Query psy6501
Match_columns 174
No_of_seqs 155 out of 2262
Neff 8.2
Searched_HMMs 46136
Date Fri Aug 16 19:44:18 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6501.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6501hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PHA01976 helix-turn-helix prot 99.8 2.7E-19 6E-24 115.1 7.1 64 31-94 1-64 (67)
2 PF12844 HTH_19: Helix-turn-he 99.7 1.3E-17 2.8E-22 106.4 6.6 60 34-93 1-60 (64)
3 KOG3398|consensus 99.7 2.2E-17 4.9E-22 115.7 8.0 90 1-90 42-131 (135)
4 PRK09706 transcriptional repre 99.7 2.5E-16 5.4E-21 114.8 11.3 66 30-95 3-68 (135)
5 PF01381 HTH_3: Helix-turn-hel 99.7 7.1E-17 1.5E-21 99.8 6.3 55 37-91 1-55 (55)
6 PRK08359 transcription factor; 99.7 3.3E-16 7.2E-21 118.1 8.1 68 26-93 79-146 (176)
7 TIGR00270 conserved hypothetic 99.7 4.3E-16 9.4E-21 115.7 7.9 66 28-93 65-130 (154)
8 COG1476 Predicted transcriptio 99.6 5.4E-16 1.2E-20 98.9 6.2 58 36-93 5-62 (68)
9 TIGR03070 couple_hipB transcri 99.6 1.3E-15 2.7E-20 94.6 7.8 57 32-88 2-58 (58)
10 PRK09726 antitoxin HipB; Provi 99.6 3E-15 6.6E-20 101.5 9.0 64 30-93 10-73 (88)
11 PRK06424 transcription factor; 99.6 2.2E-15 4.8E-20 110.6 8.2 64 28-91 80-143 (144)
12 PRK08154 anaerobic benzoate ca 99.6 1.3E-15 2.9E-20 125.2 7.5 71 26-96 22-92 (309)
13 PF13560 HTH_31: Helix-turn-he 99.6 3.2E-15 6.8E-20 95.4 6.0 60 32-91 1-61 (64)
14 PRK13890 conjugal transfer pro 99.6 7.2E-15 1.6E-19 105.1 8.2 67 30-96 3-69 (120)
15 PRK09943 DNA-binding transcrip 99.6 8.1E-15 1.8E-19 112.1 7.9 67 28-94 3-69 (185)
16 TIGR02607 antidote_HigA addict 99.5 2.1E-14 4.5E-19 94.8 6.7 62 32-93 4-66 (78)
17 TIGR02612 mob_myst_A mobile my 99.5 8.6E-14 1.9E-18 102.9 7.3 62 35-96 28-91 (150)
18 TIGR02684 dnstrm_HI1420 probab 99.4 5.2E-13 1.1E-17 90.5 7.1 58 30-89 30-87 (89)
19 KOG3398|consensus 99.4 6.4E-13 1.4E-17 93.4 6.8 82 93-174 44-125 (135)
20 PRK10072 putative transcriptio 99.4 7.2E-13 1.6E-17 90.9 6.9 56 33-89 34-89 (96)
21 PF13443 HTH_26: Cro/C1-type H 99.3 3E-12 6.4E-17 81.1 6.5 58 36-93 1-59 (63)
22 PRK04140 hypothetical protein; 99.3 3.9E-12 8.6E-17 104.4 7.8 62 30-91 124-185 (317)
23 smart00530 HTH_XRE Helix-turn- 99.3 8.2E-12 1.8E-16 75.0 6.8 56 36-91 1-56 (56)
24 COG1813 Predicted transcriptio 99.3 1.2E-11 2.5E-16 91.8 8.0 70 26-95 73-142 (165)
25 TIGR03830 CxxCG_CxxCG_HTH puta 99.3 1.1E-11 2.3E-16 89.1 6.8 61 31-92 64-124 (127)
26 cd00093 HTH_XRE Helix-turn-hel 99.2 3.5E-11 7.6E-16 72.7 7.0 58 34-91 1-58 (58)
27 PRK10856 cytoskeletal protein 99.2 3.4E-11 7.5E-16 99.8 7.4 65 30-94 12-82 (331)
28 PHA01976 helix-turn-helix prot 99.2 7E-11 1.5E-15 75.7 6.7 52 123-174 3-54 (67)
29 PF13744 HTH_37: Helix-turn-he 99.2 1.5E-10 3.3E-15 77.0 7.1 61 29-89 15-76 (80)
30 PRK13355 bifunctional HTH-doma 99.1 1.1E-10 2.5E-15 102.0 7.9 66 31-96 2-72 (517)
31 TIGR03070 couple_hipB transcri 99.1 2.3E-10 5E-15 70.6 7.0 53 122-174 2-54 (58)
32 PF01381 HTH_3: Helix-turn-hel 99.1 1.7E-10 3.6E-15 71.0 5.7 48 127-174 1-48 (55)
33 PRK08359 transcription factor; 99.1 1.7E-10 3.6E-15 87.2 6.7 57 118-174 81-137 (176)
34 COG1813 Predicted transcriptio 99.1 2.6E-10 5.7E-15 84.7 6.5 58 117-174 74-131 (165)
35 PF12844 HTH_19: Helix-turn-he 99.1 3.6E-10 7.8E-15 71.7 5.9 51 124-174 1-51 (64)
36 PRK06424 transcription factor; 99.1 5.3E-10 1.2E-14 82.1 7.1 56 119-174 81-136 (144)
37 TIGR00270 conserved hypothetic 99.1 5.4E-10 1.2E-14 83.1 7.1 57 118-174 65-121 (154)
38 PF13560 HTH_31: Helix-turn-he 99.1 7.1E-10 1.5E-14 70.5 6.6 52 123-174 2-54 (64)
39 PHA00542 putative Cro-like pro 99.0 1E-09 2.2E-14 73.3 7.6 51 34-84 20-71 (82)
40 COG1476 Predicted transcriptio 99.0 8.7E-10 1.9E-14 70.4 6.1 50 125-174 4-53 (68)
41 COG3620 Predicted transcriptio 99.0 7.8E-10 1.7E-14 81.7 6.4 53 34-86 7-59 (187)
42 COG2944 Predicted transcriptio 99.0 2E-09 4.4E-14 74.3 6.3 45 34-78 46-90 (104)
43 smart00352 POU Found in Pit-Oc 98.9 5.4E-09 1.2E-13 67.9 7.6 42 30-71 9-56 (75)
44 PRK09726 antitoxin HipB; Provi 98.9 4.3E-09 9.2E-14 71.2 7.4 55 120-174 10-64 (88)
45 PF07022 Phage_CI_repr: Bacter 98.9 7.6E-10 1.6E-14 71.0 2.7 59 36-95 2-62 (66)
46 PRK09706 transcriptional repre 98.9 4.7E-09 1E-13 76.4 7.0 53 122-174 5-57 (135)
47 PRK02866 cyanate hydratase; Va 98.8 2.2E-08 4.7E-13 73.5 8.6 62 31-92 4-65 (147)
48 TIGR00673 cynS cyanate hydrata 98.8 3.9E-08 8.4E-13 72.3 8.6 60 33-92 9-68 (150)
49 TIGR02607 antidote_HigA addict 98.8 2.4E-08 5.2E-13 65.6 6.6 52 123-174 5-57 (78)
50 PRK13890 conjugal transfer pro 98.8 2.5E-08 5.5E-13 71.3 6.8 52 123-174 6-57 (120)
51 PRK10072 putative transcriptio 98.8 2.3E-08 5.1E-13 68.6 6.0 49 125-174 36-84 (96)
52 PRK09943 DNA-binding transcrip 98.8 2.9E-08 6.3E-13 75.9 7.2 54 121-174 6-59 (185)
53 COG1396 HipB Predicted transcr 98.7 6.4E-08 1.4E-12 64.0 7.5 61 33-93 2-63 (120)
54 COG1709 Predicted transcriptio 98.7 1.5E-08 3.3E-13 78.2 4.2 55 30-84 25-80 (241)
55 TIGR02684 dnstrm_HI1420 probab 98.7 5.9E-08 1.3E-12 65.8 6.3 53 120-174 30-82 (89)
56 COG3655 Predicted transcriptio 98.7 4.5E-08 9.8E-13 63.3 5.0 62 32-93 2-64 (73)
57 PRK08154 anaerobic benzoate ca 98.7 6.8E-08 1.5E-12 79.6 7.3 56 119-174 25-80 (309)
58 COG3093 VapI Plasmid maintenan 98.6 1.1E-07 2.4E-12 65.5 6.2 59 34-92 11-70 (104)
59 TIGR02612 mob_myst_A mobile my 98.6 2E-07 4.3E-12 69.1 6.9 51 124-174 27-79 (150)
60 PF13413 HTH_25: Helix-turn-he 98.6 1.4E-07 3E-12 59.7 5.2 55 36-90 1-61 (62)
61 PRK04140 hypothetical protein; 98.6 1.9E-07 4.1E-12 77.0 6.8 54 121-174 125-178 (317)
62 COG1395 Predicted transcriptio 98.5 2.4E-07 5.2E-12 75.4 6.6 56 33-88 126-181 (313)
63 PHA00542 putative Cro-like pro 98.5 5.5E-07 1.2E-11 60.1 6.5 49 126-174 22-71 (82)
64 smart00530 HTH_XRE Helix-turn- 98.4 1.3E-06 2.8E-11 51.7 6.4 48 127-174 2-49 (56)
65 TIGR03830 CxxCG_CxxCG_HTH puta 98.4 1.1E-06 2.3E-11 62.9 6.5 50 123-173 66-115 (127)
66 COG1709 Predicted transcriptio 98.3 4.5E-07 9.7E-12 70.1 4.0 56 119-174 24-80 (241)
67 PF08667 BetR: BetR domain; I 98.3 2E-06 4.3E-11 63.2 7.1 64 30-93 3-70 (147)
68 cd00093 HTH_XRE Helix-turn-hel 98.3 2.5E-06 5.5E-11 50.8 6.2 50 125-174 2-51 (58)
69 COG2944 Predicted transcriptio 98.3 1.7E-06 3.7E-11 59.8 5.9 45 124-168 46-90 (104)
70 COG1426 Predicted transcriptio 98.3 1.5E-06 3.3E-11 70.8 6.0 63 31-93 2-70 (284)
71 COG5499 Predicted transcriptio 98.3 1.9E-06 4.2E-11 59.5 5.4 58 34-92 62-119 (120)
72 PF13443 HTH_26: Cro/C1-type H 98.2 3.3E-06 7.2E-11 53.0 5.3 48 127-174 2-50 (63)
73 cd01392 HTH_LacI Helix-turn-he 98.2 2.9E-06 6.3E-11 51.2 4.6 43 50-92 2-47 (52)
74 PRK10856 cytoskeletal protein 98.2 4.4E-06 9.4E-11 69.5 6.8 53 122-174 14-72 (331)
75 PRK02866 cyanate hydratase; Va 98.2 1E-05 2.2E-10 59.5 7.3 53 122-174 5-57 (147)
76 TIGR01321 TrpR trp operon repr 98.1 1.8E-05 3.9E-10 53.8 6.7 48 32-79 40-89 (94)
77 smart00352 POU Found in Pit-Oc 98.0 1.2E-05 2.5E-10 52.4 5.1 43 121-163 10-58 (75)
78 PF13744 HTH_37: Helix-turn-he 98.0 2.4E-05 5.1E-10 51.9 6.7 55 120-174 16-71 (80)
79 TIGR00673 cynS cyanate hydrata 98.0 3.4E-05 7.3E-10 56.9 7.0 52 123-174 9-60 (150)
80 PRK08099 bifunctional DNA-bind 97.8 4.2E-05 9E-10 65.3 5.4 46 44-89 2-48 (399)
81 PHA01083 hypothetical protein 97.7 8.6E-05 1.9E-09 54.3 5.8 58 35-92 5-65 (149)
82 COG2522 Predicted transcriptio 97.7 0.00011 2.5E-09 52.1 6.0 38 34-72 12-49 (119)
83 COG1396 HipB Predicted transcr 97.6 0.00043 9.4E-09 45.1 6.9 51 123-173 2-53 (120)
84 COG4800 Predicted transcriptio 97.5 0.00051 1.1E-08 49.8 7.4 54 30-84 14-67 (170)
85 PF08965 DUF1870: Domain of un 97.5 0.00037 8.1E-09 49.3 6.4 54 34-87 3-58 (118)
86 smart00354 HTH_LACI helix_turn 97.5 0.00033 7.2E-09 45.1 5.7 45 46-90 1-48 (70)
87 COG1395 Predicted transcriptio 97.5 0.00023 5.1E-09 58.2 6.0 51 124-174 127-177 (313)
88 PF00356 LacI: Bacterial regul 97.5 0.00048 1E-08 40.8 5.6 37 47-83 1-37 (46)
89 COG3093 VapI Plasmid maintenan 97.5 0.00038 8.1E-09 48.1 5.8 52 123-174 10-62 (104)
90 PF13413 HTH_25: Helix-turn-he 97.5 0.00048 1E-08 43.4 5.7 44 126-169 1-46 (62)
91 PHA00675 hypothetical protein 97.4 0.0006 1.3E-08 44.4 5.6 48 23-70 17-64 (78)
92 TIGR03879 near_KaiC_dom probab 97.4 0.001 2.3E-08 43.2 6.4 43 37-81 24-66 (73)
93 PF04552 Sigma54_DBD: Sigma-54 97.2 0.00012 2.6E-09 54.8 1.0 104 42-163 46-154 (160)
94 PF07022 Phage_CI_repr: Bacter 97.2 0.00035 7.5E-09 44.5 2.8 47 126-173 2-50 (66)
95 PF00157 Pou: Pou domain - N-t 97.2 0.0025 5.3E-08 41.6 6.7 50 31-82 10-65 (75)
96 COG5606 Uncharacterized conser 97.1 0.0012 2.5E-08 44.1 4.9 61 29-89 25-86 (91)
97 PF13693 HTH_35: Winged helix- 97.1 0.0011 2.3E-08 43.7 4.7 56 35-93 5-60 (78)
98 PF08965 DUF1870: Domain of un 97.1 0.0015 3.3E-08 46.2 5.7 47 126-172 5-53 (118)
99 COG3423 Nlp Predicted transcri 97.0 0.0031 6.7E-08 41.0 5.9 55 36-93 12-66 (82)
100 TIGR01321 TrpR trp operon repr 97.0 0.004 8.7E-08 42.4 6.6 41 133-173 53-93 (94)
101 TIGR02147 Fsuc_second hypothet 96.9 0.0019 4.1E-08 52.4 5.7 46 45-90 27-73 (271)
102 PRK03975 tfx putative transcri 96.9 0.0019 4.2E-08 47.3 4.8 49 43-92 19-70 (141)
103 COG3655 Predicted transcriptio 96.9 0.0033 7.1E-08 40.8 5.3 49 126-174 6-55 (73)
104 PF13384 HTH_23: Homeodomain-l 96.9 0.0022 4.8E-08 38.1 4.3 24 45-68 17-40 (50)
105 TIGR00721 tfx DNA-binding prot 96.9 0.0022 4.8E-08 46.8 4.9 32 36-68 13-44 (137)
106 PF13936 HTH_38: Helix-turn-he 96.7 0.0021 4.6E-08 37.6 3.0 29 37-66 13-41 (44)
107 PHA02591 hypothetical protein; 96.6 0.0045 9.7E-08 40.4 4.5 28 40-67 54-81 (83)
108 COG2522 Predicted transcriptio 96.6 0.01 2.2E-07 42.2 6.5 42 121-162 8-49 (119)
109 cd01392 HTH_LacI Helix-turn-he 96.6 0.0038 8.3E-08 37.3 3.8 34 140-173 2-35 (52)
110 TIGR02293 TAS_TIGR02293 putati 96.5 0.012 2.5E-07 42.7 6.8 53 34-86 25-77 (133)
111 PF14549 P22_Cro: DNA-binding 96.5 0.0052 1.1E-07 38.4 4.3 36 44-83 9-44 (60)
112 COG3636 Predicted transcriptio 96.5 0.016 3.4E-07 39.5 6.8 56 33-90 39-94 (100)
113 PHA01083 hypothetical protein 96.4 0.011 2.4E-07 43.4 5.9 50 125-174 5-56 (149)
114 PF02796 HTH_7: Helix-turn-hel 96.4 0.0053 1.1E-07 36.0 3.4 33 34-67 11-43 (45)
115 PF00356 LacI: Bacterial regul 96.4 0.015 3.2E-07 34.4 5.2 37 137-173 1-37 (46)
116 PF13412 HTH_24: Winged helix- 96.3 0.011 2.5E-07 34.7 4.8 33 34-66 6-38 (48)
117 PF08535 KorB: KorB domain; I 96.3 0.0036 7.8E-08 42.5 2.9 29 43-71 1-29 (93)
118 PF01710 HTH_Tnp_IS630: Transp 96.3 0.02 4.3E-07 40.6 6.7 88 31-156 5-92 (119)
119 PRK10344 DNA-binding transcrip 96.1 0.021 4.6E-07 38.4 5.7 56 35-93 11-66 (92)
120 cd04763 HTH_MlrA-like Helix-Tu 96.1 0.072 1.6E-06 33.7 8.0 22 46-67 1-22 (68)
121 PF04545 Sigma70_r4: Sigma-70, 96.0 0.017 3.7E-07 34.3 4.5 32 36-67 11-42 (50)
122 PF07037 DUF1323: Putative tra 96.0 0.0066 1.4E-07 42.9 2.8 24 46-69 1-24 (122)
123 PF04814 HNF-1_N: Hepatocyte n 96.0 0.013 2.7E-07 44.5 4.5 38 30-67 116-153 (180)
124 PRK01381 Trp operon repressor; 96.0 0.021 4.6E-07 39.2 5.2 56 31-86 39-96 (99)
125 TIGR02844 spore_III_D sporulat 95.9 0.083 1.8E-06 35.0 7.8 49 36-85 11-60 (80)
126 COG4197 Uncharacterized protei 95.9 0.0068 1.5E-07 40.9 2.5 46 47-92 14-61 (96)
127 smart00354 HTH_LACI helix_turn 95.9 0.021 4.7E-07 36.5 4.8 38 136-173 1-38 (70)
128 PF06056 Terminase_5: Putative 95.8 0.011 2.5E-07 36.6 3.1 27 43-69 11-37 (58)
129 cd04762 HTH_MerR-trunc Helix-T 95.8 0.017 3.6E-07 33.4 3.7 27 46-72 1-27 (49)
130 PF05269 Phage_CII: Bacterioph 95.8 0.0038 8.3E-08 42.3 0.9 45 40-88 18-62 (91)
131 COG1191 FliA DNA-directed RNA 95.7 0.19 4E-06 40.3 10.4 122 30-157 83-234 (247)
132 COG1356 tfx Transcriptional re 95.7 0.0092 2E-07 42.6 2.6 50 42-92 20-72 (143)
133 TIGR02531 yecD_yerC TrpR-relat 95.7 0.023 5E-07 38.3 4.5 28 41-68 46-73 (88)
134 PF08523 MBF1: Multiprotein br 95.7 0.0029 6.3E-08 40.9 0.1 29 1-29 42-71 (71)
135 PRK10014 DNA-binding transcrip 95.6 0.031 6.8E-07 45.7 6.0 45 45-89 6-53 (342)
136 PF13551 HTH_29: Winged helix- 95.6 0.18 3.8E-06 34.5 9.0 27 42-68 8-35 (112)
137 PHA00675 hypothetical protein 95.6 0.043 9.4E-07 35.8 5.1 43 118-160 22-64 (78)
138 COG4800 Predicted transcriptio 95.5 0.064 1.4E-06 39.1 6.4 51 122-173 16-66 (170)
139 TIGR01610 phage_O_Nterm phage 95.5 0.023 5E-07 38.7 3.9 54 12-65 6-67 (95)
140 PRK09492 treR trehalose repres 95.5 0.029 6.3E-07 45.4 5.3 45 45-89 4-51 (315)
141 PRK11303 DNA-binding transcrip 95.4 0.034 7.3E-07 45.3 5.5 44 46-89 1-50 (328)
142 PF05225 HTH_psq: helix-turn-h 95.4 0.037 7.9E-07 32.5 4.0 38 32-70 4-41 (45)
143 PRK05932 RNA polymerase factor 95.4 0.011 2.5E-07 51.3 2.6 103 44-164 342-449 (455)
144 TIGR02405 trehalos_R_Ecol treh 95.4 0.039 8.4E-07 44.8 5.6 45 46-90 2-49 (311)
145 TIGR03879 near_KaiC_dom probab 95.3 0.093 2E-06 34.1 6.1 44 125-170 22-65 (73)
146 PF02001 DUF134: Protein of un 95.3 0.057 1.2E-06 37.7 5.4 38 40-84 52-89 (106)
147 PF02376 CUT: CUT domain; Int 95.3 0.05 1.1E-06 36.6 5.0 38 30-67 11-49 (87)
148 TIGR02395 rpoN_sigma RNA polym 95.3 0.012 2.6E-07 50.8 2.5 103 44-163 317-424 (429)
149 PRK09526 lacI lac repressor; R 95.3 0.028 6.2E-07 46.0 4.6 47 44-90 4-53 (342)
150 PRK08558 adenine phosphoribosy 95.3 0.074 1.6E-06 42.4 6.7 53 33-87 13-65 (238)
151 PF04218 CENP-B_N: CENP-B N-te 95.2 0.018 4E-07 34.9 2.5 28 42-69 19-46 (53)
152 PF01371 Trp_repressor: Trp re 95.2 0.062 1.3E-06 36.1 5.3 36 31-66 33-70 (87)
153 PF10668 Phage_terminase: Phag 95.2 0.024 5.2E-07 35.4 3.0 24 44-67 21-44 (60)
154 TIGR01481 ccpA catabolite cont 95.2 0.044 9.6E-07 44.6 5.5 45 46-90 2-49 (329)
155 PRK10703 DNA-binding transcrip 95.2 0.045 9.7E-07 44.9 5.5 44 46-89 2-48 (341)
156 PRK04217 hypothetical protein; 95.2 0.084 1.8E-06 37.1 6.0 77 8-92 22-98 (110)
157 COG2842 Uncharacterized ATPase 95.1 0.068 1.5E-06 43.8 6.2 62 28-90 2-64 (297)
158 PRK13698 plasmid-partitioning 95.1 0.045 9.8E-07 45.4 5.1 43 30-72 160-203 (323)
159 COG2390 DeoR Transcriptional r 95.1 0.15 3.3E-06 42.4 8.2 64 30-93 11-87 (321)
160 cd01104 HTH_MlrA-CarA Helix-Tu 95.0 0.037 8E-07 34.8 3.6 22 46-67 1-22 (68)
161 cd04764 HTH_MlrA-like_sg1 Heli 95.0 0.068 1.5E-06 33.6 4.8 22 46-67 1-22 (67)
162 PF00325 Crp: Bacterial regula 94.9 0.034 7.4E-07 30.2 2.7 22 45-66 2-23 (32)
163 cd04761 HTH_MerR-SF Helix-Turn 94.9 0.048 1E-06 31.8 3.7 27 46-72 1-27 (49)
164 COG5499 Predicted transcriptio 94.9 0.075 1.6E-06 37.0 5.1 53 121-174 59-111 (120)
165 PRK10727 DNA-binding transcrip 94.9 0.055 1.2E-06 44.5 5.3 45 46-90 2-49 (343)
166 TIGR01764 excise DNA binding d 94.9 0.046 1E-06 31.6 3.5 28 46-73 2-29 (49)
167 cd00569 HTH_Hin_like Helix-tur 94.9 0.13 2.8E-06 27.0 5.2 23 43-65 19-41 (42)
168 PF08279 HTH_11: HTH domain; 94.8 0.043 9.3E-07 33.1 3.4 31 36-66 5-36 (55)
169 PRK10401 DNA-binding transcrip 94.8 0.066 1.4E-06 44.0 5.6 44 46-89 2-48 (346)
170 cd04774 HTH_YfmP Helix-Turn-He 94.8 0.19 4E-06 34.3 6.9 24 46-69 1-24 (96)
171 cd04765 HTH_MlrA-like_sg2 Heli 94.8 0.5 1.1E-05 32.4 9.0 22 46-67 1-22 (99)
172 PRK14987 gluconate operon tran 94.8 0.049 1.1E-06 44.5 4.7 45 45-89 5-52 (331)
173 PRK12469 RNA polymerase factor 94.8 0.026 5.6E-07 49.4 3.1 104 43-164 367-475 (481)
174 PF02954 HTH_8: Bacterial regu 94.7 0.096 2.1E-06 30.0 4.4 31 34-64 7-37 (42)
175 TIGR00180 parB_part ParB-like 94.6 0.084 1.8E-06 40.3 5.3 52 30-82 105-156 (187)
176 TIGR02417 fruct_sucro_rep D-fr 94.6 0.076 1.6E-06 43.2 5.3 44 47-90 1-50 (327)
177 cd04778 HTH_MerR-like_sg2 Heli 94.6 0.7 1.5E-05 36.4 10.5 24 46-69 2-25 (219)
178 PRK09744 DNA-binding transcrip 94.5 0.061 1.3E-06 34.8 3.6 34 47-83 12-45 (75)
179 COG1342 Predicted DNA-binding 94.5 0.11 2.4E-06 35.4 4.9 43 34-84 39-81 (99)
180 COG1609 PurR Transcriptional r 94.5 0.082 1.8E-06 43.9 5.4 46 46-91 1-49 (333)
181 PF12728 HTH_17: Helix-turn-he 94.5 0.066 1.4E-06 31.8 3.6 29 46-74 2-30 (51)
182 TIGR03764 ICE_PFGI_1_parB inte 94.4 0.091 2E-06 42.3 5.2 51 31-81 116-177 (258)
183 COG1513 CynS Cyanate lyase [In 94.4 0.21 4.5E-06 36.0 6.4 62 31-92 7-68 (151)
184 PF13518 HTH_28: Helix-turn-he 94.4 0.1 2.3E-06 30.7 4.3 24 44-67 11-34 (52)
185 KOG3802|consensus 94.4 0.066 1.4E-06 45.3 4.4 54 30-85 208-267 (398)
186 PF13936 HTH_38: Helix-turn-he 94.3 0.062 1.3E-06 31.2 3.1 31 125-156 11-41 (44)
187 PRK15418 transcriptional regul 94.3 0.066 1.4E-06 44.4 4.4 60 33-92 17-89 (318)
188 PF01047 MarR: MarR family; I 94.3 0.068 1.5E-06 32.6 3.4 32 35-66 7-38 (59)
189 PF00376 MerR: MerR family reg 94.3 0.064 1.4E-06 30.3 3.0 25 47-71 1-25 (38)
190 PF13613 HTH_Tnp_4: Helix-turn 94.2 0.07 1.5E-06 32.2 3.3 29 39-67 13-41 (53)
191 PF04967 HTH_10: HTH DNA bindi 94.2 0.062 1.4E-06 32.7 3.0 23 44-66 22-44 (53)
192 cd00131 PAX Paired Box domain 94.2 1.5 3.2E-05 31.5 11.1 35 32-67 21-55 (128)
193 cd01105 HTH_GlnR-like Helix-Tu 94.1 0.15 3.2E-06 34.2 5.0 24 45-68 1-24 (88)
194 KOG1168|consensus 94.1 0.029 6.4E-07 45.5 1.8 39 31-69 220-267 (385)
195 PRK10339 DNA-binding transcrip 94.1 0.059 1.3E-06 44.0 3.7 45 46-90 2-51 (327)
196 cd06171 Sigma70_r4 Sigma70, re 94.0 0.15 3.3E-06 29.5 4.4 29 39-67 20-48 (55)
197 PF13384 HTH_23: Homeodomain-l 93.9 0.12 2.5E-06 30.5 3.8 24 135-158 17-40 (50)
198 PF08667 BetR: BetR domain; I 93.9 0.3 6.4E-06 36.1 6.7 52 123-174 6-61 (147)
199 cd04782 HTH_BltR Helix-Turn-He 93.9 0.21 4.7E-06 34.0 5.6 22 46-67 1-22 (97)
200 cd04787 HTH_HMRTR_unk Helix-Tu 93.9 0.36 7.8E-06 34.8 7.0 46 46-91 1-63 (133)
201 PF13411 MerR_1: MerR HTH fami 93.8 0.064 1.4E-06 33.8 2.7 25 46-70 1-25 (69)
202 smart00342 HTH_ARAC helix_turn 93.8 0.95 2.1E-05 28.6 8.5 22 45-66 1-22 (84)
203 COG1191 FliA DNA-directed RNA 93.8 0.1 2.2E-06 41.9 4.3 45 34-85 201-245 (247)
204 cd04784 HTH_CadR-PbrR Helix-Tu 93.6 0.16 3.5E-06 36.3 4.7 46 46-91 1-63 (127)
205 cd01109 HTH_YyaN Helix-Turn-He 93.5 0.25 5.4E-06 34.5 5.6 46 46-91 1-63 (113)
206 cd04788 HTH_NolA-AlbR Helix-Tu 93.5 0.21 4.6E-06 33.9 5.0 22 46-67 1-22 (96)
207 cd04767 HTH_HspR-like_MBC Heli 93.5 0.49 1.1E-05 33.7 7.0 71 46-150 2-72 (120)
208 PRK12427 flagellar biosynthesi 93.4 1.3 2.8E-05 34.9 10.0 32 126-157 190-221 (231)
209 cd04768 HTH_BmrR-like Helix-Tu 93.4 0.24 5.1E-06 33.7 5.1 23 46-68 1-23 (96)
210 PRK03975 tfx putative transcri 93.4 0.16 3.5E-06 37.2 4.5 26 133-158 19-44 (141)
211 PHA02591 hypothetical protein; 93.3 0.21 4.5E-06 32.7 4.4 29 129-157 53-81 (83)
212 PF13404 HTH_AsnC-type: AsnC-t 93.3 0.19 4.2E-06 28.9 3.9 30 35-64 7-36 (42)
213 TIGR02147 Fsuc_second hypothet 93.3 0.31 6.7E-06 39.6 6.5 41 134-174 26-67 (271)
214 PRK10423 transcriptional repre 93.3 0.16 3.5E-06 41.2 5.0 41 49-89 2-45 (327)
215 TIGR02293 TAS_TIGR02293 putati 93.3 0.43 9.4E-06 34.5 6.6 48 126-173 27-74 (133)
216 PF01527 HTH_Tnp_1: Transposas 93.3 0.15 3.2E-06 32.7 3.7 32 36-67 14-45 (76)
217 cd00092 HTH_CRP helix_turn_hel 93.2 0.28 6E-06 30.3 4.9 24 43-66 23-46 (67)
218 TIGR02844 spore_III_D sporulat 93.2 0.75 1.6E-05 30.4 7.1 48 124-172 9-57 (80)
219 cd06571 Bac_DnaA_C C-terminal 93.2 0.53 1.1E-05 31.5 6.5 61 75-154 3-64 (90)
220 cd01106 HTH_TipAL-Mta Helix-Tu 93.2 0.27 5.9E-06 33.7 5.2 22 46-67 1-22 (103)
221 smart00422 HTH_MERR helix_turn 93.1 0.16 3.5E-06 31.9 3.8 22 46-67 1-22 (70)
222 PF14549 P22_Cro: DNA-binding 93.1 0.1 2.2E-06 32.6 2.7 27 137-165 11-37 (60)
223 PF08281 Sigma70_r4_2: Sigma-7 93.1 0.18 4E-06 30.1 3.8 32 35-66 16-47 (54)
224 smart00351 PAX Paired Box doma 93.1 0.32 6.9E-06 34.8 5.6 38 29-67 18-55 (125)
225 PRK10458 DNA cytosine methylas 93.0 0.37 7.9E-06 42.2 6.8 49 36-84 20-77 (467)
226 TIGR02997 Sig70-cyanoRpoD RNA 93.0 0.37 8.1E-06 39.4 6.6 25 133-157 267-291 (298)
227 PF01418 HTH_6: Helix-turn-hel 92.9 0.18 3.8E-06 32.9 3.7 47 32-78 20-67 (77)
228 PRK00118 putative DNA-binding 92.9 0.25 5.5E-06 34.3 4.6 47 36-86 24-70 (104)
229 cd04786 HTH_MerR-like_sg7 Heli 92.8 1.4 3.1E-05 31.7 8.7 46 46-91 1-63 (131)
230 PRK08558 adenine phosphoribosy 92.8 0.36 7.7E-06 38.5 6.0 36 136-171 24-59 (238)
231 cd01111 HTH_MerD Helix-Turn-He 92.7 0.26 5.7E-06 34.3 4.6 22 46-67 1-22 (107)
232 cd04775 HTH_Cfa-like Helix-Tur 92.7 0.31 6.7E-06 33.5 4.9 22 46-67 2-23 (102)
233 PF13412 HTH_24: Winged helix- 92.7 0.39 8.4E-06 28.0 4.7 33 124-156 6-38 (48)
234 smart00421 HTH_LUXR helix_turn 92.6 0.17 3.7E-06 29.8 3.2 25 43-67 16-40 (58)
235 smart00550 Zalpha Z-DNA-bindin 92.6 0.27 5.9E-06 31.3 4.2 28 38-65 13-42 (68)
236 PRK09413 IS2 repressor TnpA; R 92.5 0.37 8E-06 34.1 5.3 38 30-67 14-51 (121)
237 PF13545 HTH_Crp_2: Crp-like h 92.5 0.16 3.5E-06 32.4 3.1 23 44-66 27-49 (76)
238 PF05225 HTH_psq: helix-turn-h 92.4 0.29 6.3E-06 28.6 3.9 38 122-160 4-41 (45)
239 TIGR02479 FliA_WhiG RNA polyme 92.4 0.52 1.1E-05 36.7 6.5 29 129-157 185-213 (224)
240 TIGR00721 tfx DNA-binding prot 92.3 0.33 7.1E-06 35.5 4.8 26 133-158 19-44 (137)
241 PRK07408 RNA polymerase sigma 92.2 1.1 2.5E-05 35.7 8.4 29 129-157 213-241 (256)
242 cd01282 HTH_MerR-like_sg3 Heli 92.2 0.42 9.1E-06 33.4 5.2 46 46-91 1-62 (112)
243 PF10078 DUF2316: Uncharacteri 92.2 0.57 1.2E-05 31.6 5.5 54 33-87 11-64 (89)
244 PF06056 Terminase_5: Putative 92.2 0.18 4E-06 31.2 2.9 27 133-159 11-37 (58)
245 PRK07598 RNA polymerase sigma 92.2 0.51 1.1E-05 40.6 6.6 24 134-157 369-392 (415)
246 PF14590 DUF4447: Domain of un 92.2 0.76 1.7E-05 33.0 6.4 41 34-74 9-49 (166)
247 TIGR02044 CueR Cu(I)-responsiv 92.0 0.47 1E-05 33.9 5.4 46 46-91 1-63 (127)
248 PRK13752 putative transcriptio 92.0 1 2.2E-05 33.0 7.3 47 45-91 7-70 (144)
249 TIGR02051 MerR Hg(II)-responsi 92.0 0.91 2E-05 32.3 6.8 21 47-67 1-21 (124)
250 TIGR02047 CadR-PbrR Cd(II)/Pb( 92.0 0.54 1.2E-05 33.7 5.6 46 46-91 1-63 (127)
251 PRK11511 DNA-binding transcrip 92.0 3 6.5E-05 29.6 9.5 23 45-67 25-47 (127)
252 PF08535 KorB: KorB domain; I 91.9 0.13 2.8E-06 34.7 2.2 31 133-163 1-31 (93)
253 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 91.9 0.35 7.5E-06 29.1 3.8 32 38-69 13-44 (50)
254 COG2512 Predicted membrane-ass 91.9 0.34 7.4E-06 39.1 4.9 50 17-66 181-231 (258)
255 COG2973 TrpR Trp operon repres 91.9 0.89 1.9E-05 31.1 6.1 54 31-84 44-99 (103)
256 smart00419 HTH_CRP helix_turn_ 91.9 0.22 4.9E-06 28.6 3.0 23 44-66 7-29 (48)
257 cd04773 HTH_TioE_rpt2 Second H 91.9 0.26 5.7E-06 34.3 3.8 24 46-69 1-24 (108)
258 cd00592 HTH_MerR-like Helix-Tu 91.7 0.53 1.1E-05 31.9 5.1 22 46-67 1-22 (100)
259 cd01108 HTH_CueR Helix-Turn-He 91.6 0.52 1.1E-05 33.7 5.3 46 46-91 1-63 (127)
260 PF12802 MarR_2: MarR family; 91.6 0.23 4.9E-06 30.4 3.0 32 35-66 9-42 (62)
261 PF07900 DUF1670: Protein of u 91.5 0.34 7.4E-06 38.0 4.3 105 39-156 98-218 (220)
262 cd04770 HTH_HMRTR Helix-Turn-H 91.4 0.67 1.5E-05 32.7 5.6 46 46-91 1-63 (123)
263 PRK05911 RNA polymerase sigma 91.4 0.82 1.8E-05 36.6 6.7 31 127-157 213-243 (257)
264 TIGR02392 rpoH_proteo alternat 91.4 0.6 1.3E-05 37.6 5.9 24 134-157 235-258 (270)
265 cd04785 HTH_CadR-PbrR-like Hel 91.4 0.65 1.4E-05 33.1 5.5 46 46-91 1-63 (126)
266 smart00420 HTH_DEOR helix_turn 91.3 0.55 1.2E-05 27.3 4.4 27 40-66 9-35 (53)
267 PRK04132 replication factor C 91.3 0.6 1.3E-05 43.7 6.5 44 48-91 420-463 (846)
268 PRK10227 DNA-binding transcrip 91.2 0.67 1.5E-05 33.6 5.5 46 46-91 1-63 (135)
269 TIGR02054 MerD mercuric resist 91.2 0.53 1.2E-05 33.5 4.8 47 45-91 3-66 (120)
270 PF07638 Sigma70_ECF: ECF sigm 91.2 0.38 8.3E-06 36.5 4.4 32 35-66 141-172 (185)
271 TIGR02885 spore_sigF RNA polym 91.0 6.1 0.00013 30.7 11.8 29 129-157 193-221 (231)
272 PF00157 Pou: Pou domain - N-t 91.0 0.43 9.3E-06 31.1 3.8 40 121-160 10-55 (75)
273 PF05930 Phage_AlpA: Prophage 91.0 0.07 1.5E-06 32.0 0.1 29 46-74 4-32 (51)
274 COG1522 Lrp Transcriptional re 90.9 0.62 1.3E-05 33.8 5.2 32 34-65 11-42 (154)
275 cd01110 HTH_SoxR Helix-Turn-He 90.9 0.52 1.1E-05 34.3 4.7 45 46-90 2-62 (139)
276 PF13022 HTH_Tnp_1_2: Helix-tu 90.9 0.23 5E-06 36.3 2.7 26 44-69 33-58 (142)
277 PF02796 HTH_7: Helix-turn-hel 90.9 0.61 1.3E-05 27.0 4.1 25 133-157 19-43 (45)
278 PRK07405 RNA polymerase sigma 90.9 0.62 1.4E-05 38.6 5.7 24 134-157 275-298 (317)
279 PRK09514 zntR zinc-responsive 90.8 0.64 1.4E-05 33.9 5.1 46 46-91 2-64 (140)
280 PF13542 HTH_Tnp_ISL3: Helix-t 90.8 1 2.3E-05 26.5 5.2 35 31-66 14-48 (52)
281 cd04762 HTH_MerR-trunc Helix-T 90.8 0.4 8.7E-06 27.3 3.3 28 136-163 1-28 (49)
282 TIGR02885 spore_sigF RNA polym 90.7 0.48 1E-05 37.1 4.7 29 39-67 193-221 (231)
283 PF08220 HTH_DeoR: DeoR-like h 90.7 0.35 7.7E-06 29.6 3.1 30 36-65 5-34 (57)
284 PRK13749 transcriptional regul 90.6 0.9 2E-05 32.4 5.6 47 45-91 3-66 (121)
285 TIGR02394 rpoS_proteo RNA poly 90.6 0.37 8E-06 39.1 4.1 46 43-92 240-285 (285)
286 PF00165 HTH_AraC: Bacterial r 90.6 0.37 8E-06 27.3 2.9 25 43-67 6-30 (42)
287 cd04790 HTH_Cfa-like_unk Helix 90.6 0.78 1.7E-05 34.6 5.5 46 46-91 2-64 (172)
288 PRK13355 bifunctional HTH-doma 90.5 0.3 6.5E-06 42.9 3.7 29 146-174 32-60 (517)
289 TIGR02980 SigBFG RNA polymeras 90.5 2.7 5.8E-05 32.6 8.7 38 119-157 179-216 (227)
290 TIGR01636 phage_rinA phage tra 90.5 1.1 2.4E-05 32.3 6.1 34 46-86 101-134 (134)
291 TIGR02043 ZntR Zn(II)-responsi 90.5 0.73 1.6E-05 33.1 5.1 46 46-91 2-64 (131)
292 TIGR02850 spore_sigG RNA polym 90.4 3.5 7.6E-05 32.8 9.5 37 120-157 208-244 (254)
293 cd04783 HTH_MerR1 Helix-Turn-H 90.4 0.8 1.7E-05 32.6 5.2 46 46-91 1-63 (126)
294 PRK06596 RNA polymerase factor 90.3 1.3 2.7E-05 36.1 7.0 24 134-157 247-270 (284)
295 TIGR02393 RpoD_Cterm RNA polym 90.3 0.76 1.7E-05 36.2 5.5 25 133-157 194-218 (238)
296 PF09339 HTH_IclR: IclR helix- 90.2 0.26 5.6E-06 29.4 2.2 23 44-66 17-39 (52)
297 PRK13869 plasmid-partitioning 90.2 1 2.2E-05 38.6 6.6 59 28-86 21-101 (405)
298 cd04789 HTH_Cfa Helix-Turn-Hel 90.2 0.48 1E-05 32.5 3.8 25 46-70 2-26 (102)
299 PRK09744 DNA-binding transcrip 90.1 0.49 1.1E-05 30.7 3.4 29 137-167 12-40 (75)
300 PRK11512 DNA-binding transcrip 90.1 0.81 1.7E-05 33.1 5.1 43 24-66 33-75 (144)
301 cd01107 HTH_BmrR Helix-Turn-He 90.0 0.48 1E-05 32.8 3.7 23 46-68 1-23 (108)
302 cd04772 HTH_TioE_rpt1 First He 89.9 0.52 1.1E-05 32.2 3.8 27 46-72 1-27 (99)
303 PF04545 Sigma70_r4: Sigma-70, 89.9 1.1 2.4E-05 26.3 4.7 33 125-157 10-42 (50)
304 PRK10219 DNA-binding transcrip 89.9 4.6 0.0001 27.4 9.0 35 44-92 20-54 (107)
305 cd04764 HTH_MlrA-like_sg1 Heli 89.8 0.51 1.1E-05 29.5 3.4 22 136-157 1-22 (67)
306 PF13011 LZ_Tnp_IS481: leucine 89.7 0.85 1.8E-05 30.5 4.4 33 35-67 13-47 (85)
307 cd04761 HTH_MerR-SF Helix-Turn 89.6 0.6 1.3E-05 27.0 3.4 27 136-162 1-27 (49)
308 PF02954 HTH_8: Bacterial regu 89.5 1.1 2.3E-05 25.6 4.3 31 124-154 7-37 (42)
309 COG1508 RpoN DNA-directed RNA 89.4 0.66 1.4E-05 40.2 4.7 102 46-164 331-437 (444)
310 COG0789 SoxR Predicted transcr 89.3 0.87 1.9E-05 31.9 4.7 46 46-91 1-63 (124)
311 cd01279 HTH_HspR-like Helix-Tu 89.2 0.62 1.4E-05 31.8 3.7 24 46-69 2-25 (98)
312 cd04780 HTH_MerR-like_sg5 Heli 89.2 0.64 1.4E-05 31.6 3.8 27 46-72 1-27 (95)
313 PRK15043 transcriptional regul 89.0 0.69 1.5E-05 37.0 4.3 47 45-91 3-66 (243)
314 cd06170 LuxR_C_like C-terminal 89.0 0.6 1.3E-05 27.5 3.1 25 43-67 13-37 (57)
315 cd01104 HTH_MlrA-CarA Helix-Tu 89.0 0.63 1.4E-05 29.0 3.4 22 136-157 1-22 (68)
316 PF12840 HTH_20: Helix-turn-he 88.8 0.67 1.4E-05 28.5 3.3 29 36-64 15-43 (61)
317 PF00376 MerR: MerR family reg 88.8 0.41 8.9E-06 26.9 2.1 26 137-162 1-26 (38)
318 cd04779 HTH_MerR-like_sg4 Heli 88.7 1 2.3E-05 32.6 4.8 46 46-91 1-62 (134)
319 PF08299 Bac_DnaA_C: Bacterial 88.6 1.2 2.5E-05 28.5 4.4 60 75-153 4-64 (70)
320 cd04766 HTH_HspR Helix-Turn-He 88.6 0.71 1.5E-05 30.9 3.6 24 46-69 2-25 (91)
321 PF10668 Phage_terminase: Phag 88.5 0.57 1.2E-05 29.2 2.8 24 135-158 22-45 (60)
322 cd04763 HTH_MlrA-like Helix-Tu 88.5 0.69 1.5E-05 29.0 3.3 22 136-157 1-22 (68)
323 COG5606 Uncharacterized conser 88.5 0.73 1.6E-05 30.9 3.5 41 121-161 27-67 (91)
324 PF00196 GerE: Bacterial regul 88.5 0.51 1.1E-05 28.7 2.6 26 42-67 15-40 (58)
325 PRK00215 LexA repressor; Valid 88.5 1.1 2.5E-05 34.3 5.2 56 31-92 7-72 (205)
326 COG3415 Transposase and inacti 88.4 1.2 2.6E-05 32.5 4.9 32 36-67 12-43 (138)
327 PF13730 HTH_36: Helix-turn-he 88.3 0.6 1.3E-05 27.9 2.8 21 47-67 27-47 (55)
328 PRK11891 aspartate carbamoyltr 88.3 0.7 1.5E-05 40.0 4.2 34 35-68 6-39 (429)
329 COG1318 Predicted transcriptio 88.3 0.71 1.5E-05 34.9 3.7 33 39-71 55-87 (182)
330 PRK08215 sporulation sigma fac 88.3 0.89 1.9E-05 36.3 4.6 30 38-67 218-247 (258)
331 PF12728 HTH_17: Helix-turn-he 88.2 0.78 1.7E-05 27.0 3.3 29 136-164 2-30 (51)
332 PRK05572 sporulation sigma fac 88.2 0.91 2E-05 36.1 4.6 29 39-67 212-240 (252)
333 cd04769 HTH_MerR2 Helix-Turn-H 88.1 0.57 1.2E-05 32.9 3.0 23 46-68 1-23 (116)
334 smart00345 HTH_GNTR helix_turn 88.0 1.2 2.5E-05 26.5 4.0 21 45-65 19-40 (60)
335 PRK12427 flagellar biosynthesi 87.8 1.1 2.3E-05 35.4 4.7 29 39-67 193-221 (231)
336 PF13411 MerR_1: MerR HTH fami 87.8 0.54 1.2E-05 29.4 2.5 28 136-163 1-28 (69)
337 PRK00430 fis global DNA-bindin 87.7 1.1 2.5E-05 30.5 4.2 32 35-66 58-89 (95)
338 TIGR00122 birA_repr_reg BirA b 87.7 1.3 2.7E-05 27.9 4.2 27 40-66 8-34 (69)
339 PRK07500 rpoH2 RNA polymerase 87.6 0.57 1.2E-05 38.2 3.2 24 134-157 244-267 (289)
340 TIGR03453 partition_RepA plasm 87.6 2.1 4.6E-05 36.3 6.7 43 44-86 32-86 (387)
341 TIGR01764 excise DNA binding d 87.5 0.92 2E-05 25.9 3.2 28 136-163 2-29 (49)
342 PF09048 Cro: Cro; InterPro: 87.5 1 2.2E-05 27.9 3.4 30 39-70 8-37 (59)
343 PF05269 Phage_CII: Bacterioph 87.5 0.52 1.1E-05 31.9 2.3 24 134-157 22-45 (91)
344 TIGR02392 rpoH_proteo alternat 87.4 0.91 2E-05 36.6 4.2 24 44-67 235-258 (270)
345 cd04781 HTH_MerR-like_sg6 Heli 87.4 0.93 2E-05 32.0 3.8 24 46-69 1-24 (120)
346 PF01978 TrmB: Sugar-specific 87.4 0.9 2E-05 28.5 3.3 33 34-66 11-43 (68)
347 COG3311 AlpA Predicted transcr 87.3 0.57 1.2E-05 30.1 2.4 32 46-77 14-45 (70)
348 PRK05949 RNA polymerase sigma 87.2 1.3 2.9E-05 36.8 5.2 24 134-157 285-308 (327)
349 TIGR03209 P21_Cbot clostridium 87.2 0.77 1.7E-05 32.9 3.3 27 37-63 115-141 (142)
350 PRK15320 transcriptional activ 87.1 0.66 1.4E-05 36.1 3.0 39 41-90 175-213 (251)
351 TIGR02850 spore_sigG RNA polym 87.1 1.1 2.4E-05 35.7 4.4 28 40-67 217-244 (254)
352 PRK09863 putative frv operon r 87.1 13 0.00027 33.4 11.6 98 43-155 15-112 (584)
353 PRK11179 DNA-binding transcrip 87.0 1.7 3.6E-05 31.9 5.1 31 34-64 12-42 (153)
354 PRK09210 RNA polymerase sigma 87.0 1.8 4E-05 36.6 5.9 24 134-157 324-347 (367)
355 PF01022 HTH_5: Bacterial regu 86.9 0.74 1.6E-05 26.8 2.6 29 37-66 8-36 (47)
356 PRK01381 Trp operon repressor; 86.9 1.9 4.2E-05 29.6 4.9 51 123-173 41-93 (99)
357 TIGR03697 NtcA_cyano global ni 86.8 1.7 3.8E-05 32.4 5.2 23 44-66 142-164 (193)
358 PF07453 NUMOD1: NUMOD1 domain 86.8 0.88 1.9E-05 25.1 2.7 19 47-65 18-36 (37)
359 PF01527 HTH_Tnp_1: Transposas 86.8 1 2.2E-05 28.6 3.4 36 122-157 10-45 (76)
360 COG1356 tfx Transcriptional re 86.7 0.63 1.4E-05 33.4 2.5 26 132-157 20-45 (143)
361 PF13693 HTH_35: Winged helix- 86.7 2.9 6.2E-05 27.5 5.5 47 125-174 5-51 (78)
362 PF04297 UPF0122: Putative hel 86.7 0.64 1.4E-05 32.1 2.5 45 40-88 28-72 (101)
363 PF04218 CENP-B_N: CENP-B N-te 86.7 0.77 1.7E-05 27.7 2.6 27 132-158 19-45 (53)
364 PF02042 RWP-RK: RWP-RK domain 86.6 2.4 5.1E-05 25.7 4.6 29 37-65 7-35 (52)
365 TIGR02393 RpoD_Cterm RNA polym 86.6 1.1 2.4E-05 35.3 4.2 25 43-67 194-218 (238)
366 PRK07122 RNA polymerase sigma 86.5 7.4 0.00016 31.3 9.0 31 127-157 223-253 (264)
367 PRK06596 RNA polymerase factor 86.5 0.7 1.5E-05 37.6 3.1 24 44-67 247-270 (284)
368 TIGR02337 HpaR homoprotocatech 86.5 1.6 3.5E-05 30.4 4.6 38 28-65 25-62 (118)
369 smart00760 Bac_DnaA_C Bacteria 86.4 3 6.4E-05 25.6 5.2 53 75-146 4-56 (60)
370 smart00497 IENR1 Intron encode 86.4 1.2 2.5E-05 26.3 3.3 25 47-71 19-43 (53)
371 PRK13832 plasmid partitioning 86.3 1.5 3.3E-05 38.7 5.1 50 30-81 104-153 (520)
372 PRK11161 fumarate/nitrate redu 86.2 1.3 2.9E-05 34.3 4.4 22 45-66 184-205 (235)
373 PRK10572 DNA-binding transcrip 86.1 5.4 0.00012 32.0 8.1 15 134-148 247-261 (290)
374 PRK06986 fliA flagellar biosyn 86.1 7 0.00015 30.6 8.5 32 126-157 191-222 (236)
375 PRK13182 racA polar chromosome 86.1 1 2.2E-05 34.3 3.5 46 46-91 1-62 (175)
376 PRK13413 mpi multiple promoter 86.0 1.5 3.2E-05 33.6 4.5 33 35-68 163-195 (200)
377 PRK08215 sporulation sigma fac 86.0 3.8 8.1E-05 32.7 7.0 29 129-157 219-247 (258)
378 PF00325 Crp: Bacterial regula 85.8 1 2.3E-05 24.4 2.5 22 135-156 2-23 (32)
379 PRK11924 RNA polymerase sigma 85.7 1.5 3.3E-05 32.1 4.4 29 39-67 135-163 (179)
380 COG1974 LexA SOS-response tran 85.7 1.2 2.7E-05 34.5 3.9 53 40-93 7-59 (201)
381 PRK06288 RNA polymerase sigma 85.6 3.3 7.3E-05 33.2 6.6 30 127-156 220-249 (268)
382 PRK07037 extracytoplasmic-func 85.6 1.8 3.9E-05 31.5 4.7 28 38-65 118-145 (163)
383 PF06322 Phage_NinH: Phage Nin 85.5 0.98 2.1E-05 28.2 2.6 23 47-69 18-40 (64)
384 PRK11169 leucine-responsive tr 85.5 1.5 3.2E-05 32.7 4.2 32 33-64 16-47 (164)
385 PRK06759 RNA polymerase factor 85.4 1.8 4E-05 31.1 4.6 29 38-66 115-143 (154)
386 TIGR02980 SigBFG RNA polymeras 85.4 1.7 3.6E-05 33.8 4.6 29 39-67 188-216 (227)
387 PRK05901 RNA polymerase sigma 85.4 3.1 6.8E-05 36.9 6.7 24 134-157 466-489 (509)
388 TIGR02985 Sig70_bacteroi1 RNA 85.4 1.9 4.1E-05 31.0 4.6 30 38-67 122-151 (161)
389 cd07377 WHTH_GntR Winged helix 85.2 3.5 7.6E-05 24.9 5.2 19 47-65 27-45 (66)
390 smart00346 HTH_ICLR helix_turn 85.2 1.6 3.5E-05 28.6 3.9 23 44-66 19-41 (91)
391 TIGR02999 Sig-70_X6 RNA polyme 85.1 1.9 4.1E-05 32.1 4.7 30 37-66 142-171 (183)
392 cd04776 HTH_GnyR Helix-Turn-He 85.0 1.4 3.1E-05 31.0 3.7 24 46-69 1-24 (118)
393 TIGR02297 HpaA 4-hydroxyphenyl 85.0 4.6 0.0001 32.2 7.2 18 133-150 249-266 (287)
394 cd04777 HTH_MerR-like_sg1 Heli 84.9 1.5 3.2E-05 30.2 3.7 27 46-72 1-27 (107)
395 TIGR02937 sigma70-ECF RNA poly 84.8 1.8 3.9E-05 30.3 4.3 28 40-67 121-148 (158)
396 PRK12423 LexA repressor; Provi 84.8 3.7 8E-05 31.6 6.2 35 30-64 8-45 (202)
397 TIGR00180 parB_part ParB-like 84.8 3.3 7.2E-05 31.5 5.9 50 121-171 106-155 (187)
398 PF13518 HTH_28: Helix-turn-he 84.7 1.3 2.8E-05 25.9 2.9 24 134-157 11-34 (52)
399 PRK09391 fixK transcriptional 84.7 2 4.4E-05 33.5 4.8 36 30-65 156-199 (230)
400 PRK05572 sporulation sigma fac 84.7 18 0.00039 28.6 11.8 38 119-157 203-240 (252)
401 PRK13918 CRP/FNR family transc 84.4 0.98 2.1E-05 34.1 2.9 23 44-66 148-170 (202)
402 smart00344 HTH_ASNC helix_turn 84.4 1.9 4.1E-05 29.4 4.1 29 37-65 9-37 (108)
403 PRK09652 RNA polymerase sigma 84.4 2.1 4.5E-05 31.5 4.5 29 39-67 138-166 (182)
404 TIGR02895 spore_sigI RNA polym 84.3 6 0.00013 31.1 7.3 78 70-155 116-196 (218)
405 smart00422 HTH_MERR helix_turn 84.3 1.6 3.6E-05 27.1 3.4 22 136-157 1-22 (70)
406 PRK11753 DNA-binding transcrip 84.3 1 2.2E-05 34.2 2.9 22 45-66 168-189 (211)
407 PRK07408 RNA polymerase sigma 84.2 2 4.4E-05 34.3 4.7 28 40-67 214-241 (256)
408 PRK09639 RNA polymerase sigma 84.2 2.1 4.5E-05 31.3 4.5 30 36-66 119-148 (166)
409 TIGR02531 yecD_yerC TrpR-relat 84.2 1.6 3.4E-05 29.4 3.4 27 132-158 47-73 (88)
410 PRK13503 transcriptional activ 84.1 6.5 0.00014 31.2 7.6 17 134-150 235-251 (278)
411 PRK13501 transcriptional activ 84.1 6.1 0.00013 31.8 7.5 16 134-149 240-255 (290)
412 PF12833 HTH_18: Helix-turn-he 84.1 5.2 0.00011 25.5 5.9 19 132-150 42-60 (81)
413 PRK13502 transcriptional activ 83.9 5.1 0.00011 32.0 7.0 16 134-149 240-255 (282)
414 COG5484 Uncharacterized conser 83.8 0.98 2.1E-05 36.2 2.6 28 42-69 16-43 (279)
415 PF08280 HTH_Mga: M protein tr 83.7 2.1 4.5E-05 26.2 3.6 30 37-66 11-40 (59)
416 smart00347 HTH_MARR helix_turn 83.7 3.2 6.9E-05 27.2 4.9 38 29-66 8-45 (101)
417 PF09012 FeoC: FeoC like trans 83.6 1.4 3.1E-05 27.8 2.9 30 36-65 4-34 (69)
418 PHA01082 putative transcriptio 83.6 0.87 1.9E-05 32.4 2.0 41 43-83 28-69 (133)
419 COG1513 CynS Cyanate lyase [In 83.6 5.6 0.00012 28.8 6.1 54 121-174 7-60 (151)
420 TIGR02989 Sig-70_gvs1 RNA poly 83.5 2.5 5.4E-05 30.6 4.6 27 39-65 121-147 (159)
421 PRK12519 RNA polymerase sigma 83.5 1.8 3.8E-05 32.7 3.9 28 40-67 152-179 (194)
422 PRK03341 arginine repressor; P 83.5 2.2 4.8E-05 32.2 4.3 31 36-66 19-55 (168)
423 PRK09413 IS2 repressor TnpA; R 83.4 3.5 7.6E-05 29.1 5.1 38 120-157 14-51 (121)
424 PF13309 HTH_22: HTH domain 83.3 3.6 7.9E-05 25.7 4.7 28 39-66 31-63 (64)
425 PF00440 TetR_N: Bacterial reg 83.3 5.5 0.00012 22.9 5.2 29 37-65 8-36 (47)
426 PRK15411 rcsA colanic acid cap 83.3 1.3 2.9E-05 34.2 3.2 25 42-66 149-173 (207)
427 PRK08583 RNA polymerase sigma 83.3 2.3 5.1E-05 33.8 4.7 29 39-67 215-243 (257)
428 PRK07122 RNA polymerase sigma 83.3 2 4.4E-05 34.5 4.4 31 37-67 223-253 (264)
429 TIGR01950 SoxR redox-sensitive 83.2 1.8 3.9E-05 31.6 3.7 22 46-67 2-23 (142)
430 cd00569 HTH_Hin_like Helix-tur 83.2 4.5 9.7E-05 20.6 5.1 23 133-155 19-41 (42)
431 PRK13777 transcriptional regul 83.2 2.7 5.8E-05 32.2 4.8 42 24-65 38-79 (185)
432 PRK09646 RNA polymerase sigma 83.1 5.1 0.00011 30.3 6.3 42 39-87 152-193 (194)
433 PF01710 HTH_Tnp_IS630: Transp 82.9 1.4 3E-05 31.1 2.9 26 41-66 67-92 (119)
434 PRK09047 RNA polymerase factor 82.9 2.7 5.8E-05 30.4 4.6 30 38-67 115-144 (161)
435 PF13613 HTH_Tnp_4: Helix-turn 82.7 3.5 7.5E-05 24.6 4.2 32 126-157 10-41 (53)
436 PRK13919 putative RNA polymera 82.5 2.7 5.9E-05 31.3 4.6 31 37-67 143-173 (186)
437 PRK06030 hypothetical protein; 82.5 6 0.00013 28.3 6.0 62 74-153 26-87 (124)
438 PRK06986 fliA flagellar biosyn 82.5 2.4 5.2E-05 33.3 4.4 31 37-67 192-222 (236)
439 COG4565 CitB Response regulato 82.4 3 6.6E-05 32.8 4.8 36 31-66 157-194 (224)
440 PF08281 Sigma70_r4_2: Sigma-7 82.4 3.7 8E-05 24.2 4.3 31 125-155 16-46 (54)
441 PRK07500 rpoH2 RNA polymerase 82.4 2.3 4.9E-05 34.7 4.4 36 44-86 244-279 (289)
442 PRK07406 RNA polymerase sigma 82.2 4.5 9.7E-05 34.4 6.2 24 134-157 330-353 (373)
443 PRK12529 RNA polymerase sigma 82.1 3 6.5E-05 31.1 4.7 29 38-66 136-164 (178)
444 PRK01905 DNA-binding protein F 81.9 4.1 8.9E-05 26.4 4.7 33 34-66 39-71 (77)
445 TIGR02941 Sigma_B RNA polymera 81.8 15 0.00033 29.0 8.9 32 126-157 212-243 (255)
446 PRK05911 RNA polymerase sigma 81.7 2.9 6.3E-05 33.4 4.7 31 37-67 213-243 (257)
447 PF02001 DUF134: Protein of un 81.7 1.6 3.5E-05 30.4 2.8 26 132-157 54-79 (106)
448 TIGR02997 Sig70-cyanoRpoD RNA 81.6 2.4 5.1E-05 34.7 4.2 25 43-67 267-291 (298)
449 PRK15201 fimbriae regulatory p 81.5 2 4.2E-05 32.9 3.3 26 42-67 145-170 (198)
450 PRK09649 RNA polymerase sigma 81.5 2.9 6.3E-05 31.4 4.4 30 37-66 138-167 (185)
451 PRK15002 redox-sensitivie tran 81.4 2.1 4.6E-05 31.8 3.5 29 40-68 6-34 (154)
452 PRK12523 RNA polymerase sigma 81.4 3.3 7.2E-05 30.6 4.7 30 37-66 127-156 (172)
453 PRK09954 putative kinase; Prov 81.3 3 6.6E-05 34.8 4.9 33 35-67 7-39 (362)
454 PRK12537 RNA polymerase sigma 81.3 3.1 6.8E-05 31.0 4.5 29 38-66 142-170 (182)
455 PRK09642 RNA polymerase sigma 81.1 3.4 7.3E-05 30.0 4.6 30 37-66 114-143 (160)
456 PRK09645 RNA polymerase sigma 81.1 3.4 7.3E-05 30.4 4.6 30 37-66 126-155 (173)
457 PRK14845 translation initiatio 81.1 2.3 5E-05 40.9 4.4 50 33-87 323-372 (1049)
458 PRK07670 RNA polymerase sigma 80.9 7.2 0.00016 30.9 6.7 122 35-157 109-239 (251)
459 COG3413 Predicted DNA binding 80.9 1.8 3.8E-05 33.7 3.1 24 44-67 177-200 (215)
460 COG3415 Transposase and inacti 80.9 4 8.7E-05 29.8 4.7 37 121-157 7-43 (138)
461 PF08822 DUF1804: Protein of u 80.9 4.9 0.00011 30.3 5.3 37 31-67 5-41 (165)
462 cd01105 HTH_GlnR-like Helix-Tu 80.8 2.6 5.6E-05 28.0 3.5 27 135-161 1-27 (88)
463 PRK05657 RNA polymerase sigma 80.8 8.7 0.00019 31.9 7.3 40 118-157 262-304 (325)
464 COG4367 Uncharacterized protei 80.7 7.2 0.00016 26.2 5.4 52 33-86 11-62 (97)
465 PF13404 HTH_AsnC-type: AsnC-t 80.6 6.5 0.00014 22.4 4.7 30 124-153 6-35 (42)
466 PRK13509 transcriptional repre 80.6 2.5 5.4E-05 33.8 3.9 32 35-66 9-40 (251)
467 TIGR02941 Sigma_B RNA polymera 80.6 3.1 6.7E-05 33.0 4.5 31 37-67 213-243 (255)
468 PRK11050 manganese transport r 80.5 4.3 9.4E-05 29.8 4.9 36 31-66 36-72 (152)
469 PF08279 HTH_11: HTH domain; 80.5 3.6 7.9E-05 24.4 3.8 31 126-156 5-36 (55)
470 PRK09210 RNA polymerase sigma 80.5 2.7 5.9E-05 35.5 4.3 24 44-67 324-347 (367)
471 PRK10411 DNA-binding transcrip 80.4 2.6 5.6E-05 33.5 3.9 31 36-66 9-39 (240)
472 PF01371 Trp_repressor: Trp re 80.4 6.1 0.00013 26.5 5.1 36 122-157 34-71 (87)
473 TIGR02702 SufR_cyano iron-sulf 80.3 2.7 5.9E-05 32.3 4.0 31 36-66 6-36 (203)
474 PRK05602 RNA polymerase sigma 80.3 3.3 7.1E-05 31.0 4.4 29 39-67 138-166 (186)
475 PF14590 DUF4447: Domain of un 80.3 6.7 0.00015 28.3 5.5 41 126-166 11-51 (166)
476 PF01325 Fe_dep_repress: Iron 80.2 2 4.4E-05 26.6 2.6 25 42-66 19-43 (60)
477 smart00421 HTH_LUXR helix_turn 80.2 6.9 0.00015 22.6 5.0 25 133-157 16-40 (58)
478 PRK06930 positive control sigm 80.2 3.8 8.3E-05 30.8 4.6 29 39-67 124-152 (170)
479 smart00418 HTH_ARSR helix_turn 80.2 3.3 7.2E-05 24.5 3.6 24 43-66 8-31 (66)
480 PRK12524 RNA polymerase sigma 80.1 3.6 7.9E-05 31.1 4.6 32 36-67 143-174 (196)
481 cd04773 HTH_TioE_rpt2 Second H 80.1 2.6 5.6E-05 29.2 3.4 27 136-162 1-27 (108)
482 PRK05657 RNA polymerase sigma 80.0 2.2 4.7E-05 35.5 3.5 43 43-89 280-322 (325)
483 PRK12511 RNA polymerase sigma 80.0 3.6 7.9E-05 31.0 4.5 29 38-66 120-148 (182)
484 PRK10840 transcriptional regul 79.9 2.2 4.7E-05 32.6 3.3 25 43-67 163-187 (216)
485 PRK14165 winged helix-turn-hel 79.9 1.9 4.2E-05 33.9 3.0 28 39-66 15-42 (217)
486 PRK15418 transcriptional regul 79.9 1.7 3.8E-05 36.0 2.9 24 134-157 28-51 (318)
487 COG1654 BirA Biotin operon rep 79.9 4.1 8.9E-05 26.8 4.1 26 40-65 12-39 (79)
488 PF06163 DUF977: Bacterial pro 79.8 4.5 9.7E-05 29.0 4.5 43 24-66 5-47 (127)
489 cd01106 HTH_TipAL-Mta Helix-Tu 79.8 2.7 5.9E-05 28.7 3.4 26 136-161 1-26 (103)
490 TIGR02479 FliA_WhiG RNA polyme 79.8 3.7 8.1E-05 31.8 4.6 29 39-67 185-213 (224)
491 COG1595 RpoE DNA-directed RNA 79.7 2.6 5.5E-05 31.6 3.6 29 39-67 137-165 (182)
492 PRK13500 transcriptional activ 79.6 20 0.00043 29.3 9.1 17 134-150 270-286 (312)
493 PF04967 HTH_10: HTH DNA bindi 79.5 2.5 5.5E-05 25.6 2.8 22 134-155 22-43 (53)
494 PRK05901 RNA polymerase sigma 79.5 2.9 6.3E-05 37.1 4.3 24 44-67 466-489 (509)
495 TIGR01889 Staph_reg_Sar staphy 79.4 3 6.4E-05 28.8 3.6 24 43-66 41-64 (109)
496 PRK12532 RNA polymerase sigma 79.4 3.6 7.7E-05 31.1 4.3 28 39-66 146-173 (195)
497 TIGR02984 Sig-70_plancto1 RNA 79.3 3.9 8.4E-05 30.4 4.5 28 39-66 150-177 (189)
498 TIGR02959 SigZ RNA polymerase 79.2 4.4 9.6E-05 29.9 4.7 28 39-66 110-137 (170)
499 TIGR02954 Sig70_famx3 RNA poly 79.1 3.9 8.5E-05 30.0 4.4 30 37-66 127-156 (169)
500 COG3636 Predicted transcriptio 79.1 5.7 0.00012 27.2 4.7 47 126-174 42-88 (100)
No 1
>PHA01976 helix-turn-helix protein
Probab=99.79 E-value=2.7e-19 Score=115.12 Aligned_cols=64 Identities=25% Similarity=0.549 Sum_probs=61.5
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCC
Q psy6501 31 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGT 94 (174)
Q Consensus 31 ~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~ 94 (174)
|.||.+|+.+|+.+||||.+||+.+|+|+++|++||+|...|+.+.+.+||++|||+++||++.
T Consensus 1 m~~~~rl~~~R~~~glt~~~lA~~~gvs~~~v~~~e~g~~~p~~~~l~~ia~~l~v~~~~l~~g 64 (67)
T PHA01976 1 MSFAIQLIKARNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTLDWLCGR 64 (67)
T ss_pred CcHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHHHhcC
Confidence 4689999999999999999999999999999999999999999999999999999999999853
No 2
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=99.72 E-value=1.3e-17 Score=106.36 Aligned_cols=60 Identities=30% Similarity=0.432 Sum_probs=52.8
Q ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501 34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG 93 (174)
Q Consensus 34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~ 93 (174)
|++||.+|+.+|+||.+||+.+|+++++|++||+|++.|+...+.+||++|+|+++||+.
T Consensus 1 G~~lk~~r~~~~lt~~~~a~~~~i~~~~i~~~e~g~~~~~~~~l~~i~~~~~v~~~~l~~ 60 (64)
T PF12844_consen 1 GERLKELREEKGLTQKDLAEKLGISRSTISKIENGKRKPSVSTLKKIAEALGVSLDELFD 60 (64)
T ss_dssp HHHHHHHHHHCT--HHHHHHHHTS-HHHHHHHHTTSS--BHHHHHHHHHHHTS-HHHHCC
T ss_pred CHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCcCCCHHHHHHHHHHhCCCHHHHhc
Confidence 789999999999999999999999999999999999999999999999999999999984
No 3
>KOG3398|consensus
Probab=99.72 E-value=2.2e-17 Score=115.68 Aligned_cols=90 Identities=64% Similarity=0.951 Sum_probs=87.4
Q ss_pred CCCCCCCCCCCccccccccchhhcccccchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH
Q psy6501 1 NAGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKM 80 (174)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~l 80 (174)
++|.|+|--.++++++||++||++.|+.+...+|..|...|..+||||++||.+|+--++.|..||+|+..|+..+|.++
T Consensus 42 ~~g~nkq~~~~~~t~klD~etE~~~~~~v~~~Vg~aIq~aR~~KgmsqkDLA~kInekpqVv~dyEsGrAIpNqqil~km 121 (135)
T KOG3398|consen 42 PAGLNKQHPSTQSTAKLDRETEELGHDRVPLEVGKAIQQARAQKGMSQKDLAQKINEKPQVIQDYESGRAIPNQQILSKM 121 (135)
T ss_pred cccccccCCcccchhhccccccccccccccHHHHHHHHHHHHhccccHHHHHHHHccCchhhhhHhccccCchHHHHHHH
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhCccccc
Q psy6501 81 ERALGIRLRV 90 (174)
Q Consensus 81 a~~L~v~~~~ 90 (174)
.++|||.+.+
T Consensus 122 EraLgvKlrg 131 (135)
T KOG3398|consen 122 ERALGVKLRG 131 (135)
T ss_pred HHHhceeccc
Confidence 9999998765
No 4
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=99.70 E-value=2.5e-16 Score=114.84 Aligned_cols=66 Identities=17% Similarity=0.128 Sum_probs=62.5
Q ss_pred hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCC
Q psy6501 30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTN 95 (174)
Q Consensus 30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~ 95 (174)
.+.+|++|+.+|+.+||||.+||+.+|||+++|++||+|.+.|+.+.+.+||++|||+++||+...
T Consensus 3 ~~~~g~rlk~~R~~~gltq~~lA~~~gvs~~~is~~E~g~~~p~~~~l~~la~~l~vs~~~l~~g~ 68 (135)
T PRK09706 3 NLTLGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCSPTWLLFGD 68 (135)
T ss_pred hhhHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHHHhcCC
Confidence 357999999999999999999999999999999999999999999999999999999999998543
No 5
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=99.69 E-value=7.1e-17 Score=99.79 Aligned_cols=55 Identities=29% Similarity=0.438 Sum_probs=51.6
Q ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccc
Q psy6501 37 LMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVN 91 (174)
Q Consensus 37 ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l 91 (174)
|+++|+++||||+|||+.+|+|+++|++||+|.+.|+.+.+.+||++|||+++||
T Consensus 1 ik~~r~~~gls~~~la~~~gis~~~i~~~~~g~~~~~~~~~~~ia~~l~~~~~~l 55 (55)
T PF01381_consen 1 IKELRKEKGLSQKELAEKLGISRSTISRIENGKRNPSLDTLKKIAKALGVSPEYL 55 (55)
T ss_dssp HHHHHHHTTS-HHHHHHHHTS-HHHHHHHHTTSSTSBHHHHHHHHHHHTSEHHHH
T ss_pred CHHHHHHcCCCHHHHHHHhCCCcchhHHHhcCCCCCCHHHHHHHHHHHCCCHHHC
Confidence 7899999999999999999999999999999999999999999999999999986
No 6
>PRK08359 transcription factor; Validated
Probab=99.66 E-value=3.3e-16 Score=118.07 Aligned_cols=68 Identities=21% Similarity=0.220 Sum_probs=64.4
Q ss_pred cccchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501 26 HEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG 93 (174)
Q Consensus 26 ~~~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~ 93 (174)
..++...||++||++|+.+||||+|||+.+|+++++|++||+|.+.|+.+.+.+||++|+|++..++.
T Consensus 79 ~~elv~dy~~rIkeaRe~kglSQeeLA~~lgvs~stI~~iE~G~~~Ps~~~l~kLak~l~VsL~e~~~ 146 (176)
T PRK08359 79 TEDIVEDYAERVYEAIQKSGLSYEELSHEVGLSVNDLRRIAHGEYEPTIKEAKKLERYFKIKLIERVE 146 (176)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCcCCCHHHHHHHHHHhCCccccccc
Confidence 45788899999999999999999999999999999999999999999999999999999999887664
No 7
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=99.65 E-value=4.3e-16 Score=115.70 Aligned_cols=66 Identities=30% Similarity=0.545 Sum_probs=63.8
Q ss_pred cchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501 28 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG 93 (174)
Q Consensus 28 ~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~ 93 (174)
.++..+|++|+.+|+++||||++||+++|+++++|++||+|...|+++.+.+||++|||++++++.
T Consensus 65 ~l~~~~g~~Ir~~Re~~glSqeeLA~~lgvs~s~IsriE~G~~~Ps~~~l~kLa~~Lgvsl~el~~ 130 (154)
T TIGR00270 65 ELVEDYGIIIRREREKRGWSQEQLAKKIQEKESLIKKIENAEIEPEPKVVEKLEKLLKIKLREQVP 130 (154)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCCCHHHHcc
Confidence 667889999999999999999999999999999999999999999999999999999999999985
No 8
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=99.64 E-value=5.4e-16 Score=98.88 Aligned_cols=58 Identities=22% Similarity=0.239 Sum_probs=56.6
Q ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501 36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG 93 (174)
Q Consensus 36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~ 93 (174)
++|.+|...|+||+|||+.+|||++||..||+|+..||+....+||.+|+++++++|-
T Consensus 5 k~k~~R~~~~ltQ~elA~~vgVsRQTi~~iEkgky~Psl~La~kia~~f~~~iedIF~ 62 (68)
T COG1476 5 KLKELRAELGLTQEELAKLVGVSRQTIIAIEKGKYNPSLELALKIARVFGKTIEDIFQ 62 (68)
T ss_pred HHHHHHHHhCcCHHHHHHHcCcCHHHHHHHHcCCCCchHHHHHHHHHHhCCCHHHHHh
Confidence 8999999999999999999999999999999999999999999999999999999883
No 9
>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=99.64 E-value=1.3e-15 Score=94.64 Aligned_cols=57 Identities=26% Similarity=0.355 Sum_probs=55.0
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccc
Q psy6501 32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRL 88 (174)
Q Consensus 32 ~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~ 88 (174)
.+|++|+.+|+..||||++||+.+|+|+++|++||+|+..|+.+.+.+||++|||++
T Consensus 2 ~~~~~l~~~r~~~gltq~~lA~~~gvs~~~vs~~e~g~~~~~~~~~~~i~~~lgv~l 58 (58)
T TIGR03070 2 QIGMLVRARRKALGLTQADLADLAGVGLRFIRDVENGKPTVRLDKVLRVLDALGLEL 58 (58)
T ss_pred hHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHcCCCC
Confidence 489999999999999999999999999999999999999999999999999999874
No 10
>PRK09726 antitoxin HipB; Provisional
Probab=99.62 E-value=3e-15 Score=101.48 Aligned_cols=64 Identities=25% Similarity=0.418 Sum_probs=60.9
Q ss_pred hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501 30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG 93 (174)
Q Consensus 30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~ 93 (174)
...+|.+|+.+|+.+|+||++||+.+|||+++|++||+|...|+++.+.+||++|||+++++..
T Consensus 10 ~~~l~~~lk~~R~~~gltq~elA~~~gvs~~tis~~e~g~~~ps~~~l~~ia~~lgv~~~~~~~ 73 (88)
T PRK09726 10 PTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMTLCDA 73 (88)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHcCCCcchhcc
Confidence 4589999999999999999999999999999999999999999999999999999999999653
No 11
>PRK06424 transcription factor; Provisional
Probab=99.61 E-value=2.2e-15 Score=110.58 Aligned_cols=64 Identities=33% Similarity=0.455 Sum_probs=60.4
Q ss_pred cchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccc
Q psy6501 28 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVN 91 (174)
Q Consensus 28 ~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l 91 (174)
.++..+|++|+.+|+++||||+|||+.+|+++++|++||+|.+.|+.+.+.+||++||+++.+.
T Consensus 80 ~~~~~~g~~Ir~lRe~~GLSQ~eLA~~iGvs~stIskiE~G~~~Ps~~~l~kLa~~Lgvsl~e~ 143 (144)
T PRK06424 80 DIVEDYAELVKNARERLSMSQADLAAKIFERKNVIASIERGDLLPDIKTARKLEKILGITLIEK 143 (144)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCCCC
Confidence 3467899999999999999999999999999999999999999999999999999999998653
No 12
>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed
Probab=99.61 E-value=1.3e-15 Score=125.19 Aligned_cols=71 Identities=23% Similarity=0.262 Sum_probs=66.2
Q ss_pred cccchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCCC
Q psy6501 26 HEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTNK 96 (174)
Q Consensus 26 ~~~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~~ 96 (174)
++.+...+|++|+.+|+.+||||++||+++|+|+++|++||+|+..|+.+.+.+||++|||+++||++...
T Consensus 22 ~~~~~~~~g~rl~~~R~~~gltq~~lA~~~gvs~~~i~~~E~g~~~ps~~~l~~ia~~l~v~~~~l~~~~~ 92 (309)
T PRK08154 22 EAPFLAALGERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCSLADLLGDVD 92 (309)
T ss_pred hHHHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCCCHHHHhCCCC
Confidence 34556789999999999999999999999999999999999999999999999999999999999997654
No 13
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=99.59 E-value=3.2e-15 Score=95.41 Aligned_cols=60 Identities=28% Similarity=0.424 Sum_probs=52.1
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCcccccc
Q psy6501 32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG-IPNQAIIGKMERALGIRLRVN 91 (174)
Q Consensus 32 ~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~-~P~~~~l~~la~~L~v~~~~l 91 (174)
.||..|+.+|+..||||.++|+.+|+|+++|++||+|+. .|+.+.+.+||++|+++.+.+
T Consensus 1 ~lg~~lr~~R~~~gls~~~lA~~~g~s~s~v~~iE~G~~~~p~~~~l~~l~~~l~~~~~~~ 61 (64)
T PF13560_consen 1 QLGRRLRRLRERAGLSQAQLADRLGVSQSTVSRIERGRRPRPSPDTLQRLARALGVPPDER 61 (64)
T ss_dssp HHHHHHHHHHHCHTS-HHHHHHHHTS-HHHHHHHHTTSSSS-BHHHHHHHHHHTT--HHHH
T ss_pred CHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCCHHHHHHHHHHHCcCHHHH
Confidence 489999999999999999999999999999999999999 699999999999999998754
No 14
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=99.58 E-value=7.2e-15 Score=105.11 Aligned_cols=67 Identities=12% Similarity=0.189 Sum_probs=63.4
Q ss_pred hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCCC
Q psy6501 30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTNK 96 (174)
Q Consensus 30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~~ 96 (174)
.+.++.+|+.+|+++||||+|||+++|+|+++|++||+|+..|+.+.+.+||++|+|+++||+....
T Consensus 3 ~~i~~~~l~~ll~~~Glsq~eLA~~~Gis~~~is~iE~g~~~ps~~~l~kIa~aL~v~~~~L~~~~~ 69 (120)
T PRK13890 3 NYIFFTNVLRLLDERHMTKKELSERSGVSISFLSDLTTGKANPSLKVMEAIADALETPLPLLLESTD 69 (120)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCCCHHHHhccCc
Confidence 4678999999999999999999999999999999999999999999999999999999999996543
No 15
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=99.57 E-value=8.1e-15 Score=112.14 Aligned_cols=67 Identities=21% Similarity=0.192 Sum_probs=63.4
Q ss_pred cchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCC
Q psy6501 28 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGT 94 (174)
Q Consensus 28 ~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~ 94 (174)
+..+.+|.+||.+|+++||||.+||+++|+|+++|++||+|...|+...+.+||++|+|++++|+..
T Consensus 3 ~~~~~~g~~l~~~R~~~glt~~elA~~~gis~~~is~~E~g~~~p~~~~l~~ia~~l~v~~~~l~~~ 69 (185)
T PRK09943 3 DEGLAPGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFFSE 69 (185)
T ss_pred chhhHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHccC
Confidence 3456799999999999999999999999999999999999999999999999999999999999953
No 16
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized 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 uncoded by the upstream member of the gene pair.
Probab=99.54 E-value=2.1e-14 Score=94.83 Aligned_cols=62 Identities=16% Similarity=0.157 Sum_probs=59.2
Q ss_pred HHHHHHH-HHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501 32 DLAKLLM-QGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG 93 (174)
Q Consensus 32 ~ig~~ik-~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~ 93 (174)
..|++|+ .+|+++|+||.+||+.+|+|+++|++||+|.+.|+.+.+.+||++|||+++||+.
T Consensus 4 ~~g~~i~~~~~~~~~~t~~~lA~~~gis~~tis~~~~g~~~~~~~~~~~l~~~l~v~~~~l~~ 66 (78)
T TIGR02607 4 HPGEILREEFLEPLGLSIRALAKALGVSRSTLSRIVNGRRGITADMALRLAKALGTSPEFWLN 66 (78)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHcCCCHHHHHH
Confidence 3588999 8999999999999999999999999999999999999999999999999999984
No 17
>TIGR02612 mob_myst_A mobile mystery protein A. Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).
Probab=99.49 E-value=8.6e-14 Score=102.87 Aligned_cols=62 Identities=19% Similarity=0.128 Sum_probs=57.7
Q ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCC--CCCHHHHHHHHHHhCcccccccCCCC
Q psy6501 35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG--IPNQAIIGKMERALGIRLRVNAGTNK 96 (174)
Q Consensus 35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~--~P~~~~l~~la~~L~v~~~~l~~~~~ 96 (174)
.+|+.+|+.+||||.+||+++|||+++|++||+|.. .|+++.|.+||++|||+++|||.+..
T Consensus 28 ~~Ir~~R~~lGmTq~eLAerlGVS~~tIs~iE~G~~~~~psl~~L~kIA~aLgv~~~~l~~~~~ 91 (150)
T TIGR02612 28 GWVRAIRKALGMSGAQLAGRLGVTPQRVEALEKSELSGTVTLKTLRAAAEALDCTFVYAFVPKT 91 (150)
T ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCCCHHHHHHHHHHcCCCHHHHhCCcc
Confidence 589999999999999999999999999999999985 48999999999999999999996443
No 18
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein. 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=99.43 E-value=5.2e-13 Score=90.50 Aligned_cols=58 Identities=31% Similarity=0.387 Sum_probs=54.7
Q ss_pred hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccc
Q psy6501 30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLR 89 (174)
Q Consensus 30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~ 89 (174)
...++.+|+.+|+++|||| ||+++|||+++|++||+|...|+.+.+.+||++||+++.
T Consensus 30 ~~~~~~~l~~~r~~~glSq--LAe~~GIs~stLs~iE~g~~~Ps~~tL~kI~~aLgi~l~ 87 (89)
T TIGR02684 30 PAYIAHALGYIARARGMTQ--LARKTGLSRESLYKALSGKGNPTFDTILKVTKALGLKLT 87 (89)
T ss_pred HHHHHHHHHHHHHHCChHH--HHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHcCCcee
Confidence 3468999999999999995 999999999999999999999999999999999999875
No 19
>KOG3398|consensus
Probab=99.41 E-value=6.4e-13 Score=93.35 Aligned_cols=82 Identities=66% Similarity=0.966 Sum_probs=73.8
Q ss_pred CCCCCCCCCcccchhhhhhhhhhcccccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHh
Q psy6501 93 GTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMER 172 (174)
Q Consensus 93 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~ 172 (174)
+.+..+....+..+++++.+...+..++.+++..|.++|..+||||+|||.+++..++.|.+||+|+.+|+..++.++.+
T Consensus 44 g~nkq~~~~~~t~klD~etE~~~~~~v~~~Vg~aIq~aR~~KgmsqkDLA~kInekpqVv~dyEsGrAIpNqqil~kmEr 123 (135)
T KOG3398|consen 44 GLNKQHPSTQSTAKLDRETEELGHDRVPLEVGKAIQQARAQKGMSQKDLAQKINEKPQVIQDYESGRAIPNQQILSKMER 123 (135)
T ss_pred cccccCCcccchhhccccccccccccccHHHHHHHHHHHHhccccHHHHHHHHccCchhhhhHhccccCchHHHHHHHHH
Confidence 34444455566678888889999999999999999999999999999999999999999999999999999999999999
Q ss_pred hC
Q psy6501 173 AL 174 (174)
Q Consensus 173 ~l 174 (174)
+|
T Consensus 124 aL 125 (135)
T KOG3398|consen 124 AL 125 (135)
T ss_pred Hh
Confidence 86
No 20
>PRK10072 putative transcriptional regulator; Provisional
Probab=99.41 E-value=7.2e-13 Score=90.92 Aligned_cols=56 Identities=20% Similarity=0.227 Sum_probs=51.9
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccc
Q psy6501 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLR 89 (174)
Q Consensus 33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~ 89 (174)
-+..|+.+|+..||||.+||+.+|+|.+||++||+|++.|+...+. ++++|++++.
T Consensus 34 ~~~eik~LR~~~glTQ~elA~~lGvS~~TVs~WE~G~r~P~~~~l~-Ll~~L~~~P~ 89 (96)
T PRK10072 34 SFTEFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVKPSSAELK-LMRLIQANPA 89 (96)
T ss_pred ChHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH-HHHHHhhCHH
Confidence 3566999999999999999999999999999999999999999965 9999999984
No 21
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=99.35 E-value=3e-12 Score=81.13 Aligned_cols=58 Identities=22% Similarity=0.226 Sum_probs=46.3
Q ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCcccccccC
Q psy6501 36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR-GIPNQAIIGKMERALGIRLRVNAG 93 (174)
Q Consensus 36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~-~~P~~~~l~~la~~L~v~~~~l~~ 93 (174)
+|+.+..++|+|+.+||+.+|+|+++|++|-+|. ..|+.+.+.+||.+|||++++|+.
T Consensus 1 ~L~~~m~~~~it~~~La~~~gis~~tl~~~~~~~~~~~~~~~l~~ia~~l~~~~~el~~ 59 (63)
T PF13443_consen 1 KLKELMAERGITQKDLARKTGISRSTLSRILNGKPSNPSLDTLEKIAKALNCSPEELFE 59 (63)
T ss_dssp HHHHHHHHTT--HHHHHHHHT--HHHHHHHHTTT-----HHHHHHHHHHHT--HHHCTE
T ss_pred CHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcccccccHHHHHHHHHHcCCCHHHHhh
Confidence 6899999999999999999999999999999999 799999999999999999999984
No 22
>PRK04140 hypothetical protein; Provisional
Probab=99.33 E-value=3.9e-12 Score=104.43 Aligned_cols=62 Identities=21% Similarity=0.259 Sum_probs=58.6
Q ss_pred hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccc
Q psy6501 30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVN 91 (174)
Q Consensus 30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l 91 (174)
.+..|++||.+|+++||||.+||+.+|+|+++|++||+|...|+.+.+.+||++||+++.+.
T Consensus 124 v~i~GerLk~lRe~~GlSq~eLA~~lGVSr~tIskyE~G~~~Ps~e~~~kLa~~Lgv~l~~~ 185 (317)
T PRK04140 124 VKIDGDVLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDVPLTKP 185 (317)
T ss_pred ehhhHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCChHHH
Confidence 46789999999999999999999999999999999999999999999999999999986553
No 23
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=99.31 E-value=8.2e-12 Score=74.95 Aligned_cols=56 Identities=29% Similarity=0.443 Sum_probs=53.3
Q ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccc
Q psy6501 36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVN 91 (174)
Q Consensus 36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l 91 (174)
+|+.+|+..|+|+.++|+.+|+++.+|++|++|...|+...+.+|+++||++++||
T Consensus 1 ~i~~~~~~~~~s~~~la~~~~i~~~~i~~~~~~~~~~~~~~~~~i~~~~~~~~~~~ 56 (56)
T smart00530 1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56 (56)
T ss_pred CHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCCChhhC
Confidence 47889999999999999999999999999999999999999999999999999875
No 24
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=99.30 E-value=1.2e-11 Score=91.84 Aligned_cols=70 Identities=30% Similarity=0.494 Sum_probs=65.1
Q ss_pred cccchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCC
Q psy6501 26 HEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTN 95 (174)
Q Consensus 26 ~~~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~ 95 (174)
...+..+++++|+.+|+.+||||+|||.+++++.+.|.+||+|+..|+.....+|.++|+|...+....+
T Consensus 73 ~~elvedY~e~Ir~ARE~~G~SqedLA~ki~ek~svI~~iE~g~~~P~~~~akkLEk~LgIkL~e~~~~~ 142 (165)
T COG1813 73 LPELVEDYGERIREAREKRGLSQEDLAAKLKEKVSVIRRIERGEATPNIKVAKKLEKLLGIKLVEKVDEE 142 (165)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCHHHHHHHhcccHHHHHHHHhcccCccHHHHHHHHHHhCceeeeecccc
Confidence 4456789999999999999999999999999999999999999999999999999999999998887544
No 25
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=99.28 E-value=1.1e-11 Score=89.10 Aligned_cols=61 Identities=23% Similarity=0.253 Sum_probs=56.2
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501 31 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA 92 (174)
Q Consensus 31 ~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~ 92 (174)
+..+.+|+.+|+..|+||.+||+.+|+|+++|++||+|...|+.. +.++++.|+++++||.
T Consensus 64 ~~~~~~i~~~r~~~gltq~~lA~~lg~~~~tis~~e~g~~~p~~~-~~~l~~~l~~~p~~l~ 124 (127)
T TIGR03830 64 LLTPPEIRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSKA-LDKLLRLLDKHPELLE 124 (127)
T ss_pred CcCHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHH-HHHHHHHHHHChHHHH
Confidence 457889999999999999999999999999999999999999865 7889999999999974
No 26
>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=99.25 E-value=3.5e-11 Score=72.66 Aligned_cols=58 Identities=28% Similarity=0.441 Sum_probs=54.7
Q ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccc
Q psy6501 34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVN 91 (174)
Q Consensus 34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l 91 (174)
|+.|+..|+..|+|+.++|+.+|+++++|++|++|...|+...+.+|+++|+++++|+
T Consensus 1 ~~~l~~~~~~~~~s~~~~a~~~~~~~~~v~~~~~g~~~~~~~~~~~i~~~~~~~~~~l 58 (58)
T cd00093 1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58 (58)
T ss_pred ChHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCChhhC
Confidence 3578899999999999999999999999999999999999999999999999998875
No 27
>PRK10856 cytoskeletal protein RodZ; Provisional
Probab=99.21 E-value=3.4e-11 Score=99.78 Aligned_cols=65 Identities=22% Similarity=0.207 Sum_probs=60.1
Q ss_pred hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCH------HHHHHHHHHhCcccccccCC
Q psy6501 30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQ------AIIGKMERALGIRLRVNAGT 94 (174)
Q Consensus 30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~------~~l~~la~~L~v~~~~l~~~ 94 (174)
.+.+|++||.+|+++||||++||+++|+++++|++||+|...|.. .++..+|++|||+.++|+..
T Consensus 12 ~~~~G~~Lr~aRe~~GlSq~~vA~~l~l~~~~I~~iE~g~~~~~~~~tf~RGyir~yA~~lgv~~~~L~~~ 82 (331)
T PRK10856 12 ALTTGERLRQAREQLGLTQQAVAERLCLKVSTVRDIEEDKAPADLASTFLRGYIRSYARLVHIPEEELLPG 82 (331)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHCCCCCCChhHHHHHHHHHHHHHHHCcCHHHHHHh
Confidence 456999999999999999999999999999999999999988887 56899999999999999853
No 28
>PHA01976 helix-turn-helix protein
Probab=99.19 E-value=7e-11 Score=75.66 Aligned_cols=52 Identities=25% Similarity=0.561 Sum_probs=49.9
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501 123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174 (174)
Q Consensus 123 ~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l 174 (174)
++.+|+.+|+.+|+||.++|+++|+++++|++||+|...|+.+.+.+||++|
T Consensus 3 ~~~rl~~~R~~~glt~~~lA~~~gvs~~~v~~~e~g~~~p~~~~l~~ia~~l 54 (67)
T PHA01976 3 FAIQLIKARNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADAL 54 (67)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence 5789999999999999999999999999999999999999999999999976
No 29
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=99.15 E-value=1.5e-10 Score=76.99 Aligned_cols=61 Identities=21% Similarity=0.273 Sum_probs=51.1
Q ss_pred chHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCcccc
Q psy6501 29 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR-GIPNQAIIGKMERALGIRLR 89 (174)
Q Consensus 29 ~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~-~~P~~~~l~~la~~L~v~~~ 89 (174)
+...+...|+.+|+++||||.|+|+.+|++++.||++|+|+ ..++++.|.+++..||..++
T Consensus 15 ~k~~l~~~i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L~~~l~aLG~~v~ 76 (80)
T PF13744_consen 15 AKAQLMAAIRELREERGLTQAELAERLGISQPRVSRLENGKIDDFSLDTLLRYLEALGGRVE 76 (80)
T ss_dssp HHHHHHHHHHHHHHCCT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHHHHHHHHHTTEEEE
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHHHHHHHHHcCCeEE
Confidence 45678888999999999999999999999999999999987 78999999999999998875
No 30
>PRK13355 bifunctional HTH-domain containing protein/aminotransferase; Provisional
Probab=99.14 E-value=1.1e-10 Score=102.00 Aligned_cols=66 Identities=21% Similarity=0.309 Sum_probs=61.3
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHh-----CCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCCC
Q psy6501 31 LDLAKLLMQGRQAKGWSQKDLATKI-----NEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTNK 96 (174)
Q Consensus 31 ~~ig~~ik~~R~~~gltq~eLA~~i-----gvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~~ 96 (174)
+.|++||+.+|+++|+||.+||+.+ +|++++|++||+|+..|+.+.+.+||++|+|+++||++...
T Consensus 2 ~~~~~rL~~~r~~~g~tq~~la~~~~~~g~~vs~~~is~~e~g~~~p~~~~l~~la~~l~v~~~~l~~~~~ 72 (517)
T PRK13355 2 TTFAERLKQAMKARGLKQEDLVHAAEARGVKLGKSHISQYVSGKTGPRRDVLPFLAAILGVSEDWLLGGES 72 (517)
T ss_pred chHHHHHHHHHHHCCCCHHHHHHHHHhccCCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCcCHHHHccCCc
Confidence 4689999999999999999999986 69999999999999999999999999999999999985443
No 31
>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=99.14 E-value=2.3e-10 Score=70.64 Aligned_cols=53 Identities=25% Similarity=0.295 Sum_probs=50.2
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501 122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174 (174)
Q Consensus 122 ~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l 174 (174)
.++..|+..|+..|++|.++|+.+|+++++|++||+|+..|+...+.+|+++|
T Consensus 2 ~~~~~l~~~r~~~gltq~~lA~~~gvs~~~vs~~e~g~~~~~~~~~~~i~~~l 54 (58)
T TIGR03070 2 QIGMLVRARRKALGLTQADLADLAGVGLRFIRDVENGKPTVRLDKVLRVLDAL 54 (58)
T ss_pred hHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHc
Confidence 35788999999999999999999999999999999999999999999999886
No 32
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=99.12 E-value=1.7e-10 Score=70.96 Aligned_cols=48 Identities=31% Similarity=0.477 Sum_probs=43.9
Q ss_pred HHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501 127 LMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174 (174)
Q Consensus 127 i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l 174 (174)
|++.|++.|+||.++|+.+|+++++|++||+|...|+.+.+.+|+++|
T Consensus 1 ik~~r~~~gls~~~la~~~gis~~~i~~~~~g~~~~~~~~~~~ia~~l 48 (55)
T PF01381_consen 1 IKELRKEKGLSQKELAEKLGISRSTISRIENGKRNPSLDTLKKIAKAL 48 (55)
T ss_dssp HHHHHHHTTS-HHHHHHHHTS-HHHHHHHHTTSSTSBHHHHHHHHHHH
T ss_pred CHHHHHHcCCCHHHHHHHhCCCcchhHHHhcCCCCCCHHHHHHHHHHH
Confidence 578899999999999999999999999999999999999999999875
No 33
>PRK08359 transcription factor; Validated
Probab=99.12 E-value=1.7e-10 Score=87.22 Aligned_cols=57 Identities=19% Similarity=0.215 Sum_probs=54.7
Q ss_pred cccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501 118 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174 (174)
Q Consensus 118 ~~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l 174 (174)
.+..+++.+|+++|+.+||||++||+.+|++.++|+.||+|...|+.+.+.+|+++|
T Consensus 81 elv~dy~~rIkeaRe~kglSQeeLA~~lgvs~stI~~iE~G~~~Ps~~~l~kLak~l 137 (176)
T PRK08359 81 DIVEDYAERVYEAIQKSGLSYEELSHEVGLSVNDLRRIAHGEYEPTIKEAKKLERYF 137 (176)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCcCCCHHHHHHHHHHh
Confidence 566789999999999999999999999999999999999999999999999999987
No 34
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=99.09 E-value=2.6e-10 Score=84.66 Aligned_cols=58 Identities=31% Similarity=0.519 Sum_probs=54.9
Q ss_pred ccccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501 117 EKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174 (174)
Q Consensus 117 ~~~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l 174 (174)
..+..++.++|+.+|+++||||++||+++++..+.|.+||+|+..|+...+.+|.++|
T Consensus 74 ~elvedY~e~Ir~ARE~~G~SqedLA~ki~ek~svI~~iE~g~~~P~~~~akkLEk~L 131 (165)
T COG1813 74 PELVEDYGERIREAREKRGLSQEDLAAKLKEKVSVIRRIERGEATPNIKVAKKLEKLL 131 (165)
T ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHhcccHHHHHHHHhcccCccHHHHHHHHHHh
Confidence 4556889999999999999999999999999999999999999999999999999986
No 35
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=99.07 E-value=3.6e-10 Score=71.67 Aligned_cols=51 Identities=31% Similarity=0.468 Sum_probs=43.8
Q ss_pred HHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501 124 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174 (174)
Q Consensus 124 ~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l 174 (174)
+++|++.|+.+|+||.++|+.+|+++++++.||+|...|+...+.+||++|
T Consensus 1 G~~lk~~r~~~~lt~~~~a~~~~i~~~~i~~~e~g~~~~~~~~l~~i~~~~ 51 (64)
T PF12844_consen 1 GERLKELREEKGLTQKDLAEKLGISRSTISKIENGKRKPSVSTLKKIAEAL 51 (64)
T ss_dssp HHHHHHHHHHCT--HHHHHHHHTS-HHHHHHHHTTSS--BHHHHHHHHHHH
T ss_pred CHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCcCCCHHHHHHHHHHh
Confidence 468999999999999999999999999999999999999999999999875
No 36
>PRK06424 transcription factor; Provisional
Probab=99.06 E-value=5.3e-10 Score=82.15 Aligned_cols=56 Identities=32% Similarity=0.452 Sum_probs=53.3
Q ss_pred ccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501 119 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174 (174)
Q Consensus 119 ~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l 174 (174)
+..+++.+|+.+|+++||||++||+.+|++.++|+.||+|...|+.+++.+|+++|
T Consensus 81 ~~~~~g~~Ir~lRe~~GLSQ~eLA~~iGvs~stIskiE~G~~~Ps~~~l~kLa~~L 136 (144)
T PRK06424 81 IVEDYAELVKNARERLSMSQADLAAKIFERKNVIASIERGDLLPDIKTARKLEKIL 136 (144)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHh
Confidence 35778999999999999999999999999999999999999999999999999987
No 37
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=99.05 E-value=5.4e-10 Score=83.08 Aligned_cols=57 Identities=30% Similarity=0.563 Sum_probs=54.0
Q ss_pred cccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501 118 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174 (174)
Q Consensus 118 ~~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l 174 (174)
.+..+++.+|+.+|+++||||++||+++|++.++|++||+|...|+.+.+.+|+++|
T Consensus 65 ~l~~~~g~~Ir~~Re~~glSqeeLA~~lgvs~s~IsriE~G~~~Ps~~~l~kLa~~L 121 (154)
T TIGR00270 65 ELVEDYGIIIRREREKRGWSQEQLAKKIQEKESLIKKIENAEIEPEPKVVEKLEKLL 121 (154)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHh
Confidence 455678999999999999999999999999999999999999999999999999987
No 38
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=99.05 E-value=7.1e-10 Score=70.48 Aligned_cols=52 Identities=31% Similarity=0.454 Sum_probs=46.7
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCC-CCCHHHHHHHHhhC
Q psy6501 123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG-IPNQAIIGKMERAL 174 (174)
Q Consensus 123 ~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~-~P~~~~l~~i~~~l 174 (174)
++..|+..|+..||||.++|+.+|+++++|++||+|.. .|+.+.+.+|+++|
T Consensus 2 lg~~lr~~R~~~gls~~~lA~~~g~s~s~v~~iE~G~~~~p~~~~l~~l~~~l 54 (64)
T PF13560_consen 2 LGRRLRRLRERAGLSQAQLADRLGVSQSTVSRIERGRRPRPSPDTLQRLARAL 54 (64)
T ss_dssp HHHHHHHHHHCHTS-HHHHHHHHTS-HHHHHHHHTTSSSS-BHHHHHHHHHHT
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCCHHHHHHHHHHH
Confidence 67899999999999999999999999999999999999 59999999999986
No 39
>PHA00542 putative Cro-like protein
Probab=99.05 E-value=1e-09 Score=73.34 Aligned_cols=51 Identities=20% Similarity=0.346 Sum_probs=46.8
Q ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHh
Q psy6501 34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR-GIPNQAIIGKMERAL 84 (174)
Q Consensus 34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~-~~P~~~~l~~la~~L 84 (174)
..++...++..|+||.+||+.+|||+++|++||+|. ..|+.+.+.+||+++
T Consensus 20 ~~~l~~~l~~~glTq~elA~~lgIs~~tIsr~e~g~~~~p~~~~l~ki~~~~ 71 (82)
T PHA00542 20 PDELVCALIRAGWSQEQIADATDVSQPTICRIYSGRHKDPRYSVVEKLRHLV 71 (82)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHH
Confidence 446778889999999999999999999999999999 589999999999985
No 40
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=99.03 E-value=8.7e-10 Score=70.40 Aligned_cols=50 Identities=24% Similarity=0.292 Sum_probs=48.1
Q ss_pred HHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501 125 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174 (174)
Q Consensus 125 ~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l 174 (174)
..++..|...|+||.++|+.+|+++.+|..+|+|+-.|+..++.+||++|
T Consensus 4 nk~k~~R~~~~ltQ~elA~~vgVsRQTi~~iEkgky~Psl~La~kia~~f 53 (68)
T COG1476 4 NKLKELRAELGLTQEELAKLVGVSRQTIIAIEKGKYNPSLELALKIARVF 53 (68)
T ss_pred hHHHHHHHHhCcCHHHHHHHcCcCHHHHHHHHcCCCCchHHHHHHHHHHh
Confidence 37899999999999999999999999999999999999999999999987
No 41
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=99.02 E-value=7.8e-10 Score=81.67 Aligned_cols=53 Identities=25% Similarity=0.317 Sum_probs=50.2
Q ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCc
Q psy6501 34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI 86 (174)
Q Consensus 34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v 86 (174)
.+-||+.|++.|+||++||++.|||+++|.++|.|.-.|++.++.+|-++|.-
T Consensus 7 pedlrk~Rk~LGitQ~dLA~~aGVSQ~~IArlE~G~vdPrlSt~k~Il~aL~e 59 (187)
T COG3620 7 PEDLRKRRKELGITQKDLARRAGVSQPYIARLEAGKVDPRLSTVKRILEALEE 59 (187)
T ss_pred HHHHHHHHHHcCCCHHHHHHHcCccHHHHHHHhcCCCCccHHHHHHHHHHHHH
Confidence 57799999999999999999999999999999999999999999999998753
No 42
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=98.96 E-value=2e-09 Score=74.25 Aligned_cols=45 Identities=24% Similarity=0.273 Sum_probs=41.9
Q ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH
Q psy6501 34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG 78 (174)
Q Consensus 34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~ 78 (174)
+..|+.+|+..|+||.+||..+|+|.+||++||.|+..|+..-+.
T Consensus 46 ~~eIk~iRe~~~lSQ~vFA~~L~vs~~Tv~~WEqGr~kPsg~Alk 90 (104)
T COG2944 46 PTEIKAIREKLGLSQPVFARYLGVSVSTVRKWEQGRKKPSGAALK 90 (104)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHcCCcCCCCHHHH
Confidence 778999999999999999999999999999999999999976554
No 43
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=98.95 E-value=5.4e-09 Score=67.91 Aligned_cols=42 Identities=19% Similarity=0.181 Sum_probs=38.4
Q ss_pred hHHHHHHHHHHHHHcCCCHHHHHHHhC------CCHHHHHHHHcCCCC
Q psy6501 30 PLDLAKLLMQGRQAKGWSQKDLATKIN------EKPQIVNDYEGGRGI 71 (174)
Q Consensus 30 ~~~ig~~ik~~R~~~gltq~eLA~~ig------vs~~~is~~E~G~~~ 71 (174)
+..||++++..|++.|+||.|||+++| +|+++||+||+|.-.
T Consensus 9 le~~~~~lk~~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es~~ls 56 (75)
T smart00352 9 LEAFAKTFKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEALQLS 56 (75)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHhcCcc
Confidence 347999999999999999999999999 499999999998753
No 44
>PRK09726 antitoxin HipB; Provisional
Probab=98.94 E-value=4.3e-09 Score=71.20 Aligned_cols=55 Identities=29% Similarity=0.459 Sum_probs=51.8
Q ss_pred cHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501 120 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174 (174)
Q Consensus 120 ~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l 174 (174)
...++.+|+..|...|+||.++|+.+|+++++|+.||+|...|+...+.+|+++|
T Consensus 10 ~~~l~~~lk~~R~~~gltq~elA~~~gvs~~tis~~e~g~~~ps~~~l~~ia~~l 64 (88)
T PRK09726 10 PTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSL 64 (88)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHc
Confidence 3467889999999999999999999999999999999999999999999999886
No 45
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 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 [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.
Probab=98.91 E-value=7.6e-10 Score=70.97 Aligned_cols=59 Identities=17% Similarity=0.260 Sum_probs=44.4
Q ss_pred HHHHHHHHcCCCH-HHHHHHhCCCHHHHH-HHHcCCCCCCHHHHHHHHHHhCcccccccCCC
Q psy6501 36 LLMQGRQAKGWSQ-KDLATKINEKPQIVN-DYEGGRGIPNQAIIGKMERALGIRLRVNAGTN 95 (174)
Q Consensus 36 ~ik~~R~~~gltq-~eLA~~igvs~~~is-~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~ 95 (174)
+|+++++..|++. .|||+.+|||+++|+ .|......| .+.+.+||..+||+++||+...
T Consensus 2 ~i~rl~~~~g~~~~~~lA~~lgis~st~s~~~~~r~~~P-~~~l~~ia~~~gvsl~WLltG~ 62 (66)
T PF07022_consen 2 VIERLKEALGVKSDKELAERLGISKSTLSNNWKKRGSIP-AEWLIKIALETGVSLDWLLTGK 62 (66)
T ss_dssp HHHHHHHHHT-SSCHHHHCCTT--HHHHH-HHHHSSS---HHHHHHHHHHH---HHHHHC-S
T ss_pred HHHHHHHHhCCCCHHHHHHHhCcCHHHhhHHHHhCCCCC-HHHHHHHHHHHCcCHHHHHhCC
Confidence 6788888888855 699999999999999 898877777 9999999999999999998543
No 46
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=98.90 E-value=4.7e-09 Score=76.40 Aligned_cols=53 Identities=19% Similarity=0.238 Sum_probs=50.5
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501 122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174 (174)
Q Consensus 122 ~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l 174 (174)
.++.+|+..|...|+||.++|+.+|+++++|+.||+|...|+...+.+||++|
T Consensus 5 ~~g~rlk~~R~~~gltq~~lA~~~gvs~~~is~~E~g~~~p~~~~l~~la~~l 57 (135)
T PRK09706 5 TLGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKAL 57 (135)
T ss_pred hHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence 46889999999999999999999999999999999999999999999999875
No 47
>PRK02866 cyanate hydratase; Validated
Probab=98.84 E-value=2.2e-08 Score=73.46 Aligned_cols=62 Identities=19% Similarity=0.181 Sum_probs=57.9
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501 31 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA 92 (174)
Q Consensus 31 ~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~ 92 (174)
..+.+.|..+|.++|+|++++|+++|+|+.++..++.|.+.++.+...+||++|+++.+...
T Consensus 4 ~~~~e~Ll~AK~~kGLTw~~IA~~iG~S~v~vaaa~lGQ~~ls~e~A~kla~~LgL~~~~~~ 65 (147)
T PRK02866 4 EELTEKILAAKKEKGLTWADIAEAIGLSEVWVTAALLGQMTLPAEEAEKVAELLGLDEDAVA 65 (147)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHhCCCCCCHHHHHHHHHHhCCCHHHHH
Confidence 35788999999999999999999999999999999999999999999999999999977543
No 48
>TIGR00673 cynS cyanate hydratase. Alternate names include cyanate lyase, cyanase and cyanate hydrolase.
Probab=98.79 E-value=3.9e-08 Score=72.31 Aligned_cols=60 Identities=17% Similarity=0.147 Sum_probs=57.4
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA 92 (174)
Q Consensus 33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~ 92 (174)
+.+.|..+|+++|||++++|+.+|+|+.++..++.|.+.++.+...+||++|+++.+.++
T Consensus 9 ~t~~Ll~AK~~KGLTwe~IAe~iG~sevwvaaa~lGQ~~ls~e~A~kla~lLgL~~e~~~ 68 (150)
T TIGR00673 9 LADALLESKKKKGLTFADIADGLGLAEVFVAAALYGQAAAPADEARLVGAKLDLDEDSIL 68 (150)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHhCCCCCCHHHHHHHHHHhCcCHHHHH
Confidence 788999999999999999999999999999999999999999999999999999987655
No 49
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized 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 uncoded by the upstream member of the gene pair.
Probab=98.78 E-value=2.4e-08 Score=65.56 Aligned_cols=52 Identities=17% Similarity=0.187 Sum_probs=48.6
Q ss_pred HHHHHH-HHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501 123 LAKLLM-QGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174 (174)
Q Consensus 123 ~~~~i~-~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l 174 (174)
.+++|+ ..|+..|+++.++|+++|+++++|+.||+|...|+...+.+|+++|
T Consensus 5 ~g~~i~~~~~~~~~~t~~~lA~~~gis~~tis~~~~g~~~~~~~~~~~l~~~l 57 (78)
T TIGR02607 5 PGEILREEFLEPLGLSIRALAKALGVSRSTLSRIVNGRRGITADMALRLAKAL 57 (78)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHc
Confidence 456788 7899999999999999999999999999999999999999999986
No 50
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=98.77 E-value=2.5e-08 Score=71.26 Aligned_cols=52 Identities=13% Similarity=0.272 Sum_probs=49.2
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501 123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174 (174)
Q Consensus 123 ~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l 174 (174)
+...|+..+..+|+||+++|+++|+++++|++||+|+..|+...+.+||++|
T Consensus 6 ~~~~l~~ll~~~Glsq~eLA~~~Gis~~~is~iE~g~~~ps~~~l~kIa~aL 57 (120)
T PRK13890 6 FFTNVLRLLDERHMTKKELSERSGVSISFLSDLTTGKANPSLKVMEAIADAL 57 (120)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence 5678889999999999999999999999999999999999999999999986
No 51
>PRK10072 putative transcriptional regulator; Provisional
Probab=98.75 E-value=2.3e-08 Score=68.60 Aligned_cols=49 Identities=22% Similarity=0.319 Sum_probs=43.9
Q ss_pred HHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501 125 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174 (174)
Q Consensus 125 ~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l 174 (174)
..|+..|+..|+||.++|+.+|++.++|++||+|++.|+...+. ++++|
T Consensus 36 ~eik~LR~~~glTQ~elA~~lGvS~~TVs~WE~G~r~P~~~~l~-Ll~~L 84 (96)
T PRK10072 36 TEFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVKPSSAELK-LMRLI 84 (96)
T ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH-HHHHH
Confidence 45888999999999999999999999999999999999998876 55553
No 52
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=98.75 E-value=2.9e-08 Score=75.87 Aligned_cols=54 Identities=22% Similarity=0.219 Sum_probs=51.4
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501 121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174 (174)
Q Consensus 121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l 174 (174)
..++.+|+..|+.+|+||.++|+.+|+++++|++||+|...|+...+.+|+++|
T Consensus 6 ~~~g~~l~~~R~~~glt~~elA~~~gis~~~is~~E~g~~~p~~~~l~~ia~~l 59 (185)
T PRK09943 6 LAPGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVY 59 (185)
T ss_pred hHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence 447889999999999999999999999999999999999999999999999986
No 53
>COG1396 HipB Predicted transcriptional regulators [Transcription]
Probab=98.73 E-value=6.4e-08 Score=63.96 Aligned_cols=61 Identities=26% Similarity=0.444 Sum_probs=58.0
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCcccccccC
Q psy6501 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG-IPNQAIIGKMERALGIRLRVNAG 93 (174)
Q Consensus 33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~-~P~~~~l~~la~~L~v~~~~l~~ 93 (174)
+|.+++.+|+..|+||+++|..+|++..+++.||+|.. .|+...+..++..|+++..+++.
T Consensus 2 ~~~~~~~~r~~~~~s~~~~a~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 (120)
T COG1396 2 IGERLKELRKKKGLSQEELAERLGVSRSTISRIERGRSESPSLELLARLAAALGVSLDELLE 63 (120)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCCHHHHHHHHHHHCCCHHHhcC
Confidence 68999999999999999999999999999999999999 99999999999999999887663
No 54
>COG1709 Predicted transcriptional regulator [Transcription]
Probab=98.70 E-value=1.5e-08 Score=78.18 Aligned_cols=55 Identities=33% Similarity=0.471 Sum_probs=50.9
Q ss_pred hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCC-CCHHHHHHHHHHh
Q psy6501 30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGI-PNQAIIGKMERAL 84 (174)
Q Consensus 30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~-P~~~~l~~la~~L 84 (174)
....|+.||+-|+..+.||.|||+.+|+|++.||+||.|++. |....+.++.++|
T Consensus 25 S~~pge~lrKWR~~F~vSQ~elA~~l~vSpSVISDYE~GRRk~Pg~~~vkk~V~AL 80 (241)
T COG1709 25 SEDPGETLRKWREIFNVSQTELARELGVSPSVISDYESGRRKSPGIAFVKKFVEAL 80 (241)
T ss_pred cCChhHHHHHHHHHhCccHHHHHHHhCCCcceeehhhccCccCccHHHHHHHHHHH
Confidence 356899999999999999999999999999999999999988 9999999888775
No 55
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein. 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=98.69 E-value=5.9e-08 Score=65.77 Aligned_cols=53 Identities=30% Similarity=0.324 Sum_probs=48.7
Q ss_pred cHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501 120 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174 (174)
Q Consensus 120 ~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l 174 (174)
+..+...|+..|+.+|||| +|+.+|++++++++||+|...|+.+.+.+||++|
T Consensus 30 ~~~~~~~l~~~r~~~glSq--LAe~~GIs~stLs~iE~g~~~Ps~~tL~kI~~aL 82 (89)
T TIGR02684 30 PAYIAHALGYIARARGMTQ--LARKTGLSRESLYKALSGKGNPTFDTILKVTKAL 82 (89)
T ss_pred HHHHHHHHHHHHHHCChHH--HHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHc
Confidence 3446778999999999995 9999999999999999999999999999999987
No 56
>COG3655 Predicted transcriptional regulator [Transcription]
Probab=98.67 E-value=4.5e-08 Score=63.28 Aligned_cols=62 Identities=18% Similarity=0.078 Sum_probs=57.1
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCcccccccC
Q psy6501 32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR-GIPNQAIIGKMERALGIRLRVNAG 93 (174)
Q Consensus 32 ~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~-~~P~~~~l~~la~~L~v~~~~l~~ 93 (174)
.+.-++..+...++++..|||+.+|+|.+++|.+.+|+ ...+.++|.+||++|+|.+.+++.
T Consensus 2 ~i~~~l~~~l~~r~~~~~eLa~~igis~~~ls~l~~gk~k~I~~~tL~~iC~~LeCqpgDile 64 (73)
T COG3655 2 PIAVRLDVMLADRKISLKELAEAIGISEANLSKLKTGKVKAIRLSTLEKICKALECQPGDILE 64 (73)
T ss_pred cchHhHHHHHHHHhhhHHHHHHHHcccHHHHHHHHcCCcceeeHHHHHHHHHHcCCChhheeE
Confidence 35668889999999999999999999999999999998 668999999999999999999983
No 57
>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed
Probab=98.67 E-value=6.8e-08 Score=79.56 Aligned_cols=56 Identities=23% Similarity=0.294 Sum_probs=52.9
Q ss_pred ccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501 119 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174 (174)
Q Consensus 119 ~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l 174 (174)
+...++.+|+..|+.+|+||+++|+++|+++++|++||+|+..|+...+.+|+++|
T Consensus 25 ~~~~~g~rl~~~R~~~gltq~~lA~~~gvs~~~i~~~E~g~~~ps~~~l~~ia~~l 80 (309)
T PRK08154 25 FLAALGERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARAL 80 (309)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHh
Confidence 34668999999999999999999999999999999999999999999999999986
No 58
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=98.62 E-value=1.1e-07 Score=65.48 Aligned_cols=59 Identities=14% Similarity=0.219 Sum_probs=52.3
Q ss_pred HHHHHH-HHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501 34 AKLLMQ-GRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA 92 (174)
Q Consensus 34 g~~ik~-~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~ 92 (174)
|+-|++ +-+-.|+||.+||+.+||++.+|+.+-||++..+.+...+|+++||.++++.+
T Consensus 11 GEiL~eeflep~glt~~~lA~~lgV~r~~is~ling~~~iT~dmAlrL~k~fGtspefWl 70 (104)
T COG3093 11 GEILREEFLEPLGLTQTELAEALGVTRNTISELINGRRAITADMALRLAKVFGTSPEFWL 70 (104)
T ss_pred hHHHHHHHhccccCCHHHHHHHhCCCHHHHHHHHcCCcCCCHHHHHHHHHHhCCCHHHHH
Confidence 444443 34556999999999999999999999999999999999999999999999776
No 59
>TIGR02612 mob_myst_A mobile mystery protein A. Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).
Probab=98.58 E-value=2e-07 Score=69.05 Aligned_cols=51 Identities=24% Similarity=0.194 Sum_probs=47.4
Q ss_pred HHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCC--CCHHHHHHHHhhC
Q psy6501 124 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGI--PNQAIIGKMERAL 174 (174)
Q Consensus 124 ~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~--P~~~~l~~i~~~l 174 (174)
...|+..|...||||.++|+++|+++++|+.||+|... |+...+.+|+++|
T Consensus 27 ~~~Ir~~R~~lGmTq~eLAerlGVS~~tIs~iE~G~~~~~psl~~L~kIA~aL 79 (150)
T TIGR02612 27 EGWVRAIRKALGMSGAQLAGRLGVTPQRVEALEKSELSGTVTLKTLRAAAEAL 79 (150)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCCCHHHHHHHHHHc
Confidence 36899999999999999999999999999999999864 8999999999986
No 60
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=98.57 E-value=1.4e-07 Score=59.70 Aligned_cols=55 Identities=27% Similarity=0.404 Sum_probs=41.5
Q ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC--CCCCH----HHHHHHHHHhCccccc
Q psy6501 36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR--GIPNQ----AIIGKMERALGIRLRV 90 (174)
Q Consensus 36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~--~~P~~----~~l~~la~~L~v~~~~ 90 (174)
+||..|+++|+|++|+|..++|+.++|..+|+|. ..|+. ..+...|++||++.+.
T Consensus 1 ~Lr~~R~~~glsl~~va~~t~I~~~~l~aiE~~~~~~lp~~~y~rg~lr~Ya~~Lgld~~~ 61 (62)
T PF13413_consen 1 RLREAREAKGLSLEDVAEETKISVSYLEAIENGDFDSLPSPVYARGYLRKYARFLGLDPDE 61 (62)
T ss_dssp -HHHHHHCTT--HHHHHHHCS--HHHHHHHHCT-GCCSSSHHHHHHHHHHHHHHTT--HHH
T ss_pred ChHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCcChhhCCcHHHHHHHHHHHHHHhCcCccc
Confidence 4899999999999999999999999999999997 66765 4567899999998753
No 61
>PRK04140 hypothetical protein; Provisional
Probab=98.55 E-value=1.9e-07 Score=76.96 Aligned_cols=54 Identities=22% Similarity=0.287 Sum_probs=51.0
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501 121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174 (174)
Q Consensus 121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l 174 (174)
.-.+..|+..|+.+||||.++|+.+|++++++++||+|...|+.+.+.+|+++|
T Consensus 125 ~i~GerLk~lRe~~GlSq~eLA~~lGVSr~tIskyE~G~~~Ps~e~~~kLa~~L 178 (317)
T PRK04140 125 KIDGDVLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEIL 178 (317)
T ss_pred hhhHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence 335789999999999999999999999999999999999999999999999986
No 62
>COG1395 Predicted transcriptional regulator [Transcription]
Probab=98.52 E-value=2.4e-07 Score=75.39 Aligned_cols=56 Identities=27% Similarity=0.308 Sum_probs=54.0
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccc
Q psy6501 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRL 88 (174)
Q Consensus 33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~ 88 (174)
=|+.||+.|+++|+|..+||..+|||+.+|++||+|...|+++...+|-+.||.+.
T Consensus 126 dge~Lre~Ree~glSlG~lA~~lgVSRktV~~YE~G~~~~sleva~kLeei~g~~i 181 (313)
T COG1395 126 DGEKLREKREEMGLSLGDLATMLGVSRKTVYKYEKGLSDASLEVALKLEEIFGEDI 181 (313)
T ss_pred chHHHHHHHHHcCcCHHHHHHHhCccHHHHHHhccCCCCccHHHHHHHHHHhcchh
Confidence 38999999999999999999999999999999999999999999999999999874
No 63
>PHA00542 putative Cro-like protein
Probab=98.48 E-value=5.5e-07 Score=60.10 Aligned_cols=49 Identities=20% Similarity=0.354 Sum_probs=44.0
Q ss_pred HHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCC-CCCCHHHHHHHHhhC
Q psy6501 126 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR-GIPNQAIIGKMERAL 174 (174)
Q Consensus 126 ~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~-~~P~~~~l~~i~~~l 174 (174)
.+...+...|+|+.++|+.+|+++++|++||+|. ..|+.+.+.+|++++
T Consensus 22 ~l~~~l~~~glTq~elA~~lgIs~~tIsr~e~g~~~~p~~~~l~ki~~~~ 71 (82)
T PHA00542 22 ELVCALIRAGWSQEQIADATDVSQPTICRIYSGRHKDPRYSVVEKLRHLV 71 (82)
T ss_pred HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHH
Confidence 4456678899999999999999999999999999 589999999999874
No 64
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=98.41 E-value=1.3e-06 Score=51.70 Aligned_cols=48 Identities=29% Similarity=0.474 Sum_probs=44.6
Q ss_pred HHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501 127 LMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174 (174)
Q Consensus 127 i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l 174 (174)
|+..+...++|+.++|+.+|+++.+++.|++|...|+...+.+|+++|
T Consensus 2 i~~~~~~~~~s~~~la~~~~i~~~~i~~~~~~~~~~~~~~~~~i~~~~ 49 (56)
T smart00530 2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKAL 49 (56)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHh
Confidence 456788899999999999999999999999999999999999999876
No 65
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=98.39 E-value=1.1e-06 Score=62.95 Aligned_cols=50 Identities=24% Similarity=0.311 Sum_probs=43.1
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhh
Q psy6501 123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERA 173 (174)
Q Consensus 123 ~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~ 173 (174)
....|+..|...|+||.++|+.+|+++++|++||+|...|+..+ ..+.++
T Consensus 66 ~~~~i~~~r~~~gltq~~lA~~lg~~~~tis~~e~g~~~p~~~~-~~l~~~ 115 (127)
T TIGR03830 66 TPPEIRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSKAL-DKLLRL 115 (127)
T ss_pred CHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHH-HHHHHH
Confidence 34678999999999999999999999999999999999998764 445444
No 66
>COG1709 Predicted transcriptional regulator [Transcription]
Probab=98.35 E-value=4.5e-07 Score=70.14 Aligned_cols=56 Identities=32% Similarity=0.474 Sum_probs=50.8
Q ss_pred ccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCC-CCHHHHHHHHhhC
Q psy6501 119 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGI-PNQAIIGKMERAL 174 (174)
Q Consensus 119 ~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~-P~~~~l~~i~~~l 174 (174)
.+.+.++.|+.||+..+.||.++|..+|+++|.|++||+|++. |...++.++-.+|
T Consensus 24 lS~~pge~lrKWR~~F~vSQ~elA~~l~vSpSVISDYE~GRRk~Pg~~~vkk~V~AL 80 (241)
T COG1709 24 LSEDPGETLRKWREIFNVSQTELARELGVSPSVISDYESGRRKSPGIAFVKKFVEAL 80 (241)
T ss_pred ecCChhHHHHHHHHHhCccHHHHHHHhCCCcceeehhhccCccCccHHHHHHHHHHH
Confidence 3466789999999999999999999999999999999999988 9999999886654
No 67
>PF08667 BetR: BetR domain; InterPro: IPR013975 CheY-like phosphoacceptor (or receiver [REC]) domain is a common module in a variety of response regulators of the bacterial signal transduction systems. BetR is one of the many response regulators and is encoded mainly in Burkholderia spp. It is a N-terminal helix-turn-helix domain (HTH) and has been shown to be related to the XRE-type HTH domain (IPR001387 from INTERPRO), it has been suggested that BetR would have dimerization, protein-protein interaction, and activation/relief-of-inhibition properties [].
Probab=98.34 E-value=2e-06 Score=63.19 Aligned_cols=64 Identities=16% Similarity=0.118 Sum_probs=60.0
Q ss_pred hHHHHHHHHHHHHHcCCCH----HHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501 30 PLDLAKLLMQGRQAKGWSQ----KDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG 93 (174)
Q Consensus 30 ~~~ig~~ik~~R~~~gltq----~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~ 93 (174)
.+.++++|+.+..++|+.+ .+||+-+|+|.+++++--+|....++..+.+||+.||+++++|++
T Consensus 3 ~~~~~erV~~Ll~~~Gi~kr~~~s~LA~iL~Is~ssa~RKL~G~~~ftl~EI~~Ia~~fgvS~d~l~g 70 (147)
T PF08667_consen 3 DQAIAERVRELLDRKGIPKRKHASELADILGISYSSAYRKLNGKSPFTLEEIKKIAKHFGVSPDELFG 70 (147)
T ss_pred hHHHHHHHHHHHHHcCCcchhhHHHHHHHHCCCHHHHHHHhcCCCCCCHHHHHHHHHHhCcCHHHHHh
Confidence 3578999999999999977 559999999999999999999999999999999999999999995
No 68
>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=98.32 E-value=2.5e-06 Score=50.82 Aligned_cols=50 Identities=28% Similarity=0.453 Sum_probs=45.8
Q ss_pred HHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501 125 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174 (174)
Q Consensus 125 ~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l 174 (174)
..|+..+...++++.++|+.+|+++.+++.|++|...|+...+.+|++.|
T Consensus 2 ~~l~~~~~~~~~s~~~~a~~~~~~~~~v~~~~~g~~~~~~~~~~~i~~~~ 51 (58)
T cd00093 2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKAL 51 (58)
T ss_pred hHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence 35677788899999999999999999999999999999999999999875
No 69
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=98.32 E-value=1.7e-06 Score=59.79 Aligned_cols=45 Identities=24% Similarity=0.273 Sum_probs=40.8
Q ss_pred HHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHH
Q psy6501 124 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG 168 (174)
Q Consensus 124 ~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~ 168 (174)
...|+..|+..++||.+||..+|++.+++++||+|+..|+-.-+.
T Consensus 46 ~~eIk~iRe~~~lSQ~vFA~~L~vs~~Tv~~WEqGr~kPsg~Alk 90 (104)
T COG2944 46 PTEIKAIREKLGLSQPVFARYLGVSVSTVRKWEQGRKKPSGAALK 90 (104)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHcCCcCCCCHHHH
Confidence 468889999999999999999999999999999999999865543
No 70
>COG1426 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]
Probab=98.29 E-value=1.5e-06 Score=70.81 Aligned_cols=63 Identities=24% Similarity=0.332 Sum_probs=56.0
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC--CCCCH----HHHHHHHHHhCcccccccC
Q psy6501 31 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR--GIPNQ----AIIGKMERALGIRLRVNAG 93 (174)
Q Consensus 31 ~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~--~~P~~----~~l~~la~~L~v~~~~l~~ 93 (174)
..+|++||+.|+++|||++|+|.+++|.+++|..+|+|. ..|.. ..+...|++|+++.+.|+.
T Consensus 2 ~~~Ge~Lr~~Re~~gLsL~dva~~t~I~~~~L~aiEeg~~~~lp~~~y~rG~ir~YA~~l~ld~~~l~~ 70 (284)
T COG1426 2 KTLGERLRQAREEKGLSLEDVAARTKIRKSYLRALEEGNFDKLPGPVYIRGYIRSYAKFLGLDEDELLQ 70 (284)
T ss_pred ccHHHHHHHHHHHcCCCHHHHHHHhCccHHHHHHHhcCccccccchHHHHHHHHHHHHHhCCCHHHHHH
Confidence 478999999999999999999999999999999999998 44544 3567899999999998873
No 71
>COG5499 Predicted transcription regulator containing HTH domain [Transcription]
Probab=98.28 E-value=1.9e-06 Score=59.54 Aligned_cols=58 Identities=22% Similarity=0.254 Sum_probs=54.6
Q ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501 34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA 92 (174)
Q Consensus 34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~ 92 (174)
-+.|+.+.+..|+|+.+||..+| |++.+|++-+|++..+.+.+.+|.+.||++.+.|.
T Consensus 62 ve~I~t~Md~~glt~~dLa~~iG-Sks~vS~iL~~rraLTle~ikkL~q~~gIpa~~lI 119 (120)
T COG5499 62 VEVIRTLMDQYGLTLADLANEIG-SKSRVSNILSGRRALTLEHIKKLHQRFGIPADVLI 119 (120)
T ss_pred HHHHHHHHHHhCCcHHHHHHHhC-chHHHHHHHhhhhHhhHHHHHHHHHHhCcCHHHhc
Confidence 46899999999999999999999 89999999999999999999999999999988764
No 72
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=98.22 E-value=3.3e-06 Score=53.03 Aligned_cols=48 Identities=27% Similarity=0.362 Sum_probs=37.4
Q ss_pred HHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCC-CCCCHHHHHHHHhhC
Q psy6501 127 LMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR-GIPNQAIIGKMERAL 174 (174)
Q Consensus 127 i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~-~~P~~~~l~~i~~~l 174 (174)
|+.....+|+++.++|+..|++++++++|-+|. ..|+.+.+.+||++|
T Consensus 2 L~~~m~~~~it~~~La~~~gis~~tl~~~~~~~~~~~~~~~l~~ia~~l 50 (63)
T PF13443_consen 2 LKELMAERGITQKDLARKTGISRSTLSRILNGKPSNPSLDTLEKIAKAL 50 (63)
T ss_dssp HHHHHHHTT--HHHHHHHHT--HHHHHHHHTTT-----HHHHHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcccccccHHHHHHHHHHc
Confidence 667788999999999999999999999999998 799999999999986
No 73
>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=98.21 E-value=2.9e-06 Score=51.21 Aligned_cols=43 Identities=19% Similarity=0.183 Sum_probs=36.1
Q ss_pred HHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCccccccc
Q psy6501 50 DLATKINEKPQIVNDYEGGRGIPNQAI---IGKMERALGIRLRVNA 92 (174)
Q Consensus 50 eLA~~igvs~~~is~~E~G~~~P~~~~---l~~la~~L~v~~~~l~ 92 (174)
+||+++|||+++||+|++|...++... +..++..||+.++|+.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~~vs~~~~~~i~~~~~~l~~~~~~~~ 47 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKPRVSEETRERVLAAAEELGYRPNAAA 47 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHHHhCCCCCHHH
Confidence 799999999999999999997666555 4558889999888754
No 74
>PRK10856 cytoskeletal protein RodZ; Provisional
Probab=98.19 E-value=4.4e-06 Score=69.52 Aligned_cols=53 Identities=23% Similarity=0.286 Sum_probs=48.1
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCH------HHHHHHHhhC
Q psy6501 122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQ------AIIGKMERAL 174 (174)
Q Consensus 122 ~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~------~~l~~i~~~l 174 (174)
.++.+|+++|+++||||+++|+++++++++|+.||+|...|.. .+++.+|++|
T Consensus 14 ~~G~~Lr~aRe~~GlSq~~vA~~l~l~~~~I~~iE~g~~~~~~~~tf~RGyir~yA~~l 72 (331)
T PRK10856 14 TTGERLRQAREQLGLTQQAVAERLCLKVSTVRDIEEDKAPADLASTFLRGYIRSYARLV 72 (331)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHCCCCCCChhHHHHHHHHHHHHHHH
Confidence 4789999999999999999999999999999999999998877 4578888875
No 75
>PRK02866 cyanate hydratase; Validated
Probab=98.16 E-value=1e-05 Score=59.48 Aligned_cols=53 Identities=19% Similarity=0.189 Sum_probs=50.2
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501 122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174 (174)
Q Consensus 122 ~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l 174 (174)
++.+.|..+|.++|+|++++|+++|+++..+..++.|...++.+.+.+|+++|
T Consensus 5 ~~~e~Ll~AK~~kGLTw~~IA~~iG~S~v~vaaa~lGQ~~ls~e~A~kla~~L 57 (147)
T PRK02866 5 ELTEKILAAKKEKGLTWADIAEAIGLSEVWVTAALLGQMTLPAEEAEKVAELL 57 (147)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHhCCCCCCHHHHHHHHHHh
Confidence 45678999999999999999999999999999999999999999999999986
No 76
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=98.07 E-value=1.8e-05 Score=53.84 Aligned_cols=48 Identities=13% Similarity=0.085 Sum_probs=39.0
Q ss_pred HHHHHHHHHHH--HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHH
Q psy6501 32 DLAKLLMQGRQ--AKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGK 79 (174)
Q Consensus 32 ~ig~~ik~~R~--~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~ 79 (174)
.++.|++-.+. ..++||.|+|+++|||++||++++|+...-+++.-.-
T Consensus 40 ~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn~lk~~~~~~~~~ 89 (94)
T TIGR01321 40 DLGDRIRIVNELLNGNMSQREIASKLGVSIATITRGSNNLKTMDPNFKQF 89 (94)
T ss_pred HHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHHhhcccCCHHHHHH
Confidence 67788888774 5789999999999999999999999997544444333
No 77
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=98.04 E-value=1.2e-05 Score=52.39 Aligned_cols=43 Identities=19% Similarity=0.201 Sum_probs=38.4
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHhCC------ChhHHHHHhcCCCCCC
Q psy6501 121 LDLAKLLMQGRQAKGWSQKDLATKINE------KPQIVNDYEGGRGIPN 163 (174)
Q Consensus 121 ~~~~~~i~~~R~~~glsq~ela~~lg~------~~s~i~~~E~G~~~P~ 163 (174)
..++..++.+|...|+||.++|+.+|. ++++|++||+|.-.+.
T Consensus 10 e~~~~~lk~~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es~~ls~~ 58 (75)
T smart00352 10 EAFAKTFKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEALQLSFK 58 (75)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHhcCccHH
Confidence 457889999999999999999999995 9999999999876544
No 78
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=98.03 E-value=2.4e-05 Score=51.86 Aligned_cols=55 Identities=20% Similarity=0.217 Sum_probs=43.4
Q ss_pred cHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcC-CCCCCHHHHHHHHhhC
Q psy6501 120 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGG-RGIPNQAIIGKMERAL 174 (174)
Q Consensus 120 ~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G-~~~P~~~~l~~i~~~l 174 (174)
...+...|...++.+||||.++|+.+|++++.|+++++| ...++.+.+.++..+|
T Consensus 16 k~~l~~~i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L~~~l~aL 71 (80)
T PF13744_consen 16 KAQLMAAIRELREERGLTQAELAERLGISQPRVSRLENGKIDDFSLDTLLRYLEAL 71 (80)
T ss_dssp HHHHHHHHHHHHHCCT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHHHHHHHHHc
Confidence 455677799999999999999999999999999999998 5568999988887764
No 79
>TIGR00673 cynS cyanate hydratase. Alternate names include cyanate lyase, cyanase and cyanate hydrolase.
Probab=97.97 E-value=3.4e-05 Score=56.87 Aligned_cols=52 Identities=19% Similarity=0.204 Sum_probs=49.9
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501 123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174 (174)
Q Consensus 123 ~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l 174 (174)
+.+.|..+|.++|+|.+++|+++|+++..+..++.|...|+.+.+.+|+++|
T Consensus 9 ~t~~Ll~AK~~KGLTwe~IAe~iG~sevwvaaa~lGQ~~ls~e~A~kla~lL 60 (150)
T TIGR00673 9 LADALLESKKKKGLTFADIADGLGLAEVFVAAALYGQAAAPADEARLVGAKL 60 (150)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHhCCCCCCHHHHHHHHHHh
Confidence 6688999999999999999999999999999999999999999999999986
No 80
>PRK08099 bifunctional DNA-binding transcriptional repressor/ NMN adenylyltransferase; Provisional
Probab=97.77 E-value=4.2e-05 Score=65.26 Aligned_cols=46 Identities=13% Similarity=0.271 Sum_probs=43.7
Q ss_pred cCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCcccc
Q psy6501 44 KGWSQKDLATKINEKPQIVNDYEGGR-GIPNQAIIGKMERALGIRLR 89 (174)
Q Consensus 44 ~gltq~eLA~~igvs~~~is~~E~G~-~~P~~~~l~~la~~L~v~~~ 89 (174)
.|+|.+|||+.+|+|++|++.+|||+ ..||.+.|.+|+++|||+..
T Consensus 2 ~~~~~~~~~~~~~~~~~y~~~l~~~~~~~ps~~~~~~~~~~~~~~~~ 48 (399)
T PRK08099 2 QGCTLQQVADASGMTKGYLSQLLNAKIKSPSAQKLEALHRFLGLEFP 48 (399)
T ss_pred CCCcHHHHHHHhCCcHHHHHHHhcCCCCCccHHHHHHHHHHhCCChh
Confidence 68999999999999999999999999 78999999999999999944
No 81
>PHA01083 hypothetical protein
Probab=97.74 E-value=8.6e-05 Score=54.31 Aligned_cols=58 Identities=22% Similarity=0.256 Sum_probs=49.2
Q ss_pred HHHHHHHHHcCC-CHHHHHHHhCCCHHHHHHHHcC-CCCCCHHHHHHHHHHhCcccc-ccc
Q psy6501 35 KLLMQGRQAKGW-SQKDLATKINEKPQIVNDYEGG-RGIPNQAIIGKMERALGIRLR-VNA 92 (174)
Q Consensus 35 ~~ik~~R~~~gl-tq~eLA~~igvs~~~is~~E~G-~~~P~~~~l~~la~~L~v~~~-~l~ 92 (174)
+-|..+.+.+++ +-++||..+|||++.||+|.+| ++.++-+....||+.+|+++. +++
T Consensus 5 kLLda~K~a~~~~sdkqLA~~LGVs~q~IS~~R~G~r~~i~de~A~~LAe~aGiDp~eall 65 (149)
T PHA01083 5 KLLDAYKKAKNYVQYKQIAHDLGVSPQKISKMRTGVRTYISDEEAIFLAESAGIDPEIALL 65 (149)
T ss_pred HHHHHHHHHHhhccHHHHHHHhCCCHHHHHHHHcCCCCCCCHHHHHHHHHHhCCCHHHHHH
Confidence 345556666666 5578999999999999999999 999999999999999999986 554
No 82
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=97.71 E-value=0.00011 Score=52.13 Aligned_cols=38 Identities=24% Similarity=0.212 Sum_probs=33.4
Q ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCC
Q psy6501 34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIP 72 (174)
Q Consensus 34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P 72 (174)
+.--+.++++ |+||.++|+.+|+|+++||+|-.|.+.|
T Consensus 12 a~lA~~L~ee-G~Sq~~iA~LLGltqaAVS~Yls~krg~ 49 (119)
T COG2522 12 ALLAKELIEE-GLSQYRIAKLLGLTQAAVSQYLSGKRGS 49 (119)
T ss_pred HHHHHHHHHc-CCcHHHHHHHhCCCHHHHHHHHccCCch
Confidence 4445667777 9999999999999999999999999985
No 83
>COG1396 HipB Predicted transcriptional regulators [Transcription]
Probab=97.56 E-value=0.00043 Score=45.08 Aligned_cols=51 Identities=25% Similarity=0.464 Sum_probs=47.1
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCC-CCCHHHHHHHHhh
Q psy6501 123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG-IPNQAIIGKMERA 173 (174)
Q Consensus 123 ~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~-~P~~~~l~~i~~~ 173 (174)
++..++..|...|+++++++..+|++..+++.||.|.. .|....+..++..
T Consensus 2 ~~~~~~~~r~~~~~s~~~~a~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~ 53 (120)
T COG1396 2 IGERLKELRKKKGLSQEELAERLGVSRSTISRIERGRSESPSLELLARLAAA 53 (120)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCCHHHHHHHHHH
Confidence 35788999999999999999999999999999999999 9999999988864
No 84
>COG4800 Predicted transcriptional regulator with an HTH domain [Transcription]
Probab=97.54 E-value=0.00051 Score=49.79 Aligned_cols=54 Identities=13% Similarity=0.164 Sum_probs=50.1
Q ss_pred hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q psy6501 30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 84 (174)
Q Consensus 30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L 84 (174)
...|++-++.+-.++|||..|+|++.|+..+|+.++-+| +.|+.++|.+|-..+
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
Confidence 357999999999999999999999999999999999999 889999999988765
No 85
>PF08965 DUF1870: Domain of unknown function (DUF1870); InterPro: IPR015060 This family consist of hypothetical bacterial proteins. ; PDB: 1S4K_A.
Probab=97.53 E-value=0.00037 Score=49.25 Aligned_cols=54 Identities=19% Similarity=0.140 Sum_probs=41.7
Q ss_pred HHHHHHHHHHcCCCHHHHHHHhC--CCHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Q psy6501 34 AKLLMQGRQAKGWSQKDLATKIN--EKPQIVNDYEGGRGIPNQAIIGKMERALGIR 87 (174)
Q Consensus 34 g~~ik~~R~~~gltq~eLA~~ig--vs~~~is~~E~G~~~P~~~~l~~la~~L~v~ 87 (174)
+--|+.+|+..+||+.|.|..++ ++..+-.+||+|.+..+.++...+.......
T Consensus 3 ~~ELqalR~~l~lt~~EaA~~Ia~~v~~~tWq~WE~G~~~IP~~Vie~l~~m~~~R 58 (118)
T PF08965_consen 3 NLELQALRQILGLTVEEAAYYIAQDVSSRTWQQWEKGERPIPDDVIEELLEMKSQR 58 (118)
T ss_dssp HHHHHHHHHHTT--HHHHHHHTSSS--HHHHHHHHTTSS---HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHccCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHH
Confidence 45689999999999999999999 9999999999999999999988888766554
No 86
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=97.52 E-value=0.00033 Score=45.08 Aligned_cols=45 Identities=18% Similarity=0.091 Sum_probs=36.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHH---HHHHHHHHhCccccc
Q psy6501 46 WSQKDLATKINEKPQIVNDYEGGRGIPNQA---IIGKMERALGIRLRV 90 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~G~~~P~~~---~l~~la~~L~v~~~~ 90 (174)
+|+.|+|+.+|||.+|||++.||....+.+ .+.++++.+|..+..
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln~~~~v~~~t~~~i~~~~~~~gy~~~~ 48 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLNGNGRVSEETREKVLAAMEELGYIPNR 48 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCCCCH
Confidence 489999999999999999999999765544 455677778876543
No 87
>COG1395 Predicted transcriptional regulator [Transcription]
Probab=97.51 E-value=0.00023 Score=58.18 Aligned_cols=51 Identities=27% Similarity=0.322 Sum_probs=48.2
Q ss_pred HHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501 124 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174 (174)
Q Consensus 124 ~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l 174 (174)
++.+++.|++.|+|..++|..+|+|+.+|+.||.|...|+.+++.+|-..|
T Consensus 127 ge~Lre~Ree~glSlG~lA~~lgVSRktV~~YE~G~~~~sleva~kLeei~ 177 (313)
T COG1395 127 GEKLREKREEMGLSLGDLATMLGVSRKTVYKYEKGLSDASLEVALKLEEIF 177 (313)
T ss_pred hHHHHHHHHHcCcCHHHHHHHhCccHHHHHHhccCCCCccHHHHHHHHHHh
Confidence 689999999999999999999999999999999999999999999987654
No 88
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=97.48 E-value=0.00048 Score=40.79 Aligned_cols=37 Identities=16% Similarity=0.136 Sum_probs=31.7
Q ss_pred CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHH
Q psy6501 47 SQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERA 83 (174)
Q Consensus 47 tq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~ 83 (174)
|.+|+|+.+|+|.+|||++-||....+.+.-.+|-++
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~~~~vs~~tr~rI~~~ 37 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNGPPRVSEETRERILEA 37 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTTCSSSTHHHHHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHHHhCCCCCCHHHHHHHHHH
Confidence 6789999999999999999999988888776655443
No 89
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=97.48 E-value=0.00038 Score=48.13 Aligned_cols=52 Identities=13% Similarity=0.238 Sum_probs=45.5
Q ss_pred HHHHHHHHHHh-cCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501 123 LAKLLMQGRQA-KGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174 (174)
Q Consensus 123 ~~~~i~~~R~~-~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l 174 (174)
.++.|++.=.+ .|+|+.++|+.+|+++.+|+.+-+|++..+.+.+.+|+++|
T Consensus 10 PGEiL~eeflep~glt~~~lA~~lgV~r~~is~ling~~~iT~dmAlrL~k~f 62 (104)
T COG3093 10 PGEILREEFLEPLGLTQTELAEALGVTRNTISELINGRRAITADMALRLAKVF 62 (104)
T ss_pred chHHHHHHHhccccCCHHHHHHHhCCCHHHHHHHHcCCcCCCHHHHHHHHHHh
Confidence 34556555445 59999999999999999999999999999999999999987
No 90
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=97.46 E-value=0.00048 Score=43.43 Aligned_cols=44 Identities=25% Similarity=0.360 Sum_probs=34.0
Q ss_pred HHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcC--CCCCCHHHHHH
Q psy6501 126 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGG--RGIPNQAIIGK 169 (174)
Q Consensus 126 ~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G--~~~P~~~~l~~ 169 (174)
+++++|+.+|+|.+++|..++++.+.+..+|+| ...|++.++..
T Consensus 1 ~Lr~~R~~~glsl~~va~~t~I~~~~l~aiE~~~~~~lp~~~y~rg 46 (62)
T PF13413_consen 1 RLREAREAKGLSLEDVAEETKISVSYLEAIENGDFDSLPSPVYARG 46 (62)
T ss_dssp -HHHHHHCTT--HHHHHHHCS--HHHHHHHHCT-GCCSSSHHHHHH
T ss_pred ChHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCcChhhCCcHHHHHH
Confidence 478899999999999999999999999999999 56688765443
No 91
>PHA00675 hypothetical protein
Probab=97.39 E-value=0.0006 Score=44.38 Aligned_cols=48 Identities=13% Similarity=0.059 Sum_probs=42.2
Q ss_pred hcccccchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCC
Q psy6501 23 ELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG 70 (174)
Q Consensus 23 ~~~~~~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~ 70 (174)
..+...+...--+.|+.+++.-|.|+.+||.++|||+++|++|-+|++
T Consensus 17 ~h~~AKLt~~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~~gk~ 64 (78)
T PHA00675 17 DHPNAKLTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICRYER 64 (78)
T ss_pred CCCCcccCHHHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHHccch
Confidence 355566677778899999999999999999999999999999999875
No 92
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=97.35 E-value=0.001 Score=43.21 Aligned_cols=43 Identities=16% Similarity=0.217 Sum_probs=34.9
Q ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHH
Q psy6501 37 LMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKME 81 (174)
Q Consensus 37 ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la 81 (174)
....|...|+|++|+|+.+|+|.++|..+.++ .++...+.++|
T Consensus 24 f~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~--~~~~~~~~~~~ 66 (73)
T TIGR03879 24 AALAREEAGKTASEIAEELGRTEQTVRNHLKG--ETKAGGLVKLA 66 (73)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc--CcccchHHHHH
Confidence 33447889999999999999999999999974 44566666665
No 93
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 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 [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=97.21 E-value=0.00012 Score=54.79 Aligned_cols=104 Identities=19% Similarity=0.265 Sum_probs=26.2
Q ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCCCCCCCCcccchhhhhhhhhhcccccH
Q psy6501 42 QAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDRETEELKHEKVPL 121 (174)
Q Consensus 42 ~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ 121 (174)
.-.-||++|+|+.+|++.+|||+.-+|+..-.+.-+.-|...|...+..-.+ .......+..
T Consensus 46 ~l~PLt~~~iA~~lgl~~STVSRav~~Ky~~t~~Gi~plk~fF~~~~~~~~~------------------~~~S~~~ik~ 107 (160)
T PF04552_consen 46 ALKPLTMKDIADELGLHESTVSRAVKNKYIQTPRGIFPLKDFFSRSVSSGSG------------------EEFSSEAIKA 107 (160)
T ss_dssp ---------------------------------------S-----SS--SS-------------------SS---TTH-H
T ss_pred cCcCCCHHHHHHHhCCCHhHHHHHHcCceeecCCeeeeHHHhccccccCCCC------------------cccHHHHHHH
Confidence 4556899999999999999999999998654444444444443333211100 0011122234
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHh-----CCChhHHHHHhcCCCCCC
Q psy6501 122 DLAKLLMQGRQAKGWSQKDLATKI-----NEKPQIVNDYEGGRGIPN 163 (174)
Q Consensus 122 ~~~~~i~~~R~~~glsq~ela~~l-----g~~~s~i~~~E~G~~~P~ 163 (174)
.+.++|.......-+|.+++++.+ .+++-||++|=..-..|+
T Consensus 108 ~i~~lI~~Ed~~~PlSD~~i~~~L~~~gi~isRRTVaKYR~~L~Ip~ 154 (160)
T PF04552_consen 108 RIKELIEEEDKKKPLSDQEIAELLKEEGIKISRRTVAKYREELGIPS 154 (160)
T ss_dssp HHHHHHTTS-TTS---HHHHHHHHTTTTS---HHHHHHHHHHHT-S-
T ss_pred HHHHHHHhcCCCCCCCHHHHHHHHHHcCCCccHHHHHHHHHHcCCCC
Confidence 455666555555778999999998 788889988865544444
No 94
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 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 [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.
Probab=97.18 E-value=0.00035 Score=44.52 Aligned_cols=47 Identities=19% Similarity=0.320 Sum_probs=35.2
Q ss_pred HHHHHHHhcCC-CHHHHHHHhCCChhHHH-HHhcCCCCCCHHHHHHHHhh
Q psy6501 126 LLMQGRQAKGW-SQKDLATKINEKPQIVN-DYEGGRGIPNQAIIGKMERA 173 (174)
Q Consensus 126 ~i~~~R~~~gl-sq~ela~~lg~~~s~i~-~~E~G~~~P~~~~l~~i~~~ 173 (174)
+|++.++..|. ++.+||+.+|+++++++ .|......| .+.+.+|++.
T Consensus 2 ~i~rl~~~~g~~~~~~lA~~lgis~st~s~~~~~r~~~P-~~~l~~ia~~ 50 (66)
T PF07022_consen 2 VIERLKEALGVKSDKELAERLGISKSTLSNNWKKRGSIP-AEWLIKIALE 50 (66)
T ss_dssp HHHHHHHHHT-SSCHHHHCCTT--HHHHH-HHHHSSS---HHHHHHHHHH
T ss_pred HHHHHHHHhCCCCHHHHHHHhCcCHHHhhHHHHhCCCCC-HHHHHHHHHH
Confidence 45666777775 56799999999999999 899888888 8999888864
No 95
>PF00157 Pou: Pou domain - N-terminal to homeobox domain; InterPro: IPR000327 POU proteins are eukaryotic transcription factors containing a bipartite DNA binding domain referred to as the POU domain. The acronym POU (pronounced 'pow') is derived from the names of three mammalian transcription factors, the pituitary-specific Pit-1, the octamer-binding proteins Oct-1 and Oct-2, and the neural Unc-86 from Caenorhabditis elegans. POU domain genes have been identified in diverse organisms including nematodes, flies, amphibians, fish and mammals but have not been yet identified in plants and fungi. The various members of the POU family have a wide variety of functions, all of which are related to the function of the neuroendocrine system [] and the development of an organism []. Some other genes are also regulated, including those for immunoglobulin light and heavy chains (Oct-2) [, ], and trophic hormone genes, such as those for prolactin and growth hormone (Pit-1). The POU domain is a bipartite domain composed of two subunits separated by a non-conserved region of 15-55 aa. The N-terminal subunit is known as the POU-specific (POUs) domain (IPR000327 from INTERPRO), while the C-terminal subunit is a homeobox domain (IPR007103 from INTERPRO). 3D structures of complexes including both POU subdomains bound to DNA are available. Both subdomains contain the structural motif 'helix-turn-helix', which directly associates with the two components of bipartite DNA binding sites, and both are required for high affinity sequence-specific DNA-binding. The domain may also be involved in protein-protein interactions []. The subdomains are connected by a flexible linker [, , ]. In proteins a POU-specific domain is always accompanied by a homeodomain. Despite of the lack of sequence homology, 3D structure of POUs is similar to 3D structure of bacteriophage lambda repressor and other members of HTH_3 family [, ]. This entry represents the POU-specific subunit of the POU domain.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3D1N_O 1AU7_A 3L1P_A 2XSD_C 1O4X_A 1HF0_B 1GT0_C 1POU_A 1CQT_B 1E3O_C ....
Probab=97.17 E-value=0.0025 Score=41.58 Aligned_cols=50 Identities=18% Similarity=0.197 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHHHH
Q psy6501 31 LDLAKLLMQGRQAKGWSQKDLATKIN------EKPQIVNDYEGGRGIPNQAIIGKMER 82 (174)
Q Consensus 31 ~~ig~~ik~~R~~~gltq~eLA~~ig------vs~~~is~~E~G~~~P~~~~l~~la~ 82 (174)
..|+..+|..|-..|+||.+++..+| .|+++|+++|+= ..|...+.+|-=
T Consensus 10 e~Fa~~fk~rRi~LG~TQ~dVg~al~~~~G~~~SQttI~RFE~L--~LS~kn~~klkP 65 (75)
T PF00157_consen 10 EQFAKEFKQRRIKLGYTQADVGAALGRLYGKEFSQTTICRFEAL--QLSFKNMCKLKP 65 (75)
T ss_dssp HHHHHHHHHHHHHTT--HHHHHHHHHHHHSSGGSHHHHHHHHTT--TSCHHHHHHHHH
T ss_pred HHHHHHHHHhhhhcccCHHHHhHHHHHhcCccccchhhhhhHhc--ccCHHHHHHHHH
Confidence 47999999999999999999998875 489999999963 445665555543
No 96
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=97.14 E-value=0.0012 Score=44.08 Aligned_cols=61 Identities=16% Similarity=0.099 Sum_probs=52.9
Q ss_pred chHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCcccc
Q psy6501 29 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR-GIPNQAIIGKMERALGIRLR 89 (174)
Q Consensus 29 ~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~-~~P~~~~l~~la~~L~v~~~ 89 (174)
+...++..|+..-+.++|+|+++|+.+||+++.+|.+-+|+ ..-+++.|.....+.|..++
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
Confidence 34568889999999999999999999999999999999999 55788888888877777665
No 97
>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A.
Probab=97.12 E-value=0.0011 Score=43.69 Aligned_cols=56 Identities=13% Similarity=-0.000 Sum_probs=43.0
Q ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501 35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG 93 (174)
Q Consensus 35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~ 93 (174)
..|+..-+.+|+|+.+||...|++++|+++-- ..|....=..||++|||++..+..
T Consensus 5 adI~AaL~krG~sL~~lsr~~Gl~~~tl~nal---~r~~pk~E~~IA~aLgv~P~eIWP 60 (78)
T PF13693_consen 5 ADIKAALRKRGTSLAALSREAGLSSSTLRNAL---RRPWPKGERIIADALGVPPEEIWP 60 (78)
T ss_dssp HHHHHHHCTTS--HHHHHHHHSS-HHHHHHTT---TSS-HHHHHHHHHHTTS-HHHHST
T ss_pred HHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHH---cCCChHHHHHHHHHHCcCHHHhCc
Confidence 45777778999999999999999999999874 455666667899999999999985
No 98
>PF08965 DUF1870: Domain of unknown function (DUF1870); InterPro: IPR015060 This family consist of hypothetical bacterial proteins. ; PDB: 1S4K_A.
Probab=97.12 E-value=0.0015 Score=46.20 Aligned_cols=47 Identities=19% Similarity=0.174 Sum_probs=36.6
Q ss_pred HHHHHHHhcCCCHHHHHHHhC--CChhHHHHHhcCCCCCCHHHHHHHHh
Q psy6501 126 LLMQGRQAKGWSQKDLATKIN--EKPQIVNDYEGGRGIPNQAIIGKMER 172 (174)
Q Consensus 126 ~i~~~R~~~glsq~ela~~lg--~~~s~i~~~E~G~~~P~~~~l~~i~~ 172 (174)
.++.+|...+||+.+.|..++ ++..+...||+|....|++++..+..
T Consensus 5 ELqalR~~l~lt~~EaA~~Ia~~v~~~tWq~WE~G~~~IP~~Vie~l~~ 53 (118)
T PF08965_consen 5 ELQALRQILGLTVEEAAYYIAQDVSSRTWQQWEKGERPIPDDVIEELLE 53 (118)
T ss_dssp HHHHHHHHTT--HHHHHHHTSSS--HHHHHHHHTTSS---HHHHHHHHH
T ss_pred HHHHHHHHHcCCHHHHHHHHHccCCHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 567889999999999999999 88889999999999999999998865
No 99
>COG3423 Nlp Predicted transcriptional regulator [Transcription]
Probab=97.01 E-value=0.0031 Score=41.00 Aligned_cols=55 Identities=16% Similarity=0.113 Sum_probs=45.3
Q ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501 36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG 93 (174)
Q Consensus 36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~ 93 (174)
-|....+.+|+|...|+.+.|+|++|+.+.-. +.-|..+. -||++|||++.++-.
T Consensus 12 dI~A~Lkk~G~Sl~~LS~~agls~~tL~n~L~-rp~pkgEr--iIA~algv~P~eIWp 66 (82)
T COG3423 12 DIIAALKKKGTSLAALSREAGLSSSTLANALD-RPWPKGER--IIADALGVPPEEIWP 66 (82)
T ss_pred HHHHHHHHccccHHHHHHHcCCCHHHHHHHHc-CCCchHHH--HHHHHhCCCHHHhCc
Confidence 35666788999999999999999999999864 55566665 489999999988763
No 100
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=96.98 E-value=0.004 Score=42.43 Aligned_cols=41 Identities=10% Similarity=0.100 Sum_probs=35.4
Q ss_pred hcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhh
Q psy6501 133 AKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERA 173 (174)
Q Consensus 133 ~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~ 173 (174)
..++||.++|+++|+|.++|++++++...-++++..-|.+.
T Consensus 53 ~~~~tQrEIa~~lGiS~atIsR~sn~lk~~~~~~~~~l~~~ 93 (94)
T TIGR01321 53 NGNMSQREIASKLGVSIATITRGSNNLKTMDPNFKQFLRKK 93 (94)
T ss_pred hCCCCHHHHHHHhCCChhhhhHHHhhcccCCHHHHHHHHhh
Confidence 46899999999999999999999999997777777666554
No 101
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. 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 characterized.
Probab=96.95 E-value=0.0019 Score=52.40 Aligned_cols=46 Identities=24% Similarity=0.283 Sum_probs=43.4
Q ss_pred CCCHHHHHHHhCCCH-HHHHHHHcCCCCCCHHHHHHHHHHhCccccc
Q psy6501 45 GWSQKDLATKINEKP-QIVNDYEGGRGIPNQAIIGKMERALGIRLRV 90 (174)
Q Consensus 45 gltq~eLA~~igvs~-~~is~~E~G~~~P~~~~l~~la~~L~v~~~~ 90 (174)
.+|..++|+.+|++. ++++.+.+|++.++...+.++|++||.+..+
T Consensus 27 ~fS~R~fa~~~G~ss~s~L~~v~~Gkr~Ls~~~~~k~a~~l~L~~~E 73 (271)
T TIGR02147 27 AFSWRFFAEKAGFSSTSYLNDIIKGKKNLTKRMIPKFAEALGLDEKE 73 (271)
T ss_pred CcCHHHHHHHhCCCCHHHHHHHHcCCCCCCHHHHHHHHHHcCCCHHH
Confidence 699999999999888 9999999999999999999999999999664
No 102
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=96.90 E-value=0.0019 Score=47.33 Aligned_cols=49 Identities=16% Similarity=0.260 Sum_probs=37.9
Q ss_pred HcCCCHHHHHHHhCCCHHHHHHHHcCCCC---CCHHHHHHHHHHhCccccccc
Q psy6501 43 AKGWSQKDLATKINEKPQIVNDYEGGRGI---PNQAIIGKMERALGIRLRVNA 92 (174)
Q Consensus 43 ~~gltq~eLA~~igvs~~~is~~E~G~~~---P~~~~l~~la~~L~v~~~~l~ 92 (174)
..|+||+|+|+.+|+|+++|+.||++-.. =...+| +++..|+-++...+
T Consensus 19 ~~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~tl-~~~~~l~a~~~v~~ 70 (141)
T PRK03975 19 ERGLTQQEIADILGTSRANVSSIEKRARENIEKARETL-AFAETLNAPVRVTI 70 (141)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH-HHHHHcCCCeEEEe
Confidence 69999999999999999999999986421 011233 77778888877666
No 103
>COG3655 Predicted transcriptional regulator [Transcription]
Probab=96.89 E-value=0.0033 Score=40.76 Aligned_cols=49 Identities=20% Similarity=0.133 Sum_probs=42.6
Q ss_pred HHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCC-CCHHHHHHHHhhC
Q psy6501 126 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGI-PNQAIIGKMERAL 174 (174)
Q Consensus 126 ~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~-P~~~~l~~i~~~l 174 (174)
.+.....+++++..++++.+|++.++++.+..|+.. ....++.+||++|
T Consensus 6 ~l~~~l~~r~~~~~eLa~~igis~~~ls~l~~gk~k~I~~~tL~~iC~~L 55 (73)
T COG3655 6 RLDVMLADRKISLKELAEAIGISEANLSKLKTGKVKAIRLSTLEKICKAL 55 (73)
T ss_pred hHHHHHHHHhhhHHHHHHHHcccHHHHHHHHcCCcceeeHHHHHHHHHHc
Confidence 445556778899999999999999999999998665 7899999999986
No 104
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=96.88 E-value=0.0022 Score=38.10 Aligned_cols=24 Identities=21% Similarity=0.495 Sum_probs=19.3
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHcC
Q psy6501 45 GWSQKDLATKINEKPQIVNDYEGG 68 (174)
Q Consensus 45 gltq~eLA~~igvs~~~is~~E~G 68 (174)
|+|+.++|+.+|+|++||++|-+-
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT-
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 999999999999999999999764
No 105
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=96.86 E-value=0.0022 Score=46.80 Aligned_cols=32 Identities=28% Similarity=0.370 Sum_probs=27.5
Q ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcC
Q psy6501 36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGG 68 (174)
Q Consensus 36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G 68 (174)
.+-.+| ..|+||+|+|+.+|+|+++|+.+|+.
T Consensus 13 ~VL~Lr-~~GlTq~EIAe~LgiS~stV~~~e~r 44 (137)
T TIGR00721 13 KVLELR-EKGLSQKEIAKELKTTRANVSAIEKR 44 (137)
T ss_pred HHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHh
Confidence 344455 69999999999999999999999975
No 106
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=96.69 E-value=0.0021 Score=37.56 Aligned_cols=29 Identities=14% Similarity=0.189 Sum_probs=19.8
Q ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 37 LMQGRQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 37 ik~~R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
|..+ ...|+|+.++|+.+|+|++||+++-
T Consensus 13 I~~l-~~~G~s~~~IA~~lg~s~sTV~rel 41 (44)
T PF13936_consen 13 IEAL-LEQGMSIREIAKRLGRSRSTVSREL 41 (44)
T ss_dssp HHHH-HCS---HHHHHHHTT--HHHHHHHH
T ss_pred HHHH-HHcCCCHHHHHHHHCcCcHHHHHHH
Confidence 4444 3699999999999999999999874
No 107
>PHA02591 hypothetical protein; Provisional
Probab=96.65 E-value=0.0045 Score=40.43 Aligned_cols=28 Identities=18% Similarity=0.270 Sum_probs=24.6
Q ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 40 GRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 40 ~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
-..++|+||+++|+.+|+++.+|++|-.
T Consensus 54 eL~eqGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 54 ELARKGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 3456899999999999999999999854
No 108
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=96.60 E-value=0.01 Score=42.24 Aligned_cols=42 Identities=21% Similarity=0.240 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCC
Q psy6501 121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIP 162 (174)
Q Consensus 121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P 162 (174)
+.++..+.......|+||.++|+.+|++++.|+.|-+|++.|
T Consensus 8 PaiRa~lA~~L~eeG~Sq~~iA~LLGltqaAVS~Yls~krg~ 49 (119)
T COG2522 8 PAIRALLAKELIEEGLSQYRIAKLLGLTQAAVSQYLSGKRGS 49 (119)
T ss_pred HHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHccCCch
Confidence 444455544444559999999999999999999999999986
No 109
>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=96.58 E-value=0.0038 Score=37.25 Aligned_cols=34 Identities=15% Similarity=0.106 Sum_probs=29.5
Q ss_pred HHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhh
Q psy6501 140 DLATKINEKPQIVNDYEGGRGIPNQAIIGKMERA 173 (174)
Q Consensus 140 ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~ 173 (174)
++|+.+|+++++|+.|++|...+++....+|.++
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~~vs~~~~~~i~~~ 35 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKPRVSEETRERVLAA 35 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 6899999999999999999988888887776543
No 110
>TIGR02293 TAS_TIGR02293 putative toxin-antitoxin system antitoxin component, TIGR02293 family. Proteins in this family are found almost exclusively in the Proteobacteria, but also in Gloeobacter violaceus PCC 7421, a cyanobacterium. This family was proposed by Makarova, et al. (2009) to be the antitoxin component of a new class of type 2 toxin-antitoxin system, or addiction module.
Probab=96.55 E-value=0.012 Score=42.72 Aligned_cols=53 Identities=4% Similarity=-0.048 Sum_probs=41.1
Q ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCc
Q psy6501 34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI 86 (174)
Q Consensus 34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v 86 (174)
...+..+-+..|+|++|+|..+|+|++|++++-++...++.+.-.++.....|
T Consensus 25 ~~~~~~l~~~l~ls~~el~~~lgis~~Tl~R~~~~~~~Ls~~~serl~~l~ri 77 (133)
T TIGR02293 25 IGALDRLAHLLAIGKAEIFKATGIPKATLQRRKMAHQRLSSEESDRLARVARV 77 (133)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHhhcCCCCCHHHHHHHHHHHHH
Confidence 34567778999999999999999999999999987656666655554444333
No 111
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=96.54 E-value=0.0052 Score=38.43 Aligned_cols=36 Identities=31% Similarity=0.487 Sum_probs=25.6
Q ss_pred cCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHH
Q psy6501 44 KGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERA 83 (174)
Q Consensus 44 ~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~ 83 (174)
.| ++..||+.+|||+++|++| |...|. .....|...
T Consensus 9 ~G-~~~~lAkalGVs~~aVs~W--~~~IP~-~ra~~Ie~~ 44 (60)
T PF14549_consen 9 FG-GQSKLAKALGVSPQAVSQW--GERIPA-ERAYQIEKL 44 (60)
T ss_dssp HS-SHHHHHHHHTS-HHHHHHH--HTS--H-HHHHHHHHH
T ss_pred HC-CHHHHHHHHCCCHHHHHHh--cCccCH-HHHHHHHHH
Confidence 44 8999999999999999999 455544 555556554
No 112
>COG3636 Predicted transcriptional regulator [Transcription]
Probab=96.52 E-value=0.016 Score=39.52 Aligned_cols=56 Identities=25% Similarity=0.242 Sum_probs=46.9
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccc
Q psy6501 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRV 90 (174)
Q Consensus 33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~ 90 (174)
|...+-..-..+||| ++|++.|+|+..+.+=-+...+|++.++.+++++||+....
T Consensus 39 i~~alg~var~~GMs--qvA~~aGlsRe~LYkaLS~~GNPtf~Til~V~kAlG~rl~~ 94 (100)
T COG3636 39 IAAALGVVARSRGMS--QVARKAGLSREGLYKALSPGGNPTFDTILAVLKALGLRLSA 94 (100)
T ss_pred HHHHHHHHHHhcCHH--HHHHHhCccHHHHHHHhCCCCCCcHHHHHHHHHHcCceeec
Confidence 444444455567776 58999999999999999999999999999999999998654
No 113
>PHA01083 hypothetical protein
Probab=96.40 E-value=0.011 Score=43.35 Aligned_cols=50 Identities=22% Similarity=0.268 Sum_probs=42.4
Q ss_pred HHHHHHHHhcCC-CHHHHHHHhCCChhHHHHHhcC-CCCCCHHHHHHHHhhC
Q psy6501 125 KLLMQGRQAKGW-SQKDLATKINEKPQIVNDYEGG-RGIPNQAIIGKMERAL 174 (174)
Q Consensus 125 ~~i~~~R~~~gl-sq~ela~~lg~~~s~i~~~E~G-~~~P~~~~l~~i~~~l 174 (174)
++|...+++..+ +-+++|+.+|++++.|++|-+| +..++.+.+..||+.+
T Consensus 5 kLLda~K~a~~~~sdkqLA~~LGVs~q~IS~~R~G~r~~i~de~A~~LAe~a 56 (149)
T PHA01083 5 KLLDAYKKAKNYVQYKQIAHDLGVSPQKISKMRTGVRTYISDEEAIFLAESA 56 (149)
T ss_pred HHHHHHHHHHhhccHHHHHHHhCCCHHHHHHHHcCCCCCCCHHHHHHHHHHh
Confidence 466666777664 5689999999999999999999 9999999999998753
No 114
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=96.38 E-value=0.0053 Score=35.98 Aligned_cols=33 Identities=18% Similarity=0.189 Sum_probs=24.1
Q ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
-+.+++++ ..|+|..++|+.+|||++||.+|-+
T Consensus 11 ~~~i~~l~-~~G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 11 IEEIKELY-AEGMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHHH-HTT--HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHHH-HCCCCHHHHHHHHCcCHHHHHHHHh
Confidence 45566655 4569999999999999999999865
No 115
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=96.36 E-value=0.015 Score=34.40 Aligned_cols=37 Identities=16% Similarity=0.136 Sum_probs=33.5
Q ss_pred CHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhh
Q psy6501 137 SQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERA 173 (174)
Q Consensus 137 sq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~ 173 (174)
|.+|+|+..|+|+++++++-+|....+++...+|-++
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~~~~vs~~tr~rI~~~ 37 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNGPPRVSEETRERILEA 37 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTTCSSSTHHHHHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHHHhCCCCCCHHHHHHHHHH
Confidence 5789999999999999999999999999998887654
No 116
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=96.33 E-value=0.011 Score=34.73 Aligned_cols=33 Identities=33% Similarity=0.351 Sum_probs=26.6
Q ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
-.-|..+++.-++|+.|+|+.+|+|.++++.+-
T Consensus 6 ~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l 38 (48)
T PF13412_consen 6 RKILNYLRENPRITQKELAEKLGISRSTVNRYL 38 (48)
T ss_dssp HHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHH
Confidence 455777888888999999999999999998864
No 117
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains 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 []. ; PDB: 1R71_C.
Probab=96.33 E-value=0.0036 Score=42.46 Aligned_cols=29 Identities=17% Similarity=0.391 Sum_probs=20.7
Q ss_pred HcCCCHHHHHHHhCCCHHHHHHHHcCCCC
Q psy6501 43 AKGWSQKDLATKINEKPQIVNDYEGGRGI 71 (174)
Q Consensus 43 ~~gltq~eLA~~igvs~~~is~~E~G~~~ 71 (174)
+.||||.|+|+++|.|+++|+++-.=-..
T Consensus 1 ~~G~tq~eIA~~lGks~s~Vs~~l~Ll~l 29 (93)
T PF08535_consen 1 EFGWTQEEIAKRLGKSRSWVSNHLALLDL 29 (93)
T ss_dssp HTT--HHHHHHHTT--HHHHHHHHGGGS-
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHcC
Confidence 47999999999999999999999864443
No 118
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=96.31 E-value=0.02 Score=40.62 Aligned_cols=88 Identities=17% Similarity=0.213 Sum_probs=55.5
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCCCCCCCCcccchhhhh
Q psy6501 31 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDRE 110 (174)
Q Consensus 31 ~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~~~~~~~~~~~~l~~~ 110 (174)
.+|-+++-...+. |.|..+.|...+||.+||.+|-+ +..+. + +.... .. . .+++
T Consensus 5 ~DlR~rVl~~~~~-g~s~~eaa~~F~VS~~Tv~~W~k-~~~~G-~----------~~~k~----r~-----~--~Kid-- 58 (119)
T PF01710_consen 5 LDLRQRVLAYIEK-GKSIREAAKRFGVSRNTVYRWLK-RKETG-D----------LEPKP----RG-----R--KKID-- 58 (119)
T ss_pred HHHHHHHHHHHHc-cchHHHHHHHhCcHHHHHHHHHH-hcccc-c----------ccccc----cc-----c--cccc--
Confidence 3455666665555 88999999999999999999987 32211 0 00000 00 0 0111
Q ss_pred hhhhhcccccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHh
Q psy6501 111 TEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE 156 (174)
Q Consensus 111 ~~~~~~~~~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E 156 (174)
...+... .......++.|+|+.+|+++++|...-
T Consensus 59 ---------~~~L~~~---v~~~pd~tl~Ela~~l~Vs~~ti~~~L 92 (119)
T PF01710_consen 59 ---------RDELKAL---VEENPDATLRELAERLGVSPSTIWRAL 92 (119)
T ss_pred ---------HHHHHHH---HHHCCCcCHHHHHHHcCCCHHHHHHHH
Confidence 1112223 344678999999999999999887654
No 119
>PRK10344 DNA-binding transcriptional regulator Nlp; Provisional
Probab=96.15 E-value=0.021 Score=38.37 Aligned_cols=56 Identities=18% Similarity=0.119 Sum_probs=44.7
Q ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501 35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG 93 (174)
Q Consensus 35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~ 93 (174)
.-|+..-+.+|+|..+||...|+|.+|+.+--. +..|..+ ..||++|||.+..+-.
T Consensus 11 adI~AaL~KrG~sLa~lsr~~Gls~~TL~nAL~-rp~PKgE--riIA~aLGv~P~eIWP 66 (92)
T PRK10344 11 ADIIAGLRKKGTSMAAESRRNGLSSSTLANALS-RPWPKGE--MIIAKALGTDPWVIWP 66 (92)
T ss_pred HHHHHHHHHcCCcHHHHHHHcCCChHHHHHHHc-CCCchHH--HHHHHHHCcCHHHhCc
Confidence 345666778999999999999999999988754 3445555 4699999999998874
No 120
>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=96.11 E-value=0.072 Score=33.65 Aligned_cols=22 Identities=18% Similarity=0.407 Sum_probs=20.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q psy6501 46 WSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~ 67 (174)
+|..|+|+.+|||+++|..||.
T Consensus 1 ~~i~e~A~~~gVs~~tlr~ye~ 22 (68)
T cd04763 1 YTIGEVALLTGIKPHVLRAWER 22 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999996
No 121
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 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 recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is 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.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=96.03 E-value=0.017 Score=34.30 Aligned_cols=32 Identities=13% Similarity=0.170 Sum_probs=26.5
Q ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
.|-.+|--.|+|++|+|+.+|+|.++|+++++
T Consensus 11 ~vi~~~y~~~~t~~eIa~~lg~s~~~V~~~~~ 42 (50)
T PF04545_consen 11 EVIRLRYFEGLTLEEIAERLGISRSTVRRILK 42 (50)
T ss_dssp HHHHHHHTST-SHHHHHHHHTSCHHHHHHHHH
T ss_pred HHHHHHhcCCCCHHHHHHHHCCcHHHHHHHHH
Confidence 34456668999999999999999999999874
No 122
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=95.99 E-value=0.0066 Score=42.91 Aligned_cols=24 Identities=17% Similarity=0.195 Sum_probs=21.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501 46 WSQKDLATKINEKPQIVNDYEGGR 69 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~G~ 69 (174)
||++|||+.+|+|++||++|-+-.
T Consensus 1 MT~eELA~~tG~srQTINrWvRke 24 (122)
T PF07037_consen 1 MTPEELAELTGYSRQTINRWVRKE 24 (122)
T ss_pred CCHHHHHHHhCccHHHHHHHHHhc
Confidence 799999999999999999997543
No 123
>PF04814 HNF-1_N: Hepatocyte nuclear factor 1 (HNF-1), N terminus; InterPro: IPR006899 This domain consists of the N terminus of homeobox-containing transcription factor HNF-1. This region contains a dimerisation 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) [].; GO: 0045893 positive regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2GYP_B 1IC8_B 2H8R_B 1G2Y_D 1F93_H 1G39_D 1G2Z_B 1JB6_B.
Probab=95.98 E-value=0.013 Score=44.53 Aligned_cols=38 Identities=11% Similarity=0.059 Sum_probs=31.5
Q ss_pred hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
...+.+-||.+...++++|.++++..|||+++||.|-+
T Consensus 116 ~~~VkeeIK~fl~~h~IsQ~~V~q~TGisQS~lSq~L~ 153 (180)
T PF04814_consen 116 PWRVKEEIKAFLQQHNISQREVVQVTGISQSHLSQHLN 153 (180)
T ss_dssp HHHHHHHHHHHHHHCT--CHHHHHHHT--HHHHHHHHC
T ss_pred HHHHHHHHHHHHHHcCCcHHHHHHHhhhhHHHHHHHHH
Confidence 35689999999999999999999999999999999974
No 124
>PRK01381 Trp operon repressor; Provisional
Probab=95.97 E-value=0.021 Score=39.23 Aligned_cols=56 Identities=9% Similarity=-0.002 Sum_probs=43.7
Q ss_pred HHHHHHHHHHHH--HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCc
Q psy6501 31 LDLAKLLMQGRQ--AKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI 86 (174)
Q Consensus 31 ~~ig~~ik~~R~--~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v 86 (174)
..++.|++-.+. .-++||.|+|+.+|||.+||++--|--..-+.+...-|...|+-
T Consensus 39 ~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn~Lk~~~~~~k~~l~~~l~~ 96 (99)
T PRK01381 39 EALGTRVRIVEELLRGELSQREIKQELGVGIATITRGSNSLKTAPPEFKEWLEQQLLK 96 (99)
T ss_pred HHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhHHHhccCCHHHHHHHHHHhcc
Confidence 468889988885 34599999999999999999988776655556666666666543
No 125
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=95.94 E-value=0.083 Score=34.95 Aligned_cols=49 Identities=10% Similarity=-0.004 Sum_probs=40.6
Q ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhC
Q psy6501 36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR-GIPNQAIIGKMERALG 85 (174)
Q Consensus 36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~-~~P~~~~l~~la~~L~ 85 (174)
-+..+++ ..+|.+++|+.+|||.+|||+.-++. ...+.++-.++-++..
T Consensus 11 I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L~~~~~~Vs~~Tr~rV~~aa~ 60 (80)
T TIGR02844 11 IGKYIVE-TKATVRETAKVFGVSKSTVHKDVTERLPEINPELAEEVKEVLD 60 (80)
T ss_pred HHHHHHH-CCCCHHHHHHHhCCCHHHHHHHhcCCCCCCCHHHHHHHHHHHc
Confidence 3445556 88999999999999999999999986 6778888888777766
No 126
>COG4197 Uncharacterized protein conserved in bacteria, prophage-related [Function unknown]
Probab=95.90 E-value=0.0068 Score=40.89 Aligned_cols=46 Identities=26% Similarity=0.230 Sum_probs=42.1
Q ss_pred CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC--ccccccc
Q psy6501 47 SQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALG--IRLRVNA 92 (174)
Q Consensus 47 tq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~--v~~~~l~ 92 (174)
.|+.||..+|||+++|++|-+|.+....+....|+++-+ |+..+|-
T Consensus 14 ~q~a~a~LLgvsp~~vnQw~~g~r~~~a~r~~aIerAt~g~Vs~~elr 61 (96)
T COG4197 14 GQKALARLLGVSPPSVNQWIKGRRQVAAERALAIERATSGQVSREELR 61 (96)
T ss_pred cHHHHHHHHccCchHHHHHhhheeecCcccchHHHHHhcCCccHHHHc
Confidence 689999999999999999999999999999999999988 8777664
No 127
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=95.89 E-value=0.021 Score=36.52 Aligned_cols=38 Identities=21% Similarity=0.130 Sum_probs=33.0
Q ss_pred CCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhh
Q psy6501 136 WSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERA 173 (174)
Q Consensus 136 lsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~ 173 (174)
.++.|+|+.+|++.++|+++.+|....++....+|.++
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln~~~~v~~~t~~~i~~~ 38 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLNGNGRVSEETREKVLAA 38 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHH
Confidence 36889999999999999999999888888887777654
No 128
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 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.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=95.82 E-value=0.011 Score=36.61 Aligned_cols=27 Identities=22% Similarity=0.471 Sum_probs=24.1
Q ss_pred HcCCCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501 43 AKGWSQKDLATKINEKPQIVNDYEGGR 69 (174)
Q Consensus 43 ~~gltq~eLA~~igvs~~~is~~E~G~ 69 (174)
-.|++++++|+.+|++.+||.+|-.-.
T Consensus 11 ~~G~~~~eIA~~Lg~~~~TV~~W~~r~ 37 (58)
T PF06056_consen 11 LQGWSIKEIAEELGVPRSTVYSWKDRY 37 (58)
T ss_pred HcCCCHHHHHHHHCCChHHHHHHHHhh
Confidence 469999999999999999999997544
No 129
>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=95.79 E-value=0.017 Score=33.39 Aligned_cols=27 Identities=11% Similarity=0.206 Sum_probs=23.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCC
Q psy6501 46 WSQKDLATKINEKPQIVNDYEGGRGIP 72 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~G~~~P 72 (174)
+|..|+|+.+|||++||.+|++-...|
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~g~~~ 27 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKEGKLK 27 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCCC
Confidence 588999999999999999998655444
No 130
>PF05269 Phage_CII: Bacteriophage CII protein; InterPro: IPR007933 The CII protein is a transcription activator, conserved in bacteriophage lambda and related phages, that plays a key role in the decision between lytic or lysogenic phage development. CII is regulated at multiple levels including transcription, translation initiation, mRNA stability, and proteolysis []. Conditions that stabilise cII favour lysogenic development. The lambda CII protein activates three specific promoters, binding to direct repeat sequences rather than the more usual inverted repeats. Structurally, CII is a homotetramer where each monomer is composed of four alpha helices and a disordered C terminus [, ]. The alpha helical region is responsible for DNA binding and multimerisation. The homotetramer has an unusual spatial arrangement that allows recognition of the direct repeat sequences.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ZS4_C 1ZPQ_C 1XWR_A.
Probab=95.77 E-value=0.0038 Score=42.28 Aligned_cols=45 Identities=11% Similarity=0.130 Sum_probs=32.2
Q ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccc
Q psy6501 40 GRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRL 88 (174)
Q Consensus 40 ~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~ 88 (174)
++.-..++|+.+|+.+|++.++||+|-++ -...+..|..+|++.+
T Consensus 18 L~rlA~~gq~~vA~~~Gv~eStISR~k~~----~~~~~a~lLa~L~~~v 62 (91)
T PF05269_consen 18 LNRLASVGQKKVAEAMGVDESTISRWKND----FIEKMAMLLAALELGV 62 (91)
T ss_dssp HHHHHHHHHHHHHHHHTSSTTTHHHHHHH----HHHHHHHHHHHTTTTH
T ss_pred HHHHHHHhhHHHHHHhCCCHHHHHHHHhh----HHHHHHHHHHHHHhcc
Confidence 34455679999999999999999999653 2345555555555543
No 131
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=95.71 E-value=0.19 Score=40.34 Aligned_cols=122 Identities=15% Similarity=0.150 Sum_probs=72.6
Q ss_pred hHHHHHHHHHHHHHc--CC--CHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCccccccc------------
Q psy6501 30 PLDLAKLLMQGRQAK--GW--SQKDLATKINEKPQIVNDYEGGR-GIPNQAIIGKMERALGIRLRVNA------------ 92 (174)
Q Consensus 30 ~~~ig~~ik~~R~~~--gl--tq~eLA~~igvs~~~is~~E~G~-~~P~~~~l~~la~~L~v~~~~l~------------ 92 (174)
....|.-+..+|+.- .+ +..+.+.++. ..+..++.-. +.|+.. .||+.||++.++..
T Consensus 83 ~~I~Gei~d~LR~~~~v~vpR~~~~~~~~i~---~~~~~l~~el~r~pt~~---EIA~~L~i~~ee~~~~~~~~~~~~~~ 156 (247)
T COG1191 83 RRIRGEILDYLRKNDSVKVPRSLRELGRRIE---EAIDELEQELGREPTDE---EIAEELGIDKEEYIEALLAINGSQLL 156 (247)
T ss_pred HHHHHHHHHHHHhCCCccCcHHHHHHHHHHH---HHHHHHHHHhCCCCcHH---HHHHHhCCCHHHHHHHHHHhcccccc
Confidence 355788888898877 44 4566777775 4444444333 667766 58999999977332
Q ss_pred CCCCCCC--CCcc----c----chhhhhhh--h-hhcccccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 93 GTNKQPG--TTKN----T----AKLDRETE--E-LKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 93 ~~~~~~~--~~~~----~----~~l~~~~~--~-~~~~~~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
.-..... .... . ..+..... . ........+-.+.+-..|-..++|++++|+.+|+|.+.|+++++
T Consensus 157 sld~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~ai~~L~EREk~Vl~l~y~eelt~kEI~~~LgISes~VSql~k 234 (247)
T COG1191 157 SLDEDVLKDDDDDVDDQIENPDDGVEKEELLEILKEAIEPLPEREKLVLVLRYKEELTQKEIAEVLGISESRVSRLHK 234 (247)
T ss_pred chhhhhccccccchhhccccchhHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCHHHHHHHhCccHHHHHHHHH
Confidence 0000000 0000 0 00000000 0 00011234456677788888999999999999999999999886
No 132
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=95.71 E-value=0.0092 Score=42.63 Aligned_cols=50 Identities=14% Similarity=0.112 Sum_probs=37.0
Q ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH---HHHHHHhCccccccc
Q psy6501 42 QAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAII---GKMERALGIRLRVNA 92 (174)
Q Consensus 42 ~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l---~~la~~L~v~~~~l~ 92 (174)
.++||||+|+|+.+|.++..||-+|+--. -+++.. ..|.+.++-++....
T Consensus 20 RekG~tQ~eIA~~L~TTraNvSaIEkrA~-enIekarnTL~l~~~i~spv~i~v 72 (143)
T COG1356 20 REKGLTQSEIARILKTTRANVSAIEKRAL-ENIEKARNTLLLWEQINSPVSITV 72 (143)
T ss_pred hhccccHHHHHHHHccchhhHHHHHHHHH-HHHHHHHHHHHHHHHhCCCeEEEe
Confidence 46899999999999999999999996321 233322 357777777776665
No 133
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=95.70 E-value=0.023 Score=38.29 Aligned_cols=28 Identities=7% Similarity=0.123 Sum_probs=25.3
Q ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHcC
Q psy6501 41 RQAKGWSQKDLATKINEKPQIVNDYEGG 68 (174)
Q Consensus 41 R~~~gltq~eLA~~igvs~~~is~~E~G 68 (174)
....|+|..++|+.+|+|++||++|-+|
T Consensus 46 ll~~G~S~~eIA~~LgISrsTIyRi~R~ 73 (88)
T TIGR02531 46 MLKQGKTYSDIEAETGASTATISRVKRC 73 (88)
T ss_pred HHHCCCCHHHHHHHHCcCHHHHHHHHHh
Confidence 3567999999999999999999999875
No 134
>PF08523 MBF1: Multiprotein bridging factor 1; InterPro: IPR013729 This domain is found in the multiprotein bridging factor 1 (MBF1) which forms a heterodimer with MBF2. It has been shown to make direct contact with the TATA-box binding protein (TBP) and interacts with Ftz-F1, stabilising the Ftz-F1-DNA complex []. It is also found in the endothelial differentiation-related factor (EDF-1). Human EDF-1 is involved in the repression of endothelial differentiation, interacts with CaM and is phosphorylated by PKC []. The domain is found in a wide range of eukaryotic proteins including metazoans, fungi and plants. A helix-turn-helix motif (IPR001387 from INTERPRO) is found to its C terminus. ; PDB: 1X57_A.
Probab=95.70 E-value=0.0029 Score=40.91 Aligned_cols=29 Identities=76% Similarity=0.982 Sum_probs=0.8
Q ss_pred CCCCCC-CCCCCccccccccchhhcccccc
Q psy6501 1 NAGTNK-QPGTTKNTAKLDRETEELKHEKV 29 (174)
Q Consensus 1 ~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~ 29 (174)
.+|+|+ +.+...++.+|||+||+++|+.+
T Consensus 42 ~~g~Nk~~~~~~~n~~KLD~etE~~~~~kV 71 (71)
T PF08523_consen 42 GAGNNKHQHGEGQNAAKLDRETEELKHEKV 71 (71)
T ss_dssp ---------------------------S--
T ss_pred eccccccCCCcccccccccccccccCCCCC
Confidence 378999 89999999999999999998764
No 135
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=95.65 E-value=0.031 Score=45.74 Aligned_cols=45 Identities=18% Similarity=0.113 Sum_probs=38.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH---HHHhCcccc
Q psy6501 45 GWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKM---ERALGIRLR 89 (174)
Q Consensus 45 gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~l---a~~L~v~~~ 89 (174)
..|.+|+|+++|||.+|||+.-||+...+.++-.++ ++.||..+.
T Consensus 6 ~~Ti~dIA~~agVS~~TVSr~Ln~~~~vs~~tr~~V~~~a~elgY~p~ 53 (342)
T PRK10014 6 KITIHDVALAAGVSVSTVSLVLSGKGRISTATGERVNQAIEELGFVRN 53 (342)
T ss_pred CCcHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCCcC
Confidence 579999999999999999999999987888777665 777887664
No 136
>PF13551 HTH_29: Winged helix-turn helix
Probab=95.64 E-value=0.18 Score=34.51 Aligned_cols=27 Identities=15% Similarity=0.213 Sum_probs=23.6
Q ss_pred HHcCC-CHHHHHHHhCCCHHHHHHHHcC
Q psy6501 42 QAKGW-SQKDLATKINEKPQIVNDYEGG 68 (174)
Q Consensus 42 ~~~gl-tq~eLA~~igvs~~~is~~E~G 68 (174)
...|+ |..++|+.+|+|++||.+|-+.
T Consensus 8 ~~~g~~~~~~ia~~lg~s~~Tv~r~~~~ 35 (112)
T PF13551_consen 8 LAEGVSTIAEIARRLGISRRTVYRWLKR 35 (112)
T ss_pred HHcCCCcHHHHHHHHCcCHHHHHHHHHH
Confidence 56788 5999999999999999999754
No 137
>PHA00675 hypothetical protein
Probab=95.55 E-value=0.043 Score=35.79 Aligned_cols=43 Identities=14% Similarity=0.054 Sum_probs=36.8
Q ss_pred cccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCC
Q psy6501 118 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG 160 (174)
Q Consensus 118 ~~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~ 160 (174)
.+.....+.|+..++..|.|..++|+++|+++++|+.+-+|++
T Consensus 22 KLt~~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~~gk~ 64 (78)
T PHA00675 22 KLTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICRYER 64 (78)
T ss_pred ccCHHHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHHccch
Confidence 3445556788888888999999999999999999999999875
No 138
>COG4800 Predicted transcriptional regulator with an HTH domain [Transcription]
Probab=95.50 E-value=0.064 Score=39.06 Aligned_cols=51 Identities=14% Similarity=0.184 Sum_probs=42.9
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhh
Q psy6501 122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERA 173 (174)
Q Consensus 122 ~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~ 173 (174)
.++.-+...-.+.|++..+||++.|+++|++..+-+| +-|..+.+.+|-+.
T Consensus 16 ~F~~~l~~~l~Elglt~~eFak~anIP~StLYKil~G-~dpr~~tl~~I~kt 66 (170)
T COG4800 16 DFGSCLQKLLDELGLTPSEFAKRANIPLSTLYKILKG-SDPRYDTLTRIFKT 66 (170)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHhC-CCccHHHHHHHHHH
Confidence 3445555556679999999999999999999999999 88999999888653
No 139
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=95.49 E-value=0.023 Score=38.73 Aligned_cols=54 Identities=15% Similarity=0.045 Sum_probs=42.6
Q ss_pred ccccccccchhhcccccchHHHHHHHHHH-H-------HHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501 12 KNTAKLDRETEELKHEKVPLDLAKLLMQG-R-------QAKGWSQKDLATKINEKPQIVNDY 65 (174)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~~~~ig~~ik~~-R-------~~~gltq~eLA~~igvs~~~is~~ 65 (174)
-|++-.++..+.+....+.......|-.+ | ....+||.|||+.+|+++.+|++.
T Consensus 6 g~t~~~~~~~e~l~~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~ 67 (95)
T TIGR01610 6 GYTRMANELQEALPGADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDA 67 (95)
T ss_pred chhhhhHHHHHHHHhCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHH
Confidence 36677777778888777777777766643 3 577899999999999999999884
No 140
>PRK09492 treR trehalose repressor; Provisional
Probab=95.49 E-value=0.029 Score=45.39 Aligned_cols=45 Identities=11% Similarity=0.018 Sum_probs=37.2
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHH---HHHHhCcccc
Q psy6501 45 GWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGK---MERALGIRLR 89 (174)
Q Consensus 45 gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~---la~~L~v~~~ 89 (174)
.+|.+|+|+++|||.+|||+.-||....+.++-.+ .++.||..+.
T Consensus 4 ~~ti~dIA~~agVS~~TVSrvLn~~~~vs~~tr~rV~~~a~elgY~pn 51 (315)
T PRK09492 4 KLTIKDIARLSGVGKSTVSRVLNNESGVSEETRERVEAVINQHGFSPS 51 (315)
T ss_pred CCcHHHHHHHhCCCHHHHhHHhCCCCCCCHHHHHHHHHHHHHHCCCcC
Confidence 47999999999999999999999987777766554 5777886554
No 141
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=95.45 E-value=0.034 Score=45.28 Aligned_cols=44 Identities=7% Similarity=0.031 Sum_probs=35.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCC---CCCHHHHH---HHHHHhCcccc
Q psy6501 46 WSQKDLATKINEKPQIVNDYEGGRG---IPNQAIIG---KMERALGIRLR 89 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~G~~---~P~~~~l~---~la~~L~v~~~ 89 (174)
||.+|+|+.+|||.+|||+.-||.. ..+.++-. +.|+.||-.+.
T Consensus 1 ~ti~dIA~~aGVS~~TVSrvLn~~~~~~~Vs~~tr~rV~~~a~elgY~pn 50 (328)
T PRK11303 1 MKLDEIARLAGVSRTTASYVINGKAKQYRVSDKTVEKVMAVVREHNYHPN 50 (328)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCCcCHHHHHHHHHHHHHhCCCCC
Confidence 5899999999999999999999985 46665554 55777886554
No 142
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=95.38 E-value=0.037 Score=32.47 Aligned_cols=38 Identities=21% Similarity=0.192 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCC
Q psy6501 32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG 70 (174)
Q Consensus 32 ~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~ 70 (174)
.+-..|..++... +|+.+.|+..||+++||+++-+|..
T Consensus 4 ~l~~Ai~~v~~g~-~S~r~AA~~ygVp~sTL~~r~~g~~ 41 (45)
T PF05225_consen 4 DLQKAIEAVKNGK-MSIRKAAKKYGVPRSTLRRRLRGKP 41 (45)
T ss_dssp HHHHHHHHHHTTS-S-HHHHHHHHT--HHHHHHHHHHTT
T ss_pred HHHHHHHHHHhCC-CCHHHHHHHHCcCHHHHHHHHcCCC
Confidence 4667788888555 9999999999999999999988764
No 143
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=95.37 E-value=0.011 Score=51.27 Aligned_cols=103 Identities=16% Similarity=0.182 Sum_probs=64.0
Q ss_pred cCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCCCCCCCCcccchhhhhhhhhhcccccHHH
Q psy6501 44 KGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDRETEELKHEKVPLDL 123 (174)
Q Consensus 44 ~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~ 123 (174)
+-||++++|+.+|+..||||+.-+|+..-++.-+ +++.+||........+ .......+...+
T Consensus 342 kPLtlkdvAe~lglheSTVSRav~~Kyv~tp~Gi--------~~lk~FFs~~~~~~~g----------~~~S~~~Ik~~I 403 (455)
T PRK05932 342 KPLVLKDIAEELGMHESTISRATTNKYMATPRGI--------FELKYFFSSAVSTDGG----------GEASSTAIRALI 403 (455)
T ss_pred cCccHHHHHHHhCCCccchhhhhcCceeecCCce--------EEHHHhcccccCCCCC----------ccccHHHHHHHH
Confidence 5579999999999999999999999954333333 3444555322110000 001111222334
Q ss_pred HHHHHHHHHhcCCCHHHHHHHh-----CCChhHHHHHhcCCCCCCH
Q psy6501 124 AKLLMQGRQAKGWSQKDLATKI-----NEKPQIVNDYEGGRGIPNQ 164 (174)
Q Consensus 124 ~~~i~~~R~~~glsq~ela~~l-----g~~~s~i~~~E~G~~~P~~ 164 (174)
..+|...-..+-+|-.++++.+ .+++-||++|=..-..|+-
T Consensus 404 k~lI~~Ed~~~PlSD~~I~~~L~~~Gi~IaRRTVaKYRe~L~Ip~s 449 (455)
T PRK05932 404 KKLIAAENPKKPLSDSKIAELLKEQGIDVARRTVAKYREALNIPSS 449 (455)
T ss_pred HHHHHhcCCCCCCCHHHHHHHHHHcCCCeehHHHHHHHHHcCCCCh
Confidence 4555444444569999999888 6777799999777666664
No 144
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
Probab=95.37 E-value=0.039 Score=44.79 Aligned_cols=45 Identities=11% Similarity=-0.017 Sum_probs=35.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH---HHHHHhCccccc
Q psy6501 46 WSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG---KMERALGIRLRV 90 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~---~la~~L~v~~~~ 90 (174)
.|.+|+|+.+|||++|||++-||....+.++-. +.++.||..+..
T Consensus 2 ~ti~dIA~~agVS~sTVSr~Ln~~~~vs~~tr~rV~~~a~~lgY~pn~ 49 (311)
T TIGR02405 2 LTIKDIARLAGVGKSTVSRVLNNEPKVSIETRERVEQVIQQSGFVPSK 49 (311)
T ss_pred CcHHHHHHHhCCCHHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCCcCH
Confidence 589999999999999999999998666665544 456777776543
No 145
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=95.33 E-value=0.093 Score=34.10 Aligned_cols=44 Identities=16% Similarity=0.200 Sum_probs=32.8
Q ss_pred HHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHH
Q psy6501 125 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKM 170 (174)
Q Consensus 125 ~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i 170 (174)
....-.|...|+|++++|+.+|+++++|..+.++ .+....+.++
T Consensus 22 ~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~--~~~~~~~~~~ 65 (73)
T TIGR03879 22 AAAALAREEAGKTASEIAEELGRTEQTVRNHLKG--ETKAGGLVKL 65 (73)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc--CcccchHHHH
Confidence 3333336679999999999999999999999994 3444444444
No 146
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=95.32 E-value=0.057 Score=37.67 Aligned_cols=38 Identities=18% Similarity=0.144 Sum_probs=30.2
Q ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q psy6501 40 GRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 84 (174)
Q Consensus 40 ~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L 84 (174)
|-.-.||||+|-|+.+|||++|+.++-+ .--.+||++|
T Consensus 52 L~D~egl~QeeaA~~MgVSR~T~~ril~-------~ARkKiA~AL 89 (106)
T PF02001_consen 52 LVDYEGLSQEEAAERMGVSRPTFQRILE-------SARKKIADAL 89 (106)
T ss_pred HHHHcCCCHHHHHHHcCCcHHHHHHHHH-------HHHHHHHHHH
Confidence 3456899999999999999999999875 2334677665
No 147
>PF02376 CUT: CUT domain; InterPro: IPR003350 A class, also called ONECUT, of homeodomain proteins. The CUT domain is a DNA-binding motif which can bind independently or in cooperation with the homeodomain (IPR001356 from INTERPRO), often found downstream of the CUT domain. Proteins display two modes of DNA binding, which hinge on the homeodomain and on the linker that separates it from the cut domain, and two modes of transcriptional stimulation, which hinge on the homeodomain [].; GO: 0003677 DNA binding; PDB: 1WH6_A 2D5V_A 2CSF_A 1X2L_A 2O49_A 2O4A_A 1YSE_A 1S7E_A 1WIZ_A 1WH8_A.
Probab=95.31 E-value=0.05 Score=36.58 Aligned_cols=38 Identities=18% Similarity=0.223 Sum_probs=32.5
Q ss_pred hHHHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHHc
Q psy6501 30 PLDLAKLLMQGRQAKGWSQKDLATKI-NEKPQIVNDYEG 67 (174)
Q Consensus 30 ~~~ig~~ik~~R~~~gltq~eLA~~i-gvs~~~is~~E~ 67 (174)
...|..+|+...+..++||+.||+.+ |.|+.++|.+-+
T Consensus 11 T~~I~~~ik~~L~~~~IsQ~~Fa~~vL~rsqgtlsdlL~ 49 (87)
T PF02376_consen 11 TKEIARRIKEWLKRNNISQRVFAKKVLNRSQGTLSDLLR 49 (87)
T ss_dssp HHHHHHHHHHHHHHTT--HHHHHHHTTSS-HHHHHHHHH
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHhccChhHHHHHhC
Confidence 56899999999999999999999976 999999999987
No 148
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=95.30 E-value=0.012 Score=50.81 Aligned_cols=103 Identities=14% Similarity=0.206 Sum_probs=64.4
Q ss_pred cCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCCCCCCCCcccchhhhhhhhhhcccccHHH
Q psy6501 44 KGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDRETEELKHEKVPLDL 123 (174)
Q Consensus 44 ~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~ 123 (174)
+-||++++|+.+|++.||||+.-+|+..-++.-+ +++.+||.......... .......+...+
T Consensus 317 kPLtlkdiA~~lglheSTVSRav~~Kyi~tp~Gi--------~~lk~FFs~~~~~~~~g---------~~~S~~~Ik~~I 379 (429)
T TIGR02395 317 KPLTLREVAEELGLHESTISRAINNKYLQTPRGV--------FELKYFFSRGVQTDSGE---------GEVSSTAIKALI 379 (429)
T ss_pred cCCcHHHHHHHhCCCccchhhhhcCceEecCCce--------EEHHHhcCCccCCCCCC---------CccCHHHHHHHH
Confidence 4589999999999999999999999954333333 24445553221100000 001111233444
Q ss_pred HHHHHHHHHhcCCCHHHHHHHh-----CCChhHHHHHhcCCCCCC
Q psy6501 124 AKLLMQGRQAKGWSQKDLATKI-----NEKPQIVNDYEGGRGIPN 163 (174)
Q Consensus 124 ~~~i~~~R~~~glsq~ela~~l-----g~~~s~i~~~E~G~~~P~ 163 (174)
.++|...-..+=+|-.++++.+ .+++-||++|=..-..|+
T Consensus 380 ~~lI~~E~~~~PlSD~~I~~~L~~~Gi~IaRRTVaKYRe~L~Ip~ 424 (429)
T TIGR02395 380 KELIAAEDKRKPLSDQKIAELLKEKGIKIARRTVAKYREELGIPS 424 (429)
T ss_pred HHHHHhcCCCCCCCHHHHHHHHHhcCCCeehHHHHHHHHHcCCCc
Confidence 5556555555569999999888 777779999976666665
No 149
>PRK09526 lacI lac repressor; Reviewed
Probab=95.29 E-value=0.028 Score=45.98 Aligned_cols=47 Identities=13% Similarity=-0.096 Sum_probs=37.2
Q ss_pred cCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH---HHHHHHhCccccc
Q psy6501 44 KGWSQKDLATKINEKPQIVNDYEGGRGIPNQAII---GKMERALGIRLRV 90 (174)
Q Consensus 44 ~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l---~~la~~L~v~~~~ 90 (174)
+..|.+|+|+++|||.+|||+.-||....+.++- .++++.||..+..
T Consensus 4 ~~~ti~dIA~~aGVS~~TVSrvLn~~~~vs~~tr~rV~~~a~elgY~pn~ 53 (342)
T PRK09526 4 KPVTLYDVARYAGVSYQTVSRVLNQASHVSAKTREKVEAAMAELNYVPNR 53 (342)
T ss_pred CCCcHHHHHHHhCCCHHHHHHHhcCCCCCCHHHHHHHHHHHHHHCCCcCH
Confidence 3469999999999999999999999876666554 4566677776543
No 150
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=95.26 E-value=0.074 Score=42.36 Aligned_cols=53 Identities=15% Similarity=0.296 Sum_probs=41.8
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Q psy6501 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIR 87 (174)
Q Consensus 33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~ 87 (174)
.-.-||.+.+- +|.+||++.+|++.+.+++|-||+..|+.+....|.+.|.-.
T Consensus 13 ~v~~lr~lk~~--~ty~el~~~~g~p~~~l~RYv~g~~~P~~~~a~~~~~~l~~~ 65 (238)
T PRK08558 13 AVRVLRSLKKT--YTYEELSSITGLPESVLNRYVNGHVLPSVERAREIVEKLGPY 65 (238)
T ss_pred HHHHHHHHhcc--cCHHHHHHHHCCCHHHHHHHHcCCcCCCHHHHHHHHHHHHHh
Confidence 34455555544 599999999999999999999999999999777666654433
No 151
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 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 [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=95.24 E-value=0.018 Score=34.95 Aligned_cols=28 Identities=18% Similarity=0.244 Sum_probs=22.1
Q ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501 42 QAKGWSQKDLATKINEKPQIVNDYEGGR 69 (174)
Q Consensus 42 ~~~gltq~eLA~~igvs~~~is~~E~G~ 69 (174)
.+.|.++.++|+..||+++||++|-+.+
T Consensus 19 ~e~g~s~~~ia~~fgv~~sTv~~I~K~k 46 (53)
T PF04218_consen 19 LEEGESKRDIAREFGVSRSTVSTILKNK 46 (53)
T ss_dssp HHCTT-HHHHHHHHT--CCHHHHHHHCH
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHhH
Confidence 4788899999999999999999997654
No 152
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 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.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=95.22 E-value=0.062 Score=36.14 Aligned_cols=36 Identities=14% Similarity=0.134 Sum_probs=31.0
Q ss_pred HHHHHHHHHHH--HHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 31 LDLAKLLMQGR--QAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 31 ~~ig~~ik~~R--~~~gltq~eLA~~igvs~~~is~~E 66 (174)
..+++|++-++ -..|+||.|+|+.+|+|-.||++.=
T Consensus 33 ~~l~~R~~va~~lL~~g~syreIa~~tgvS~aTItRvs 70 (87)
T PF01371_consen 33 EALAQRWQVAKELLDEGKSYREIAEETGVSIATITRVS 70 (87)
T ss_dssp HHHHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHH
Confidence 36888888887 4589999999999999999999864
No 153
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=95.20 E-value=0.024 Score=35.39 Aligned_cols=24 Identities=17% Similarity=0.291 Sum_probs=22.0
Q ss_pred cCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 44 KGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 44 ~gltq~eLA~~igvs~~~is~~E~ 67 (174)
-+++..++|+.+|||.+||+.|-+
T Consensus 21 g~i~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 21 GKIKLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred CCccHHHHHHHHCCCHHHHHHHhh
Confidence 469999999999999999999964
No 154
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=95.19 E-value=0.044 Score=44.58 Aligned_cols=45 Identities=16% Similarity=0.068 Sum_probs=37.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH---HHHHHhCccccc
Q psy6501 46 WSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG---KMERALGIRLRV 90 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~---~la~~L~v~~~~ 90 (174)
.|.+|+|+.+|||.+|||+.-||....+.++-. +.|+.||-.++.
T Consensus 2 ~ti~dIA~~agvS~~TVSrvLn~~~~vs~~tr~rV~~~a~~lgY~pn~ 49 (329)
T TIGR01481 2 VTIYDVAREAGVSMATVSRVVNGNPNVKPATRKKVLEVIKRLDYRPNA 49 (329)
T ss_pred CcHHHHHHHhCCCHHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCCCCH
Confidence 488999999999999999999999777776655 567778876653
No 155
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=95.19 E-value=0.045 Score=44.85 Aligned_cols=44 Identities=11% Similarity=0.036 Sum_probs=35.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCcccc
Q psy6501 46 WSQKDLATKINEKPQIVNDYEGGRGIPNQAI---IGKMERALGIRLR 89 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~G~~~P~~~~---l~~la~~L~v~~~ 89 (174)
.|.+|+|+.+|||.+|||+.-||+...+.++ +.++|+.||-.+.
T Consensus 2 ~Ti~dIA~~agVS~~TVSrvLn~~~~vs~~tr~~V~~~a~elgY~pn 48 (341)
T PRK10703 2 ATIKDVAKRAGVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPS 48 (341)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHCCCcC
Confidence 4899999999999999999999986556555 5567777876654
No 156
>PRK04217 hypothetical protein; Provisional
Probab=95.16 E-value=0.084 Score=37.08 Aligned_cols=77 Identities=8% Similarity=-0.056 Sum_probs=53.3
Q ss_pred CCCCccccccccchhhcccccchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Q psy6501 8 PGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIR 87 (174)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~ 87 (174)
|.|-.|.-+.--.-..+++..+...-- .+-.++...|+|++|+|+.+|+|.+||.++-. ....+|.+.+...
T Consensus 22 ~~~~~~~~~~~~~~~~~p~~~Lt~eer-eai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~-------RArkkLre~L~~~ 93 (110)
T PRK04217 22 PQVRHFYPAIPPVGPPKPPIFMTYEEF-EALRLVDYEGLTQEEAGKRMGVSRGTVWRALT-------SARKKVAQMLVEG 93 (110)
T ss_pred CCcceEeCCCCCccCCCCcccCCHHHH-HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH-------HHHHHHHHHHHhc
Confidence 444444444444445566666665553 55577888999999999999999999999975 3555677776655
Q ss_pred ccccc
Q psy6501 88 LRVNA 92 (174)
Q Consensus 88 ~~~l~ 92 (174)
....+
T Consensus 94 ~~~~~ 98 (110)
T PRK04217 94 RELII 98 (110)
T ss_pred cceeE
Confidence 55444
No 157
>COG2842 Uncharacterized ATPase, putative transposase [General function prediction only]
Probab=95.14 E-value=0.068 Score=43.76 Aligned_cols=62 Identities=21% Similarity=0.109 Sum_probs=50.9
Q ss_pred cchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH-HHHHHhCccccc
Q psy6501 28 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG-KMERALGIRLRV 90 (174)
Q Consensus 28 ~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~-~la~~L~v~~~~ 90 (174)
++.+..-+.++++-+-.|++|+.+|..+|+|+.+||.|-|| ..+...... +|+..++-....
T Consensus 2 ~~n~~~~k~~k~f~e~~~~~q~~~a~gi~~~~~~vsk~L~g-~~g~~~~~~a~ia~~le~~~~q 64 (297)
T COG2842 2 QINFIEIKKLKEFAEFSGMCQKYLARGIGTSAPALSKYLNG-YKGDYATNEAKIAAFLEKKGVQ 64 (297)
T ss_pred chhHHHHHHHHHHHHhhhhhHHHHHHHhccCchhHHHHhcC-cCchHHHHHHHHHHHHcCCCcc
Confidence 34566778899999999999999999999999999999999 555555554 888888876443
No 158
>PRK13698 plasmid-partitioning protein; Provisional
Probab=95.09 E-value=0.045 Score=45.38 Aligned_cols=43 Identities=12% Similarity=0.034 Sum_probs=36.4
Q ss_pred hHHHHHHH-HHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCC
Q psy6501 30 PLDLAKLL-MQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIP 72 (174)
Q Consensus 30 ~~~ig~~i-k~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P 72 (174)
..+.|... +.+....|+||++||+.+|+|+++|++.-+=-..|
T Consensus 160 ~iE~A~ay~~~L~~~~~~tQeeLA~~lG~SRs~Vsn~Lrla~LP 203 (323)
T PRK13698 160 AYERGLRYASRLQNEFAGNISALADAENISRKIITRCINTAKLP 203 (323)
T ss_pred HHHHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHcCC
Confidence 36778887 66888999999999999999999999998655553
No 159
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=95.06 E-value=0.15 Score=42.40 Aligned_cols=64 Identities=9% Similarity=0.052 Sum_probs=51.2
Q ss_pred hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH-------------cCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501 30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE-------------GGRGIPNQAIIGKMERALGIRLRVNAG 93 (174)
Q Consensus 30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E-------------~G~~~P~~~~l~~la~~L~v~~~~l~~ 93 (174)
......++..+.-..||||.|+|+++|+|+.+|+++- +.......+.-.+|.+.||+.-.+...
T Consensus 11 ~~~l~~~~A~lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I~i~~~~~~~~~Le~~L~~~fgL~~a~VVp 87 (321)
T COG2390 11 EERLLARAAWLYYVEGLTQSEIAERLGISRATVSRLLAKAREEGIVKISINSPVEGCLELEQQLKERFGLKEAIVVP 87 (321)
T ss_pred HHHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEEEeCCCCcchHHHHHHHHHhcCCCeEEEEc
Confidence 4568889999999999999999999999999999985 222334444557899999998776664
No 160
>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=95.02 E-value=0.037 Score=34.77 Aligned_cols=22 Identities=14% Similarity=0.283 Sum_probs=20.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q psy6501 46 WSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~ 67 (174)
+|..|+|+.+|||++||..|++
T Consensus 1 ~s~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5789999999999999999996
No 161
>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=95.01 E-value=0.068 Score=33.63 Aligned_cols=22 Identities=27% Similarity=0.513 Sum_probs=20.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q psy6501 46 WSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~ 67 (174)
+|..|+|+.+|||++||..||.
T Consensus 1 ~~i~evA~~~gvs~~tlR~~~~ 22 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEK 22 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5789999999999999999986
No 162
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=94.94 E-value=0.034 Score=30.24 Aligned_cols=22 Identities=14% Similarity=0.167 Sum_probs=17.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHH
Q psy6501 45 GWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 45 gltq~eLA~~igvs~~~is~~E 66 (174)
.||.+|+|+.+|+++.|||+.-
T Consensus 2 ~mtr~diA~~lG~t~ETVSR~l 23 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVSRIL 23 (32)
T ss_dssp E--HHHHHHHHTS-HHHHHHHH
T ss_pred CcCHHHHHHHhCCcHHHHHHHH
Confidence 4899999999999999999863
No 163
>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=94.94 E-value=0.048 Score=31.83 Aligned_cols=27 Identities=19% Similarity=0.223 Sum_probs=22.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCC
Q psy6501 46 WSQKDLATKINEKPQIVNDYEGGRGIP 72 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~G~~~P 72 (174)
||..|+|+.+||++++|..|++-...|
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~~~g~l~ 27 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERIGLLS 27 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHCCCCC
Confidence 578999999999999999998655444
No 164
>COG5499 Predicted transcription regulator containing HTH domain [Transcription]
Probab=94.93 E-value=0.075 Score=37.04 Aligned_cols=53 Identities=21% Similarity=0.229 Sum_probs=46.5
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501 121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174 (174)
Q Consensus 121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l 174 (174)
..-.+.|+......|+|+.+++..+| |.+.++++-+|++.-+.+.+.++.+-|
T Consensus 59 P~pve~I~t~Md~~glt~~dLa~~iG-Sks~vS~iL~~rraLTle~ikkL~q~~ 111 (120)
T COG5499 59 PDPVEVIRTLMDQYGLTLADLANEIG-SKSRVSNILSGRRALTLEHIKKLHQRF 111 (120)
T ss_pred CCHHHHHHHHHHHhCCcHHHHHHHhC-chHHHHHHHhhhhHhhHHHHHHHHHHh
Confidence 34457889999999999999999999 578999999999999999999987643
No 165
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=94.91 E-value=0.055 Score=44.47 Aligned_cols=45 Identities=13% Similarity=-0.026 Sum_probs=36.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH---HHHHHhCccccc
Q psy6501 46 WSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG---KMERALGIRLRV 90 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~---~la~~L~v~~~~ 90 (174)
.|.+|+|+.+|||.+|||+.-||....+.++-. +.|+.||..+..
T Consensus 2 ~ti~dIA~~aGVS~~TVSrvLn~~~~Vs~~tr~rV~~~a~elgY~pn~ 49 (343)
T PRK10727 2 ATIKDVARLAGVSVATVSRVINNSPKASEASRLAVHSAMESLSYHPNA 49 (343)
T ss_pred CCHHHHHHHhCCCHHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCCCCH
Confidence 389999999999999999999999777766555 556677776554
No 166
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model 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 model 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 (pfam00376).
Probab=94.88 E-value=0.046 Score=31.60 Aligned_cols=28 Identities=11% Similarity=0.102 Sum_probs=24.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q psy6501 46 WSQKDLATKINEKPQIVNDYEGGRGIPN 73 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~G~~~P~ 73 (174)
||.+|+|+.+|+|+++|.+|.+-...|.
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g~i~~ 29 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEGELPA 29 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcCCCCe
Confidence 6889999999999999999997666664
No 167
>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=94.86 E-value=0.13 Score=27.01 Aligned_cols=23 Identities=22% Similarity=0.335 Sum_probs=21.3
Q ss_pred HcCCCHHHHHHHhCCCHHHHHHH
Q psy6501 43 AKGWSQKDLATKINEKPQIVNDY 65 (174)
Q Consensus 43 ~~gltq~eLA~~igvs~~~is~~ 65 (174)
..|+|..++|+.+|+|+++|++|
T Consensus 19 ~~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 19 AAGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHh
Confidence 46889999999999999999987
No 168
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=94.85 E-value=0.043 Score=33.08 Aligned_cols=31 Identities=16% Similarity=0.156 Sum_probs=24.2
Q ss_pred HHHHHHHHcC-CCHHHHHHHhCCCHHHHHHHH
Q psy6501 36 LLMQGRQAKG-WSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 36 ~ik~~R~~~g-ltq~eLA~~igvs~~~is~~E 66 (174)
-|+.+.+..+ +|.++||+.+|||+.||.+.-
T Consensus 5 il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i 36 (55)
T PF08279_consen 5 ILKLLLESKEPITAKELAEELGVSRRTIRRDI 36 (55)
T ss_dssp HHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHH
T ss_pred HHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHH
Confidence 3555655555 999999999999999998864
No 169
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=94.81 E-value=0.066 Score=44.03 Aligned_cols=44 Identities=16% Similarity=0.136 Sum_probs=35.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH---HHHHHhCcccc
Q psy6501 46 WSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG---KMERALGIRLR 89 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~---~la~~L~v~~~ 89 (174)
.|.+|+|+++|||.+|||+.-||....+.++-. +.++.||..+.
T Consensus 2 ~ti~dIA~~aGVS~~TVSrvLn~~~~Vs~~tr~kV~~~a~elgY~pn 48 (346)
T PRK10401 2 ITIRDVARQAGVSVATVSRVLNNSALVSADTREAVMKAVSELGYRPN 48 (346)
T ss_pred CCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCC
Confidence 589999999999999999999998766665554 55666776543
No 170
>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=94.80 E-value=0.19 Score=34.29 Aligned_cols=24 Identities=13% Similarity=0.260 Sum_probs=21.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501 46 WSQKDLATKINEKPQIVNDYEGGR 69 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~G~ 69 (174)
|+..|+|+.+|||.+||..||+-.
T Consensus 1 ~~I~e~a~~~gvs~~tLR~ye~~G 24 (96)
T cd04774 1 YKVDEVAKRLGLTKRTLKYYEEIG 24 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCC
Confidence 578899999999999999998643
No 171
>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=94.79 E-value=0.5 Score=32.37 Aligned_cols=22 Identities=18% Similarity=0.382 Sum_probs=20.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q psy6501 46 WSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~ 67 (174)
+|..|+|+.+|||.+||..||.
T Consensus 1 yti~EvA~~~gVs~~tLR~ye~ 22 (99)
T cd04765 1 FSIGEVAEILGLPPHVLRYWET 22 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999985
No 172
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=94.78 E-value=0.049 Score=44.47 Aligned_cols=45 Identities=16% Similarity=0.109 Sum_probs=36.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH---HHHHHhCcccc
Q psy6501 45 GWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG---KMERALGIRLR 89 (174)
Q Consensus 45 gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~---~la~~L~v~~~ 89 (174)
..|.+|+|+.+|||.+|||+.-||....+.++-. ++++.||-.+.
T Consensus 5 ~~ti~dIA~~agVS~~TVSrvLn~~~~vs~~tr~rV~~~a~elgY~pn 52 (331)
T PRK14987 5 RPVLQDVADRVGVTKMTVSRFLRNPEQVSVALRGKIAAALDELGYIPN 52 (331)
T ss_pred CCcHHHHHHHhCCCHHHhhhhhCCCCCCCHHHHHHHHHHHHHhCCCcc
Confidence 4699999999999999999999998766766554 56677776554
No 173
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=94.76 E-value=0.026 Score=49.36 Aligned_cols=104 Identities=14% Similarity=0.164 Sum_probs=64.2
Q ss_pred HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCCCCCCCCcccchhhhhhhhhhcccccHH
Q psy6501 43 AKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDRETEELKHEKVPLD 122 (174)
Q Consensus 43 ~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ 122 (174)
.+=||++++|+.+|+..||||+.-+|+..-++.-+..|-.+|.-.+..--| .......+...
T Consensus 367 LkPLtlkdVAe~lglHeSTVSRa~~~KY~~tp~GifeLK~FFs~~v~~~~g------------------~~~Ss~~Ik~~ 428 (481)
T PRK12469 367 LKPLVLRDVAEELGLHESTISRATGNKYMATPRGTFEFKHFFPRKLEAAGG------------------GECSAAAVRAL 428 (481)
T ss_pred CcCCcHHHHHHHhCCCcchhhHHhcCceeecCCceEeHHHhhccccCCCCC------------------ccccHHHHHHH
Confidence 356799999999999999999999999554444444444444433210000 00011112233
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHh-----CCChhHHHHHhcCCCCCCH
Q psy6501 123 LAKLLMQGRQAKGWSQKDLATKI-----NEKPQIVNDYEGGRGIPNQ 164 (174)
Q Consensus 123 ~~~~i~~~R~~~glsq~ela~~l-----g~~~s~i~~~E~G~~~P~~ 164 (174)
+.++|...-..+=+|-.++++.+ .+++-||++|=..-..|+-
T Consensus 429 Ik~lI~~Ed~~kPLSD~~I~~~L~~~GI~IARRTVAKYRe~L~IpsS 475 (481)
T PRK12469 429 IKEMIAAEQAGDPLSDVALAEMLAGRGVLIARRTVAKYREAMKIPPA 475 (481)
T ss_pred HHHHHHhcCCCCCCCHHHHHHHHHhcCCCeechhHHHHHHHcCCCCh
Confidence 44455444445568999988887 4555699999777666654
No 174
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=94.68 E-value=0.096 Score=30.04 Aligned_cols=31 Identities=13% Similarity=0.085 Sum_probs=26.2
Q ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHH
Q psy6501 34 AKLLMQGRQAKGWSQKDLATKINEKPQIVND 64 (174)
Q Consensus 34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~ 64 (174)
-..|...-+..+.++.+.|+.+|||++++.+
T Consensus 7 ~~~i~~aL~~~~gn~~~aA~~Lgisr~tL~~ 37 (42)
T PF02954_consen 7 KQLIRQALERCGGNVSKAARLLGISRRTLYR 37 (42)
T ss_dssp HHHHHHHHHHTTT-HHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHHHHhCCCHHHHHHHHCCCHHHHHH
Confidence 4578889999999999999999999999975
No 175
>TIGR00180 parB_part ParB-like partition proteins. This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.
Probab=94.61 E-value=0.084 Score=40.31 Aligned_cols=52 Identities=17% Similarity=0.142 Sum_probs=39.2
Q ss_pred hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHH
Q psy6501 30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMER 82 (174)
Q Consensus 30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~ 82 (174)
..+.+..++.+....|+|++++|+.+|+|+++|+++-.=.. .+.+.+..+..
T Consensus 105 ~~e~a~~~~~l~~~~g~s~~~iA~~lg~s~~~V~r~l~l~~-lp~~v~~~~~~ 156 (187)
T TIGR00180 105 PIEEAQAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLRLLK-LPSEIQSAIPE 156 (187)
T ss_pred HHHHHHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHHHHc-CCHHHHHHHHh
Confidence 35567777787777999999999999999999999976444 33355555554
No 176
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized 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.
Probab=94.58 E-value=0.076 Score=43.22 Aligned_cols=44 Identities=14% Similarity=0.156 Sum_probs=35.6
Q ss_pred CHHHHHHHhCCCHHHHHHHHcCCC---CCCHHHHH---HHHHHhCccccc
Q psy6501 47 SQKDLATKINEKPQIVNDYEGGRG---IPNQAIIG---KMERALGIRLRV 90 (174)
Q Consensus 47 tq~eLA~~igvs~~~is~~E~G~~---~P~~~~l~---~la~~L~v~~~~ 90 (174)
|.+|+|+.+|||.+|||+.-||.. ..+.++-. +.|+.||-.++.
T Consensus 1 ti~dIA~~aGVS~~TVSrvLn~~~~~~~vs~~tr~rV~~~a~~lgY~pn~ 50 (327)
T TIGR02417 1 TLSDIAKLAGVSKTTASYVINGKAKEYRISQETVERVMAVVREQGYQPNI 50 (327)
T ss_pred CHHHHHHHhCCCHHHHHHHHcCCCCCCccCHHHHHHHHHHHHHhCCCCCH
Confidence 678999999999999999999986 46666655 567778877654
No 177
>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=94.58 E-value=0.7 Score=36.36 Aligned_cols=24 Identities=21% Similarity=0.286 Sum_probs=21.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501 46 WSQKDLATKINEKPQIVNDYEGGR 69 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~G~ 69 (174)
++..|||+.+|||.++|..||+-.
T Consensus 2 y~i~elA~~~Gvs~~tIR~Ye~~G 25 (219)
T cd04778 2 YRIDDLARAAGTTVRNVRAYQDRG 25 (219)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCC
Confidence 688999999999999999999543
No 178
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=94.52 E-value=0.061 Score=34.83 Aligned_cols=34 Identities=21% Similarity=0.313 Sum_probs=26.2
Q ss_pred CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHH
Q psy6501 47 SQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERA 83 (174)
Q Consensus 47 tq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~ 83 (174)
|...+|+.+|||+++||+| |...|. ....+|...
T Consensus 12 s~~kvA~aLGIs~~AVsQW--Ge~VPe-~rA~~ie~~ 45 (75)
T PRK09744 12 SKTKLANAAGVRLASVAAW--GELVPE-GRAMRLQEA 45 (75)
T ss_pred cHHHHHHHHCCCHHHHHHH--hccCcH-HHHHHHHHH
Confidence 6788999999999999999 666665 444455544
No 179
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=94.51 E-value=0.11 Score=35.39 Aligned_cols=43 Identities=19% Similarity=0.101 Sum_probs=32.4
Q ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q psy6501 34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 84 (174)
Q Consensus 34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L 84 (174)
-+.|| +..-.||||+|-|.++|||++|+.+.-+ .--.++|++|
T Consensus 39 lEAlR-LvD~~~l~QeeAA~rMgISr~Tfwr~l~-------sAR~KvA~aL 81 (99)
T COG1342 39 LEALR-LVDYEGLTQEEAALRMGISRQTFWRLLT-------SARKKVADAL 81 (99)
T ss_pred HHHHH-HHhHhhccHHHHHHHhcccHHHHHHHHH-------HHHHHHHHHH
Confidence 34443 5567899999999999999999998875 2334666664
No 180
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=94.49 E-value=0.082 Score=43.93 Aligned_cols=46 Identities=17% Similarity=0.100 Sum_probs=36.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH---HHHHHhCcccccc
Q psy6501 46 WSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG---KMERALGIRLRVN 91 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~---~la~~L~v~~~~l 91 (174)
.|.+|+|+.+|||.+|||+..||....+.++-. +.++.||-.++..
T Consensus 1 ~TikDVA~~AGVS~sTVSrvln~~~~Vs~eTr~kV~~a~~elgY~pN~~ 49 (333)
T COG1609 1 ATIKDVAKLAGVSKATVSRVLNGSPYVSEETREKVLAAIKELGYRPNAV 49 (333)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHCCCCCHH
Confidence 378999999999999999999999877776655 5566677765543
No 181
>PF12728 HTH_17: Helix-turn-helix domain
Probab=94.48 E-value=0.066 Score=31.77 Aligned_cols=29 Identities=17% Similarity=0.124 Sum_probs=25.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCH
Q psy6501 46 WSQKDLATKINEKPQIVNDYEGGRGIPNQ 74 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~G~~~P~~ 74 (174)
||.+|+|+.+|||.+||.+|-+-...|..
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g~i~~~ 30 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQGKIPPF 30 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCCCeE
Confidence 68999999999999999999876666654
No 182
>TIGR03764 ICE_PFGI_1_parB integrating conjugative element, PFGI_1 class, ParB family protein. Members of this protein family carry the ParB-type nuclease domain and are found in integrating conjugative elements (ICE) in the same class as PFGI-1 of Pseudomonas fluorescens Pf-5.
Probab=94.42 E-value=0.091 Score=42.26 Aligned_cols=51 Identities=16% Similarity=0.162 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHH---H---cCCCHHHHHHHhCC-----CHHHHHHHHcCCCCCCHHHHHHHH
Q psy6501 31 LDLAKLLMQGRQ---A---KGWSQKDLATKINE-----KPQIVNDYEGGRGIPNQAIIGKME 81 (174)
Q Consensus 31 ~~ig~~ik~~R~---~---~gltq~eLA~~igv-----s~~~is~~E~G~~~P~~~~l~~la 81 (174)
.+-+..++.++. + .++||+|||+++|- |+++||++..=-..........|+
T Consensus 116 IE~A~~~~~l~~l~e~~~g~~ltq~ela~~lgk~g~~isrs~Isn~lrll~~L~~~i~~~l~ 177 (258)
T TIGR03764 116 IEKALGVQKARALYEKELGESLSQRELARRLSADGYPISQSHISRMGDTVEYLYPAIPNLLY 177 (258)
T ss_pred HHHHHHHHHHHHHHHhhccCCCCHHHHHHHhcccCCCCCHHHHHHHHHHHHhChHHHHHHHH
Confidence 334555555653 4 68999999999976 999999988433333333333333
No 183
>COG1513 CynS Cyanate lyase [Inorganic ion transport and metabolism]
Probab=94.37 E-value=0.21 Score=35.96 Aligned_cols=62 Identities=24% Similarity=0.203 Sum_probs=58.0
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501 31 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA 92 (174)
Q Consensus 31 ~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~ 92 (174)
..+.+.|-...+.+|+|-++||+.+|.+.-.+...--|....+.+...++++.||++-+.+.
T Consensus 7 ~~l~~~ll~~Kk~kgLsfaDl~~~lG~~ev~vaa~~ygqa~~~~~ear~v~e~L~L~~~~v~ 68 (151)
T COG1513 7 LDLADALLLAKKKKGLSFADLADGLGLAEVFVAAALYGQAALPADEARAVGEALDLDEDAIL 68 (151)
T ss_pred HHHHHHHHHHHHhcCCcHHHHHhhcCccHHHHHHHHHhhccCCHHHHHHHHHHhCCCHHHHH
Confidence 46788899999999999999999999999999999999999999999999999999988775
No 184
>PF13518 HTH_28: Helix-turn-helix domain
Probab=94.37 E-value=0.1 Score=30.73 Aligned_cols=24 Identities=17% Similarity=0.215 Sum_probs=21.9
Q ss_pred cCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 44 KGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 44 ~gltq~eLA~~igvs~~~is~~E~ 67 (174)
.|.|..++|..+|||+++|.+|-+
T Consensus 11 ~g~s~~~~a~~~gis~~tv~~w~~ 34 (52)
T PF13518_consen 11 EGESVREIAREFGISRSTVYRWIK 34 (52)
T ss_pred cCCCHHHHHHHHCCCHhHHHHHHH
Confidence 477999999999999999999974
No 185
>KOG3802|consensus
Probab=94.35 E-value=0.066 Score=45.30 Aligned_cols=54 Identities=19% Similarity=0.175 Sum_probs=44.4
Q ss_pred hHHHHHHHHHHHHHcCCCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q psy6501 30 PLDLAKLLMQGRQAKGWSQKDLATKIN------EKPQIVNDYEGGRGIPNQAIIGKMERALG 85 (174)
Q Consensus 30 ~~~ig~~ik~~R~~~gltq~eLA~~ig------vs~~~is~~E~G~~~P~~~~l~~la~~L~ 85 (174)
...|++.+|..|-..|+||.|+..++| .|+.||++||.= ..|...+.||-=.|+
T Consensus 208 LEqFAK~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEAL--qLSFKNMCKLKPLL~ 267 (398)
T KOG3802|consen 208 LEQFAKTFKQRRIKLGFTQADVGLALGALYGNVFSQTTICRFEAL--QLSFKNMCKLKPLLE 267 (398)
T ss_pred HHHHHHHHHhheeccccchhHHHHHHHhhhCcccchhhhhHhHhh--ccCHHHHhhhHHHHH
Confidence 356999999999999999999999887 689999999963 446677777665554
No 186
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=94.32 E-value=0.062 Score=31.24 Aligned_cols=31 Identities=13% Similarity=0.162 Sum_probs=19.7
Q ss_pred HHHHHHHHhcCCCHHHHHHHhCCChhHHHHHh
Q psy6501 125 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYE 156 (174)
Q Consensus 125 ~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E 156 (174)
..|..+. ..|+|+.++|+.+|.+++||+++-
T Consensus 11 ~~I~~l~-~~G~s~~~IA~~lg~s~sTV~rel 41 (44)
T PF13936_consen 11 NQIEALL-EQGMSIREIAKRLGRSRSTVSREL 41 (44)
T ss_dssp -HHHHHH-CS---HHHHHHHTT--HHHHHHHH
T ss_pred HHHHHHH-HcCCCHHHHHHHHCcCcHHHHHHH
Confidence 3454443 689999999999999999998763
No 187
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=94.31 E-value=0.066 Score=44.43 Aligned_cols=60 Identities=8% Similarity=0.005 Sum_probs=45.1
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH-----cCC--------CCCCHHHHHHHHHHhCccccccc
Q psy6501 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE-----GGR--------GIPNQAIIGKMERALGIRLRVNA 92 (174)
Q Consensus 33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E-----~G~--------~~P~~~~l~~la~~L~v~~~~l~ 92 (174)
+--++-.+--..||||+|+|+++|+|+.+||++- .|- .....+.-.+|.+.||+.--...
T Consensus 17 l~~~vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~I~I~~~~~~~~~Le~~L~~~fgLk~~iVv 89 (318)
T PRK15418 17 LVARIAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQINSRFEGCLELENALRQHFSLQHIRVL 89 (318)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEEEEEeCCCccHHHHHHHHHHHhCCCEEEEE
Confidence 4557788888999999999999999999999985 332 12233444588888888765554
No 188
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=94.28 E-value=0.068 Score=32.56 Aligned_cols=32 Identities=22% Similarity=0.219 Sum_probs=27.5
Q ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
.-|..+.+.-++|+.+||+.+++++++++++-
T Consensus 7 ~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i 38 (59)
T PF01047_consen 7 RILRILYENGGITQSELAEKLGISRSTVTRII 38 (59)
T ss_dssp HHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHcCCCCHHHHHHHHCCChhHHHHHH
Confidence 45677889999999999999999999999874
No 189
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=94.26 E-value=0.064 Score=30.26 Aligned_cols=25 Identities=16% Similarity=0.263 Sum_probs=20.5
Q ss_pred CHHHHHHHhCCCHHHHHHHHcCCCC
Q psy6501 47 SQKDLATKINEKPQIVNDYEGGRGI 71 (174)
Q Consensus 47 tq~eLA~~igvs~~~is~~E~G~~~ 71 (174)
|..|+|+.+|||.+||..||.-.-.
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~Gll 25 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYEREGLL 25 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHTTSS
T ss_pred CHHHHHHHHCCCHHHHHHHHHCCCC
Confidence 4579999999999999999976544
No 190
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=94.22 E-value=0.07 Score=32.23 Aligned_cols=29 Identities=14% Similarity=-0.032 Sum_probs=25.0
Q ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 39 QGRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 39 ~~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
-.+-+.|.++.+||...|||++|+++|=+
T Consensus 13 L~~LR~~~~~~~La~~FgIs~stvsri~~ 41 (53)
T PF13613_consen 13 LMYLRLNLTFQDLAYRFGISQSTVSRIFH 41 (53)
T ss_pred HHHHHcCCcHhHHhhheeecHHHHHHHHH
Confidence 34566899999999999999999999853
No 191
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=94.20 E-value=0.062 Score=32.70 Aligned_cols=23 Identities=13% Similarity=0.187 Sum_probs=20.2
Q ss_pred cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 44 KGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 44 ~gltq~eLA~~igvs~~~is~~E 66 (174)
++.|..|||+.+|||++|++..-
T Consensus 22 R~~tl~elA~~lgis~st~~~~L 44 (53)
T PF04967_consen 22 RRITLEELAEELGISKSTVSEHL 44 (53)
T ss_pred CcCCHHHHHHHhCCCHHHHHHHH
Confidence 56799999999999999998754
No 192
>cd00131 PAX Paired Box domain
Probab=94.19 E-value=1.5 Score=31.52 Aligned_cols=35 Identities=9% Similarity=0.138 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 32 ~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
+.=.+|-.+- +.|+|+.++|+.+|||+++|++|-+
T Consensus 21 d~R~rIv~~~-~~G~s~~~iA~~~~Vs~~tV~r~i~ 55 (128)
T cd00131 21 SIRQRIVELA-QSGIRPCDISRQLRVSHGCVSKILN 55 (128)
T ss_pred HHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3444555443 4899999999999999999999954
No 193
>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=94.12 E-value=0.15 Score=34.18 Aligned_cols=24 Identities=8% Similarity=0.088 Sum_probs=21.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHcC
Q psy6501 45 GWSQKDLATKINEKPQIVNDYEGG 68 (174)
Q Consensus 45 gltq~eLA~~igvs~~~is~~E~G 68 (174)
++|..|+|+.+|||.+||..||.-
T Consensus 1 ~~ti~evA~~~gvs~~tLR~ye~~ 24 (88)
T cd01105 1 VIGIGEVSKLTGVSPRQLRYWEEK 24 (88)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHC
Confidence 478999999999999999999843
No 194
>KOG1168|consensus
Probab=94.11 E-value=0.029 Score=45.53 Aligned_cols=39 Identities=18% Similarity=0.201 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHh---------CCCHHHHHHHHcCC
Q psy6501 31 LDLAKLLMQGRQAKGWSQKDLATKI---------NEKPQIVNDYEGGR 69 (174)
Q Consensus 31 ~~ig~~ik~~R~~~gltq~eLA~~i---------gvs~~~is~~E~G~ 69 (174)
+.|++|.|+.|-+.|.||.++++.+ .+|++||.++|.=.
T Consensus 220 EaFAErFKQRRIKLGVTQADVG~ALAnLKiPGVGsLSQSTICRFESLT 267 (385)
T KOG1168|consen 220 EAFAERFKQRRIKLGVTQADVGKALANLKIPGVGSLSQSTICRFESLT 267 (385)
T ss_pred HHHHHHHHhhhhhhcccHHHHHHHHHhCcCCCcccccccceeeeeeec
Confidence 4899999999999999999999987 47899999999643
No 195
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=94.10 E-value=0.059 Score=43.97 Aligned_cols=45 Identities=13% Similarity=0.068 Sum_probs=35.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCC--CCHHH---HHHHHHHhCccccc
Q psy6501 46 WSQKDLATKINEKPQIVNDYEGGRGI--PNQAI---IGKMERALGIRLRV 90 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~G~~~--P~~~~---l~~la~~L~v~~~~ 90 (174)
.|.+|+|+++|||++|||+.-||+.. .+.++ +.+.++.||..+..
T Consensus 2 ~ti~dIA~~agVS~~TVSrvln~~~~~~vs~~tr~rV~~~a~~lgY~pn~ 51 (327)
T PRK10339 2 ATLKDIAIEAGVSLATVSRVLNDDPTLNVKEETKHRILEIAEKLEYKTSS 51 (327)
T ss_pred CCHHHHHHHhCCCHHhhhhhhcCCCCCCcCHHHHHHHHHHHHHhCCCCch
Confidence 48999999999999999999999852 45444 45668888887664
No 196
>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=93.95 E-value=0.15 Score=29.50 Aligned_cols=29 Identities=17% Similarity=0.106 Sum_probs=24.9
Q ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 39 QGRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 39 ~~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
.++-..|+|++++|+.+|+|.++|.+|.+
T Consensus 20 ~~~~~~~~~~~~ia~~~~~s~~~i~~~~~ 48 (55)
T cd06171 20 LLRFGEGLSYEEIAEILGISRSTVRQRLH 48 (55)
T ss_pred HHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34445899999999999999999999864
No 197
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=93.94 E-value=0.12 Score=30.48 Aligned_cols=24 Identities=21% Similarity=0.495 Sum_probs=19.1
Q ss_pred CCCHHHHHHHhCCChhHHHHHhcC
Q psy6501 135 GWSQKDLATKINEKPQIVNDYEGG 158 (174)
Q Consensus 135 glsq~ela~~lg~~~s~i~~~E~G 158 (174)
|+|..++|+.+|+++++|.+|-+-
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT-
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 999999999999999999999764
No 198
>PF08667 BetR: BetR domain; InterPro: IPR013975 CheY-like phosphoacceptor (or receiver [REC]) domain is a common module in a variety of response regulators of the bacterial signal transduction systems. BetR is one of the many response regulators and is encoded mainly in Burkholderia spp. It is a N-terminal helix-turn-helix domain (HTH) and has been shown to be related to the XRE-type HTH domain (IPR001387 from INTERPRO), it has been suggested that BetR would have dimerization, protein-protein interaction, and activation/relief-of-inhibition properties [].
Probab=93.93 E-value=0.3 Score=36.06 Aligned_cols=52 Identities=15% Similarity=0.121 Sum_probs=44.7
Q ss_pred HHHHHHHHHHhcCCCH----HHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501 123 LAKLLMQGRQAKGWSQ----KDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174 (174)
Q Consensus 123 ~~~~i~~~R~~~glsq----~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l 174 (174)
+..+++.+-..+|+.+ .++|..||++.++.++--+|+...+..-+.+|++.|
T Consensus 6 ~~erV~~Ll~~~Gi~kr~~~s~LA~iL~Is~ssa~RKL~G~~~ftl~EI~~Ia~~f 61 (147)
T PF08667_consen 6 IAERVRELLDRKGIPKRKHASELADILGISYSSAYRKLNGKSPFTLEEIKKIAKHF 61 (147)
T ss_pred HHHHHHHHHHHcCCcchhhHHHHHHHHCCCHHHHHHHhcCCCCCCHHHHHHHHHHh
Confidence 4566777777777655 679999999999999999999999999999999876
No 199
>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=93.89 E-value=0.21 Score=33.97 Aligned_cols=22 Identities=14% Similarity=0.241 Sum_probs=20.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q psy6501 46 WSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~ 67 (174)
+|..|+|+.+|||.+||.-||+
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~ 22 (97)
T cd04782 1 FTTGEFAKLCGISKQTLFHYDK 22 (97)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5789999999999999999983
No 200
>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=93.85 E-value=0.36 Score=34.79 Aligned_cols=46 Identities=24% Similarity=0.292 Sum_probs=32.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc------------CCCCCCHHHHH-----HHHHHhCcccccc
Q psy6501 46 WSQKDLATKINEKPQIVNDYEG------------GRGIPNQAIIG-----KMERALGIRLRVN 91 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~------------G~~~P~~~~l~-----~la~~L~v~~~~l 91 (174)
|+..|+|+.+|||.+||.-||+ |.|.-+.+.+. +..+.+|++++++
T Consensus 1 m~IgE~A~~~gvs~~TLRyYE~~GLl~p~r~~~~gyR~Y~~~~~~~l~~I~~lr~~G~sL~eI 63 (133)
T cd04787 1 MKVKELANAAGVTPDTVRFYTRIGLLRPTRDPVNGYRLYSEKDLSRLRFILSARQLGFSLKDI 63 (133)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCCcCCCCCeeeCCHHHHHHHHHHHHHHHcCCCHHHH
Confidence 6789999999999999999994 33333333333 3345577777664
No 201
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=93.84 E-value=0.064 Score=33.75 Aligned_cols=25 Identities=20% Similarity=0.320 Sum_probs=21.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCC
Q psy6501 46 WSQKDLATKINEKPQIVNDYEGGRG 70 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~G~~ 70 (174)
+|..|+|+.+|||+++|..||+-.-
T Consensus 1 yti~eva~~~gvs~~tlr~y~~~gl 25 (69)
T PF13411_consen 1 YTIKEVAKLLGVSPSTLRYYEREGL 25 (69)
T ss_dssp EEHHHHHHHTTTTHHHHHHHHHTTS
T ss_pred CcHHHHHHHHCcCHHHHHHHHHhcC
Confidence 4788999999999999999996443
No 202
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=93.82 E-value=0.95 Score=28.58 Aligned_cols=22 Identities=18% Similarity=0.243 Sum_probs=18.4
Q ss_pred CCCHHHHHHHhCCCHHHHHHHH
Q psy6501 45 GWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 45 gltq~eLA~~igvs~~~is~~E 66 (174)
.+|.++||+.+|+|.++++++=
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f 22 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLF 22 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHH
Confidence 4788999999999999887763
No 203
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=93.80 E-value=0.1 Score=41.86 Aligned_cols=45 Identities=22% Similarity=0.284 Sum_probs=35.8
Q ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q psy6501 34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALG 85 (174)
Q Consensus 34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~ 85 (174)
=+.|-.+|-..++||+|+|+.+|||+++||++++ ..+.+|-..|+
T Consensus 201 Ek~Vl~l~y~eelt~kEI~~~LgISes~VSql~k-------kai~kLr~~l~ 245 (247)
T COG1191 201 EKLVLVLRYKEELTQKEIAEVLGISESRVSRLHK-------KAIKKLRKELN 245 (247)
T ss_pred HHHHHHHHHHhccCHHHHHHHhCccHHHHHHHHH-------HHHHHHHHHhc
Confidence 3456678889999999999999999999999985 45555555543
No 204
>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=93.59 E-value=0.16 Score=36.27 Aligned_cols=46 Identities=17% Similarity=0.200 Sum_probs=34.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHH------------cCCCCCCHHHHH-----HHHHHhCcccccc
Q psy6501 46 WSQKDLATKINEKPQIVNDYE------------GGRGIPNQAIIG-----KMERALGIRLRVN 91 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E------------~G~~~P~~~~l~-----~la~~L~v~~~~l 91 (174)
|+..|+|+.+|||..||.-|| +|.+..+.+.+. ...+.+|+++.++
T Consensus 1 m~IgevA~~~gvs~~tLRyYe~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI 63 (127)
T cd04784 1 MKIGELAKKTGCSVETIRYYEKEGLLPAPARSANNYRLYDEEHLERLLFIRRCRSLDMSLDEI 63 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHH
Confidence 578999999999999999999 455666666654 3345677776654
No 205
>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=93.53 E-value=0.25 Score=34.50 Aligned_cols=46 Identities=20% Similarity=0.266 Sum_probs=32.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHH------------cCCCCCCHHHHHHHH-----HHhCcccccc
Q psy6501 46 WSQKDLATKINEKPQIVNDYE------------GGRGIPNQAIIGKME-----RALGIRLRVN 91 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E------------~G~~~P~~~~l~~la-----~~L~v~~~~l 91 (174)
||..|+|+.+|||.+||..|| +|.+.-+.+.+..|. +.+|+++.++
T Consensus 1 ~~i~e~a~~~gvs~~tlr~ye~~gll~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI 63 (113)
T cd01109 1 YTIKEVAEKTGLSADTLRYYEKEGLLPPVKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDI 63 (113)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHH
Confidence 578999999999999999999 444555555555443 3356665543
No 206
>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=93.47 E-value=0.21 Score=33.93 Aligned_cols=22 Identities=18% Similarity=0.480 Sum_probs=20.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q psy6501 46 WSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~ 67 (174)
|+..|+|+.+|||..||.-||+
T Consensus 1 m~i~eva~~~gvs~~tlR~ye~ 22 (96)
T cd04788 1 WKIGELARRTGLSVRTLHHYDH 22 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 6789999999999999999994
No 207
>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=93.46 E-value=0.49 Score=33.74 Aligned_cols=71 Identities=14% Similarity=0.116 Sum_probs=46.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCCCCCCCCcccchhhhhhhhhhcccccHHHHH
Q psy6501 46 WSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAK 125 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~ 125 (174)
+|..++|+.+|||++||..||+-.-.+... + + -.-++ +.. ....-.
T Consensus 2 ysI~eVA~~~GVs~~TLR~wE~~GLl~p~r------~--~--G~R~Y---------------s~~---------dv~rL~ 47 (120)
T cd04767 2 YPIGVVAELLNIHPETLRIWERHGLIKPAR------R--N--GQRLY---------------SNN---------DLKRLR 47 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCcC------C--C--CcEEE---------------CHH---------HHHHHH
Confidence 688999999999999999998754333210 0 0 00111 111 112235
Q ss_pred HHHHHHHhcCCCHHHHHHHhCCChh
Q psy6501 126 LLMQGRQAKGWSQKDLATKINEKPQ 150 (174)
Q Consensus 126 ~i~~~R~~~glsq~ela~~lg~~~s 150 (174)
.|+.++...|++.+++...+..-+.
T Consensus 48 ~I~~L~~e~G~~l~eI~~~L~l~~~ 72 (120)
T cd04767 48 FIKKLINEKGLNIAGVKQILSMYPC 72 (120)
T ss_pred HHHHHHHHcCCCHHHHHHHHHhCcc
Confidence 7788888899999999988876554
No 208
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=93.38 E-value=1.3 Score=34.91 Aligned_cols=32 Identities=13% Similarity=0.121 Sum_probs=26.2
Q ss_pred HHHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 126 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 126 ~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
.+-.++-..|+|++++|+.+|++.+.|+.++.
T Consensus 190 ~vi~l~~~~~~t~~EIA~~lgis~~~V~q~~~ 221 (231)
T PRK12427 190 LILHLYYQHEMSLKEIALVLDLTEARICQLNK 221 (231)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 33345556799999999999999999998875
No 209
>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=93.37 E-value=0.24 Score=33.68 Aligned_cols=23 Identities=9% Similarity=0.112 Sum_probs=20.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Q psy6501 46 WSQKDLATKINEKPQIVNDYEGG 68 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~G 68 (174)
+|..|+|+.+|||.+||.-||+-
T Consensus 1 ~ti~eva~~~gvs~~tLRyye~~ 23 (96)
T cd04768 1 LTIGEFAKLAGVSIRTLRHYDDI 23 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 57899999999999999999954
No 210
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=93.37 E-value=0.16 Score=37.24 Aligned_cols=26 Identities=19% Similarity=0.322 Sum_probs=24.9
Q ss_pred hcCCCHHHHHHHhCCChhHHHHHhcC
Q psy6501 133 AKGWSQKDLATKINEKPQIVNDYEGG 158 (174)
Q Consensus 133 ~~glsq~ela~~lg~~~s~i~~~E~G 158 (174)
..|+||+++|+.+|+++++|+.||++
T Consensus 19 ~~GlTq~EIAe~LGiS~~tVs~ie~r 44 (141)
T PRK03975 19 ERGLTQQEIADILGTSRANVSSIEKR 44 (141)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 69999999999999999999999986
No 211
>PHA02591 hypothetical protein; Provisional
Probab=93.35 E-value=0.21 Score=32.72 Aligned_cols=29 Identities=17% Similarity=0.274 Sum_probs=24.9
Q ss_pred HHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 129 QGRQAKGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 129 ~~R~~~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
....+.|+||+++|..+|++..+++.|-+
T Consensus 53 ~eL~eqGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 53 HELARKGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 33457999999999999999999998854
No 212
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=93.33 E-value=0.19 Score=28.91 Aligned_cols=30 Identities=20% Similarity=0.167 Sum_probs=23.1
Q ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHH
Q psy6501 35 KLLMQGRQAKGWSQKDLATKINEKPQIVND 64 (174)
Q Consensus 35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~ 64 (174)
.-|..+.+....|..++|+.+|+|+++|.+
T Consensus 7 ~Il~~Lq~d~r~s~~~la~~lglS~~~v~~ 36 (42)
T PF13404_consen 7 KILRLLQEDGRRSYAELAEELGLSESTVRR 36 (42)
T ss_dssp HHHHHHHH-TTS-HHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHHcCCccHHHHHHHHCcCHHHHHH
Confidence 456778888999999999999999998864
No 213
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. 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 characterized.
Probab=93.33 E-value=0.31 Score=39.63 Aligned_cols=41 Identities=24% Similarity=0.255 Sum_probs=38.1
Q ss_pred cCCCHHHHHHHhCCCh-hHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501 134 KGWSQKDLATKINEKP-QIVNDYEGGRGIPNQAIIGKMERAL 174 (174)
Q Consensus 134 ~glsq~ela~~lg~~~-s~i~~~E~G~~~P~~~~l~~i~~~l 174 (174)
..+|-.++|+++|++. +.++.+.+|++.++...+.+++++|
T Consensus 26 p~fS~R~fa~~~G~ss~s~L~~v~~Gkr~Ls~~~~~k~a~~l 67 (271)
T TIGR02147 26 PAFSWRFFAEKAGFSSTSYLNDIIKGKKNLTKRMIPKFAEAL 67 (271)
T ss_pred cCcCHHHHHHHhCCCCHHHHHHHHcCCCCCCHHHHHHHHHHc
Confidence 3699999999999888 9999999999999999999999876
No 214
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=93.33 E-value=0.16 Score=41.16 Aligned_cols=41 Identities=17% Similarity=0.114 Sum_probs=33.2
Q ss_pred HHHHHHhCCCHHHHHHHHcCCCCCCHHHHH---HHHHHhCcccc
Q psy6501 49 KDLATKINEKPQIVNDYEGGRGIPNQAIIG---KMERALGIRLR 89 (174)
Q Consensus 49 ~eLA~~igvs~~~is~~E~G~~~P~~~~l~---~la~~L~v~~~ 89 (174)
+|+|+.+|||.+|||+.-||....+.++-. +.|+.||-.+.
T Consensus 2 ~dIA~~agVS~~TVSrvLn~~~~vs~~tr~rV~~~a~~lgY~pn 45 (327)
T PRK10423 2 KDVARLAGVSTSTVSHVINKDRFVSEAITAKVEAAIKELNYAPS 45 (327)
T ss_pred hhHHHHhCCcHHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCCcc
Confidence 689999999999999999998777777655 45666776554
No 215
>TIGR02293 TAS_TIGR02293 putative toxin-antitoxin system antitoxin component, TIGR02293 family. Proteins in this family are found almost exclusively in the Proteobacteria, but also in Gloeobacter violaceus PCC 7421, a cyanobacterium. This family was proposed by Makarova, et al. (2009) to be the antitoxin component of a new class of type 2 toxin-antitoxin system, or addiction module.
Probab=93.29 E-value=0.43 Score=34.46 Aligned_cols=48 Identities=4% Similarity=-0.047 Sum_probs=39.3
Q ss_pred HHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhh
Q psy6501 126 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERA 173 (174)
Q Consensus 126 ~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~ 173 (174)
.+.......++++++++..+|++++|++++-++...++.+.-.++.++
T Consensus 27 ~~~~l~~~l~ls~~el~~~lgis~~Tl~R~~~~~~~Ls~~~serl~~l 74 (133)
T TIGR02293 27 ALDRLAHLLAIGKAEIFKATGIPKATLQRRKMAHQRLSSEESDRLARV 74 (133)
T ss_pred HHHHHHHHHCCCHHHHHHHHCCCHHHHHHHhhcCCCCCHHHHHHHHHH
Confidence 444446778999999999999999999999998778888777666553
No 216
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=93.25 E-value=0.15 Score=32.67 Aligned_cols=32 Identities=13% Similarity=0.184 Sum_probs=25.0
Q ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
.+-..-..-|.|..++|...||++++|++|.+
T Consensus 14 ~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 14 QAVREYLESGESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp HHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHCCCceEeeecccccccccccHHHH
Confidence 33333356799999999999999999999974
No 217
>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=93.24 E-value=0.28 Score=30.34 Aligned_cols=24 Identities=8% Similarity=0.082 Sum_probs=20.7
Q ss_pred HcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 43 AKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 43 ~~gltq~eLA~~igvs~~~is~~E 66 (174)
...+|+.+||+.+|+|+++++++-
T Consensus 23 ~~~~s~~ela~~~g~s~~tv~r~l 46 (67)
T cd00092 23 QLPLTRQEIADYLGLTRETVSRTL 46 (67)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHH
Confidence 345999999999999999998764
No 218
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=93.22 E-value=0.75 Score=30.40 Aligned_cols=48 Identities=8% Similarity=-0.033 Sum_probs=37.7
Q ss_pred HHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCC-CCCCHHHHHHHHh
Q psy6501 124 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR-GIPNQAIIGKMER 172 (174)
Q Consensus 124 ~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~-~~P~~~~l~~i~~ 172 (174)
...+...+. ...+..++|+..|+|.++|++.-++. ...++.+-.++-+
T Consensus 9 ~~I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L~~~~~~Vs~~Tr~rV~~ 57 (80)
T TIGR02844 9 LEIGKYIVE-TKATVRETAKVFGVSKSTVHKDVTERLPEINPELAEEVKE 57 (80)
T ss_pred HHHHHHHHH-CCCCHHHHHHHhCCCHHHHHHHhcCCCCCCCHHHHHHHHH
Confidence 344445556 66899999999999999999999875 6677777777654
No 219
>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=93.17 E-value=0.53 Score=31.54 Aligned_cols=61 Identities=15% Similarity=0.225 Sum_probs=43.0
Q ss_pred HHHHHHHHHhCcccccccCCCCCCCCCcccchhhhhhhhhhcccccHHHHHHHHHHHHhcCCCHHHHHHHhC-CChhHHH
Q psy6501 75 AIIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKIN-EKPQIVN 153 (174)
Q Consensus 75 ~~l~~la~~L~v~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~R~~~glsq~ela~~lg-~~~s~i~ 153 (174)
..+..+|+.|||+.+++.++.-.. .+...=.-.+--++...|+|..++++.+| .+.++|.
T Consensus 3 ~Ii~~Va~~~~v~~~~i~~~~R~~-------------------~~~~aR~ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~ 63 (90)
T cd06571 3 LIIEAVAEYFGISVEDLRSKSRKK-------------------EIALARQIAMYLARELTGLSLPEIGRAFGGRDHSTVL 63 (90)
T ss_pred HHHHHHHHHhCCCHHHHhcCCCCc-------------------CcchHHHHHHHHHHHHhCCCHHHHHHHhCCCCHhHHH
Confidence 567899999999999998644321 11111122344467778999999999999 8888765
Q ss_pred H
Q psy6501 154 D 154 (174)
Q Consensus 154 ~ 154 (174)
.
T Consensus 64 ~ 64 (90)
T cd06571 64 H 64 (90)
T ss_pred H
Confidence 4
No 220
>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=93.15 E-value=0.27 Score=33.73 Aligned_cols=22 Identities=9% Similarity=0.228 Sum_probs=20.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q psy6501 46 WSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~ 67 (174)
+|..|+|+.+|||++||..||+
T Consensus 1 ~ti~eva~~~gvs~~tlR~ye~ 22 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYDE 22 (103)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5789999999999999999984
No 221
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=93.12 E-value=0.16 Score=31.86 Aligned_cols=22 Identities=14% Similarity=0.215 Sum_probs=20.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q psy6501 46 WSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~ 67 (174)
||..|+|+.+|||+++|..|+.
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5789999999999999999986
No 222
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=93.12 E-value=0.1 Score=32.61 Aligned_cols=27 Identities=33% Similarity=0.598 Sum_probs=20.9
Q ss_pred CHHHHHHHhCCChhHHHHHhcCCCCCCHH
Q psy6501 137 SQKDLATKINEKPQIVNDYEGGRGIPNQA 165 (174)
Q Consensus 137 sq~ela~~lg~~~s~i~~~E~G~~~P~~~ 165 (174)
++..+|+++|++++.|+.| |...|...
T Consensus 11 ~~~~lAkalGVs~~aVs~W--~~~IP~~r 37 (60)
T PF14549_consen 11 GQSKLAKALGVSPQAVSQW--GERIPAER 37 (60)
T ss_dssp SHHHHHHHHTS-HHHHHHH--HTS--HHH
T ss_pred CHHHHHHHHCCCHHHHHHh--cCccCHHH
Confidence 7899999999999999999 66666654
No 223
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 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 recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=93.11 E-value=0.18 Score=30.12 Aligned_cols=32 Identities=16% Similarity=0.116 Sum_probs=23.4
Q ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
..+-.++.-.|+|.+|+|+.+|+|.++|..+-
T Consensus 16 r~i~~l~~~~g~s~~eIa~~l~~s~~~v~~~l 47 (54)
T PF08281_consen 16 REIFLLRYFQGMSYAEIAEILGISESTVKRRL 47 (54)
T ss_dssp HHHHHHHHTS---HHHHHHHCTS-HHHHHHHH
T ss_pred HHHHHHHHHHCcCHHHHHHHHCcCHHHHHHHH
Confidence 44556778899999999999999999998763
No 224
>smart00351 PAX Paired Box domain.
Probab=93.07 E-value=0.32 Score=34.77 Aligned_cols=38 Identities=16% Similarity=0.205 Sum_probs=30.0
Q ss_pred chHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 29 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 29 ~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
+.+++=.+|-.+-. .|+|+.++|+.+|||++||++|-+
T Consensus 18 ~s~~~R~riv~~~~-~G~s~~~iA~~~gvs~~tV~kwi~ 55 (125)
T smart00351 18 LPDEERQRIVELAQ-NGVRPCDISRQLCVSHGCVSKILG 55 (125)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHH
Confidence 44555556655543 799999999999999999999964
No 225
>PRK10458 DNA cytosine methylase; Provisional
Probab=92.97 E-value=0.37 Score=42.18 Aligned_cols=49 Identities=16% Similarity=0.250 Sum_probs=38.2
Q ss_pred HHHHHHHHcCCCHHHHHHHhC------CCHHHHHHHHcCCCC---CCHHHHHHHHHHh
Q psy6501 36 LLMQGRQAKGWSQKDLATKIN------EKPQIVNDYEGGRGI---PNQAIIGKMERAL 84 (174)
Q Consensus 36 ~ik~~R~~~gltq~eLA~~ig------vs~~~is~~E~G~~~---P~~~~l~~la~~L 84 (174)
.....|...++||+++|..++ .|+.+|.+||+|... ++...+..|-+.+
T Consensus 20 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (467)
T PRK10458 20 QALLEKLLEIYDVKTLAAQLNGVGENHWSRAILKRWLAGKSAWHRLSEAEFAHLQTLL 77 (467)
T ss_pred HHHHHHHHHhcCHHHHHHHHhhcccCccCHHHHHHHHcCCCCCCCccHHHHHHHHHhc
Confidence 345566778899999999997 788999999999974 3446666676666
No 226
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=92.96 E-value=0.37 Score=39.42 Aligned_cols=25 Identities=12% Similarity=0.238 Sum_probs=22.7
Q ss_pred hcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 133 AKGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 133 ~~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
..++|.+++|+.+|+++++|..+++
T Consensus 267 ~~~~Tl~EIa~~lgiS~erVrq~~~ 291 (298)
T TIGR02997 267 GEPLTLAEIGRRLNLSRERVRQIEA 291 (298)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 4689999999999999999998875
No 227
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=92.89 E-value=0.18 Score=32.87 Aligned_cols=47 Identities=15% Similarity=0.175 Sum_probs=31.6
Q ss_pred HHHHHHHH-HHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH
Q psy6501 32 DLAKLLMQ-GRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG 78 (174)
Q Consensus 32 ~ig~~ik~-~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~ 78 (174)
.+++-|-. ..+-..+|..|||+.+|||+++|.++-+--..-....+.
T Consensus 20 ~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~kkLG~~gf~efk 67 (77)
T PF01418_consen 20 KIADYILENPDEIAFMSISELAEKAGVSPSTIVRFCKKLGFSGFKEFK 67 (77)
T ss_dssp HHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHHHHCTTTCHHHHH
T ss_pred HHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHHHHhCCCCHHHHH
Confidence 34444444 556778999999999999999999987665555554443
No 228
>PRK00118 putative DNA-binding protein; Validated
Probab=92.87 E-value=0.25 Score=34.32 Aligned_cols=47 Identities=19% Similarity=0.197 Sum_probs=34.2
Q ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCc
Q psy6501 36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI 86 (174)
Q Consensus 36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v 86 (174)
.+-.++...|+|.+|+|+.+|+|++||.++-.- ....+.++-..+|.
T Consensus 24 evl~L~y~eg~S~~EIAe~lGIS~~TV~r~L~R----ArkkLr~~~~~~~~ 70 (104)
T PRK00118 24 NYMELYYLDDYSLGEIAEEFNVSRQAVYDNIKR----TEKLLEDYEEKLHL 70 (104)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHH----HHHHHHHHHHHHCh
Confidence 344667788999999999999999999998642 23444555555444
No 229
>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=92.82 E-value=1.4 Score=31.71 Aligned_cols=46 Identities=15% Similarity=0.094 Sum_probs=32.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc------------CCCCCCHHHHH-----HHHHHhCcccccc
Q psy6501 46 WSQKDLATKINEKPQIVNDYEG------------GRGIPNQAIIG-----KMERALGIRLRVN 91 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~------------G~~~P~~~~l~-----~la~~L~v~~~~l 91 (174)
|+..|+|+.+|||..||.-||+ |.+.-+...+. +.++.+|++++++
T Consensus 1 m~Ige~a~~~gvs~~tLRyYE~~GLl~p~~r~~~gyR~Y~~~~v~~l~~I~~lr~~GfsL~eI 63 (131)
T cd04786 1 MKIGELAKRSGMAASRIRFYEAEGLLSSVERSANGYRDYPPETVWVLEIISSAQQAGFSLDEI 63 (131)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHH
Confidence 5789999999999999999983 44444433333 2345577776654
No 230
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=92.76 E-value=0.36 Score=38.46 Aligned_cols=36 Identities=14% Similarity=0.320 Sum_probs=32.8
Q ss_pred CCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHH
Q psy6501 136 WSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKME 171 (174)
Q Consensus 136 lsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~ 171 (174)
+|-+||++.+|++.+.+.+|=+|...|+...+..+-
T Consensus 24 ~ty~el~~~~g~p~~~l~RYv~g~~~P~~~~a~~~~ 59 (238)
T PRK08558 24 YTYEELSSITGLPESVLNRYVNGHVLPSVERAREIV 59 (238)
T ss_pred cCHHHHHHHHCCCHHHHHHHHcCCcCCCHHHHHHHH
Confidence 699999999999999999999999999998666554
No 231
>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=92.70 E-value=0.26 Score=34.27 Aligned_cols=22 Identities=32% Similarity=0.323 Sum_probs=20.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q psy6501 46 WSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~ 67 (174)
+|..|+|+.+|||..||..||+
T Consensus 1 y~Ige~A~~~gvs~~tlR~ye~ 22 (107)
T cd01111 1 YSISQLALDAGVSVHIVRDYLL 22 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999994
No 232
>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=92.68 E-value=0.31 Score=33.49 Aligned_cols=22 Identities=14% Similarity=0.252 Sum_probs=20.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q psy6501 46 WSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~ 67 (174)
+|..|+|+.+|||++||.-||+
T Consensus 2 ~~i~eva~~~gvs~~tLR~ye~ 23 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYES 23 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 6889999999999999999994
No 233
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=92.65 E-value=0.39 Score=28.00 Aligned_cols=33 Identities=33% Similarity=0.351 Sum_probs=25.7
Q ss_pred HHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHh
Q psy6501 124 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE 156 (174)
Q Consensus 124 ~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E 156 (174)
...+....+..++|+.++|+.+|++.++++.+-
T Consensus 6 ~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l 38 (48)
T PF13412_consen 6 RKILNYLRENPRITQKELAEKLGISRSTVNRYL 38 (48)
T ss_dssp HHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHH
Confidence 456667777888999999999999999987753
No 234
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=92.59 E-value=0.17 Score=29.85 Aligned_cols=25 Identities=20% Similarity=0.348 Sum_probs=22.8
Q ss_pred HcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 43 AKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 43 ~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
..|+|.+++|+.+|+|+++|..+-+
T Consensus 16 ~~g~s~~eia~~l~is~~tv~~~~~ 40 (58)
T smart00421 16 AEGLTNKEIAERLGISEKTVKTHLS 40 (58)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 5799999999999999999998864
No 235
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=92.58 E-value=0.27 Score=31.25 Aligned_cols=28 Identities=14% Similarity=0.004 Sum_probs=22.4
Q ss_pred HHHHHHcC--CCHHHHHHHhCCCHHHHHHH
Q psy6501 38 MQGRQAKG--WSQKDLATKINEKPQIVNDY 65 (174)
Q Consensus 38 k~~R~~~g--ltq~eLA~~igvs~~~is~~ 65 (174)
..++..-+ +|+.|||+.+|++.++|++.
T Consensus 13 ~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~ 42 (68)
T smart00550 13 EFLENSGDETSTALQLAKNLGLPKKEVNRV 42 (68)
T ss_pred HHHHHCCCCCcCHHHHHHHHCCCHHHHHHH
Confidence 33444445 99999999999999999876
No 236
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=92.52 E-value=0.37 Score=34.15 Aligned_cols=38 Identities=8% Similarity=-0.035 Sum_probs=29.6
Q ss_pred hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
..+|=..+-..-...|.|..++|+.+|||+++|++|-+
T Consensus 14 s~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r 51 (121)
T PRK09413 14 TTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRK 51 (121)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34444444444566799999999999999999999964
No 237
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=92.45 E-value=0.16 Score=32.44 Aligned_cols=23 Identities=13% Similarity=0.141 Sum_probs=20.4
Q ss_pred cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 44 KGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 44 ~gltq~eLA~~igvs~~~is~~E 66 (174)
..+||++||+.+|+|+.+|++.-
T Consensus 27 ~~lt~~~iA~~~g~sr~tv~r~l 49 (76)
T PF13545_consen 27 LPLTQEEIADMLGVSRETVSRIL 49 (76)
T ss_dssp EESSHHHHHHHHTSCHHHHHHHH
T ss_pred ecCCHHHHHHHHCCCHHHHHHHH
Confidence 46899999999999999998764
No 238
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=92.45 E-value=0.29 Score=28.58 Aligned_cols=38 Identities=21% Similarity=0.192 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCC
Q psy6501 122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG 160 (174)
Q Consensus 122 ~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~ 160 (174)
.+...|...+... +|+.+.|++.|++.+|+.++-+|..
T Consensus 4 ~l~~Ai~~v~~g~-~S~r~AA~~ygVp~sTL~~r~~g~~ 41 (45)
T PF05225_consen 4 DLQKAIEAVKNGK-MSIRKAAKKYGVPRSTLRRRLRGKP 41 (45)
T ss_dssp HHHHHHHHHHTTS-S-HHHHHHHHT--HHHHHHHHHHTT
T ss_pred HHHHHHHHHHhCC-CCHHHHHHHHCcCHHHHHHHHcCCC
Confidence 3455666666333 9999999999999999999888754
No 239
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. 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.
Probab=92.42 E-value=0.52 Score=36.69 Aligned_cols=29 Identities=7% Similarity=-0.002 Sum_probs=24.3
Q ss_pred HHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 129 QGRQAKGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 129 ~~R~~~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
..+-..|+|.+++|+.+|++.+++.....
T Consensus 185 ~l~y~~~~s~~eIA~~lgis~~tV~~~~~ 213 (224)
T TIGR02479 185 SLYYYEELNLKEIGEVLGLTESRVSQIHS 213 (224)
T ss_pred HHHHhCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 44556899999999999999999987654
No 240
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=92.30 E-value=0.33 Score=35.46 Aligned_cols=26 Identities=31% Similarity=0.397 Sum_probs=24.4
Q ss_pred hcCCCHHHHHHHhCCChhHHHHHhcC
Q psy6501 133 AKGWSQKDLATKINEKPQIVNDYEGG 158 (174)
Q Consensus 133 ~~glsq~ela~~lg~~~s~i~~~E~G 158 (174)
..|+||+++|+.+|+++++|+.+|+.
T Consensus 19 ~~GlTq~EIAe~LgiS~stV~~~e~r 44 (137)
T TIGR00721 19 EKGLSQKEIAKELKTTRANVSAIEKR 44 (137)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHh
Confidence 69999999999999999999999874
No 241
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=92.25 E-value=1.1 Score=35.73 Aligned_cols=29 Identities=17% Similarity=0.116 Sum_probs=24.6
Q ss_pred HHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 129 QGRQAKGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 129 ~~R~~~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
.++--.|+|++++|+.+|++.++|+.+..
T Consensus 213 ~l~y~~~~s~~eIA~~lgvs~~~V~~~~~ 241 (256)
T PRK07408 213 EFVFLHDLTQKEAAERLGISPVTVSRRVK 241 (256)
T ss_pred HHHHHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 44445799999999999999999988765
No 242
>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=92.23 E-value=0.42 Score=33.40 Aligned_cols=46 Identities=20% Similarity=0.244 Sum_probs=31.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHH-----------cCCCCCCHHHHHHHH-----HHhCcccccc
Q psy6501 46 WSQKDLATKINEKPQIVNDYE-----------GGRGIPNQAIIGKME-----RALGIRLRVN 91 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E-----------~G~~~P~~~~l~~la-----~~L~v~~~~l 91 (174)
|+..|+|+.+|||.+||.-|| +|.+.-+...+..|. +.+|+++..+
T Consensus 1 m~i~eva~~~gvs~~tlR~Ye~~GLl~p~r~~~g~R~Y~~~~~~~l~~I~~lr~~G~sl~eI 62 (112)
T cd01282 1 MRIGELAARTGVSVRSLRYYEEQGLLVPERSANGYRDYDEAAVDRVRQIRRLLAAGLTLEEI 62 (112)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHH
Confidence 578999999999999999999 455555555444333 3355555443
No 243
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=92.21 E-value=0.57 Score=31.61 Aligned_cols=54 Identities=13% Similarity=0.129 Sum_probs=43.1
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Q psy6501 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIR 87 (174)
Q Consensus 33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~ 87 (174)
-.+-|+.-.+..|+|.+++|..+|+|...|.++-+=. .+.+.....+-++|+--
T Consensus 11 T~~ELq~nf~~~~ls~~~ia~dL~~s~~~le~vL~l~-~~~~~~vW~lRdyL~~~ 64 (89)
T PF10078_consen 11 TRQELQANFELSGLSLEQIAADLGTSPEHLEQVLNLK-QPFPEDVWILRDYLNDK 64 (89)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC-CCCcccchHHHHHHHHH
Confidence 3566788889999999999999999999999987644 55667777777776544
No 244
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 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.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=92.19 E-value=0.18 Score=31.18 Aligned_cols=27 Identities=22% Similarity=0.471 Sum_probs=23.8
Q ss_pred hcCCCHHHHHHHhCCChhHHHHHhcCC
Q psy6501 133 AKGWSQKDLATKINEKPQIVNDYEGGR 159 (174)
Q Consensus 133 ~~glsq~ela~~lg~~~s~i~~~E~G~ 159 (174)
..|++++++|+.+|+++++|..|-.-.
T Consensus 11 ~~G~~~~eIA~~Lg~~~~TV~~W~~r~ 37 (58)
T PF06056_consen 11 LQGWSIKEIAEELGVPRSTVYSWKDRY 37 (58)
T ss_pred HcCCCHHHHHHHHCCChHHHHHHHHhh
Confidence 379999999999999999999987643
No 245
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=92.19 E-value=0.51 Score=40.64 Aligned_cols=24 Identities=13% Similarity=0.249 Sum_probs=22.3
Q ss_pred cCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 134 KGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 134 ~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
.++|.+++|+.+|++.++|..+++
T Consensus 369 ~~~Tl~EIA~~LGvS~erVRqie~ 392 (415)
T PRK07598 369 HTYSLAEIGRALDLSRERVRQIES 392 (415)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHH
Confidence 569999999999999999999886
No 246
>PF14590 DUF4447: Domain of unknown function (DUF4447); PDB: 2OX6_B.
Probab=92.18 E-value=0.76 Score=33.03 Aligned_cols=41 Identities=17% Similarity=0.088 Sum_probs=31.8
Q ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCH
Q psy6501 34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQ 74 (174)
Q Consensus 34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~ 74 (174)
+--|+.+|...|+|..++|+..+.|..-|-.||.|....+.
T Consensus 9 aie~~ylr~slgl~~aqv~~l~k~se~dv~aweage~~~~~ 49 (166)
T PF14590_consen 9 AIEIKYLRLSLGLTTAQVAELTKASEADVLAWEAGEKPAPG 49 (166)
T ss_dssp HHHHHHHHHHTT--HHHHHHHHTS-HHHHHHHHTTSS---H
T ss_pred HHHHHHHHHHcCCCHHHHHHhhccCHHHhhhhhccCCcCch
Confidence 34688999999999999999999999999999999965443
No 247
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model 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 (pfam00376) 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.
Probab=92.02 E-value=0.47 Score=33.86 Aligned_cols=46 Identities=17% Similarity=0.222 Sum_probs=32.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc------------CCCCCCHHHHHH-----HHHHhCcccccc
Q psy6501 46 WSQKDLATKINEKPQIVNDYEG------------GRGIPNQAIIGK-----MERALGIRLRVN 91 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~------------G~~~P~~~~l~~-----la~~L~v~~~~l 91 (174)
|+..|+|+.+|||..||.-||. |.+.-+.+.+.. .++.+|+++.++
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI 63 (127)
T TIGR02044 1 MNIGQVAKLTGLSSKMIRYYEEKGLIPPPLRSEGGYRTYTQQHLDELRLISRARQVGFSLEEC 63 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHCCCCHHHH
Confidence 6789999999999999999994 444444444443 345577776654
No 248
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=92.01 E-value=1 Score=33.01 Aligned_cols=47 Identities=15% Similarity=0.137 Sum_probs=34.1
Q ss_pred CCCHHHHHHHhCCCHHHHHHHH------------cCCCCCCHHHHHH-----HHHHhCcccccc
Q psy6501 45 GWSQKDLATKINEKPQIVNDYE------------GGRGIPNQAIIGK-----MERALGIRLRVN 91 (174)
Q Consensus 45 gltq~eLA~~igvs~~~is~~E------------~G~~~P~~~~l~~-----la~~L~v~~~~l 91 (174)
.+|..|||+.+|||..||.-|| ||.+.-+...+.. ..+.+|++++++
T Consensus 7 ~~~IgevAk~~Gvs~~TLRyYE~~GLl~p~~r~~~gyR~Y~~~~l~rl~~I~~lr~~G~sL~eI 70 (144)
T PRK13752 7 NLTIGVFAKAAGVNVETIRFYQRKGLLPEPDKPYGSIRRYGEADVTRVRFVKSAQRLGFSLDEI 70 (144)
T ss_pred cccHHHHHHHHCcCHHHHHHHHHCCCCCCCccCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHH
Confidence 3899999999999999999999 3445445554443 345567776654
No 249
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model 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 (pfam00376) 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.
Probab=91.98 E-value=0.91 Score=32.29 Aligned_cols=21 Identities=19% Similarity=0.257 Sum_probs=19.0
Q ss_pred CHHHHHHHhCCCHHHHHHHHc
Q psy6501 47 SQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 47 tq~eLA~~igvs~~~is~~E~ 67 (174)
|..|+|+.+|||.+||.-||.
T Consensus 1 ~I~e~a~~~gvs~~tlR~Ye~ 21 (124)
T TIGR02051 1 TIGELAKAAGVNVETIRYYER 21 (124)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 467999999999999999984
No 250
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model 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 (pfam00376) 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=91.97 E-value=0.54 Score=33.65 Aligned_cols=46 Identities=17% Similarity=0.216 Sum_probs=34.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHH------------cCCCCCCHHHHHHHH-----HHhCcccccc
Q psy6501 46 WSQKDLATKINEKPQIVNDYE------------GGRGIPNQAIIGKME-----RALGIRLRVN 91 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E------------~G~~~P~~~~l~~la-----~~L~v~~~~l 91 (174)
|+..|+|+.+|||..||.-|| ||.+..+.+.+..|. +.+|+++..+
T Consensus 1 m~I~e~a~~~gvs~~tlR~Ye~~GLl~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~lG~sL~eI 63 (127)
T TIGR02047 1 MKIGELAQKTGVSVETIRFYEKQGLLPPPARTDNNYRVYTVGHVERLAFIRNCRTLDMSLAEI 63 (127)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCCCcCCHHHHHHHHHHHHHHHcCCCHHHH
Confidence 578999999999999999999 455555555554443 4567777655
No 251
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=91.96 E-value=3 Score=29.62 Aligned_cols=23 Identities=4% Similarity=-0.098 Sum_probs=20.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 45 GWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 45 gltq~eLA~~igvs~~~is~~E~ 67 (174)
.+|.++||+.+|+|+.+++++=+
T Consensus 25 ~~sl~~lA~~~g~S~~~l~r~Fk 47 (127)
T PRK11511 25 PLSLEKVSERSGYSKWHLQRMFK 47 (127)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHH
Confidence 59999999999999999988744
No 252
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains 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 []. ; PDB: 1R71_C.
Probab=91.93 E-value=0.13 Score=34.70 Aligned_cols=31 Identities=19% Similarity=0.457 Sum_probs=21.6
Q ss_pred hcCCCHHHHHHHhCCChhHHHHHhcCCCCCC
Q psy6501 133 AKGWSQKDLATKINEKPQIVNDYEGGRGIPN 163 (174)
Q Consensus 133 ~~glsq~ela~~lg~~~s~i~~~E~G~~~P~ 163 (174)
..||||.++|+++|-+++.|+.+-.=-..|+
T Consensus 1 ~~G~tq~eIA~~lGks~s~Vs~~l~Ll~lP~ 31 (93)
T PF08535_consen 1 EFGWTQEEIAKRLGKSRSWVSNHLALLDLPE 31 (93)
T ss_dssp HTT--HHHHHHHTT--HHHHHHHHGGGS--H
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHcCCH
Confidence 3699999999999999999999888655554
No 253
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=91.92 E-value=0.35 Score=29.05 Aligned_cols=32 Identities=13% Similarity=0.256 Sum_probs=24.4
Q ss_pred HHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501 38 MQGRQAKGWSQKDLATKINEKPQIVNDYEGGR 69 (174)
Q Consensus 38 k~~R~~~gltq~eLA~~igvs~~~is~~E~G~ 69 (174)
-....+.|+|..++|+.+|-|+..|.+|-++-
T Consensus 13 id~m~qlG~s~~~isr~i~RSr~~Ir~yl~dP 44 (50)
T PF11427_consen 13 IDVMHQLGMSLREISRRIGRSRTCIRRYLKDP 44 (50)
T ss_dssp HHHHHHTT--HHHHHHHHT--HHHHHHHHHSC
T ss_pred HHHHHHhchhHHHHHHHhCccHHHHHHHhcCh
Confidence 35678999999999999999999999998753
No 254
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=91.91 E-value=0.34 Score=39.10 Aligned_cols=50 Identities=16% Similarity=0.075 Sum_probs=42.2
Q ss_pred cccchhhcccccchHHHHHHHHHHHHHcC-CCHHHHHHHhCCCHHHHHHHH
Q psy6501 17 LDRETEELKHEKVPLDLAKLLMQGRQAKG-WSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 17 ~~~~~~~~~~~~~~~~ig~~ik~~R~~~g-ltq~eLA~~igvs~~~is~~E 66 (174)
.++....-....+..+--+.|+.+|..-| ++|+||.+++|.|++|+|++-
T Consensus 181 ~~~~~~~~~~~~L~~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L 231 (258)
T COG2512 181 GDELRVLVNEYDLNEDEKEILDLIRERGGRITQAELRRALGLSKTTVSRIL 231 (258)
T ss_pred ccccccccccCCCCHHHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHH
Confidence 35555555567778888899999999999 999999999999999999864
No 255
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=91.87 E-value=0.89 Score=31.10 Aligned_cols=54 Identities=13% Similarity=0.102 Sum_probs=40.3
Q ss_pred HHHHHHHHHHHH--HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q psy6501 31 LDLAKLLMQGRQ--AKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 84 (174)
Q Consensus 31 ~~ig~~ik~~R~--~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L 84 (174)
..+|.|++-.++ ...+||.|++.++|+|-.+|.+=-|.-..-+++...-+.+.+
T Consensus 44 eal~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITRGSN~LK~~~~~~k~~L~~~l 99 (103)
T COG2973 44 EALGTRVRIVEELLRGELSQREIAQKLGVSIATITRGSNSLKTADPEFKQWLEKVL 99 (103)
T ss_pred HHHHHHHHHHHHHHhccccHHHHHHHhCcchhhhccchhhhccCCHHHHHHHHHHh
Confidence 478898887776 467999999999999999998766655554555555555544
No 256
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=91.86 E-value=0.22 Score=28.58 Aligned_cols=23 Identities=9% Similarity=0.086 Sum_probs=20.0
Q ss_pred cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 44 KGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 44 ~gltq~eLA~~igvs~~~is~~E 66 (174)
..+|+.++|+.+|+|++++++.-
T Consensus 7 ~~~s~~~la~~l~~s~~tv~~~l 29 (48)
T smart00419 7 LPLTRQEIAELLGLTRETVSRTL 29 (48)
T ss_pred eccCHHHHHHHHCCCHHHHHHHH
Confidence 35799999999999999998754
No 257
>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=91.85 E-value=0.26 Score=34.26 Aligned_cols=24 Identities=17% Similarity=0.271 Sum_probs=21.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501 46 WSQKDLATKINEKPQIVNDYEGGR 69 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~G~ 69 (174)
||..|+|+.+|||++||..||.-.
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~G 24 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEKEG 24 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCC
Confidence 688999999999999999999543
No 258
>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=91.68 E-value=0.53 Score=31.88 Aligned_cols=22 Identities=14% Similarity=0.273 Sum_probs=20.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q psy6501 46 WSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~ 67 (174)
||..|+|+.+||++++|..|++
T Consensus 1 ~~~~eva~~~gi~~~tlr~~~~ 22 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYEE 22 (100)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5789999999999999999974
No 259
>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=91.65 E-value=0.52 Score=33.66 Aligned_cols=46 Identities=24% Similarity=0.300 Sum_probs=32.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHH------------cCCCCCCHHHHHHH-----HHHhCcccccc
Q psy6501 46 WSQKDLATKINEKPQIVNDYE------------GGRGIPNQAIIGKM-----ERALGIRLRVN 91 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E------------~G~~~P~~~~l~~l-----a~~L~v~~~~l 91 (174)
||..|+|+.+|||..||.-|| +|.+.-+.+.+..| .+.+|+++.++
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe~~GLl~~~~r~~~g~R~Y~~~~~~~l~~I~~lr~~G~sL~eI 63 (127)
T cd01108 1 MNIGEAAKLTGLSAKMIRYYEEIGLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEI 63 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCceecCHHHHHHHHHHHHHHHcCCCHHHH
Confidence 678999999999999999999 44455555555443 34456665543
No 260
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=91.64 E-value=0.23 Score=30.37 Aligned_cols=32 Identities=22% Similarity=0.320 Sum_probs=25.0
Q ss_pred HHHHHHHHHcC--CCHHHHHHHhCCCHHHHHHHH
Q psy6501 35 KLLMQGRQAKG--WSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 35 ~~ik~~R~~~g--ltq~eLA~~igvs~~~is~~E 66 (174)
.-|..+...-+ +|+.|||+.++++++++++.-
T Consensus 9 ~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v 42 (62)
T PF12802_consen 9 RVLMALARHPGEELTQSELAERLGISKSTVSRIV 42 (62)
T ss_dssp HHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHH
Confidence 34555666666 999999999999999999864
No 261
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=91.47 E-value=0.34 Score=37.98 Aligned_cols=105 Identities=18% Similarity=0.301 Sum_probs=56.0
Q ss_pred HHHHHcC-CCHHHHHHHhCCCHHHHHHHH------cCCCCCCHHHHHHHHHHhCcc---cc-cccCCCCCCCCCcccchh
Q psy6501 39 QGRQAKG-WSQKDLATKINEKPQIVNDYE------GGRGIPNQAIIGKMERALGIR---LR-VNAGTNKQPGTTKNTAKL 107 (174)
Q Consensus 39 ~~R~~~g-ltq~eLA~~igvs~~~is~~E------~G~~~P~~~~l~~la~~L~v~---~~-~l~~~~~~~~~~~~~~~l 107 (174)
++.++-| |||.|||..+|+|..||++.- +|.-.|+-.....|-..+--. +. +|-+... ..+
T Consensus 98 EAy~QgglLT~~Dla~LL~~S~~TI~~~i~~yq~e~g~vvPtrG~i~DiGp~~tHK~~ii~~~l~g~~~--------~ei 169 (220)
T PF07900_consen 98 EAYDQGGLLTQEDLAMLLGISPRTISKDIKEYQKEHGVVVPTRGTIHDIGPGVTHKKIIIRLYLKGKPT--------PEI 169 (220)
T ss_pred HHHHcCCcccHHHHHHHHCCCHHHHHHHHHHHHHHcCceeccCCcccccCCcchHHHHHHHHHHcCCCH--------HHH
Confidence 3333333 699999999999999999863 355556655444332110000 00 1111000 000
Q ss_pred hhhhhhhhcccccHHHHHHHHHH-----HHhcCCCHHHHHHHhCCChhHHHHHh
Q psy6501 108 DRETEELKHEKVPLDLAKLLMQG-----RQAKGWSQKDLATKINEKPQIVNDYE 156 (174)
Q Consensus 108 ~~~~~~~~~~~~~~~~~~~i~~~-----R~~~glsq~ela~~lg~~~s~i~~~E 156 (174)
.. .. ..-...+...|+.- -..+|++..+++..+|+|...+..|+
T Consensus 170 ar---~t--~HS~~av~rYi~~F~rV~~l~~~~~~~~eia~~tg~S~~Lv~eY~ 218 (220)
T PF07900_consen 170 AR---RT--NHSPEAVDRYIKDFKRVLMLYEKGMSPEEIAFITGMSERLVKEYL 218 (220)
T ss_pred HH---Hh--ccCHHHHHHHHHhhHHhHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 00 00 11112222222211 13588999999999999999998886
No 262
>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=91.40 E-value=0.67 Score=32.73 Aligned_cols=46 Identities=24% Similarity=0.367 Sum_probs=33.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHH------------cCCCCCCHHHHHHHH-----HHhCcccccc
Q psy6501 46 WSQKDLATKINEKPQIVNDYE------------GGRGIPNQAIIGKME-----RALGIRLRVN 91 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E------------~G~~~P~~~~l~~la-----~~L~v~~~~l 91 (174)
||..|+|+.+|||.+||.-|| +|.+.-+.+.+..|. +.+|+++.++
T Consensus 1 ~~I~eva~~~gvs~~tLRyYe~~GLl~p~~r~~~gyR~Y~~~~i~~l~~I~~lr~~G~sl~eI 63 (123)
T cd04770 1 MKIGELAKAAGVSPDTIRYYERIGLLPPPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEI 63 (123)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCCCCCCCccCCHHHHHHHHHHHHHHHCCCCHHHH
Confidence 578999999999999999999 455555555555433 4456665544
No 263
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=91.39 E-value=0.82 Score=36.62 Aligned_cols=31 Identities=10% Similarity=0.046 Sum_probs=25.6
Q ss_pred HHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 127 LMQGRQAKGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 127 i~~~R~~~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
+-..+-..++|.+++|+.+|++.++|+.++.
T Consensus 213 vi~l~y~e~~t~~EIA~~lgis~~~V~~~~~ 243 (257)
T PRK05911 213 VMALYYYEELVLKEIGKILGVSESRVSQIHS 243 (257)
T ss_pred HHHHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3344556899999999999999999988865
No 264
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. 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.
Probab=91.36 E-value=0.6 Score=37.61 Aligned_cols=24 Identities=13% Similarity=0.205 Sum_probs=22.2
Q ss_pred cCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 134 KGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 134 ~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
.++|++++|+.+|+++.+|+.++.
T Consensus 235 ~~~t~~eIA~~lgvS~~~V~q~~~ 258 (270)
T TIGR02392 235 DKLTLQELAAEYGVSAERIRQIEK 258 (270)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHH
Confidence 479999999999999999998876
No 265
>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=91.35 E-value=0.65 Score=33.14 Aligned_cols=46 Identities=24% Similarity=0.347 Sum_probs=32.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc------------CCCCCCHHHHHHH-----HHHhCcccccc
Q psy6501 46 WSQKDLATKINEKPQIVNDYEG------------GRGIPNQAIIGKM-----ERALGIRLRVN 91 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~------------G~~~P~~~~l~~l-----a~~L~v~~~~l 91 (174)
||..|+|+.+|||.+||.-||+ |.+.-+.+.+..| .+.+|+++.++
T Consensus 1 ~~I~e~a~~~gvs~~tlR~Ye~~Gll~~~~r~~~g~R~Y~~~~l~~l~~I~~lr~~G~sL~eI 63 (126)
T cd04785 1 LSIGELARRTGVNVETIRYYESIGLLPEPARTAGGYRLYGAAHVERLRFIRRARDLGFSLEEI 63 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCccccCHHHHHHHHHHHHHHHCCCCHHHH
Confidence 5789999999999999999993 4444555555444 34456665544
No 266
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=91.34 E-value=0.55 Score=27.27 Aligned_cols=27 Identities=15% Similarity=-0.018 Sum_probs=22.5
Q ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 40 GRQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 40 ~R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
+....++|..++|+.+++|+++++++-
T Consensus 9 l~~~~~~s~~~l~~~l~~s~~tv~~~l 35 (53)
T smart00420 9 LAQQGKVSVEELAELLGVSEMTIRRDL 35 (53)
T ss_pred HHHcCCcCHHHHHHHHCCCHHHHHHHH
Confidence 334568999999999999999998764
No 267
>PRK04132 replication factor C small subunit; Provisional
Probab=91.33 E-value=0.6 Score=43.73 Aligned_cols=44 Identities=27% Similarity=0.416 Sum_probs=40.4
Q ss_pred HHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccc
Q psy6501 48 QKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVN 91 (174)
Q Consensus 48 q~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l 91 (174)
.+|+|++.|+....+-.|-.|++.|+...-.+||.+||++++..
T Consensus 420 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 463 (846)
T PRK04132 420 RKEIAEKTGIRADRILEYIKGKRKPSLKNYIKIAKALGINLEKT 463 (846)
T ss_pred HHHHHHHhCCcHHHHHHHHhcCCCccHHHHHHHHHHhcccHHHH
Confidence 47899999999999999999999999999999999999997543
No 268
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=91.19 E-value=0.67 Score=33.61 Aligned_cols=46 Identities=20% Similarity=0.289 Sum_probs=33.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHH------------cCCCCCCHHHHHHH-----HHHhCcccccc
Q psy6501 46 WSQKDLATKINEKPQIVNDYE------------GGRGIPNQAIIGKM-----ERALGIRLRVN 91 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E------------~G~~~P~~~~l~~l-----a~~L~v~~~~l 91 (174)
|+..|||+.+|||..||.-|| ||.+.-+...+..| ++.+|++++.+
T Consensus 1 m~Ige~a~~~gvs~~tlRyYE~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sl~eI 63 (135)
T PRK10227 1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEES 63 (135)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCcccCCCCcccCCHHHHHHHHHHHHHHHCCCCHHHH
Confidence 678999999999999999999 44555555555433 34567777664
No 269
>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD. This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.
Probab=91.16 E-value=0.53 Score=33.50 Aligned_cols=47 Identities=26% Similarity=0.303 Sum_probs=33.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHc------------CCCCCCHHHHHH-----HHHHhCcccccc
Q psy6501 45 GWSQKDLATKINEKPQIVNDYEG------------GRGIPNQAIIGK-----MERALGIRLRVN 91 (174)
Q Consensus 45 gltq~eLA~~igvs~~~is~~E~------------G~~~P~~~~l~~-----la~~L~v~~~~l 91 (174)
.||..|||+.+|||..||.-||+ |.+.-+...+.. .++.+|++++.+
T Consensus 3 ~~tI~elA~~~gvs~~tlR~Ye~~GLL~p~~r~~~gyR~Y~~~~l~rL~~I~~lr~~G~~L~eI 66 (120)
T TIGR02054 3 AYTISRLAEDAGVSVHVVRDYLLRGLLHPVRRTTSGYGIFDDASLQRLRFVRAAFEAGIGLGEL 66 (120)
T ss_pred CCcHHHHHHHHCcCHHHHHHHHHCCCCCCCccCCCCCeeCCHHHHHHHHHHHHHHHcCCCHHHH
Confidence 58999999999999999999994 334333444433 334566666554
No 270
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=91.15 E-value=0.38 Score=36.48 Aligned_cols=32 Identities=16% Similarity=0.213 Sum_probs=27.2
Q ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
.++-.+|.-.|+|.+|+|+.+|+|..||.+.-
T Consensus 141 ~~~v~l~~~~Gls~~EIA~~lgiS~~tV~r~l 172 (185)
T PF07638_consen 141 RRVVELRFFEGLSVEEIAERLGISERTVRRRL 172 (185)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHH
Confidence 34556788899999999999999999998753
No 271
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=91.03 E-value=6.1 Score=30.73 Aligned_cols=29 Identities=21% Similarity=0.105 Sum_probs=25.1
Q ss_pred HHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 129 QGRQAKGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 129 ~~R~~~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
..+-..|+|++++|+.+|+++.+|+.+++
T Consensus 193 ~~~~~~~~t~~eIA~~lgis~~~V~~~~~ 221 (231)
T TIGR02885 193 MLRYFKDKTQTEVANMLGISQVQVSRLEK 221 (231)
T ss_pred HHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 33445799999999999999999999886
No 272
>PF00157 Pou: Pou domain - N-terminal to homeobox domain; InterPro: IPR000327 POU proteins are eukaryotic transcription factors containing a bipartite DNA binding domain referred to as the POU domain. The acronym POU (pronounced 'pow') is derived from the names of three mammalian transcription factors, the pituitary-specific Pit-1, the octamer-binding proteins Oct-1 and Oct-2, and the neural Unc-86 from Caenorhabditis elegans. POU domain genes have been identified in diverse organisms including nematodes, flies, amphibians, fish and mammals but have not been yet identified in plants and fungi. The various members of the POU family have a wide variety of functions, all of which are related to the function of the neuroendocrine system [] and the development of an organism []. Some other genes are also regulated, including those for immunoglobulin light and heavy chains (Oct-2) [, ], and trophic hormone genes, such as those for prolactin and growth hormone (Pit-1). The POU domain is a bipartite domain composed of two subunits separated by a non-conserved region of 15-55 aa. The N-terminal subunit is known as the POU-specific (POUs) domain (IPR000327 from INTERPRO), while the C-terminal subunit is a homeobox domain (IPR007103 from INTERPRO). 3D structures of complexes including both POU subdomains bound to DNA are available. Both subdomains contain the structural motif 'helix-turn-helix', which directly associates with the two components of bipartite DNA binding sites, and both are required for high affinity sequence-specific DNA-binding. The domain may also be involved in protein-protein interactions []. The subdomains are connected by a flexible linker [, , ]. In proteins a POU-specific domain is always accompanied by a homeodomain. Despite of the lack of sequence homology, 3D structure of POUs is similar to 3D structure of bacteriophage lambda repressor and other members of HTH_3 family [, ]. This entry represents the POU-specific subunit of the POU domain.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3D1N_O 1AU7_A 3L1P_A 2XSD_C 1O4X_A 1HF0_B 1GT0_C 1POU_A 1CQT_B 1E3O_C ....
Probab=91.02 E-value=0.43 Score=31.13 Aligned_cols=40 Identities=20% Similarity=0.277 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHhCC------ChhHHHHHhcCCC
Q psy6501 121 LDLAKLLMQGRQAKGWSQKDLATKINE------KPQIVNDYEGGRG 160 (174)
Q Consensus 121 ~~~~~~i~~~R~~~glsq~ela~~lg~------~~s~i~~~E~G~~ 160 (174)
..+....+..|-..|+||.+++..+|. +.++|+++|+=.-
T Consensus 10 e~Fa~~fk~rRi~LG~TQ~dVg~al~~~~G~~~SQttI~RFE~L~L 55 (75)
T PF00157_consen 10 EQFAKEFKQRRIKLGYTQADVGAALGRLYGKEFSQTTICRFEALQL 55 (75)
T ss_dssp HHHHHHHHHHHHHTT--HHHHHHHHHHHHSSGGSHHHHHHHHTTTS
T ss_pred HHHHHHHHHhhhhcccCHHHHhHHHHHhcCccccchhhhhhHhccc
Confidence 456778899999999999999887653 5679999998543
No 273
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.
Probab=90.99 E-value=0.07 Score=31.95 Aligned_cols=29 Identities=10% Similarity=0.117 Sum_probs=21.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCH
Q psy6501 46 WSQKDLATKINEKPQIVNDYEGGRGIPNQ 74 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~G~~~P~~ 74 (174)
++.+|+++.+|+|++||.++.+....|.+
T Consensus 4 l~~~ev~~~~g~s~~ti~~~~k~g~FP~p 32 (51)
T PF05930_consen 4 LRIKEVAELLGVSRSTIYRLIKDGKFPKP 32 (51)
T ss_dssp E-HHHHHHHHSS-HHHHHHHHHHHH---S
T ss_pred ccHHHHHHHHCCCHHHHHHHHhcccCCCC
Confidence 57889999999999999999986666654
No 274
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=90.95 E-value=0.62 Score=33.85 Aligned_cols=32 Identities=19% Similarity=0.225 Sum_probs=27.5
Q ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501 34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDY 65 (174)
Q Consensus 34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~ 65 (174)
-.-|+.+++....|+.+||+++|+|++++++-
T Consensus 11 ~~IL~~L~~d~r~~~~eia~~lglS~~~v~~R 42 (154)
T COG1522 11 RRILRLLQEDARISNAELAERVGLSPSTVLRR 42 (154)
T ss_pred HHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHH
Confidence 45678888888999999999999999987753
No 275
>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=90.93 E-value=0.52 Score=34.33 Aligned_cols=45 Identities=18% Similarity=0.301 Sum_probs=32.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHH-----------cCCCCCCHHHHHHHH-----HHhCccccc
Q psy6501 46 WSQKDLATKINEKPQIVNDYE-----------GGRGIPNQAIIGKME-----RALGIRLRV 90 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E-----------~G~~~P~~~~l~~la-----~~L~v~~~~ 90 (174)
||..|+|+.+|||.+||.-|| +|.+.-+.+.+..|. +.+|+++..
T Consensus 2 ~~I~EvA~~~Gvs~~tLRyYE~~GLl~p~r~~~g~R~Y~~~dl~~l~~I~~lr~~G~sl~e 62 (139)
T cd01110 2 LSVGEVAKRSGVAVSALHFYEQKGLIASWRNAGNQRRYPRDVLRRIAFIKVAQRLGLSLAE 62 (139)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCCcCCCCCeEECHHHHHHHHHHHHHHHcCCCHHH
Confidence 788999999999999999998 455555555555443 335555544
No 276
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=90.92 E-value=0.23 Score=36.27 Aligned_cols=26 Identities=8% Similarity=0.180 Sum_probs=19.5
Q ss_pred cCCCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501 44 KGWSQKDLATKINEKPQIVNDYEGGR 69 (174)
Q Consensus 44 ~gltq~eLA~~igvs~~~is~~E~G~ 69 (174)
-..|+.++|+.+||+++|+.+|-+..
T Consensus 33 ~r~T~~eiAee~Gis~~tLYrWr~~~ 58 (142)
T PF13022_consen 33 ERRTQAEIAEEVGISRSTLYRWRQQN 58 (142)
T ss_dssp --S-HHHHHHHHTS-HHHHHHHHHH-
T ss_pred ccchHHHHHHHhCCCHHHHHHHHhcC
Confidence 35799999999999999999997543
No 277
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=90.92 E-value=0.61 Score=27.03 Aligned_cols=25 Identities=24% Similarity=0.322 Sum_probs=19.5
Q ss_pred hcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 133 AKGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 133 ~~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
..|++..++|+.+|+++++|.+|-.
T Consensus 19 ~~G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 19 AEGMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HTT--HHHHHHHTTS-HHHHHHHHC
T ss_pred HCCCCHHHHHHHHCcCHHHHHHHHh
Confidence 5679999999999999999998864
No 278
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=90.90 E-value=0.62 Score=38.58 Aligned_cols=24 Identities=13% Similarity=0.196 Sum_probs=22.2
Q ss_pred cCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 134 KGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 134 ~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
.++|.+++|+.+|+++++|..+|.
T Consensus 275 ~~~Tl~EIa~~lgiS~erVRqi~~ 298 (317)
T PRK07405 275 QPLTLAKIGERLNISRERVRQIER 298 (317)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHH
Confidence 669999999999999999999886
No 279
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=90.84 E-value=0.64 Score=33.89 Aligned_cols=46 Identities=20% Similarity=0.325 Sum_probs=32.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc------------CCCCCCHHHHHHH-----HHHhCcccccc
Q psy6501 46 WSQKDLATKINEKPQIVNDYEG------------GRGIPNQAIIGKM-----ERALGIRLRVN 91 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~------------G~~~P~~~~l~~l-----a~~L~v~~~~l 91 (174)
++..|+|+.+|||..||.-||+ |.+.-+...+..| .+.+|+++..+
T Consensus 2 ~~I~e~a~~~gvs~~tlR~Ye~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI 64 (140)
T PRK09514 2 YRIGELAKLAEVTPDTLRFYEKQGLMDPEVRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEI 64 (140)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHCCCCCCcccCCCCCeeeCHHHHHHHHHHHHHHHcCCCHHHH
Confidence 6889999999999999999994 3444444444433 34466666544
No 280
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=90.81 E-value=1 Score=26.48 Aligned_cols=35 Identities=17% Similarity=0.108 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 31 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 31 ~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
..+-..|-.+-... .|++++|+.+|+|.+||.++=
T Consensus 14 ~~~~~~i~~~~~~~-~s~~~vA~~~~vs~~TV~ri~ 48 (52)
T PF13542_consen 14 KRLEQYILKLLRES-RSFKDVARELGVSWSTVRRIF 48 (52)
T ss_pred HHHHHHHHHHHhhc-CCHHHHHHHHCCCHHHHHHHH
Confidence 34444444444444 799999999999999999874
No 281
>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=90.81 E-value=0.4 Score=27.30 Aligned_cols=28 Identities=11% Similarity=0.195 Sum_probs=22.7
Q ss_pred CCHHHHHHHhCCChhHHHHHhcCCCCCC
Q psy6501 136 WSQKDLATKINEKPQIVNDYEGGRGIPN 163 (174)
Q Consensus 136 lsq~ela~~lg~~~s~i~~~E~G~~~P~ 163 (174)
++..++|+.+|++++++..|.+-...|.
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~g~~~~ 28 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKEGKLKA 28 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCCCc
Confidence 5788999999999999999976444443
No 282
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=90.71 E-value=0.48 Score=37.06 Aligned_cols=29 Identities=21% Similarity=0.105 Sum_probs=25.6
Q ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 39 QGRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 39 ~~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
.+|-..|+|++|+|+.+|+|+.+|+++++
T Consensus 193 ~~~~~~~~t~~eIA~~lgis~~~V~~~~~ 221 (231)
T TIGR02885 193 MLRYFKDKTQTEVANMLGISQVQVSRLEK 221 (231)
T ss_pred HHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34556899999999999999999999986
No 283
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=90.66 E-value=0.35 Score=29.57 Aligned_cols=30 Identities=17% Similarity=0.112 Sum_probs=25.5
Q ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501 36 LLMQGRQAKGWSQKDLATKINEKPQIVNDY 65 (174)
Q Consensus 36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~ 65 (174)
-+..+.+...+|-+|||+.+|||..||.+-
T Consensus 5 Il~~l~~~~~~s~~ela~~~~VS~~TiRRD 34 (57)
T PF08220_consen 5 ILELLKEKGKVSVKELAEEFGVSEMTIRRD 34 (57)
T ss_pred HHHHHHHcCCEEHHHHHHHHCcCHHHHHHH
Confidence 455667788899999999999999999864
No 284
>PRK13749 transcriptional regulator MerD; Provisional
Probab=90.62 E-value=0.9 Score=32.41 Aligned_cols=47 Identities=28% Similarity=0.424 Sum_probs=34.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHH------------cCCCCCCHHHHHHH-----HHHhCcccccc
Q psy6501 45 GWSQKDLATKINEKPQIVNDYE------------GGRGIPNQAIIGKM-----ERALGIRLRVN 91 (174)
Q Consensus 45 gltq~eLA~~igvs~~~is~~E------------~G~~~P~~~~l~~l-----a~~L~v~~~~l 91 (174)
.||..|||+++|+|..||.-|| ||.+.-+...+..| ++.+|++++++
T Consensus 3 ~~tIgelA~~~gvS~~tiR~YE~~GLl~p~~r~~~gyR~Y~~~~l~rL~~I~~~r~~G~sL~eI 66 (121)
T PRK13749 3 AYTVSRLALDAGVSVHIVRDYLLRGLLRPVACTTGGYGLFDDAALQRLCFVRAAFEAGIGLDAL 66 (121)
T ss_pred CCcHHHHHHHHCCCHHHHHHHHHCCCCCCCCcCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHH
Confidence 4799999999999999999998 45555555554433 35677776654
No 285
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=90.60 E-value=0.37 Score=39.12 Aligned_cols=46 Identities=7% Similarity=0.019 Sum_probs=37.1
Q ss_pred HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501 43 AKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA 92 (174)
Q Consensus 43 ~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~ 92 (174)
-.|+|++|+|+.+|+|.++|+.+..- ....|.+.-...+++++.||
T Consensus 240 ~e~~s~~EIA~~Lgis~~tVk~~l~r----AlkkLr~~l~~~~~~~~~~~ 285 (285)
T TIGR02394 240 YEPATLEEVAAEVGLTRERVRQIQVE----ALKKLRRILERDGVDREALF 285 (285)
T ss_pred CCCccHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHHHhhhhhhccC
Confidence 67899999999999999999999853 34666666667778777664
No 286
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=90.57 E-value=0.37 Score=27.31 Aligned_cols=25 Identities=12% Similarity=0.142 Sum_probs=18.1
Q ss_pred HcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 43 AKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 43 ~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
..+||.+++|+.+|+|++++++.-+
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~Fk 30 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRLFK 30 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3579999999999999999987643
No 287
>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=90.57 E-value=0.78 Score=34.63 Aligned_cols=46 Identities=15% Similarity=0.186 Sum_probs=33.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHH------------cCCCCCCHHHHHHH-----HHHhCcccccc
Q psy6501 46 WSQKDLATKINEKPQIVNDYE------------GGRGIPNQAIIGKM-----ERALGIRLRVN 91 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E------------~G~~~P~~~~l~~l-----a~~L~v~~~~l 91 (174)
+|..|||+.+|||.+||.-|| ||.+..+.+.+..| .+.+|+++..+
T Consensus 2 ~~I~evA~~~gvs~~tLRyYe~~GLl~p~~r~~~gyR~Y~~~dl~rL~~I~~lr~~G~sL~eI 64 (172)
T cd04790 2 LTISQLARQFGLSRSTLLYYERIGLLSPSARSESNYRLYGERDLERLEQICAYRSAGVSLEDI 64 (172)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCCccCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHH
Confidence 688999999999999999999 45555555544433 34467776654
No 288
>PRK13355 bifunctional HTH-domain containing protein/aminotransferase; Provisional
Probab=90.54 E-value=0.3 Score=42.94 Aligned_cols=29 Identities=14% Similarity=0.285 Sum_probs=27.5
Q ss_pred CCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501 146 NEKPQIVNDYEGGRGIPNQAIIGKMERAL 174 (174)
Q Consensus 146 g~~~s~i~~~E~G~~~P~~~~l~~i~~~l 174 (174)
++++++|+.||+|+..|+.+.+.+|+++|
T Consensus 32 ~vs~~~is~~e~g~~~p~~~~l~~la~~l 60 (517)
T PRK13355 32 KLGKSHISQYVSGKTGPRRDVLPFLAAIL 60 (517)
T ss_pred CcCHHHHHHHHCCCCCCCHHHHHHHHHHh
Confidence 69999999999999999999999999876
No 289
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=90.50 E-value=2.7 Score=32.65 Aligned_cols=38 Identities=16% Similarity=0.144 Sum_probs=27.9
Q ss_pred ccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 119 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 119 ~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
++..-...+ ..+-..|+|.+++|+.+|+++++|..+.+
T Consensus 179 L~~~~r~vl-~l~y~~~~s~~eIA~~lgis~~~v~~~~~ 216 (227)
T TIGR02980 179 LPERERRIL-LLRFFEDKTQSEIAERLGISQMHVSRLLR 216 (227)
T ss_pred CCHHHHHHH-HHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 333333333 34456899999999999999999988764
No 290
>TIGR01636 phage_rinA phage transcriptional activator, RinA family. This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.
Probab=90.50 E-value=1.1 Score=32.30 Aligned_cols=34 Identities=18% Similarity=0.217 Sum_probs=30.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCc
Q psy6501 46 WSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI 86 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v 86 (174)
+|..++|..+|+|+++++++.+ ..+.+||..||.
T Consensus 101 ~t~~~Ia~~l~iS~~t~~r~r~-------~~l~kla~~lG~ 134 (134)
T TIGR01636 101 LTLVGLAQQLFISKSTAYRLRN-------HIIEAVAEELGM 134 (134)
T ss_pred CCHHHHHHHhCCCHHHHHHHHH-------HHHHHHHHHhCc
Confidence 5999999999999999999975 788899988873
No 291
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model 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 (pfam00376) 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=90.49 E-value=0.73 Score=33.15 Aligned_cols=46 Identities=17% Similarity=0.235 Sum_probs=32.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHH------------cCCCCCCHHHHHHH-----HHHhCcccccc
Q psy6501 46 WSQKDLATKINEKPQIVNDYE------------GGRGIPNQAIIGKM-----ERALGIRLRVN 91 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E------------~G~~~P~~~~l~~l-----a~~L~v~~~~l 91 (174)
++..|+|+.+|||..||.-|| +|.+.-+.+.+..| .+.+|+++..+
T Consensus 2 ~~I~e~a~~~gvs~~tlR~Ye~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sl~eI 64 (131)
T TIGR02043 2 FQIGELAKLCGVTSDTLRFYEKNGLIKPAGRTDSGYRLYTDEDQKRLRFILKAKELGFTLDEI 64 (131)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCceecCHHHHHHHHHHHHHHHcCCCHHHH
Confidence 688999999999999999999 34444444444443 44567776544
No 292
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=90.44 E-value=3.5 Score=32.77 Aligned_cols=37 Identities=22% Similarity=0.149 Sum_probs=27.8
Q ss_pred cHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 120 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 120 ~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
+..-...+ .+|-..++|++++|+.+|+++++|+.++.
T Consensus 208 ~~rer~vi-~~~~~~~~t~~eIA~~lgis~~~V~~~~~ 244 (254)
T TIGR02850 208 NEREKMIL-NMRFFEGKTQMEVAEEIGISQAQVSRLEK 244 (254)
T ss_pred CHHHHHHH-HHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 33333333 34445789999999999999999998875
No 293
>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=90.41 E-value=0.8 Score=32.61 Aligned_cols=46 Identities=15% Similarity=0.229 Sum_probs=32.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc------------CCCCCCHHHHHHH-----HHHhCcccccc
Q psy6501 46 WSQKDLATKINEKPQIVNDYEG------------GRGIPNQAIIGKM-----ERALGIRLRVN 91 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~------------G~~~P~~~~l~~l-----a~~L~v~~~~l 91 (174)
||..|+|+.+|||.+||.-||. |.+..+.+.+..| .+.+|+++.++
T Consensus 1 m~I~e~a~~~gvs~~tlR~Ye~~GLl~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI 63 (126)
T cd04783 1 LTIGELAKAAGVNVETIRYYQRRGLLPEPPRPEGGYRRYPEETVTRLRFIKRAQELGFTLDEI 63 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHH
Confidence 5789999999999999999993 4455555555443 34466666544
No 294
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=90.34 E-value=1.3 Score=36.11 Aligned_cols=24 Identities=17% Similarity=0.173 Sum_probs=22.3
Q ss_pred cCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 134 KGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 134 ~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
.++|++++|+.+|++++.|+.+++
T Consensus 247 ~~~Tl~EIA~~lgvS~~rVrqi~~ 270 (284)
T PRK06596 247 DKSTLQELAAEYGVSAERVRQIEK 270 (284)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHH
Confidence 479999999999999999999986
No 295
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=90.34 E-value=0.76 Score=36.21 Aligned_cols=25 Identities=8% Similarity=0.231 Sum_probs=22.8
Q ss_pred hcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 133 AKGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 133 ~~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
..++|++++|+.+|++.+.|+.++.
T Consensus 194 ~~~~t~~EIA~~lgis~~~V~q~~~ 218 (238)
T TIGR02393 194 GRPHTLEEVGKEFNVTRERIRQIES 218 (238)
T ss_pred CCCccHHHHHHHHCCCHHHHHHHHH
Confidence 4779999999999999999998876
No 296
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=90.23 E-value=0.26 Score=29.43 Aligned_cols=23 Identities=9% Similarity=0.063 Sum_probs=19.7
Q ss_pred cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 44 KGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 44 ~gltq~eLA~~igvs~~~is~~E 66 (174)
.++|..|+|+.+|+++++++++-
T Consensus 17 ~~~t~~eia~~~gl~~stv~r~L 39 (52)
T PF09339_consen 17 GPLTLSEIARALGLPKSTVHRLL 39 (52)
T ss_dssp SCEEHHHHHHHHTS-HHHHHHHH
T ss_pred CCCCHHHHHHHHCcCHHHHHHHH
Confidence 44899999999999999999875
No 297
>PRK13869 plasmid-partitioning protein RepA; Provisional
Probab=90.20 E-value=1 Score=38.61 Aligned_cols=59 Identities=12% Similarity=0.146 Sum_probs=47.0
Q ss_pred cchHHHHHHHHHHHH----------HcCCCHHHHHHHhCCCHHHHHHHH------------cCCCCCCHHHHHHHHHHhC
Q psy6501 28 KVPLDLAKLLMQGRQ----------AKGWSQKDLATKINEKPQIVNDYE------------GGRGIPNQAIIGKMERALG 85 (174)
Q Consensus 28 ~~~~~ig~~ik~~R~----------~~gltq~eLA~~igvs~~~is~~E------------~G~~~P~~~~l~~la~~L~ 85 (174)
.+...+++.+..+|+ .+.+|..|+|+.+|||.+||..|+ +|++.-+.+.+..+.+.|.
T Consensus 21 ~~~~~~~~~~~~~~~~~~~p~~~k~~r~ft~~e~A~~lgvs~~tlr~~~~~g~~~~~~~~~~grR~yt~~di~~lr~~l~ 100 (405)
T PRK13869 21 EHAEQLSSQLQAMSEALFPPTSHKSLRKFTSGEAARLMKISDSTLRKMTLAGEGPQPELASNGRRFYTLGQINEIRQMLA 100 (405)
T ss_pred HHHHHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHHhCcCHHHHHHHHHcCCCCCCccCCCCceeecHHHHHHHHHHHH
Confidence 344556666666665 257899999999999999999994 5677788899999999987
Q ss_pred c
Q psy6501 86 I 86 (174)
Q Consensus 86 v 86 (174)
-
T Consensus 101 ~ 101 (405)
T PRK13869 101 G 101 (405)
T ss_pred h
Confidence 4
No 298
>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=90.17 E-value=0.48 Score=32.54 Aligned_cols=25 Identities=20% Similarity=0.112 Sum_probs=22.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCC
Q psy6501 46 WSQKDLATKINEKPQIVNDYEGGRG 70 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~G~~ 70 (174)
+|..|+|+.+|||++||.-||+-.-
T Consensus 2 ~~i~eva~~~gvs~~tlR~ye~~Gl 26 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEKLGL 26 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 6889999999999999999996443
No 299
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=90.12 E-value=0.49 Score=30.70 Aligned_cols=29 Identities=21% Similarity=0.324 Sum_probs=24.5
Q ss_pred CHHHHHHHhCCChhHHHHHhcCCCCCCHHHH
Q psy6501 137 SQKDLATKINEKPQIVNDYEGGRGIPNQAII 167 (174)
Q Consensus 137 sq~ela~~lg~~~s~i~~~E~G~~~P~~~~l 167 (174)
+...+|+.+|++++.|+.| |+.+|.....
T Consensus 12 s~~kvA~aLGIs~~AVsQW--Ge~VPe~rA~ 40 (75)
T PRK09744 12 SKTKLANAAGVRLASVAAW--GELVPEGRAM 40 (75)
T ss_pred cHHHHHHHHCCCHHHHHHH--hccCcHHHHH
Confidence 5678999999999999999 8888876543
No 300
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=90.10 E-value=0.81 Score=33.15 Aligned_cols=43 Identities=14% Similarity=0.036 Sum_probs=30.4
Q ss_pred cccccchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 24 LKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 24 ~~~~~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
+.+-.+...-...|..+...-++||.+||+.+++++++|++.-
T Consensus 33 l~~~glt~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l 75 (144)
T PRK11512 33 LSPLDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRML 75 (144)
T ss_pred hcccCCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHH
Confidence 3333444344445666666778999999999999999998764
No 301
>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=90.04 E-value=0.48 Score=32.85 Aligned_cols=23 Identities=13% Similarity=0.130 Sum_probs=20.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Q psy6501 46 WSQKDLATKINEKPQIVNDYEGG 68 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~G 68 (174)
+|..|+|+.+|||++||.-||.-
T Consensus 1 ~~i~eva~~~gis~~tlR~ye~~ 23 (108)
T cd01107 1 FTIGEFAKLSNLSIKALRYYDKI 23 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc
Confidence 57899999999999999999954
No 302
>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=89.90 E-value=0.52 Score=32.20 Aligned_cols=27 Identities=41% Similarity=0.539 Sum_probs=22.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCC
Q psy6501 46 WSQKDLATKINEKPQIVNDYEGGRGIP 72 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~G~~~P 72 (174)
++..|+|+.+|||.+||..||.-.-.|
T Consensus 1 y~i~e~A~~~gvs~~tlR~Ye~~Gll~ 27 (99)
T cd04772 1 YRTVDLARAIGLSPQTVRNYESLGLIP 27 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCCC
Confidence 467899999999999999999644433
No 303
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 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 recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is 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.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=89.88 E-value=1.1 Score=26.29 Aligned_cols=33 Identities=12% Similarity=0.192 Sum_probs=26.2
Q ss_pred HHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 125 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 125 ~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
..+-..+-..++|..++|+.+|++.++++.+..
T Consensus 10 r~vi~~~y~~~~t~~eIa~~lg~s~~~V~~~~~ 42 (50)
T PF04545_consen 10 REVIRLRYFEGLTLEEIAERLGISRSTVRRILK 42 (50)
T ss_dssp HHHHHHHHTST-SHHHHHHHHTSCHHHHHHHHH
T ss_pred HHHHHHHhcCCCCHHHHHHHHCCcHHHHHHHHH
Confidence 344455668899999999999999999998764
No 304
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=89.88 E-value=4.6 Score=27.44 Aligned_cols=35 Identities=9% Similarity=-0.071 Sum_probs=26.6
Q ss_pred cCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501 44 KGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA 92 (174)
Q Consensus 44 ~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~ 92 (174)
..+|.++||+.+|+|+.++++. +.+.+|+++..++
T Consensus 20 ~~~~~~~lA~~~~~S~~~l~r~--------------f~~~~g~s~~~~i 54 (107)
T PRK10219 20 QPLNIDVVAKKSGYSKWYLQRM--------------FRTVTHQTLGDYI 54 (107)
T ss_pred CCCCHHHHHHHHCCCHHHHHHH--------------HHHHHCcCHHHHH
Confidence 3599999999999999998875 4455666665443
No 305
>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=89.80 E-value=0.51 Score=29.51 Aligned_cols=22 Identities=27% Similarity=0.513 Sum_probs=20.2
Q ss_pred CCHHHHHHHhCCChhHHHHHhc
Q psy6501 136 WSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 136 lsq~ela~~lg~~~s~i~~~E~ 157 (174)
++..++|+.+|++++++..||.
T Consensus 1 ~~i~evA~~~gvs~~tlR~~~~ 22 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEK 22 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4678999999999999999986
No 306
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=89.67 E-value=0.85 Score=30.51 Aligned_cols=33 Identities=15% Similarity=0.255 Sum_probs=26.7
Q ss_pred HHHHHHHH--HcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 35 KLLMQGRQ--AKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 35 ~~ik~~R~--~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
.|+...+. ..|++..++|+..|||..|.++|-.
T Consensus 13 gR~~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~ 47 (85)
T PF13011_consen 13 GRLRLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLA 47 (85)
T ss_pred HHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHH
Confidence 34444443 4899999999999999999999964
No 307
>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=89.56 E-value=0.6 Score=26.96 Aligned_cols=27 Identities=19% Similarity=0.223 Sum_probs=22.5
Q ss_pred CCHHHHHHHhCCChhHHHHHhcCCCCC
Q psy6501 136 WSQKDLATKINEKPQIVNDYEGGRGIP 162 (174)
Q Consensus 136 lsq~ela~~lg~~~s~i~~~E~G~~~P 162 (174)
++..++|+.+|++++++..|+.-...|
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~~~g~l~ 27 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERIGLLS 27 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHCCCCC
Confidence 577899999999999999997754444
No 308
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=89.54 E-value=1.1 Score=25.58 Aligned_cols=31 Identities=13% Similarity=0.085 Sum_probs=25.2
Q ss_pred HHHHHHHHHhcCCCHHHHHHHhCCChhHHHH
Q psy6501 124 AKLLMQGRQAKGWSQKDLATKINEKPQIVND 154 (174)
Q Consensus 124 ~~~i~~~R~~~glsq~ela~~lg~~~s~i~~ 154 (174)
...|.++-+..++++.+.|+.+|++++++..
T Consensus 7 ~~~i~~aL~~~~gn~~~aA~~Lgisr~tL~~ 37 (42)
T PF02954_consen 7 KQLIRQALERCGGNVSKAARLLGISRRTLYR 37 (42)
T ss_dssp HHHHHHHHHHTTT-HHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHHHHhCCCHHHHHHHHCCCHHHHHH
Confidence 4678888889999999999999999998754
No 309
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=89.36 E-value=0.66 Score=40.20 Aligned_cols=102 Identities=15% Similarity=0.189 Sum_probs=61.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCCCCCCCCcccchhhhhhhhhhcccccHHHHH
Q psy6501 46 WSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAK 125 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~ 125 (174)
|+.+++|+.+|+..+|||+.-+++..-++.-+..|-.+|-..+..-.+.... ....+..-+.+
T Consensus 331 L~LrdvA~~i~~HESTISRai~nKy~~tprG~feLK~FFs~~i~s~~gg~~~-----------------S~~~Ik~~Ik~ 393 (444)
T COG1508 331 LVLRDVADEIGMHESTISRAITNKYLATPRGLFELKYFFSSSLASSEGGEAS-----------------STEAIKALIKK 393 (444)
T ss_pred ccHHHHHHHhCccHHHHHHHHhcccccCCcceeeHHHHHHHhccCCCCCccc-----------------cHHHHHHHHHH
Confidence 8999999999999999999999995555555555555554444332221110 00112233444
Q ss_pred HHHHHHHhcCCCHHHHHHHh-----CCChhHHHHHhcCCCCCCH
Q psy6501 126 LLMQGRQAKGWSQKDLATKI-----NEKPQIVNDYEGGRGIPNQ 164 (174)
Q Consensus 126 ~i~~~R~~~glsq~ela~~l-----g~~~s~i~~~E~G~~~P~~ 164 (174)
+|......+=+|...++..+ .+++-||++|=..-+.|+-
T Consensus 394 lI~~E~~~~pLSD~kIa~lLkekGi~iARRTVAKYRe~L~I~sS 437 (444)
T COG1508 394 LIEAEDKKKPLSDSKIAELLKEKGIDVARRTVAKYREELNIPSS 437 (444)
T ss_pred HHhhccCCCCCCHHHHHHHHHHcCCchhHHhHHHHHHHcCCCch
Confidence 55555555556776666544 3445588888776666654
No 310
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=89.33 E-value=0.87 Score=31.89 Aligned_cols=46 Identities=20% Similarity=0.229 Sum_probs=32.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHH------------cCCCCCCHHHHHHH-----HHHhCcccccc
Q psy6501 46 WSQKDLATKINEKPQIVNDYE------------GGRGIPNQAIIGKM-----ERALGIRLRVN 91 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E------------~G~~~P~~~~l~~l-----a~~L~v~~~~l 91 (174)
||-.|+|+.+|||..||.-|| +|.+.-+...+..+ .+.+|+++..+
T Consensus 1 ~~I~eva~~~gvs~~tLRyYE~~GLl~p~~~~~~gyR~Ys~~dl~~l~~I~~~r~~G~~L~~I 63 (124)
T COG0789 1 YTIGEVAKLTGVSVRTLRFYERKGLLSPERRDEGGYRYYTPEDLELLQIIKTLRELGFSLAEI 63 (124)
T ss_pred CcHHHHHHHhCCCHHHHHHHHHcCCCCCcccCCCCceecCHHHHHHHHHHHHHHHcCCCHHHH
Confidence 578899999999999999999 35555555544433 33456665543
No 311
>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=89.22 E-value=0.62 Score=31.76 Aligned_cols=24 Identities=17% Similarity=0.181 Sum_probs=21.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501 46 WSQKDLATKINEKPQIVNDYEGGR 69 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~G~ 69 (174)
+|..|+|+.+|||.++|..||+-.
T Consensus 2 ~~i~eva~~~gVs~~tLR~ye~~G 25 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVYDRLG 25 (98)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCC
Confidence 578999999999999999998633
No 312
>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=89.22 E-value=0.64 Score=31.57 Aligned_cols=27 Identities=11% Similarity=0.150 Sum_probs=22.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCC
Q psy6501 46 WSQKDLATKINEKPQIVNDYEGGRGIP 72 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~G~~~P 72 (174)
|+..|+|+.+|||.+||.-||+-.-.|
T Consensus 1 m~I~eva~~~gvs~~tlR~Ye~~GLl~ 27 (95)
T cd04780 1 MRMSELSKRSGVSVATIKYYLREGLLP 27 (95)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCC
Confidence 578999999999999999999844433
No 313
>PRK15043 transcriptional regulator MirA; Provisional
Probab=89.02 E-value=0.69 Score=37.00 Aligned_cols=47 Identities=17% Similarity=0.299 Sum_probs=35.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHH------------cCCCCCCHHHHHHHH-----HHhCcccccc
Q psy6501 45 GWSQKDLATKINEKPQIVNDYE------------GGRGIPNQAIIGKME-----RALGIRLRVN 91 (174)
Q Consensus 45 gltq~eLA~~igvs~~~is~~E------------~G~~~P~~~~l~~la-----~~L~v~~~~l 91 (174)
-+|..|+|+.+|||+.||..|| +|.|..+.+.+..|. ...|+++..+
T Consensus 3 ~ytIgeVA~~~GVs~~TLR~wErr~GLL~P~Rt~~G~R~Ys~~dv~rL~~I~~l~~~G~~i~eI 66 (243)
T PRK15043 3 LYTIGEVALLCDINPVTLRAWQRRYGLLKPQRTDGGHRLFNDADIDRIREIKRWIDNGVQVSKV 66 (243)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHhcCCCCCccCCCCCEEECHHHHHHHHHHHHHHHcCCCHHHH
Confidence 4789999999999999999998 344566666676666 5566666543
No 314
>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=88.97 E-value=0.6 Score=27.51 Aligned_cols=25 Identities=20% Similarity=0.230 Sum_probs=22.5
Q ss_pred HcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 43 AKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 43 ~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
..|+|.+++|+.+|+|.++|..+-.
T Consensus 13 ~~~~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 13 AEGKTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4799999999999999999998864
No 315
>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=88.96 E-value=0.63 Score=28.99 Aligned_cols=22 Identities=14% Similarity=0.283 Sum_probs=20.3
Q ss_pred CCHHHHHHHhCCChhHHHHHhc
Q psy6501 136 WSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 136 lsq~ela~~lg~~~s~i~~~E~ 157 (174)
++..++|+.+|++++++..|+.
T Consensus 1 ~s~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4778999999999999999997
No 316
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=88.82 E-value=0.67 Score=28.52 Aligned_cols=29 Identities=14% Similarity=0.077 Sum_probs=23.6
Q ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHH
Q psy6501 36 LLMQGRQAKGWSQKDLATKINEKPQIVND 64 (174)
Q Consensus 36 ~ik~~R~~~gltq~eLA~~igvs~~~is~ 64 (174)
-|+.+....++|..|||+.+|+++++++.
T Consensus 15 Il~~L~~~~~~t~~ela~~l~~~~~t~s~ 43 (61)
T PF12840_consen 15 ILRLLASNGPMTVSELAEELGISQSTVSY 43 (61)
T ss_dssp HHHHHHHCSTBEHHHHHHHHTS-HHHHHH
T ss_pred HHHHHhcCCCCCHHHHHHHHCCCHHHHHH
Confidence 34455678999999999999999999885
No 317
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=88.78 E-value=0.41 Score=26.91 Aligned_cols=26 Identities=19% Similarity=0.350 Sum_probs=20.6
Q ss_pred CHHHHHHHhCCChhHHHHHhcCCCCC
Q psy6501 137 SQKDLATKINEKPQIVNDYEGGRGIP 162 (174)
Q Consensus 137 sq~ela~~lg~~~s~i~~~E~G~~~P 162 (174)
|..++|+.+|+++.++..||.-.-.|
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~Gll~ 26 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYEREGLLP 26 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHTTSS-
T ss_pred CHHHHHHHHCCCHHHHHHHHHCCCCC
Confidence 35789999999999999999865553
No 318
>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=88.69 E-value=1 Score=32.61 Aligned_cols=46 Identities=9% Similarity=0.176 Sum_probs=31.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHH-----------cCCCCCCHHHHHHHH-----HHhCcccccc
Q psy6501 46 WSQKDLATKINEKPQIVNDYE-----------GGRGIPNQAIIGKME-----RALGIRLRVN 91 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E-----------~G~~~P~~~~l~~la-----~~L~v~~~~l 91 (174)
++..|+|+.+|||++||..|| +|.+.-+.+.+..|. ..+|++++.+
T Consensus 1 y~I~e~a~~~gvs~~TLR~Ye~~GLl~p~r~~~g~R~Y~~~~l~~l~~I~~lr~~G~sL~eI 62 (134)
T cd04779 1 YRIGQLAHLAGVSKRTIDYYTNLGLLTPERSDSNYRYYDETALDRLQLIEHLKGQRLSLAEI 62 (134)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCccCCCCCeeECHHHHHHHHHHHHHHHCCCCHHHH
Confidence 578899999999999999999 345544554444332 3456665543
No 319
>PF08299 Bac_DnaA_C: Bacterial dnaA protein helix-turn-helix; InterPro: IPR013159 This entry represents the C-terminal domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; GO: 0005524 ATP binding, 0043565 sequence-specific DNA binding, 0006270 DNA-dependent DNA replication initiation, 0006275 regulation of DNA replication; PDB: 2HCB_B 3R8F_C 1L8Q_A 3PVP_B 3PVV_A 1J1V_A.
Probab=88.57 E-value=1.2 Score=28.50 Aligned_cols=60 Identities=13% Similarity=0.205 Sum_probs=35.9
Q ss_pred HHHHHHHHHhCcccccccCCCCCCCCCcccchhhhhhhhhhcccccHHHHHHHHHHHHhcCCCHHHHHHHhC-CChhHHH
Q psy6501 75 AIIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKIN-EKPQIVN 153 (174)
Q Consensus 75 ~~l~~la~~L~v~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~R~~~glsq~ela~~lg-~~~s~i~ 153 (174)
..+..+|+.|||+.+++.++... .. +...=.-.+--.|+..++|..+++..+| ...+++.
T Consensus 4 ~Ii~~Va~~~~v~~~~i~s~~R~-----------~~--------i~~aR~va~yL~r~~~~~sl~~Ig~~fg~rdHstV~ 64 (70)
T PF08299_consen 4 DIIEAVAEYFGVSVEDIRSKSRK-----------RK--------IVEARQVAMYLARELTGLSLSEIGRYFGGRDHSTVI 64 (70)
T ss_dssp HHHHHHHHHTT--HHHHHSS--------------HH--------HHHHHHHHHHHHHHHS---HHHHHHHCTSSTHHHHH
T ss_pred HHHHHHHHHHCCCHHHHhCCCCC-----------hh--------hcchHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHH
Confidence 56778999999999999864421 00 0111112344467778999999999999 8888764
No 320
>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=88.56 E-value=0.71 Score=30.91 Aligned_cols=24 Identities=21% Similarity=0.105 Sum_probs=21.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501 46 WSQKDLATKINEKPQIVNDYEGGR 69 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~G~ 69 (174)
+|..++|+.+|||++||..||.-.
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye~~G 25 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYERLG 25 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCC
Confidence 578999999999999999998643
No 321
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=88.52 E-value=0.57 Score=29.25 Aligned_cols=24 Identities=17% Similarity=0.292 Sum_probs=21.9
Q ss_pred CCCHHHHHHHhCCChhHHHHHhcC
Q psy6501 135 GWSQKDLATKINEKPQIVNDYEGG 158 (174)
Q Consensus 135 glsq~ela~~lg~~~s~i~~~E~G 158 (174)
.++..++|+++|+++++|+.|-+-
T Consensus 22 ~i~lkdIA~~Lgvs~~tIr~WK~~ 45 (60)
T PF10668_consen 22 KIKLKDIAEKLGVSESTIRKWKSR 45 (60)
T ss_pred CccHHHHHHHHCCCHHHHHHHhhh
Confidence 489999999999999999999764
No 322
>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=88.52 E-value=0.69 Score=29.02 Aligned_cols=22 Identities=18% Similarity=0.407 Sum_probs=20.0
Q ss_pred CCHHHHHHHhCCChhHHHHHhc
Q psy6501 136 WSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 136 lsq~ela~~lg~~~s~i~~~E~ 157 (174)
++..++|+.+|++++++..||.
T Consensus 1 ~~i~e~A~~~gVs~~tlr~ye~ 22 (68)
T cd04763 1 YTIGEVALLTGIKPHVLRAWER 22 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4678999999999999999986
No 323
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=88.52 E-value=0.73 Score=30.86 Aligned_cols=41 Identities=20% Similarity=0.122 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCC
Q psy6501 121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGI 161 (174)
Q Consensus 121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~ 161 (174)
..+...|..+-+..+++|+++++.+|++.+.++.+-+|+.-
T Consensus 27 ~~l~~~i~~~i~q~~l~Q~qiae~lgV~qprvS~l~~gk~~ 67 (91)
T COG5606 27 SALMMAIKQWIEQAALSQAQIAELLGVTQPRVSDLARGKIQ 67 (91)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHhcchh
Confidence 45667888888999999999999999999999999998753
No 324
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=88.49 E-value=0.51 Score=28.70 Aligned_cols=26 Identities=23% Similarity=0.334 Sum_probs=22.0
Q ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 42 QAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 42 ~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
-..|+|.+|+|+.+|+|..||..+-+
T Consensus 15 l~~G~~~~eIA~~l~is~~tV~~~~~ 40 (58)
T PF00196_consen 15 LAQGMSNKEIAEELGISEKTVKSHRR 40 (58)
T ss_dssp HHTTS-HHHHHHHHTSHHHHHHHHHH
T ss_pred HHhcCCcchhHHhcCcchhhHHHHHH
Confidence 46899999999999999999988753
No 325
>PRK00215 LexA repressor; Validated
Probab=88.47 E-value=1.1 Score=34.32 Aligned_cols=56 Identities=14% Similarity=0.237 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHHH--cCCCHHHHHHHhCC-CHHHHHHH-----HcCC--CCCCHHHHHHHHHHhCccccccc
Q psy6501 31 LDLAKLLMQGRQA--KGWSQKDLATKINE-KPQIVNDY-----EGGR--GIPNQAIIGKMERALGIRLRVNA 92 (174)
Q Consensus 31 ~~ig~~ik~~R~~--~gltq~eLA~~igv-s~~~is~~-----E~G~--~~P~~~~l~~la~~L~v~~~~l~ 92 (174)
..+-..|++.+.. ..+|+.|||+.+|+ ++++++++ ++|. +.+.. ++.+.+..+++.
T Consensus 7 ~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~~~------~r~~~l~~~~~~ 72 (205)
T PRK00215 7 QEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALERKGFIRRDPGR------SRAIEVAAPAQL 72 (205)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCCCC------cceEEecccccc
Confidence 3456667765544 45599999999999 99999999 6676 33322 456666544443
No 326
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=88.42 E-value=1.2 Score=32.51 Aligned_cols=32 Identities=13% Similarity=0.163 Sum_probs=26.6
Q ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
++-..-...|+|..|+|+++|||.+||.+|-+
T Consensus 12 ~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~ 43 (138)
T COG3415 12 RVVDAVVGEGLSCREAAKRFGVSISTVYRWVR 43 (138)
T ss_pred HHHHHHHHcCccHHHHHHHhCccHHHHHHHHH
Confidence 33344467899999999999999999999965
No 327
>PF13730 HTH_36: Helix-turn-helix domain
Probab=88.35 E-value=0.6 Score=27.92 Aligned_cols=21 Identities=24% Similarity=0.197 Sum_probs=19.2
Q ss_pred CHHHHHHHhCCCHHHHHHHHc
Q psy6501 47 SQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 47 tq~eLA~~igvs~~~is~~E~ 67 (174)
|++.||+.+|+|++||+++-+
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~ 47 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIK 47 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 999999999999999998753
No 328
>PRK11891 aspartate carbamoyltransferase; Provisional
Probab=88.33 E-value=0.7 Score=40.00 Aligned_cols=34 Identities=9% Similarity=0.149 Sum_probs=31.2
Q ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcC
Q psy6501 35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGG 68 (174)
Q Consensus 35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G 68 (174)
+.|+++..+.|||.++||+++|++..++.+|--=
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~wl~p 39 (429)
T PRK11891 6 AFLRDAMRRLNMTREAFANRIGVSRRALDTWLLP 39 (429)
T ss_pred HHHHHHHHHhCCCHHHHHHHhCCcHHhHHhhcCC
Confidence 5689999999999999999999999999999743
No 329
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=88.33 E-value=0.71 Score=34.87 Aligned_cols=33 Identities=18% Similarity=0.281 Sum_probs=29.9
Q ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCC
Q psy6501 39 QGRQAKGWSQKDLATKINEKPQIVNDYEGGRGI 71 (174)
Q Consensus 39 ~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~ 71 (174)
-+|...|+|..++|+.+|.+++||.++-.|...
T Consensus 55 ~arekag~Ti~EIAeelG~TeqTir~hlkgetk 87 (182)
T COG1318 55 LAREKAGMTISEIAEELGRTEQTVRNHLKGETK 87 (182)
T ss_pred HHHHHccCcHHHHHHHhCCCHHHHHHHHhcchh
Confidence 356999999999999999999999999988764
No 330
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=88.33 E-value=0.89 Score=36.28 Aligned_cols=30 Identities=23% Similarity=0.227 Sum_probs=25.8
Q ss_pred HHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 38 MQGRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 38 k~~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
-.+|-..|+|++|+|+.+|+|+++|+++++
T Consensus 218 i~~~~~~~~t~~eIA~~lgis~~~V~~~~~ 247 (258)
T PRK08215 218 LNLRFFQGKTQMEVAEEIGISQAQVSRLEK 247 (258)
T ss_pred HHHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 344556799999999999999999999986
No 331
>PF12728 HTH_17: Helix-turn-helix domain
Probab=88.23 E-value=0.78 Score=26.98 Aligned_cols=29 Identities=17% Similarity=0.124 Sum_probs=24.3
Q ss_pred CCHHHHHHHhCCChhHHHHHhcCCCCCCH
Q psy6501 136 WSQKDLATKINEKPQIVNDYEGGRGIPNQ 164 (174)
Q Consensus 136 lsq~ela~~lg~~~s~i~~~E~G~~~P~~ 164 (174)
+|.+|+|+.+|++.+++..|-+-...|..
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g~i~~~ 30 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQGKIPPF 30 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCCCeE
Confidence 68899999999999999999766566543
No 332
>PRK05572 sporulation sigma factor SigF; Validated
Probab=88.21 E-value=0.91 Score=36.09 Aligned_cols=29 Identities=21% Similarity=0.139 Sum_probs=25.5
Q ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 39 QGRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 39 ~~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
.+|-..|+|++|+|+.+|+|+++|+++++
T Consensus 212 ~l~~~~~~s~~eIA~~lgis~~~V~~~~~ 240 (252)
T PRK05572 212 YLRYFKDKTQSEVAKRLGISQVQVSRLEK 240 (252)
T ss_pred HHHHhCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34556799999999999999999999986
No 333
>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=88.13 E-value=0.57 Score=32.88 Aligned_cols=23 Identities=17% Similarity=0.143 Sum_probs=21.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Q psy6501 46 WSQKDLATKINEKPQIVNDYEGG 68 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~G 68 (174)
||..|+|+.+|||..||.-||.-
T Consensus 1 ~~ige~a~~~gvs~~tLryYe~~ 23 (116)
T cd04769 1 MYIGELAQQTGVTIKAIRLYEEK 23 (116)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 68899999999999999999953
No 334
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=87.96 E-value=1.2 Score=26.54 Aligned_cols=21 Identities=19% Similarity=0.321 Sum_probs=18.3
Q ss_pred CC-CHHHHHHHhCCCHHHHHHH
Q psy6501 45 GW-SQKDLATKINEKPQIVNDY 65 (174)
Q Consensus 45 gl-tq~eLA~~igvs~~~is~~ 65 (174)
.+ |+.+||+.+|+|+++|++.
T Consensus 19 ~l~s~~~la~~~~vs~~tv~~~ 40 (60)
T smart00345 19 KLPSERELAAQLGVSRTTVREA 40 (60)
T ss_pred cCcCHHHHHHHHCCCHHHHHHH
Confidence 35 8999999999999998864
No 335
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=87.80 E-value=1.1 Score=35.42 Aligned_cols=29 Identities=10% Similarity=0.023 Sum_probs=25.4
Q ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 39 QGRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 39 ~~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
.+|-..|+|++|+|+.+|+|+++|+++++
T Consensus 193 ~l~~~~~~t~~EIA~~lgis~~~V~q~~~ 221 (231)
T PRK12427 193 HLYYQHEMSLKEIALVLDLTEARICQLNK 221 (231)
T ss_pred HHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34556799999999999999999999985
No 336
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=87.76 E-value=0.54 Score=29.41 Aligned_cols=28 Identities=21% Similarity=0.399 Sum_probs=23.0
Q ss_pred CCHHHHHHHhCCChhHHHHHhcCCCCCC
Q psy6501 136 WSQKDLATKINEKPQIVNDYEGGRGIPN 163 (174)
Q Consensus 136 lsq~ela~~lg~~~s~i~~~E~G~~~P~ 163 (174)
++..|+|+.+|++++++..||.-.-.|+
T Consensus 1 yti~eva~~~gvs~~tlr~y~~~gll~~ 28 (69)
T PF13411_consen 1 YTIKEVAKLLGVSPSTLRYYEREGLLPP 28 (69)
T ss_dssp EEHHHHHHHTTTTHHHHHHHHHTTSSTT
T ss_pred CcHHHHHHHHCcCHHHHHHHHHhcCccc
Confidence 3678999999999999999998544443
No 337
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=87.72 E-value=1.1 Score=30.46 Aligned_cols=32 Identities=16% Similarity=-0.076 Sum_probs=28.2
Q ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
..|+...+..+..+.+.|+.+|+|++++.+.-
T Consensus 58 ~~i~~aL~~~~gn~s~AAr~LGIsRsTL~rKL 89 (95)
T PRK00430 58 PLLDMVMQYTRGNQTRAALMLGINRGTLRKKL 89 (95)
T ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 35888889999999999999999999987654
No 338
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=87.70 E-value=1.3 Score=27.91 Aligned_cols=27 Identities=15% Similarity=0.064 Sum_probs=22.1
Q ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 40 GRQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 40 ~R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
+.....+|..+||+.+|+|+++|++.-
T Consensus 8 ~L~~~~~~~~eLa~~l~vS~~tv~~~l 34 (69)
T TIGR00122 8 LLADNPFSGEKLGEALGMSRTAVNKHI 34 (69)
T ss_pred HHHcCCcCHHHHHHHHCCCHHHHHHHH
Confidence 344556899999999999999998764
No 339
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=87.63 E-value=0.57 Score=38.25 Aligned_cols=24 Identities=17% Similarity=0.241 Sum_probs=22.4
Q ss_pred cCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 134 KGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 134 ~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
.++|.+++|+.+|+++++|+.++.
T Consensus 244 ~~~t~~EIa~~lgvs~~~V~q~~~ 267 (289)
T PRK07500 244 DGATLEALGEELGISKERVRQIEA 267 (289)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Confidence 689999999999999999999876
No 340
>TIGR03453 partition_RepA plasmid partitioning protein RepA. Members of this family are the RepA (or ParA) protein involved in replicon partitioning. All known examples occur in bacterial species with two or more replicons, on a plasmid or the smaller chromosome. Note that an apparent exception may be seen as a pseudomolecule from assembly of an incompletely sequenced genome. Members of this family belong to a larger family that also includes the enzyme cobyrinic acid a,c-diamide synthase, but assignment of that name to members of this family would be in error.
Probab=87.61 E-value=2.1 Score=36.25 Aligned_cols=43 Identities=14% Similarity=0.251 Sum_probs=36.7
Q ss_pred cCCCHHHHHHHhCCCHHHHHHHH------------cCCCCCCHHHHHHHHHHhCc
Q psy6501 44 KGWSQKDLATKINEKPQIVNDYE------------GGRGIPNQAIIGKMERALGI 86 (174)
Q Consensus 44 ~gltq~eLA~~igvs~~~is~~E------------~G~~~P~~~~l~~la~~L~v 86 (174)
+-+|..|+|+.+|||.+||..|| +|++..+.+.+..|...+..
T Consensus 32 ~~~~i~eva~~~gv~~~tlr~~e~~~~~~~~~r~~~g~r~yt~~di~~l~~~~~~ 86 (387)
T TIGR03453 32 RKFTSGEVAKLLGVSDSYLRQLSLEGKGPEPETLSNGRRSYTLEQINELRRHLAQ 86 (387)
T ss_pred ccCCHHHHHHHHCcCHHHHHHHHHcCCCCCCCcCCCCceeeCHHHHHHHHHHHHh
Confidence 56899999999999999999997 45666778888888887765
No 341
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model 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 model 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 (pfam00376).
Probab=87.55 E-value=0.92 Score=25.87 Aligned_cols=28 Identities=11% Similarity=0.102 Sum_probs=23.5
Q ss_pred CCHHHHHHHhCCChhHHHHHhcCCCCCC
Q psy6501 136 WSQKDLATKINEKPQIVNDYEGGRGIPN 163 (174)
Q Consensus 136 lsq~ela~~lg~~~s~i~~~E~G~~~P~ 163 (174)
+|.+++|+.+|++++++..|-+-...|.
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g~i~~ 29 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEGELPA 29 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcCCCCe
Confidence 6789999999999999998886555554
No 342
>PF09048 Cro: Cro; InterPro: IPR000655 Bacteriophage lambda encodes two repressors: the Cro repressor that acts to turn off early gene transcription during the lytic cycle, and the lambda or cI repressor that is required to maintain lysogenic growth. Together the Cro and cI repressors form a helix-turn-helix (HTH) superfamily. The lambda Cro repressor binds to DNA as a highly flexible dimer. The crystal structure of the lambda Cro repressor [] reveals a HTH DNA-binding protein with an alpha/beta fold that differs from other Cro family members, possibly by an evolutionary fold change []. Most Cro proteins, such as Enterobacteria phage P22 Cro and Bacteriophage 434 Cro, have an all-alpha structure that is thought to be ancestral to lambda Cro, where the fourth and fifth helices are replaced by a beta-sheet, possibly as a result of secondary structure switching rather than by nonhomologous replacement []. This entry represents the lambda-type Cro repressor with an alpha/beta topology.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 5CRO_A 2ECS_A 2OVG_A 6CRO_A 1D1L_A 2ORC_A 1D1M_B 3ORC_A 1ORC_A 2A63_A ....
Probab=87.49 E-value=1 Score=27.93 Aligned_cols=30 Identities=10% Similarity=0.062 Sum_probs=22.0
Q ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCC
Q psy6501 39 QGRQAKGWSQKDLATKINEKPQIVNDYEGGRG 70 (174)
Q Consensus 39 ~~R~~~gltq~eLA~~igvs~~~is~~E~G~~ 70 (174)
+.=++.| |.+.|+.+||++++||+--+-.|
T Consensus 8 eyv~~~G--Q~kaA~~lGV~Q~AIsKAlr~gR 37 (59)
T PF09048_consen 8 EYVKEHG--QAKAARALGVTQSAISKALRAGR 37 (59)
T ss_dssp HHHHHHH--HHHHHHHHTS-HHHHHHHHHCT-
T ss_pred HHHHHhC--hHHHHHHcCCcHHHHHHHHHcCC
Confidence 3444555 99999999999999998766554
No 343
>PF05269 Phage_CII: Bacteriophage CII protein; InterPro: IPR007933 The CII protein is a transcription activator, conserved in bacteriophage lambda and related phages, that plays a key role in the decision between lytic or lysogenic phage development. CII is regulated at multiple levels including transcription, translation initiation, mRNA stability, and proteolysis []. Conditions that stabilise cII favour lysogenic development. The lambda CII protein activates three specific promoters, binding to direct repeat sequences rather than the more usual inverted repeats. Structurally, CII is a homotetramer where each monomer is composed of four alpha helices and a disordered C terminus [, ]. The alpha helical region is responsible for DNA binding and multimerisation. The homotetramer has an unusual spatial arrangement that allows recognition of the direct repeat sequences.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ZS4_C 1ZPQ_C 1XWR_A.
Probab=87.47 E-value=0.52 Score=31.93 Aligned_cols=24 Identities=13% Similarity=0.250 Sum_probs=21.7
Q ss_pred cCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 134 KGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 134 ~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
...+|..+|+.+|++.|+|++|..
T Consensus 22 A~~gq~~vA~~~Gv~eStISR~k~ 45 (91)
T PF05269_consen 22 ASVGQKKVAEAMGVDESTISRWKN 45 (91)
T ss_dssp HHHHHHHHHHHHTSSTTTHHHHHH
T ss_pred HHHhhHHHHHHhCCCHHHHHHHHh
Confidence 457899999999999999999975
No 344
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. 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.
Probab=87.44 E-value=0.91 Score=36.56 Aligned_cols=24 Identities=13% Similarity=0.205 Sum_probs=22.4
Q ss_pred cCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 44 KGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 44 ~gltq~eLA~~igvs~~~is~~E~ 67 (174)
.|+|++|+|+.+|||+.+|+++++
T Consensus 235 ~~~t~~eIA~~lgvS~~~V~q~~~ 258 (270)
T TIGR02392 235 DKLTLQELAAEYGVSAERIRQIEK 258 (270)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHH
Confidence 379999999999999999999985
No 345
>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=87.39 E-value=0.93 Score=31.99 Aligned_cols=24 Identities=13% Similarity=0.122 Sum_probs=21.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501 46 WSQKDLATKINEKPQIVNDYEGGR 69 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~G~ 69 (174)
||..|+|+.+|||..||.-||+-.
T Consensus 1 m~IgevA~~~gvs~~tlRyYe~~G 24 (120)
T cd04781 1 LDIAEVARQSGLPASTLRYYEEKG 24 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCC
Confidence 678999999999999999999543
No 346
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=87.36 E-value=0.9 Score=28.48 Aligned_cols=33 Identities=12% Similarity=0.061 Sum_probs=27.7
Q ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
.+.+..+....++|..|+|+.+|+++++|++.-
T Consensus 11 ~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L 43 (68)
T PF01978_consen 11 AKVYLALLKNGPATAEEIAEELGISRSTVYRAL 43 (68)
T ss_dssp HHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHH
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence 445566668899999999999999999998764
No 347
>COG3311 AlpA Predicted transcriptional regulator [Transcription]
Probab=87.32 E-value=0.57 Score=30.15 Aligned_cols=32 Identities=6% Similarity=0.035 Sum_probs=27.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH
Q psy6501 46 WSQKDLATKINEKPQIVNDYEGGRGIPNQAII 77 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~G~~~P~~~~l 77 (174)
+...|++..+|+|+++|.++.+....|....|
T Consensus 14 lrl~ev~~~~GlSrstiYr~i~~~~FPkpvkl 45 (70)
T COG3311 14 LRLPEVAQLTGLSRSTIYRLIKDGTFPKPVKL 45 (70)
T ss_pred hhHHHHHHHHCccHHHHHHHHccCCCCCCeec
Confidence 45679999999999999999999999987644
No 348
>PRK05949 RNA polymerase sigma factor; Validated
Probab=87.23 E-value=1.3 Score=36.81 Aligned_cols=24 Identities=21% Similarity=0.230 Sum_probs=22.0
Q ss_pred cCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 134 KGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 134 ~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
.++|.+++|+.+|++.++|..++.
T Consensus 285 e~~Tl~EIa~~lgiS~erVrq~~~ 308 (327)
T PRK05949 285 KELSLAKVGERLNLSRERVRQLEH 308 (327)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHH
Confidence 569999999999999999998876
No 349
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=87.21 E-value=0.77 Score=32.86 Aligned_cols=27 Identities=19% Similarity=0.181 Sum_probs=23.2
Q ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHH
Q psy6501 37 LMQGRQAKGWSQKDLATKINEKPQIVN 63 (174)
Q Consensus 37 ik~~R~~~gltq~eLA~~igvs~~~is 63 (174)
+=.++.-.|+|.+|+|+.+|+|.+||.
T Consensus 115 v~~l~~~~~~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 115 IIYMKFFEDMKEIDIAKKLHISRQSVY 141 (142)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHhhc
Confidence 344667899999999999999999985
No 350
>PRK15320 transcriptional activator SprB; Provisional
Probab=87.12 E-value=0.66 Score=36.14 Aligned_cols=39 Identities=23% Similarity=0.249 Sum_probs=31.6
Q ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccc
Q psy6501 41 RQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRV 90 (174)
Q Consensus 41 R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~ 90 (174)
.-..|+|++|+|+.+++|.+||+.+-+ +|-+.|++.-.-
T Consensus 175 LLAkG~SNKEIAekL~LS~KTVSTYKn-----------RLLeKLgAkN~~ 213 (251)
T PRK15320 175 LLSSGHPAIELAKKFGLGTKTVSIYRK-----------KVMYRLGMDSSP 213 (251)
T ss_pred HHHcCCCHHHHHHHhccchhhHHHHHH-----------HHHHHcCCCCCc
Confidence 457899999999999999999998854 666677776443
No 351
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=87.07 E-value=1.1 Score=35.70 Aligned_cols=28 Identities=25% Similarity=0.209 Sum_probs=24.8
Q ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 40 GRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 40 ~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
+|--.|+|++|+|+.+|+|+.+|+++++
T Consensus 217 ~~~~~~~t~~eIA~~lgis~~~V~~~~~ 244 (254)
T TIGR02850 217 MRFFEGKTQMEVAEEIGISQAQVSRLEK 244 (254)
T ss_pred HHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 4445799999999999999999999985
No 352
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=87.06 E-value=13 Score=33.39 Aligned_cols=98 Identities=18% Similarity=0.049 Sum_probs=50.4
Q ss_pred HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCCCCCCCCcccchhhhhhhhhhcccccHH
Q psy6501 43 AKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDRETEELKHEKVPLD 122 (174)
Q Consensus 43 ~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ 122 (174)
...+|-++||+.+|||..||.+.- ..+....+..++.... +.....-....-..+... .. ......
T Consensus 15 ~~~~t~~~LA~~l~VS~RTIr~dI--------~~in~~l~~~~~~~i~--~~~Gy~l~~~~~~~~~~~---~~-~~~~e~ 80 (584)
T PRK09863 15 QQDRSGGELAQQLGVSRRTIVRDI--------AYINFTLNGKAIGSIS--GSAKYHLEILNRRSLFQL---LQ-KSDNED 80 (584)
T ss_pred cCCCCHHHHHHHhCCCHHHHHHHH--------HHHHHHHHhcchhhee--cCCceEEEeCCHHHHHHH---Hh-cCCHHH
Confidence 468999999999999999998843 3444333332332110 000000000000000000 00 000111
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHH
Q psy6501 123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDY 155 (174)
Q Consensus 123 ~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~ 155 (174)
. ..+...-.....+..++|+.+.+|++++...
T Consensus 81 ~-~il~~Ll~~~~~~~~~La~~l~vS~sTi~~d 112 (584)
T PRK09863 81 R-LLLLRLLLNTFTPMAQLASALNLSRTWVAER 112 (584)
T ss_pred H-HHHHHHHHcCCccHHHHHHHhCCCHHHHHHH
Confidence 1 1222223356789999999999999988754
No 353
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=86.96 E-value=1.7 Score=31.95 Aligned_cols=31 Identities=13% Similarity=0.102 Sum_probs=26.4
Q ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHH
Q psy6501 34 AKLLMQGRQAKGWSQKDLATKINEKPQIVND 64 (174)
Q Consensus 34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~ 64 (174)
-.-|..+.+.-..|..+||+.+|+|++++.+
T Consensus 12 ~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~ 42 (153)
T PRK11179 12 RGILEALMENARTPYAELAKQFGVSPGTIHV 42 (153)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHH
Confidence 4456778888999999999999999998764
No 354
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=86.96 E-value=1.8 Score=36.57 Aligned_cols=24 Identities=4% Similarity=0.144 Sum_probs=22.0
Q ss_pred cCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 134 KGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 134 ~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
.++|.+++|+.+|++.+.|+.+|.
T Consensus 324 ~~~tl~EIa~~lgvs~erVrQi~~ 347 (367)
T PRK09210 324 RTRTLEEVGKVFGVTRERIRQIEA 347 (367)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHH
Confidence 448999999999999999999986
No 355
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=86.90 E-value=0.74 Score=26.81 Aligned_cols=29 Identities=14% Similarity=0.055 Sum_probs=22.5
Q ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 37 LMQGRQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 37 ik~~R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
|+.+.+ ..++..|+|+.+|+|+++||..-
T Consensus 8 l~~L~~-~~~~~~el~~~l~~s~~~vs~hL 36 (47)
T PF01022_consen 8 LKLLSE-GPLTVSELAEELGLSQSTVSHHL 36 (47)
T ss_dssp HHHHTT-SSEEHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHh-CCCchhhHHHhccccchHHHHHH
Confidence 344444 77899999999999999999753
No 356
>PRK01381 Trp operon repressor; Provisional
Probab=86.87 E-value=1.9 Score=29.60 Aligned_cols=51 Identities=8% Similarity=0.034 Sum_probs=35.9
Q ss_pred HHHHHHHHHH--hcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhh
Q psy6501 123 LAKLLMQGRQ--AKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERA 173 (174)
Q Consensus 123 ~~~~i~~~R~--~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~ 173 (174)
+..+++-.+. ..++||.++++.+|+|.++|++.=+--..-++.+..-|.+.
T Consensus 41 l~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn~Lk~~~~~~k~~l~~~ 93 (99)
T PRK01381 41 LGTRVRIVEELLRGELSQREIKQELGVGIATITRGSNSLKTAPPEFKEWLEQQ 93 (99)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhHHHhccCCHHHHHHHHHH
Confidence 3444444443 34599999999999999999988776555556666665543
No 357
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=86.82 E-value=1.7 Score=32.38 Aligned_cols=23 Identities=13% Similarity=0.114 Sum_probs=19.8
Q ss_pred cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 44 KGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 44 ~gltq~eLA~~igvs~~~is~~E 66 (174)
..+||+|||..+|+|+.+||+.-
T Consensus 142 ~~~t~~~iA~~lG~tretvsR~l 164 (193)
T TIGR03697 142 LRLSHQAIAEAIGSTRVTITRLL 164 (193)
T ss_pred CCCCHHHHHHHhCCcHHHHHHHH
Confidence 34799999999999999998853
No 358
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [].
Probab=86.81 E-value=0.88 Score=25.08 Aligned_cols=19 Identities=16% Similarity=0.282 Sum_probs=17.6
Q ss_pred CHHHHHHHhCCCHHHHHHH
Q psy6501 47 SQKDLATKINEKPQIVNDY 65 (174)
Q Consensus 47 tq~eLA~~igvs~~~is~~ 65 (174)
|..|.|+.+|+++++|+++
T Consensus 18 Si~eAa~~l~i~~~~I~~~ 36 (37)
T PF07453_consen 18 SIREAARYLGISHSTISKY 36 (37)
T ss_pred CHHHHHHHhCCCHHHHHHh
Confidence 7899999999999999975
No 359
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=86.77 E-value=1 Score=28.65 Aligned_cols=36 Identities=11% Similarity=0.184 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 122 ~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
++...+-..-...|.|..++|...|++++++..|..
T Consensus 10 e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 10 EFKLQAVREYLESGESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp HHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHHCCCceEeeecccccccccccHHHH
Confidence 333344333456789999999999999999999975
No 360
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=86.74 E-value=0.63 Score=33.41 Aligned_cols=26 Identities=23% Similarity=0.335 Sum_probs=23.8
Q ss_pred HhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 132 QAKGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 132 ~~~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
.++||+|+++|+.+|....-||.+|.
T Consensus 20 RekG~tQ~eIA~~L~TTraNvSaIEk 45 (143)
T COG1356 20 REKGLTQSEIARILKTTRANVSAIEK 45 (143)
T ss_pred hhccccHHHHHHHHccchhhHHHHHH
Confidence 46899999999999999999998886
No 361
>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A.
Probab=86.74 E-value=2.9 Score=27.50 Aligned_cols=47 Identities=13% Similarity=0.020 Sum_probs=33.5
Q ss_pred HHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501 125 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174 (174)
Q Consensus 125 ~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l 174 (174)
..|..+-+++|+|..++|...|+++++++..- ..|.+..-..||.+|
T Consensus 5 adI~AaL~krG~sL~~lsr~~Gl~~~tl~nal---~r~~pk~E~~IA~aL 51 (78)
T PF13693_consen 5 ADIKAALRKRGTSLAALSREAGLSSSTLRNAL---RRPWPKGERIIADAL 51 (78)
T ss_dssp HHHHHHHCTTS--HHHHHHHHSS-HHHHHHTT---TSS-HHHHHHHHHHT
T ss_pred HHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHH---cCCChHHHHHHHHHH
Confidence 45666777899999999999999999988765 456676677777664
No 362
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). 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 [].; PDB: 1S7O_A 1XSV_B.
Probab=86.68 E-value=0.64 Score=32.13 Aligned_cols=45 Identities=18% Similarity=0.136 Sum_probs=29.7
Q ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccc
Q psy6501 40 GRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRL 88 (174)
Q Consensus 40 ~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~ 88 (174)
+--.-++|..|+|+.+|||+++|+++-+- ....|..+-+.|++--
T Consensus 28 lyy~eDlSlsEIAe~~~iSRqaV~d~ikr----~~~~L~~yE~kL~l~~ 72 (101)
T PF04297_consen 28 LYYEEDLSLSEIAEELGISRQAVYDSIKR----AEKKLEEYEEKLGLVE 72 (101)
T ss_dssp HHCTS---HHHHHHHCTS-HHHHHHHHHH----HHHHHHHHHHHH-HHH
T ss_pred HHHccCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHHHHhhHH
Confidence 44456899999999999999999998753 2366667776666543
No 363
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 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 [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=86.65 E-value=0.77 Score=27.72 Aligned_cols=27 Identities=19% Similarity=0.219 Sum_probs=20.6
Q ss_pred HhcCCCHHHHHHHhCCChhHHHHHhcC
Q psy6501 132 QAKGWSQKDLATKINEKPQIVNDYEGG 158 (174)
Q Consensus 132 ~~~glsq~ela~~lg~~~s~i~~~E~G 158 (174)
-+.|.++.++|..+|++.++|+.|-..
T Consensus 19 ~e~g~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 19 LEEGESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp HHCTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 368889999999999999999988653
No 364
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=86.62 E-value=2.4 Score=25.65 Aligned_cols=29 Identities=14% Similarity=0.000 Sum_probs=23.6
Q ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501 37 LMQGRQAKGWSQKDLATKINEKPQIVNDY 65 (174)
Q Consensus 37 ik~~R~~~gltq~eLA~~igvs~~~is~~ 65 (174)
+.+++.-..++++|.|+.+||+.+++-+.
T Consensus 7 ~~~L~~~fhlp~~eAA~~Lgv~~T~LKr~ 35 (52)
T PF02042_consen 7 LEDLSQYFHLPIKEAAKELGVSVTTLKRR 35 (52)
T ss_pred HHHHHHHhCCCHHHHHHHhCCCHHHHHHH
Confidence 45778888999999999999888766544
No 365
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=86.56 E-value=1.1 Score=35.27 Aligned_cols=25 Identities=8% Similarity=0.231 Sum_probs=23.3
Q ss_pred HcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 43 AKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 43 ~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
..++|++|+|+.+|+|+++|++++.
T Consensus 194 ~~~~t~~EIA~~lgis~~~V~q~~~ 218 (238)
T TIGR02393 194 GRPHTLEEVGKEFNVTRERIRQIES 218 (238)
T ss_pred CCCccHHHHHHHHCCCHHHHHHHHH
Confidence 4789999999999999999999985
No 366
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=86.55 E-value=7.4 Score=31.27 Aligned_cols=31 Identities=13% Similarity=0.124 Sum_probs=25.4
Q ss_pred HHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 127 LMQGRQAKGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 127 i~~~R~~~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
+-.++-..++|.+++|+.+|++.++|..++.
T Consensus 223 vl~l~y~~~~t~~EIA~~lgis~~~V~~~~~ 253 (264)
T PRK07122 223 VLVLRFFESMTQTQIAERVGISQMHVSRLLA 253 (264)
T ss_pred HHHHHhcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3344445799999999999999999998765
No 367
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=86.53 E-value=0.7 Score=37.60 Aligned_cols=24 Identities=17% Similarity=0.173 Sum_probs=22.5
Q ss_pred cCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 44 KGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 44 ~gltq~eLA~~igvs~~~is~~E~ 67 (174)
.++|++|+|+.+|||+.+|+++++
T Consensus 247 ~~~Tl~EIA~~lgvS~~rVrqi~~ 270 (284)
T PRK06596 247 DKSTLQELAAEYGVSAERVRQIEK 270 (284)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHH
Confidence 379999999999999999999996
No 368
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=86.50 E-value=1.6 Score=30.37 Aligned_cols=38 Identities=8% Similarity=-0.060 Sum_probs=27.8
Q ss_pred cchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501 28 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDY 65 (174)
Q Consensus 28 ~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~ 65 (174)
.+...-...|..+...-++|+.+||+.+|++++++++.
T Consensus 25 ~lt~~q~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~ 62 (118)
T TIGR02337 25 GLTEQQWRILRILAEQGSMEFTQLANQACILRPSLTGI 62 (118)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHHhCCCchhHHHH
Confidence 33333334566666778899999999999999999744
No 369
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=86.40 E-value=3 Score=25.59 Aligned_cols=53 Identities=11% Similarity=0.188 Sum_probs=35.8
Q ss_pred HHHHHHHHHhCcccccccCCCCCCCCCcccchhhhhhhhhhcccccHHHHHHHHHHHHhcCCCHHHHHHHhC
Q psy6501 75 AIIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKIN 146 (174)
Q Consensus 75 ~~l~~la~~L~v~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~R~~~glsq~ela~~lg 146 (174)
+.+..+|+.|||+.+++.++.... .+...=.-.+--.+...++|..+++..+|
T Consensus 4 ~I~~~Va~~~~i~~~~i~s~~R~~-------------------~~~~aR~iamyla~~~~~~sl~~Ig~~fg 56 (60)
T smart00760 4 EIIEAVAEYFGVKPEDLKSKSRKR-------------------EIVLARQIAMYLARELTDLSLPEIGKIFG 56 (60)
T ss_pred HHHHHHHHHhCCCHHHHhcCCCCc-------------------chhHHHHHHHHHHHHHHCCCHHHHHHHhC
Confidence 567799999999999998644311 11111112333467778999999999887
No 370
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=86.36 E-value=1.2 Score=26.30 Aligned_cols=25 Identities=12% Similarity=0.101 Sum_probs=22.6
Q ss_pred CHHHHHHHhCCCHHHHHHHHcCCCC
Q psy6501 47 SQKDLATKINEKPQIVNDYEGGRGI 71 (174)
Q Consensus 47 tq~eLA~~igvs~~~is~~E~G~~~ 71 (174)
|+.|.|+.+|++.++|++.-+|...
T Consensus 19 S~~eAa~~lg~~~~~I~~~~~~~~~ 43 (53)
T smart00497 19 SIREAAKYLGISHSSISKYLNTGKK 43 (53)
T ss_pred CHHHHHHHhCCCHHHHHHHHhCCCc
Confidence 7899999999999999999998643
No 371
>PRK13832 plasmid partitioning protein; Provisional
Probab=86.35 E-value=1.5 Score=38.66 Aligned_cols=50 Identities=16% Similarity=0.244 Sum_probs=37.7
Q ss_pred hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHH
Q psy6501 30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKME 81 (174)
Q Consensus 30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la 81 (174)
..+-...++.+. ..|+|++++|..+|+|+++|+++-. -...++..+..++
T Consensus 104 PiEea~AfkrLi-e~G~T~EeIA~~lG~S~~~V~rlll-LA~L~P~lLdal~ 153 (520)
T PRK13832 104 PVDQWRAIERLV-ALGWTEEAIAVALALPVRQIRKLRL-LANVLPAMLDHMA 153 (520)
T ss_pred HHHHHHHHHHHH-hcCCCHHHHHHHHCCCHHHHHHHHH-HcCCCHHHHHHHH
Confidence 355677778887 7999999999999999999998643 2334555555555
No 372
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=86.17 E-value=1.3 Score=34.34 Aligned_cols=22 Identities=5% Similarity=0.107 Sum_probs=19.3
Q ss_pred CCCHHHHHHHhCCCHHHHHHHH
Q psy6501 45 GWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 45 gltq~eLA~~igvs~~~is~~E 66 (174)
.+||++||+.+|+|+.+||+.-
T Consensus 184 ~lt~~~iA~~lG~sr~tvsR~l 205 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETISRLL 205 (235)
T ss_pred cccHHHHHHHhCCcHHHHHHHH
Confidence 4899999999999999999854
No 373
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=86.15 E-value=5.4 Score=32.01 Aligned_cols=15 Identities=0% Similarity=0.034 Sum_probs=11.3
Q ss_pred cCCCHHHHHHHhCCC
Q psy6501 134 KGWSQKDLATKINEK 148 (174)
Q Consensus 134 ~glsq~ela~~lg~~ 148 (174)
.+++..++|..+|.+
T Consensus 247 t~~sI~eIA~~~GF~ 261 (290)
T PRK10572 247 TRMPIATIGRNVGYD 261 (290)
T ss_pred CCCCHHHHHHHhCCC
Confidence 457788888888776
No 374
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=86.14 E-value=7 Score=30.59 Aligned_cols=32 Identities=9% Similarity=0.125 Sum_probs=25.9
Q ss_pred HHHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 126 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 126 ~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
.+-.++-..|+|.+++|+.+|++.++|.....
T Consensus 191 ~vl~l~~~~g~s~~EIA~~lgis~~tV~~~~~ 222 (236)
T PRK06986 191 LVLSLYYQEELNLKEIGAVLGVSESRVSQIHS 222 (236)
T ss_pred HHHHhHhccCCCHHHHHHHHCCCHHHHHHHHH
Confidence 33345557899999999999999999987654
No 375
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=86.09 E-value=1 Score=34.28 Aligned_cols=46 Identities=15% Similarity=0.155 Sum_probs=32.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHH-----------cCCCCCCHHHHHHH-----HHHhCcccccc
Q psy6501 46 WSQKDLATKINEKPQIVNDYE-----------GGRGIPNQAIIGKM-----ERALGIRLRVN 91 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E-----------~G~~~P~~~~l~~l-----a~~L~v~~~~l 91 (174)
||..++|+.+|||..||..|+ +|.+.-+.+.+..| ....|+++.++
T Consensus 1 mti~evA~~lGVS~~TLRrw~k~g~L~~~R~~~G~R~y~~~dl~~L~~I~~l~~~Gm~i~~i 62 (175)
T PRK13182 1 MKTPFVAKKLGVSPKTVQRWVKQLNLPCEKNEYGHYIFTEEDLQLLEYVKSQIEEGQNMQDT 62 (175)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCCCCCcCCCCCEEECHHHHHHHHHHHHHHHcCCCHHHH
Confidence 578999999999999999997 55555554444433 23355665554
No 376
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=86.04 E-value=1.5 Score=33.63 Aligned_cols=33 Identities=15% Similarity=0.177 Sum_probs=27.0
Q ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcC
Q psy6501 35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGG 68 (174)
Q Consensus 35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G 68 (174)
..|..++ ..|+|..++|+.+|||++||.+|-+.
T Consensus 163 ~~i~~~~-~~g~s~~~iak~lgis~~Tv~r~~k~ 195 (200)
T PRK13413 163 EKIKKLL-DKGTSKSEIARKLGVSRTTLARFLKT 195 (200)
T ss_pred HHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 3455553 56999999999999999999999763
No 377
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=85.98 E-value=3.8 Score=32.66 Aligned_cols=29 Identities=24% Similarity=0.203 Sum_probs=25.0
Q ss_pred HHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 129 QGRQAKGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 129 ~~R~~~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
.+|-..|+|++++|+.+|+++++|+.+++
T Consensus 219 ~~~~~~~~t~~eIA~~lgis~~~V~~~~~ 247 (258)
T PRK08215 219 NLRFFQGKTQMEVAEEIGISQAQVSRLEK 247 (258)
T ss_pred HHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 44556799999999999999999998876
No 378
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=85.77 E-value=1 Score=24.37 Aligned_cols=22 Identities=14% Similarity=0.167 Sum_probs=16.6
Q ss_pred CCCHHHHHHHhCCChhHHHHHh
Q psy6501 135 GWSQKDLATKINEKPQIVNDYE 156 (174)
Q Consensus 135 glsq~ela~~lg~~~s~i~~~E 156 (174)
.+|.+|+|..+|.++.++++.-
T Consensus 2 ~mtr~diA~~lG~t~ETVSR~l 23 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVSRIL 23 (32)
T ss_dssp E--HHHHHHHHTS-HHHHHHHH
T ss_pred CcCHHHHHHHhCCcHHHHHHHH
Confidence 3789999999999999998753
No 379
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=85.72 E-value=1.5 Score=32.10 Aligned_cols=29 Identities=17% Similarity=0.111 Sum_probs=25.1
Q ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 39 QGRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 39 ~~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
.++...|+|++|+|+.+|+|+++|.++..
T Consensus 135 ~l~~~~~~~~~eIA~~lgis~~tv~~~~~ 163 (179)
T PRK11924 135 LLRYVEGLSYREIAEILGVPVGTVKSRLR 163 (179)
T ss_pred hHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34556899999999999999999999864
No 380
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=85.65 E-value=1.2 Score=34.55 Aligned_cols=53 Identities=11% Similarity=0.085 Sum_probs=48.4
Q ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501 40 GRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG 93 (174)
Q Consensus 40 ~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~ 93 (174)
.+++.+.+++++++..|+++ ++..|.++-..++...+...+++|+..--+...
T Consensus 7 rq~el~~~~~~~~~~~g~~p-s~~e~~~~~~~~s~~~~~~~l~~L~~~g~i~~~ 59 (201)
T COG1974 7 RQKELLDFIRSLIKETGYPP-SIREIGDALGLASPSAIHSHLKALERKGYIRRD 59 (201)
T ss_pred HHHHHHHHHHHHHHHhCCCc-cHHHHHHhhCCCChHHHHHHHHHHhcCCcEEec
Confidence 77888999999999999999 899999999999999999999999998766553
No 381
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=85.61 E-value=3.3 Score=33.17 Aligned_cols=30 Identities=3% Similarity=0.055 Sum_probs=24.6
Q ss_pred HHHHHHhcCCCHHHHHHHhCCChhHHHHHh
Q psy6501 127 LMQGRQAKGWSQKDLATKINEKPQIVNDYE 156 (174)
Q Consensus 127 i~~~R~~~glsq~ela~~lg~~~s~i~~~E 156 (174)
+-.++-..|+|.+++|+.+|+++++|....
T Consensus 220 vl~l~~~~~~s~~eIA~~lgis~~tV~~~~ 249 (268)
T PRK06288 220 VLILYYYEDLTLKEIGKVLGVTESRISQLH 249 (268)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence 334555689999999999999999998665
No 382
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=85.60 E-value=1.8 Score=31.53 Aligned_cols=28 Identities=29% Similarity=0.404 Sum_probs=24.8
Q ss_pred HHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501 38 MQGRQAKGWSQKDLATKINEKPQIVNDY 65 (174)
Q Consensus 38 k~~R~~~gltq~eLA~~igvs~~~is~~ 65 (174)
-.++--.|+|.+|+|+.+|+|.++|...
T Consensus 118 ~~l~~~~~~s~~EIA~~lgis~~tV~~~ 145 (163)
T PRK07037 118 FEMYRLHGETQKDIARELGVSPTLVNFM 145 (163)
T ss_pred HHHHHHcCCCHHHHHHHHCCCHHHHHHH
Confidence 3466788999999999999999999976
No 383
>PF06322 Phage_NinH: Phage NinH protein; InterPro: IPR010454 This entry is represented by Bacteriophage 933W, NinH. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=85.54 E-value=0.98 Score=28.18 Aligned_cols=23 Identities=17% Similarity=0.384 Sum_probs=20.7
Q ss_pred CHHHHHHHhCCCHHHHHHHHcCC
Q psy6501 47 SQKDLATKINEKPQIVNDYEGGR 69 (174)
Q Consensus 47 tq~eLA~~igvs~~~is~~E~G~ 69 (174)
.|.|+|+.+++++.||.+|-...
T Consensus 18 nqtEvaR~l~c~R~TVrKY~~D~ 40 (64)
T PF06322_consen 18 NQTEVARRLGCNRATVRKYSRDK 40 (64)
T ss_pred cHHHHHHHhcccHHHHHHHhccc
Confidence 79999999999999999997543
No 384
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=85.49 E-value=1.5 Score=32.68 Aligned_cols=32 Identities=13% Similarity=0.150 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHH
Q psy6501 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVND 64 (174)
Q Consensus 33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~ 64 (174)
=-+-|..+.+.-.+|..+||+++|+|++++.+
T Consensus 16 D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~ 47 (164)
T PRK11169 16 DRNILNELQKDGRISNVELSKRVGLSPTPCLE 47 (164)
T ss_pred HHHHHHHhccCCCCCHHHHHHHHCcCHHHHHH
Confidence 34567788899999999999999999988754
No 385
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=85.45 E-value=1.8 Score=31.12 Aligned_cols=29 Identities=14% Similarity=-0.063 Sum_probs=25.2
Q ss_pred HHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 38 MQGRQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 38 k~~R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
-.++--.|+|.+|+|+.+|+|.++|..+-
T Consensus 115 i~l~~~~~~s~~EIA~~l~is~~tV~~~~ 143 (154)
T PRK06759 115 IFERFFVGKTMGEIALETEMTYYQVRWIY 143 (154)
T ss_pred HHHHHhcCCCHHHHHHHHCCCHHHHHHHH
Confidence 34567789999999999999999998875
No 386
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=85.43 E-value=1.7 Score=33.81 Aligned_cols=29 Identities=14% Similarity=0.046 Sum_probs=25.3
Q ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 39 QGRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 39 ~~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
.++-..|+|++|+|+.+|+|+++|..+.+
T Consensus 188 ~l~y~~~~s~~eIA~~lgis~~~v~~~~~ 216 (227)
T TIGR02980 188 LLRFFEDKTQSEIAERLGISQMHVSRLLR 216 (227)
T ss_pred HHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 44556899999999999999999999874
No 387
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=85.41 E-value=3.1 Score=36.85 Aligned_cols=24 Identities=4% Similarity=0.072 Sum_probs=22.4
Q ss_pred cCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 134 KGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 134 ~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
.++|+.++|+.+|++++.|+.+|.
T Consensus 466 e~~TL~EIa~~lGVSrERVRQIe~ 489 (509)
T PRK05901 466 QPKTLDEIGQVYGVTRERIRQIES 489 (509)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Confidence 569999999999999999999987
No 388
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=85.39 E-value=1.9 Score=30.96 Aligned_cols=30 Identities=17% Similarity=0.091 Sum_probs=25.5
Q ss_pred HHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 38 MQGRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 38 k~~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
-.++--.|+|..|+|+.+|+|+++|.....
T Consensus 122 l~l~~~~~~~~~eIA~~lgis~~tv~~~~~ 151 (161)
T TIGR02985 122 FILSRFEGKSYKEIAEELGISVKTVEYHIS 151 (161)
T ss_pred HHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 345667899999999999999999988753
No 389
>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=85.24 E-value=3.5 Score=24.90 Aligned_cols=19 Identities=21% Similarity=0.368 Sum_probs=16.8
Q ss_pred CHHHHHHHhCCCHHHHHHH
Q psy6501 47 SQKDLATKINEKPQIVNDY 65 (174)
Q Consensus 47 tq~eLA~~igvs~~~is~~ 65 (174)
|..+||+.+|+|+++|++.
T Consensus 27 ~~~~la~~~~is~~~v~~~ 45 (66)
T cd07377 27 SERELAEELGVSRTTVREA 45 (66)
T ss_pred CHHHHHHHHCCCHHHHHHH
Confidence 4999999999999998854
No 390
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=85.18 E-value=1.6 Score=28.59 Aligned_cols=23 Identities=13% Similarity=0.200 Sum_probs=20.8
Q ss_pred cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 44 KGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 44 ~gltq~eLA~~igvs~~~is~~E 66 (174)
.++|..|+|+.+|+++++++++-
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~l 41 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLL 41 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHH
Confidence 47999999999999999998874
No 391
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=85.11 E-value=1.9 Score=32.07 Aligned_cols=30 Identities=13% Similarity=0.117 Sum_probs=25.5
Q ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 37 LMQGRQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 37 ik~~R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
+-.++.-.|+|.+|+|+.+|+|.+||...-
T Consensus 142 v~~l~~~~g~s~~EIA~~lgis~~tVk~~l 171 (183)
T TIGR02999 142 VVELRFFAGLTVEEIAELLGVSVRTVERDW 171 (183)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 445577899999999999999999998764
No 392
>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=85.05 E-value=1.4 Score=31.02 Aligned_cols=24 Identities=21% Similarity=0.429 Sum_probs=21.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501 46 WSQKDLATKINEKPQIVNDYEGGR 69 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~G~ 69 (174)
++..|+|+.+|||..||.-||+-.
T Consensus 1 ~~Igeva~~~gvs~~tlRyYe~~G 24 (118)
T cd04776 1 YTISELAREFDVTPRTLRFYEDKG 24 (118)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCC
Confidence 578899999999999999999643
No 393
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=85.04 E-value=4.6 Score=32.23 Aligned_cols=18 Identities=17% Similarity=0.088 Sum_probs=14.1
Q ss_pred hcCCCHHHHHHHhCCChh
Q psy6501 133 AKGWSQKDLATKINEKPQ 150 (174)
Q Consensus 133 ~~glsq~ela~~lg~~~s 150 (174)
..+++..++|..+|.+..
T Consensus 249 ~t~~sI~eIA~~~GF~s~ 266 (287)
T TIGR02297 249 FTQHSINQIAYDLGYKDP 266 (287)
T ss_pred cCCCCHHHHHHHhCCCCH
Confidence 466889999999988753
No 394
>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=84.86 E-value=1.5 Score=30.20 Aligned_cols=27 Identities=19% Similarity=0.004 Sum_probs=23.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCC
Q psy6501 46 WSQKDLATKINEKPQIVNDYEGGRGIP 72 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~G~~~P 72 (174)
|+..|+|+.+|||..||.-||+-.-.|
T Consensus 1 m~Ige~a~~~gvs~~tlRyYe~~GLl~ 27 (107)
T cd04777 1 MKIGKFAKKNNITIDTVRHYIDLGLLI 27 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCcC
Confidence 578999999999999999999755443
No 395
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=84.85 E-value=1.8 Score=30.34 Aligned_cols=28 Identities=21% Similarity=0.113 Sum_probs=24.2
Q ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 40 GRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 40 ~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
++--.|+|..++|+.+|+|+++|+++-+
T Consensus 121 ~~~~~g~s~~eIA~~l~~s~~~v~~~~~ 148 (158)
T TIGR02937 121 LRYLEGLSYKEIAEILGISVGTVKRRLK 148 (158)
T ss_pred hHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3446799999999999999999998864
No 396
>PRK12423 LexA repressor; Provisional
Probab=84.81 E-value=3.7 Score=31.64 Aligned_cols=35 Identities=9% Similarity=0.153 Sum_probs=30.0
Q ss_pred hHHHHHHHHHHHHHcCC--CHHHHHHHhC-CCHHHHHH
Q psy6501 30 PLDLAKLLMQGRQAKGW--SQKDLATKIN-EKPQIVND 64 (174)
Q Consensus 30 ~~~ig~~ik~~R~~~gl--tq~eLA~~ig-vs~~~is~ 64 (174)
...+-++|+..-.+.|+ |..|||+.+| +|+++|+.
T Consensus 8 q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~ 45 (202)
T PRK12423 8 RAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARK 45 (202)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHH
Confidence 45778888888888898 9999999999 59998873
No 397
>TIGR00180 parB_part ParB-like partition proteins. This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.
Probab=84.77 E-value=3.3 Score=31.45 Aligned_cols=50 Identities=18% Similarity=0.190 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHH
Q psy6501 121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKME 171 (174)
Q Consensus 121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~ 171 (174)
.+....+.......|++++++|+.+|++.++|+++-+=-..|+ .++..+.
T Consensus 106 ~e~a~~~~~l~~~~g~s~~~iA~~lg~s~~~V~r~l~l~~lp~-~v~~~~~ 155 (187)
T TIGR00180 106 IEEAQAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLRLLKLPS-EIQSAIP 155 (187)
T ss_pred HHHHHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHHHHcCCH-HHHHHHH
Confidence 3344455555556899999999999999999999988766443 4444443
No 398
>PF13518 HTH_28: Helix-turn-helix domain
Probab=84.71 E-value=1.3 Score=25.89 Aligned_cols=24 Identities=17% Similarity=0.215 Sum_probs=21.5
Q ss_pred cCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 134 KGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 134 ~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
.|.|..++|..+|++++++..|-.
T Consensus 11 ~g~s~~~~a~~~gis~~tv~~w~~ 34 (52)
T PF13518_consen 11 EGESVREIAREFGISRSTVYRWIK 34 (52)
T ss_pred cCCCHHHHHHHHCCCHhHHHHHHH
Confidence 577999999999999999988865
No 399
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=84.70 E-value=2 Score=33.49 Aligned_cols=36 Identities=17% Similarity=0.154 Sum_probs=26.0
Q ss_pred hHHHHHHHHHHHHH--------cCCCHHHHHHHhCCCHHHHHHH
Q psy6501 30 PLDLAKLLMQGRQA--------KGWSQKDLATKINEKPQIVNDY 65 (174)
Q Consensus 30 ~~~ig~~ik~~R~~--------~gltq~eLA~~igvs~~~is~~ 65 (174)
...+...|..+.+. ..+||++||..+|+++.++|+.
T Consensus 156 ~~Rla~~Ll~l~~~~g~~~~i~i~lt~~~IA~~lGisretlsR~ 199 (230)
T PRK09391 156 MERVAAFLLEMDERLGGAGMMALPMSRRDIADYLGLTIETVSRA 199 (230)
T ss_pred HHHHHHHHHHHHHHhCCCCEEEecCCHHHHHHHHCCCHHHHHHH
Confidence 34455555555443 3479999999999999998884
No 400
>PRK05572 sporulation sigma factor SigF; Validated
Probab=84.69 E-value=18 Score=28.62 Aligned_cols=38 Identities=16% Similarity=0.081 Sum_probs=28.6
Q ss_pred ccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 119 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 119 ~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
++......+ ..+-..|+|++++|+.+|+++++|+.+++
T Consensus 203 L~~~~~~v~-~l~~~~~~s~~eIA~~lgis~~~V~~~~~ 240 (252)
T PRK05572 203 LDERERLIV-YLRYFKDKTQSEVAKRLGISQVQVSRLEK 240 (252)
T ss_pred CCHHHHHHH-HHHHhCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 333333444 34556899999999999999999998876
No 401
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=84.44 E-value=0.98 Score=34.12 Aligned_cols=23 Identities=13% Similarity=0.083 Sum_probs=20.2
Q ss_pred cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 44 KGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 44 ~gltq~eLA~~igvs~~~is~~E 66 (174)
..+||++||..+|+++.+||+.-
T Consensus 148 ~~~t~~~iA~~lG~tretvsR~l 170 (202)
T PRK13918 148 IYATHDELAAAVGSVRETVTKVI 170 (202)
T ss_pred ecCCHHHHHHHhCccHHHHHHHH
Confidence 35799999999999999999854
No 402
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=84.43 E-value=1.9 Score=29.39 Aligned_cols=29 Identities=24% Similarity=0.282 Sum_probs=23.6
Q ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501 37 LMQGRQAKGWSQKDLATKINEKPQIVNDY 65 (174)
Q Consensus 37 ik~~R~~~gltq~eLA~~igvs~~~is~~ 65 (174)
|+.+...-.+|..+||+.+|+|++++++.
T Consensus 9 l~~L~~~~~~~~~~la~~l~~s~~tv~~~ 37 (108)
T smart00344 9 LEELQKDARISLAELAKKVGLSPSTVHNR 37 (108)
T ss_pred HHHHHHhCCCCHHHHHHHHCcCHHHHHHH
Confidence 44555556799999999999999998764
No 403
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=84.35 E-value=2.1 Score=31.49 Aligned_cols=29 Identities=17% Similarity=0.063 Sum_probs=24.8
Q ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 39 QGRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 39 ~~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
.++.-.|+|.+|+|+.+|+|.++|+.+-.
T Consensus 138 ~l~~~~~~s~~eIA~~lgis~~tV~~~l~ 166 (182)
T PRK09652 138 TLREIEGLSYEEIAEIMGCPIGTVRSRIF 166 (182)
T ss_pred HHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34566899999999999999999987754
No 404
>TIGR02895 spore_sigI RNA polymerase sigma-I factor. Members of this sigma factor protein family are strictly limited to endospore-forming species in the Firmicutes lineage of bacteria, but are not universally present among such species. Sigma-I was shown to be induced by heat shock (PubMed:11157964) in Bacillus subtilis and is suggested by its phylogenetic profile to be connected to the program of sporulation (PubMed:16311624).
Probab=84.33 E-value=6 Score=31.06 Aligned_cols=78 Identities=15% Similarity=0.177 Sum_probs=48.9
Q ss_pred CCCCHHHHH---HHHHHhCcccccccCCCCCCCCCcccchhhhhhhhhhcccccHHHHHHHHHHHHhcCCCHHHHHHHhC
Q psy6501 70 GIPNQAIIG---KMERALGIRLRVNAGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKIN 146 (174)
Q Consensus 70 ~~P~~~~l~---~la~~L~v~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~R~~~glsq~ela~~lg 146 (174)
+.|..+.+. +.-..||++.++|......|.. .-...............+.....+.+.+..+++++.++
T Consensus 116 ~~~~~eEI~~~~~~L~~~gi~~~dLv~~sPkh~d--------~r~~~i~ia~~~~~~~~l~~~l~~kk~LP~k~l~~~~~ 187 (218)
T TIGR02895 116 NENRRLEILEYKKLLKQFGIEFVELVKVSPKHRD--------TRKKAIKIAKVIVENEELLEYLIRKKKLPIKEIEERVR 187 (218)
T ss_pred cccHHHHHHHHHHHHHHcCCcHHHHhhcCCCCHH--------HHHHHHHHHHHHhcCHHHHHHHHHhCCCCHHHHHHHcC
Confidence 455555544 4445689999999854443321 11111111122223345667778889999999999999
Q ss_pred CChhHHHHH
Q psy6501 147 EKPQIVNDY 155 (174)
Q Consensus 147 ~~~s~i~~~ 155 (174)
+++.|+.++
T Consensus 188 v~rktier~ 196 (218)
T TIGR02895 188 ISRKTIERY 196 (218)
T ss_pred CCHHHHHHh
Confidence 999998654
No 405
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=84.28 E-value=1.6 Score=27.11 Aligned_cols=22 Identities=14% Similarity=0.215 Sum_probs=19.9
Q ss_pred CCHHHHHHHhCCChhHHHHHhc
Q psy6501 136 WSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 136 lsq~ela~~lg~~~s~i~~~E~ 157 (174)
++..++|+.+|++++++..|+.
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999976
No 406
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=84.28 E-value=1 Score=34.20 Aligned_cols=22 Identities=5% Similarity=0.135 Sum_probs=20.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHH
Q psy6501 45 GWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 45 gltq~eLA~~igvs~~~is~~E 66 (174)
.+||++||+.+|+++.+||+.-
T Consensus 168 ~~t~~~lA~~lG~tr~tvsR~l 189 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGRVL 189 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHHHH
Confidence 5899999999999999999864
No 407
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=84.19 E-value=2 Score=34.31 Aligned_cols=28 Identities=18% Similarity=0.100 Sum_probs=24.8
Q ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 40 GRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 40 ~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
+|--.|+|++|+|+.+|+|.++|+++..
T Consensus 214 l~y~~~~s~~eIA~~lgvs~~~V~~~~~ 241 (256)
T PRK07408 214 FVFLHDLTQKEAAERLGISPVTVSRRVK 241 (256)
T ss_pred HHHHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 4555799999999999999999999974
No 408
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=84.19 E-value=2.1 Score=31.25 Aligned_cols=30 Identities=23% Similarity=0.246 Sum_probs=25.7
Q ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
.+-.++. .|+|.+|+|+.+|+|.++|...-
T Consensus 119 ~il~l~~-~g~s~~eIA~~lgis~~tV~~~i 148 (166)
T PRK09639 119 TVLLLRF-SGYSYKEIAEALGIKESSVGTTL 148 (166)
T ss_pred HHHHHHH-cCCCHHHHHHHHCCCHHHHHHHH
Confidence 3445667 99999999999999999998875
No 409
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=84.18 E-value=1.6 Score=29.40 Aligned_cols=27 Identities=7% Similarity=0.148 Sum_probs=24.5
Q ss_pred HhcCCCHHHHHHHhCCChhHHHHHhcC
Q psy6501 132 QAKGWSQKDLATKINEKPQIVNDYEGG 158 (174)
Q Consensus 132 ~~~glsq~ela~~lg~~~s~i~~~E~G 158 (174)
...|+|..++|+.+|++++||.++-+|
T Consensus 47 l~~G~S~~eIA~~LgISrsTIyRi~R~ 73 (88)
T TIGR02531 47 LKQGKTYSDIEAETGASTATISRVKRC 73 (88)
T ss_pred HHCCCCHHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999999999885
No 410
>PRK13503 transcriptional activator RhaS; Provisional
Probab=84.08 E-value=6.5 Score=31.15 Aligned_cols=17 Identities=18% Similarity=0.040 Sum_probs=14.1
Q ss_pred cCCCHHHHHHHhCCChh
Q psy6501 134 KGWSQKDLATKINEKPQ 150 (174)
Q Consensus 134 ~glsq~ela~~lg~~~s 150 (174)
.+++..++|..+|.+..
T Consensus 235 ~~~sI~eIA~~~GF~~~ 251 (278)
T PRK13503 235 SDASVTDIAYRCGFGDS 251 (278)
T ss_pred CCCCHHHHHHHhCCCCH
Confidence 46899999999998764
No 411
>PRK13501 transcriptional activator RhaR; Provisional
Probab=84.07 E-value=6.1 Score=31.79 Aligned_cols=16 Identities=13% Similarity=0.119 Sum_probs=10.2
Q ss_pred cCCCHHHHHHHhCCCh
Q psy6501 134 KGWSQKDLATKINEKP 149 (174)
Q Consensus 134 ~glsq~ela~~lg~~~ 149 (174)
-.++..++|..+|.+-
T Consensus 240 t~~sI~eIA~~~GF~~ 255 (290)
T PRK13501 240 SEHRISDIAARCGFED 255 (290)
T ss_pred CCCCHHHHHHHhCCCC
Confidence 4466777777777643
No 412
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=84.06 E-value=5.2 Score=25.54 Aligned_cols=19 Identities=21% Similarity=0.167 Sum_probs=11.9
Q ss_pred HhcCCCHHHHHHHhCCChh
Q psy6501 132 QAKGWSQKDLATKINEKPQ 150 (174)
Q Consensus 132 ~~~glsq~ela~~lg~~~s 150 (174)
...+++..++|..+|.+..
T Consensus 42 ~~~~~~i~~ia~~~Gf~~~ 60 (81)
T PF12833_consen 42 QNTDLSIAEIAEECGFSSQ 60 (81)
T ss_dssp HHTT--HHHHHHHTT-SSH
T ss_pred HhhcccHHHHHHHcCCCCH
Confidence 3467888888888888753
No 413
>PRK13502 transcriptional activator RhaR; Provisional
Probab=83.94 E-value=5.1 Score=31.96 Aligned_cols=16 Identities=0% Similarity=-0.039 Sum_probs=12.3
Q ss_pred cCCCHHHHHHHhCCCh
Q psy6501 134 KGWSQKDLATKINEKP 149 (174)
Q Consensus 134 ~glsq~ela~~lg~~~ 149 (174)
-.++..++|..+|.+-
T Consensus 240 t~~sI~eIA~~~GF~d 255 (282)
T PRK13502 240 SPLMISEISMQCGFED 255 (282)
T ss_pred CCCCHHHHHHHcCCCC
Confidence 3578888888888775
No 414
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=83.77 E-value=0.98 Score=36.23 Aligned_cols=28 Identities=25% Similarity=0.443 Sum_probs=24.5
Q ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501 42 QAKGWSQKDLATKINEKPQIVNDYEGGR 69 (174)
Q Consensus 42 ~~~gltq~eLA~~igvs~~~is~~E~G~ 69 (174)
--.||..+++|+++|||++||..|-+-.
T Consensus 16 yl~gmk~~dIAeklGvspntiksWKrr~ 43 (279)
T COG5484 16 YLKGMKLKDIAEKLGVSPNTIKSWKRRD 43 (279)
T ss_pred HHhhccHHHHHHHhCCChHHHHHHHHhc
Confidence 3467999999999999999999998644
No 415
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 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 [].; PDB: 2WTE_A 3SQN_A.
Probab=83.72 E-value=2.1 Score=26.24 Aligned_cols=30 Identities=23% Similarity=0.145 Sum_probs=23.8
Q ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 37 LMQGRQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 37 ik~~R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
|..+-+...+|..+||+.+|+|..+|.++-
T Consensus 11 l~~L~~~~~~~~~ela~~l~~S~rti~~~i 40 (59)
T PF08280_consen 11 LELLLKNKWITLKELAKKLNISERTIKNDI 40 (59)
T ss_dssp HHHHHHHTSBBHHHHHHHCTS-HHHHHHHH
T ss_pred HHHHHcCCCCcHHHHHHHHCCCHHHHHHHH
Confidence 344556788999999999999999998764
No 416
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=83.66 E-value=3.2 Score=27.24 Aligned_cols=38 Identities=16% Similarity=0.080 Sum_probs=28.1
Q ss_pred chHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 29 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 29 ~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
+...--.-|..+....++|+.++|+.+++++++|++.-
T Consensus 8 l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l 45 (101)
T smart00347 8 LTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVL 45 (101)
T ss_pred CCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHH
Confidence 33344445556666668999999999999999888654
No 417
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=83.62 E-value=1.4 Score=27.81 Aligned_cols=30 Identities=20% Similarity=0.194 Sum_probs=20.8
Q ss_pred HHHH-HHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501 36 LLMQ-GRQAKGWSQKDLATKINEKPQIVNDY 65 (174)
Q Consensus 36 ~ik~-~R~~~gltq~eLA~~igvs~~~is~~ 65 (174)
.|+. +++...+|..|||..+++++++|..+
T Consensus 4 ~i~~~l~~~~~~S~~eLa~~~~~s~~~ve~m 34 (69)
T PF09012_consen 4 EIRDYLRERGRVSLAELAREFGISPEAVEAM 34 (69)
T ss_dssp HHHHHHHHS-SEEHHHHHHHTT--HHHHHHH
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHH
Confidence 3455 66677789999999999999877543
No 418
>PHA01082 putative transcription regulator
Probab=83.62 E-value=0.87 Score=32.38 Aligned_cols=41 Identities=17% Similarity=0.198 Sum_probs=34.7
Q ss_pred HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCC-HHHHHHHHHH
Q psy6501 43 AKGWSQKDLATKINEKPQIVNDYEGGRGIPN-QAIIGKMERA 83 (174)
Q Consensus 43 ~~gltq~eLA~~igvs~~~is~~E~G~~~P~-~~~l~~la~~ 83 (174)
+.|+|.+|-|+.+--|.++|.+|-.|+..|+ ...|.++-..
T Consensus 28 eCgLsveeaa~LCfKsVrtVk~WD~G~~IPPeCkRLMr~~~g 69 (133)
T PHA01082 28 ECGLSVEEAAKLCFKTVSEVKQWDAGEKIPPICKRLMRWHSR 69 (133)
T ss_pred ccCccHHHHHHHHHHhHHHHhhccCCCcCChHHHHHHHHhcc
Confidence 7899999999999999999999999997654 5666666544
No 419
>COG1513 CynS Cyanate lyase [Inorganic ion transport and metabolism]
Probab=83.59 E-value=5.6 Score=28.78 Aligned_cols=54 Identities=28% Similarity=0.260 Sum_probs=47.7
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501 121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174 (174)
Q Consensus 121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l 174 (174)
..+.+.+-...+.+|+|=+|++..+|.++-.+...-.|....+.+-+++++++|
T Consensus 7 ~~l~~~ll~~Kk~kgLsfaDl~~~lG~~ev~vaa~~ygqa~~~~~ear~v~e~L 60 (151)
T COG1513 7 LDLADALLLAKKKKGLSFADLADGLGLAEVFVAAALYGQAALPADEARAVGEAL 60 (151)
T ss_pred HHHHHHHHHHHHhcCCcHHHHHhhcCccHHHHHHHHHhhccCCHHHHHHHHHHh
Confidence 445667777888999999999999999999999999999999999999888765
No 420
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=83.51 E-value=2.5 Score=30.56 Aligned_cols=27 Identities=26% Similarity=0.225 Sum_probs=23.6
Q ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501 39 QGRQAKGWSQKDLATKINEKPQIVNDY 65 (174)
Q Consensus 39 ~~R~~~gltq~eLA~~igvs~~~is~~ 65 (174)
.++.-.|+|.+|+|+.+|+|.++|...
T Consensus 121 ~l~~~~g~~~~eIA~~l~is~~tv~~~ 147 (159)
T TIGR02989 121 QLRYQRGVSLTALAEQLGRTVNAVYKA 147 (159)
T ss_pred HHHHhcCCCHHHHHHHhCCCHHHHHHH
Confidence 346778999999999999999999865
No 421
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=83.51 E-value=1.8 Score=32.65 Aligned_cols=28 Identities=18% Similarity=0.133 Sum_probs=24.7
Q ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 40 GRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 40 ~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
+|.-.|+|++|+|+.+|+|.++|..+-.
T Consensus 152 l~~~~g~s~~EIA~~lgis~~tV~~~l~ 179 (194)
T PRK12519 152 LAYYEGLSQSEIAKRLGIPLGTVKARAR 179 (194)
T ss_pred hhhhcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 4566899999999999999999998863
No 422
>PRK03341 arginine repressor; Provisional
Probab=83.47 E-value=2.2 Score=32.19 Aligned_cols=31 Identities=13% Similarity=0.041 Sum_probs=23.5
Q ss_pred HHHHH-HHHcCCCHHHHHHHh-----CCCHHHHHHHH
Q psy6501 36 LLMQG-RQAKGWSQKDLATKI-----NEKPQIVNDYE 66 (174)
Q Consensus 36 ~ik~~-R~~~gltq~eLA~~i-----gvs~~~is~~E 66 (174)
.|+++ ++..=-||+||++.+ ++|+.|||+.-
T Consensus 19 ~I~~li~~~~i~tQ~eL~~~L~~~Gi~vTQaTiSRDl 55 (168)
T PRK03341 19 RIVAILSRQSVRSQAELAALLADEGIEVTQATLSRDL 55 (168)
T ss_pred HHHHHHHHCCCccHHHHHHHHHHcCCcccHHHHHHHH
Confidence 34444 444455999999999 99999999854
No 423
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=83.37 E-value=3.5 Score=29.09 Aligned_cols=38 Identities=8% Similarity=-0.035 Sum_probs=29.1
Q ss_pred cHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 120 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 120 ~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
+.++...+-..-...|.+..++|..+|++++++.+|-+
T Consensus 14 s~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r 51 (121)
T PRK09413 14 TTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRK 51 (121)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34444444444456899999999999999999999954
No 424
>PF13309 HTH_22: HTH domain
Probab=83.32 E-value=3.6 Score=25.75 Aligned_cols=28 Identities=21% Similarity=0.186 Sum_probs=22.1
Q ss_pred HHHHHcCC-----CHHHHHHHhCCCHHHHHHHH
Q psy6501 39 QGRQAKGW-----SQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 39 ~~R~~~gl-----tq~eLA~~igvs~~~is~~E 66 (174)
....++|+ +-..+|+.+|||+.||.+|-
T Consensus 31 ~~L~~~G~F~lKgav~~vA~~L~iS~~TVY~YL 63 (64)
T PF13309_consen 31 RQLYEKGIFLLKGAVEYVAEKLGISRATVYRYL 63 (64)
T ss_pred HHHHHCCCcccCcHHHHHHHHHCCCHHHHHHHc
Confidence 34455665 77889999999999999884
No 425
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=83.29 E-value=5.5 Score=22.92 Aligned_cols=29 Identities=17% Similarity=0.223 Sum_probs=23.4
Q ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501 37 LMQGRQAKGWSQKDLATKINEKPQIVNDY 65 (174)
Q Consensus 37 ik~~R~~~gltq~eLA~~igvs~~~is~~ 65 (174)
+-.-+--.++|..++|+++|+|++++.++
T Consensus 8 l~~~~G~~~~s~~~Ia~~~gvs~~~~y~~ 36 (47)
T PF00440_consen 8 LFAEKGYEAVSIRDIARRAGVSKGSFYRY 36 (47)
T ss_dssp HHHHHHTTTSSHHHHHHHHTSCHHHHHHH
T ss_pred HHHHhCHHhCCHHHHHHHHccchhhHHHH
Confidence 33344556889999999999999999876
No 426
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=83.28 E-value=1.3 Score=34.15 Aligned_cols=25 Identities=16% Similarity=0.222 Sum_probs=22.9
Q ss_pred HHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 42 QAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 42 ~~~gltq~eLA~~igvs~~~is~~E 66 (174)
-..|+|-+|+|+++++|.+||..+-
T Consensus 149 la~G~snkeIA~~L~iS~~TVk~h~ 173 (207)
T PRK15411 149 WMAGQGTIQISDQMNIKAKTVSSHK 173 (207)
T ss_pred HHcCCCHHHHHHHcCCCHHHHHHHH
Confidence 4689999999999999999999875
No 427
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=83.27 E-value=2.3 Score=33.76 Aligned_cols=29 Identities=17% Similarity=0.146 Sum_probs=25.6
Q ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 39 QGRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 39 ~~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
.++--.|+|++|+|+.+|+|.++|+.+..
T Consensus 215 ~l~~~~g~s~~eIA~~l~is~~tV~~~~~ 243 (257)
T PRK08583 215 QCTFIENLSQKETGERLGISQMHVSRLQR 243 (257)
T ss_pred HHHHhCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34567899999999999999999999974
No 428
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=83.25 E-value=2 Score=34.50 Aligned_cols=31 Identities=13% Similarity=0.124 Sum_probs=26.2
Q ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 37 LMQGRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 37 ik~~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
+-.+|-..|+|++|+|+.+|+|.++|++++.
T Consensus 223 vl~l~y~~~~t~~EIA~~lgis~~~V~~~~~ 253 (264)
T PRK07122 223 VLVLRFFESMTQTQIAERVGISQMHVSRLLA 253 (264)
T ss_pred HHHHHhcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3345556799999999999999999999875
No 429
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR. 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-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.
Probab=83.24 E-value=1.8 Score=31.64 Aligned_cols=22 Identities=18% Similarity=0.219 Sum_probs=20.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q psy6501 46 WSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 46 ltq~eLA~~igvs~~~is~~E~ 67 (174)
||..|+|+.+|||..||.-||+
T Consensus 2 ~~IgevA~~~Gvs~~tLRyYE~ 23 (142)
T TIGR01950 2 LTVGELAKRSGVAVSALHFYES 23 (142)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 6889999999999999999994
No 430
>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=83.23 E-value=4.5 Score=20.56 Aligned_cols=23 Identities=22% Similarity=0.335 Sum_probs=20.6
Q ss_pred hcCCCHHHHHHHhCCChhHHHHH
Q psy6501 133 AKGWSQKDLATKINEKPQIVNDY 155 (174)
Q Consensus 133 ~~glsq~ela~~lg~~~s~i~~~ 155 (174)
..+++..++++.+|++.+++..|
T Consensus 19 ~~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 19 AAGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHh
Confidence 46789999999999999999876
No 431
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=83.19 E-value=2.7 Score=32.20 Aligned_cols=42 Identities=14% Similarity=0.109 Sum_probs=29.2
Q ss_pred cccccchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501 24 LKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDY 65 (174)
Q Consensus 24 ~~~~~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~ 65 (174)
+++-.+...=...|..+....|+||++||+.++++++|++++
T Consensus 38 l~~~gLt~~q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~ 79 (185)
T PRK13777 38 IKPYDLNINEHHILWIAYHLKGASISEIAKFGVMHVSTAFNF 79 (185)
T ss_pred HHHCCCCHHHHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHH
Confidence 333344434345566677777899999999999988887764
No 432
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=83.09 E-value=5.1 Score=30.27 Aligned_cols=42 Identities=12% Similarity=0.133 Sum_probs=32.2
Q ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Q psy6501 39 QGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIR 87 (174)
Q Consensus 39 ~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~ 87 (174)
.++--.|+|.+|+|+.+|+|.++|...-. .-+.+|...|+++
T Consensus 152 ~l~~~~~~s~~EIA~~Lgis~~tVk~~l~-------ra~~~Lr~~l~~~ 193 (194)
T PRK09646 152 TLAYYGGLTYREVAERLAVPLGTVKTRMR-------DGLIRLRDCLGVS 193 (194)
T ss_pred HHHHHcCCCHHHHHHHhCCChHhHHHHHH-------HHHHHHHHHhccC
Confidence 36678999999999999999999988753 4455666665543
No 433
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=82.94 E-value=1.4 Score=31.10 Aligned_cols=26 Identities=12% Similarity=0.192 Sum_probs=22.4
Q ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 41 RQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 41 R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
-..-++|+.|+|+.+|||.++|+..-
T Consensus 67 ~~~pd~tl~Ela~~l~Vs~~ti~~~L 92 (119)
T PF01710_consen 67 EENPDATLRELAERLGVSPSTIWRAL 92 (119)
T ss_pred HHCCCcCHHHHHHHcCCCHHHHHHHH
Confidence 34689999999999999999988765
No 434
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=82.87 E-value=2.7 Score=30.45 Aligned_cols=30 Identities=10% Similarity=-0.064 Sum_probs=25.4
Q ss_pred HHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 38 MQGRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 38 k~~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
-.++.-.|+|.+|+|+.+|+|.++|...-.
T Consensus 115 ~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ 144 (161)
T PRK09047 115 FLLRYWEDMDVAETAAAMGCSEGSVKTHCS 144 (161)
T ss_pred HHHHHHhcCCHHHHHHHHCCCHHHHHHHHH
Confidence 345677899999999999999999987753
No 435
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=82.71 E-value=3.5 Score=24.64 Aligned_cols=32 Identities=19% Similarity=0.048 Sum_probs=26.1
Q ss_pred HHHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 126 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 126 ~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
.+--.+-+.+.+..++|...|++.+++++|=+
T Consensus 10 ll~L~~LR~~~~~~~La~~FgIs~stvsri~~ 41 (53)
T PF13613_consen 10 LLTLMYLRLNLTFQDLAYRFGISQSTVSRIFH 41 (53)
T ss_pred HHHHHHHHcCCcHhHHhhheeecHHHHHHHHH
Confidence 44445667899999999999999999988743
No 436
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=82.51 E-value=2.7 Score=31.33 Aligned_cols=31 Identities=6% Similarity=0.128 Sum_probs=26.2
Q ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 37 LMQGRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 37 ik~~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
+-.++.-.|+|.+|+|+.+|+|.++|...-.
T Consensus 143 vl~l~~~~~~s~~eIA~~lgis~~~V~~~l~ 173 (186)
T PRK13919 143 VIEVLYYQGYTHREAAQLLGLPLGTLKTRAR 173 (186)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3345778999999999999999999998764
No 437
>PRK06030 hypothetical protein; Provisional
Probab=82.47 E-value=6 Score=28.35 Aligned_cols=62 Identities=16% Similarity=0.232 Sum_probs=40.8
Q ss_pred HHHHHHHHHHhCcccccccCCCCCCCCCcccchhhhhhhhhhcccccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHH
Q psy6501 74 QAIIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVN 153 (174)
Q Consensus 74 ~~~l~~la~~L~v~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~ 153 (174)
...+..+|++|||+++++.+......... ..-.+...| .|+..++|..++++.+|.+.++|.
T Consensus 26 d~Ii~~Va~~f~I~~~di~sk~R~rk~i~----------------~aRqIAMYL--~r~~~~~sl~~IG~~FGRDHSTV~ 87 (124)
T PRK06030 26 EAVIDLLALAFGVSGAEIASPLRGRREVS----------------RIRQIAMYV--AHVSLGWPMNEVALAFGRDRTTVG 87 (124)
T ss_pred HHHHHHHHHHhCCCHHHHhCCCCCCcccc----------------hHHHHHHHH--HHHHcCCCHHHHHHHHCCChhHHH
Confidence 45566899999999999986443211000 112222333 577789999999999998777653
No 438
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=82.46 E-value=2.4 Score=33.26 Aligned_cols=31 Identities=6% Similarity=0.086 Sum_probs=26.4
Q ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 37 LMQGRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 37 ik~~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
+-.+|-..|+|.+|+|+.+|+|.++|..+..
T Consensus 192 vl~l~~~~g~s~~EIA~~lgis~~tV~~~~~ 222 (236)
T PRK06986 192 VLSLYYQEELNLKEIGAVLGVSESRVSQIHS 222 (236)
T ss_pred HHHhHhccCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3345667899999999999999999998874
No 439
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=82.44 E-value=3 Score=32.77 Aligned_cols=36 Identities=8% Similarity=0.052 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHH--HcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 31 LDLAKLLMQGRQ--AKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 31 ~~ig~~ik~~R~--~~gltq~eLA~~igvs~~~is~~E 66 (174)
..--..|++.-+ ...+|-+|+|+.+|+|+.|+.+|-
T Consensus 157 ~~Tl~~i~~~~~~~~~~~Taeela~~~giSRvTaRRYL 194 (224)
T COG4565 157 ELTLQKVREALKEPDQELTAEELAQALGISRVTARRYL 194 (224)
T ss_pred HHHHHHHHHHHhCcCCccCHHHHHHHhCccHHHHHHHH
Confidence 333445555555 678999999999999999999984
No 440
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 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 recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=82.39 E-value=3.7 Score=24.22 Aligned_cols=31 Identities=16% Similarity=0.149 Sum_probs=21.6
Q ss_pred HHHHHHHHhcCCCHHHHHHHhCCChhHHHHH
Q psy6501 125 KLLMQGRQAKGWSQKDLATKINEKPQIVNDY 155 (174)
Q Consensus 125 ~~i~~~R~~~glsq~ela~~lg~~~s~i~~~ 155 (174)
..+-..+-..|+|.+++|+.+|++++++..+
T Consensus 16 r~i~~l~~~~g~s~~eIa~~l~~s~~~v~~~ 46 (54)
T PF08281_consen 16 REIFLLRYFQGMSYAEIAEILGISESTVKRR 46 (54)
T ss_dssp HHHHHHHHTS---HHHHHHHCTS-HHHHHHH
T ss_pred HHHHHHHHHHCcCHHHHHHHHCcCHHHHHHH
Confidence 3444566779999999999999999988765
No 441
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=82.38 E-value=2.3 Score=34.73 Aligned_cols=36 Identities=22% Similarity=0.271 Sum_probs=29.4
Q ss_pred cCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCc
Q psy6501 44 KGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI 86 (174)
Q Consensus 44 ~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v 86 (174)
.|+|++|+|+.+|||+.+|++++. .-+.+|-..|..
T Consensus 244 ~~~t~~EIa~~lgvs~~~V~q~~~-------~Al~kLr~~l~~ 279 (289)
T PRK07500 244 DGATLEALGEELGISKERVRQIEA-------RALEKLRRALLS 279 (289)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH-------HHHHHHHHHHHh
Confidence 689999999999999999999985 455566665543
No 442
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=82.21 E-value=4.5 Score=34.44 Aligned_cols=24 Identities=8% Similarity=0.138 Sum_probs=21.9
Q ss_pred cCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 134 KGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 134 ~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
.++|.+++|+.+|+++..|..+|.
T Consensus 330 ~~~Tl~EIA~~lgiS~eRVRQie~ 353 (373)
T PRK07406 330 RMKTLEEIGQIFNVTRERIRQIEA 353 (373)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHH
Confidence 358999999999999999999886
No 443
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=82.13 E-value=3 Score=31.11 Aligned_cols=29 Identities=24% Similarity=0.288 Sum_probs=25.0
Q ss_pred HHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 38 MQGRQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 38 k~~R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
-.+|.-.|+|.+|+|+.+|+|.+||...-
T Consensus 136 ~~L~~~~g~s~~EIA~~lgis~~tVk~~l 164 (178)
T PRK12529 136 FLMATLDGMKQKDIAQALDIALPTVKKYI 164 (178)
T ss_pred HHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 44667789999999999999999998764
No 444
>PRK01905 DNA-binding protein Fis; Provisional
Probab=81.86 E-value=4.1 Score=26.42 Aligned_cols=33 Identities=15% Similarity=-0.006 Sum_probs=28.8
Q ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
...|+...+..|-++.+.|+.+|+|++++...-
T Consensus 39 ~~~i~~aL~~~~gn~s~aAr~LGIsrstL~rkl 71 (77)
T PRK01905 39 KPLLEVVMEQAGGNQSLAAEYLGINRNTLRKKL 71 (77)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 446888999999999999999999999987654
No 445
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=81.75 E-value=15 Score=29.02 Aligned_cols=32 Identities=13% Similarity=0.158 Sum_probs=26.1
Q ss_pred HHHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 126 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 126 ~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
.+-.++-..|+|.+++|+.+|+++++|..+.+
T Consensus 212 ~ii~l~~~~g~s~~eIA~~lgis~~~V~~~~~ 243 (255)
T TIGR02941 212 SIIHCTFEENLSQKETGERLGISQMHVSRLQR 243 (255)
T ss_pred HHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34455557899999999999999999987764
No 446
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=81.67 E-value=2.9 Score=33.43 Aligned_cols=31 Identities=10% Similarity=0.046 Sum_probs=26.5
Q ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 37 LMQGRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 37 ik~~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
|-.+|--.|+|++|+|+.+|+|.++|++++.
T Consensus 213 vi~l~y~e~~t~~EIA~~lgis~~~V~~~~~ 243 (257)
T PRK05911 213 VMALYYYEELVLKEIGKILGVSESRVSQIHS 243 (257)
T ss_pred HHHHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3345556899999999999999999999985
No 447
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=81.66 E-value=1.6 Score=30.39 Aligned_cols=26 Identities=15% Similarity=0.182 Sum_probs=22.1
Q ss_pred HhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 132 QAKGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 132 ~~~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
-..|++|++.|+.+|+|.+|+.++-.
T Consensus 54 D~egl~QeeaA~~MgVSR~T~~ril~ 79 (106)
T PF02001_consen 54 DYEGLSQEEAAERMGVSRPTFQRILE 79 (106)
T ss_pred HHcCCCHHHHHHHcCCcHHHHHHHHH
Confidence 35889999999999999998877543
No 448
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=81.61 E-value=2.4 Score=34.70 Aligned_cols=25 Identities=12% Similarity=0.238 Sum_probs=23.1
Q ss_pred HcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 43 AKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 43 ~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
..++|.+|+|+.+|+|+.+|.+++.
T Consensus 267 ~~~~Tl~EIa~~lgiS~erVrq~~~ 291 (298)
T TIGR02997 267 GEPLTLAEIGRRLNLSRERVRQIEA 291 (298)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 3689999999999999999999985
No 449
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=81.52 E-value=2 Score=32.95 Aligned_cols=26 Identities=12% Similarity=0.167 Sum_probs=22.8
Q ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 42 QAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 42 ~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
-..|+|-+|+|+.+++|++||..+-+
T Consensus 145 LAqGkTnKEIAe~L~IS~rTVkth~s 170 (198)
T PRK15201 145 IASGYHLSETAALLSLSEEQTKSLRR 170 (198)
T ss_pred HHCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 35799999999999999999988753
No 450
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=81.46 E-value=2.9 Score=31.45 Aligned_cols=30 Identities=17% Similarity=-0.018 Sum_probs=25.9
Q ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 37 LMQGRQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 37 ik~~R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
+-.+|.-.|+|.+|+|+.+|+|.++|...-
T Consensus 138 v~~L~~~~g~s~~EIA~~lgis~~tVk~~l 167 (185)
T PRK09649 138 ALLLTQLLGLSYADAAAVCGCPVGTIRSRV 167 (185)
T ss_pred HhhhHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 344678899999999999999999998775
No 451
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=81.44 E-value=2.1 Score=31.76 Aligned_cols=29 Identities=14% Similarity=0.098 Sum_probs=24.7
Q ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHHcC
Q psy6501 40 GRQAKGWSQKDLATKINEKPQIVNDYEGG 68 (174)
Q Consensus 40 ~R~~~gltq~eLA~~igvs~~~is~~E~G 68 (174)
-|...=||..|+|+.+|||..||.-||.-
T Consensus 6 ~~~~~~~~IgevAk~~gvs~~TlRyYE~~ 34 (154)
T PRK15002 6 PRIKALLTPGEVAKRSGVAVSALHFYESK 34 (154)
T ss_pred hhhcccccHHHHHHHHCcCHHHHHHHHHC
Confidence 35555689999999999999999999943
No 452
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=81.39 E-value=3.3 Score=30.56 Aligned_cols=30 Identities=13% Similarity=0.226 Sum_probs=25.7
Q ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 37 LMQGRQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 37 ik~~R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
+-.++.-.|+|.+|+|+.+|+|.++|...-
T Consensus 127 v~~L~~~~g~s~~EIA~~lgis~~tV~~~l 156 (172)
T PRK12523 127 AFLYNRLDGMGHAEIAERLGVSVSRVRQYL 156 (172)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 335567799999999999999999998775
No 453
>PRK09954 putative kinase; Provisional
Probab=81.33 E-value=3 Score=34.77 Aligned_cols=33 Identities=15% Similarity=0.021 Sum_probs=27.8
Q ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
+-|+.+++...+|+.|||+.+|+|+++|.+.-+
T Consensus 7 ~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~ 39 (362)
T PRK09954 7 EILAILRRNPLIQQNEIADILQISRSRVAAHIM 39 (362)
T ss_pred HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 456777788899999999999999998877654
No 454
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=81.31 E-value=3.1 Score=31.05 Aligned_cols=29 Identities=14% Similarity=0.243 Sum_probs=25.3
Q ss_pred HHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 38 MQGRQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 38 k~~R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
-.++.-.|+|.+|+|+.+|+|.++|..+-
T Consensus 142 ~~l~~~~~~s~~eIA~~lgis~~tV~~~l 170 (182)
T PRK12537 142 ILHAYVDGCSHAEIAQRLGAPLGTVKAWI 170 (182)
T ss_pred HHHHHHcCCCHHHHHHHHCCChhhHHHHH
Confidence 44566799999999999999999998875
No 455
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=81.14 E-value=3.4 Score=30.01 Aligned_cols=30 Identities=10% Similarity=-0.007 Sum_probs=25.1
Q ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 37 LMQGRQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 37 ik~~R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
+-.++.-.|+|.+|+|+.+|+|.++|...-
T Consensus 114 v~~l~~~~g~s~~EIA~~lgis~~tV~~~l 143 (160)
T PRK09642 114 VVLAHYLEEKSYQEIALQEKIEVKTVEMKL 143 (160)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCHHHHHHHH
Confidence 344667789999999999999999997653
No 456
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=81.14 E-value=3.4 Score=30.43 Aligned_cols=30 Identities=17% Similarity=0.317 Sum_probs=25.0
Q ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 37 LMQGRQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 37 ik~~R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
+-.+|.-.|+|.+|+|+.+|+|.++|...-
T Consensus 126 vl~L~~~~g~s~~EIA~~lgis~~tV~~~l 155 (173)
T PRK09645 126 VLVRSYYRGWSTAQIAADLGIPEGTVKSRL 155 (173)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence 344567789999999999999999997654
No 457
>PRK14845 translation initiation factor IF-2; Provisional
Probab=81.10 E-value=2.3 Score=40.88 Aligned_cols=50 Identities=16% Similarity=0.291 Sum_probs=43.0
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Q psy6501 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIR 87 (174)
Q Consensus 33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~ 87 (174)
+..-|+.+|+..|+|+.|++. .+++.+.||+ ...|+.+.+..+-..|.-.
T Consensus 323 i~~el~~lr~~~~lt~~e~~~----~~~~Y~~~e~-~~~~s~~~l~~~l~~~~~~ 372 (1049)
T PRK14845 323 INEELKRLRLLFGFTRNELSS----NIPFYSKYES-EEAPSYEILMEILNSIERG 372 (1049)
T ss_pred cHHHHHHHHHhcCcchhhccc----cchhhhhhhc-ccCCCHHHHHHHHHHHHhc
Confidence 445689999999999999987 6899999999 9999999999887776633
No 458
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=80.94 E-value=7.2 Score=30.89 Aligned_cols=122 Identities=8% Similarity=-0.027 Sum_probs=0.0
Q ss_pred HHHHHHHHH------cCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccc---ccccCCCCCCCCCcccc
Q psy6501 35 KLLMQGRQA------KGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRL---RVNAGTNKQPGTTKNTA 105 (174)
Q Consensus 35 ~~ik~~R~~------~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~---~~l~~~~~~~~~~~~~~ 105 (174)
.+++..++. +.-+.+++|+.+|++...|...-.....+....|......-+-.. ..+..............
T Consensus 109 ~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 188 (251)
T PRK07670 109 KKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQDDGENVSVTIRDDKTPTPEEKLLK 188 (251)
T ss_pred HHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCccccCCCCcchhhhhhcCcCCCCHHHHHHH
Q ss_pred hhhhhhhhhhcccccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 106 KLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 106 ~l~~~~~~~~~~~~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
.-....-......++......+ .++-..|+|.+++|+.+|+++++|.....
T Consensus 189 ~~~~~~l~~~l~~L~~~~r~vl-~l~~~~~~s~~EIA~~lgis~~tV~~~~~ 239 (251)
T PRK07670 189 EELIEELAEKIKQLSEKEQLVI-SLFYKEELTLTEIGQVLNLSTSRISQIHS 239 (251)
T ss_pred HHHHHHHHHHHhcCCHHHHHHH-HHHHhcCCCHHHHHHHHCcCHHHHHHHHH
No 459
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=80.94 E-value=1.8 Score=33.68 Aligned_cols=24 Identities=21% Similarity=0.201 Sum_probs=20.7
Q ss_pred cCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 44 KGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 44 ~gltq~eLA~~igvs~~~is~~E~ 67 (174)
++.|.+|||+.+|||++|++..-+
T Consensus 177 R~~~l~dLA~~lGISkst~~ehLR 200 (215)
T COG3413 177 RRVSLKDLAKELGISKSTLSEHLR 200 (215)
T ss_pred ccCCHHHHHHHhCCCHHHHHHHHH
Confidence 456999999999999999987653
No 460
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=80.90 E-value=4 Score=29.80 Aligned_cols=37 Identities=16% Similarity=0.197 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
.++..++-..-...|+|..++|+.+|++.+|+.+|-+
T Consensus 7 ~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~ 43 (138)
T COG3415 7 NDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVR 43 (138)
T ss_pred HHHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHH
Confidence 3445555556667999999999999999999888855
No 461
>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry is represented by Bacteriophage D3112, Orf24. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=80.88 E-value=4.9 Score=30.26 Aligned_cols=37 Identities=8% Similarity=-0.002 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 31 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 31 ~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
.+.-..+|.+---.++|.+..|..+|||.+|+.+|-.
T Consensus 5 ~e~R~~~R~~YV~~~~sLe~aA~~~gVs~~TarrWK~ 41 (165)
T PF08822_consen 5 QETRDAVRRAYVFDRLSLEQAAAKCGVSYATARRWKR 41 (165)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 4556778888888999999999999999999999975
No 462
>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=80.85 E-value=2.6 Score=28.03 Aligned_cols=27 Identities=11% Similarity=0.062 Sum_probs=22.7
Q ss_pred CCCHHHHHHHhCCChhHHHHHhcCCCC
Q psy6501 135 GWSQKDLATKINEKPQIVNDYEGGRGI 161 (174)
Q Consensus 135 glsq~ela~~lg~~~s~i~~~E~G~~~ 161 (174)
+++..++|+.+|++++++..||.-.-.
T Consensus 1 ~~ti~evA~~~gvs~~tLR~ye~~Gll 27 (88)
T cd01105 1 VIGIGEVSKLTGVSPRQLRYWEEKGLI 27 (88)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 368899999999999999999874333
No 463
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=80.79 E-value=8.7 Score=31.94 Aligned_cols=40 Identities=13% Similarity=0.052 Sum_probs=28.2
Q ss_pred cccHHHHHHHHH---HHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 118 KVPLDLAKLLMQ---GRQAKGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 118 ~~~~~~~~~i~~---~R~~~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
.++......|.. ++...|+|.+++|+.+|+++++|..+..
T Consensus 262 ~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~ 304 (325)
T PRK05657 262 ELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQV 304 (325)
T ss_pred cCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 334444444432 2235789999999999999999988764
No 464
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=80.71 E-value=7.2 Score=26.23 Aligned_cols=52 Identities=15% Similarity=0.029 Sum_probs=40.9
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCc
Q psy6501 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI 86 (174)
Q Consensus 33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v 86 (174)
-.+-++.-++...+|-+++|.++|+|.--|-++++=...| .....+.++|.-
T Consensus 11 Tk~elqan~el~~LS~~~iA~~Ln~t~~~lekil~~tqr~--~dvW~lRd~l~~ 62 (97)
T COG4367 11 TKQELQANFELCPLSDEEIATALNWTEVKLEKILQVTQRP--ADVWRLRDFLVQ 62 (97)
T ss_pred HHHHHHHhhhhccccHHHHHHHhCCCHHHHHHHHHHhhcc--chhHHHHHHHHH
Confidence 3556777888999999999999999999999999877666 445556555543
No 465
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=80.60 E-value=6.5 Score=22.42 Aligned_cols=30 Identities=20% Similarity=0.163 Sum_probs=22.2
Q ss_pred HHHHHHHHHhcCCCHHHHHHHhCCChhHHH
Q psy6501 124 AKLLMQGRQAKGWSQKDLATKINEKPQIVN 153 (174)
Q Consensus 124 ~~~i~~~R~~~glsq~ela~~lg~~~s~i~ 153 (174)
..+|......-..+..++|+.+|++++++.
T Consensus 6 ~~Il~~Lq~d~r~s~~~la~~lglS~~~v~ 35 (42)
T PF13404_consen 6 RKILRLLQEDGRRSYAELAEELGLSESTVR 35 (42)
T ss_dssp HHHHHHHHH-TTS-HHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHHcCCccHHHHHHHHCcCHHHHH
Confidence 456777777778999999999999998764
No 466
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=80.58 E-value=2.5 Score=33.76 Aligned_cols=32 Identities=13% Similarity=-0.026 Sum_probs=26.4
Q ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
.-++.+++...++.+|||+.+|||+.||.+.-
T Consensus 9 ~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL 40 (251)
T PRK13509 9 ILLELLAQLGFVTVEKVIERLGISPATARRDI 40 (251)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHH
Confidence 34556667777999999999999999998764
No 467
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=80.56 E-value=3.1 Score=33.01 Aligned_cols=31 Identities=13% Similarity=0.186 Sum_probs=26.6
Q ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 37 LMQGRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 37 ik~~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
+-.+|...|+|.+|+|+.+|+|.++|+.+..
T Consensus 213 ii~l~~~~g~s~~eIA~~lgis~~~V~~~~~ 243 (255)
T TIGR02941 213 IIHCTFEENLSQKETGERLGISQMHVSRLQR 243 (255)
T ss_pred HHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 4456667899999999999999999998864
No 468
>PRK11050 manganese transport regulator MntR; Provisional
Probab=80.53 E-value=4.3 Score=29.84 Aligned_cols=36 Identities=17% Similarity=0.121 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 31 LDLAKLLMQGRQ-AKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 31 ~~ig~~ik~~R~-~~gltq~eLA~~igvs~~~is~~E 66 (174)
..+-..|..+.. .-++++.+||+.+++|+++|+.+-
T Consensus 36 e~~l~~I~~~l~~~~~~t~~eLA~~l~is~stVsr~l 72 (152)
T PRK11050 36 EDYVELIADLIAEVGEARQVDIAARLGVSQPTVAKML 72 (152)
T ss_pred HHHHHHHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHH
Confidence 344455554443 367899999999999999999875
No 469
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=80.46 E-value=3.6 Score=24.36 Aligned_cols=31 Identities=16% Similarity=0.156 Sum_probs=22.5
Q ss_pred HHHHHHHhcC-CCHHHHHHHhCCChhHHHHHh
Q psy6501 126 LLMQGRQAKG-WSQKDLATKINEKPQIVNDYE 156 (174)
Q Consensus 126 ~i~~~R~~~g-lsq~ela~~lg~~~s~i~~~E 156 (174)
.+....+..+ +|.+++|+.+++|..+|.++-
T Consensus 5 il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i 36 (55)
T PF08279_consen 5 ILKLLLESKEPITAKELAEELGVSRRTIRRDI 36 (55)
T ss_dssp HHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHH
T ss_pred HHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHH
Confidence 4444444444 999999999999999987753
No 470
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=80.46 E-value=2.7 Score=35.52 Aligned_cols=24 Identities=4% Similarity=0.144 Sum_probs=22.2
Q ss_pred cCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 44 KGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 44 ~gltq~eLA~~igvs~~~is~~E~ 67 (174)
.++|++|+|+.+|||+..|+++|.
T Consensus 324 ~~~tl~EIa~~lgvs~erVrQi~~ 347 (367)
T PRK09210 324 RTRTLEEVGKVFGVTRERIRQIEA 347 (367)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHH
Confidence 458999999999999999999985
No 471
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=80.37 E-value=2.6 Score=33.47 Aligned_cols=31 Identities=10% Similarity=0.068 Sum_probs=26.3
Q ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
-+..+.+...+|++|||+.+|||..||++.-
T Consensus 9 Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL 39 (240)
T PRK10411 9 IVDLLLNHTSLTTEALAEQLNVSKETIRRDL 39 (240)
T ss_pred HHHHHHHcCCCcHHHHHHHHCcCHHHHHHHH
Confidence 4556667789999999999999999998864
No 472
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 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.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=80.35 E-value=6.1 Score=26.50 Aligned_cols=36 Identities=14% Similarity=0.150 Sum_probs=26.9
Q ss_pred HHHHHHHHHH--HhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 122 DLAKLLMQGR--QAKGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 122 ~~~~~i~~~R--~~~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
++..++.-++ -..|.||.++++.+|+|..+|++.=+
T Consensus 34 ~l~~R~~va~~lL~~g~syreIa~~tgvS~aTItRvsr 71 (87)
T PF01371_consen 34 ALAQRWQVAKELLDEGKSYREIAEETGVSIATITRVSR 71 (87)
T ss_dssp HHHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 3444554444 34789999999999999999987643
No 473
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=80.34 E-value=2.7 Score=32.30 Aligned_cols=31 Identities=19% Similarity=0.078 Sum_probs=25.5
Q ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
-|..+...-++|+.+||+.+|+++++|++.-
T Consensus 6 IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L 36 (203)
T TIGR02702 6 ILSYLLKQGQATAAALAEALAISPQAVRRHL 36 (203)
T ss_pred HHHHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence 3455666778999999999999999998763
No 474
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=80.30 E-value=3.3 Score=30.96 Aligned_cols=29 Identities=10% Similarity=0.048 Sum_probs=25.7
Q ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 39 QGRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 39 ~~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
.+|.-.|+|.+|+|+.+|+|.++|.....
T Consensus 138 ~l~~~~g~s~~EIA~~lgis~~tV~~~l~ 166 (186)
T PRK05602 138 VLQYYQGLSNIEAAAVMDISVDALESLLA 166 (186)
T ss_pred hHHHhcCCCHHHHHHHhCcCHHHHHHHHH
Confidence 36677899999999999999999998863
No 475
>PF14590 DUF4447: Domain of unknown function (DUF4447); PDB: 2OX6_B.
Probab=80.27 E-value=6.7 Score=28.26 Aligned_cols=41 Identities=15% Similarity=0.070 Sum_probs=30.7
Q ss_pred HHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHH
Q psy6501 126 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAI 166 (174)
Q Consensus 126 ~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~ 166 (174)
.|...|...|++..++++..+.+..-+-.||.|....+.-.
T Consensus 11 e~~ylr~slgl~~aqv~~l~k~se~dv~aweage~~~~~la 51 (166)
T PF14590_consen 11 EIKYLRLSLGLTTAQVAELTKASEADVLAWEAGEKPAPGLA 51 (166)
T ss_dssp HHHHHHHHTT--HHHHHHHHTS-HHHHHHHHTTSS---HHH
T ss_pred HHHHHHHHcCCCHHHHHHhhccCHHHhhhhhccCCcCchHH
Confidence 56778999999999999999999999999999988765443
No 476
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=80.24 E-value=2 Score=26.56 Aligned_cols=25 Identities=20% Similarity=0.324 Sum_probs=20.5
Q ss_pred HHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 42 QAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 42 ~~~gltq~eLA~~igvs~~~is~~E 66 (174)
+....+..+||+.+|||+++++..-
T Consensus 19 ~~~~v~~~~iA~~L~vs~~tvt~ml 43 (60)
T PF01325_consen 19 EGGPVRTKDIAERLGVSPPTVTEML 43 (60)
T ss_dssp CTSSBBHHHHHHHHTS-HHHHHHHH
T ss_pred CCCCccHHHHHHHHCCChHHHHHHH
Confidence 5567899999999999999998753
No 477
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=80.21 E-value=6.9 Score=22.58 Aligned_cols=25 Identities=20% Similarity=0.348 Sum_probs=22.3
Q ss_pred hcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 133 AKGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 133 ~~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
..|++..++|+.+|++++++..+-.
T Consensus 16 ~~g~s~~eia~~l~is~~tv~~~~~ 40 (58)
T smart00421 16 AEGLTNKEIAERLGISEKTVKTHLS 40 (58)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 5789999999999999999987754
No 478
>PRK06930 positive control sigma-like factor; Validated
Probab=80.18 E-value=3.8 Score=30.83 Aligned_cols=29 Identities=21% Similarity=0.171 Sum_probs=25.5
Q ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 39 QGRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 39 ~~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
.++...|+|.+|+|+.+|+|.++|..+..
T Consensus 124 ~L~~~eg~s~~EIA~~lgiS~~tVk~~l~ 152 (170)
T PRK06930 124 LMHRGYGLSYSEIADYLNIKKSTVQSMIE 152 (170)
T ss_pred HHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34567999999999999999999998864
No 479
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=80.16 E-value=3.3 Score=24.53 Aligned_cols=24 Identities=13% Similarity=-0.002 Sum_probs=20.9
Q ss_pred HcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 43 AKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 43 ~~gltq~eLA~~igvs~~~is~~E 66 (174)
...+|..++++.+|+|++++++.-
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l 31 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHL 31 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHH
Confidence 567899999999999999888764
No 480
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=80.10 E-value=3.6 Score=31.12 Aligned_cols=32 Identities=16% Similarity=0.183 Sum_probs=27.2
Q ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
.+-.++.-.|+|.+|+|+.+|+|.++|...-.
T Consensus 143 ~i~~L~~~~g~s~~eIA~~lgis~~tV~~~l~ 174 (196)
T PRK12524 143 QAVVLRHIEGLSNPEIAEVMEIGVEAVESLTA 174 (196)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34556778999999999999999999998763
No 481
>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=80.09 E-value=2.6 Score=29.17 Aligned_cols=27 Identities=15% Similarity=0.226 Sum_probs=22.8
Q ss_pred CCHHHHHHHhCCChhHHHHHhcCCCCC
Q psy6501 136 WSQKDLATKINEKPQIVNDYEGGRGIP 162 (174)
Q Consensus 136 lsq~ela~~lg~~~s~i~~~E~G~~~P 162 (174)
++..++|+.+|+++.++..||.-.-.|
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~Gll~ 27 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEKEGLLS 27 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCC
Confidence 578899999999999999999854443
No 482
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=80.01 E-value=2.2 Score=35.53 Aligned_cols=43 Identities=12% Similarity=0.151 Sum_probs=30.2
Q ss_pred HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccc
Q psy6501 43 AKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLR 89 (174)
Q Consensus 43 ~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~ 89 (174)
-.|+|++|+|+.+|+|.++|.++..- ....|.+....-|++.+
T Consensus 280 ~e~~s~~EIA~~Lgis~~tV~~~~~r----Al~kLr~~l~~~~~~~~ 322 (325)
T PRK05657 280 YEAATLEDVAREIGLTRERVRQIQVE----ALRRLREILQTQGLSIE 322 (325)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHH----HHHHHHHHHHhCccchh
Confidence 56899999999999999999999852 22344444444444433
No 483
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=79.96 E-value=3.6 Score=30.95 Aligned_cols=29 Identities=10% Similarity=0.000 Sum_probs=25.2
Q ss_pred HHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 38 MQGRQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 38 k~~R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
-.++.-.|+|.+|+|+.+|+|.++|...-
T Consensus 120 ~~L~~~eg~s~~EIA~~lgis~~tV~~~l 148 (182)
T PRK12511 120 LHLVAIEGLSYQEAAAVLGIPIGTLMSRI 148 (182)
T ss_pred HHHHHHcCCCHHHHHHHhCcCHHHHHHHH
Confidence 34567789999999999999999998885
No 484
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=79.93 E-value=2.2 Score=32.57 Aligned_cols=25 Identities=20% Similarity=0.399 Sum_probs=22.4
Q ss_pred HcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 43 AKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 43 ~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
..|+|-+|+|+.+++|.+||..+-+
T Consensus 163 ~~G~s~~eIA~~l~iS~~TV~~h~~ 187 (216)
T PRK10840 163 AEGFLVTEIAKKLNRSIKTISSQKK 187 (216)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4899999999999999999988753
No 485
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=79.90 E-value=1.9 Score=33.87 Aligned_cols=28 Identities=7% Similarity=0.018 Sum_probs=23.1
Q ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 39 QGRQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 39 ~~R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
.+.+.-++|+.+||+.+++|+++++++-
T Consensus 15 ~l~~~~~IS~~eLA~~L~iS~~Tvsr~L 42 (217)
T PRK14165 15 AVNNTVKISSSEFANHTGTSSKTAARIL 42 (217)
T ss_pred ccCCCCCcCHHHHHHHHCcCHHHHHHHH
Confidence 3444557899999999999999998874
No 486
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=79.87 E-value=1.7 Score=36.02 Aligned_cols=24 Identities=13% Similarity=0.219 Sum_probs=22.0
Q ss_pred cCCCHHHHHHHhCCChhHHHHHhc
Q psy6501 134 KGWSQKDLATKINEKPQIVNDYEG 157 (174)
Q Consensus 134 ~glsq~ela~~lg~~~s~i~~~E~ 157 (174)
.|+||+|+|+++|+|+.+|+++-.
T Consensus 28 ~g~tQ~eIA~~lgiSR~~VsRlL~ 51 (318)
T PRK15418 28 DGLTQSEIGERLGLTRLKVSRLLE 51 (318)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHH
Confidence 789999999999999999998753
No 487
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=79.86 E-value=4.1 Score=26.81 Aligned_cols=26 Identities=19% Similarity=0.029 Sum_probs=20.9
Q ss_pred HHHHcC--CCHHHHHHHhCCCHHHHHHH
Q psy6501 40 GRQAKG--WSQKDLATKINEKPQIVNDY 65 (174)
Q Consensus 40 ~R~~~g--ltq~eLA~~igvs~~~is~~ 65 (174)
+....+ .|.++||+.+|+|+.+|.+-
T Consensus 12 l~~~~~~~~SGe~La~~LgiSRtaVwK~ 39 (79)
T COG1654 12 LLLLTGNFVSGEKLAEELGISRTAVWKH 39 (79)
T ss_pred HHHcCCCcccHHHHHHHHCccHHHHHHH
Confidence 334444 79999999999999999764
No 488
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=79.83 E-value=4.5 Score=29.04 Aligned_cols=43 Identities=19% Similarity=0.146 Sum_probs=36.6
Q ss_pred cccccchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 24 LKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 24 ~~~~~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
+++++.....+.-|...|+.-.+|..|++...|+|+.++..+-
T Consensus 5 ~T~eer~eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~l 47 (127)
T PF06163_consen 5 FTPEEREELKARIVELVREHGRITIKQLVAKTGASRNTVKRYL 47 (127)
T ss_pred CCHHHHHHHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHH
Confidence 4455566677888888999999999999999999999999874
No 489
>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=79.83 E-value=2.7 Score=28.66 Aligned_cols=26 Identities=8% Similarity=0.102 Sum_probs=21.9
Q ss_pred CCHHHHHHHhCCChhHHHHHhcCCCC
Q psy6501 136 WSQKDLATKINEKPQIVNDYEGGRGI 161 (174)
Q Consensus 136 lsq~ela~~lg~~~s~i~~~E~G~~~ 161 (174)
++..++|+.+|+++.++..||.-.-.
T Consensus 1 ~ti~eva~~~gvs~~tlR~ye~~Gll 26 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYDEIGLL 26 (103)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 47889999999999999999874443
No 490
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. 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.
Probab=79.78 E-value=3.7 Score=31.84 Aligned_cols=29 Identities=7% Similarity=-0.002 Sum_probs=25.0
Q ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 39 QGRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 39 ~~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
.+|--.|+|++|+|+.+|+|.++|..+..
T Consensus 185 ~l~y~~~~s~~eIA~~lgis~~tV~~~~~ 213 (224)
T TIGR02479 185 SLYYYEELNLKEIGEVLGLTESRVSQIHS 213 (224)
T ss_pred HHHHhCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 35567899999999999999999998764
No 491
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=79.67 E-value=2.6 Score=31.58 Aligned_cols=29 Identities=17% Similarity=0.074 Sum_probs=25.5
Q ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 39 QGRQAKGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 39 ~~R~~~gltq~eLA~~igvs~~~is~~E~ 67 (174)
.++.-.|+|++|+|+.+|+|.+||...-.
T Consensus 137 ~l~~~~gls~~EIA~~l~i~~~tVks~l~ 165 (182)
T COG1595 137 LLRYLEGLSYEEIAEILGISVGTVKSRLH 165 (182)
T ss_pred hhHhhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 46777899999999999999999988763
No 492
>PRK13500 transcriptional activator RhaR; Provisional
Probab=79.61 E-value=20 Score=29.32 Aligned_cols=17 Identities=12% Similarity=0.059 Sum_probs=12.4
Q ss_pred cCCCHHHHHHHhCCChh
Q psy6501 134 KGWSQKDLATKINEKPQ 150 (174)
Q Consensus 134 ~glsq~ela~~lg~~~s 150 (174)
-.++..++|..+|..-+
T Consensus 270 t~~sI~eIA~~~GF~d~ 286 (312)
T PRK13500 270 SRLLISDISTECGFEDS 286 (312)
T ss_pred CCCCHHHHHHHhCCCCH
Confidence 35788888888887553
No 493
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=79.52 E-value=2.5 Score=25.59 Aligned_cols=22 Identities=14% Similarity=0.238 Sum_probs=18.9
Q ss_pred cCCCHHHHHHHhCCChhHHHHH
Q psy6501 134 KGWSQKDLATKINEKPQIVNDY 155 (174)
Q Consensus 134 ~glsq~ela~~lg~~~s~i~~~ 155 (174)
++.+..++|+.+|+++++++..
T Consensus 22 R~~tl~elA~~lgis~st~~~~ 43 (53)
T PF04967_consen 22 RRITLEELAEELGISKSTVSEH 43 (53)
T ss_pred CcCCHHHHHHHhCCCHHHHHHH
Confidence 4578999999999999998754
No 494
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=79.47 E-value=2.9 Score=37.06 Aligned_cols=24 Identities=4% Similarity=0.072 Sum_probs=22.5
Q ss_pred cCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501 44 KGWSQKDLATKINEKPQIVNDYEG 67 (174)
Q Consensus 44 ~gltq~eLA~~igvs~~~is~~E~ 67 (174)
.++|++|+|+.+|||+..|+++|+
T Consensus 466 e~~TL~EIa~~lGVSrERVRQIe~ 489 (509)
T PRK05901 466 QPKTLDEIGQVYGVTRERIRQIES 489 (509)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Confidence 469999999999999999999996
No 495
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=79.44 E-value=3 Score=28.77 Aligned_cols=24 Identities=13% Similarity=0.052 Sum_probs=20.6
Q ss_pred HcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 43 AKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 43 ~~gltq~eLA~~igvs~~~is~~E 66 (174)
..++||.+||+.+++++++|++.-
T Consensus 41 ~~~~t~~eL~~~l~~~~stvs~~i 64 (109)
T TIGR01889 41 EGKLTLKEIIKEILIKQSALVKII 64 (109)
T ss_pred CCcCcHHHHHHHHCCCHHHHHHHH
Confidence 356999999999999999998764
No 496
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=79.41 E-value=3.6 Score=31.06 Aligned_cols=28 Identities=7% Similarity=0.070 Sum_probs=24.6
Q ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 39 QGRQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 39 ~~R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
.+|.-.|+|.+|+|+.+|+|.++|...-
T Consensus 146 ~L~~~~g~s~~EIA~~lgis~~tVk~~l 173 (195)
T PRK12532 146 TLKEILGFSSDEIQQMCGISTSNYHTIM 173 (195)
T ss_pred hhHHHhCCCHHHHHHHHCCCHHHHHHHH
Confidence 3567789999999999999999998764
No 497
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=79.32 E-value=3.9 Score=30.38 Aligned_cols=28 Identities=18% Similarity=0.174 Sum_probs=24.3
Q ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 39 QGRQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 39 ~~R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
.++.-.|+|++|+|+.+|+|.++|....
T Consensus 150 ~l~~~~g~s~~eIA~~lgis~~~v~~~l 177 (189)
T TIGR02984 150 LLRHLEGLSFAEVAERMDRSEGAVSMLW 177 (189)
T ss_pred HHHHhcCCCHHHHHHHHCcCHHHHHHHH
Confidence 4556689999999999999999998764
No 498
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=79.16 E-value=4.4 Score=29.94 Aligned_cols=28 Identities=18% Similarity=0.163 Sum_probs=25.0
Q ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 39 QGRQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 39 ~~R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
.++.-.|+|.+|+|+.+|+|.++|...-
T Consensus 110 ~l~~~~g~s~~eIA~~lgis~~tV~~~l 137 (170)
T TIGR02959 110 RLTELEGLSQQEIAEKLGLSLSGAKSRV 137 (170)
T ss_pred HHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 3677899999999999999999998775
No 499
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=79.13 E-value=3.9 Score=30.00 Aligned_cols=30 Identities=20% Similarity=0.210 Sum_probs=24.9
Q ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501 37 LMQGRQAKGWSQKDLATKINEKPQIVNDYE 66 (174)
Q Consensus 37 ik~~R~~~gltq~eLA~~igvs~~~is~~E 66 (174)
|-.++--.|+|.+|+|+.+|+|.++|...-
T Consensus 127 i~~l~~~~g~s~~eiA~~lgis~~tv~~~l 156 (169)
T TIGR02954 127 AIILRYYHDLTIKEIAEVMNKPEGTVKTYL 156 (169)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 334566789999999999999999998764
No 500
>COG3636 Predicted transcriptional regulator [Transcription]
Probab=79.10 E-value=5.7 Score=27.21 Aligned_cols=47 Identities=21% Similarity=0.126 Sum_probs=38.2
Q ss_pred HHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501 126 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174 (174)
Q Consensus 126 ~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l 174 (174)
.+...-..+||+ ++|++.|+++..+.+--+....|+.+.+-++.++|
T Consensus 42 alg~var~~GMs--qvA~~aGlsRe~LYkaLS~~GNPtf~Til~V~kAl 88 (100)
T COG3636 42 ALGVVARSRGMS--QVARKAGLSREGLYKALSPGGNPTFDTILAVLKAL 88 (100)
T ss_pred HHHHHHHhcCHH--HHHHHhCccHHHHHHHhCCCCCCcHHHHHHHHHHc
Confidence 333333446665 58999999999999999999999999999999876
Done!