Q gi|254781218|r 123 KDKGMSQIEFGKLLGMPNSTLSNYEQ 148 (205)
Q Consensus 123 ~~~glsq~elA~~lgis~~tis~~E~ 148 (205)
...+++..|+|+.+|++++++.++-+
T Consensus 15 ~~~~~~l~eia~~~gl~kstv~RlL~ 40 (52)
T pfam09339 15 APGGLSLTEIARRTGLPKSTAHRLLQ 40 (52)
T ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 89998999999998919999999999
No 333
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=61.46 E-value=11 Score=17.96 Aligned_cols=28 Identities=25% Similarity=0.405 Sum_probs=18.6
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 9999997298389999997799999999
Q gi|254781218|r 118 LKSIRKDKGMSQIEFGKLLGMPNSTLSN 145 (205)
Q Consensus 118 Lk~lR~~~glsq~elA~~lgis~~tis~ 145 (205)
+..+.+..-++..|+|+.+|+|..|+.+
T Consensus 6 l~~l~~~~~~~i~~La~~~~VS~~TiRR 33 (53)
T smart00420 6 LELLAQQGKVSVEELAELLGVSEMTIRR 33 (53)
T ss_pred HHHHHHCCCEEHHHHHHHHCCCHHHHHH
T ss_conf 9999986979799999998979999999
No 334
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=61.43 E-value=11 Score=17.93 Aligned_cols=28 Identities=18% Similarity=0.103 Sum_probs=23.7
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 9999729838999999779999999974
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~E 147 (205)
.++...|+|..|.|+.+|+|..|+...-
T Consensus 163 ~L~~~egls~~EIA~~l~is~~TVksrl 190 (206)
T PRK12526 163 KGVYFQELSQEQLAQQLNVPLGTVKSRL 190 (206)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9999859999999999893999999999
No 335
>pfam04760 IF2_N Translation initiation factor IF-2, N-terminal region. This conserved feature at the N-terminus of bacterial translation initiation factor IF2 has recently had its structure solved. It shows structural similarity to the tRNA anticodon Stem Contact Fold domains of the methionyl-tRNA and glutaminyl-tRNA synthetases, and a similar fold is also found in the B5 domain of the phenylalanine-tRNA synthetase.
Probab=60.89 E-value=13 Score=17.48 Aligned_cols=42 Identities=14% Similarity=0.112 Sum_probs=19.6
Q ss_pred CCCHHHHHHHHCCCHHHHHHHH-------CCCCCCCHHHHHHHHHHHCC
Q ss_conf 9838999999779999999974-------14889998999999998289
Q gi|254781218|r 126 GMSQIEFGKLLGMPNSTLSNYE-------QGRTIPEIKPARKIKQVTKK 167 (205)
Q Consensus 126 glsq~elA~~lgis~~tis~~E-------~g~~~Ps~~~l~kIa~~lgv 167 (205)
+++..|||+.+|++..-+-+.. +-....+.+.+..|++.||.
T Consensus 3 ~itV~elA~~l~~~~~~vi~~L~~~Gi~~~~n~~ld~e~a~~i~~~~~~ 51 (52)
T pfam04760 3 KIRVYELAKELGVSSKELIKKLFKLGIMKTHNSTLDEETAELLAEEFGV 51 (52)
T ss_pred CEEHHHHHHHHCCCHHHHHHHHHHCCCEECCCCCCCHHHHHHHHHHHCC
T ss_conf 1739999999888899999999987985567774599999999998198
No 336
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=60.79 E-value=11 Score=17.90 Aligned_cols=51 Identities=12% Similarity=0.252 Sum_probs=35.7
Q ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCC
Q ss_conf 9999972983899999977999999997414889998999999998289999952472
Q gi|254781218|r 119 KSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIYFGD 176 (205)
Q Consensus 119 k~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~~G~ 176 (205)
=.++...|+|..|.|+.+|+|..|+...-. ....+|.+.|+---.++=+|+
T Consensus 145 i~L~~~eg~s~~EIA~~lgis~~tVk~~l~-------Rark~Lr~~L~~~r~~~g~~~ 195 (196)
T PRK12524 145 VVLRHIEGLSNPEIAEVMQIGVEAVESLTA-------RGKRALAALLAGQRAELGYGE 195 (196)
T ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHHH-------HHHHHHHHHHHHHHHHCCCCC
T ss_conf 899998089999999998929999999999-------999999999871798749889
No 337
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=60.35 E-value=12 Score=17.74 Aligned_cols=30 Identities=23% Similarity=0.242 Sum_probs=24.9
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 999999729838999999779999999974
Q gi|254781218|r 118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 118 Lk~lR~~~glsq~elA~~lgis~~tis~~E 147 (205)
+=.+|-..|||..|.|+.+|++.+|+...-
T Consensus 137 vi~L~~~~g~s~~EIA~~l~is~~tVk~rl 166 (190)
T PRK12543 137 VIILRYLHDYSQEEVAQILHIPIGTVKSRI 166 (190)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 999999859999999999893999999999
No 338
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=60.29 E-value=11 Score=17.89 Aligned_cols=27 Identities=22% Similarity=0.310 Sum_probs=23.5
Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 997298389999997799999999741
Q gi|254781218|r 122 RKDKGMSQIEFGKLLGMPNSTLSNYEQ 148 (205)
Q Consensus 122 R~~~glsq~elA~~lgis~~tis~~E~ 148 (205)
.-..|+|.+|.|+.+++|..|+..+-+
T Consensus 148 lia~G~snkeIA~~L~IS~~TVk~h~~ 174 (196)
T PRK10360 148 KLAQGMAVKEIAAELGLSPKTVHVHRA 174 (196)
T ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 998799999999996999999999999
No 339
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=60.24 E-value=11 Score=17.95 Aligned_cols=30 Identities=17% Similarity=0.125 Sum_probs=25.1
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 999999729838999999779999999974
Q gi|254781218|r 118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 118 Lk~lR~~~glsq~elA~~lgis~~tis~~E 147 (205)
+=.++...|+|..|.|+.+|+|..|+...-
T Consensus 120 v~~L~~~~g~s~~EIA~~lgis~~tVksrl 149 (164)
T PRK12547 120 AIILIGASGFSYEEAAEICGCAVGTIKSRV 149 (164)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 999899849999999999893999999999
No 340
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=59.69 E-value=11 Score=17.92 Aligned_cols=28 Identities=21% Similarity=0.211 Sum_probs=23.9
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 9999729838999999779999999974
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~E 147 (205)
.+|...|||..|.|+.+|++..++....
T Consensus 167 ~Lr~~eglS~~EIAe~Lgis~gTVKsrl 194 (222)
T PRK09647 167 VLCDIEGLSYEEIAATLGVKLGTVRSRI 194 (222)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 8799639999999999893999999999
No 341
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=59.68 E-value=11 Score=17.86 Aligned_cols=33 Identities=24% Similarity=0.295 Sum_probs=25.8
Q ss_pred HHHHHH--HHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 999999--997298389999997799999999741
Q gi|254781218|r 116 ARLKSI--RKDKGMSQIEFGKLLGMPNSTLSNYEQ 148 (205)
Q Consensus 116 ~rLk~l--R~~~glsq~elA~~lgis~~tis~~E~ 148 (205)
.|=+++ .-..|+|.+|.|+.+++|..|+..+-+
T Consensus 152 ~RE~eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~ 186 (210)
T PRK09935 152 NREVTVLRYLANGLSNKEIAEQLLLSNKTISAHKS 186 (210)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 89999999998699999999894988999999999
No 342
>TIGR01529 argR_whole arginine repressor; InterPro: IPR001669 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia . The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 100f total cell protein . Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR . This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine . The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography . The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 transcription factor activity, 0006355 regulation of transcription DNA-dependent.
Probab=59.29 E-value=13 Score=17.42 Aligned_cols=32 Identities=22% Similarity=0.162 Sum_probs=15.5
Q ss_pred HHHHHHHHHCC-CCHHHHHHHH-----C-CCHHHHHHHH
Q ss_conf 99999999859-9889999984-----8-9999999887
Q gi|254781218|r 34 TRIKDIRKANN-KTQKEMAIGA-----N-QLESAVNLFE 65 (205)
Q Consensus 34 ~rik~lR~~~g-ltQ~elA~~~-----g-is~~~is~~E 65 (205)
++||.+=...+ =||+||...+ . ++|+++||+=
T Consensus 5 ~~Ik~Ii~~e~~~tQ~El~~~L~~~G~~nvTQaTvSRDL 43 (155)
T TIGR01529 5 EAIKEIITEEKISTQEELVALLKKEGVKNVTQATVSRDL 43 (155)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHCCCCEECCCCHHHHH
T ss_conf 999999874376798899999986597511234067878
No 343
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=59.22 E-value=11 Score=17.83 Aligned_cols=41 Identities=5% Similarity=0.224 Sum_probs=30.0
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 999999729838999999779999999974148899989999999982
Q gi|254781218|r 118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVT 165 (205)
Q Consensus 118 Lk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~l 165 (205)
+=.+|--.|||..|.|+.+|+|.+|+...-. ....+|.+.+
T Consensus 130 v~~L~~~~gls~~EIA~~L~is~~tVk~rl~-------RArk~Lr~~L 170 (185)
T PRK12542 130 VFKYKVFYNLTYQEISSVMGITEANVRKQFE-------RARKRVQNMI 170 (185)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH-------HHHHHHHHHH
T ss_conf 9767998399999999998929999999999-------9999999987
No 344
>TIGR02233 Myxo_sigma_rel Myxococcus probable DNA-binding regulatory protein.
Probab=59.14 E-value=6.8 Score=19.17 Aligned_cols=32 Identities=25% Similarity=0.465 Sum_probs=22.7
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCC
Q ss_conf 99997298389999997799999999741488
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRT 151 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~E~g~~ 151 (205)
.+.--.|+|...+|.+-|.+++|+++|-.+-.
T Consensus 34 RLH~~~gLsldR~~~lY~~hrStvaR~v~~ar 65 (106)
T TIGR02233 34 RLHHVEGLSLDRLGTLYGVHRSTVARWVAGAR 65 (106)
T ss_pred HHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf 67762365589999884788616999999999
No 345
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=58.95 E-value=12 Score=17.74 Aligned_cols=28 Identities=25% Similarity=0.183 Sum_probs=23.7
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 9999729838999999779999999974
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~E 147 (205)
.++.-.|+|..|.|+.+|+|.+++...-
T Consensus 136 ~l~~~eg~s~~EIA~~lgis~~tVk~rl 163 (178)
T PRK12536 136 VHVKLEGLSVEETAQLTGLSESAVKVGI 163 (178)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9998859999999999892999999999
No 346
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=58.88 E-value=11 Score=17.96 Aligned_cols=29 Identities=10% Similarity=0.067 Sum_probs=24.1
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 99999972983899999977999999997
Q gi|254781218|r 118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 118 Lk~lR~~~glsq~elA~~lgis~~tis~~ 146 (205)
+=.++...|+|..|.|+.+|+|.+++...
T Consensus 116 v~~L~~~~~~s~~EIA~~l~is~~tVk~r 144 (165)
T PRK09644 116 AILLCDVHELTYEEAASVLDLKENTYKSH 144 (165)
T ss_pred HHHHHHHHCCCHHHHHHHHCCCHHHHHHH
T ss_conf 99999998889999999989399999999
No 347
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=58.45 E-value=11 Score=17.87 Aligned_cols=27 Identities=15% Similarity=0.176 Sum_probs=23.4
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 999972983899999977999999997
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~ 146 (205)
.+|.-.|||..|.|+.+|+|..++...
T Consensus 116 ~L~~~egls~~EIA~~l~is~~tVk~~ 142 (161)
T PRK09047 116 LLRYWEDMDVAETAAAMGCSEGSVKTH 142 (161)
T ss_pred HHHHHHCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999998779999999989699999999
No 348
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator; InterPro: IPR011791 This entry represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system , . This protein is a member of the MerR family of transcriptional activators and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix ..
Probab=58.34 E-value=5.4 Score=19.78 Aligned_cols=25 Identities=12% Similarity=0.110 Sum_probs=14.5
Q ss_pred HHHHHHHCCCHHHHHHHHCCCCCCC
Q ss_conf 9999984899999998877998889
Q gi|254781218|r 48 KEMAIGANQLESAVNLFENGMCSTS 72 (205)
Q Consensus 48 ~elA~~~gis~~~is~~E~G~~~ps 72 (205)
-|||++.|++..||-.||.----|.
T Consensus 4 GeLA~~t~v~v~TIRFYE~~gLLPe 28 (127)
T TIGR02047 4 GELAKKTGVSVETIRFYEKEGLLPE 28 (127)
T ss_pred HHHHHHHCCCCCHHHHHHHCCCCCC
T ss_conf 3454553344002246441378538
No 349
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=58.21 E-value=12 Score=17.66 Aligned_cols=42 Identities=12% Similarity=0.193 Sum_probs=29.4
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCC
Q ss_conf 9999729838999999779999999974148899989999999982899
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKH 168 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs 168 (205)
.++.-.|+|..|.|+.+||+..|+...-.- ...++.+.|+..
T Consensus 123 ~L~~~egls~~EIAe~Lgis~gTVKsRL~R-------AR~~Lr~~Le~~ 164 (188)
T PRK12546 123 ILVGASGFSYEEAAEMCGVAVGTVKSRANR-------ARARLAELLQLE 164 (188)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHHH-------HHHHHHHHHHCC
T ss_conf 879982989999999989399999999999-------999999987272
No 350
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=57.92 E-value=13 Score=17.35 Aligned_cols=28 Identities=32% Similarity=0.450 Sum_probs=23.7
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 9999729838999999779999999974
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~E 147 (205)
.++-..|+|..|.|+.+|++..|+....
T Consensus 151 ~L~~~eg~s~~EIA~~lgis~~tVk~rl 178 (194)
T PRK12519 151 ELAYYEGLSQSEIAKRLGIPLGTVKARA 178 (194)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9999819999999999894999999999
No 351
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=57.91 E-value=14 Score=17.17 Aligned_cols=24 Identities=17% Similarity=-0.111 Sum_probs=14.3
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 859988999998489999999887
Q gi|254781218|r 42 ANNKTQKEMAIGANQLESAVNLFE 65 (205)
Q Consensus 42 ~~gltQ~elA~~~gis~~~is~~E 65 (205)
.+.||..++|..+.+|++.+++.=
T Consensus 156 ~~~wsL~dIA~~L~MSpS~LkKkL 179 (274)
T PRK09978 156 AHEWTLARIASELLMSPSLLKKKL 179 (274)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 036139999988727999999999
No 352
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=57.91 E-value=14 Score=17.17 Aligned_cols=58 Identities=21% Similarity=0.122 Sum_probs=39.4
Q ss_pred HHHHHHHHHHHHH-HHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHH-HHHHHHHC
Q ss_conf 9999999999999-9985998899999848999999988779988899999-99999828
Q gi|254781218|r 27 QYWKDVGTRIKDI-RKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYA-LYLRNEYE 84 (205)
Q Consensus 27 ~~~~~iG~rik~l-R~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l-~~la~~~~ 84 (205)
...+.|+.-|-.- -....+|-.+||+++|+|+++|.|+=+-.......-+ +.|+..+.
T Consensus 16 ~~Ek~iA~yIl~n~~~v~~~si~eLA~~~~vS~aTV~Rf~kkLGf~Gf~efK~~l~~~l~ 75 (284)
T PRK11302 16 KSERKVAEVILASPQTAIHSSIATLAKMANVSEPTVNRFCRSLDTKGFPDFKLHLAQSLA 75 (284)
T ss_pred HHHHHHHHHHHCCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHH
T ss_conf 999999999980989997666999998969988899999999578978999999999975
No 353
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=57.82 E-value=13 Score=17.33 Aligned_cols=23 Identities=26% Similarity=0.485 Sum_probs=12.0
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 72983899999977999999997
Q gi|254781218|r 124 DKGMSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 124 ~~glsq~elA~~lgis~~tis~~ 146 (205)
+..++..|+|+.+|++++++++.
T Consensus 8 ~~~~~~~ela~~l~is~~tvs~H 30 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHH 30 (66)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 39966999999988298888799
No 354
>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR; InterPro: IPR012704 At least five distinct pathways exist for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR which is, in most cases, divergently transcribed from the operon that encodes the genes involved in the methylcitric acid cycle of propionate catabolism. This protein is required for the expression of the proteins involved in this pathway . 2-methylcitric acid, an intermediate in this pathway, has been proposed to be a co-activator of PrpR .; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay), 0019629 propionate catabolic process 2-methylcitrate cycle, 0005737 cytoplasm.
Probab=57.79 E-value=13 Score=17.49 Aligned_cols=36 Identities=14% Similarity=0.085 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 779999999997298389999997799999999741
Q gi|254781218|r 113 AIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQ 148 (205)
Q Consensus 113 ~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~ 148 (205)
....-+++..+..+=...-.|+.+|||+.|+++|.+
T Consensus 622 v~a~~~~~aL~~~~G~~~a~a~~LGiSrTTLWRrL~ 657 (658)
T TIGR02329 622 VEALAVRAALERFQGDRAAAAKALGISRTTLWRRLK 657 (658)
T ss_pred CCHHHHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHC
T ss_conf 335768999987278968998542764245777613
No 355
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). 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=57.73 E-value=14 Score=17.18 Aligned_cols=27 Identities=11% Similarity=0.186 Sum_probs=21.5
Q ss_pred CHHHHHHHHCCCHHHHHHHH-CCCCCCC
Q ss_conf 88999998489999999887-7998889
Q gi|254781218|r 46 TQKEMAIGANQLESAVNLFE-NGMCSTS 72 (205)
Q Consensus 46 tQ~elA~~~gis~~~is~~E-~G~~~ps 72 (205)
+-.++|+..|+|..+|-.|| .|.-.|.
T Consensus 2 ~IgelA~~~gvs~~TlRyYe~~GLl~p~ 29 (134)
T cd04779 2 RIGQLAHLAGVSKRTIDYYTNLGLLTPE 29 (134)
T ss_pred CHHHHHHHHCCCHHHHHHHHHCCCCCCC
T ss_conf 5889999988688999999977997999
No 356
>PRK10403 transcriptional regulator NarP; Provisional
Probab=57.60 E-value=12 Score=17.55 Aligned_cols=36 Identities=14% Similarity=0.250 Sum_probs=28.0
Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCC
Q ss_conf 99729838999999779999999974148899989999999982899
Q gi|254781218|r 122 RKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKH 168 (205)
Q Consensus 122 R~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs 168 (205)
.-..|+|-+|.|+.++++..|+..+ +..|.+-||++
T Consensus 164 lla~G~snkeIA~~L~iS~~TV~~h-----------~~~I~~KLgv~ 199 (215)
T PRK10403 164 ELAQGLSNKQIASVLNISEQTVKVH-----------IRNLLRKLNVR 199 (215)
T ss_pred HHHCCCCHHHHHHHHCCCHHHHHHH-----------HHHHHHHHCCC
T ss_conf 9986999999999979829999999-----------99999986899
No 357
>PHA01082 putative transcription regulator
Probab=57.56 E-value=6.4 Score=19.33 Aligned_cols=40 Identities=15% Similarity=0.103 Sum_probs=27.6
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCH-HHHHHHHH
Q ss_conf 85998899999848999999988779988899-99999999
Q gi|254781218|r 42 ANNKTQKEMAIGANQLESAVNLFENGMCSTSI-RYALYLRN 81 (205)
Q Consensus 42 ~~gltQ~elA~~~gis~~~is~~E~G~~~psi-~~l~~la~ 81 (205)
..|||-+|-|+.+=-|.++|-.|..|+.-|+. ..|++.-.
T Consensus 28 eCgLsveeaA~LCfKtVrtVk~WD~G~~IPPeCkRLMRm~~ 68 (133)
T PHA01082 28 ECGLSVEEAAKLCFKTVSEVKQWDAGEKIPPICKRLMRMNK 68 (133)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHC
T ss_conf 13763999999999978888630489949879999998851
No 358
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=57.42 E-value=13 Score=17.45 Aligned_cols=27 Identities=19% Similarity=0.250 Sum_probs=23.1
Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 997298389999997799999999741
Q gi|254781218|r 122 RKDKGMSQIEFGKLLGMPNSTLSNYEQ 148 (205)
Q Consensus 122 R~~~glsq~elA~~lgis~~tis~~E~ 148 (205)
.-..|+|.+|.|+.+++|..|+..|-+
T Consensus 154 ll~~G~snkeIA~~L~iS~~TV~~h~~ 180 (204)
T PRK09958 154 YILDGKDNNDIAEKMFISNKTVSTYKS 180 (204)
T ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 998699999999897889999999999
No 359
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=57.36 E-value=15 Score=17.11 Aligned_cols=30 Identities=27% Similarity=0.335 Sum_probs=24.8
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 999999729838999999779999999974
Q gi|254781218|r 118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 118 Lk~lR~~~glsq~elA~~lgis~~tis~~E 147 (205)
+=.++.-.|++..|.|+.+|++.+++..+-
T Consensus 133 il~l~~~~g~s~~eIA~~lgis~~tv~~~l 162 (180)
T PRK11924 133 VFLLRYVEGLSYQEIADQLGVPLGTVKSRL 162 (180)
T ss_pred HHHHHHHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 999999968599999999894999999999
No 360
>COG3888 Predicted transcriptional regulator [Transcription]
Probab=57.21 E-value=13 Score=17.47 Aligned_cols=28 Identities=21% Similarity=0.264 Sum_probs=21.3
Q ss_pred HHHHHHHC--CCCHHHHHHHHCCCHHHHHH
Q ss_conf 99999985--99889999984899999998
Q gi|254781218|r 36 IKDIRKAN--NKTQKEMAIGANQLESAVNL 63 (205)
Q Consensus 36 ik~lR~~~--gltQ~elA~~~gis~~~is~ 63 (205)
||.++... |+.|-|+-+..|.|.|++|.
T Consensus 10 ir~Lk~a~~~GI~Q~eIeel~GlSKStvSE 39 (321)
T COG3888 10 IRELKRAGPEGIDQTEIEELMGLSKSTVSE 39 (321)
T ss_pred HHHHHHCCCCCCCHHHHHHHHCCCHHHHHH
T ss_conf 999986287776587889885745647999
No 361
>pfam06056 Terminase_5 Putative ATPase subunit of terminase (gpP-like). This family of proteins are annotated as ATPase subunits of phage terminase after. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.
Probab=56.73 E-value=11 Score=17.91 Aligned_cols=29 Identities=17% Similarity=0.279 Sum_probs=20.5
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHHCCCCC
Q ss_conf 72983899999977999999997414889
Q gi|254781218|r 124 DKGMSQIEFGKLLGMPNSTLSNYEQGRTI 152 (205)
Q Consensus 124 ~~glsq~elA~~lgis~~tis~~E~g~~~ 152 (205)
-+|.+..+.|+.+|++..|+..|-.-..=
T Consensus 11 ~qg~~~~eIA~~Lg~~~~tVysWk~r~~W 39 (58)
T pfam06056 11 WQGYRPAEIAQELGLKARTVYSWKDRDKW 39 (58)
T ss_pred HCCCCHHHHHHHHCCCCCHHHHHHHHCCC
T ss_conf 96898999999978993145658652483
No 362
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=56.72 E-value=13 Score=17.33 Aligned_cols=28 Identities=14% Similarity=0.010 Sum_probs=23.7
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 9999729838999999779999999974
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~E 147 (205)
.+|.-.|||..|.|+.+|++.+++....
T Consensus 159 ~Lr~~eglS~~EIAe~Lgis~~tVks~L 186 (207)
T PRK12544 159 MMREFIELETPEICHNEDLTVSNLNVML 186 (207)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9999819999999999797999999999
No 363
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=56.69 E-value=15 Score=17.04 Aligned_cols=29 Identities=21% Similarity=0.394 Sum_probs=24.4
Q ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 99999729838999999779999999974
Q gi|254781218|r 119 KSIRKDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 119 k~lR~~~glsq~elA~~lgis~~tis~~E 147 (205)
=.++-..|+|..|.|+.+|+|..|+...-
T Consensus 137 ~~L~~~~g~s~~EIA~~l~is~~tVk~~l 165 (186)
T PRK05602 137 IVLQYYQGLSNIEAARVMGLSVDALESLL 165 (186)
T ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 99998638999999999893999999999
No 364
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=56.31 E-value=15 Score=17.00 Aligned_cols=47 Identities=17% Similarity=0.155 Sum_probs=30.5
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCC
Q ss_conf 999999729838999999779999999974148899989999999982899
Q gi|254781218|r 118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKH 168 (205)
Q Consensus 118 Lk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs 168 (205)
+=.++--.|+|.+|.|+.+|+|..|+...-.- ....|.+.-+-.||+
T Consensus 124 v~~l~~~~g~s~~EIA~~l~is~~tVk~~l~r----a~~~Lr~~L~~~gi~ 170 (171)
T PRK09645 124 VLVRSYYRGWSTAQIAADLGIPEGTVKSRLHY----AVRALRLTLQEMGVT 170 (171)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHHHCCCC
T ss_conf 98999986999999999989299999999999----999999999970999
No 365
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=56.29 E-value=12 Score=17.72 Aligned_cols=57 Identities=16% Similarity=0.123 Sum_probs=36.4
Q ss_pred HHHHHHHH-HHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCH-HHHHHHHHHHCC
Q ss_conf 99999999-9999985998899999848999999988779988899-999999998289
Q gi|254781218|r 29 WKDVGTRI-KDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSI-RYALYLRNEYEI 85 (205)
Q Consensus 29 ~~~iG~ri-k~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi-~~l~~la~~~~v 85 (205)
.+.|++-| ....+...+|-.+||+.+|||+++|.|+=+-...-.. ++=..|+..+..
T Consensus 20 er~iA~yil~~~~~~~~~si~elA~~a~VS~aTv~Rf~~kLGf~Gf~efk~~l~~~l~~ 78 (281)
T COG1737 20 ERKIADYILANPDEVALLSIAELAERAGVSPATVVRFARKLGFEGFSEFKLALAQELAE 78 (281)
T ss_pred HHHHHHHHHHCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf 99999999939678856149999988199888999999985999889999999999763
No 366
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=56.27 E-value=15 Score=17.00 Aligned_cols=23 Identities=26% Similarity=0.095 Sum_probs=12.6
Q ss_pred HHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 98599889999984899999998
Q gi|254781218|r 41 KANNKTQKEMAIGANQLESAVNL 63 (205)
Q Consensus 41 ~~~gltQ~elA~~~gis~~~is~ 63 (205)
....+|..++|+.+|.++|++++
T Consensus 39 ~~~~~tvdelae~lnr~rStv~r 61 (126)
T COG3355 39 ENGPLTVDELAEILNRSRSTVYR 61 (126)
T ss_pred HCCCCCHHHHHHHHCCCHHHHHH
T ss_conf 46995799999997831999999
No 367
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=56.16 E-value=15 Score=16.99 Aligned_cols=26 Identities=19% Similarity=0.036 Sum_probs=21.9
Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 99729838999999779999999974
Q gi|254781218|r 122 RKDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 122 R~~~glsq~elA~~lgis~~tis~~E 147 (205)
+--.|+|..|.|+.+|+|..++....
T Consensus 166 ~~~eg~s~~EIA~~l~is~~tV~~~l 191 (209)
T PRK08295 166 LYLDGKSYQEIAEELNRHVKSIDNAL 191 (209)
T ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 99869999999999892999999999
No 368
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=55.75 E-value=14 Score=17.22 Aligned_cols=27 Identities=19% Similarity=0.247 Sum_probs=23.9
Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 997298389999997799999999741
Q gi|254781218|r 122 RKDKGMSQIEFGKLLGMPNSTLSNYEQ 148 (205)
Q Consensus 122 R~~~glsq~elA~~lgis~~tis~~E~ 148 (205)
.-..|+|-+|.|+.+++|..|+..+-+
T Consensus 159 lla~G~snkeIA~~L~iS~~TVk~h~~ 185 (211)
T COG2197 159 LLAEGLSNKEIAEELNLSEKTVKTHVS 185 (211)
T ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 998799889999997878989999999
No 369
>PRK13502 transcriptional activator RhaR; Provisional
Probab=55.63 E-value=16 Score=16.93 Aligned_cols=28 Identities=11% Similarity=0.024 Sum_probs=20.5
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHHCCCC
Q ss_conf 7298389999997799999999741488
Q gi|254781218|r 124 DKGMSQIEFGKLLGMPNSTLSNYEQGRT 151 (205)
Q Consensus 124 ~~glsq~elA~~lgis~~tis~~E~g~~ 151 (205)
...++..++|+.+|+|+..+++.-+...
T Consensus 190 ~~~isl~~lA~~~~~S~~~lsr~FK~~t 217 (282)
T PRK13502 190 ECPFALDAFCQQEQCSERVLRQQFRAQT 217 (282)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 6998899999897979999999999998
No 370
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=55.56 E-value=14 Score=17.22 Aligned_cols=42 Identities=12% Similarity=0.146 Sum_probs=29.8
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCC
Q ss_conf 9999729838999999779999999974148899989999999982899
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKH 168 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs 168 (205)
.++...|+|..|.|+.+|+|..|+...-. ....++.+.|..+
T Consensus 121 ~L~~~egls~~EIA~iL~is~gTVKsRL~-------RAr~kLr~~L~~~ 162 (181)
T PRK12540 121 ILVGASGFSYEDAAAICGCAVGTIKSRVN-------RARSKLSALLYVD 162 (181)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHH-------HHHHHHHHHHHHC
T ss_conf 87998099999999998949999999999-------9999999998746
No 371
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=55.53 E-value=15 Score=17.11 Aligned_cols=27 Identities=15% Similarity=0.076 Sum_probs=23.3
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 999972983899999977999999997
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~ 146 (205)
.+|.-.|+|..|.|+.+|+|.+++...
T Consensus 146 ~Lr~~~~ls~~EIA~~l~is~~tVksr 172 (191)
T PRK12530 146 MMREFLELSSEQICQECHITTSNLHVL 172 (191)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999992999999999989699999999
No 372
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=55.30 E-value=15 Score=17.10 Aligned_cols=47 Identities=13% Similarity=0.017 Sum_probs=30.9
Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHCC----CCCCCHHHHHHHHHHHCCC
Q ss_conf 9972983899999977999999997414----8899989999999982899
Q gi|254781218|r 122 RKDKGMSQIEFGKLLGMPNSTLSNYEQG----RTIPEIKPARKIKQVTKKH 168 (205)
Q Consensus 122 R~~~glsq~elA~~lgis~~tis~~E~g----~~~Ps~~~l~kIa~~lgvs 168 (205)
.-..|+|-+|.|+.+++|..|+..+-+. -..-+.-.|...+..+|..
T Consensus 161 lla~G~snkeIA~~L~iS~~TV~~h~~~i~~KLgv~n~~eLv~ya~~~gl~ 211 (216)
T PRK10840 161 LFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLNYLSSVTLS 211 (216)
T ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC
T ss_conf 998699999999896989999999999999982999899999999986999
No 373
>PRK09483 response regulator; Provisional
Probab=55.03 E-value=15 Score=17.03 Aligned_cols=51 Identities=14% Similarity=0.109 Sum_probs=32.7
Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHCCC----CCCCHHHHHHHHHHHC-CCHHHH
Q ss_conf 99729838999999779999999974148----8999899999999828-999995
Q gi|254781218|r 122 RKDKGMSQIEFGKLLGMPNSTLSNYEQGR----TIPEIKPARKIKQVTK-KHLDWI 172 (205)
Q Consensus 122 R~~~glsq~elA~~lgis~~tis~~E~g~----~~Ps~~~l~kIa~~lg-vs~d~L 172 (205)
.-..|+|-+|.|+.+++|..|+..+-+.- ..-+.-.+...|.-.| ++.|.|
T Consensus 159 ll~~G~snkeIA~~L~iS~~TV~~h~~~i~~KL~v~~r~el~~~A~~~gli~~~~~ 214 (216)
T PRK09483 159 MITKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDVELTHLAIRHGLLNAETL 214 (216)
T ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCHHHC
T ss_conf 99879999999999698999999999999998099999999999999599188884
No 374
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Probab=54.34 E-value=16 Score=16.80 Aligned_cols=54 Identities=11% Similarity=0.108 Sum_probs=34.2
Q ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHCCCC------------------------------CCCHHHHHHHHHHHCCCHHHH
Q ss_conf 97298389999997799999999741488------------------------------999899999999828999995
Q gi|254781218|r 123 KDKGMSQIEFGKLLGMPNSTLSNYEQGRT------------------------------IPEIKPARKIKQVTKKHLDWI 172 (205)
Q Consensus 123 ~~~glsq~elA~~lgis~~tis~~E~g~~------------------------------~Ps~~~l~kIa~~lgvs~d~L 172 (205)
...|=|...+|...|++...+.+|-+-.. .=+-++|..||+.|||+++-|
T Consensus 348 Vr~GDtL~~IA~ky~vsv~~L~~~N~L~~~~L~~Gq~L~Ip~~~~~~~~~~~~~~~~Y~Vk~GDTL~~IArry~Vsv~~L 427 (449)
T PRK10783 348 VRSGDTLSGIASRLGVSTKDLQQWNNLRGSTLKVGQSLTIGAGSSAQRLANNSDSITYRVRKGDSLSSIAKRHGVNIKDV 427 (449)
T ss_pred ECCCCCHHHHHHHHCCCHHHHHHHCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCEEEEECCCCCHHHHHHHHCCCHHHH
T ss_conf 58999899999997979999999839994447899878737887555565678965899899997999999969899999
Q ss_pred HCCC
Q ss_conf 2472
Q gi|254781218|r 173 YFGD 176 (205)
Q Consensus 173 ~~G~ 176 (205)
..=+
T Consensus 428 ~~wN 431 (449)
T PRK10783 428 MRWN 431 (449)
T ss_pred HHHC
T ss_conf 9865
No 375
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=54.25 E-value=13 Score=17.32 Aligned_cols=26 Identities=23% Similarity=0.054 Sum_probs=21.8
Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 99859988999998489999999887
Q gi|254781218|r 40 RKANNKTQKEMAIGANQLESAVNLFE 65 (205)
Q Consensus 40 R~~~gltQ~elA~~~gis~~~is~~E 65 (205)
+.+-...|+|.|+++|||.+.||.+=
T Consensus 21 ~~qp~v~q~eIA~~lgiT~QaVsehi 46 (260)
T COG1497 21 VRQPRVKQKEIAKKLGITLQAVSEHI 46 (260)
T ss_pred HHCCCCCHHHHHHHCCCCHHHHHHHH
T ss_conf 75887788899987098799999999
No 376
>pfam08220 HTH_DeoR DeoR-like helix-turn-helix domain.
Probab=53.93 E-value=17 Score=16.76 Aligned_cols=29 Identities=24% Similarity=0.415 Sum_probs=19.4
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 99999997298389999997799999999
Q gi|254781218|r 117 RLKSIRKDKGMSQIEFGKLLGMPNSTLSN 145 (205)
Q Consensus 117 rLk~lR~~~glsq~elA~~lgis~~tis~ 145 (205)
-+..+....-++..|+|+.+++|..|+.+
T Consensus 5 Il~~l~~~~~v~i~~La~~f~VS~~TiRR 33 (57)
T pfam08220 5 ILELLKQQGTLSVEELAELLGVSEMTIRR 33 (57)
T ss_pred HHHHHHHCCCEEHHHHHHHHCCCHHHHHH
T ss_conf 99999986979799999998959999999
No 377
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=53.91 E-value=17 Score=16.76 Aligned_cols=29 Identities=10% Similarity=0.138 Sum_probs=24.6
Q ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 99999729838999999779999999974
Q gi|254781218|r 119 KSIRKDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 119 k~lR~~~glsq~elA~~lgis~~tis~~E 147 (205)
=.++...|+|..|.|+.+|++..|+..+.
T Consensus 180 l~L~~~egls~~EIA~~Lgis~~TVKsrL 208 (233)
T PRK12538 180 VILSYHENMSNGEIAEVMDTTVAAVESLL 208 (233)
T ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 99999849999999999892999999999
No 378
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=53.83 E-value=16 Score=16.79 Aligned_cols=30 Identities=17% Similarity=0.035 Sum_probs=24.6
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 999999729838999999779999999974
Q gi|254781218|r 118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 118 Lk~lR~~~glsq~elA~~lgis~~tis~~E 147 (205)
+=.++.-.|+|..|.|+.+|+|.+++....
T Consensus 139 vi~L~~~~g~s~~EIA~~lgis~~tVk~~l 168 (184)
T PRK12512 139 VVQSIAVEGASIKETAAKLSMSEGAVRVAL 168 (184)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 999998559799999999891999999999
No 379
>TIGR02899 spore_safA spore coat assembly protein SafA; InterPro: IPR014248 This entry represents a domain of about 40 residues long which is found in a variety of enzymes involved in bacterial cell wall degradation , and which may have a general peptidoglycan binding function. Proteins containing this domain include SafA of Bacillus subtilis, which is a protein found at the interface of the spore cortex and spore coat, and which is dependent on SpoVID for its localization. This domain is generally found towards the N-terminus of these proteins. The C-terminal region of these proteins are more variable and may contain blocks of 12-residue and 13-residue repeats, tandem LysM domains (IPR002482 from INTERPRO), or an SCP-like domain (IPR014258 from INTERPRO)..
Probab=53.45 E-value=8.1 Score=18.70 Aligned_cols=20 Identities=10% Similarity=0.244 Sum_probs=15.5
Q ss_pred HHHHHHHHHHCCCHHHHHCC
Q ss_conf 99999999828999996145
Q gi|254781218|r 74 RYALYLRNEYEISFDWIYDG 93 (205)
Q Consensus 74 ~~l~~la~~~~vs~d~Ll~g 93 (205)
++|-+||+-|+|++|.|...
T Consensus 5 DtlWkiA~kygV~~~~Li~~ 24 (44)
T TIGR02899 5 DTLWKIAKKYGVDLDELIQA 24 (44)
T ss_pred CHHHHHHHHHCCCHHHHHHH
T ss_conf 21477787717876788641
No 380
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=53.44 E-value=17 Score=16.72 Aligned_cols=27 Identities=19% Similarity=0.364 Sum_probs=23.6
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 999972983899999977999999997
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~ 146 (205)
.++...|+|..|.|+.+|+|..|+...
T Consensus 148 ~L~~~egls~~EIA~~l~is~~tVk~r 174 (193)
T PRK11923 148 TLREFDGLSYEDIASVMQCPVGTVRSR 174 (193)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999994999999999989299999999
No 381
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=53.40 E-value=16 Score=16.82 Aligned_cols=28 Identities=18% Similarity=0.172 Sum_probs=23.9
Q ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 9999972983899999977999999997
Q gi|254781218|r 119 KSIRKDKGMSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 119 k~lR~~~glsq~elA~~lgis~~tis~~ 146 (205)
=.++...|+|..|.|+.+|+|.+|+...
T Consensus 128 i~L~~~~~~s~~EIA~~l~is~~tVksr 155 (173)
T PRK12522 128 LVLYYYEQYSYKEMSEILNIPIGTVKYR 155 (173)
T ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 9999983999999999989399999999
No 382
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=53.04 E-value=17 Score=16.77 Aligned_cols=30 Identities=13% Similarity=0.067 Sum_probs=25.0
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 999999972983899999977999999997
Q gi|254781218|r 117 RLKSIRKDKGMSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 117 rLk~lR~~~glsq~elA~~lgis~~tis~~ 146 (205)
.+=.+|-..|+|..|.|+.+|++.+|+...
T Consensus 141 ~vl~L~~~~~ls~~EIA~~l~is~~tVksr 170 (188)
T PRK09640 141 EILVLRFVAELEFQEIADIMHMGLSATKMR 170 (188)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999999992999999999989299999999
No 383
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=52.97 E-value=16 Score=16.79 Aligned_cols=28 Identities=18% Similarity=0.204 Sum_probs=23.0
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 9999729838999999779999999974
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~E 147 (205)
.++-..|+|..|.|+.+|+|.+|+...-
T Consensus 139 ~l~~~eg~s~~EIA~~l~is~~tVk~~l 166 (179)
T PRK12514 139 RRAYLEGLSYKELAERHDVPLNTMRTWL 166 (179)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9996069989999998890999999999
No 384
>pfam11268 DUF3071 Protein of unknown function (DUF3071). Some members in this family of proteins are annotated as DNA-binding proteins however this cannot be confirmed. Currently no function is known.
Probab=52.96 E-value=17 Score=16.67 Aligned_cols=28 Identities=25% Similarity=0.444 Sum_probs=17.1
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 9999729838999999779999999974
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~E 147 (205)
+.|...|.|..++|+..|++...+.+|+
T Consensus 62 QarIRaGas~eevA~~~g~~~~rVerfa 89 (169)
T pfam11268 62 QARIRAGASAEEVAEAAGVPEERVERFE 89 (169)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHCC
T ss_conf 9998879999999999599999987422
No 385
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=52.84 E-value=17 Score=16.66 Aligned_cols=29 Identities=24% Similarity=0.395 Sum_probs=24.3
Q ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 99999729838999999779999999974
Q gi|254781218|r 119 KSIRKDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 119 k~lR~~~glsq~elA~~lgis~~tis~~E 147 (205)
=.++-..|+|..|.|+.+|+|.+|+...-
T Consensus 136 ~~L~~~eg~s~~EIA~~l~is~~tVk~~l 164 (177)
T PRK09638 136 FILKHYYGYTYEEIAKMLGIPEGTVKSRV 164 (177)
T ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 99999919999999999893999999999
No 386
>pfam07278 DUF1441 Protein of unknown function (DUF1441). This family consists of several hypothetical Enterobacterial proteins of around 160 residues in length. The function of this family is unknown. However, it appears to be distantly related to other HTH families so may act as a transcriptional regulator.
Probab=52.76 E-value=17 Score=16.65 Aligned_cols=25 Identities=12% Similarity=-0.001 Sum_probs=21.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHHCCCC
Q ss_conf 9889999984899999998877998
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFENGMC 69 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E~G~~ 69 (205)
|+-.++|+..|+.++|+++=-.|..
T Consensus 2 lnI~qlA~~~GlhRqTV~~RL~~~~ 26 (152)
T pfam07278 2 LNINQLAALTGLHRQTVAARLAGVN 26 (152)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCC
T ss_conf 8789999998532999999984599
No 387
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=52.69 E-value=17 Score=16.64 Aligned_cols=29 Identities=24% Similarity=0.351 Sum_probs=24.7
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 99997298389999997799999999741
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNYEQ 148 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~E~ 148 (205)
.++.-.|+|+.|.|+.+|++.+|+..+..
T Consensus 137 ~l~~~~gls~~EIA~~l~i~~~tVks~l~ 165 (182)
T COG1595 137 LLRYLEGLSYEEIAEILGISVGTVKSRLH 165 (182)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 99998599999999895999999999999
No 388
>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]
Probab=52.56 E-value=14 Score=17.26 Aligned_cols=55 Identities=22% Similarity=0.230 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHH--HCCCCHHHHHHHHCCCHHHHH----HHHCCCCCCCHHHHHHHHHHHCCCHHHHHCC
Q ss_conf 999999999999--859988999998489999999----8877998889999999999828999996145
Q gi|254781218|r 30 KDVGTRIKDIRK--ANNKTQKEMAIGANQLESAVN----LFENGMCSTSIRYALYLRNEYEISFDWIYDG 93 (205)
Q Consensus 30 ~~iG~rik~lR~--~~gltQ~elA~~~gis~~~is----~~E~G~~~psi~~l~~la~~~~vs~d~Ll~g 93 (205)
++|-+-|+..|+ .+|||..|.|..+|+|+.+.. +-+.+...|. --+|.+||---|
T Consensus 2 k~IeeLi~kA~eLk~~Glt~gEIAdELNvSreTa~WL~~r~~~~~~~~~---------p~Di~i~W~siG 62 (203)
T COG0856 2 KNIEELIKKARELKSKGLTTGEIADELNVSRETATWLLTRAFKKESVPA---------PVDIKIDWRSIG 62 (203)
T ss_pred CCHHHHHHHHHHHHHCCCCHHHHHHHHCCHHHHHHHHHHHHHHCCCCCC---------CCCEEEEHHHHC
T ss_conf 6589999999999877985777676641048778888754431147888---------752587326725
No 389
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=52.54 E-value=17 Score=16.63 Aligned_cols=28 Identities=25% Similarity=0.284 Sum_probs=22.8
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 9999729838999999779999999974
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~E 147 (205)
.++...|+|..|.|+.+|++..|+...-
T Consensus 145 ~l~~~eg~s~~EIA~~l~is~~TVk~rl 172 (184)
T PRK12537 145 LHAYVDGCSHAEIAQRLGAPLGTVKAWI 172 (184)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9988439999999999892999999999
No 390
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=52.45 E-value=18 Score=16.62 Aligned_cols=121 Identities=15% Similarity=0.133 Sum_probs=69.9
Q ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCC
Q ss_conf 56689999999999999999859988999998489999999887799888999999999982899999614532210000
Q gi|254781218|r 22 TPEIRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYE 101 (205)
Q Consensus 22 ~~~~~~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~ 101 (205)
++.+.+|.+.|=.-. ......+-.++|..+||++++++. ++.+|.+.==| ... .+...
T Consensus 3 T~s~EdYLe~Iy~L~---~~~~~vr~~dIA~~L~Vs~~SVs~-----------mikkL~~~Glv-----~~~---~y~~i 60 (142)
T PRK03902 3 TPSMEDYIEQIYLLI---EEKGYARVSDIAEALSVHPSSVTK-----------MVQKLDKDEYL-----IYE---KYRGL 60 (142)
T ss_pred CCHHHHHHHHHHHHH---HCCCCCCHHHHHHHHCCCCHHHHH-----------HHHHHHHCCCC-----EEC---CCCCE
T ss_conf 942999999999998---258971299999997899533999-----------99999987992-----455---89875
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHH-HHCCCCCCCHHHHHHHHHHHC---CCHHHH
Q ss_conf 23213455467779999999997298389999997799999999-741488999899999999828---999995
Q gi|254781218|r 102 DVTNKKRLDPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSN-YEQGRTIPEIKPARKIKQVTK---KHLDWI 172 (205)
Q Consensus 102 ~~~~~~~~d~~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~-~E~g~~~Ps~~~l~kIa~~lg---vs~d~L 172 (205)
..+ .-|.++......+.--...|=..+|++...... -+.=....|.+++.+|.+.++ ..+||+
T Consensus 61 ~LT--------~~G~~~A~~i~~rHrlle~FL~~LGv~~~~a~~eAc~lEH~iS~~~~~~l~~~l~~~~~~P~~~ 127 (142)
T PRK03902 61 VLT--------PKGKKIGKRLVYRHELLEQFLRIIGVDESKIYNDVEGIEHHLSWNAIDRIGDLVQYFEEDPDRL 127 (142)
T ss_pred EEC--------HHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHCCHHHCCHHH
T ss_conf 689--------8799999999999999999999919987699999988141698999999999973654296999
No 391
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=52.11 E-value=13 Score=17.50 Aligned_cols=24 Identities=25% Similarity=0.379 Sum_probs=16.0
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 729838999999779999999974
Q gi|254781218|r 124 DKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 124 ~~glsq~elA~~lgis~~tis~~E 147 (205)
..+++..|+|+.+|++++|+.++.
T Consensus 18 ~~~~sl~eia~~~~l~ksT~~RlL 41 (91)
T smart00346 18 PGGLTLAELAERLGLSKSTAHRLL 41 (91)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 999899999999890999999999
No 392
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=51.95 E-value=18 Score=16.60 Aligned_cols=28 Identities=14% Similarity=0.106 Sum_probs=23.9
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 9999729838999999779999999974
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~E 147 (205)
.++.-.|||..|.|+.+|++..|+...-
T Consensus 142 ~L~~~~g~s~~EIA~ilgi~~gTVKsRl 169 (195)
T PRK12535 142 ILTQVLGYTYEEAAKIADVRVGTIRSRV 169 (195)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9999829989999999893999999999
No 393
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=51.71 E-value=18 Score=16.60 Aligned_cols=28 Identities=18% Similarity=0.235 Sum_probs=23.8
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 9999729838999999779999999974
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~E 147 (205)
-++.-.|||..|.|+.+|+|..|+....
T Consensus 140 ~L~~~egls~~EIA~~lg~~~gTVKsRl 167 (185)
T PRK09649 140 LLTQLLGLSYADAAAVCGCPVGTIRSRV 167 (185)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9899729999999999893999999999
No 394
>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=51.39 E-value=18 Score=16.51 Aligned_cols=28 Identities=25% Similarity=0.389 Sum_probs=16.7
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 99999972983899999977999999997
Q gi|254781218|r 118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 118 Lk~lR~~~glsq~elA~~lgis~~tis~~ 146 (205)
|..+. ..+++..|+|+.+|++++++++.
T Consensus 13 l~~L~-~~~~~~~eia~~l~is~~~vs~h 40 (78)
T cd00090 13 LRLLL-EGPLTVSELAERLGLSQSTVSRH 40 (78)
T ss_pred HHHHH-HCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 99998-48906999987778487899999
No 395
>TIGR00491 aIF-2 translation initiation factor aIF-2; InterPro: IPR004544 Initiation factor 2 (IF-2) is one of the three factors required for the initiation of protein biosynthesis in bacteria. IF-2 promotes the GTP-dependent binding of the initiator tRNA to the small subunit of the ribosome. IF-2 is a protein of about 70 to 95 Kd which contains a central GTP-binding domain flanked by a highly variable N-terminal domain and a more conserved C-terminal domain. Some members of this family undergo protein self splicing that involves a post-translational excision of the intein followed by peptide ligation.; GO: 0003743 translation initiation factor activity, 0005525 GTP binding, 0006413 translational initiation, 0005622 intracellular.
Probab=51.36 E-value=4.6 Score=20.23 Aligned_cols=47 Identities=21% Similarity=0.183 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHC
Q ss_conf 99999999998599889999984899999998877998889999999999828
Q gi|254781218|r 32 VGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYE 84 (205)
Q Consensus 32 iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~ 84 (205)
|..-+|.+|-..|+|..++ ..|++.+||||+.-||.+.+.+..+.+.
T Consensus 415 inkdmkrlrilfGmtrnev------nvsyyakyenGkeiPsyeivkkflnslk 461 (1145)
T TIGR00491 415 INKDMKRLRILFGMTRNEV------NVSYYAKYENGKEIPSYEIVKKFLNSLK 461 (1145)
T ss_pred CHHHHHHHHHHHCCCCCCE------EEEEEEEECCCCCCCHHHHHHHHHHHCC
T ss_conf 3034455344321210003------4555543047863750899999985227
No 396
>TIGR01817 nifA Nif-specific regulatory protein; InterPro: IPR010113 This entry represents NifA, a DNA-binding regulatory protein for nitrogen fixation. Not included in this group are: the homologue in Aquifex aeolicus (which lacks nitrogenase), transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms. In diazotrophic proteobacteria, the sigma54-dependent activator NifA activates transcription of the nif (nitrogen fixation) genes by a conserved mechanism common to members of the enhancer binding protein family. Although NifA proteins have similar domain structures, both transcriptional regulation of nifA expression and posttranslational regulation of NifA activity by oxygen and fixed nitrogen vary significantly from one organism to another. In Klebsiella pneumoniae and Azotobacter vinelandii, nifA is co-ordinately transcribed with a second gene, nifL, whose product inhibits NifA activity in response to oxygen and fixed nitrogen .; GO: 0003677 DNA binding, 0016563 transcription activator activity, 0009399 nitrogen fixation.
Probab=51.32 E-value=18 Score=16.51 Aligned_cols=30 Identities=23% Similarity=0.355 Sum_probs=26.5
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 999999997298389999997799999999
Q gi|254781218|r 116 ARLKSIRKDKGMSQIEFGKLLGMPNSTLSN 145 (205)
Q Consensus 116 ~rLk~lR~~~glsq~elA~~lgis~~tis~ 145 (205)
+||-.++++-|+-|..-|.+||+++..+.-
T Consensus 533 ERli~AlE~aGWVQAKAARlLg~TPRQVgY 562 (574)
T TIGR01817 533 ERLIAALEKAGWVQAKAARLLGLTPRQVGY 562 (574)
T ss_pred HHHHHHHHHCCHHHHHHHHHHCCCHHHHHH
T ss_conf 899999975153799999973786558999
No 397
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=51.24 E-value=18 Score=16.50 Aligned_cols=42 Identities=7% Similarity=0.038 Sum_probs=29.2
Q ss_pred HHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCH
Q ss_conf 79999999997--2983899999977999999997414889998
Q gi|254781218|r 114 IGARLKSIRKD--KGMSQIEFGKLLGMPNSTLSNYEQGRTIPEI 155 (205)
Q Consensus 114 iG~rLk~lR~~--~glsq~elA~~lgis~~tis~~E~g~~~Ps~ 155 (205)
+-.-|.-+.+. ..+|..++|+.+|+++..++++-+...--+.
T Consensus 193 v~~il~YI~~hY~e~IsL~diA~~~~lS~~y~sr~FKk~tG~T~ 236 (302)
T PRK10371 193 VSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQRVMQLTM 236 (302)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCH
T ss_conf 99999999998289999999998979599999999999989099
No 398
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=51.17 E-value=18 Score=16.49 Aligned_cols=59 Identities=10% Similarity=-0.024 Sum_probs=39.9
Q ss_pred HHHHHHHHHHHH-HHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHH-HHHHHHHCC
Q ss_conf 999999999999-99985998899999848999999988779988899999-999998289
Q gi|254781218|r 27 QYWKDVGTRIKD-IRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYA-LYLRNEYEI 85 (205)
Q Consensus 27 ~~~~~iG~rik~-lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l-~~la~~~~v 85 (205)
...+.|++-|-. ......+|-.+||+.+|+|+++|.|+=+-...-...-+ ..|+..+..
T Consensus 29 ~sEk~IA~yIL~~~~~v~~~si~eLA~~~~vS~aTVvRf~kkLGf~Gf~efK~~l~~~~~~ 89 (293)
T PRK11337 29 ENESRVVDWLLKPGNLSCATALKDVAEALAVSEAMIVKVAKLLGFSGFRNLRSALEDYFSQ 89 (293)
T ss_pred HHHHHHHHHHHCCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHC
T ss_conf 9999999999829899976669999989599888999999995789789999999999860
No 399
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=51.01 E-value=18 Score=16.48 Aligned_cols=27 Identities=19% Similarity=0.311 Sum_probs=23.5
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 999972983899999977999999997
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~ 146 (205)
.++-..|+|..|.|+.+|+|.+|+...
T Consensus 146 ~L~~~~~~s~~EIA~~l~is~~tVk~~ 172 (187)
T PRK09641 146 VLKYIEELSLKEISEILDLPVGTVKTR 172 (187)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999982998999999989399999999
No 400
>KOG3647 consensus
Probab=50.81 E-value=19 Score=16.46 Aligned_cols=136 Identities=16% Similarity=0.198 Sum_probs=75.2
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHH---------HHHHHHHHCCCHHHHHCCCC
Q ss_conf 899999999999999998599889999984899999998877998889999---------99999982899999614532
Q gi|254781218|r 25 IRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRY---------ALYLRNEYEISFDWIYDGEV 95 (205)
Q Consensus 25 ~~~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~---------l~~la~~~~vs~d~Ll~ge~ 95 (205)
..||..-||.+|..+|+.+. ||..+-.+..+|+..-+-.--.+-.. |...-+.+.+.+-.+...-
T Consensus 48 ~~q~~~~i~~k~~e~r~~r~-----lat~l~~~g~~i~e~ls~~~~~~~~~~~aa~Rplel~e~Ekvlk~aIq~i~~~~- 121 (338)
T KOG3647 48 RDQYRSLIGDKIEELRKARE-----LATDLTQRGTTICEMLSKELLHKESLMSAAQRPLELLEVEKVLKSAIQAIQVRL- 121 (338)
T ss_pred HHHHHHHHHHHHHHHHHHHH-----HHHHCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH-
T ss_conf 89999998789999999999-----874054111399999879999999999987177207889999999999999999-
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHC---CCHHHH
Q ss_conf 21000023213455467779999999997298389999997799999999741488999899999999828---999995
Q gi|254781218|r 96 IDRRYEDVTNKKRLDPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTK---KHLDWI 172 (205)
Q Consensus 96 ~~~~~~~~~~~~~~d~~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lg---vs~d~L 172 (205)
.+..+.-+-...|..++|.+|...+.+.--+++-|+.+-.+-+..+..||.-. +.|.++-+.|= -.++||
T Consensus 122 --q~~~~~Lnnvasdea~L~~Kierrk~ElEr~rkRle~LqsiRP~~MdEyE~~E-----eeLqkly~~Y~l~f~nl~yL 194 (338)
T KOG3647 122 --QSSRAQLNNVASDEAALGSKIERRKAELERTRKRLEALQSIRPAHMDEYEDCE-----EELQKLYQRYFLRFHNLDYL 194 (338)
T ss_pred --HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHH
T ss_conf --99999998775378788779999999999999999998720658788898899-----99999999999987418999
Q ss_pred H
Q ss_conf 2
Q gi|254781218|r 173 Y 173 (205)
Q Consensus 173 ~ 173 (205)
-
T Consensus 195 ~ 195 (338)
T KOG3647 195 K 195 (338)
T ss_pred H
T ss_conf 9
No 401
>PRK10651 transcriptional regulator NarL; Provisional
Probab=50.35 E-value=19 Score=16.41 Aligned_cols=25 Identities=20% Similarity=0.231 Sum_probs=22.0
Q ss_pred HHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 9729838999999779999999974
Q gi|254781218|r 123 KDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 123 ~~~glsq~elA~~lgis~~tis~~E 147 (205)
-..|+|-++.|+.+++|..|+..+-
T Consensus 167 l~~G~snkeIA~~L~iS~~TV~~h~ 191 (216)
T PRK10651 167 IAQGLSNKMIARRLDITESTVKVHV 191 (216)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9859999999999697899999999
No 402
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=50.34 E-value=19 Score=16.41 Aligned_cols=81 Identities=10% Similarity=-0.053 Sum_probs=47.3
Q ss_pred HHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHH
Q ss_conf 999999999985--998899999848999999988779988899999999998289999961453221000023213455
Q gi|254781218|r 32 VGTRIKDIRKAN--NKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRL 109 (205)
Q Consensus 32 iG~rik~lR~~~--gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~ 109 (205)
|-.-+..+.... .+|.++||+.+|+|++++++.=+ ..++.++-..+..
T Consensus 7 i~~~~~yI~~h~~~~i~l~~lA~~~~~S~~~l~r~Fk--------------~~~g~t~~~yi~~---------------- 56 (107)
T PRK10219 7 IQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFR--------------TVTHQTLGDYIRQ---------------- 56 (107)
T ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHH--------------HHHCCCHHHHHHH----------------
T ss_conf 9999999998669999999999898939999999999--------------9989099999999----------------
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHCC-CHHHHHH
Q ss_conf 46777999999999729838999999779-9999999
Q gi|254781218|r 110 DPYAIGARLKSIRKDKGMSQIEFGKLLGM-PNSTLSN 145 (205)
Q Consensus 110 d~~~iG~rLk~lR~~~glsq~elA~~lgi-s~~tis~ 145 (205)
..+ .+-+.+...-+++..|.|..+|. +.+.+++
T Consensus 57 --~Rl-~~A~~lL~~t~~~I~eIA~~~Gf~~~~~Fsr 90 (107)
T PRK10219 57 --RRL-LLAAVELRTTERPIFDIAMDLGYVSQQTFSR 90 (107)
T ss_pred --HHH-HHHHHHHHCCCCCHHHHHHHHCCCCHHHHHH
T ss_conf --999-9999998869998999999928998899999
No 403
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=50.08 E-value=19 Score=16.39 Aligned_cols=30 Identities=10% Similarity=-0.043 Sum_probs=24.9
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 999999729838999999779999999974
Q gi|254781218|r 118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 118 Lk~lR~~~glsq~elA~~lgis~~tis~~E 147 (205)
+=.+|.-.|||..|.|+.+|++..++.-..
T Consensus 147 v~~Lr~~egls~~EIA~~L~is~~tVksrL 176 (201)
T PRK12545 147 VFMMREFLDFEIDDICTELTLTANHCSVLL 176 (201)
T ss_pred HHHHHHHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 989999928989999999896999999999
No 404
>pfam02042 RWP-RK RWP-RK domain. This domain is named RWP-RK after a conserved motif at the C terminus of the presumed domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development.
Probab=50.05 E-value=19 Score=16.38 Aligned_cols=33 Identities=21% Similarity=0.128 Sum_probs=21.3
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCC
Q ss_conf 999999729838999999779999999974148
Q gi|254781218|r 118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGR 150 (205)
Q Consensus 118 Lk~lR~~~glsq~elA~~lgis~~tis~~E~g~ 150 (205)
+..++....+++.+.|..+|++..++-+..+..
T Consensus 7 ~~dl~~~F~lpi~~AA~~Lgv~~T~LKk~CR~~ 39 (52)
T pfam02042 7 LEDLSKYFHLPIKEAAKELGVCLTVLKKICRQL 39 (52)
T ss_pred HHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHC
T ss_conf 999999818759999999687799999999987
No 405
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=49.91 E-value=19 Score=16.37 Aligned_cols=48 Identities=19% Similarity=0.248 Sum_probs=32.0
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHH
Q ss_conf 9999729838999999779999999974148899989999999982899999
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDW 171 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~ 171 (205)
.++-..|+|..|.|+.+|+|..|+...-.- ....|.+.-+..|+...|
T Consensus 141 ~l~~~e~~s~~EIA~~lgis~~tV~~~l~R----Ar~~Lr~~L~~~g~~~g~ 188 (189)
T PRK12515 141 DLVYYHEKSVEEVGEIVGIPESTVKTRMFY----ARKKLAELLKAAGVERGW 188 (189)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHHHHCCCCCC
T ss_conf 999984999999999989299999999999----999999999972833589
No 406
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=49.85 E-value=10 Score=18.13 Aligned_cols=26 Identities=31% Similarity=0.420 Sum_probs=22.5
Q ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 99972983899999977999999997
Q gi|254781218|r 121 IRKDKGMSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 121 lR~~~glsq~elA~~lgis~~tis~~ 146 (205)
++.-.|+|..|.|+.+|||..|+...
T Consensus 122 L~~~egls~~EIAe~Lgis~gTVKsr 147 (182)
T PRK12511 122 LVAIEGLSYQEAANVLGIPIGTLMSR 147 (182)
T ss_pred EEEECCCCHHHHHHHHCCCHHHHHHH
T ss_conf 41007999999999989399999999
No 407
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator; InterPro: IPR011788 This entry represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system . This protein is a member of the MerR family of transcriptional activators and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix . .
Probab=49.70 E-value=7.7 Score=18.84 Aligned_cols=27 Identities=19% Similarity=0.290 Sum_probs=21.7
Q ss_pred HHHHHHHHCCCHHHHHHHH-CCCCCCCH
Q ss_conf 8999998489999999887-79988899
Q gi|254781218|r 47 QKEMAIGANQLESAVNLFE-NGMCSTSI 73 (205)
Q Consensus 47 Q~elA~~~gis~~~is~~E-~G~~~psi 73 (205)
--+||+..+|+.-|+-.|| +|...|+-
T Consensus 4 IGeLAklc~V~~DTlRfYEK~gl~~p~~ 31 (132)
T TIGR02043 4 IGELAKLCDVTADTLRFYEKNGLLKPAE 31 (132)
T ss_pred HHHHHHHCCCCCCHHHHHHHHHHCCCCC
T ss_conf 0224766179843334776774305566
No 408
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=49.63 E-value=19 Score=16.34 Aligned_cols=19 Identities=16% Similarity=0.004 Sum_probs=10.5
Q ss_pred CCHHHHHHHHCCCHHHHHH
Q ss_conf 9889999984899999998
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNL 63 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~ 63 (205)
.+.++||+.+|+|+.+|.+
T Consensus 20 ~SGe~La~~LgiSRtaVwK 38 (79)
T COG1654 20 VSGEKLAEELGISRTAVWK 38 (79)
T ss_pred CCHHHHHHHHCCCHHHHHH
T ss_conf 6689999997865999999
No 409
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=49.27 E-value=20 Score=16.31 Aligned_cols=30 Identities=7% Similarity=0.119 Sum_probs=24.9
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 999999729838999999779999999974
Q gi|254781218|r 118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 118 Lk~lR~~~glsq~elA~~lgis~~tis~~E 147 (205)
+-.++...|+|..|.|+.+|+|.+|+...-
T Consensus 149 vi~L~~~e~~s~~EIAe~l~is~~TVKsrl 178 (194)
T PRK12531 149 VLQAVYLEELPHQQVAEMFDIPLGTVKSRL 178 (194)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 999998869999999999892999999999
No 410
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=49.11 E-value=15 Score=17.00 Aligned_cols=25 Identities=16% Similarity=0.021 Sum_probs=21.9
Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 9985998899999848999999988
Q gi|254781218|r 40 RKANNKTQKEMAIGANQLESAVNLF 64 (205)
Q Consensus 40 R~~~gltQ~elA~~~gis~~~is~~ 64 (205)
+...++|..|+|..+|++++++.++
T Consensus 22 ~~~~~lslsela~~lglpksTv~Rl 46 (264)
T PRK09834 22 RLDGGATVGLLAELTGLHRTTVRRL 46 (264)
T ss_pred HCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 1799979999999979099999999
No 411
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=48.88 E-value=20 Score=16.27 Aligned_cols=30 Identities=17% Similarity=0.213 Sum_probs=25.0
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 999999729838999999779999999974
Q gi|254781218|r 118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 118 Lk~lR~~~glsq~elA~~lgis~~tis~~E 147 (205)
+=.++...|+|..|.|+.+|+|..|+....
T Consensus 139 vl~L~~~eg~s~~EIA~~lgis~~tVKsrl 168 (197)
T PRK09643 139 ALVAVDMQGYSVADTARMLGVAEGTVKSRC 168 (197)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 999999819999999999893999999999
No 412
>TIGR01369 CPSaseII_lrg carbamoyl-phosphate synthase, large subunit; InterPro: IPR006275 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates , . CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate . The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain . CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites . The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein . The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP . There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia . CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains . This entry represents glutamine-dependent CPSase (6.3.5.5 from EC) from prokaryotes and eukaryotes (CPSase II). ; GO: 0004086 carbamoyl-phosphate synthase activity, 0006807 nitrogen compound metabolic process.
Probab=48.22 E-value=7.5 Score=18.91 Aligned_cols=117 Identities=14% Similarity=0.216 Sum_probs=83.4
Q ss_pred HHHHHHHHCCCCCCCHHH---HHHHHHHH--CCCHHHHHCCCCCCCCC----CCCCCHHHH-H----H-H---HHHHHHH
Q ss_conf 999998877998889999---99999982--89999961453221000----023213455-4----6-7---7799999
Q gi|254781218|r 58 ESAVNLFENGMCSTSIRY---ALYLRNEY--EISFDWIYDGEVIDRRY----EDVTNKKRL-D----P-Y---AIGARLK 119 (205)
Q Consensus 58 ~~~is~~E~G~~~psi~~---l~~la~~~--~vs~d~Ll~ge~~~~~~----~~~~~~~~~-d----~-~---~iG~rLk 119 (205)
.-....++.-...|+-+. +..|+++| ++|+|.|+.--.+|.=| ..+...... . . . .+-.-+=
T Consensus 416 ~~~~~~~~~~l~~p~d~RPYW~f~i~~Al~~G~~V~~~~ElT~ID~wFL~k~~~iV~~e~~l~~~~n~~~~I~~~~~e~L 495 (1089)
T TIGR01369 416 VESDEDLEEALKKPTDRRPYWIFAIAEALRRGVSVEEIHELTKIDRWFLHKIKNIVELEKELEELKNKLTGIEELDKELL 495 (1089)
T ss_pred CCCHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHH
T ss_conf 03578999997286988761899899998758868999865278888999999999999998753012445334898899
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHH------HHHHHCCC-CCCCHHHHHHHHHHHCCCHHHHHC
Q ss_conf 99997298389999997799999------99974148-899989999999982899999524
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNST------LSNYEQGR-TIPEIKPARKIKQVTKKHLDWIYF 174 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~t------is~~E~g~-~~Ps~~~l~kIa~~lgvs~d~L~~ 174 (205)
+--|.+|+|=.++|..++++... +.++=... ..|..+.+--.|--|...+.||+.
T Consensus 496 ~~aK~lGFSD~~iA~~~~~~~~~~~~~~~vR~~R~~~gi~Pv~K~vDTcAAEF~A~TpY~YS 557 (1089)
T TIGR01369 496 RKAKKLGFSDAQIARLVNVTEAESIEELEVRKLRKELGIIPVYKRVDTCAAEFEAKTPYLYS 557 (1089)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHCCCHHHHHHHHHHCCCEEEEEEEECCCCCCCCCCCCCCC
T ss_conf 99864188878999986897444200689999998469747787752321202015688525
No 413
>pfam00325 Crp Bacterial regulatory proteins, crp family.
Probab=48.09 E-value=16 Score=16.89 Aligned_cols=22 Identities=32% Similarity=0.427 Sum_probs=14.8
Q ss_pred CCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 9838999999779999999974
Q gi|254781218|r 126 GMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 126 glsq~elA~~lgis~~tis~~E 147 (205)
-||..|.|+.+|++..|+|+..
T Consensus 2 pmsrqdIadylGlt~ETVsR~l 23 (32)
T pfam00325 2 PMSRQEIADYLGLTRETVSRLL 23 (32)
T ss_pred CCCHHHHHHHHCCHHHHHHHHH
T ss_conf 8658899998472599999999
No 414
>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional
Probab=47.68 E-value=21 Score=16.15 Aligned_cols=94 Identities=16% Similarity=0.049 Sum_probs=49.8
Q ss_pred CCCHHHHHHHHCCCCCCCHHHHHHHHHH-------HCCCHHHHHCCC--------CCCCCCCCCCCHHHHHHH----HH-
Q ss_conf 8999999988779988899999999998-------289999961453--------221000023213455467----77-
Q gi|254781218|r 55 NQLESAVNLFENGMCSTSIRYALYLRNE-------YEISFDWIYDGE--------VIDRRYEDVTNKKRLDPY----AI- 114 (205)
Q Consensus 55 gis~~~is~~E~G~~~psi~~l~~la~~-------~~vs~d~Ll~ge--------~~~~~~~~~~~~~~~d~~----~i- 114 (205)
++++.++..+.+=.-.=.+.-|.++.+. -.+.+|.++-.. .......+.......+-. .+
T Consensus 208 ~~s~~a~~~L~~y~WPGNvrEL~n~ierav~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~E 287 (325)
T PRK11608 208 GFTERARETLLNYRWPGNIRELKNVVERSVYRHGTSDYPLDDIIIDPFKRRPPEEAIAVSEATSLPTLPLDLREFQHQQE 287 (325)
T ss_pred CCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHCCCHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHH
T ss_conf 88999999996199996599999999999985688765555421371210565567787775456677868999999999
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 9999999997298389999997799999999741
Q gi|254781218|r 115 GARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQ 148 (205)
Q Consensus 115 G~rLk~lR~~~glsq~elA~~lgis~~tis~~E~ 148 (205)
-.-|....+..+..+...|+.+||++.|+.+..+
T Consensus 288 k~~I~~aL~~~~gn~~~aA~~LGIsR~tL~~klk 321 (325)
T PRK11608 288 KELLQRSLQQAKFNQKRAAELLGLTYHQFRALLK 321 (325)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9999999999399899999998889999999999
No 415
>PRK04182 cytidylate kinase; Provisional
Probab=47.67 E-value=21 Score=16.15 Aligned_cols=113 Identities=12% Similarity=0.018 Sum_probs=55.0
Q ss_pred HCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHH-----HHHHHHHHCCCHHHHHCC
Q ss_conf 001566899999999999999998599889999984899999998877998889999-----999999828999996145
Q gi|254781218|r 19 LIITPEIRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRY-----ALYLRNEYEISFDWIYDG 93 (205)
Q Consensus 19 ~~~~~~~~~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~-----l~~la~~~~vs~d~Ll~g 93 (205)
.++++...+--+.+++++-.---..|..-.++|+..|++...++++ +...|.++. +..+|+.=+| .+.|
T Consensus 7 g~~GSGk~tIak~LA~~lg~~~~d~g~i~r~~a~~~g~~~~~~~~~--~e~~~~id~~~~~~~~~~a~~~~~----Vi~G 80 (178)
T PRK04182 7 GPPGSGKTTVARLLAEKLGLKLVSAGDIFRELARERGMSLEEFNKY--AEEDPEIDKEIDRRQLELAKRGNV----VLEG 80 (178)
T ss_pred CCCCCCHHHHHHHHHHHHCCEEECHHHHHHHHHHHCCCCHHHHHHH--HHCCHHHHHHHHHHHHHHHHCCCE----EEEC
T ss_conf 8998887999999999959938721299999999859999999999--851926899999999999853998----9983
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHC
Q ss_conf 32210000232134554677799999999972983899999977
Q gi|254781218|r 94 EVIDRRYEDVTNKKRLDPYAIGARLKSIRKDKGMSQIEFGKLLG 137 (205)
Q Consensus 94 e~~~~~~~~~~~~~~~d~~~iG~rLk~lR~~~glsq~elA~~lg 137 (205)
-..+....+...........+..|++.+.+..|++..+..+.+-
T Consensus 81 R~~~~il~~~~~l~ifl~A~~e~R~~Ri~~r~~~~~~~a~~~i~ 124 (178)
T PRK04182 81 RLAGWIVKNYADLKIYLKAPLEVRAKRIAEREGISVEEALEETI 124 (178)
T ss_pred CCCCEEECCCCCEEEEEECCHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf 88876972798779999899999999999732999999999999
No 416
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=46.71 E-value=22 Score=16.06 Aligned_cols=53 Identities=13% Similarity=0.142 Sum_probs=34.2
Q ss_pred HHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHC
Q ss_conf 9999999982899999614532210000232134554677799999999972983899999977
Q gi|254781218|r 74 RYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRKDKGMSQIEFGKLLG 137 (205)
Q Consensus 74 ~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~~~glsq~elA~~lg 137 (205)
+.+-.+|+.|+|+.+.|....- .+....+..++ .--+|+..++|..+.+..+|
T Consensus 4 ~I~~~Va~~~~v~~~~i~s~~R---------~~~i~~aR~ia--myL~r~~~~~s~~~IG~~fg 56 (60)
T smart00760 4 EIIEAVAEYFGVKPEDLKSKSR---------KREIVLARQIA--MYLARELTDLSLPEIGKIFG 56 (60)
T ss_pred HHHHHHHHHHCCCHHHHHCCCC---------CHHHHHHHHHH--HHHHHHHHCCCHHHHHHHHC
T ss_conf 9999999883997999856799---------81688899999--99999986799999999977
No 417
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=46.31 E-value=22 Score=16.03 Aligned_cols=25 Identities=4% Similarity=0.037 Sum_probs=21.7
Q ss_pred HHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 9859988999998489999999887
Q gi|254781218|r 41 KANNKTQKEMAIGANQLESAVNLFE 65 (205)
Q Consensus 41 ~~~gltQ~elA~~~gis~~~is~~E 65 (205)
...++|..|+|+.+|++++++.++=
T Consensus 37 ~~~~ltl~eia~~lglpksT~~RlL 61 (271)
T PRK10163 37 SGGSSSVSDISLNLDLPLSTTFRLL 61 (271)
T ss_pred CCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 7999799999999791999999999
No 418
>PRK01905 DNA-binding protein Fis; Provisional
Probab=46.05 E-value=22 Score=16.00 Aligned_cols=32 Identities=22% Similarity=0.236 Sum_probs=26.9
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 99999999729838999999779999999974
Q gi|254781218|r 116 ARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 116 ~rLk~lR~~~glsq~elA~~lgis~~tis~~E 147 (205)
.=|..+.+.-+-.|...|+.+||++.|+.+-.
T Consensus 40 pLi~~vl~~~~gNQ~kAA~~LGinR~TLRkKl 71 (77)
T PRK01905 40 PLLEVVMEQAGGNQSLAAEYLGINRNTLRKKL 71 (77)
T ss_pred HHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 99999999845949999999786588899999
No 419
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=46.02 E-value=22 Score=16.00 Aligned_cols=25 Identities=28% Similarity=0.504 Sum_probs=11.3
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHH
Q ss_conf 9999729838999999779999999
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLS 144 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis 144 (205)
.++..-+|...|+|+.+|+++++++
T Consensus 31 lL~~k~plNvneiAe~lgLpqst~s 55 (308)
T COG4189 31 LLHRKGPLNVNEIAEALGLPQSTMS 55 (308)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHH
T ss_conf 9987179878999988588656666
No 420
>pfam00440 TetR_N Bacterial regulatory proteins, tetR family.
Probab=45.79 E-value=22 Score=15.97 Aligned_cols=33 Identities=15% Similarity=0.101 Sum_probs=19.4
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCC
Q ss_conf 999999729838999999779999999974148
Q gi|254781218|r 118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGR 150 (205)
Q Consensus 118 Lk~lR~~~glsq~elA~~lgis~~tis~~E~g~ 150 (205)
+=.-+--.+.|..++|+.+|+++.++.+|-.++
T Consensus 8 l~~~~G~~~~s~~~Ia~~agvs~~~iy~~F~~K 40 (47)
T pfam00440 8 LFAEKGYDATTVREIAKEAGVSKGALYRHFPSK 40 (47)
T ss_pred HHHHHCCCCCCHHHHHHHHCCCHHHHHHHCCCH
T ss_conf 999869150779999999796988999887699
No 421
>PRK11569 transcriptional repressor IclR; Provisional
Probab=45.54 E-value=22 Score=15.98 Aligned_cols=24 Identities=17% Similarity=0.113 Sum_probs=21.1
Q ss_pred HHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 985998899999848999999988
Q gi|254781218|r 41 KANNKTQKEMAIGANQLESAVNLF 64 (205)
Q Consensus 41 ~~~gltQ~elA~~~gis~~~is~~ 64 (205)
...++|..|+|+.+|++++++.++
T Consensus 40 ~~~~lsl~eia~~lglpksT~~Rl 63 (274)
T PRK11569 40 SNGSVALTELAQQAGLPNSTTHRL 63 (274)
T ss_pred CCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 899989999999879199999999
No 422
>pfam09572 RE_XamI XamI restriction endonuclease. This family includes the XamI (recognizes GTCGAC but cleavage site unknown) restriction endonuclease.
Probab=44.65 E-value=23 Score=15.87 Aligned_cols=74 Identities=14% Similarity=0.152 Sum_probs=48.1
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHH------HHHHHHHHCCCH----
Q ss_conf 015668999999999999999985--99889999984899999998877998889999------999999828999----
Q gi|254781218|r 20 IITPEIRQYWKDVGTRIKDIRKAN--NKTQKEMAIGANQLESAVNLFENGMCSTSIRY------ALYLRNEYEISF---- 87 (205)
Q Consensus 20 ~~~~~~~~~~~~iG~rik~lR~~~--gltQ~elA~~~gis~~~is~~E~G~~~psi~~------l~~la~~~~vs~---- 87 (205)
.|+||.-. .-..-+-.+|..- -+.-..|...+|+|.+.+-.+|.|+-.|...- |-+++....-.+
T Consensus 6 ~itp~~l~---~~p~~L~~LR~~t~ppia~d~l~~lagvsk~lv~~le~~kl~~~~~~~~l~~~l~ki~~iI~~~lDpdi 82 (251)
T pfam09572 6 AITPDVLK---AYPLTLPTLRMLTCPPIARDRLVGLAGGSKNLVKSLEPKKLPPKMKADVLDEHLQKVVAVIEKMLDPDR 82 (251)
T ss_pred CCCHHHHH---HCCHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf 17889987---380477787861399830878766516667888764227898322243689999999999998518430
Q ss_pred -HHHHCCCCC
Q ss_conf -996145322
Q gi|254781218|r 88 -DWIYDGEVI 96 (205)
Q Consensus 88 -d~Ll~ge~~ 96 (205)
.|+-.|...
T Consensus 83 F~Wl~~g~~p 92 (251)
T pfam09572 83 FPWVGRGRTP 92 (251)
T ss_pred CCEECCCCCC
T ss_conf 1011589999
No 423
>TIGR03454 partition_RepB plasmid partitioning protein RepB. Members of this family are the RepB protein involved in replicon partitioning. RepB is found, in general, as part of a repABC operon in plasmids and small chromosomes, separate from the main chromosome, in various bacteria. This model describes a rather narrow clade of proteins; it should be noted that additional homologs scoring below the trusted cutoff have very similar functions, although they may be named differently.
Probab=44.59 E-value=23 Score=15.86 Aligned_cols=57 Identities=12% Similarity=0.090 Sum_probs=45.4
Q ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHH-HHHCC
Q ss_conf 9999972983899999977999999997414889998999999998289999-95247
Q gi|254781218|r 119 KSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLD-WIYFG 175 (205)
Q Consensus 119 k~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d-~L~~G 175 (205)
....++.|+++...+..++++++++|++.+=-...+.+.+..|.-+-++-.+ |+-..
T Consensus 170 A~~l~~~g~~r~~I~~aL~vdks~lSrml~Va~~iP~elI~aIGpAp~iGR~RW~~La 227 (325)
T TIGR03454 170 AQRLEDRGFDRDTIMAALSVDKTELSRMISVARRIPEELIEAIGPAPGIGRPRWMELA 227 (325)
T ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCHHHHHHHCCCCCCCCHHHHHHH
T ss_conf 9999984999999999988899999999999997899999973798734733799999
No 424
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=44.08 E-value=24 Score=15.81 Aligned_cols=21 Identities=10% Similarity=0.143 Sum_probs=11.0
Q ss_pred CCCHHHHHHHHCCCHHHHHHH
Q ss_conf 983899999977999999997
Q gi|254781218|r 126 GMSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 126 glsq~elA~~lgis~~tis~~ 146 (205)
.+.-.|+++.+|++++++|+.
T Consensus 28 elcV~eL~~~l~~sQs~vS~H 48 (106)
T PRK10141 28 ELCVCDLCTALDQSQPKISRH 48 (106)
T ss_pred CCCHHHHHHHHCCCHHHHHHH
T ss_conf 956999998869988899999
No 425
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=43.94 E-value=24 Score=15.80 Aligned_cols=27 Identities=26% Similarity=0.504 Sum_probs=22.2
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 999972983899999977999999997
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~ 146 (205)
.++--.|+|..|.|+.+|+|.+++...
T Consensus 147 ~l~~~~~~s~~EIA~~lgis~~tVk~~ 173 (192)
T PRK09652 147 TLREIEGLSYEEIAEIMGCPIGTVRSR 173 (192)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 899972999999999989399999999
No 426
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=43.64 E-value=24 Score=15.77 Aligned_cols=27 Identities=33% Similarity=0.284 Sum_probs=23.4
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 999972983899999977999999997
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~ 146 (205)
.+|--.|+|..|.|+.+|+|.+|+...
T Consensus 138 ~l~~~~~~s~~EIA~~l~is~~tVk~r 164 (185)
T PRK06811 138 IKRYLLGESIEEIAKKLGLTRSAIDNR 164 (185)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999994999999999989299999999
No 427
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=43.51 E-value=24 Score=15.76 Aligned_cols=29 Identities=17% Similarity=0.190 Sum_probs=23.4
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 99999972983899999977999999997
Q gi|254781218|r 118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 118 Lk~lR~~~glsq~elA~~lgis~~tis~~ 146 (205)
+=.++-..|+|..|.|+.+|+|..|+...
T Consensus 145 vi~l~~~eg~s~~EIA~~l~i~~gTVksr 173 (187)
T PRK12534 145 LIRTAFFEGITYEELAARTDTPIGTVKSW 173 (187)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 99999984999999999989199999999
No 428
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=42.68 E-value=25 Score=15.68 Aligned_cols=29 Identities=17% Similarity=0.282 Sum_probs=24.5
Q ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 99999729838999999779999999974
Q gi|254781218|r 119 KSIRKDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 119 k~lR~~~glsq~elA~~lgis~~tis~~E 147 (205)
=.++...|+|..|.|+.+|+|.+|+...-
T Consensus 129 i~l~~~~~~s~~EIA~~l~is~~tVk~~l 157 (175)
T PRK12518 129 LVLHDLEDLPQKEIAEILNIPVGTVKSRL 157 (175)
T ss_pred HHHHHHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 99999929999999999895999999999
No 429
>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=42.56 E-value=25 Score=15.67 Aligned_cols=26 Identities=23% Similarity=0.367 Sum_probs=17.1
Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 99729838999999779999999974
Q gi|254781218|r 122 RKDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 122 R~~~glsq~elA~~lgis~~tis~~E 147 (205)
..+.-++..|+|+.+|++++++|+..
T Consensus 11 L~~~~~~v~el~~~l~~sq~~vS~HL 36 (47)
T pfam01022 11 LSEGELCVCELAEILGLSQSTVSHHL 36 (47)
T ss_pred HHCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 98089969999999895886999999
No 430
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=42.55 E-value=25 Score=15.67 Aligned_cols=40 Identities=10% Similarity=0.053 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCC-CHHHHHHH
Q ss_conf 89999999999999999859988999998489-99999988
Q gi|254781218|r 25 IRQYWKDVGTRIKDIRKANNKTQKEMAIGANQ-LESAVNLF 64 (205)
Q Consensus 25 ~~~~~~~iG~rik~lR~~~gltQ~elA~~~gi-s~~~is~~ 64 (205)
++.|..+.-.++-.+....|.|..++|...|| +.+++.+|
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W 45 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKW 45 (116)
T ss_pred CCCCCHHHHHHHHHHHHCCCCHHHHHHHHHCCCCHHHHHHH
T ss_conf 36489999999999998178359999999487753789999
No 431
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=42.50 E-value=25 Score=15.66 Aligned_cols=27 Identities=11% Similarity=-0.141 Sum_probs=23.3
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 999972983899999977999999997
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~ 146 (205)
.++--.|+|..|.|+.+|+|.+|+...
T Consensus 116 ~L~~~e~~s~~EIA~~l~is~~tVk~~ 142 (160)
T PRK09642 116 LAHYLEEKSYQEIALQENIEVKTVEMK 142 (160)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999982999999999989199999999
No 432
>pfam02540 NAD_synthase NAD synthase. NAD synthase (EC:6.3.5.1) is involved in the de novo synthesis of NAD and is induced by stress factors such as heat shock and glucose limitation.
Probab=42.39 E-value=25 Score=15.65 Aligned_cols=32 Identities=22% Similarity=0.219 Sum_probs=17.7
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 99999999729838999999779999999974
Q gi|254781218|r 116 ARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 116 ~rLk~lR~~~glsq~elA~~lgis~~tis~~E 147 (205)
..+=....+.+++..+.++.+|++...+.++.
T Consensus 199 D~~l~~~~~~~~~~~~i~~~~g~~~~~v~~i~ 230 (243)
T pfam02540 199 DQILKGLIEKKLSPEEIIGDLGLPAEVVERVE 230 (243)
T ss_pred HHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHH
T ss_conf 99999998759999999987298999999999
No 433
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR; InterPro: IPR010211 SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulphur cluster activates SoxR. The physiological role in Escherichia coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In Escherichia coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0005506 iron ion binding, 0006118 electron transport, 0006355 regulation of transcription DNA-dependent, 0006979 response to oxidative stress.
Probab=42.06 E-value=12 Score=17.54 Aligned_cols=25 Identities=32% Similarity=0.389 Sum_probs=20.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHH-CCCC
Q ss_conf 988999998489999999887-7998
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFE-NGMC 69 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E-~G~~ 69 (205)
||--+||+..||..|++..|| +|.-
T Consensus 2 lTvG~lA~R~GVAVSALHFYE~KGLI 27 (142)
T TIGR01950 2 LTVGELAKRAGVAVSALHFYESKGLI 27 (142)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHCCCE
T ss_conf 86101655655788877654103561
No 434
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=41.97 E-value=26 Score=15.61 Aligned_cols=31 Identities=10% Similarity=-0.045 Sum_probs=18.9
Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHCCCCC
Q ss_conf 9972983899999977999999997414889
Q gi|254781218|r 122 RKDKGMSQIEFGKLLGMPNSTLSNYEQGRTI 152 (205)
Q Consensus 122 R~~~glsq~elA~~lgis~~tis~~E~g~~~ 152 (205)
.-...++..++|+.+|+|..++.+.-+...-
T Consensus 228 ~l~~~ls~~~lA~~~~~S~R~l~R~Fk~~~G 258 (320)
T PRK09393 228 HLAQPHTVASLAARAAMSPRTFLRRFEAATG 258 (320)
T ss_pred HHCCCCCHHHHHHHHCCCHHHHHHHHHHHHC
T ss_conf 1114788999999978798799989978869
No 435
>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=41.72 E-value=25 Score=15.68 Aligned_cols=27 Identities=15% Similarity=0.026 Sum_probs=13.1
Q ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 999998599889999984899999998
Q gi|254781218|r 37 KDIRKANNKTQKEMAIGANQLESAVNL 63 (205)
Q Consensus 37 k~lR~~~gltQ~elA~~~gis~~~is~ 63 (205)
..|-+.-..|-.+||+.++||+++|-+
T Consensus 8 ~~LL~~Gq~sA~~lA~~L~iSpQAvRr 34 (215)
T TIGR02702 8 EYLLKEGQASALALAEELAISPQAVRR 34 (215)
T ss_pred HHHHHHHHHHHHHHHHHHCCCHHHHHH
T ss_conf 998860048899999972788678876
No 436
>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=40.89 E-value=27 Score=15.51 Aligned_cols=45 Identities=11% Similarity=0.108 Sum_probs=39.1
Q ss_pred HHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHH
Q ss_conf 9999999985--99889999984899999998877998889999999
Q gi|254781218|r 34 TRIKDIRKAN--NKTQKEMAIGANQLESAVNLFENGMCSTSIRYALY 78 (205)
Q Consensus 34 ~rik~lR~~~--gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~ 78 (205)
+.||.|+... -||...||+...||+.+|.+|-+.+-.|+.+.-++
T Consensus 17 e~IR~Lh~~~Pe~~t~~~LAe~F~VSpeaIrRILKSKw~Pt~e~klK 63 (225)
T pfam06413 17 EQIRYLKQEFPEEWTVPRLAEGFDVSTDVIRRVLKSKFVPTLERKLK 63 (225)
T ss_pred HHHHHHHHHCCHHCCHHHHHHHCCCCHHHHHHHHHCCCCCCHHHHHH
T ss_conf 99999987384011589998607889999999997157886888754
No 437
>pfam04645 DUF603 Protein of unknown function, DUF603. This family includes several uncharacterized proteins from Borrelia species.
Probab=40.04 E-value=27 Score=15.42 Aligned_cols=30 Identities=20% Similarity=0.133 Sum_probs=25.4
Q ss_pred CC-CCHHHHHHHHCCCHHHHH----HHHCCCCCCC
Q ss_conf 59-988999998489999999----8877998889
Q gi|254781218|r 43 NN-KTQKEMAIGANQLESAVN----LFENGMCSTS 72 (205)
Q Consensus 43 ~g-ltQ~elA~~~gis~~~is----~~E~G~~~ps 72 (205)
.| |+-.++|..+||++..|. +||.|...+.
T Consensus 17 eG~L~D~eIA~~LGVsr~nV~kmRqKwes~~dsv~ 51 (181)
T pfam04645 17 EGSLSDAEIAKELGVSRVNVWRMRQKWESGEDSVN 51 (181)
T ss_pred CCCCCHHHHHHHHCCHHHHHHHHHHHHHHCCCCCC
T ss_conf 17875799999978309999999999981278855
No 438
>pfam04458 DUF505 Protein of unknown function (DUF505). Family of uncharacterized prokaryotic proteins.
Probab=39.94 E-value=27 Score=15.41 Aligned_cols=47 Identities=9% Similarity=0.017 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH-CCCCCCCHHHHHHHHHHH
Q ss_conf 9999999999859988999998489999999887-799888999999999982
Q gi|254781218|r 32 VGTRIKDIRKANNKTQKEMAIGANQLESAVNLFE-NGMCSTSIRYALYLRNEY 83 (205)
Q Consensus 32 iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E-~G~~~psi~~l~~la~~~ 83 (205)
++.++-..-+.+|+.++ -|++.....-+| --...|-+..-..|+.+.
T Consensus 105 vp~~w~e~L~ERgla~e-----~~LT~~gk~lle~Y~et~P~l~vt~ela~~i 152 (591)
T pfam04458 105 VPERWEEALSERGLAEE-----GGLTEYGKAVLEIYRETHPKLYVTPEVAGYI 152 (591)
T ss_pred CCHHHHHHHHHCCCCCC-----CCCCHHHHHHHHHHHHCCCEEEECHHHHHHH
T ss_conf 96779999987245322-----5734999999999986298299878999999
No 439
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=39.87 E-value=28 Score=15.41 Aligned_cols=115 Identities=10% Similarity=-0.004 Sum_probs=64.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCC
Q ss_conf 66899999999999999998599889999984899999998877998889999999999828999996145322100002
Q gi|254781218|r 23 PEIRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYED 102 (205)
Q Consensus 23 ~~~~~~~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~ 102 (205)
+...+|.+.|=.-++ ..--....++|..++|++++++.. +.+|++.==|.. ..+....
T Consensus 6 ~~~edYL~~Iy~l~~---~~~~~~~~diA~~L~Vsp~sVt~m-----------l~rL~~~GlV~~--------~~y~gi~ 63 (154)
T COG1321 6 ETEEDYLETIYELLE---EKGFARTKDIAERLKVSPPSVTEM-----------LKRLERLGLVEY--------EPYGGVT 63 (154)
T ss_pred HHHHHHHHHHHHHHH---CCCCCCHHHHHHHHCCCCHHHHHH-----------HHHHHHCCCEEE--------ECCCCEE
T ss_conf 168999999999984---368751999999858992789999-----------999987899788--------4588867
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHCCCCHHH-HHHHHCCCHHHHHH-HHCCCCCCCHHHHHHHHHHHCC
Q ss_conf 32134554677799999999972983899-99997799999999-7414889998999999998289
Q gi|254781218|r 103 VTNKKRLDPYAIGARLKSIRKDKGMSQIE-FGKLLGMPNSTLSN-YEQGRTIPEIKPARKIKQVTKK 167 (205)
Q Consensus 103 ~~~~~~~d~~~iG~rLk~lR~~~glsq~e-lA~~lgis~~tis~-~E~g~~~Ps~~~l~kIa~~lgv 167 (205)
.. .-|.++..-.-.+...... |.+.+|++...... -+.=....+.+.+.+|.+.++-
T Consensus 64 LT--------~~G~~~a~~~~r~hrlle~fL~~~lg~~~~~~~~ea~~leh~~s~~~~~rl~~~l~~ 122 (154)
T COG1321 64 LT--------EKGREKAKELLRKHRLLERFLVDVLGLDWEEAHEEAEGLEHALSDETAERLDELLGF 122 (154)
T ss_pred EC--------CCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHCC
T ss_conf 88--------354899999999999999999998589889999999888621999999999999579
No 440
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=39.64 E-value=20 Score=16.33 Aligned_cols=24 Identities=33% Similarity=0.429 Sum_probs=15.6
Q ss_pred CHHHHHHHHCCCHHHHHHHHCCCC
Q ss_conf 389999997799999999741488
Q gi|254781218|r 128 SQIEFGKLLGMPNSTLSNYEQGRT 151 (205)
Q Consensus 128 sq~elA~~lgis~~tis~~E~g~~ 151 (205)
|..|.|+.+|+++++|+++.++..
T Consensus 19 Si~~aak~l~~~~~~I~~~l~~~~ 42 (53)
T smart00497 19 SIREAAKYLGISHSSISKYLNTGK 42 (53)
T ss_pred HHHHHHHHHCCCCCCHHHHHCCCC
T ss_conf 799999985888323888706775
No 441
>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=39.61 E-value=12 Score=17.60 Aligned_cols=116 Identities=10% Similarity=0.141 Sum_probs=62.5
Q ss_pred HHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHH--CCCCCC-CCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999848999999988779988899999999998289999961--453221-000023213455467779999999997
Q gi|254781218|r 48 KEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIY--DGEVID-RRYEDVTNKKRLDPYAIGARLKSIRKD 124 (205)
Q Consensus 48 ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll--~ge~~~-~~~~~~~~~~~~d~~~iG~rLk~lR~~ 124 (205)
.|||++||||+.|+- |+|.+||+= -||- .|+++- +.+-+.....+++-. -++ +
T Consensus 34 RELsElIGVTRTTLR-----------EVLQRLARD-----GWLTIQHGKPTKVNnfWETSGLNILeTL------~~L--D 89 (275)
T TIGR02812 34 RELSELIGVTRTTLR-----------EVLQRLARD-----GWLTIQHGKPTKVNNFWETSGLNILETL------IRL--D 89 (275)
T ss_pred HHHHHHCCCCCCHHH-----------HHHHHHHHH-----CCCCCCCCCCCCCCCHHHCCCCCHHHHH------HHH--C
T ss_conf 657542376630378-----------999887641-----1343658899862762430273578999------861--8
Q ss_pred CC----CCHHHHHHHHCCCHHHHHHHHCCCCCCC-----HHHHHHHHHHHCCCH--HHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 29----8389999997799999999741488999-----899999999828999--9952472102545677754235
Q gi|254781218|r 125 KG----MSQIEFGKLLGMPNSTLSNYEQGRTIPE-----IKPARKIKQVTKKHL--DWIYFGDEVIVPKSIKRAKGNQ 191 (205)
Q Consensus 125 ~g----lsq~elA~~lgis~~tis~~E~g~~~Ps-----~~~l~kIa~~lgvs~--d~L~~G~e~~~~~~~~~~~~~~ 191 (205)
.. +.-.=|+.+++||.-.+..=-+ ..|. +..+.+=+++|.-.- +-|+ +.....+.+++.-.+.
T Consensus 90 ~~~~P~l~dnLLSARTnIS~IYir~A~K--~np~~~~~~~~~VI~s~e~L~~~~s~~~F~--~~SP~~~~~~~~l~d~ 163 (275)
T TIGR02812 90 GESVPSLIDNLLSARTNISAIYIRAAFK--NNPEESEELIENVIKSLEVLANAESFAEFV--EASPLAEKVKKELEDT 163 (275)
T ss_pred CCCCCHHHHHHHHHHHCCCHHHHHHHHH--CCHHHHHHHHHHHHHHHHHHHCCCCHHHHH--HHCCHHHHHHHHHHCC
T ss_conf 7777079999997764137788999862--283568999999999999983040179998--5082689999874203
No 442
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=39.29 E-value=28 Score=15.35 Aligned_cols=27 Identities=19% Similarity=0.180 Sum_probs=22.7
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 999972983899999977999999997
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~ 146 (205)
.+|--.|+|..|.|+.+|++..++...
T Consensus 147 ~L~~~~g~s~~EIA~~lg~s~~tVk~~ 173 (187)
T PRK09648 147 ILRVVVGLSAEETAEAVGSTPGAVRVA 173 (187)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999984999999999989399999999
No 443
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=39.28 E-value=28 Score=15.35 Aligned_cols=28 Identities=25% Similarity=0.355 Sum_probs=23.8
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 9999729838999999779999999974
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~E 147 (205)
.++-..|||..|.|+.+|+|.+|+...-
T Consensus 149 ~L~~~~g~s~~EIA~~l~is~~tVk~~l 176 (194)
T PRK12513 149 LLREHGDLSLEEIAQLTGVPLETVKSRL 176 (194)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9999849999999999894999999999
No 444
>PRK10365 transcriptional regulatory protein ZraR; Provisional
Probab=38.82 E-value=29 Score=15.31 Aligned_cols=32 Identities=19% Similarity=0.202 Sum_probs=26.5
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 99999999729838999999779999999974
Q gi|254781218|r 116 ARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 116 ~rLk~lR~~~glsq~elA~~lgis~~tis~~E 147 (205)
.-|....+..+-.+.+.|+.+||+++|+.+..
T Consensus 408 ~~I~~aL~~~~gn~~~aA~~LGisR~tLyrKl 439 (441)
T PRK10365 408 EVILAALEKTGGNKTEAARQLGITRKTLLAKL 439 (441)
T ss_pred HHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 99999999939989999999788999999996
No 445
>PRK09409 insertion element IS2 transposase InsD; Reviewed
Probab=38.52 E-value=29 Score=15.28 Aligned_cols=26 Identities=4% Similarity=-0.117 Sum_probs=21.2
Q ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 98599889999984899999998877
Q gi|254781218|r 41 KANNKTQKEMAIGANQLESAVNLFEN 66 (205)
Q Consensus 41 ~~~gltQ~elA~~~gis~~~is~~E~ 66 (205)
-+.|+.-+-++..+|||+|.+..|-+
T Consensus 8 ~a~g~~v~~~cr~LgVSRS~~y~~~~ 33 (301)
T PRK09409 8 IARGWGVSLVSRCLRVSRAQLHVILR 33 (301)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHCC
T ss_conf 96897499999997866877444302
No 446
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family; InterPro: IPR014325 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 the sigE factor from Streptomyces coelicolor . The protein appears to include a paralogous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives..
Probab=38.31 E-value=15 Score=16.97 Aligned_cols=59 Identities=17% Similarity=0.127 Sum_probs=37.7
Q ss_pred HHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHH----------HHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 996145322100002321345546777999999----------99972983899999977999999997
Q gi|254781218|r 88 DWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKS----------IRKDKGMSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 88 d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~----------lR~~~glsq~elA~~lgis~~tis~~ 146 (205)
+.+...+.+|-...+-......+...+-.-|+. +|---+||-.|.|+.+|||..|+...
T Consensus 81 ~e~~~~~~Pd~~ga~d~~~~~~~r~~l~~AL~~LP~rQR~vvVLRY~eDlSe~~~A~~LG~SvGTVKS~ 149 (165)
T TIGR02983 81 LELPTEELPDAAGAPDPAADVALRAALARALRRLPARQRAVVVLRYYEDLSEAEVAEVLGISVGTVKSR 149 (165)
T ss_pred HHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCHHCCEEEEEECCCCCCHHHHHHHHCCCCHHHHHH
T ss_conf 421466864888898753112269999999973564123672320457898689998819993228998
No 447
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family; InterPro: IPR014305 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 appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution and represent a conserved family.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=38.25 E-value=29 Score=15.25 Aligned_cols=24 Identities=25% Similarity=0.426 Sum_probs=14.3
Q ss_pred HHHHCCCCHHHHHHHHCCCHHHHH
Q ss_conf 999729838999999779999999
Q gi|254781218|r 121 IRKDKGMSQIEFGKLLGMPNSTLS 144 (205)
Q Consensus 121 lR~~~glsq~elA~~lgis~~tis 144 (205)
+|+-.|++-.|.|+.+|.|..+++
T Consensus 154 LRdvlGw~A~E~A~~L~~s~ASVn 177 (329)
T TIGR02960 154 LRDVLGWKAAEVAELLGTSVASVN 177 (329)
T ss_pred HHHHHCCCHHHHHHHHCCCHHHHH
T ss_conf 898835555689987438326786
No 448
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=37.80 E-value=30 Score=15.21 Aligned_cols=28 Identities=7% Similarity=0.088 Sum_probs=23.8
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 9999998599889999984899999998
Q gi|254781218|r 36 IKDIRKANNKTQKEMAIGANQLESAVNL 63 (205)
Q Consensus 36 ik~lR~~~gltQ~elA~~~gis~~~is~ 63 (205)
+..+++..-++-.+||+.+|+|..||-|
T Consensus 11 l~~l~~~g~v~v~eLa~~~~VS~~TIRR 38 (252)
T PRK10906 11 IELVKQQGYVSTEELVEHFSVSPQTIRR 38 (252)
T ss_pred HHHHHHCCCEEHHHHHHHHCCCHHHHHH
T ss_conf 9999986989999999987969989988
No 449
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=37.60 E-value=22 Score=16.01 Aligned_cols=33 Identities=21% Similarity=0.072 Sum_probs=22.0
Q ss_pred HHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 9999999999-85998899999848999999988
Q gi|254781218|r 32 VGTRIKDIRK-ANNKTQKEMAIGANQLESAVNLF 64 (205)
Q Consensus 32 iG~rik~lR~-~~gltQ~elA~~~gis~~~is~~ 64 (205)
+|.=.-.+=- ..-||..|+++.+|+|.+.+|.-
T Consensus 28 VG~iYgilyls~~Pmtl~Ei~E~lg~Sks~vS~~ 61 (177)
T COG1510 28 VGQIYGILYLSRKPLTLDEIAEALGMSKSNVSMG 61 (177)
T ss_pred HHHHHHHHEECCCCCCHHHHHHHHCCCCCHHHHH
T ss_conf 7778654000699966999999977780128899
No 450
>pfam04297 UPF0122 Putative helix-turn-helix protein, YlxM / p13 like. Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13. Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway.
Probab=37.38 E-value=30 Score=15.17 Aligned_cols=22 Identities=23% Similarity=0.078 Sum_probs=13.1
Q ss_pred HCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 8599889999984899999998
Q gi|254781218|r 42 ANNKTQKEMAIGANQLESAVNL 63 (205)
Q Consensus 42 ~~gltQ~elA~~~gis~~~is~ 63 (205)
...+|..|.|+..|||+++|..
T Consensus 31 ~eDlSL~EIAe~~~iSRQaV~D 52 (101)
T pfam04297 31 LDDLSLSEIAEEFNVSRQAVYD 52 (101)
T ss_pred HCCCCHHHHHHHHCCCHHHHHH
T ss_conf 7639899999881985999999
No 451
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=37.35 E-value=30 Score=15.16 Aligned_cols=29 Identities=3% Similarity=-0.123 Sum_probs=24.8
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 99999985998899999848999999988
Q gi|254781218|r 36 IKDIRKANNKTQKEMAIGANQLESAVNLF 64 (205)
Q Consensus 36 ik~lR~~~gltQ~elA~~~gis~~~is~~ 64 (205)
+..+++..-++-++||+.+|+|..||-|-
T Consensus 11 l~~L~~~g~v~v~eLa~~~~VS~~TIRRD 39 (251)
T PRK13509 11 LDMLAQLGFVTVEKVIERLGISPATARRD 39 (251)
T ss_pred HHHHHHCCCEEHHHHHHHHCCCHHHHHHH
T ss_conf 99999869898999999989699899983
No 452
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=36.96 E-value=31 Score=15.13 Aligned_cols=28 Identities=7% Similarity=0.107 Sum_probs=24.1
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 9999998599889999984899999998
Q gi|254781218|r 36 IKDIRKANNKTQKEMAIGANQLESAVNL 63 (205)
Q Consensus 36 ik~lR~~~gltQ~elA~~~gis~~~is~ 63 (205)
+..+++..-++-.+||+.+|||..||-|
T Consensus 23 l~~L~~~g~v~v~eLae~~~VS~~TIRR 50 (269)
T PRK09802 23 IQRLRQQGSVQVNDLSALYGVSTVTIRN 50 (269)
T ss_pred HHHHHHCCCEEHHHHHHHHCCCHHHHHH
T ss_conf 9999986989999999987969889998
No 453
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=36.70 E-value=31 Score=15.10 Aligned_cols=28 Identities=21% Similarity=0.245 Sum_probs=24.0
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 9999729838999999779999999974
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~E 147 (205)
-+|.-.|||..|.|+.+|++..|+....
T Consensus 147 ~Lr~~eglS~~EIAeiLgip~gTVKSRL 174 (217)
T PRK12533 147 VLRELEDMSYREIAAIADVPVGTVMSRL 174 (217)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9999809999999999894999999999
No 454
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=36.31 E-value=31 Score=15.06 Aligned_cols=32 Identities=22% Similarity=0.172 Sum_probs=27.5
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 99999999729838999999779999999974
Q gi|254781218|r 116 ARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 116 ~rLk~lR~~~glsq~elA~~lgis~~tis~~E 147 (205)
..|.......|..+.+.|+.+||+++|+.+..
T Consensus 594 ~~I~~aL~~~~gN~s~aA~~LGIsR~TLYRKl 625 (639)
T PRK11388 594 QAIINAAQVCGGRIQEMAALLGIGRTTLWRKM 625 (639)
T ss_pred HHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 99999999949979999999898999999999
No 455
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=35.76 E-value=32 Score=15.01 Aligned_cols=22 Identities=18% Similarity=0.108 Sum_probs=19.2
Q ss_pred CCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 5998899999848999999988
Q gi|254781218|r 43 NNKTQKEMAIGANQLESAVNLF 64 (205)
Q Consensus 43 ~gltQ~elA~~~gis~~~is~~ 64 (205)
.+++..++|+++|++++++.++
T Consensus 18 ~~l~l~ela~~~glpksT~~Rl 39 (246)
T COG1414 18 GGLSLAELAERLGLPKSTVHRL 39 (246)
T ss_pred CCCCHHHHHHHHCCCHHHHHHH
T ss_conf 8887999999879198899999
No 456
>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=35.74 E-value=32 Score=15.01 Aligned_cols=17 Identities=18% Similarity=0.257 Sum_probs=7.5
Q ss_pred CHHHHHHHHCCCHHHHH
Q ss_conf 88999998489999999
Q gi|254781218|r 46 TQKEMAIGANQLESAVN 62 (205)
Q Consensus 46 tQ~elA~~~gis~~~is 62 (205)
|..+||+..|+|+.+|.
T Consensus 27 s~~~La~~~~vSr~tvr 43 (66)
T cd07377 27 SERELAEELGVSRTTVR 43 (66)
T ss_pred CHHHHHHHHCCCHHHHH
T ss_conf 79999999798889999
No 457
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=35.71 E-value=32 Score=15.00 Aligned_cols=24 Identities=25% Similarity=0.290 Sum_probs=20.8
Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 729838999999779999999974
Q gi|254781218|r 124 DKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 124 ~~glsq~elA~~lgis~~tis~~E 147 (205)
..|+|..|.|+.+|+|.+|+...-
T Consensus 125 ~~g~s~~EIA~~l~is~~tVk~~l 148 (166)
T PRK09639 125 FSGYSYKEIAQALGIDESSVGTTL 148 (166)
T ss_pred HHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 938999999999891999999999
No 458
>PRK13501 transcriptional activator RhaR; Provisional
Probab=35.53 E-value=32 Score=14.98 Aligned_cols=31 Identities=13% Similarity=0.045 Sum_probs=24.0
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCH
Q ss_conf 2983899999977999999997414889998
Q gi|254781218|r 125 KGMSQIEFGKLLGMPNSTLSNYEQGRTIPEI 155 (205)
Q Consensus 125 ~glsq~elA~~lgis~~tis~~E~g~~~Ps~ 155 (205)
..++..++|+.+++++..++++-+..+--+.
T Consensus 191 ~~~~l~~lA~~~~lS~~~lsrlFK~~tG~T~ 221 (290)
T PRK13501 191 AYFDMADFCHKNQLVERSLKQLFRQQTGMSI 221 (290)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHCCCH
T ss_conf 8999999999969899999999999989399
No 459
>pfam07453 NUMOD1 NUMOD1 domain. This domain probably represents a DNA-binding helix-turn-helix based on its similarity to other families (Bateman A pers obs).
Probab=35.46 E-value=24 Score=15.77 Aligned_cols=19 Identities=37% Similarity=0.578 Sum_probs=10.3
Q ss_pred CHHHHHHHHCCCHHHHHHH
Q ss_conf 3899999977999999997
Q gi|254781218|r 128 SQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 128 sq~elA~~lgis~~tis~~ 146 (205)
|..++|+.+|+++.+++++
T Consensus 18 Si~~aa~~L~i~~~tI~~~ 36 (37)
T pfam07453 18 SIREAARALGISHSTINKY 36 (37)
T ss_pred HHHHHHHHHCCCHHHHHCC
T ss_conf 7999999847646566502
No 460
>pfam05732 RepL Firmicute plasmid replication protein (RepL). This family consists of Firmicute RepL proteins which are involved in plasmid replication.
Probab=34.53 E-value=31 Score=15.08 Aligned_cols=46 Identities=26% Similarity=0.386 Sum_probs=24.7
Q ss_pred CCHHHHHHHHCCCHHHHHHH----HCCCCCCCHHHHHHHH-HHHCCCHHHHHCCCCC
Q ss_conf 83899999977999999997----4148899989999999-9828999995247210
Q gi|254781218|r 127 MSQIEFGKLLGMPNSTLSNY----EQGRTIPEIKPARKIK-QVTKKHLDWIYFGDEV 178 (205)
Q Consensus 127 lsq~elA~~lgis~~tis~~----E~g~~~Ps~~~l~kIa-~~lgvs~d~L~~G~e~ 178 (205)
.|+.++|+.+|+|.+|+..- +.+.-. .+.. -++=++|+-+|-|++.
T Consensus 76 ~T~R~lae~~gvs~~TV~~tmK~L~e~~fI------kk~t~GvymiNP~i~~kG~~~ 126 (165)
T pfam05732 76 MTQREIAEETGISLETVRQTMKALEEGNFL------KKKTSGVYMINPDLLFKGDDT 126 (165)
T ss_pred EEHHHHHHHHCCCHHHHHHHHHHHHHCCCE------EEECCCEEEECHHHHHCCCHH
T ss_conf 878999998395299999999999758926------861387699885895068727
No 461
>PRK00430 fis DNA-binding protein Fis; Provisional
Probab=34.36 E-value=34 Score=14.87 Aligned_cols=61 Identities=21% Similarity=0.232 Sum_probs=38.5
Q ss_pred HHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 999999982899999614532210000232134554677799999999972983899999977999999997
Q gi|254781218|r 75 YALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 75 ~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~ 146 (205)
+-..+.++|. -++|+....-|..+-..- =..=|..+.+.-+-.|...|+.+||++.|+.+-
T Consensus 31 V~~al~~Yf~-----~L~g~~~~~ly~~vl~ev------E~pLl~~vL~~t~gNqskAA~~LGInR~TLRkK 91 (98)
T PRK00430 31 VKQALKNYFA-----QLDGQDVNDLYELVLAEV------EAPLLDMVMQYTRGNQTRAALMLGINRGTLRKK 91 (98)
T ss_pred HHHHHHHHHH-----HCCCCCCHHHHHHHHHHH------HHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHH
T ss_conf 9999999999-----749999206999999998------999999999996695999999978778899999
No 462
>COG0656 ARA1 Aldo/keto reductases, related to diketogulonate reductase [General function prediction only]
Probab=34.31 E-value=34 Score=14.86 Aligned_cols=59 Identities=17% Similarity=0.253 Sum_probs=42.1
Q ss_pred HHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH-----HHHHCCCCCCCHHHHHHH
Q ss_conf 89999997799999999741488999899999999828999-----995247210254567775
Q gi|254781218|r 129 QIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHL-----DWIYFGDEVIVPKSIKRA 187 (205)
Q Consensus 129 q~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~-----d~L~~G~e~~~~~~~~~~ 187 (205)
.-+||+.-||....+|-..+|.....-..+..||+.+|.|+ .|.+...-...|++.+..
T Consensus 175 l~~~~~~~gI~v~AysPL~~g~~l~~~~~l~~Ia~k~g~t~AQv~L~W~i~~gv~~Ipks~~~~ 238 (280)
T COG0656 175 LLPFCQRHGIAVEAYSPLAKGGKLLDNPVLAEIAKKYGKTPAQVALRWHIQRGVIVIPKSTTPE 238 (280)
T ss_pred HHHHHHHCCCEEEEECCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHCCCEEECCCCCHH
T ss_conf 9999998799899978722366312586999999984898799999988757948755789889
No 463
>PRK10923 glnG nitrogen regulation protein NR(I); Provisional
Probab=34.13 E-value=34 Score=14.84 Aligned_cols=33 Identities=21% Similarity=0.221 Sum_probs=27.4
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 999999997298389999997799999999741
Q gi|254781218|r 116 ARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQ 148 (205)
Q Consensus 116 ~rLk~lR~~~glsq~elA~~lgis~~tis~~E~ 148 (205)
.-|.+..+..+..+.+.|+.+||+++|+.+..+
T Consensus 432 ~~I~~aL~~~~gn~~~aA~~LGisR~TLyrKlk 464 (469)
T PRK10923 432 TLLTTALRHTQGHKQEAARLLGWGRNTLTRKLK 464 (469)
T ss_pred HHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 999999999099899999998989999999999
No 464
>pfam02084 Bindin Bindin.
Probab=33.99 E-value=34 Score=14.85 Aligned_cols=52 Identities=21% Similarity=0.294 Sum_probs=38.2
Q ss_pred HHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 988779988899999999998289999961453221000023213455467779999999997298
Q gi|254781218|r 62 NLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRKDKGM 127 (205)
Q Consensus 62 s~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~~~gl 127 (205)
|.++-+...+|.+++-+|-.+|+.+- +|. .--+.||+.+|--||.+|...+|
T Consensus 90 ss~~e~etTIsAkvm~~IKAVLGATK--------IDL------PVDINDPYDLGLLLRHLRHHSNL 141 (239)
T pfam02084 90 SSIEEGDTTISADVMEKIKAVLGATK--------IDL------PVDINDPYDLGLLLRHLRHHSNL 141 (239)
T ss_pred CCCCCCCCEEEHHHHHHHHHHHCCCC--------CCC------CCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 22347875350999998999857543--------467------44368733678999998877778
No 465
>PRK00118 putative DNA-binding protein; Validated
Probab=33.91 E-value=34 Score=14.82 Aligned_cols=23 Identities=22% Similarity=0.027 Sum_probs=14.8
Q ss_pred HHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 98599889999984899999998
Q gi|254781218|r 41 KANNKTQKEMAIGANQLESAVNL 63 (205)
Q Consensus 41 ~~~gltQ~elA~~~gis~~~is~ 63 (205)
-..++|-.|.|+..|||+++|+.
T Consensus 30 y~~DlSl~EIAe~~~iSRQaV~D 52 (105)
T PRK00118 30 YLDDYSLGEIAEEFNVSRQAVYD 52 (105)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHH
T ss_conf 88549999998996985999999
No 466
>PRK09480 slmA nucleoid occlusion protein; Provisional
Probab=33.90 E-value=34 Score=14.82 Aligned_cols=30 Identities=13% Similarity=0.028 Sum_probs=24.2
Q ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHCCCCC
Q ss_conf 985998899999848999999988779988
Q gi|254781218|r 41 KANNKTQKEMAIGANQLESAVNLFENGMCS 70 (205)
Q Consensus 41 ~~~gltQ~elA~~~gis~~~is~~E~G~~~ 70 (205)
.-.++|..++|+.+|||+.++.++=.++..
T Consensus 27 ~~~~iTt~~iA~~~gvs~aalYrHF~sK~~ 56 (194)
T PRK09480 27 PGERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred CCCCCCHHHHHHHHCCCHHHHHHHCCCHHH
T ss_conf 976422999998909978999997587999
No 467
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=33.48 E-value=35 Score=14.78 Aligned_cols=30 Identities=10% Similarity=0.137 Sum_probs=25.6
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 999999998599889999984899999998
Q gi|254781218|r 34 TRIKDIRKANNKTQKEMAIGANQLESAVNL 63 (205)
Q Consensus 34 ~rik~lR~~~gltQ~elA~~~gis~~~is~ 63 (205)
.=+..+++..-++-.+||+.+|+|..||-|
T Consensus 11 ~Il~~L~~~g~v~v~eLa~~~~VS~~TIRR 40 (252)
T PRK10681 11 QLLQALKRSDKLHLKDAAALLGVSEMTIRR 40 (252)
T ss_pred HHHHHHHHCCCEEHHHHHHHHCCCHHHHHH
T ss_conf 999999986979999999887979989987
No 468
>KOG0774 consensus
Probab=33.33 E-value=17 Score=16.72 Aligned_cols=23 Identities=26% Similarity=0.297 Sum_probs=11.6
Q ss_pred HHHHHHHCCCHHHHHHHHCCCCC
Q ss_conf 99999977999999997414889
Q gi|254781218|r 130 IEFGKLLGMPNSTLSNYEQGRTI 152 (205)
Q Consensus 130 ~elA~~lgis~~tis~~E~g~~~ 152 (205)
.+||...||+.+.+++|.-.+++
T Consensus 222 ~eLAkqCnItvsQvsnwfgnkrI 244 (334)
T KOG0774 222 EELAKQCNITVSQVSNWFGNKRI 244 (334)
T ss_pred HHHHHHCCCEEHHHCCCCCCCEE
T ss_conf 99998729340563232245403
No 469
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=33.12 E-value=35 Score=14.74 Aligned_cols=37 Identities=11% Similarity=0.140 Sum_probs=19.7
Q ss_pred HHHHHHHHHH---HCCCCHHHHHHHHCCCHHHHHHHHCCC
Q ss_conf 7999999999---729838999999779999999974148
Q gi|254781218|r 114 IGARLKSIRK---DKGMSQIEFGKLLGMPNSTLSNYEQGR 150 (205)
Q Consensus 114 iG~rLk~lR~---~~glsq~elA~~lgis~~tis~~E~g~ 150 (205)
++.+++.+-. .+.++..++|+.+.++.+++.+.....
T Consensus 135 ~s~Kv~~II~sDis~~W~L~dIA~~L~mSEStLkRkLk~E 174 (253)
T PRK09940 135 VSGKVRNIVNMKLAHPWKLKDICDCLYISESLLKKKLKQE 174 (253)
T ss_pred HHHHHHHHHHCCCCCCCCHHHHHHHHCCCHHHHHHHHHHC
T ss_conf 5698999996483004609999988745899999999986
No 470
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=32.92 E-value=36 Score=14.72 Aligned_cols=27 Identities=15% Similarity=0.164 Sum_probs=23.0
Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 999972983899999977999999997
Q gi|254781218|r 120 SIRKDKGMSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 120 ~lR~~~glsq~elA~~lgis~~tis~~ 146 (205)
.+|-..|+|..|.|+.+|++.+++...
T Consensus 137 ~l~~~~~~s~~EIA~~l~is~~tV~~r 163 (177)
T PRK09415 137 YLFYYEELSIKEIATVTGVNENTIKTR 163 (177)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999980998999999889299999999
No 471
>PRK05234 mgsA methylglyoxal synthase; Validated
Probab=32.89 E-value=36 Score=14.72 Aligned_cols=45 Identities=13% Similarity=0.268 Sum_probs=29.6
Q ss_pred HCCCHHHHHHHHCCC---------------CCCCHHHHHHHHHHHCCCH-------HHHHCCCCCCC
Q ss_conf 489999999887799---------------8889999999999828999-------99614532210
Q gi|254781218|r 54 ANQLESAVNLFENGM---------------CSTSIRYALYLRNEYEISF-------DWIYDGEVIDR 98 (205)
Q Consensus 54 ~gis~~~is~~E~G~---------------~~psi~~l~~la~~~~vs~-------d~Ll~ge~~~~ 98 (205)
+|=.++-=+++..|. ..|++..|+++|..++|++ |.|+.+-..+.
T Consensus 62 lGGDqQIga~Ia~g~id~viFF~DPl~~~phd~Dv~aLlRlc~v~nIP~AtN~aTAe~li~~~~~~~ 128 (146)
T PRK05234 62 LGGDQQIGALIAEGKIDMLIFFWDPLTAQPHDPDVKALLRLADVWNIPVATNRATADFLISSPLFND 128 (146)
T ss_pred CCHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCC
T ss_conf 4189999999983998789994088755777520999999998728764268978999970822365
No 472
>PRK04280 arginine repressor; Provisional
Probab=32.88 E-value=33 Score=14.89 Aligned_cols=29 Identities=24% Similarity=0.224 Sum_probs=19.3
Q ss_pred HHHHH-HHCCCCHHHHHHHH-----CCCHHHHHHH
Q ss_conf 99999-98599889999984-----8999999988
Q gi|254781218|r 36 IKDIR-KANNKTQKEMAIGA-----NQLESAVNLF 64 (205)
Q Consensus 36 ik~lR-~~~gltQ~elA~~~-----gis~~~is~~ 64 (205)
|+.+= ...=-||+||.+.+ .+||.+|||-
T Consensus 10 I~~lI~~~~I~tQeeL~~~L~~~Gi~vTQATlSRD 44 (149)
T PRK04280 10 IREIITNEEIETQDELVDRLREYGFNVTQATVSRD 44 (149)
T ss_pred HHHHHHHCCCCCHHHHHHHHHHCCCCEEHHHHHHH
T ss_conf 99999748977899999999985975538988987
No 473
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=32.67 E-value=36 Score=14.70 Aligned_cols=26 Identities=15% Similarity=0.005 Sum_probs=21.7
Q ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 999859988999998489999999887
Q gi|254781218|r 39 IRKANNKTQKEMAIGANQLESAVNLFE 65 (205)
Q Consensus 39 lR~~~gltQ~elA~~~gis~~~is~~E 65 (205)
.|. .++|-.+||+.+|+|+++.++|=
T Consensus 15 ~~~-~~~t~~ela~~l~~S~qta~R~l 40 (214)
T COG1339 15 VRG-VKVTSSELAKRLGVSSQTAARKL 40 (214)
T ss_pred HCC-CCCCHHHHHHHHCCCCHHHHHHH
T ss_conf 037-60208999988574707788998
No 474
>PRK13500 transcriptional activator RhaR; Provisional
Probab=31.88 E-value=37 Score=14.62 Aligned_cols=42 Identities=10% Similarity=0.040 Sum_probs=27.3
Q ss_pred HHHHHHHHHH--HCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCH
Q ss_conf 7999999999--72983899999977999999997414889998
Q gi|254781218|r 114 IGARLKSIRK--DKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEI 155 (205)
Q Consensus 114 iG~rLk~lR~--~~glsq~elA~~lgis~~tis~~E~g~~~Ps~ 155 (205)
+.+-|..+.. ..-++..+||+..|+|..++++.-+...--+.
T Consensus 208 L~~ll~~l~~~~~ep~~l~~lA~~~~lS~r~L~R~Fk~~tG~Tp 251 (312)
T PRK13500 208 LDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMTI 251 (312)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCH
T ss_conf 99999999987449998999998978899999999999989199
No 475
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=31.77 E-value=37 Score=14.61 Aligned_cols=39 Identities=13% Similarity=0.026 Sum_probs=27.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHCC-------------CCCCCHHHHHHHHHHH
Q ss_conf 83899999977999999997414-------------8899989999999982
Q gi|254781218|r 127 MSQIEFGKLLGMPNSTLSNYEQG-------------RTIPEIKPARKIKQVT 165 (205)
Q Consensus 127 lsq~elA~~lgis~~tis~~E~g-------------~~~Ps~~~l~kIa~~l 165 (205)
.++.|+|+.+|+++.++++..+. -..-+.+.|.+||.-+
T Consensus 157 ~~~~elA~~lG~Sretl~R~L~~f~~eGiI~~~~~~i~I~D~~~L~~LA~~~ 208 (213)
T PRK10402 157 EKHTQAAEYLGVSYRHLLYVLAQFCQDGYLIKSKRGYLIKNRKQLSGLALEL 208 (213)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCEEEEECHHHHHHHHHHC
T ss_conf 6799999997988999999999999889889749999995799999998644
No 476
>TIGR00651 pta phosphate acetyltransferase; InterPro: IPR004614 Phosphate acetyltransferase (2.3.1.8 from EC) catalyses the conversion of acetyl-CoA and phosphate to CoA and acetyl phosphate in the last two steps in the conversion of actetae to acetyl-CoA.; GO: 0016407 acetyltransferase activity.
Probab=31.50 E-value=38 Score=14.58 Aligned_cols=34 Identities=18% Similarity=0.239 Sum_probs=23.7
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf 1566899999999999999998599889999984
Q gi|254781218|r 21 ITPEIRQYWKDVGTRIKDIRKANNKTQKEMAIGA 54 (205)
Q Consensus 21 ~~~~~~~~~~~iG~rik~lR~~~gltQ~elA~~~ 54 (205)
+.+......+...+++-++||.+|+|.++..+.+
T Consensus 55 ~~~~~~~~~E~Y~~~~~e~RK~KG~t~~~A~~~l 88 (322)
T TIGR00651 55 IDPDVSPDRESYAERYYELRKHKGVTLAQARKQL 88 (322)
T ss_pred ECCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHH
T ss_conf 2786742279999999987415560479999973
No 477
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=31.48 E-value=38 Score=14.58 Aligned_cols=33 Identities=18% Similarity=0.266 Sum_probs=24.6
Q ss_pred HHHHHH--HHHCCCCHHHHHHHHCCCHHHHHHHHC
Q ss_conf 999999--997298389999997799999999741
Q gi|254781218|r 116 ARLKSI--RKDKGMSQIEFGKLLGMPNSTLSNYEQ 148 (205)
Q Consensus 116 ~rLk~l--R~~~glsq~elA~~lgis~~tis~~E~ 148 (205)
.|=+++ .-..|+|-++.|+.+++|..|+..+-.
T Consensus 144 ~RE~eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~ 178 (202)
T PRK09390 144 ERERQVMDGLVAGLSNKVIARDLDISPRTVEVYRA 178 (202)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 89999999998389689999997987889999999
No 478
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=31.37 E-value=38 Score=14.56 Aligned_cols=29 Identities=10% Similarity=0.103 Sum_probs=22.4
Q ss_pred HHHHHHHH--CCCCHHHHHHHHCCCHHHHHH
Q ss_conf 99999998--599889999984899999998
Q gi|254781218|r 35 RIKDIRKA--NNKTQKEMAIGANQLESAVNL 63 (205)
Q Consensus 35 rik~lR~~--~gltQ~elA~~~gis~~~is~ 63 (205)
.+|.++.. .|++..+-|+++++||++||+
T Consensus 5 QLryf~~va~~~~n~t~AA~~L~iSQPavS~ 35 (324)
T PRK12681 5 QLRYIVEVVNHNLNVSATAESLYTSQPGISK 35 (324)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf 9999999997699999999997897779999
No 479
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=30.96 E-value=38 Score=14.52 Aligned_cols=36 Identities=14% Similarity=0.235 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHHHHHCC-------CCHHHHHHHHCCCHHHHHH
Q ss_conf 99999999999999859-------9889999984899999998
Q gi|254781218|r 28 YWKDVGTRIKDIRKANN-------KTQKEMAIGANQLESAVNL 63 (205)
Q Consensus 28 ~~~~iG~rik~lR~~~g-------ltQ~elA~~~gis~~~is~ 63 (205)
-+.+|.++|+..=-..- -|..+||..++|++.|+++
T Consensus 12 IY~QI~~qIk~~I~~g~l~pGdkLPSvRelA~~~~VNpnTv~r 54 (125)
T COG1725 12 IYEQIANQIKEQIASGELKPGDKLPSVRELAKDLGVNPNTVQR 54 (125)
T ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCHHHHHH
T ss_conf 7999999999999808868888897599999981989889999
No 480
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=30.76 E-value=39 Score=14.50 Aligned_cols=31 Identities=10% Similarity=0.044 Sum_probs=25.9
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 9999999998599889999984899999998
Q gi|254781218|r 33 GTRIKDIRKANNKTQKEMAIGANQLESAVNL 63 (205)
Q Consensus 33 G~rik~lR~~~gltQ~elA~~~gis~~~is~ 63 (205)
..=+..+++..-++.++||+.+|||..||-|
T Consensus 8 ~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRR 38 (253)
T COG1349 8 QKILELLKEKGKVSVEELAELFGVSEMTIRR 38 (253)
T ss_pred HHHHHHHHHCCCEEHHHHHHHHCCCHHHHHH
T ss_conf 9999999985969799999885978999986
No 481
>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]
Probab=30.71 E-value=39 Score=14.50 Aligned_cols=49 Identities=8% Similarity=-0.048 Sum_probs=20.4
Q ss_pred HHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCC
Q ss_conf 99999848999999988779988899999999998289999961453221
Q gi|254781218|r 48 KEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVID 97 (205)
Q Consensus 48 ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~ 97 (205)
.++.+.+|+..+...+|=+-.+. --..-+.||+++-+.+.+|+-+|.++
T Consensus 122 ~~~L~~VgL~~~~l~R~P~eLSG-GQ~QRiaIARAL~~~PklLIlDEptS 170 (252)
T COG1124 122 AELLDQVGLPPSFLDRRPHELSG-GQRQRIAIARALIPEPKLLILDEPTS 170 (252)
T ss_pred HHHHHHCCCCHHHHHCCCHHCCH-HHHHHHHHHHHHCCCCCEEEECCCHH
T ss_conf 99999849998998539421281-68999999998636888799538234
No 482
>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=30.07 E-value=40 Score=14.43 Aligned_cols=22 Identities=23% Similarity=0.129 Sum_probs=13.8
Q ss_pred CCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 5998899999848999999988
Q gi|254781218|r 43 NNKTQKEMAIGANQLESAVNLF 64 (205)
Q Consensus 43 ~gltQ~elA~~~gis~~~is~~ 64 (205)
...+..++|..+|+++++++..
T Consensus 19 ~~v~~~~iA~~L~Vs~~SVt~m 40 (58)
T pfam01325 19 GVVKTKDLAERLNVSPSTVSEM 40 (58)
T ss_pred CCEEHHHHHHHHCCCCHHHHHH
T ss_conf 9612999999959992529999
No 483
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=30.05 E-value=40 Score=14.43 Aligned_cols=28 Identities=11% Similarity=0.147 Sum_probs=23.5
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 9999998599889999984899999998
Q gi|254781218|r 36 IKDIRKANNKTQKEMAIGANQLESAVNL 63 (205)
Q Consensus 36 ik~lR~~~gltQ~elA~~~gis~~~is~ 63 (205)
+..+++..-++-.+||+.+|||..||-|
T Consensus 11 l~~L~~~g~v~v~eLa~~l~VS~~TIRR 38 (256)
T PRK10434 11 LEYLQKQGKCSVEELAQYFDTTGTTIRK 38 (256)
T ss_pred HHHHHHCCCEEHHHHHHHHCCCHHHHHH
T ss_conf 9999986979999999987969989998
No 484
>PRK05294 carB carbamoyl phosphate synthase large subunit; Reviewed
Probab=29.73 E-value=40 Score=14.39 Aligned_cols=107 Identities=16% Similarity=0.225 Sum_probs=65.6
Q ss_pred HHCCCCCCCHHHHHHHHHHH--CCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHH------------HHHHHCCCCH
Q ss_conf 87799888999999999982--899999614532210000232134554677799999------------9999729838
Q gi|254781218|r 64 FENGMCSTSIRYALYLRNEY--EISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLK------------SIRKDKGMSQ 129 (205)
Q Consensus 64 ~E~G~~~psi~~l~~la~~~--~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk------------~lR~~~glsq 129 (205)
++.-...|+-..+..|+++| +++++.+-.-..+|.=|...-+.= ..+.++|+ ..-+..|+|-
T Consensus 419 l~~~L~~p~~~Rl~~i~eAlrrG~sveeI~elT~ID~wFL~ki~~I----v~~e~~l~~~~~~~l~~~~L~~aK~~GFSD 494 (1063)
T PRK05294 419 IRRELKKPTPERIFYIAEAFRRGASVEEIHELTKIDPWFLEQIEEI----VELEEELKEGGLPGLDAELLRELKRLGFSD 494 (1063)
T ss_pred HHHHHCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHCCCCCCCHHHHHHHHHHCCCH
T ss_conf 9998637993599999999985999999999878769999999999----999999984898879999999999809985
Q ss_pred HHHHHHHCCCHHHHHHHHCC-CCCCCHHHHHHHHHHHCCCHHHHHC
Q ss_conf 99999977999999997414-8899989999999982899999524
Q gi|254781218|r 130 IEFGKLLGMPNSTLSNYEQG-RTIPEIKPARKIKQVTKKHLDWIYF 174 (205)
Q Consensus 130 ~elA~~lgis~~tis~~E~g-~~~Ps~~~l~kIa~~lgvs~d~L~~ 174 (205)
.++|+.+|++...+.++-.. ...|....+.-.|-.|.-...|++.
T Consensus 495 ~~IA~l~~~~~~~Vr~~R~~~~I~P~yK~VDTcAgEF~a~T~Y~YS 540 (1063)
T PRK05294 495 ARIAKLLGVTEDEVRKLRKELGIHPVYKRVDTCAAEFEADTPYMYS 540 (1063)
T ss_pred HHHHHHHCCCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCEEEE
T ss_conf 9999884999999999999879953898415632345667872676
No 485
>PRK13980 NAD synthetase; Provisional
Probab=29.55 E-value=40 Score=14.37 Aligned_cols=71 Identities=17% Similarity=0.116 Sum_probs=32.0
Q ss_pred HHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHH-HHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 99999998289999961453221000023213455-4677799999999972983899999977999999997
Q gi|254781218|r 75 YALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRL-DPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 75 ~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~-d~~~iG~rLk~lR~~~glsq~elA~~lgis~~tis~~ 146 (205)
.+..||++++|+ +.++.-.+...-..++.....+ -+..+=..+=....+.+++..+.++.+|+++..+.++
T Consensus 167 ~V~~La~~l~vP-~~Ii~k~PSa~L~~~Q~DE~~LG~~Y~~lD~iL~~~ie~~~~~~~i~~~~g~~~~~v~~i 238 (264)
T PRK13980 167 QVRELARHLGVP-EDIIEKPPSADLWEGQTDEDELGFSYEEIDEILYALFDKKMPREEILAQLGIDEELVDRV 238 (264)
T ss_pred HHHHHHHHHCCC-HHHEECCCCCCCCCCCCCHHHCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHH
T ss_conf 999999993996-644036999776799998777199999999999999976999999998719899999999
No 486
>pfam08822 DUF1804 Protein of unknown function (DUF1804). This family of bacterial protein is uncharacterized.
Probab=29.44 E-value=41 Score=14.36 Aligned_cols=118 Identities=15% Similarity=0.165 Sum_probs=65.3
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCC--CCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCH
Q ss_conf 999999999999985998899999848999999988779988--899999999998289999961453221000023213
Q gi|254781218|r 29 WKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCS--TSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNK 106 (205)
Q Consensus 29 ~~~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~E~G~~~--psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~ 106 (205)
..+.-.++|..=-..+++.+..|.+.||+.++--+|-..-.. -+-+.+-.- ..+.|..++. ..+
T Consensus 4 ~~e~r~~vR~~Yv~~~~~Le~aA~~~gV~~~TArrWK~~Ak~~GDDWDkaRaA---------~~maggg~ed-----var 69 (165)
T pfam08822 4 PKETRDAVRRLYVFDRLTLEVAAAKAGVSYSTARRWKREAKAKGDDWDKARAA---------YTLAGGGIED-----LAR 69 (165)
T ss_pred CHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHHHHHCCCCHHHHHHH---------HHHHCCCHHH-----HHH
T ss_conf 68999999999996678799999880998888999999888758838999999---------9985687889-----999
Q ss_pred HHHHHHH--HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH--CCCCCCCHHHHHH
Q ss_conf 4554677--7999999999729838999999779999999974--1488999899999
Q gi|254781218|r 107 KRLDPYA--IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYE--QGRTIPEIKPARK 160 (205)
Q Consensus 107 ~~~d~~~--iG~rLk~lR~~~glsq~elA~~lgis~~tis~~E--~g~~~Ps~~~l~k 160 (205)
..+.-+. .-.-+.+++..-.|+..+=++.+.-=..++++.- +++..|.++.+--
T Consensus 70 ~~l~~f~~Q~~~tmeeL~~~~~l~~~~Kv~lLAsLaDsf~K~vaAskr~lPets~LA~ 127 (165)
T pfam08822 70 QMLTGFVVQYQATMDELQEDEDLPPSDKAKLLASLADSFSKTVAASKRVLPETSKLAT 127 (165)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf 9999999999999999872556998899999999999999999987133841899999
No 487
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=29.41 E-value=41 Score=14.36 Aligned_cols=34 Identities=18% Similarity=0.202 Sum_probs=28.6
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCC
Q ss_conf 9999999972983899999977999999997414
Q gi|254781218|r 116 ARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQG 149 (205)
Q Consensus 116 ~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g 149 (205)
.-|+.+....+-+....|+.+||+++|+.++..-
T Consensus 523 ~~I~~aL~~~~gn~~~aAk~LgIsrttL~rKlkk 556 (560)
T COG3829 523 HLIREALERHGGNKSKAAKELGISRTTLYRKLKK 556 (560)
T ss_pred HHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 9999999982798989999969978999999998
No 488
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=29.39 E-value=41 Score=14.36 Aligned_cols=17 Identities=24% Similarity=0.393 Sum_probs=6.8
Q ss_pred HHHHHHCCCHHHHHHHH
Q ss_conf 99999779999999974
Q gi|254781218|r 131 EFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 131 elA~~lgis~~tis~~E 147 (205)
++|..+|++...|..|-
T Consensus 32 ~La~~~~l~~~qV~~WF 48 (59)
T cd00086 32 ELAKELGLTERQVKIWF 48 (59)
T ss_pred HHHHHHCCCHHHHHHHH
T ss_conf 99999792999999999
No 489
>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional
Probab=29.38 E-value=41 Score=14.35 Aligned_cols=31 Identities=10% Similarity=0.121 Sum_probs=25.9
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 9999999729838999999779999999974
Q gi|254781218|r 117 RLKSIRKDKGMSQIEFGKLLGMPNSTLSNYE 147 (205)
Q Consensus 117 rLk~lR~~~glsq~elA~~lgis~~tis~~E 147 (205)
-|.+..+..+-.+.+.|+.+||+++|+.+..
T Consensus 421 ~i~~aL~~~~gn~~~aA~~LGisR~tLyrKl 451 (457)
T PRK11361 421 IIMEVLEQQEGNRTRTALMLGISRRALMYKL 451 (457)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9999999829989999999898999999999
No 490
>cd04778 HTH_MerR-like_sg2 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 2). 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=29.37 E-value=41 Score=14.35 Aligned_cols=28 Identities=14% Similarity=0.237 Sum_probs=20.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHH-CCCCCCC
Q ss_conf 988999998489999999887-7998889
Q gi|254781218|r 45 KTQKEMAIGANQLESAVNLFE-NGMCSTS 72 (205)
Q Consensus 45 ltQ~elA~~~gis~~~is~~E-~G~~~ps 72 (205)
++-.+||...|++..+|-.|+ .|.-.|+
T Consensus 2 y~i~eLa~~~g~~~rtiR~Y~~~GLlppp 30 (219)
T cd04778 2 YRIDDLARAAGTTVRNVRAYQDRGLLPPP 30 (219)
T ss_pred CCHHHHHHHHCCCCHHHHHHHHCCCCCCC
T ss_conf 75999999829981112798876899998
No 491
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=29.29 E-value=41 Score=14.35 Aligned_cols=34 Identities=15% Similarity=-0.023 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 9999999999985998899999848999999988
Q gi|254781218|r 31 DVGTRIKDIRKANNKTQKEMAIGANQLESAVNLF 64 (205)
Q Consensus 31 ~iG~rik~lR~~~gltQ~elA~~~gis~~~is~~ 64 (205)
-+-.=|..+|..+.+|..+||+..+||..+|.+-
T Consensus 9 RL~~ii~~L~~~~~vta~~lA~~~~VS~RTi~RD 42 (311)
T COG2378 9 RLLQIIQILRAKETVTAAELADEFEVSVRTIYRD 42 (311)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHH
T ss_conf 9999999998576045999998729889999999
No 492
>PHA02519 plasmid partition protein SopA; Reviewed
Probab=28.86 E-value=42 Score=14.30 Aligned_cols=64 Identities=11% Similarity=-0.020 Sum_probs=48.9
Q ss_pred HHHHHHHHHHHHHHHHHHHH----------CCCCHHHHHHHHCCCHHHHHHHHCC----------------CCCCCHHHH
Q ss_conf 66899999999999999998----------5998899999848999999988779----------------988899999
Q gi|254781218|r 23 PEIRQYWKDVGTRIKDIRKA----------NNKTQKEMAIGANQLESAVNLFENG----------------MCSTSIRYA 76 (205)
Q Consensus 23 ~~~~~~~~~iG~rik~lR~~----------~gltQ~elA~~~gis~~~is~~E~G----------------~~~psi~~l 76 (205)
..|.+-..++.++|+.+|-. +-+|-.|+|+.+||+.+++-+.+.. ++.=+++.+
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~P~~~k~lR~Fs~~E~A~l~gvs~~~lR~~~~~g~~P~p~~~~~gr~~~rr~ytl~~i 87 (387)
T PHA02519 8 NSCIERGQEMTQAIAIAQFGDDSPEARAITRRWGITEVADLIGVTPQAIRDAEKSGRLPPPDFETRGRVERRAGYTIDQI 87 (387)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHH
T ss_conf 99999899999999999721589633124477888999999599989998787568999997688887553343579999
Q ss_pred HHHHHHHCCC
Q ss_conf 9999982899
Q gi|254781218|r 77 LYLRNEYEIS 86 (205)
Q Consensus 77 ~~la~~~~vs 86 (205)
..|..+|+..
T Consensus 88 ~~lR~~l~~~ 97 (387)
T PHA02519 88 SHMRDHFGNP 97 (387)
T ss_pred HHHHHHHCCC
T ss_conf 9999986456
No 493
>COG1582 FlgEa Uncharacterized protein, possibly involved in motility [Cell motility and secretion]
Probab=28.84 E-value=28 Score=15.32 Aligned_cols=46 Identities=13% Similarity=0.286 Sum_probs=37.2
Q ss_pred CCCHHHHHHHHHHHHHHHHCCCHH----HHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 933077776665433310001566----8999999999999999985998
Q gi|254781218|r 1 MFLNPFLETSLKSLQEYTLIITPE----IRQYWKDVGTRIKDIRKANNKT 46 (205)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~iG~rik~lR~~~glt 46 (205)
.+|||.+--++++.++-|+.+... +++.-.++-+||+..|++-+.-
T Consensus 12 ~~lN~~~IE~ie~~PDttItLinGkkyvVkEsveEVi~kI~~y~rkI~~~ 61 (67)
T COG1582 12 FWLNAHHIETIEAFPDTTITLINGKKYVVKESVEEVINKIIEYRRKIGSL 61 (67)
T ss_pred EEECHHHHHHHHCCCCCEEEEECCCEEEECCCHHHHHHHHHHHHHHHHEE
T ss_conf 25378784432216973899976828997023999999999999876230
No 494
>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=28.59 E-value=42 Score=14.27 Aligned_cols=46 Identities=22% Similarity=0.119 Sum_probs=26.6
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf 999999997298389999997799999999741488999899999999828999
Q gi|254781218|r 116 ARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHL 169 (205)
Q Consensus 116 ~rLk~lR~~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~ 169 (205)
+-|..+-.....+..+||+.+.+|.+|+.+. +..+..+-+-+|+.+
T Consensus 20 ~il~~lf~~~~~s~~~~a~~l~iS~sTl~R~--------ik~l~~~L~~~~l~i 65 (87)
T pfam05043 20 QLLKFLFFHEFFSLTSLAQKLFISESTLYRL--------IKKLNKLLKEFDLSI 65 (87)
T ss_pred HHHHHHHCCCCCCHHHHHHHHCCCHHHHHHH--------HHHHHHHHHHCCEEE
T ss_conf 9999998189998999999978899999999--------999999999859688
No 495
>TIGR01132 pgm phosphoglucomutase, alpha-D-glucose phosphate-specific; InterPro: IPR005852 Phosphoglucomutase, alpha-D-glucose phosphate-specific () links the anaerobic or aerobic glycolysis of glucose-6-phosphate and glucose-1-phosphate produced by various glycan phosphorylases by catalysing the transfer of a phosphate group between C-1 and C-6 of glucose . Alpha-D-glucose 1-phosphate = alpha-D-glucose 6-phosphate.; GO: 0004614 phosphoglucomutase activity, 0005975 carbohydrate metabolic process.
Probab=28.54 E-value=32 Score=14.99 Aligned_cols=27 Identities=19% Similarity=0.487 Sum_probs=15.7
Q ss_pred HHHHHHHHHHCCCHH-----HHHHHHHHHHHH
Q ss_conf 665433310001566-----899999999999
Q gi|254781218|r 10 SLKSLQEYTLIITPE-----IRQYWKDVGTRI 36 (205)
Q Consensus 10 ~~~~~~~~~~~~~~~-----~~~~~~~iG~ri 36 (205)
-+.++++..+.++.| --+||++||.+.
T Consensus 224 D~aaI~~Agl~lGvDPLGGa~v~YW~~Ia~~y 255 (553)
T TIGR01132 224 DLAAIRKAGLRLGVDPLGGAGVDYWKEIAEKY 255 (553)
T ss_pred EHHHHHHCCCEECCCCCCCCCHHHHHHHHHHH
T ss_conf 06678658977723467778736789999875
No 496
>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=28.45 E-value=42 Score=14.26 Aligned_cols=36 Identities=11% Similarity=-0.078 Sum_probs=0.0
Q ss_pred HCCCCHHHHHHHHCC-CHHHHHHHHCCCCCCCHHHHH
Q ss_conf 859988999998489-999999887799888999999
Q gi|254781218|r 42 ANNKTQKEMAIGANQ-LESAVNLFENGMCSTSIRYAL 77 (205)
Q Consensus 42 ~~gltQ~elA~~~gi-s~~~is~~E~G~~~psi~~l~ 77 (205)
..+|+-.++|..+|. ++++.++.-+-....+.....
T Consensus 6 ~~~~~i~~IA~~~g~~s~~~f~r~fk~~~G~tP~~~r 42 (43)
T pfam00165 6 STNWTIADIAEELGFSSQSYFSRLFKKYTGVTPSQYR 42 (43)
T ss_pred CCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHC
T ss_conf 0899799999996899768999999998890989982
No 497
>cd01422 MGS Methylglyoxal synthase catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The first part of the catalytic mechanism is believed to be similar to TIM (triosephosphate isomerase) in that both enzymes utilize DHAP to form an ene-diolate phosphate intermediate. In MGS, the second catalytic step is characterized by the elimination of phosphate and collapse of the enediolate to form methylglyoxal instead of reprotonation to form the isomer glyceraldehyde 3-phosphate, as in TIM. This is the first reaction in the methylglyoxal bypass of the Embden-Myerhoff glycolytic pathway and is believed to provide physiological benefits under non-ideal growth conditions in bacteria.
Probab=28.28 E-value=38 Score=14.51 Aligned_cols=18 Identities=22% Similarity=0.420 Sum_probs=0.0
Q ss_pred CCCHHHHHHHHHHHCCCH
Q ss_conf 889999999999828999
Q gi|254781218|r 70 STSIRYALYLRNEYEISF 87 (205)
Q Consensus 70 ~psi~~l~~la~~~~vs~ 87 (205)
.|++..|+++|..++|++
T Consensus 87 ~~Di~aLlRlc~v~niP~ 104 (115)
T cd01422 87 EPDVKALLRLCDVYNIPL 104 (115)
T ss_pred CCCHHHHHHHHHHCCCCC
T ss_conf 702999999998619612
No 498
>PRK04435 hypothetical protein; Provisional
Probab=28.22 E-value=33 Score=14.89 Aligned_cols=28 Identities=25% Similarity=0.307 Sum_probs=0.0
Q ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf 9999972983899999977999999997
Q gi|254781218|r 119 KSIRKDKGMSQIEFGKLLGMPNSTLSNY 146 (205)
Q Consensus 119 k~lR~~~glsq~elA~~lgis~~tis~~ 146 (205)
+-+...+-.+..|.++.+|+|++++.+|
T Consensus 26 ~LL~~g~~~~i~EAvk~vGISRSafYKY 53 (146)
T PRK04435 26 ELLKSGKVKSITEAVKQVGISRSAFYKY 53 (146)
T ss_pred HHHHCCCCCCHHHHHHHHCCCHHHEECC
T ss_conf 9997389774999999839652101123
No 499
>pfam04936 DUF658 Protein of unknown function (DUF658). Protein of unknown function found in Lactococcus lactis bacteriophages.
Probab=28.19 E-value=43 Score=14.23 Aligned_cols=27 Identities=4% Similarity=0.201 Sum_probs=0.0
Q ss_pred CHHHHHHHHCCCHHHHHHHHCCCCCCC
Q ss_conf 389999997799999999741488999
Q gi|254781218|r 128 SQIEFGKLLGMPNSTLSNYEQGRTIPE 154 (205)
Q Consensus 128 sq~elA~~lgis~~tis~~E~g~~~Ps 154 (205)
|..|+|+.+.+|+.+++-|-.....|.
T Consensus 16 TidElad~f~vs~~svs~WIknGk~~~ 42 (134)
T pfam04936 16 TIDEIADMFDLSPHSIAGWIKNGKANK 42 (134)
T ss_pred CHHHHHHHHCCCCHHHHHHHHCCCCCC
T ss_conf 399999997457014478886488862
No 500
>pfam01316 Arg_repressor Arginine repressor, DNA binding domain.
Probab=28.07 E-value=36 Score=14.65 Aligned_cols=18 Identities=28% Similarity=0.243 Sum_probs=0.0
Q ss_pred CHHHHHHHH-----CCCHHHHHH
Q ss_conf 889999984-----899999998
Q gi|254781218|r 46 TQKEMAIGA-----NQLESAVNL 63 (205)
Q Consensus 46 tQ~elA~~~-----gis~~~is~ 63 (205)
||+||...+ .+++++||+
T Consensus 21 tQ~eL~~~L~~~G~~vTQATlSR 43 (70)
T pfam01316 21 TQEELVALLKAEGINVTQATVSR 43 (70)
T ss_pred CHHHHHHHHHHCCCCEEEHHHHH
T ss_conf 99999999997698564178887
Done!