Query 032366
Match_columns 142
No_of_seqs 396 out of 2492
Neff 7.0
Searched_HMMs 46136
Date Fri Mar 29 13:09:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032366.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032366hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3398 Transcription factor M 100.0 9.4E-31 2E-35 185.2 11.5 132 8-142 1-133 (135)
2 PF08523 MBF1: Multiprotein br 99.8 5.2E-22 1.1E-26 129.5 0.1 70 9-79 1-71 (71)
3 PRK06424 transcription factor; 99.7 1.3E-15 2.7E-20 112.0 10.5 65 78-142 80-144 (144)
4 PHA01976 helix-turn-helix prot 99.6 9.7E-16 2.1E-20 98.0 6.5 58 82-139 2-59 (67)
5 PRK08359 transcription factor; 99.6 7.7E-15 1.7E-19 110.9 9.1 63 78-140 81-143 (176)
6 TIGR03070 couple_hipB transcri 99.6 2.4E-14 5.2E-19 88.0 8.1 57 82-138 2-58 (58)
7 TIGR00270 conserved hypothetic 99.6 2.2E-14 4.7E-19 106.6 8.5 63 78-140 65-127 (154)
8 PF12844 HTH_19: Helix-turn-he 99.5 1.2E-14 2.6E-19 92.1 5.4 56 84-139 1-56 (64)
9 PF01381 HTH_3: Helix-turn-hel 99.5 2.2E-14 4.7E-19 88.2 5.4 53 87-139 1-53 (55)
10 COG1476 Predicted transcriptio 99.5 5E-14 1.1E-18 90.9 5.7 56 85-140 4-59 (68)
11 PRK09726 antitoxin HipB; Provi 99.5 3.7E-13 8E-18 91.0 8.5 60 80-139 10-69 (88)
12 PF13560 HTH_31: Helix-turn-he 99.5 1E-13 2.3E-18 88.1 5.0 58 82-139 1-59 (64)
13 PRK09706 transcriptional repre 99.4 4E-13 8.7E-18 97.2 7.4 59 81-139 4-62 (135)
14 COG1813 Predicted transcriptio 99.4 1.4E-12 3E-17 97.3 7.2 66 76-141 73-138 (165)
15 PRK09943 DNA-binding transcrip 99.3 2.9E-12 6.4E-17 96.9 7.1 60 80-139 5-64 (185)
16 PRK13890 conjugal transfer pro 99.3 4.1E-12 9E-17 90.7 7.5 60 80-139 3-62 (120)
17 TIGR02607 antidote_HigA addict 99.3 4.4E-12 9.6E-17 83.0 6.8 58 82-139 4-62 (78)
18 PRK08154 anaerobic benzoate ca 99.3 7.7E-12 1.7E-16 101.8 7.8 62 78-139 24-85 (309)
19 TIGR02684 dnstrm_HI1420 probab 99.3 1.2E-11 2.7E-16 84.1 7.2 58 80-139 30-87 (89)
20 PRK10072 putative transcriptio 99.2 4.1E-11 8.8E-16 82.6 7.2 53 85-138 36-88 (96)
21 PF13443 HTH_26: Cro/C1-type H 99.2 3E-11 6.5E-16 76.1 4.9 55 86-140 1-56 (63)
22 TIGR02612 mob_myst_A mobile my 99.2 9.9E-11 2.1E-15 86.7 7.0 55 85-139 28-84 (150)
23 PRK04140 hypothetical protein; 99.1 2E-10 4.3E-15 94.1 8.0 61 79-139 123-183 (317)
24 smart00530 HTH_XRE Helix-turn- 99.1 3.7E-10 8.1E-15 66.4 6.8 53 87-139 2-54 (56)
25 cd00093 HTH_XRE Helix-turn-hel 99.0 1.2E-09 2.5E-14 64.7 7.0 55 85-139 2-56 (58)
26 TIGR03830 CxxCG_CxxCG_HTH puta 99.0 1.1E-09 2.3E-14 77.7 6.7 58 81-139 64-121 (127)
27 PF13744 HTH_37: Helix-turn-he 98.9 3E-09 6.5E-14 70.6 6.0 61 79-139 15-76 (80)
28 PRK10856 cytoskeletal protein 98.9 2.9E-09 6.3E-14 87.8 6.9 60 80-139 12-77 (331)
29 PHA00542 putative Cro-like pro 98.9 9.1E-09 2E-13 68.8 7.5 49 86-134 22-71 (82)
30 COG3620 Predicted transcriptio 98.9 6.8E-09 1.5E-13 77.5 6.7 52 84-135 7-58 (187)
31 smart00352 POU Found in Pit-Oc 98.8 4.4E-08 9.6E-13 64.4 7.5 49 81-131 10-64 (75)
32 COG2944 Predicted transcriptio 98.7 3E-08 6.6E-13 69.0 6.2 45 83-127 45-89 (104)
33 PRK13355 bifunctional HTH-doma 98.7 3.2E-08 7E-13 85.3 7.5 58 82-139 3-65 (517)
34 PRK02866 cyanate hydratase; Va 98.7 7.6E-08 1.6E-12 70.9 8.3 59 81-139 4-62 (147)
35 COG3093 VapI Plasmid maintenan 98.7 7.1E-08 1.5E-12 67.0 6.5 57 83-139 10-67 (104)
36 COG1709 Predicted transcriptio 98.6 2.7E-08 5.8E-13 77.4 4.0 56 79-134 24-80 (241)
37 TIGR00673 cynS cyanate hydrata 98.6 3.4E-07 7.4E-12 67.7 8.0 56 83-138 9-64 (150)
38 COG1396 HipB Predicted transcr 98.4 2.7E-06 5.9E-11 54.2 8.0 56 83-138 2-58 (120)
39 COG1395 Predicted transcriptio 98.4 9.1E-07 2E-11 72.2 6.5 57 83-139 126-182 (313)
40 COG3655 Predicted transcriptio 98.3 1.2E-06 2.5E-11 57.4 5.3 57 83-139 3-60 (73)
41 PF07022 Phage_CI_repr: Bacter 98.3 1.9E-07 4.2E-12 59.8 1.6 53 86-139 2-56 (66)
42 PF13413 HTH_25: Helix-turn-he 98.2 6.4E-06 1.4E-10 52.3 6.1 54 86-139 1-60 (62)
43 PF08667 BetR: BetR domain; I 98.0 1.8E-05 3.9E-10 58.4 6.8 59 81-139 4-66 (147)
44 COG1426 Predicted transcriptio 98.0 1.3E-05 2.9E-10 64.9 5.3 58 82-139 3-66 (284)
45 COG5499 Predicted transcriptio 98.0 1.8E-05 3.9E-10 55.5 5.1 56 83-139 61-116 (120)
46 cd01392 HTH_LacI Helix-turn-he 97.9 3.3E-05 7.2E-10 46.3 5.3 40 100-139 2-44 (52)
47 TIGR01321 TrpR trp operon repr 97.8 0.00012 2.5E-09 50.3 6.8 50 82-131 40-91 (94)
48 PHA01083 hypothetical protein 97.8 4.8E-05 1E-09 56.0 5.1 54 86-139 6-61 (149)
49 COG2522 Predicted transcriptio 97.7 0.00017 3.7E-09 51.5 6.5 45 78-122 5-49 (119)
50 COG4800 Predicted transcriptio 97.6 0.00027 5.9E-09 51.8 7.2 54 80-134 14-67 (170)
51 PF00356 LacI: Bacterial regul 97.6 0.0003 6.5E-09 42.1 5.7 42 97-138 1-45 (46)
52 smart00354 HTH_LACI helix_turn 97.6 0.00026 5.7E-09 45.5 5.7 44 96-139 1-47 (70)
53 PF08965 DUF1870: Domain of un 97.6 0.00028 6E-09 50.3 6.1 50 85-134 4-55 (118)
54 PRK08099 bifunctional DNA-bind 97.3 0.00047 1E-08 58.3 5.8 47 93-139 1-48 (399)
55 COG3636 Predicted transcriptio 97.2 0.0021 4.5E-08 44.3 6.5 54 83-138 39-92 (100)
56 PF01710 HTH_Tnp_IS630: Transp 97.1 0.002 4.3E-08 45.6 6.5 73 29-117 19-93 (119)
57 COG5606 Uncharacterized conser 97.0 0.0016 3.4E-08 44.0 4.8 61 79-139 25-86 (91)
58 PHA00675 hypothetical protein 97.0 0.0028 6.1E-08 41.8 5.7 42 79-120 23-64 (78)
59 TIGR03879 near_KaiC_dom probab 96.9 0.0052 1.1E-07 40.3 6.5 49 81-131 18-66 (73)
60 PF00157 Pou: Pou domain - N-t 96.9 0.0065 1.4E-07 40.0 6.7 50 81-132 10-65 (75)
61 TIGR02147 Fsuc_second hypothet 96.8 0.0034 7.4E-08 50.7 6.3 46 95-140 27-73 (271)
62 PF13693 HTH_35: Winged helix- 96.8 0.0033 7.2E-08 41.7 4.8 52 85-139 5-56 (78)
63 PF13384 HTH_23: Homeodomain-l 96.7 0.0037 8.1E-08 37.1 4.3 24 95-118 17-40 (50)
64 PF02796 HTH_7: Helix-turn-hel 96.6 0.0042 9E-08 36.6 4.0 33 84-117 11-43 (45)
65 PHA02591 hypothetical protein; 96.5 0.0066 1.4E-07 40.2 4.5 31 87-117 51-81 (83)
66 TIGR02293 TAS_TIGR02293 putati 96.3 0.014 3.1E-07 42.1 6.2 49 85-133 26-74 (133)
67 PRK10014 DNA-binding transcrip 96.3 0.014 3.1E-07 46.7 6.4 46 94-139 5-53 (342)
68 PF13936 HTH_38: Helix-turn-he 96.2 0.0063 1.4E-07 35.7 3.2 30 87-117 13-42 (44)
69 PF14549 P22_Cro: DNA-binding 96.2 0.013 2.8E-07 36.9 4.7 41 93-137 8-48 (60)
70 PF13412 HTH_24: Winged helix- 96.2 0.019 4.2E-07 33.8 5.1 34 84-117 6-39 (48)
71 TIGR02844 spore_III_D sporulat 96.1 0.062 1.3E-06 35.8 7.8 50 85-135 10-60 (80)
72 COG3423 Nlp Predicted transcri 96.1 0.02 4.3E-07 37.8 5.1 52 86-140 12-63 (82)
73 PRK09492 treR trehalose repres 96.0 0.016 3.5E-07 45.9 5.6 44 95-138 4-50 (315)
74 PF04814 HNF-1_N: Hepatocyte n 96.0 0.026 5.6E-07 43.0 6.3 57 78-134 114-170 (180)
75 PRK03975 tfx putative transcri 96.0 0.011 2.4E-07 43.4 4.1 45 93-138 19-66 (141)
76 PRK09526 lacI lac repressor; R 95.9 0.015 3.3E-07 46.6 5.1 44 95-138 5-51 (342)
77 TIGR01481 ccpA catabolite cont 95.9 0.019 4.2E-07 45.7 5.5 44 96-139 2-48 (329)
78 PRK10703 DNA-binding transcrip 95.9 0.019 4.2E-07 46.0 5.6 43 96-138 2-47 (341)
79 TIGR02405 trehalos_R_Ecol treh 95.9 0.021 4.5E-07 45.5 5.7 44 96-139 2-48 (311)
80 TIGR00721 tfx DNA-binding prot 95.9 0.021 4.6E-07 41.7 5.2 34 84-118 11-44 (137)
81 PRK10727 DNA-binding transcrip 95.7 0.023 4.9E-07 45.8 5.4 44 96-139 2-48 (343)
82 PF08535 KorB: KorB domain; I 95.7 0.012 2.7E-07 39.6 3.1 25 93-117 1-25 (93)
83 cd00131 PAX Paired Box domain 95.6 0.069 1.5E-06 38.3 7.0 75 30-117 35-125 (128)
84 PRK14987 gluconate operon tran 95.5 0.022 4.8E-07 45.6 4.7 44 95-138 5-51 (331)
85 PRK10401 DNA-binding transcrip 95.5 0.033 7.2E-07 44.9 5.6 44 96-139 2-48 (346)
86 PF02001 DUF134: Protein of un 95.5 0.041 8.8E-07 38.6 5.3 28 90-117 52-79 (106)
87 PF05225 HTH_psq: helix-turn-h 95.5 0.036 7.8E-07 32.7 4.3 39 81-120 3-41 (45)
88 PF04545 Sigma70_r4: Sigma-70, 95.5 0.042 9E-07 32.6 4.6 33 85-117 10-42 (50)
89 PRK10344 DNA-binding transcrip 95.5 0.053 1.1E-06 36.9 5.5 51 87-140 13-63 (92)
90 cd04762 HTH_MerR-trunc Helix-T 95.5 0.028 6E-07 32.2 3.7 23 96-118 1-23 (49)
91 COG4197 Uncharacterized protei 95.4 0.0089 1.9E-07 40.8 1.7 39 97-135 14-52 (96)
92 PRK01381 Trp operon repressor; 95.3 0.052 1.1E-06 37.6 5.1 57 80-136 38-96 (99)
93 PRK08558 adenine phosphoribosy 95.3 0.064 1.4E-06 42.4 6.3 48 85-134 15-62 (238)
94 TIGR02531 yecD_yerC TrpR-relat 95.1 0.047 1E-06 37.0 4.4 28 91-118 46-73 (88)
95 PRK10339 DNA-binding transcrip 95.1 0.03 6.5E-07 44.8 4.0 44 96-139 2-50 (327)
96 COG1513 CynS Cyanate lyase [In 95.0 0.17 3.6E-06 36.8 7.1 59 80-138 6-64 (151)
97 PF02376 CUT: CUT domain; Int 94.9 0.29 6.2E-06 33.0 7.9 42 79-120 10-52 (87)
98 PF06056 Terminase_5: Putative 94.9 0.073 1.6E-06 33.2 4.6 25 93-117 11-35 (58)
99 PF02954 HTH_8: Bacterial regu 94.9 0.078 1.7E-06 30.6 4.4 32 84-115 7-38 (42)
100 cd00569 HTH_Hin_like Helix-tur 94.7 0.19 4.1E-06 26.0 5.6 23 93-115 19-41 (42)
101 PF12728 HTH_17: Helix-turn-he 94.7 0.054 1.2E-06 32.1 3.6 28 96-123 2-29 (51)
102 PF05269 Phage_CII: Bacterioph 94.7 0.0054 1.2E-07 41.8 -1.1 41 94-138 22-62 (91)
103 TIGR01764 excise DNA binding d 94.6 0.062 1.4E-06 30.9 3.7 27 96-122 2-28 (49)
104 PF07037 DUF1323: Putative tra 94.6 0.035 7.6E-07 39.6 2.9 23 96-118 1-23 (122)
105 COG1356 tfx Transcriptional re 94.6 0.032 6.9E-07 40.3 2.7 28 91-118 19-46 (143)
106 KOG3802 Transcription factor O 94.6 0.033 7.2E-07 47.0 3.2 49 80-130 208-262 (398)
107 PF04218 CENP-B_N: CENP-B N-te 94.5 0.051 1.1E-06 33.1 3.2 38 82-119 8-46 (53)
108 PF01371 Trp_repressor: Trp re 94.4 0.14 3.1E-06 34.5 5.5 38 80-117 32-71 (87)
109 PF01527 HTH_Tnp_1: Transposas 94.4 0.054 1.2E-06 34.5 3.3 40 78-117 6-45 (76)
110 PRK13698 plasmid-partitioning 94.3 0.091 2E-06 43.5 5.1 43 79-121 159-202 (323)
111 cd04761 HTH_MerR-SF Helix-Turn 94.3 0.081 1.8E-06 30.7 3.6 23 96-118 1-23 (49)
112 PF13518 HTH_28: Helix-turn-he 94.2 0.12 2.6E-06 30.4 4.3 24 94-117 11-34 (52)
113 cd04764 HTH_MlrA-like_sg1 Heli 94.2 0.15 3.2E-06 31.9 4.9 22 96-117 1-22 (67)
114 PF00325 Crp: Bacterial regula 94.2 0.064 1.4E-06 29.6 2.8 23 95-117 2-24 (32)
115 COG2944 Predicted transcriptio 94.0 0.046 1E-06 38.2 2.4 24 32-55 61-84 (104)
116 PF08279 HTH_11: HTH domain; 93.8 0.11 2.4E-06 31.2 3.6 32 86-117 5-37 (55)
117 cd04763 HTH_MlrA-like Helix-Tu 93.8 0.25 5.3E-06 31.0 5.4 61 33-105 5-67 (68)
118 PRK15418 transcriptional regul 93.7 0.14 3.1E-06 42.0 5.2 55 83-137 17-84 (318)
119 PF13551 HTH_29: Winged helix- 93.7 0.46 9.9E-06 32.0 7.0 80 31-117 15-109 (112)
120 PF00376 MerR: MerR family reg 93.7 0.096 2.1E-06 29.8 3.0 25 97-121 1-25 (38)
121 TIGR00180 parB_part ParB-like 93.7 0.28 6.1E-06 37.1 6.4 53 79-132 104-156 (187)
122 cd01104 HTH_MlrA-CarA Helix-Tu 93.7 0.12 2.6E-06 32.2 3.7 22 96-117 1-22 (68)
123 cd01104 HTH_MlrA-CarA Helix-Tu 93.4 0.45 9.8E-06 29.5 6.2 61 33-105 5-67 (68)
124 PF10668 Phage_terminase: Phag 93.4 0.11 2.3E-06 32.8 3.0 24 95-118 22-45 (60)
125 cd06171 Sigma70_r4 Sigma70, re 93.3 0.25 5.4E-06 28.2 4.5 29 89-117 20-48 (55)
126 COG2390 DeoR Transcriptional r 93.3 0.18 4E-06 41.7 5.2 57 81-137 12-81 (321)
127 PRK09413 IS2 repressor TnpA; R 93.3 0.27 5.9E-06 34.7 5.4 40 78-117 12-51 (121)
128 PRK04217 hypothetical protein; 93.3 0.31 6.8E-06 34.3 5.6 32 86-117 49-80 (110)
129 COG1342 Predicted DNA-binding 93.2 0.11 2.4E-06 35.7 3.2 28 90-117 44-71 (99)
130 cd04764 HTH_MlrA-like_sg1 Heli 93.2 0.34 7.4E-06 30.2 5.3 62 33-106 5-67 (67)
131 smart00351 PAX Paired Box doma 93.1 0.34 7.4E-06 34.4 5.8 38 79-117 18-55 (125)
132 PF13542 HTH_Tnp_ISL3: Helix-t 93.0 0.38 8.3E-06 28.4 5.1 38 79-117 12-49 (52)
133 cd00092 HTH_CRP helix_turn_hel 93.0 0.33 7.2E-06 29.8 5.0 24 94-117 24-47 (67)
134 PF08281 Sigma70_r4_2: Sigma-7 92.9 0.29 6.2E-06 29.2 4.4 34 83-116 14-47 (54)
135 PF04552 Sigma54_DBD: Sigma-54 92.8 0.026 5.7E-07 42.2 -0.3 46 93-138 47-92 (160)
136 PF01047 MarR: MarR family; I 92.8 0.3 6.5E-06 29.5 4.5 34 84-117 6-39 (59)
137 COG2842 Uncharacterized ATPase 92.8 0.36 7.9E-06 39.5 6.1 60 79-138 3-62 (297)
138 PF13411 MerR_1: MerR HTH fami 92.7 0.12 2.7E-06 32.2 2.7 22 96-117 1-22 (69)
139 PF13613 HTH_Tnp_4: Helix-turn 92.7 0.13 2.9E-06 31.1 2.7 28 90-117 14-41 (53)
140 cd04763 HTH_MlrA-like Helix-Tu 92.6 0.15 3.3E-06 32.0 3.1 22 96-117 1-22 (68)
141 COG1191 FliA DNA-directed RNA 92.6 0.19 4.2E-06 40.1 4.3 34 84-117 201-234 (247)
142 PF04967 HTH_10: HTH DNA bindi 92.6 0.19 4E-06 30.9 3.3 24 94-117 22-45 (53)
143 PF13411 MerR_1: MerR HTH fami 92.5 0.57 1.2E-05 29.1 5.7 62 33-106 5-67 (69)
144 TIGR01610 phage_O_Nterm phage 92.4 0.28 6E-06 33.2 4.3 25 92-116 44-68 (95)
145 smart00422 HTH_MERR helix_turn 92.4 0.24 5.2E-06 30.8 3.8 22 96-117 1-22 (70)
146 cd04774 HTH_YfmP Helix-Turn-He 92.4 0.6 1.3E-05 31.7 6.0 67 33-110 5-72 (96)
147 smart00421 HTH_LUXR helix_turn 92.3 0.61 1.3E-05 27.1 5.4 25 93-117 16-40 (58)
148 TIGR03764 ICE_PFGI_1_parB inte 92.2 0.27 5.9E-06 39.5 4.6 42 94-135 135-181 (258)
149 PF13404 HTH_AsnC-type: AsnC-t 92.0 0.45 9.8E-06 27.6 4.3 30 85-114 7-36 (42)
150 PF14590 DUF4447: Domain of un 91.9 1 2.2E-05 32.8 6.8 40 85-124 10-49 (166)
151 cd04784 HTH_CadR-PbrR Helix-Tu 91.7 0.35 7.6E-06 34.2 4.4 22 96-117 1-22 (127)
152 PF12802 MarR_2: MarR family; 91.7 0.46 1E-05 28.8 4.4 34 84-117 8-43 (62)
153 cd01392 HTH_LacI Helix-turn-he 91.7 0.57 1.2E-05 27.4 4.7 21 34-54 3-23 (52)
154 smart00351 PAX Paired Box doma 91.7 0.86 1.9E-05 32.4 6.4 74 30-116 35-124 (125)
155 cd00131 PAX Paired Box domain 91.4 0.72 1.6E-05 33.0 5.7 39 78-117 17-55 (128)
156 PF13545 HTH_Crp_2: Crp-like h 91.3 0.27 5.8E-06 31.1 3.1 24 94-117 27-50 (76)
157 smart00550 Zalpha Z-DNA-bindin 91.3 0.52 1.1E-05 29.9 4.4 29 88-116 13-43 (68)
158 PF01418 HTH_6: Helix-turn-hel 91.3 0.34 7.4E-06 31.4 3.6 42 82-123 20-62 (77)
159 PRK09744 DNA-binding transcrip 91.2 0.75 1.6E-05 30.2 5.1 36 97-135 12-47 (75)
160 PRK00118 putative DNA-binding 91.1 0.53 1.2E-05 32.8 4.6 33 85-117 23-55 (104)
161 COG3415 Transposase and inacti 90.8 0.68 1.5E-05 33.9 5.2 36 82-117 8-43 (138)
162 smart00419 HTH_CRP helix_turn_ 90.7 0.37 7.9E-06 27.5 3.1 24 94-117 7-30 (48)
163 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 90.7 0.99 2.1E-05 27.4 5.0 35 85-119 10-44 (50)
164 cd01105 HTH_GlnR-like Helix-Tu 90.5 0.48 1E-05 31.6 3.9 23 95-117 1-23 (88)
165 cd04773 HTH_TioE_rpt2 Second H 90.3 0.46 1E-05 32.9 3.8 22 96-117 1-22 (108)
166 PF07638 Sigma70_ECF: ECF sigm 90.3 0.56 1.2E-05 35.2 4.5 32 85-116 141-172 (185)
167 PF05930 Phage_AlpA: Prophage 90.2 0.09 1.9E-06 31.6 0.1 28 96-123 4-31 (51)
168 PF13551 HTH_29: Winged helix- 90.2 0.5 1.1E-05 31.8 3.8 27 91-117 7-34 (112)
169 PRK10072 putative transcriptio 90.1 0.29 6.3E-06 33.6 2.6 27 29-55 47-73 (96)
170 cd04780 HTH_MerR-like_sg5 Heli 90.1 1.7 3.7E-05 29.4 6.4 65 33-107 5-70 (95)
171 cd00592 HTH_MerR-like Helix-Tu 90.0 0.94 2E-05 30.4 5.1 22 96-117 1-22 (100)
172 KOG1168 Transcription factor A 90.0 0.16 3.6E-06 41.6 1.5 38 80-117 219-265 (385)
173 PF13022 HTH_Tnp_1_2: Helix-tu 89.9 0.33 7.2E-06 35.6 2.9 25 95-119 34-58 (142)
174 PF02042 RWP-RK: RWP-RK domain 89.8 0.87 1.9E-05 27.8 4.2 31 87-117 7-37 (52)
175 smart00420 HTH_DEOR helix_turn 89.8 1 2.2E-05 25.9 4.5 26 91-116 10-35 (53)
176 cd01105 HTH_GlnR-like Helix-Tu 89.5 2.1 4.6E-05 28.4 6.4 63 33-106 6-69 (88)
177 cd04766 HTH_HspR Helix-Turn-He 89.5 2 4.3E-05 28.5 6.3 63 33-106 6-69 (91)
178 cd01106 HTH_TipAL-Mta Helix-Tu 89.5 0.6 1.3E-05 31.8 3.8 22 96-117 1-22 (103)
179 PF09339 HTH_IclR: IclR helix- 89.3 0.34 7.4E-06 28.9 2.2 25 93-117 16-40 (52)
180 COG2512 Predicted membrane-ass 89.2 0.88 1.9E-05 36.5 5.1 41 77-117 191-232 (258)
181 COG0789 SoxR Predicted transcr 89.1 0.64 1.4E-05 32.2 3.8 22 96-117 1-22 (124)
182 cd01107 HTH_BmrR Helix-Turn-He 89.0 0.66 1.4E-05 32.0 3.8 22 96-117 1-22 (108)
183 cd04789 HTH_Cfa Helix-Turn-Hel 88.8 0.72 1.6E-05 31.6 3.8 22 96-117 2-23 (102)
184 cd04768 HTH_BmrR-like Helix-Tu 88.8 0.71 1.5E-05 31.2 3.8 23 96-118 1-23 (96)
185 PRK04132 replication factor C 88.8 0.67 1.5E-05 43.1 4.6 43 98-140 420-462 (846)
186 COG1522 Lrp Transcriptional re 88.8 0.86 1.9E-05 32.6 4.4 33 84-116 11-43 (154)
187 cd04774 HTH_YfmP Helix-Turn-He 88.7 0.74 1.6E-05 31.2 3.8 22 96-117 1-22 (96)
188 cd04769 HTH_MerR2 Helix-Turn-H 88.7 0.72 1.6E-05 32.2 3.8 22 96-117 1-22 (116)
189 COG3311 AlpA Predicted transcr 88.6 0.43 9.3E-06 31.0 2.4 31 96-126 14-44 (70)
190 PF08220 HTH_DeoR: DeoR-like h 88.6 0.97 2.1E-05 27.6 4.0 31 86-116 5-35 (57)
191 TIGR02885 spore_sigF RNA polym 88.5 0.9 1.9E-05 35.0 4.6 28 91-118 195-222 (231)
192 cd04765 HTH_MlrA-like_sg2 Heli 88.5 0.53 1.2E-05 32.2 3.0 22 96-117 1-22 (99)
193 cd04788 HTH_NolA-AlbR Helix-Tu 88.5 0.79 1.7E-05 31.0 3.8 22 96-117 1-22 (96)
194 PF00356 LacI: Bacterial regul 88.5 1.1 2.3E-05 26.6 3.9 21 33-53 4-24 (46)
195 cd04772 HTH_TioE_rpt1 First He 88.4 0.79 1.7E-05 31.2 3.8 22 96-117 1-22 (99)
196 PHA01976 helix-turn-helix prot 88.3 0.42 9.2E-06 29.6 2.2 26 29-54 16-41 (67)
197 TIGR03070 couple_hipB transcri 88.3 0.5 1.1E-05 27.9 2.4 25 30-54 17-41 (58)
198 PRK10458 DNA cytosine methylas 88.2 1.7 3.7E-05 37.8 6.5 46 90-135 24-78 (467)
199 cd04782 HTH_BltR Helix-Turn-He 88.2 0.83 1.8E-05 30.9 3.8 22 96-117 1-22 (97)
200 cd04775 HTH_Cfa-like Helix-Tur 88.1 0.85 1.8E-05 31.2 3.8 22 96-117 2-23 (102)
201 PRK11891 aspartate carbamoyltr 88.1 0.87 1.9E-05 39.2 4.6 35 83-117 4-38 (429)
202 smart00497 IENR1 Intron encode 87.9 0.87 1.9E-05 26.8 3.3 25 97-121 19-43 (53)
203 cd04780 HTH_MerR-like_sg5 Heli 87.7 0.94 2E-05 30.7 3.8 22 96-117 1-22 (95)
204 cd01107 HTH_BmrR Helix-Turn-He 87.7 3.1 6.8E-05 28.6 6.5 67 33-109 5-72 (108)
205 smart00422 HTH_MERR helix_turn 87.7 4 8.6E-05 25.1 6.5 63 32-106 4-68 (70)
206 cd04765 HTH_MlrA-like_sg2 Heli 87.4 2.9 6.2E-05 28.5 6.1 63 33-106 5-69 (99)
207 TIGR03697 NtcA_cyano global ni 87.3 1.5 3.3E-05 32.1 5.1 24 94-117 142-165 (193)
208 PF00165 HTH_AraC: Bacterial r 87.3 0.97 2.1E-05 25.6 3.2 27 94-120 7-33 (42)
209 smart00345 HTH_GNTR helix_turn 87.3 1.7 3.6E-05 25.7 4.4 22 95-116 19-41 (60)
210 cd04766 HTH_HspR Helix-Turn-He 87.3 0.97 2.1E-05 30.1 3.6 22 96-117 2-23 (91)
211 PF01978 TrmB: Sugar-specific 87.2 1.1 2.4E-05 28.0 3.7 34 84-117 11-44 (68)
212 cd01109 HTH_YyaN Helix-Turn-He 87.2 1 2.2E-05 31.2 3.8 22 96-117 1-22 (113)
213 cd04786 HTH_MerR-like_sg7 Heli 87.2 1 2.2E-05 32.4 3.9 22 96-117 1-22 (131)
214 PRK11512 DNA-binding transcrip 87.2 1.9 4.1E-05 30.9 5.3 36 81-116 40-75 (144)
215 cd06170 LuxR_C_like C-terminal 87.1 0.96 2.1E-05 26.4 3.2 25 93-117 13-37 (57)
216 PRK15043 transcriptional regul 87.1 0.94 2E-05 36.1 4.0 23 95-117 3-25 (243)
217 cd01279 HTH_HspR-like Helix-Tu 87.0 1.1 2.3E-05 30.5 3.8 22 96-117 2-23 (98)
218 PF13730 HTH_36: Helix-turn-he 87.0 0.83 1.8E-05 27.2 2.9 21 97-117 27-47 (55)
219 PF13011 LZ_Tnp_IS481: leucine 87.0 2.9 6.3E-05 28.1 5.7 32 86-117 16-47 (85)
220 TIGR03209 P21_Cbot clostridium 87.0 1.1 2.3E-05 31.7 4.0 30 84-113 112-141 (142)
221 PF12840 HTH_20: Helix-turn-he 87.0 1.2 2.5E-05 27.4 3.6 30 86-115 15-44 (61)
222 smart00354 HTH_LACI helix_turn 86.9 2.4 5.1E-05 26.8 5.1 50 32-105 4-53 (70)
223 cd01282 HTH_MerR-like_sg3 Heli 86.9 1.1 2.4E-05 31.1 3.8 22 96-117 1-22 (112)
224 PRK13413 mpi multiple promoter 86.8 1.3 2.9E-05 33.5 4.6 32 86-118 164-195 (200)
225 cd04767 HTH_HspR-like_MBC Heli 86.8 3.1 6.7E-05 29.7 6.1 68 33-112 6-74 (120)
226 PRK08215 sporulation sigma fac 86.7 1.3 2.9E-05 34.8 4.7 29 89-117 219-247 (258)
227 cd01111 HTH_MerD Helix-Turn-He 86.5 1.2 2.6E-05 30.9 3.8 22 96-117 1-22 (107)
228 PRK05572 sporulation sigma fac 86.4 1.4 3E-05 34.6 4.6 30 89-118 212-241 (252)
229 PRK11169 leucine-responsive tr 86.2 1.1 2.4E-05 33.1 3.7 31 84-114 17-47 (164)
230 COG1974 LexA SOS-response tran 86.2 0.9 2E-05 35.2 3.4 48 89-137 6-53 (201)
231 COG2973 TrpR Trp operon repres 86.2 2.4 5.1E-05 29.4 5.0 55 80-134 43-99 (103)
232 TIGR02044 CueR Cu(I)-responsiv 86.2 1.2 2.6E-05 31.6 3.8 22 96-117 1-22 (127)
233 TIGR00122 birA_repr_reg BirA b 86.1 2.1 4.5E-05 26.8 4.5 27 91-117 9-35 (69)
234 PF01710 HTH_Tnp_IS630: Transp 86.0 1.7 3.7E-05 30.5 4.5 37 80-117 4-40 (119)
235 COG1318 Predicted transcriptio 86.0 1.2 2.6E-05 33.9 3.8 33 89-121 55-87 (182)
236 cd04788 HTH_NolA-AlbR Helix-Tu 85.9 6.5 0.00014 26.4 7.2 65 33-108 5-70 (96)
237 PRK00215 LexA repressor; Valid 85.9 1.8 3.9E-05 32.8 5.0 35 82-116 8-45 (205)
238 PRK12427 flagellar biosynthesi 85.9 1.6 3.4E-05 34.1 4.6 29 89-117 193-221 (231)
239 cd04781 HTH_MerR-like_sg6 Heli 85.8 1.3 2.8E-05 31.1 3.8 22 96-117 1-22 (120)
240 PRK06759 RNA polymerase factor 85.7 1.9 4E-05 30.6 4.6 33 85-117 112-144 (154)
241 PF13309 HTH_22: HTH domain 85.7 2.5 5.3E-05 26.6 4.7 21 97-117 44-64 (64)
242 TIGR02395 rpoN_sigma RNA polym 85.6 0.27 5.9E-06 42.1 0.3 42 95-136 318-359 (429)
243 TIGR01636 phage_rinA phage tra 85.6 3.9 8.5E-05 29.3 6.3 35 95-136 100-134 (134)
244 TIGR03001 Sig-70_gmx1 RNA poly 85.6 1.4 3.1E-05 34.7 4.3 55 85-139 167-222 (244)
245 cd01279 HTH_HspR-like Helix-Tu 85.5 4.9 0.00011 27.2 6.5 64 33-107 6-70 (98)
246 cd04783 HTH_MerR1 Helix-Turn-H 85.4 0.97 2.1E-05 31.9 3.0 22 96-117 1-22 (126)
247 TIGR02999 Sig-70_X6 RNA polyme 85.4 1.9 4E-05 31.6 4.7 32 85-116 140-171 (183)
248 PF00196 GerE: Bacterial regul 85.3 0.94 2E-05 27.5 2.5 26 92-117 15-40 (58)
249 TIGR02850 spore_sigG RNA polym 85.2 1.7 3.7E-05 34.2 4.6 28 90-117 217-244 (254)
250 PF00440 TetR_N: Bacterial reg 85.2 4.2 9.1E-05 23.5 5.3 32 86-117 7-38 (47)
251 TIGR02392 rpoH_proteo alternat 85.2 1.6 3.5E-05 34.7 4.5 24 94-117 235-258 (270)
252 cd01108 HTH_CueR Helix-Turn-He 85.2 1.2 2.7E-05 31.5 3.5 22 96-117 1-22 (127)
253 PRK07037 extracytoplasmic-func 84.8 2.1 4.6E-05 30.7 4.7 30 87-116 117-146 (163)
254 PF07453 NUMOD1: NUMOD1 domain 84.8 1.3 2.8E-05 24.5 2.8 19 97-115 18-36 (37)
255 TIGR02985 Sig70_bacteroi1 RNA 84.7 2.2 4.8E-05 30.0 4.7 29 89-117 123-151 (161)
256 PRK12469 RNA polymerase factor 84.7 0.45 9.8E-06 41.5 1.2 44 95-138 369-412 (481)
257 PRK10840 transcriptional regul 84.5 2.9 6.3E-05 31.3 5.5 49 93-141 163-215 (216)
258 PRK09526 lacI lac repressor; R 84.4 2.1 4.5E-05 34.2 4.8 50 31-104 8-57 (342)
259 cd04777 HTH_MerR-like_sg1 Heli 84.4 1.7 3.6E-05 29.8 3.7 22 96-117 1-22 (107)
260 PRK11924 RNA polymerase sigma 84.3 2 4.4E-05 30.9 4.4 28 90-117 136-163 (179)
261 TIGR02393 RpoD_Cterm RNA polym 84.2 1.9 4.2E-05 33.5 4.5 25 93-117 194-218 (238)
262 PRK13832 plasmid partitioning 84.2 3.2 7E-05 36.6 6.1 49 81-131 105-153 (520)
263 PF01381 HTH_3: Helix-turn-hel 84.2 0.93 2E-05 26.8 2.1 25 30-54 11-35 (55)
264 PRK05932 RNA polymerase factor 84.1 0.49 1.1E-05 40.9 1.2 43 95-137 343-385 (455)
265 cd04767 HTH_HspR-like_MBC Heli 84.1 1.7 3.7E-05 31.0 3.8 22 96-117 2-23 (120)
266 TIGR02054 MerD mercuric resist 84.1 1.9 4.2E-05 30.6 4.1 23 95-117 3-25 (120)
267 PRK11161 fumarate/nitrate redu 83.9 2.3 4.9E-05 32.5 4.7 22 95-116 184-205 (235)
268 PRK14987 gluconate operon tran 83.9 2.2 4.7E-05 34.0 4.7 50 31-104 8-57 (331)
269 TIGR02980 SigBFG RNA polymeras 83.8 2.2 4.8E-05 32.6 4.6 31 87-117 186-216 (227)
270 cd01110 HTH_SoxR Helix-Turn-He 83.7 1.7 3.8E-05 31.4 3.8 22 96-117 2-23 (139)
271 PRK09391 fixK transcriptional 83.7 2.2 4.8E-05 32.8 4.6 23 94-116 178-200 (230)
272 PF01022 HTH_5: Bacterial regu 83.7 1.8 3.8E-05 25.2 3.1 26 91-116 11-36 (47)
273 PRK11179 DNA-binding transcrip 83.5 2.3 5E-05 31.0 4.4 31 84-114 12-42 (153)
274 PRK01905 DNA-binding protein F 83.5 3.2 6.9E-05 26.9 4.6 34 84-117 39-72 (77)
275 PRK13918 CRP/FNR family transc 83.5 1.2 2.6E-05 33.1 2.9 23 94-116 148-170 (202)
276 PRK00430 fis global DNA-bindin 83.4 3 6.6E-05 28.4 4.7 33 85-117 58-90 (95)
277 PF09048 Cro: Cro; InterPro: 83.4 1.1 2.4E-05 28.1 2.2 32 87-120 6-37 (59)
278 smart00346 HTH_ICLR helix_turn 83.4 2.9 6.3E-05 27.1 4.5 23 94-116 19-41 (91)
279 cd04785 HTH_CadR-PbrR-like Hel 83.4 1.9 4.2E-05 30.5 3.8 22 96-117 1-22 (126)
280 PHA01082 putative transcriptio 83.3 0.94 2E-05 32.5 2.1 40 92-131 27-67 (133)
281 cd04769 HTH_MerR2 Helix-Turn-H 83.3 6 0.00013 27.5 6.3 63 33-107 5-68 (116)
282 TIGR02989 Sig-70_gvs1 RNA poly 83.2 2.7 5.8E-05 29.9 4.6 32 85-116 117-148 (159)
283 smart00344 HTH_ASNC helix_turn 83.1 2.8 6.1E-05 28.2 4.4 30 87-116 9-38 (108)
284 PRK09047 RNA polymerase factor 83.0 2.6 5.7E-05 30.0 4.5 31 87-117 114-144 (161)
285 PRK12529 RNA polymerase sigma 83.0 2.7 5.8E-05 31.0 4.7 33 85-117 133-165 (178)
286 cd04776 HTH_GnyR Helix-Turn-He 83.0 2 4.4E-05 30.1 3.8 22 96-117 1-22 (118)
287 PRK11753 DNA-binding transcrip 83.0 1.3 2.9E-05 33.0 3.0 23 95-117 168-190 (211)
288 PRK09652 RNA polymerase sigma 82.8 2.7 5.9E-05 30.3 4.6 29 89-117 138-166 (182)
289 PRK12519 RNA polymerase sigma 82.8 2 4.4E-05 31.8 4.0 29 89-117 151-179 (194)
290 PF09571 RE_XcyI: XcyI restric 82.8 0.8 1.7E-05 37.4 1.8 65 71-135 61-128 (318)
291 COG2963 Transposase and inacti 82.8 3.9 8.5E-05 28.1 5.1 40 78-117 7-47 (116)
292 cd04770 HTH_HMRTR Helix-Turn-H 82.8 2.1 4.6E-05 29.9 3.8 22 96-117 1-22 (123)
293 smart00347 HTH_MARR helix_turn 82.7 4.8 0.0001 26.0 5.4 37 80-116 9-45 (101)
294 cd04787 HTH_HMRTR_unk Helix-Tu 82.7 2.1 4.6E-05 30.5 3.8 22 96-117 1-22 (133)
295 PRK10727 DNA-binding transcrip 82.5 2.4 5.2E-05 34.0 4.6 21 33-53 6-26 (343)
296 PF00376 MerR: MerR family reg 82.5 1.2 2.5E-05 25.3 1.9 19 33-51 4-22 (38)
297 PRK06986 fliA flagellar biosyn 82.5 2.5 5.5E-05 32.7 4.5 33 85-117 190-222 (236)
298 TIGR02937 sigma70-ECF RNA poly 82.3 2.9 6.2E-05 28.6 4.3 27 91-117 122-148 (158)
299 PRK10423 transcriptional repre 82.2 3 6.4E-05 33.0 4.9 20 33-52 3-22 (327)
300 TIGR02047 CadR-PbrR Cd(II)/Pb( 82.2 1.9 4.2E-05 30.6 3.4 22 96-117 1-22 (127)
301 PRK09514 zntR zinc-responsive 82.2 2.1 4.6E-05 30.9 3.7 22 96-117 2-23 (140)
302 PRK10227 DNA-binding transcrip 82.2 2 4.4E-05 31.0 3.6 22 96-117 1-22 (135)
303 PRK09639 RNA polymerase sigma 82.2 3 6.4E-05 30.0 4.5 32 85-117 118-149 (166)
304 PRK08583 RNA polymerase sigma 82.1 2.8 6.2E-05 32.8 4.7 29 89-117 215-243 (257)
305 PRK09642 RNA polymerase sigma 81.9 3.1 6.7E-05 29.8 4.5 32 85-116 112-143 (160)
306 PRK09954 putative kinase; Prov 81.9 3.3 7.2E-05 34.0 5.2 33 85-117 7-39 (362)
307 PF08822 DUF1804: Protein of u 81.9 4.2 9.2E-05 30.6 5.3 37 81-117 5-41 (165)
308 TIGR01950 SoxR redox-sensitive 81.8 2.3 4.9E-05 31.0 3.7 22 96-117 2-23 (142)
309 PF06322 Phage_NinH: Phage Nin 81.7 2.9 6.3E-05 26.5 3.7 24 96-119 17-40 (64)
310 TIGR02043 ZntR Zn(II)-responsi 81.6 2.4 5.3E-05 30.2 3.8 22 96-117 2-23 (131)
311 TIGR02947 SigH_actino RNA poly 81.6 0.95 2E-05 33.7 1.7 49 90-139 142-191 (193)
312 PRK15411 rcsA colanic acid cap 81.5 2 4.2E-05 32.8 3.5 26 92-117 149-174 (207)
313 PRK15002 redox-sensitivie tran 81.5 7.8 0.00017 28.7 6.6 64 32-107 15-79 (154)
314 PF04552 Sigma54_DBD: Sigma-54 81.4 1.6 3.4E-05 32.7 2.8 90 33-122 54-153 (160)
315 TIGR02366 DHAK_reg probable di 81.3 4.3 9.2E-05 29.5 5.2 38 82-119 7-47 (176)
316 PF13560 HTH_31: Helix-turn-he 81.3 1.6 3.4E-05 26.9 2.4 25 30-54 16-40 (64)
317 PRK12523 RNA polymerase sigma 81.3 3.5 7.5E-05 30.1 4.7 32 85-116 125-156 (172)
318 PRK07408 RNA polymerase sigma 81.2 3.1 6.8E-05 32.8 4.7 27 91-117 215-241 (256)
319 PRK06596 RNA polymerase factor 81.1 1.7 3.7E-05 35.0 3.1 24 94-117 247-270 (284)
320 PRK09645 RNA polymerase sigma 81.1 3.5 7.5E-05 29.9 4.6 31 86-116 125-155 (173)
321 PRK12537 RNA polymerase sigma 81.0 3.3 7.1E-05 30.5 4.5 31 87-117 141-171 (182)
322 cd04782 HTH_BltR Helix-Turn-He 81.0 6.2 0.00014 26.5 5.5 64 33-107 5-69 (97)
323 TIGR02051 MerR Hg(II)-responsi 80.9 1.8 3.9E-05 30.6 2.9 21 97-117 1-21 (124)
324 PRK07122 RNA polymerase sigma 80.9 3 6.6E-05 33.1 4.5 29 89-117 225-253 (264)
325 cd00592 HTH_MerR-like Helix-Tu 80.8 9.5 0.00021 25.4 6.4 62 33-106 5-67 (100)
326 PRK13749 transcriptional regul 80.8 2.8 6E-05 29.9 3.8 23 95-117 3-25 (121)
327 PRK15320 transcriptional activ 80.8 2 4.4E-05 33.8 3.3 27 91-117 175-201 (251)
328 cd07377 WHTH_GntR Winged helix 80.6 7.5 0.00016 23.2 5.4 20 97-116 27-46 (66)
329 cd04773 HTH_TioE_rpt2 Second H 80.6 9.9 0.00021 26.1 6.5 63 33-106 5-68 (108)
330 PRK09649 RNA polymerase sigma 80.6 3.3 7.2E-05 30.7 4.4 33 84-116 135-167 (185)
331 cd04790 HTH_Cfa-like_unk Helix 80.6 2.6 5.7E-05 31.6 3.8 22 96-117 2-23 (172)
332 PF01325 Fe_dep_repress: Iron 80.3 4.3 9.3E-05 25.1 4.1 34 83-116 9-43 (60)
333 PRK13919 putative RNA polymera 80.3 3.8 8.2E-05 30.1 4.6 31 87-117 143-173 (186)
334 PRK15002 redox-sensitivie tran 80.0 3.1 6.7E-05 30.8 4.0 27 91-117 7-33 (154)
335 cd01111 HTH_MerD Helix-Turn-He 79.9 12 0.00025 25.8 6.7 63 33-106 5-68 (107)
336 COG3413 Predicted DNA binding 79.8 2.1 4.6E-05 32.9 3.2 24 94-117 177-200 (215)
337 PRK12423 LexA repressor; Provi 79.8 5 0.00011 30.6 5.3 35 80-114 8-45 (202)
338 TIGR02337 HpaR homoprotocatech 79.8 5 0.00011 27.5 4.9 34 83-116 30-63 (118)
339 TIGR02051 MerR Hg(II)-responsi 79.7 6.2 0.00013 27.8 5.4 65 33-108 4-69 (124)
340 TIGR02405 trehalos_R_Ecol treh 79.7 4.1 8.8E-05 32.3 4.9 21 32-52 5-25 (311)
341 PRK12547 RNA polymerase sigma 79.7 4.2 9.1E-05 29.4 4.6 33 85-117 118-150 (164)
342 PRK12511 RNA polymerase sigma 79.6 3.8 8.3E-05 30.5 4.5 31 87-117 119-149 (182)
343 cd01109 HTH_YyaN Helix-Turn-He 79.6 11 0.00024 25.9 6.6 63 33-106 5-68 (113)
344 TIGR02394 rpoS_proteo RNA poly 79.5 4.5 9.8E-05 32.3 5.1 43 93-139 240-282 (285)
345 PRK13752 putative transcriptio 79.4 2.1 4.6E-05 31.2 2.9 23 95-117 7-29 (144)
346 TIGR02941 Sigma_B RNA polymera 79.4 3.9 8.4E-05 32.0 4.6 32 86-117 212-243 (255)
347 PRK05911 RNA polymerase sigma 79.3 3.9 8.5E-05 32.3 4.7 29 89-117 215-243 (257)
348 cd08316 Death_FAS_TNFRSF6 Deat 79.3 8.2 0.00018 26.4 5.6 39 82-120 6-45 (97)
349 TIGR01481 ccpA catabolite cont 79.3 3.7 7.9E-05 32.5 4.5 20 33-52 6-25 (329)
350 TIGR02954 Sig70_famx3 RNA poly 79.3 3.9 8.5E-05 29.6 4.4 33 85-117 125-157 (169)
351 TIGR02479 FliA_WhiG RNA polyme 79.3 4.1 8.9E-05 31.2 4.7 30 88-117 184-213 (224)
352 PF13556 HTH_30: PucR C-termin 79.3 7 0.00015 23.8 4.9 37 93-140 10-46 (59)
353 PF10078 DUF2316: Uncharacteri 79.2 6.5 0.00014 26.7 5.0 36 83-118 11-46 (89)
354 PRK12534 RNA polymerase sigma 79.2 4 8.7E-05 30.0 4.4 29 89-117 147-175 (187)
355 PRK08301 sporulation sigma fac 79.2 4 8.6E-05 31.4 4.6 25 93-117 196-220 (234)
356 PRK13869 plasmid-partitioning 79.1 3.4 7.5E-05 35.0 4.5 43 94-136 47-101 (405)
357 cd04779 HTH_MerR-like_sg4 Heli 79.1 3.2 6.9E-05 30.0 3.7 22 96-117 1-22 (134)
358 TIGR03453 partition_RepA plasm 79.1 5 0.00011 33.5 5.4 43 94-136 32-86 (387)
359 cd04768 HTH_BmrR-like Helix-Tu 79.1 16 0.00036 24.4 7.6 65 33-108 5-70 (96)
360 PRK12516 RNA polymerase sigma 79.0 4.2 9.2E-05 30.3 4.6 33 85-117 122-154 (187)
361 TIGR02959 SigZ RNA polymerase 79.0 4.6 0.0001 29.5 4.7 33 85-117 106-138 (170)
362 TIGR02952 Sig70_famx2 RNA poly 78.9 4.7 0.0001 28.9 4.6 31 86-116 129-159 (170)
363 TIGR02983 SigE-fam_strep RNA p 78.9 4 8.6E-05 29.2 4.3 32 86-117 117-148 (162)
364 TIGR02984 Sig-70_plancto1 RNA 78.8 4.7 0.0001 29.4 4.7 30 87-116 148-177 (189)
365 cd01106 HTH_TipAL-Mta Helix-Tu 78.7 13 0.00029 25.1 6.6 65 33-108 5-70 (103)
366 TIGR02417 fruct_sucro_rep D-fr 78.6 4.2 9.1E-05 32.3 4.7 21 33-53 4-24 (327)
367 COG1609 PurR Transcriptional r 78.5 4.2 9.2E-05 33.3 4.8 50 33-106 5-54 (333)
368 PRK11608 pspF phage shock prot 78.5 3.8 8.3E-05 33.5 4.5 33 85-117 289-321 (326)
369 PRK05602 RNA polymerase sigma 78.5 4.2 9.1E-05 29.9 4.4 29 89-117 138-166 (186)
370 PRK09492 treR trehalose repres 78.4 4.4 9.6E-05 31.9 4.7 22 31-52 7-28 (315)
371 PRK12542 RNA polymerase sigma 78.4 4.5 9.8E-05 29.8 4.5 32 85-116 128-159 (185)
372 PRK12528 RNA polymerase sigma 78.2 5.1 0.00011 28.7 4.7 32 85-116 119-150 (161)
373 PRK13749 transcriptional regul 78.2 13 0.00029 26.4 6.7 63 32-107 7-72 (121)
374 cd01110 HTH_SoxR Helix-Turn-He 78.1 12 0.00026 27.0 6.5 62 33-106 6-68 (139)
375 cd04776 HTH_GnyR Helix-Turn-He 78.1 11 0.00025 26.3 6.3 62 33-107 5-67 (118)
376 PRK12524 RNA polymerase sigma 78.1 4.7 0.0001 30.1 4.6 32 86-117 143-174 (196)
377 TIGR02997 Sig70-cyanoRpoD RNA 78.1 4.1 8.9E-05 32.9 4.5 25 93-117 267-291 (298)
378 PF00126 HTH_1: Bacterial regu 78.1 5.6 0.00012 24.2 4.2 31 97-138 15-45 (60)
379 PF08280 HTH_Mga: M protein tr 78.0 4.9 0.00011 24.6 3.9 31 87-117 11-41 (59)
380 PF07900 DUF1670: Protein of u 78.0 5.1 0.00011 31.5 4.8 29 88-116 97-126 (220)
381 PRK12532 RNA polymerase sigma 77.8 4.3 9.4E-05 30.2 4.3 31 87-117 144-174 (195)
382 PF07471 Phage_Nu1: Phage DNA 77.8 1.3 2.8E-05 33.2 1.4 23 95-117 2-24 (164)
383 PRK09647 RNA polymerase sigma 77.7 4.9 0.00011 30.5 4.6 30 88-117 147-176 (203)
384 COG0789 SoxR Predicted transcr 77.7 13 0.00028 25.5 6.4 65 33-108 5-70 (124)
385 PRK12545 RNA polymerase sigma 77.6 4.5 9.8E-05 30.5 4.4 33 85-117 145-177 (201)
386 PRK12527 RNA polymerase sigma 77.5 5 0.00011 28.7 4.4 33 85-117 111-143 (159)
387 PRK12530 RNA polymerase sigma 77.5 4.9 0.00011 29.9 4.5 33 85-117 140-172 (189)
388 PRK09726 antitoxin HipB; Provi 77.5 2.2 4.7E-05 28.2 2.3 27 28-54 25-51 (88)
389 PRK06930 positive control sigm 77.4 5.3 0.00012 29.9 4.6 31 87-117 122-152 (170)
390 COG2771 CsgD DNA-binding HTH d 77.3 7.9 0.00017 23.1 4.7 29 89-117 13-41 (65)
391 cd04775 HTH_Cfa-like Helix-Tur 77.2 15 0.00032 24.9 6.5 64 33-108 6-70 (102)
392 PRK13509 transcriptional repre 77.2 5.4 0.00012 31.5 4.9 33 85-117 9-41 (251)
393 COG4565 CitB Response regulato 77.1 6.7 0.00015 30.9 5.2 38 80-117 156-195 (224)
394 PRK07500 rpoH2 RNA polymerase 77.0 4.6 0.0001 32.6 4.5 24 94-117 244-267 (289)
395 COG2197 CitB Response regulato 77.0 3.2 7E-05 31.8 3.5 27 91-117 159-185 (211)
396 smart00418 HTH_ARSR helix_turn 76.9 5.5 0.00012 23.2 3.9 25 93-117 8-32 (66)
397 TIGR02702 SufR_cyano iron-sulf 76.9 5.2 0.00011 30.4 4.6 30 87-116 7-36 (203)
398 PRK09706 transcriptional repre 76.9 2 4.3E-05 30.6 2.1 25 30-54 20-44 (135)
399 PRK10046 dpiA two-component re 76.9 2.7 5.9E-05 31.9 3.0 23 95-117 177-199 (225)
400 COG1595 RpoE DNA-directed RNA 76.7 4.8 0.0001 29.7 4.3 30 88-117 136-165 (182)
401 PRK10411 DNA-binding transcrip 76.6 6.5 0.00014 30.9 5.2 33 85-117 8-40 (240)
402 cd04786 HTH_MerR-like_sg7 Heli 76.6 9.4 0.0002 27.3 5.6 63 33-106 5-68 (131)
403 TIGR02974 phageshock_pspF psp 76.6 4.9 0.00011 33.1 4.6 34 84-117 294-327 (329)
404 PRK10014 DNA-binding transcrip 76.4 5.4 0.00012 31.8 4.7 24 30-53 8-31 (342)
405 PRK11923 algU RNA polymerase s 76.3 5.4 0.00012 29.5 4.4 33 85-117 144-176 (193)
406 PRK11361 acetoacetate metaboli 76.0 4.9 0.00011 33.8 4.6 34 84-117 419-452 (457)
407 PRK11050 manganese transport r 76.0 8 0.00017 28.2 5.2 34 83-116 38-72 (152)
408 smart00342 HTH_ARAC helix_turn 76.0 6.8 0.00015 24.1 4.3 22 96-117 2-23 (84)
409 PRK09483 response regulator; P 75.9 6.5 0.00014 28.7 4.8 44 92-135 160-207 (217)
410 cd04779 HTH_MerR-like_sg4 Heli 75.9 13 0.00028 26.8 6.2 62 33-106 5-67 (134)
411 PRK10401 DNA-binding transcrip 75.8 5.4 0.00012 32.0 4.6 20 33-52 6-25 (346)
412 PRK12525 RNA polymerase sigma 75.8 6.4 0.00014 28.5 4.6 30 87-116 126-155 (168)
413 PRK09648 RNA polymerase sigma 75.7 6.3 0.00014 29.1 4.7 32 85-116 145-176 (189)
414 PRK12515 RNA polymerase sigma 75.7 6.2 0.00013 29.1 4.6 31 86-116 138-168 (189)
415 PRK06288 RNA polymerase sigma 75.7 6.1 0.00013 31.2 4.8 30 88-117 221-250 (268)
416 PRK12520 RNA polymerase sigma 75.5 6.1 0.00013 29.2 4.6 32 86-117 138-169 (191)
417 PRK12526 RNA polymerase sigma 75.5 6.1 0.00013 29.9 4.6 28 89-116 163-190 (206)
418 PRK03573 transcriptional regul 75.5 7 0.00015 27.7 4.7 32 85-116 35-67 (144)
419 TIGR02054 MerD mercuric resist 75.5 15 0.00033 26.0 6.3 65 32-107 7-72 (120)
420 PRK09646 RNA polymerase sigma 75.4 6.1 0.00013 29.4 4.6 30 87-116 150-179 (194)
421 PRK15201 fimbriae regulatory p 75.2 4.8 0.0001 31.0 3.9 26 92-117 145-170 (198)
422 PF06892 Phage_CP76: Phage reg 75.1 17 0.00037 27.1 6.8 53 81-135 8-62 (162)
423 TIGR02044 CueR Cu(I)-responsiv 75.1 19 0.0004 25.4 6.8 63 33-106 5-68 (127)
424 PRK10365 transcriptional regul 75.1 5.9 0.00013 33.1 4.8 33 84-116 407-439 (441)
425 PF04703 FaeA: FaeA-like prote 75.1 4.6 0.0001 25.4 3.2 25 93-117 13-37 (62)
426 TIGR02043 ZntR Zn(II)-responsi 75.1 16 0.00036 25.9 6.5 63 33-106 6-69 (131)
427 PRK15115 response regulator Gl 75.0 4.9 0.00011 33.7 4.3 33 85-117 401-433 (444)
428 PRK12514 RNA polymerase sigma 74.9 6.5 0.00014 28.7 4.5 28 89-116 139-166 (179)
429 PRK09641 RNA polymerase sigma 74.8 6.1 0.00013 28.8 4.3 29 89-117 146-174 (187)
430 TIGR03826 YvyF flagellar opero 74.8 5.3 0.00011 29.2 3.9 57 83-139 32-92 (137)
431 PRK03341 arginine repressor; P 74.8 6.1 0.00013 29.7 4.3 35 83-117 16-56 (168)
432 cd04785 HTH_CadR-PbrR-like Hel 74.8 17 0.00037 25.6 6.5 64 33-107 5-69 (126)
433 PRK12536 RNA polymerase sigma 74.7 6.7 0.00014 28.8 4.6 28 89-116 139-166 (181)
434 PRK12543 RNA polymerase sigma 74.7 6.9 0.00015 28.7 4.6 33 85-117 123-155 (179)
435 PF01726 LexA_DNA_bind: LexA D 74.7 9.5 0.0002 24.0 4.6 36 81-116 9-47 (65)
436 COG1309 AcrR Transcriptional r 74.6 2.3 5.1E-05 29.4 2.0 30 91-120 28-57 (201)
437 PF13463 HTH_27: Winged helix 74.6 5.7 0.00012 24.2 3.6 31 87-117 9-40 (68)
438 PRK12540 RNA polymerase sigma 74.4 6.6 0.00014 29.1 4.5 31 87-117 119-149 (182)
439 PF04297 UPF0122: Putative hel 74.3 3.1 6.7E-05 28.9 2.4 44 88-135 26-69 (101)
440 TIGR01818 ntrC nitrogen regula 74.3 5.9 0.00013 33.4 4.7 32 85-116 429-460 (463)
441 cd00090 HTH_ARSR Arsenical Res 74.2 11 0.00024 22.4 4.9 23 95-117 20-42 (78)
442 PRK11303 DNA-binding transcrip 74.2 6.7 0.00014 31.0 4.7 21 33-53 5-25 (328)
443 PRK12531 RNA polymerase sigma 74.1 6.5 0.00014 29.3 4.4 29 87-115 149-177 (194)
444 PRK10219 DNA-binding transcrip 74.1 18 0.00039 24.2 6.3 26 94-119 20-45 (107)
445 TIGR01884 cas_HTH CRISPR locus 74.0 9 0.00019 29.1 5.2 33 85-117 147-179 (203)
446 PRK13777 transcriptional regul 73.9 8.9 0.00019 29.2 5.1 37 79-115 43-79 (185)
447 PRK09637 RNA polymerase sigma 73.8 6.8 0.00015 29.0 4.4 31 86-116 113-143 (181)
448 TIGR01889 Staph_reg_Sar staphy 73.8 9.9 0.00021 25.9 4.9 25 93-117 41-65 (109)
449 COG1654 BirA Biotin operon rep 73.8 4 8.6E-05 27.0 2.8 21 96-116 20-40 (79)
450 PRK11475 DNA-binding transcrip 73.6 4.9 0.00011 30.8 3.7 26 92-117 146-171 (207)
451 PRK12546 RNA polymerase sigma 73.6 6.5 0.00014 29.4 4.3 33 85-117 119-151 (188)
452 PRK10703 DNA-binding transcrip 73.5 7.1 0.00015 31.1 4.8 20 33-52 6-25 (341)
453 PRK09480 slmA division inhibit 73.5 3.2 7E-05 30.3 2.6 27 94-120 29-55 (194)
454 PRK12533 RNA polymerase sigma 73.4 6.2 0.00013 30.4 4.2 31 87-117 142-172 (216)
455 PRK11302 DNA-binding transcrip 73.3 3.6 7.7E-05 32.5 2.9 37 83-119 21-58 (284)
456 TIGR02948 SigW_bacill RNA poly 73.2 6.5 0.00014 28.7 4.2 29 89-117 146-174 (187)
457 cd08804 Death_ank2 Death domai 73.2 12 0.00026 24.7 5.0 33 86-118 6-38 (84)
458 PRK09514 zntR zinc-responsive 73.1 19 0.00041 26.0 6.5 64 33-107 6-70 (140)
459 TIGR02943 Sig70_famx1 RNA poly 72.9 7.7 0.00017 28.9 4.6 30 87-116 139-168 (188)
460 cd04781 HTH_MerR-like_sg6 Heli 72.9 22 0.00047 24.8 6.6 64 33-108 5-69 (120)
461 TIGR01950 SoxR redox-sensitive 72.9 19 0.00042 26.1 6.5 62 33-106 6-68 (142)
462 PHA02535 P terminase ATPase su 72.9 7.2 0.00016 34.9 5.0 38 80-118 4-41 (581)
463 PRK15435 bifunctional DNA-bind 72.9 19 0.0004 30.1 7.2 37 83-119 87-123 (353)
464 PRK12517 RNA polymerase sigma 72.9 7.5 0.00016 28.9 4.5 28 90-117 139-166 (188)
465 PRK12512 RNA polymerase sigma 72.8 7.8 0.00017 28.4 4.5 30 87-116 139-168 (184)
466 smart00342 HTH_ARAC helix_turn 72.8 10 0.00022 23.3 4.5 26 92-117 47-73 (84)
467 PRK09651 RNA polymerase sigma 72.7 6.5 0.00014 28.7 4.1 31 86-116 126-156 (172)
468 PRK06811 RNA polymerase factor 72.6 8 0.00017 28.6 4.6 29 89-117 141-169 (189)
469 cd04778 HTH_MerR-like_sg2 Heli 72.6 5 0.00011 31.3 3.6 23 96-118 2-24 (219)
470 TIGR03454 partition_RepB plasm 72.4 8.1 0.00018 32.1 4.9 40 91-130 173-212 (325)
471 PRK07670 RNA polymerase sigma 72.2 7.7 0.00017 30.3 4.6 33 85-117 207-239 (251)
472 TIGR02329 propionate_PrpR prop 72.2 7 0.00015 34.5 4.7 34 84-117 492-525 (526)
473 PRK12522 RNA polymerase sigma 72.2 7.8 0.00017 28.1 4.4 28 89-116 129-156 (173)
474 TIGR02047 CadR-PbrR Cd(II)/Pb( 72.1 25 0.00053 24.8 6.8 64 33-107 5-69 (127)
475 TIGR02915 PEP_resp_reg putativ 72.0 6.4 0.00014 33.1 4.3 33 85-117 408-440 (445)
476 PRK09643 RNA polymerase sigma 72.0 7.7 0.00017 28.9 4.4 32 85-116 140-171 (192)
477 PRK05803 sporulation sigma fac 72.0 7.8 0.00017 29.9 4.5 24 94-117 194-217 (233)
478 COG3620 Predicted transcriptio 72.0 5.4 0.00012 30.3 3.4 25 30-54 20-44 (187)
479 PRK13752 putative transcriptio 71.9 20 0.00043 26.1 6.4 64 33-107 12-76 (144)
480 PF11268 DUF3071: Protein of u 71.9 5.4 0.00012 30.2 3.4 31 87-117 61-91 (170)
481 COG5484 Uncharacterized conser 71.9 6.6 0.00014 31.7 4.1 31 89-119 13-43 (279)
482 PHA00542 putative Cro-like pro 71.8 2.4 5.3E-05 27.8 1.4 25 30-54 33-57 (82)
483 cd04777 HTH_MerR-like_sg1 Heli 71.8 11 0.00024 25.6 4.8 62 33-107 5-67 (107)
484 PRK09415 RNA polymerase factor 71.7 7.6 0.00016 28.5 4.2 28 89-116 137-164 (179)
485 TIGR02846 spore_sigmaK RNA pol 71.7 8.3 0.00018 29.7 4.6 24 94-117 193-216 (227)
486 PRK14165 winged helix-turn-hel 71.7 4.1 8.8E-05 31.9 2.8 26 92-117 18-43 (217)
487 TIGR02939 RpoE_Sigma70 RNA pol 71.6 6.7 0.00015 28.7 3.9 28 89-116 148-175 (190)
488 COG1508 RpoN DNA-directed RNA 71.6 2.8 6.1E-05 36.3 2.1 43 96-138 331-373 (444)
489 PRK10430 DNA-binding transcrip 71.6 4.1 8.9E-05 31.1 2.9 25 93-117 176-200 (239)
490 PRK12513 RNA polymerase sigma 71.4 3.6 7.9E-05 30.5 2.5 25 92-116 152-176 (194)
491 PRK11557 putative DNA-binding 71.4 4.1 9E-05 32.1 2.9 35 83-117 17-52 (278)
492 PRK13866 plasmid partitioning 71.4 6.5 0.00014 32.9 4.1 42 89-130 173-214 (336)
493 PRK05901 RNA polymerase sigma 71.2 7.2 0.00016 34.4 4.5 25 94-118 466-490 (509)
494 PRK10923 glnG nitrogen regulat 71.1 7 0.00015 33.1 4.4 33 85-117 432-464 (469)
495 PRK10402 DNA-binding transcrip 71.0 4.1 8.9E-05 31.1 2.7 22 95-116 169-190 (226)
496 cd04787 HTH_HMRTR_unk Helix-Tu 71.0 24 0.00052 25.0 6.6 64 33-107 5-69 (133)
497 PRK11511 DNA-binding transcrip 70.9 14 0.0003 25.9 5.3 25 95-119 25-49 (127)
498 PF12116 SpoIIID: Stage III sp 70.9 6.6 0.00014 26.2 3.3 49 87-135 11-60 (82)
499 cd06571 Bac_DnaA_C C-terminal 70.8 8.3 0.00018 25.6 3.9 31 87-117 36-67 (90)
500 PRK10100 DNA-binding transcrip 70.7 8.6 0.00019 29.6 4.5 24 94-117 169-192 (216)
No 1
>KOG3398 consensus Transcription factor MBF1 [Transcription]
Probab=99.97 E-value=9.4e-31 Score=185.20 Aligned_cols=132 Identities=68% Similarity=0.951 Sum_probs=123.8
Q ss_pred CCCCCcee-eccCCCCCccccCHHHHHHHHHcCCChhHHHhhhcCCCCCCCCCCCcccccchhhhccccCCcchHHHHHH
Q 032366 8 TQDWEPVV-IKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKA 86 (142)
Q Consensus 8 ~~~w~~~~-~~~~~~~~~~~~~~~~~~~a~r~G~~v~t~kk~~~g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~ 86 (142)
.+|||||+ |+++. +..+.++++++|+|+|+|+.|+|+++|.+|.++. .+.+++..++|++++++.+..+..+++..
T Consensus 1 ~~dw~~vt~~~~~~-~s~~~k~~~~vnaa~r~g~~v~t~~k~~~g~nkq--~~~~~~t~klD~etE~~~~~~v~~~Vg~a 77 (135)
T KOG3398|consen 1 TSDWDPVTVLKKKA-KAATLKDEKAVNAARRAGVDVETVKKFPAGLNKQ--HPSTQSTAKLDRETEELGHDRVPLEVGKA 77 (135)
T ss_pred CCCcccceeeeccc-ccccccCHHHHHHHHHhcchhhhhhhhccccccc--CCcccchhhccccccccccccccHHHHHH
Confidence 47999985 66554 8889999999999999999999999999999985 45578899999999999999999999999
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCCCC
Q 032366 87 IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRGKK 142 (142)
Q Consensus 87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~e~~ 142 (142)
|...|.++||||++||.+++..++.|..||+|+.+|+..+|.+|.++|||.+++++
T Consensus 78 Iq~aR~~KgmsqkDLA~kInekpqVv~dyEsGrAIpNqqil~kmEraLgvKlrgk~ 133 (135)
T KOG3398|consen 78 IQQARAQKGMSQKDLAQKINEKPQVIQDYESGRAIPNQQILSKMERALGVKLRGKN 133 (135)
T ss_pred HHHHHHhccccHHHHHHHHccCchhhhhHhccccCchHHHHHHHHHHhceeccccc
Confidence 99999999999999999999999999999999999999999999999999999985
No 2
>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=99.83 E-value=5.2e-22 Score=129.51 Aligned_cols=70 Identities=51% Similarity=0.774 Sum_probs=0.7
Q ss_pred CCCCce-eeccCCCCCccccCHHHHHHHHHcCCChhHHHhhhcCCCCCCCCCCCcccccchhhhccccCCcc
Q 032366 9 QDWEPV-VIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLAHDRV 79 (142)
Q Consensus 9 ~~w~~~-~~~~~~~~~~~~~~~~~~~~a~r~G~~v~t~kk~~~g~~~~~~~~~~~~~~kl~~~~~~~~~~~~ 79 (142)
|||||| ||||+.|++++++++++||+|||+|..|+|++||.+|+|+ ++.+.++++.|||+++++|+++.+
T Consensus 1 qDWd~vtvi~kk~p~~~~~r~~~avNaArR~G~~v~T~KK~~~g~Nk-~~~~~~~n~~KLD~etE~~~~~kV 71 (71)
T PF08523_consen 1 QDWDPVTVIGKKGPRAKVARSESAVNAARRSGAVVETEKKYGAGNNK-HQHGEGQNAAKLDRETEELKHEKV 71 (71)
T ss_dssp ---------------------------------------------------------------------S--
T ss_pred CCCcccceecccCCCccccCCHHHHHHHHHcCCceEEEEeeeccccc-cCCCcccccccccccccccCCCCC
Confidence 799999 8999999999999999999999999999999999999999 667889999999999999998753
No 3
>PRK06424 transcription factor; Provisional
Probab=99.65 E-value=1.3e-15 Score=112.04 Aligned_cols=65 Identities=29% Similarity=0.452 Sum_probs=61.7
Q ss_pred cchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCCCC
Q 032366 78 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRGKK 142 (142)
Q Consensus 78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~e~~ 142 (142)
.+...|+.+|+.+|+++||||.+||+.+|+++++|++||+|+..|+.+.+.+|+++||+++.|++
T Consensus 80 ~~~~~~g~~Ir~lRe~~GLSQ~eLA~~iGvs~stIskiE~G~~~Ps~~~l~kLa~~Lgvsl~e~~ 144 (144)
T PRK06424 80 DIVEDYAELVKNARERLSMSQADLAAKIFERKNVIASIERGDLLPDIKTARKLEKILGITLIEKA 144 (144)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCCCCC
Confidence 34578999999999999999999999999999999999999999999999999999999999874
No 4
>PHA01976 helix-turn-helix protein
Probab=99.63 E-value=9.7e-16 Score=97.95 Aligned_cols=58 Identities=28% Similarity=0.509 Sum_probs=56.3
Q ss_pred HHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366 82 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 139 (142)
Q Consensus 82 ~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~ 139 (142)
.|+.+|+.+|..+|+||.+||+.+|+++++|++||+|...|+.+.+.+||++|||+++
T Consensus 2 ~~~~rl~~~R~~~glt~~~lA~~~gvs~~~v~~~e~g~~~p~~~~l~~ia~~l~v~~~ 59 (67)
T PHA01976 2 SFAIQLIKARNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTLD 59 (67)
T ss_pred cHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHH
Confidence 5899999999999999999999999999999999999999999999999999999985
No 5
>PRK08359 transcription factor; Validated
Probab=99.59 E-value=7.7e-15 Score=110.93 Aligned_cols=63 Identities=17% Similarity=0.245 Sum_probs=60.8
Q ss_pred cchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 032366 78 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG 140 (142)
Q Consensus 78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~e 140 (142)
.+...|+++|+++|+.+||||.+||+.+|+++++|++||+|+..|+.+++.+||++|+|++.+
T Consensus 81 elv~dy~~rIkeaRe~kglSQeeLA~~lgvs~stI~~iE~G~~~Ps~~~l~kLak~l~VsL~e 143 (176)
T PRK08359 81 DIVEDYAERVYEAIQKSGLSYEELSHEVGLSVNDLRRIAHGEYEPTIKEAKKLERYFKIKLIE 143 (176)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCcCCCHHHHHHHHHHhCCcccc
Confidence 577899999999999999999999999999999999999999999999999999999999875
No 6
>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=99.56 E-value=2.4e-14 Score=88.04 Aligned_cols=57 Identities=26% Similarity=0.353 Sum_probs=54.9
Q ss_pred HHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 032366 82 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 138 (142)
Q Consensus 82 ~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl 138 (142)
.++.+|+.+|...||||.+||+.+|+|+++|++||+|+..|+.+.+.+|+++|||++
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 488999999999999999999999999999999999999999999999999999985
No 7
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=99.55 E-value=2.2e-14 Score=106.58 Aligned_cols=63 Identities=30% Similarity=0.469 Sum_probs=60.1
Q ss_pred cchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 032366 78 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG 140 (142)
Q Consensus 78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~e 140 (142)
.+...|+.+|+.+|+++||||.+||+++|+++++|++||+|...|+.+.+.+|+++|||++.+
T Consensus 65 ~l~~~~g~~Ir~~Re~~glSqeeLA~~lgvs~s~IsriE~G~~~Ps~~~l~kLa~~Lgvsl~e 127 (154)
T TIGR00270 65 ELVEDYGIIIRREREKRGWSQEQLAKKIQEKESLIKKIENAEIEPEPKVVEKLEKLLKIKLRE 127 (154)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCCCHHH
Confidence 566789999999999999999999999999999999999999999999999999999999864
No 8
>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=99.54 E-value=1.2e-14 Score=92.07 Aligned_cols=56 Identities=34% Similarity=0.484 Sum_probs=48.4
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366 84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 139 (142)
Q Consensus 84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~ 139 (142)
|++|+++|+.+|+||.+||+.+|+++++|++||+|+..|+...+.+||++|||+++
T Consensus 1 G~~lk~~r~~~~lt~~~~a~~~~i~~~~i~~~e~g~~~~~~~~l~~i~~~~~v~~~ 56 (64)
T PF12844_consen 1 GERLKELREEKGLTQKDLAEKLGISRSTISKIENGKRKPSVSTLKKIAEALGVSLD 56 (64)
T ss_dssp HHHHHHHHHHCT--HHHHHHHHTS-HHHHHHHHTTSS--BHHHHHHHHHHHTS-HH
T ss_pred CHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCcCCCHHHHHHHHHHhCCCHH
Confidence 68999999999999999999999999999999999999999999999999999975
No 9
>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=99.52 E-value=2.2e-14 Score=88.21 Aligned_cols=53 Identities=34% Similarity=0.494 Sum_probs=49.0
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366 87 IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 139 (142)
Q Consensus 87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~ 139 (142)
|+++|+++|+||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||+++
T Consensus 1 ik~~r~~~gls~~~la~~~gis~~~i~~~~~g~~~~~~~~~~~ia~~l~~~~~ 53 (55)
T PF01381_consen 1 IKELRKEKGLSQKELAEKLGISRSTISRIENGKRNPSLDTLKKIAKALGVSPE 53 (55)
T ss_dssp HHHHHHHTTS-HHHHHHHHTS-HHHHHHHHTTSSTSBHHHHHHHHHHHTSEHH
T ss_pred CHHHHHHcCCCHHHHHHHhCCCcchhHHHhcCCCCCCHHHHHHHHHHHCCCHH
Confidence 68899999999999999999999999999999999999999999999999875
No 10
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=99.50 E-value=5e-14 Score=90.94 Aligned_cols=56 Identities=29% Similarity=0.431 Sum_probs=53.5
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG 140 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~e 140 (142)
.+|+.+|.+.|+||.+||+.+|||++||..||+|+..|+.....+||++|++++++
T Consensus 4 nk~k~~R~~~~ltQ~elA~~vgVsRQTi~~iEkgky~Psl~La~kia~~f~~~ied 59 (68)
T COG1476 4 NKLKELRAELGLTQEELAKLVGVSRQTIIAIEKGKYNPSLELALKIARVFGKTIED 59 (68)
T ss_pred hHHHHHHHHhCcCHHHHHHHcCcCHHHHHHHHcCCCCchHHHHHHHHHHhCCCHHH
Confidence 48999999999999999999999999999999999999999999999999998763
No 11
>PRK09726 antitoxin HipB; Provisional
Probab=99.46 E-value=3.7e-13 Score=90.97 Aligned_cols=60 Identities=25% Similarity=0.361 Sum_probs=57.2
Q ss_pred hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366 80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 139 (142)
Q Consensus 80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~ 139 (142)
...++.+|+.+|..+|+||.+||+.+||++++|++||+|...|+.+.+.+||++|||+++
T Consensus 10 ~~~l~~~lk~~R~~~gltq~elA~~~gvs~~tis~~e~g~~~ps~~~l~~ia~~lgv~~~ 69 (88)
T PRK09726 10 PTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMT 69 (88)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHcCCCcc
Confidence 457999999999999999999999999999999999999999999999999999999975
No 12
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=99.45 E-value=1e-13 Score=88.10 Aligned_cols=58 Identities=29% Similarity=0.461 Sum_probs=50.4
Q ss_pred HHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCC
Q 032366 82 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA-IPNQQILTKLERALGVKLR 139 (142)
Q Consensus 82 ~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~-~p~~~~l~kLa~~Lgvsl~ 139 (142)
.||..|+.+|...||||.++|+.+|+|+++|++||+|+. .|+.+.+.+||++||++++
T Consensus 1 ~lg~~lr~~R~~~gls~~~lA~~~g~s~s~v~~iE~G~~~~p~~~~l~~l~~~l~~~~~ 59 (64)
T PF13560_consen 1 QLGRRLRRLRERAGLSQAQLADRLGVSQSTVSRIERGRRPRPSPDTLQRLARALGVPPD 59 (64)
T ss_dssp HHHHHHHHHHHCHTS-HHHHHHHHTS-HHHHHHHHTTSSSS-BHHHHHHHHHHTT--HH
T ss_pred CHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCCHHHHHHHHHHHCcCHH
Confidence 378999999999999999999999999999999999999 5999999999999999864
No 13
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=99.43 E-value=4e-13 Score=97.18 Aligned_cols=59 Identities=25% Similarity=0.294 Sum_probs=56.5
Q ss_pred HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366 81 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 139 (142)
Q Consensus 81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~ 139 (142)
..++++|+.+|..+||||.+||+.+|||+++|++||+|...|+.+.+.+||++|||+++
T Consensus 4 ~~~g~rlk~~R~~~gltq~~lA~~~gvs~~~is~~E~g~~~p~~~~l~~la~~l~vs~~ 62 (135)
T PRK09706 4 LTLGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCSPT 62 (135)
T ss_pred hhHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHH
Confidence 45999999999999999999999999999999999999999999999999999999875
No 14
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=99.38 E-value=1.4e-12 Score=97.30 Aligned_cols=66 Identities=36% Similarity=0.528 Sum_probs=62.4
Q ss_pred CCcchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCCC
Q 032366 76 HDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRGK 141 (142)
Q Consensus 76 ~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~e~ 141 (142)
...+..+++++|+.+|+.+||||++||++|+++.+.|.+||+|+..|+...+.+|.++|||.+.++
T Consensus 73 ~~elvedY~e~Ir~ARE~~G~SqedLA~ki~ek~svI~~iE~g~~~P~~~~akkLEk~LgIkL~e~ 138 (165)
T COG1813 73 LPELVEDYGERIREAREKRGLSQEDLAAKLKEKVSVIRRIERGEATPNIKVAKKLEKLLGIKLVEK 138 (165)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCHHHHHHHhcccHHHHHHHHhcccCccHHHHHHHHHHhCceeeee
Confidence 346788999999999999999999999999999999999999999999999999999999999764
No 15
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=99.34 E-value=2.9e-12 Score=96.94 Aligned_cols=60 Identities=25% Similarity=0.300 Sum_probs=57.3
Q ss_pred hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366 80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 139 (142)
Q Consensus 80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~ 139 (142)
.+.++.+|+.+|+++||||.+||+++|+|+++|++||+|+..|+...+.+||++|||+++
T Consensus 5 ~~~~g~~l~~~R~~~glt~~elA~~~gis~~~is~~E~g~~~p~~~~l~~ia~~l~v~~~ 64 (185)
T PRK09943 5 GLAPGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLS 64 (185)
T ss_pred hhHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHH
Confidence 455899999999999999999999999999999999999999999999999999999975
No 16
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=99.34 E-value=4.1e-12 Score=90.71 Aligned_cols=60 Identities=15% Similarity=0.295 Sum_probs=56.5
Q ss_pred hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366 80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 139 (142)
Q Consensus 80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~ 139 (142)
...|+.+|+++|.++||||.+||+++|+|+++|++||+|+..|+.+++.+||++|||+++
T Consensus 3 ~~i~~~~l~~ll~~~Glsq~eLA~~~Gis~~~is~iE~g~~~ps~~~l~kIa~aL~v~~~ 62 (120)
T PRK13890 3 NYIFFTNVLRLLDERHMTKKELSERSGVSISFLSDLTTGKANPSLKVMEAIADALETPLP 62 (120)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCCCHH
Confidence 356899999999999999999999999999999999999999999999999999999654
No 17
>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=99.33 E-value=4.4e-12 Score=82.98 Aligned_cols=58 Identities=14% Similarity=0.163 Sum_probs=54.7
Q ss_pred HHHHHHH-HHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366 82 ELKKAIV-QARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 139 (142)
Q Consensus 82 ~~g~~Lk-~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~ 139 (142)
..+++|+ .+|+++|+||.+||+.+|+|+++|++||+|...|+.+.+.+||++|||+++
T Consensus 4 ~~g~~i~~~~~~~~~~t~~~lA~~~gis~~tis~~~~g~~~~~~~~~~~l~~~l~v~~~ 62 (78)
T TIGR02607 4 HPGEILREEFLEPLGLSIRALAKALGVSRSTLSRIVNGRRGITADMALRLAKALGTSPE 62 (78)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHcCCCHH
Confidence 3688899 899999999999999999999999999999999999999999999999864
No 18
>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed
Probab=99.30 E-value=7.7e-12 Score=101.81 Aligned_cols=62 Identities=23% Similarity=0.324 Sum_probs=58.9
Q ss_pred cchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366 78 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 139 (142)
Q Consensus 78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~ 139 (142)
.+...++++|+.+|+.+||||.+||+++|+|+++|++||+|+..|+.+.+.+||++|||+++
T Consensus 24 ~~~~~~g~rl~~~R~~~gltq~~lA~~~gvs~~~i~~~E~g~~~ps~~~l~~ia~~l~v~~~ 85 (309)
T PRK08154 24 PFLAALGERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCSLA 85 (309)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCCCHH
Confidence 45577999999999999999999999999999999999999999999999999999999875
No 19
>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=99.29 E-value=1.2e-11 Score=84.06 Aligned_cols=58 Identities=28% Similarity=0.368 Sum_probs=54.2
Q ss_pred hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366 80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 139 (142)
Q Consensus 80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~ 139 (142)
...++.+|+.+|+++|||| ||+++|||+++|++||+|+..|+.+.+.+||++||+++.
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 3458899999999999995 999999999999999999999999999999999999874
No 20
>PRK10072 putative transcriptional regulator; Provisional
Probab=99.22 E-value=4.1e-11 Score=82.58 Aligned_cols=53 Identities=21% Similarity=0.323 Sum_probs=49.5
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 138 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl 138 (142)
..|+.+|...||||.+||+.+|+|.++|++||+|++.|+...+. |+++|++++
T Consensus 36 ~eik~LR~~~glTQ~elA~~lGvS~~TVs~WE~G~r~P~~~~l~-Ll~~L~~~P 88 (96)
T PRK10072 36 TEFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVKPSSAELK-LMRLIQANP 88 (96)
T ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH-HHHHHhhCH
Confidence 44999999999999999999999999999999999999998864 999999987
No 21
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=99.19 E-value=3e-11 Score=76.10 Aligned_cols=55 Identities=20% Similarity=0.291 Sum_probs=42.5
Q ss_pred HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCCCCCC
Q 032366 86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK-AIPNQQILTKLERALGVKLRG 140 (142)
Q Consensus 86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~-~~p~~~~l~kLa~~Lgvsl~e 140 (142)
+|+.++.++|+|+.+||+.+|+++++|++|.+|+ ..|+.+.+.+||++|||++++
T Consensus 1 ~L~~~m~~~~it~~~La~~~gis~~tl~~~~~~~~~~~~~~~l~~ia~~l~~~~~e 56 (63)
T PF13443_consen 1 KLKELMAERGITQKDLARKTGISRSTLSRILNGKPSNPSLDTLEKIAKALNCSPEE 56 (63)
T ss_dssp HHHHHHHHTT--HHHHHHHHT--HHHHHHHHTTT-----HHHHHHHHHHHT--HHH
T ss_pred CHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcccccccHHHHHHHHHHcCCCHHH
Confidence 5889999999999999999999999999999998 689999999999999999753
No 22
>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=99.16 E-value=9.9e-11 Score=86.66 Aligned_cols=55 Identities=18% Similarity=0.194 Sum_probs=51.4
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCC--CCHHHHHHHHHHhCCCCC
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAI--PNQQILTKLERALGVKLR 139 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~--p~~~~l~kLa~~Lgvsl~ 139 (142)
..|+.+|..+||||.+||+++|||+++|++||+|... |+.+.+.+||++|||++.
T Consensus 28 ~~Ir~~R~~lGmTq~eLAerlGVS~~tIs~iE~G~~~~~psl~~L~kIA~aLgv~~~ 84 (150)
T TIGR02612 28 GWVRAIRKALGMSGAQLAGRLGVTPQRVEALEKSELSGTVTLKTLRAAAEALDCTFV 84 (150)
T ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCCCHHHHHHHHHHcCCCHH
Confidence 5799999999999999999999999999999999864 899999999999999853
No 23
>PRK04140 hypothetical protein; Provisional
Probab=99.12 E-value=2e-10 Score=94.14 Aligned_cols=61 Identities=25% Similarity=0.302 Sum_probs=57.2
Q ss_pred chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366 79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 139 (142)
Q Consensus 79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~ 139 (142)
+....+++|+.+|+++||||.+||+.+|+|+++|++||+|+..|+.+.+.+|+++||+++.
T Consensus 123 ~v~i~GerLk~lRe~~GlSq~eLA~~lGVSr~tIskyE~G~~~Ps~e~~~kLa~~Lgv~l~ 183 (317)
T PRK04140 123 YVKIDGDVLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDVPLT 183 (317)
T ss_pred eehhhHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCChH
Confidence 4455799999999999999999999999999999999999999999999999999999864
No 24
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=99.11 E-value=3.7e-10 Score=66.41 Aligned_cols=53 Identities=36% Similarity=0.543 Sum_probs=50.3
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366 87 IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 139 (142)
Q Consensus 87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~ 139 (142)
|+.+|...++|+.+||+.+|++..+|++|++|...|+.+.+.+|+++||+++.
T Consensus 2 i~~~~~~~~~s~~~la~~~~i~~~~i~~~~~~~~~~~~~~~~~i~~~~~~~~~ 54 (56)
T smart00530 2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLD 54 (56)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCCChh
Confidence 67789999999999999999999999999999999999999999999999875
No 25
>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=99.04 E-value=1.2e-09 Score=64.69 Aligned_cols=55 Identities=36% Similarity=0.529 Sum_probs=51.6
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 139 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~ 139 (142)
+.|+..+...|+|+.++|+.+|+++.+|++|++|...|+...+.+|++.||++++
T Consensus 2 ~~l~~~~~~~~~s~~~~a~~~~~~~~~v~~~~~g~~~~~~~~~~~i~~~~~~~~~ 56 (58)
T cd00093 2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLD 56 (58)
T ss_pred hHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCChh
Confidence 4578889999999999999999999999999999999999999999999999875
No 26
>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=99.00 E-value=1.1e-09 Score=77.73 Aligned_cols=58 Identities=26% Similarity=0.324 Sum_probs=51.8
Q ss_pred HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366 81 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 139 (142)
Q Consensus 81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~ 139 (142)
...+..|+.+|...|+||.+||+.+|+++++|++||+|...|+.. +..|.++|+++++
T Consensus 64 ~~~~~~i~~~r~~~gltq~~lA~~lg~~~~tis~~e~g~~~p~~~-~~~l~~~l~~~p~ 121 (127)
T TIGR03830 64 LLTPPEIRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSKA-LDKLLRLLDKHPE 121 (127)
T ss_pred CcCHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHH-HHHHHHHHHHChH
Confidence 346778999999999999999999999999999999999988865 6778899999875
No 27
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=98.92 E-value=3e-09 Score=70.62 Aligned_cols=61 Identities=26% Similarity=0.344 Sum_probs=49.3
Q ss_pred chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCCCCC
Q 032366 79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK-AIPNQQILTKLERALGVKLR 139 (142)
Q Consensus 79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~-~~p~~~~l~kLa~~Lgvsl~ 139 (142)
....+...|.++|+++||||.++|+.+|++++.|+++++|+ ..++.+.+..++..||..++
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 44567888999999999999999999999999999999986 56899999999999997653
No 28
>PRK10856 cytoskeletal protein RodZ; Provisional
Probab=98.91 E-value=2.9e-09 Score=87.80 Aligned_cols=60 Identities=20% Similarity=0.211 Sum_probs=54.5
Q ss_pred hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCH------HHHHHHHHHhCCCCC
Q 032366 80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQ------QILTKLERALGVKLR 139 (142)
Q Consensus 80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~------~~l~kLa~~Lgvsl~ 139 (142)
.+.+|.+|+.+|+++||||.+||+++++++++|++||+|+..+.. .++..+|++|||+.+
T Consensus 12 ~~~~G~~Lr~aRe~~GlSq~~vA~~l~l~~~~I~~iE~g~~~~~~~~tf~RGyir~yA~~lgv~~~ 77 (331)
T PRK10856 12 ALTTGERLRQAREQLGLTQQAVAERLCLKVSTVRDIEEDKAPADLASTFLRGYIRSYARLVHIPEE 77 (331)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHCCCCCCChhHHHHHHHHHHHHHHHCcCHH
Confidence 345899999999999999999999999999999999999987766 458899999999875
No 29
>PHA00542 putative Cro-like protein
Probab=98.89 E-value=9.1e-09 Score=68.75 Aligned_cols=49 Identities=22% Similarity=0.247 Sum_probs=45.0
Q ss_pred HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHh
Q 032366 86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK-AIPNQQILTKLERAL 134 (142)
Q Consensus 86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~-~~p~~~~l~kLa~~L 134 (142)
.+..++...|+||.+||+.+|||+++|++||+|. ..|+.+.+.+||+++
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 4667788999999999999999999999999999 479999999999886
No 30
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=98.86 E-value=6.8e-09 Score=77.52 Aligned_cols=52 Identities=23% Similarity=0.319 Sum_probs=48.9
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 032366 84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALG 135 (142)
Q Consensus 84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lg 135 (142)
.+-|++.|+++|+||++||++.|+|+++|.++|.|+..|....+.+|-++|.
T Consensus 7 pedlrk~Rk~LGitQ~dLA~~aGVSQ~~IArlE~G~vdPrlSt~k~Il~aL~ 58 (187)
T COG3620 7 PEDLRKRRKELGITQKDLARRAGVSQPYIARLEAGKVDPRLSTVKRILEALE 58 (187)
T ss_pred HHHHHHHHHHcCCCHHHHHHHcCccHHHHHHHhcCCCCccHHHHHHHHHHHH
Confidence 4569999999999999999999999999999999999999999999988874
No 31
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=98.77 E-value=4.4e-08 Score=64.38 Aligned_cols=49 Identities=18% Similarity=0.203 Sum_probs=42.1
Q ss_pred HHHHHHHHHHHHhCCCCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHHH
Q 032366 81 SELKKAIVQARNDKKLTQSQLAQLIN------EKPQVIQEYESGKAIPNQQILTKLE 131 (142)
Q Consensus 81 ~~~g~~Lk~~R~~~glTQ~eLA~~lg------is~stIs~~E~G~~~p~~~~l~kLa 131 (142)
..|+++|+..|...|+||.+||+.+| +|+++|++||+|.- +...+.+|-
T Consensus 10 e~~~~~lk~~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es~~l--s~~n~~kl~ 64 (75)
T smart00352 10 EAFAKTFKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEALQL--SFKNMCKLK 64 (75)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHhcCc--cHHHHHHHH
Confidence 46999999999999999999999999 59999999999864 555555553
No 32
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=98.74 E-value=3e-08 Score=69.01 Aligned_cols=45 Identities=20% Similarity=0.338 Sum_probs=40.7
Q ss_pred HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH
Q 032366 83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQIL 127 (142)
Q Consensus 83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l 127 (142)
-+..|+.+|+..||||.+||..+|+|.+||++||.|+..|+..-+
T Consensus 45 s~~eIk~iRe~~~lSQ~vFA~~L~vs~~Tv~~WEqGr~kPsg~Al 89 (104)
T COG2944 45 SPTEIKAIREKLGLSQPVFARYLGVSVSTVRKWEQGRKKPSGAAL 89 (104)
T ss_pred CHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHcCCcCCCCHHH
Confidence 356799999999999999999999999999999999999975543
No 33
>PRK13355 bifunctional HTH-domain containing protein/aminotransferase; Provisional
Probab=98.73 E-value=3.2e-08 Score=85.28 Aligned_cols=58 Identities=28% Similarity=0.358 Sum_probs=55.0
Q ss_pred HHHHHHHHHHHhCCCCHHHHHHHh-----CCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366 82 ELKKAIVQARNDKKLTQSQLAQLI-----NEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 139 (142)
Q Consensus 82 ~~g~~Lk~~R~~~glTQ~eLA~~l-----gis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~ 139 (142)
.|+++|+.+|+++|+||.+||+.+ +|++++|++||+|+..|+.+.+.+||++|||+++
T Consensus 3 ~~~~rL~~~r~~~g~tq~~la~~~~~~g~~vs~~~is~~e~g~~~p~~~~l~~la~~l~v~~~ 65 (517)
T PRK13355 3 TFAERLKQAMKARGLKQEDLVHAAEARGVKLGKSHISQYVSGKTGPRRDVLPFLAAILGVSED 65 (517)
T ss_pred hHHHHHHHHHHHCCCCHHHHHHHHHhccCCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCcCHH
Confidence 588999999999999999999996 6999999999999999999999999999999975
No 34
>PRK02866 cyanate hydratase; Validated
Probab=98.72 E-value=7.6e-08 Score=70.92 Aligned_cols=59 Identities=22% Similarity=0.254 Sum_probs=55.4
Q ss_pred HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366 81 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 139 (142)
Q Consensus 81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~ 139 (142)
.++.+.|..+|.++|||+.++|+.+|+|...+..+|.|+..++.+.+.+|+++||++.+
T Consensus 4 ~~~~e~Ll~AK~~kGLTw~~IA~~iG~S~v~vaaa~lGQ~~ls~e~A~kla~~LgL~~~ 62 (147)
T PRK02866 4 EELTEKILAAKKEKGLTWADIAEAIGLSEVWVTAALLGQMTLPAEEAEKVAELLGLDED 62 (147)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHhCCCCCCHHHHHHHHHHhCCCHH
Confidence 45788999999999999999999999999999999999999999999999999998754
No 35
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=98.68 E-value=7.1e-08 Score=67.05 Aligned_cols=57 Identities=18% Similarity=0.257 Sum_probs=51.2
Q ss_pred HHHHHHHH-HHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366 83 LKKAIVQA-RNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 139 (142)
Q Consensus 83 ~g~~Lk~~-R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~ 139 (142)
.|+.|++. .+..|+||.+||+.+||++.+|+++.+|++..+.+++.+|+++||.+++
T Consensus 10 PGEiL~eeflep~glt~~~lA~~lgV~r~~is~ling~~~iT~dmAlrL~k~fGtspe 67 (104)
T COG3093 10 PGEILREEFLEPLGLTQTELAEALGVTRNTISELINGRRAITADMALRLAKVFGTSPE 67 (104)
T ss_pred chHHHHHHHhccccCCHHHHHHHhCCCHHHHHHHHcCCcCCCHHHHHHHHHHhCCCHH
Confidence 56667654 5667999999999999999999999999999999999999999999864
No 36
>COG1709 Predicted transcriptional regulator [Transcription]
Probab=98.64 E-value=2.7e-08 Score=77.39 Aligned_cols=56 Identities=27% Similarity=0.444 Sum_probs=51.2
Q ss_pred chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCC-CCHHHHHHHHHHh
Q 032366 79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAI-PNQQILTKLERAL 134 (142)
Q Consensus 79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~-p~~~~l~kLa~~L 134 (142)
+....|+.|+++|+..+.||.+||+.+|+|+|.|++||.|++. |....+.++-.+|
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 4566899999999999999999999999999999999999987 8998888887665
No 37
>TIGR00673 cynS cyanate hydratase. Alternate names include cyanate lyase, cyanase and cyanate hydrolase.
Probab=98.57 E-value=3.4e-07 Score=67.65 Aligned_cols=56 Identities=16% Similarity=0.174 Sum_probs=53.8
Q ss_pred HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 032366 83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 138 (142)
Q Consensus 83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl 138 (142)
+.+.|..+|.++|||++++|+.+|+|+..+..++.|+..++.+.+.+|+++||++.
T Consensus 9 ~t~~Ll~AK~~KGLTwe~IAe~iG~sevwvaaa~lGQ~~ls~e~A~kla~lLgL~~ 64 (150)
T TIGR00673 9 LADALLESKKKKGLTFADIADGLGLAEVFVAAALYGQAAAPADEARLVGAKLDLDE 64 (150)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHhCCCCCCHHHHHHHHHHhCcCH
Confidence 77889999999999999999999999999999999999999999999999999874
No 38
>COG1396 HipB Predicted transcriptional regulators [Transcription]
Probab=98.39 E-value=2.7e-06 Score=54.21 Aligned_cols=56 Identities=30% Similarity=0.520 Sum_probs=52.6
Q ss_pred HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCC
Q 032366 83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA-IPNQQILTKLERALGVKL 138 (142)
Q Consensus 83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~-~p~~~~l~kLa~~Lgvsl 138 (142)
++.+++.+|...|+||.++|..+|++..+++.||+|.. .|....+..++..|++..
T Consensus 2 ~~~~~~~~r~~~~~s~~~~a~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~ 58 (120)
T COG1396 2 IGERLKELRKKKGLSQEELAERLGVSRSTISRIERGRSESPSLELLARLAAALGVSL 58 (120)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCCHHHHHHHHHHHCCCH
Confidence 67899999999999999999999999999999999999 899999999999988754
No 39
>COG1395 Predicted transcriptional regulator [Transcription]
Probab=98.37 E-value=9.1e-07 Score=72.15 Aligned_cols=57 Identities=19% Similarity=0.330 Sum_probs=54.1
Q ss_pred HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366 83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 139 (142)
Q Consensus 83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~ 139 (142)
-|+.|++.|.++|+|..+||..+|+|+.+|+.||+|...|+.+.+.+|.+.||.++-
T Consensus 126 dge~Lre~Ree~glSlG~lA~~lgVSRktV~~YE~G~~~~sleva~kLeei~g~~iv 182 (313)
T COG1395 126 DGEKLREKREEMGLSLGDLATMLGVSRKTVYKYEKGLSDASLEVALKLEEIFGEDIV 182 (313)
T ss_pred chHHHHHHHHHcCcCHHHHHHHhCccHHHHHHhccCCCCccHHHHHHHHHHhcchhh
Confidence 478899999999999999999999999999999999999999999999999998763
No 40
>COG3655 Predicted transcriptional regulator [Transcription]
Probab=98.35 E-value=1.2e-06 Score=57.41 Aligned_cols=57 Identities=19% Similarity=0.236 Sum_probs=50.9
Q ss_pred HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCC-CCHHHHHHHHHHhCCCCC
Q 032366 83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAI-PNQQILTKLERALGVKLR 139 (142)
Q Consensus 83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~-p~~~~l~kLa~~Lgvsl~ 139 (142)
+.-++...+.+++++..+||+.+|||.++++.+.+|+.. ...++|.+||++|+|.+-
T Consensus 3 i~~~l~~~l~~r~~~~~eLa~~igis~~~ls~l~~gk~k~I~~~tL~~iC~~LeCqpg 60 (73)
T COG3655 3 IAVRLDVMLADRKISLKELAEAIGISEANLSKLKTGKVKAIRLSTLEKICKALECQPG 60 (73)
T ss_pred chHhHHHHHHHHhhhHHHHHHHHcccHHHHHHHHcCCcceeeHHHHHHHHHHcCCChh
Confidence 345677888999999999999999999999999988864 589999999999999875
No 41
>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=98.34 E-value=1.9e-07 Score=59.78 Aligned_cols=53 Identities=19% Similarity=0.332 Sum_probs=38.7
Q ss_pred HHHHHHHhCCCC-HHHHHHHhCCCHHHHH-HHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366 86 AIVQARNDKKLT-QSQLAQLINEKPQVIQ-EYESGKAIPNQQILTKLERALGVKLR 139 (142)
Q Consensus 86 ~Lk~~R~~~glT-Q~eLA~~lgis~stIs-~~E~G~~~p~~~~l~kLa~~Lgvsl~ 139 (142)
.|+++++..|++ +.+||+.+|||+++|+ .|......| .+.+.+||..+||+++
T Consensus 2 ~i~rl~~~~g~~~~~~lA~~lgis~st~s~~~~~r~~~P-~~~l~~ia~~~gvsl~ 56 (66)
T PF07022_consen 2 VIERLKEALGVKSDKELAERLGISKSTLSNNWKKRGSIP-AEWLIKIALETGVSLD 56 (66)
T ss_dssp HHHHHHHHHT-SSCHHHHCCTT--HHHHH-HHHHSSS---HHHHHHHHHHH---HH
T ss_pred HHHHHHHHhCCCCHHHHHHHhCcCHHHhhHHHHhCCCCC-HHHHHHHHHHHCcCHH
Confidence 467777777775 5699999999999999 898877777 9999999999999975
No 42
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=98.19 E-value=6.4e-06 Score=52.27 Aligned_cols=54 Identities=24% Similarity=0.374 Sum_probs=40.3
Q ss_pred HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC--CCCCH----HHHHHHHHHhCCCCC
Q 032366 86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK--AIPNQ----QILTKLERALGVKLR 139 (142)
Q Consensus 86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~--~~p~~----~~l~kLa~~Lgvsl~ 139 (142)
+|+..|..+|+|..++|..++|+.+.|..+|+|. ..|+. ..+..+|++||++.+
T Consensus 1 ~Lr~~R~~~glsl~~va~~t~I~~~~l~aiE~~~~~~lp~~~y~rg~lr~Ya~~Lgld~~ 60 (62)
T PF13413_consen 1 RLREAREAKGLSLEDVAEETKISVSYLEAIENGDFDSLPSPVYARGYLRKYARFLGLDPD 60 (62)
T ss_dssp -HHHHHHCTT--HHHHHHHCS--HHHHHHHHCT-GCCSSSHHHHHHHHHHHHHHTT--HH
T ss_pred ChHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCcChhhCCcHHHHHHHHHHHHHHhCcCcc
Confidence 4899999999999999999999999999999986 44553 468899999998754
No 43
>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=98.04 E-value=1.8e-05 Score=58.41 Aligned_cols=59 Identities=15% Similarity=0.218 Sum_probs=54.4
Q ss_pred HHHHHHHHHHHHhCCCCH----HHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366 81 SELKKAIVQARNDKKLTQ----SQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 139 (142)
Q Consensus 81 ~~~g~~Lk~~R~~~glTQ----~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~ 139 (142)
..+.++|+++...+|+.+ .+||+.||||.+++++-.+|+..++...+.+|++.||++++
T Consensus 4 ~~~~erV~~Ll~~~Gi~kr~~~s~LA~iL~Is~ssa~RKL~G~~~ftl~EI~~Ia~~fgvS~d 66 (147)
T PF08667_consen 4 QAIAERVRELLDRKGIPKRKHASELADILGISYSSAYRKLNGKSPFTLEEIKKIAKHFGVSPD 66 (147)
T ss_pred HHHHHHHHHHHHHcCCcchhhHHHHHHHHCCCHHHHHHHhcCCCCCCHHHHHHHHHHhCcCHH
Confidence 458899999999999876 56999999999999999999999999999999999999975
No 44
>COG1426 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]
Probab=97.96 E-value=1.3e-05 Score=64.93 Aligned_cols=58 Identities=21% Similarity=0.357 Sum_probs=51.1
Q ss_pred HHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC--CCC----HHHHHHHHHHhCCCCC
Q 032366 82 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA--IPN----QQILTKLERALGVKLR 139 (142)
Q Consensus 82 ~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~--~p~----~~~l~kLa~~Lgvsl~ 139 (142)
++|++||+.|+++|||+.|+|.+++|..++|..+|.|.. .|. ...+...|++||++.+
T Consensus 3 ~~Ge~Lr~~Re~~gLsL~dva~~t~I~~~~L~aiEeg~~~~lp~~~y~rG~ir~YA~~l~ld~~ 66 (284)
T COG1426 3 TLGERLRQAREEKGLSLEDVAARTKIRKSYLRALEEGNFDKLPGPVYIRGYIRSYAKFLGLDED 66 (284)
T ss_pred cHHHHHHHHHHHcCCCHHHHHHHhCccHHHHHHHhcCccccccchHHHHHHHHHHHHHhCCCHH
Confidence 589999999999999999999999999999999999973 333 3468899999999865
No 45
>COG5499 Predicted transcription regulator containing HTH domain [Transcription]
Probab=97.95 E-value=1.8e-05 Score=55.50 Aligned_cols=56 Identities=20% Similarity=0.225 Sum_probs=52.0
Q ss_pred HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366 83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 139 (142)
Q Consensus 83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~ 139 (142)
--+.|+.++...|+|+.+||..+| |.+.++++.+|++..+.+.+.+|.+-||++.+
T Consensus 61 pve~I~t~Md~~glt~~dLa~~iG-Sks~vS~iL~~rraLTle~ikkL~q~~gIpa~ 116 (120)
T COG5499 61 PVEVIRTLMDQYGLTLADLANEIG-SKSRVSNILSGRRALTLEHIKKLHQRFGIPAD 116 (120)
T ss_pred HHHHHHHHHHHhCCcHHHHHHHhC-chHHHHHHHhhhhHhhHHHHHHHHHHhCcCHH
Confidence 456789999999999999999999 88999999999999999999999999999864
No 46
>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=97.92 E-value=3.3e-05 Score=46.35 Aligned_cols=40 Identities=13% Similarity=0.170 Sum_probs=33.2
Q ss_pred HHHHHhCCCHHHHHHHHcCCCCCCHH---HHHHHHHHhCCCCC
Q 032366 100 QLAQLINEKPQVIQEYESGKAIPNQQ---ILTKLERALGVKLR 139 (142)
Q Consensus 100 eLA~~lgis~stIs~~E~G~~~p~~~---~l~kLa~~Lgvsl~ 139 (142)
+||+.+|||+++|++|++|...++.. .+..+++.||+.+.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~~vs~~~~~~i~~~~~~l~~~~~ 44 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKPRVSEETRERVLAAAEELGYRPN 44 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHHHhCCCCC
Confidence 79999999999999999999766544 45568888888764
No 47
>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=97.79 E-value=0.00012 Score=50.27 Aligned_cols=50 Identities=12% Similarity=0.098 Sum_probs=38.7
Q ss_pred HHHHHHHHHH--HhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHH
Q 032366 82 ELKKAIVQAR--NDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLE 131 (142)
Q Consensus 82 ~~g~~Lk~~R--~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa 131 (142)
.+..|++-.+ ...++||+++|+.+|||.+||++++++-...+++.-.-|.
T Consensus 40 ~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn~lk~~~~~~~~~l~ 91 (94)
T TIGR01321 40 DLGDRIRIVNELLNGNMSQREIASKLGVSIATITRGSNNLKTMDPNFKQFLR 91 (94)
T ss_pred HHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHHhhcccCCHHHHHHHH
Confidence 4555655554 3578999999999999999999999998866666555444
No 48
>PHA01083 hypothetical protein
Probab=97.78 E-value=4.8e-05 Score=56.01 Aligned_cols=54 Identities=17% Similarity=0.242 Sum_probs=45.8
Q ss_pred HHHHHHHhCCC-CHHHHHHHhCCCHHHHHHHHcC-CCCCCHHHHHHHHHHhCCCCC
Q 032366 86 AIVQARNDKKL-TQSQLAQLINEKPQVIQEYESG-KAIPNQQILTKLERALGVKLR 139 (142)
Q Consensus 86 ~Lk~~R~~~gl-TQ~eLA~~lgis~stIs~~E~G-~~~p~~~~l~kLa~~Lgvsl~ 139 (142)
.|....+.+++ +-++||..+||+++.|++|-+| ++.++.+.+..||+.+|+++.
T Consensus 6 LLda~K~a~~~~sdkqLA~~LGVs~q~IS~~R~G~r~~i~de~A~~LAe~aGiDp~ 61 (149)
T PHA01083 6 LLDAYKKAKNYVQYKQIAHDLGVSPQKISKMRTGVRTYISDEEAIFLAESAGIDPE 61 (149)
T ss_pred HHHHHHHHHhhccHHHHHHHhCCCHHHHHHHHcCCCCCCCHHHHHHHHHHhCCCHH
Confidence 34455555555 4568999999999999999999 999999999999999999874
No 49
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=97.68 E-value=0.00017 Score=51.47 Aligned_cols=45 Identities=20% Similarity=0.327 Sum_probs=36.6
Q ss_pred cchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCC
Q 032366 78 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIP 122 (142)
Q Consensus 78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p 122 (142)
.+.+.+...|.+...+.|+||.++|+.+|+|++.||+|.+|++.+
T Consensus 5 ~vlPaiRa~lA~~L~eeG~Sq~~iA~LLGltqaAVS~Yls~krg~ 49 (119)
T COG2522 5 EVLPAIRALLAKELIEEGLSQYRIAKLLGLTQAAVSQYLSGKRGS 49 (119)
T ss_pred HHHHHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHccCCch
Confidence 345567777755555559999999999999999999999998873
No 50
>COG4800 Predicted transcriptional regulator with an HTH domain [Transcription]
Probab=97.64 E-value=0.00027 Score=51.81 Aligned_cols=54 Identities=17% Similarity=0.242 Sum_probs=49.2
Q ss_pred hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q 032366 80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERAL 134 (142)
Q Consensus 80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~L 134 (142)
.+.|+.-|+.+..++|||..|||++.||+.+|+.++.+| +.|+.+++.+|-+.+
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 356899999999999999999999999999999999999 689999998887765
No 51
>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=97.58 E-value=0.0003 Score=42.06 Aligned_cols=42 Identities=12% Similarity=0.131 Sum_probs=32.9
Q ss_pred CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH---HHHHHHhCCCC
Q 032366 97 TQSQLAQLINEKPQVIQEYESGKAIPNQQIL---TKLERALGVKL 138 (142)
Q Consensus 97 TQ~eLA~~lgis~stIs~~E~G~~~p~~~~l---~kLa~~Lgvsl 138 (142)
|.+|+|+.+|+|.+||+++.+|....+.+.. ..+++.||..+
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~~~~vs~~tr~rI~~~a~~lgY~p 45 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNGPPRVSEETRERILEAAEELGYRP 45 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTTCSSSTHHHHHHHHHHHHHHTB-S
T ss_pred CHHHHHHHHCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHCCCC
Confidence 6789999999999999999999987777654 44555666443
No 52
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=97.57 E-value=0.00026 Score=45.53 Aligned_cols=44 Identities=14% Similarity=0.138 Sum_probs=35.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCC
Q 032366 96 LTQSQLAQLINEKPQVIQEYESGKAIPNQQI---LTKLERALGVKLR 139 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~G~~~p~~~~---l~kLa~~Lgvsl~ 139 (142)
+|+.|||+.+|+|.+||+++.+|....+.+. +.++++.||..+.
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln~~~~v~~~t~~~i~~~~~~~gy~~~ 47 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLNGNGRVSEETREKVLAAMEELGYIPN 47 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCCCC
Confidence 4789999999999999999999987665554 5667777776543
No 53
>PF08965 DUF1870: Domain of unknown function (DUF1870); InterPro: IPR015060 This family consist of hypothetical bacterial proteins. ; PDB: 1S4K_A.
Probab=97.55 E-value=0.00028 Score=50.26 Aligned_cols=50 Identities=18% Similarity=0.172 Sum_probs=38.5
Q ss_pred HHHHHHHHhCCCCHHHHHHHhC--CCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q 032366 85 KAIVQARNDKKLTQSQLAQLIN--EKPQVIQEYESGKAIPNQQILTKLERAL 134 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lg--is~stIs~~E~G~~~p~~~~l~kLa~~L 134 (142)
-.|+.+|...+||+.|.|..++ ++..+..+||+|...++++++..|....
T Consensus 4 ~ELqalR~~l~lt~~EaA~~Ia~~v~~~tWq~WE~G~~~IP~~Vie~l~~m~ 55 (118)
T PF08965_consen 4 LELQALRQILGLTVEEAAYYIAQDVSSRTWQQWEKGERPIPDDVIEELLEMK 55 (118)
T ss_dssp HHHHHHHHHTT--HHHHHHHTSSS--HHHHHHHHTTSS---HHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCHHHHHHHHHccCCHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence 3589999999999999999999 9999999999999999999888876653
No 54
>PRK08099 bifunctional DNA-binding transcriptional repressor/ NMN adenylyltransferase; Provisional
Probab=97.32 E-value=0.00047 Score=58.33 Aligned_cols=47 Identities=23% Similarity=0.280 Sum_probs=43.2
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCC
Q 032366 93 DKKLTQSQLAQLINEKPQVIQEYESGKA-IPNQQILTKLERALGVKLR 139 (142)
Q Consensus 93 ~~glTQ~eLA~~lgis~stIs~~E~G~~-~p~~~~l~kLa~~Lgvsl~ 139 (142)
..|+|..+||+++|+|.++++++|+|+. .|+.+.|.+|+++|||+..
T Consensus 1 ~~~~~~~~~~~~~~~~~~y~~~l~~~~~~~ps~~~~~~~~~~~~~~~~ 48 (399)
T PRK08099 1 QQGCTLQQVADASGMTKGYLSQLLNAKIKSPSAQKLEALHRFLGLEFP 48 (399)
T ss_pred CCCCcHHHHHHHhCCcHHHHHHHhcCCCCCccHHHHHHHHHHhCCChh
Confidence 3689999999999999999999999985 6999999999999999853
No 55
>COG3636 Predicted transcriptional regulator [Transcription]
Probab=97.16 E-value=0.0021 Score=44.30 Aligned_cols=54 Identities=17% Similarity=0.211 Sum_probs=46.0
Q ss_pred HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 032366 83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 138 (142)
Q Consensus 83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl 138 (142)
+...+...-..+|||| +|++.|+|+..+.+-.+...+|+.+.+.+++++||+.+
T Consensus 39 i~~alg~var~~GMsq--vA~~aGlsRe~LYkaLS~~GNPtf~Til~V~kAlG~rl 92 (100)
T COG3636 39 IAAALGVVARSRGMSQ--VARKAGLSREGLYKALSPGGNPTFDTILAVLKALGLRL 92 (100)
T ss_pred HHHHHHHHHHhcCHHH--HHHHhCccHHHHHHHhCCCCCCcHHHHHHHHHHcCcee
Confidence 3444445556678776 99999999999999999999999999999999999875
No 56
>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=97.13 E-value=0.002 Score=45.62 Aligned_cols=73 Identities=19% Similarity=0.236 Sum_probs=48.6
Q ss_pred HHHHHHHHHcCCChhHHHhhhcCCCCCCCCCCCcccc-cchhhhccccCCcchHHHHHHHHHH-HHhCCCCHHHHHHHhC
Q 032366 29 EKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTR-KLDEDTENLAHDRVPSELKKAIVQA-RNDKKLTQSQLAQLIN 106 (142)
Q Consensus 29 ~~~~~~a~r~G~~v~t~kk~~~g~~~~~~~~~~~~~~-kl~~~~~~~~~~~~~~~~g~~Lk~~-R~~~glTQ~eLA~~lg 106 (142)
.+..++|++.||+..|+.+|.. ..........+.-. +++. +.|+.. -...++|+.|+|+.+|
T Consensus 19 ~s~~eaa~~F~VS~~Tv~~W~k-~~~~G~~~~k~r~~~Kid~---------------~~L~~~v~~~pd~tl~Ela~~l~ 82 (119)
T PF01710_consen 19 KSIREAAKRFGVSRNTVYRWLK-RKETGDLEPKPRGRKKIDR---------------DELKALVEENPDATLRELAERLG 82 (119)
T ss_pred chHHHHHHHhCcHHHHHHHHHH-hcccccccccccccccccH---------------HHHHHHHHHCCCcCHHHHHHHcC
Confidence 4678899999999999999976 32211100111111 3321 123333 3457899999999999
Q ss_pred CCHHHHHHHHc
Q 032366 107 EKPQVIQEYES 117 (142)
Q Consensus 107 is~stIs~~E~ 117 (142)
||.++|+....
T Consensus 83 Vs~~ti~~~Lk 93 (119)
T PF01710_consen 83 VSPSTIWRALK 93 (119)
T ss_pred CCHHHHHHHHH
Confidence 99999999875
No 57
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=97.01 E-value=0.0016 Score=43.99 Aligned_cols=61 Identities=23% Similarity=0.250 Sum_probs=51.8
Q ss_pred chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCC
Q 032366 79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA-IPNQQILTKLERALGVKLR 139 (142)
Q Consensus 79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~-~p~~~~l~kLa~~Lgvsl~ 139 (142)
+...+...|..+.+..+|+|+++|+.+||+++.++.+-+|+. ..+.+.|.-+....|..++
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 455688889999999999999999999999999999999985 4577778777777776554
No 58
>PHA00675 hypothetical protein
Probab=96.99 E-value=0.0028 Score=41.82 Aligned_cols=42 Identities=10% Similarity=0.064 Sum_probs=35.9
Q ss_pred chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 032366 79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA 120 (142)
Q Consensus 79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~ 120 (142)
+...--+.|+.+++..|.|+.+||+.+|||+++|+.|.+|++
T Consensus 23 Lt~~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~~gk~ 64 (78)
T PHA00675 23 LTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICRYER 64 (78)
T ss_pred cCHHHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHHccch
Confidence 334455678888888899999999999999999999999874
No 59
>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=96.91 E-value=0.0052 Score=40.28 Aligned_cols=49 Identities=24% Similarity=0.255 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHH
Q 032366 81 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLE 131 (142)
Q Consensus 81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa 131 (142)
......+.-.|...|+|+.|+|+.+|+|.++|..+.+.. +....+.+|+
T Consensus 18 ~~~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~--~~~~~~~~~~ 66 (73)
T TIGR03879 18 SLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKGE--TKAGGLVKLA 66 (73)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcC--cccchHHHHH
Confidence 333444444477899999999999999999999999853 3445555554
No 60
>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=96.87 E-value=0.0065 Score=40.00 Aligned_cols=50 Identities=18% Similarity=0.166 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHHhCCCCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHHHH
Q 032366 81 SELKKAIVQARNDKKLTQSQLAQLIN------EKPQVIQEYESGKAIPNQQILTKLER 132 (142)
Q Consensus 81 ~~~g~~Lk~~R~~~glTQ~eLA~~lg------is~stIs~~E~G~~~p~~~~l~kLa~ 132 (142)
..|.+.++..|...|+||.+++..+| .|+++|+++|+= ..+...+.+|--
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 46889999999999999999988876 499999999974 356666655543
No 61
>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=96.84 E-value=0.0034 Score=50.68 Aligned_cols=46 Identities=15% Similarity=0.241 Sum_probs=43.0
Q ss_pred CCCHHHHHHHhCCCH-HHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 032366 95 KLTQSQLAQLINEKP-QVIQEYESGKAIPNQQILTKLERALGVKLRG 140 (142)
Q Consensus 95 glTQ~eLA~~lgis~-stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~e 140 (142)
.+|-.++|+.+|++. +.++.+++|++.++...+.+++++||.+..|
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 699999999999877 9999999999999999999999999998765
No 62
>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A.
Probab=96.77 E-value=0.0033 Score=41.70 Aligned_cols=52 Identities=15% Similarity=0.095 Sum_probs=39.0
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 139 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~ 139 (142)
..|+.....+|+|..+||+..|++.+|+++... .|.+..-..||++|||++.
T Consensus 5 adI~AaL~krG~sL~~lsr~~Gl~~~tl~nal~---r~~pk~E~~IA~aLgv~P~ 56 (78)
T PF13693_consen 5 ADIKAALRKRGTSLAALSREAGLSSSTLRNALR---RPWPKGERIIADALGVPPE 56 (78)
T ss_dssp HHHHHHHCTTS--HHHHHHHHSS-HHHHHHTTT---SS-HHHHHHHHHHTTS-HH
T ss_pred HHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHc---CCChHHHHHHHHHHCcCHH
Confidence 346667778999999999999999999999764 4567777889999999875
No 63
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=96.70 E-value=0.0037 Score=37.05 Aligned_cols=24 Identities=4% Similarity=0.097 Sum_probs=19.3
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHcC
Q 032366 95 KLTQSQLAQLINEKPQVIQEYESG 118 (142)
Q Consensus 95 glTQ~eLA~~lgis~stIs~~E~G 118 (142)
|+|..++|+.+|+|++||.+|.+-
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 999999999999999999999864
No 64
>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=96.62 E-value=0.0042 Score=36.59 Aligned_cols=33 Identities=9% Similarity=0.172 Sum_probs=23.9
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.+.+.+++. .|+|..++|+.+|||++||.+|.+
T Consensus 11 ~~~i~~l~~-~G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 11 IEEIKELYA-EGMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHHHH-TT--HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHh
Confidence 344555554 569999999999999999999975
No 65
>PHA02591 hypothetical protein; Provisional
Probab=96.46 E-value=0.0066 Score=40.22 Aligned_cols=31 Identities=16% Similarity=0.295 Sum_probs=26.7
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 87 IVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+.....+.|+||.++|+.+|+++.+|++|..
T Consensus 51 vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 51 VTHELARKGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 4455566899999999999999999999864
No 66
>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=96.34 E-value=0.014 Score=42.07 Aligned_cols=49 Identities=8% Similarity=0.055 Sum_probs=38.4
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHH
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERA 133 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~ 133 (142)
..+..+....|+|+++++..+|+|++|++++-++...++.+.-.++.++
T Consensus 26 ~~~~~l~~~l~ls~~el~~~lgis~~Tl~R~~~~~~~Ls~~~serl~~l 74 (133)
T TIGR02293 26 GALDRLAHLLAIGKAEIFKATGIPKATLQRRKMAHQRLSSEESDRLARV 74 (133)
T ss_pred HHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHhhcCCCCCHHHHHHHHHH
Confidence 3456667788999999999999999999999987666776655544443
No 67
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=96.25 E-value=0.014 Score=46.74 Aligned_cols=46 Identities=20% Similarity=0.126 Sum_probs=37.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH---HHHhCCCCC
Q 032366 94 KKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKL---ERALGVKLR 139 (142)
Q Consensus 94 ~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kL---a~~Lgvsl~ 139 (142)
...|.+|+|+++|||++|||+..||+...+.++-.++ ++-||..+.
T Consensus 5 ~~~Ti~dIA~~agVS~~TVSr~Ln~~~~vs~~tr~~V~~~a~elgY~p~ 53 (342)
T PRK10014 5 KKITIHDVALAAGVSVSTVSLVLSGKGRISTATGERVNQAIEELGFVRN 53 (342)
T ss_pred CCCcHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCCcC
Confidence 3579999999999999999999999887777665544 778887653
No 68
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=96.23 E-value=0.0063 Score=35.74 Aligned_cols=30 Identities=7% Similarity=0.119 Sum_probs=20.4
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 87 IVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
|..+ .+.|+|+.++|+.+|+|++||+++.+
T Consensus 13 I~~l-~~~G~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 13 IEAL-LEQGMSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp HHHH-HCS---HHHHHHHTT--HHHHHHHHH
T ss_pred HHHH-HHcCCCHHHHHHHHCcCcHHHHHHHh
Confidence 4544 46899999999999999999998753
No 69
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=96.21 E-value=0.013 Score=36.93 Aligned_cols=41 Identities=22% Similarity=0.276 Sum_probs=29.1
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Q 032366 93 DKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVK 137 (142)
Q Consensus 93 ~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvs 137 (142)
..| ++..||+.||||+++|++| +.. .+......|..+-+-.
T Consensus 8 ~~G-~~~~lAkalGVs~~aVs~W--~~~-IP~~ra~~Ie~~T~G~ 48 (60)
T PF14549_consen 8 YFG-GQSKLAKALGVSPQAVSQW--GER-IPAERAYQIEKLTNGK 48 (60)
T ss_dssp HHS-SHHHHHHHHTS-HHHHHHH--HTS---HHHHHHHHHHTTTS
T ss_pred HHC-CHHHHHHHHCCCHHHHHHh--cCc-cCHHHHHHHHHHhCCc
Confidence 345 8999999999999999999 444 4556677777765543
No 70
>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=96.15 E-value=0.019 Score=33.75 Aligned_cols=34 Identities=21% Similarity=0.371 Sum_probs=26.7
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.+.|..+...-++|+.++|+.+|+|.++++++.+
T Consensus 6 ~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~ 39 (48)
T PF13412_consen 6 RKILNYLRENPRITQKELAEKLGISRSTVNRYLK 39 (48)
T ss_dssp HHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 4456777778889999999999999999998753
No 71
>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=96.10 E-value=0.062 Score=35.77 Aligned_cols=50 Identities=10% Similarity=0.093 Sum_probs=39.4
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhC
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK-AIPNQQILTKLERALG 135 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~-~~p~~~~l~kLa~~Lg 135 (142)
..+..++. ..+|..++|+.+|+|.+||++..++. ...+.+...++-++..
T Consensus 10 ~I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L~~~~~~Vs~~Tr~rV~~aa~ 60 (80)
T TIGR02844 10 EIGKYIVE-TKATVRETAKVFGVSKSTVHKDVTERLPEINPELAEEVKEVLD 60 (80)
T ss_pred HHHHHHHH-CCCCHHHHHHHhCCCHHHHHHHhcCCCCCCCHHHHHHHHHHHc
Confidence 33445566 78999999999999999999999975 6678887777766543
No 72
>COG3423 Nlp Predicted transcriptional regulator [Transcription]
Probab=96.06 E-value=0.02 Score=37.83 Aligned_cols=52 Identities=17% Similarity=0.188 Sum_probs=41.4
Q ss_pred HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 032366 86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG 140 (142)
Q Consensus 86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~e 140 (142)
-|....+.+|+|...|+.+.|+|++|+.+...-. -|..+ ..||++|||++.|
T Consensus 12 dI~A~Lkk~G~Sl~~LS~~agls~~tL~n~L~rp-~pkgE--riIA~algv~P~e 63 (82)
T COG3423 12 DIIAALKKKGTSLAALSREAGLSSSTLANALDRP-WPKGE--RIIADALGVPPEE 63 (82)
T ss_pred HHHHHHHHccccHHHHHHHcCCCHHHHHHHHcCC-CchHH--HHHHHHhCCCHHH
Confidence 3556677799999999999999999999988543 34444 4578999999865
No 73
>PRK09492 treR trehalose repressor; Provisional
Probab=96.01 E-value=0.016 Score=45.93 Aligned_cols=44 Identities=14% Similarity=0.113 Sum_probs=35.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH---HHHHHHhCCCC
Q 032366 95 KLTQSQLAQLINEKPQVIQEYESGKAIPNQQIL---TKLERALGVKL 138 (142)
Q Consensus 95 glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l---~kLa~~Lgvsl 138 (142)
..|.+|+|+++|||.+|||++.||....+.++- .+.++.||..+
T Consensus 4 ~~ti~dIA~~agVS~~TVSrvLn~~~~vs~~tr~rV~~~a~elgY~p 50 (315)
T PRK09492 4 KLTIKDIARLSGVGKSTVSRVLNNESGVSEETRERVEAVINQHGFSP 50 (315)
T ss_pred CCcHHHHHHHhCCCHHHHhHHhCCCCCCCHHHHHHHHHHHHHHCCCc
Confidence 479999999999999999999999877776654 44577777654
No 74
>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=96.01 E-value=0.026 Score=43.01 Aligned_cols=57 Identities=16% Similarity=0.120 Sum_probs=38.7
Q ss_pred cchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q 032366 78 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERAL 134 (142)
Q Consensus 78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~L 134 (142)
+-...+.+.||..+..++++|.++++.+|||++.|++|.+-....+...-..|-..|
T Consensus 114 ~D~~~VkeeIK~fl~~h~IsQ~~V~q~TGisQS~lSq~L~kGt~Mk~qKR~alY~Wy 170 (180)
T PF04814_consen 114 RDPWRVKEEIKAFLQQHNISQREVVQVTGISQSHLSQHLNKGTPMKEQKRRALYRWY 170 (180)
T ss_dssp S-HHHHHHHHHHHHHHCT--CHHHHHHHT--HHHHHHHHCTB----HHHHHHHHHHH
T ss_pred hCHHHHHHHHHHHHHHcCCcHHHHHHHhhhhHHHHHHHHHcCCCccHHHHHHHHHHH
Confidence 445568899999999999999999999999999999999755555655555554443
No 75
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=95.98 E-value=0.011 Score=43.38 Aligned_cols=45 Identities=16% Similarity=0.283 Sum_probs=33.4
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHcCCCC-C--CHHHHHHHHHHhCCCC
Q 032366 93 DKKLTQSQLAQLINEKPQVIQEYESGKAI-P--NQQILTKLERALGVKL 138 (142)
Q Consensus 93 ~~glTQ~eLA~~lgis~stIs~~E~G~~~-p--~~~~l~kLa~~Lgvsl 138 (142)
..|+||.|+|+.+|+|+++|+.+|++-.. . ...++ ++++.|+-++
T Consensus 19 ~~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~tl-~~~~~l~a~~ 66 (141)
T PRK03975 19 ERGLTQQEIADILGTSRANVSSIEKRARENIEKARETL-AFAETLNAPV 66 (141)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH-HHHHHcCCCe
Confidence 69999999999999999999999986321 1 12233 6666666554
No 76
>PRK09526 lacI lac repressor; Reviewed
Probab=95.92 E-value=0.015 Score=46.61 Aligned_cols=44 Identities=9% Similarity=-0.005 Sum_probs=35.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCC
Q 032366 95 KLTQSQLAQLINEKPQVIQEYESGKAIPNQQI---LTKLERALGVKL 138 (142)
Q Consensus 95 glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~---l~kLa~~Lgvsl 138 (142)
..|.+|+|+++|||.+|||++.||....+.++ +.++++-||..+
T Consensus 5 ~~ti~dIA~~aGVS~~TVSrvLn~~~~vs~~tr~rV~~~a~elgY~p 51 (342)
T PRK09526 5 PVTLYDVARYAGVSYQTVSRVLNQASHVSAKTREKVEAAMAELNYVP 51 (342)
T ss_pred CCcHHHHHHHhCCCHHHHHHHhcCCCCCCHHHHHHHHHHHHHHCCCc
Confidence 46999999999999999999999987666554 556666777654
No 77
>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=95.88 E-value=0.019 Score=45.74 Aligned_cols=44 Identities=9% Similarity=0.083 Sum_probs=35.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCC
Q 032366 96 LTQSQLAQLINEKPQVIQEYESGKAIPNQQI---LTKLERALGVKLR 139 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~G~~~p~~~~---l~kLa~~Lgvsl~ 139 (142)
.|.+|+|+.+|||.+|||++.||....+.++ +.+.++-||..+.
T Consensus 2 ~ti~dIA~~agvS~~TVSrvLn~~~~vs~~tr~rV~~~a~~lgY~pn 48 (329)
T TIGR01481 2 VTIYDVAREAGVSMATVSRVVNGNPNVKPATRKKVLEVIKRLDYRPN 48 (329)
T ss_pred CcHHHHHHHhCCCHHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCCCC
Confidence 4789999999999999999999987776655 5556777877653
No 78
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=95.88 E-value=0.019 Score=46.04 Aligned_cols=43 Identities=7% Similarity=-0.009 Sum_probs=35.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHH---HHHHHHHHhCCCC
Q 032366 96 LTQSQLAQLINEKPQVIQEYESGKAIPNQQ---ILTKLERALGVKL 138 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~G~~~p~~~---~l~kLa~~Lgvsl 138 (142)
.|.+|+|+.+|+|.+|||++.+|+...+.+ .+.++++.||..+
T Consensus 2 ~Ti~dIA~~agVS~~TVSrvLn~~~~vs~~tr~~V~~~a~elgY~p 47 (341)
T PRK10703 2 ATIKDVAKRAGVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSP 47 (341)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHCCCc
Confidence 489999999999999999999998666655 4667777787655
No 79
>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=95.88 E-value=0.021 Score=45.49 Aligned_cols=44 Identities=11% Similarity=0.118 Sum_probs=35.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCC
Q 032366 96 LTQSQLAQLINEKPQVIQEYESGKAIPNQQI---LTKLERALGVKLR 139 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~G~~~p~~~~---l~kLa~~Lgvsl~ 139 (142)
.|.+|+|+.+|+|++|||++.||....+.++ +.+.++-||..+.
T Consensus 2 ~ti~dIA~~agVS~sTVSr~Ln~~~~vs~~tr~rV~~~a~~lgY~pn 48 (311)
T TIGR02405 2 LTIKDIARLAGVGKSTVSRVLNNEPKVSIETRERVEQVIQQSGFVPS 48 (311)
T ss_pred CcHHHHHHHhCCCHHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCCcC
Confidence 5899999999999999999999987666555 4555777776553
No 80
>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=95.86 E-value=0.021 Score=41.70 Aligned_cols=34 Identities=18% Similarity=0.329 Sum_probs=28.4
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 032366 84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESG 118 (142)
Q Consensus 84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G 118 (142)
...+-.+| ..|+||+|+|+.+|+|+++|+.+|+.
T Consensus 11 qr~VL~Lr-~~GlTq~EIAe~LgiS~stV~~~e~r 44 (137)
T TIGR00721 11 QIKVLELR-EKGLSQKEIAKELKTTRANVSAIEKR 44 (137)
T ss_pred HHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHh
Confidence 34444555 69999999999999999999999974
No 81
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=95.71 E-value=0.023 Score=45.82 Aligned_cols=44 Identities=9% Similarity=0.064 Sum_probs=35.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCC
Q 032366 96 LTQSQLAQLINEKPQVIQEYESGKAIPNQQI---LTKLERALGVKLR 139 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~G~~~p~~~~---l~kLa~~Lgvsl~ 139 (142)
.|.+|+|+++|||.+|||++.||+...+.++ +.+.++-||..+.
T Consensus 2 ~ti~dIA~~aGVS~~TVSrvLn~~~~Vs~~tr~rV~~~a~elgY~pn 48 (343)
T PRK10727 2 ATIKDVARLAGVSVATVSRVINNSPKASEASRLAVHSAMESLSYHPN 48 (343)
T ss_pred CCHHHHHHHhCCCHHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCCCC
Confidence 4889999999999999999999987676654 5556777776553
No 82
>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=95.65 E-value=0.012 Score=39.65 Aligned_cols=25 Identities=12% Similarity=0.145 Sum_probs=19.2
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 93 DKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 93 ~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+.||||.|+|+++|.|+++|+++..
T Consensus 1 ~~G~tq~eIA~~lGks~s~Vs~~l~ 25 (93)
T PF08535_consen 1 EFGWTQEEIAKRLGKSRSWVSNHLA 25 (93)
T ss_dssp HTT--HHHHHHHTT--HHHHHHHHG
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4799999999999999999999876
No 83
>cd00131 PAX Paired Box domain
Probab=95.60 E-value=0.069 Score=38.30 Aligned_cols=75 Identities=12% Similarity=0.140 Sum_probs=47.1
Q ss_pred HHHHHHHHcCCChhHHHhhhc-----CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHH-HHHHHhCCCCHHHHHH
Q 032366 30 KVVNAARRAGADIETVRKSHA-----GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAI-VQARNDKKLTQSQLAQ 103 (142)
Q Consensus 30 ~~~~~a~r~G~~v~t~kk~~~-----g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~L-k~~R~~~glTQ~eLA~ 103 (142)
+.-..|++.|++..|+.+|-. |...+.+.+ ++...++. ......| ...+..-.+|..||++
T Consensus 35 s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~g-g~rpr~~~------------~~~~~~i~~~v~~~p~~Tl~El~~ 101 (128)
T cd00131 35 RPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIG-GSKPRVAT------------PEVVKKIEIYKQENPGMFAWEIRD 101 (128)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCC-CCCCCcCC------------HHHHHHHHHHHHHCCCCCHHHHHH
Confidence 456679999999999999854 655543221 12122211 1111223 2456777899999998
Q ss_pred Hh---CC-------CHHHHHHHHc
Q 032366 104 LI---NE-------KPQVIQEYES 117 (142)
Q Consensus 104 ~l---gi-------s~stIs~~E~ 117 (142)
.+ |+ |.+||+++..
T Consensus 102 ~L~~~gv~~~~~~~s~stI~R~L~ 125 (128)
T cd00131 102 RLLQEGVCDKSNVPSVSSINRILR 125 (128)
T ss_pred HHHHcCCcccCCCCCHHHHHHHHH
Confidence 86 55 8888888754
No 84
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=95.55 E-value=0.022 Score=45.58 Aligned_cols=44 Identities=7% Similarity=0.083 Sum_probs=36.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCC
Q 032366 95 KLTQSQLAQLINEKPQVIQEYESGKAIPNQQI---LTKLERALGVKL 138 (142)
Q Consensus 95 glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~---l~kLa~~Lgvsl 138 (142)
..|.+|+|+++|||.+|||++.||....+.++ +.++++-||..+
T Consensus 5 ~~ti~dIA~~agVS~~TVSrvLn~~~~vs~~tr~rV~~~a~elgY~p 51 (331)
T PRK14987 5 RPVLQDVADRVGVTKMTVSRFLRNPEQVSVALRGKIAAALDELGYIP 51 (331)
T ss_pred CCcHHHHHHHhCCCHHHhhhhhCCCCCCCHHHHHHHHHHHHHhCCCc
Confidence 36999999999999999999999987666554 556677777654
No 85
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=95.51 E-value=0.033 Score=44.93 Aligned_cols=44 Identities=14% Similarity=0.160 Sum_probs=35.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCC
Q 032366 96 LTQSQLAQLINEKPQVIQEYESGKAIPNQQI---LTKLERALGVKLR 139 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~G~~~p~~~~---l~kLa~~Lgvsl~ 139 (142)
.|.+|+|+++|||.+|||++.||+...+.++ +.+.++.||..+.
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 5889999999999999999999987666554 5566777776553
No 86
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=95.51 E-value=0.041 Score=38.57 Aligned_cols=28 Identities=14% Similarity=0.096 Sum_probs=24.7
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 90 ARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 90 ~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+..-.||||.+.|+.+|||++|+.++.+
T Consensus 52 L~D~egl~QeeaA~~MgVSR~T~~ril~ 79 (106)
T PF02001_consen 52 LVDYEGLSQEEAAERMGVSRPTFQRILE 79 (106)
T ss_pred HHHHcCCCHHHHHHHcCCcHHHHHHHHH
Confidence 3455799999999999999999999875
No 87
>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=95.49 E-value=0.036 Score=32.74 Aligned_cols=39 Identities=23% Similarity=0.314 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 032366 81 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA 120 (142)
Q Consensus 81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~ 120 (142)
..+...|...+... +|+.+.|+..||+++||.++-+|..
T Consensus 3 e~l~~Ai~~v~~g~-~S~r~AA~~ygVp~sTL~~r~~g~~ 41 (45)
T PF05225_consen 3 EDLQKAIEAVKNGK-MSIRKAAKKYGVPRSTLRRRLRGKP 41 (45)
T ss_dssp HHHHHHHHHHHTTS-S-HHHHHHHHT--HHHHHHHHHHTT
T ss_pred HHHHHHHHHHHhCC-CCHHHHHHHHCcCHHHHHHHHcCCC
Confidence 34677788877544 9999999999999999999998864
No 88
>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=95.48 E-value=0.042 Score=32.61 Aligned_cols=33 Identities=12% Similarity=0.215 Sum_probs=26.9
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
..|-.+|--.++|+.|+|+.+|+|.++|++++.
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 345556668899999999999999999999874
No 89
>PRK10344 DNA-binding transcriptional regulator Nlp; Provisional
Probab=95.46 E-value=0.053 Score=36.89 Aligned_cols=51 Identities=14% Similarity=0.055 Sum_probs=40.3
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 032366 87 IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG 140 (142)
Q Consensus 87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~e 140 (142)
|......+|+|..+|+...|++.+|+.+-... |-+.-=..||++|||.+.+
T Consensus 13 I~AaL~KrG~sLa~lsr~~Gls~~TL~nAL~r---p~PKgEriIA~aLGv~P~e 63 (92)
T PRK10344 13 IIAGLRKKGTSMAAESRRNGLSSSTLANALSR---PWPKGEMIIAKALGTDPWV 63 (92)
T ss_pred HHHHHHHcCCcHHHHHHHcCCChHHHHHHHcC---CCchHHHHHHHHHCcCHHH
Confidence 55556668999999999999999999987753 3344445689999998864
No 90
>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=95.45 E-value=0.028 Score=32.21 Aligned_cols=23 Identities=22% Similarity=0.445 Sum_probs=20.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Q 032366 96 LTQSQLAQLINEKPQVIQEYESG 118 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~G 118 (142)
+|..|+|+.+|||++||.+|++-
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc
Confidence 57899999999999999999863
No 91
>COG4197 Uncharacterized protein conserved in bacteria, prophage-related [Function unknown]
Probab=95.42 E-value=0.0089 Score=40.81 Aligned_cols=39 Identities=23% Similarity=0.358 Sum_probs=35.7
Q ss_pred CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 032366 97 TQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALG 135 (142)
Q Consensus 97 TQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lg 135 (142)
.|+.||.+||+|+++|++|-+|.+.....-...|+++.+
T Consensus 14 ~q~a~a~LLgvsp~~vnQw~~g~r~~~a~r~~aIerAt~ 52 (96)
T COG4197 14 GQKALARLLGVSPPSVNQWIKGRRQVAAERALAIERATS 52 (96)
T ss_pred cHHHHHHHHccCchHHHHHhhheeecCcccchHHHHHhc
Confidence 588999999999999999999999888888888888877
No 92
>PRK01381 Trp operon repressor; Provisional
Probab=95.26 E-value=0.052 Score=37.57 Aligned_cols=57 Identities=14% Similarity=0.080 Sum_probs=42.6
Q ss_pred hHHHHHHHHHHHH--hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Q 032366 80 PSELKKAIVQARN--DKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV 136 (142)
Q Consensus 80 ~~~~g~~Lk~~R~--~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgv 136 (142)
...++.|++-.+. .-++||.++|+.+|||.+||++--+--...+...-.-|...|.-
T Consensus 38 r~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn~Lk~~~~~~k~~l~~~l~~ 96 (99)
T PRK01381 38 REALGTRVRIVEELLRGELSQREIKQELGVGIATITRGSNSLKTAPPEFKEWLEQQLLK 96 (99)
T ss_pred HHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhHHHhccCCHHHHHHHHHHhcc
Confidence 3457777776653 34599999999999999999998776555567777777666653
No 93
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=95.26 E-value=0.064 Score=42.44 Aligned_cols=48 Identities=15% Similarity=0.336 Sum_probs=37.5
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERAL 134 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~L 134 (142)
..|+.++.. +|.+||++.+|++.+.+++|-+|+..|+.+....|.+-|
T Consensus 15 ~~lr~lk~~--~ty~el~~~~g~p~~~l~RYv~g~~~P~~~~a~~~~~~l 62 (238)
T PRK08558 15 RVLRSLKKT--YTYEELSSITGLPESVLNRYVNGHVLPSVERAREIVEKL 62 (238)
T ss_pred HHHHHHhcc--cCHHHHHHHHCCCHHHHHHHHcCCcCCCHHHHHHHHHHH
Confidence 344444443 699999999999999999999999999987655554433
No 94
>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=95.10 E-value=0.047 Score=36.95 Aligned_cols=28 Identities=11% Similarity=0.004 Sum_probs=25.3
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 032366 91 RNDKKLTQSQLAQLINEKPQVIQEYESG 118 (142)
Q Consensus 91 R~~~glTQ~eLA~~lgis~stIs~~E~G 118 (142)
....|+|+.++|+.+|+|++||+++.+|
T Consensus 46 ll~~G~S~~eIA~~LgISrsTIyRi~R~ 73 (88)
T TIGR02531 46 MLKQGKTYSDIEAETGASTATISRVKRC 73 (88)
T ss_pred HHHCCCCHHHHHHHHCcCHHHHHHHHHh
Confidence 4567999999999999999999999985
No 95
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=95.06 E-value=0.03 Score=44.82 Aligned_cols=44 Identities=9% Similarity=0.054 Sum_probs=34.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCC--CCHH---HHHHHHHHhCCCCC
Q 032366 96 LTQSQLAQLINEKPQVIQEYESGKAI--PNQQ---ILTKLERALGVKLR 139 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~G~~~--p~~~---~l~kLa~~Lgvsl~ 139 (142)
.|.+|+|+++|||.+|||+..||... .+.+ .+.++++-||..+.
T Consensus 2 ~ti~dIA~~agVS~~TVSrvln~~~~~~vs~~tr~rV~~~a~~lgY~pn 50 (327)
T PRK10339 2 ATLKDIAIEAGVSLATVSRVLNDDPTLNVKEETKHRILEIAEKLEYKTS 50 (327)
T ss_pred CCHHHHHHHhCCCHHhhhhhhcCCCCCCcCHHHHHHHHHHHHHhCCCCc
Confidence 48899999999999999999998752 4444 46666888887553
No 96
>COG1513 CynS Cyanate lyase [Inorganic ion transport and metabolism]
Probab=94.95 E-value=0.17 Score=36.84 Aligned_cols=59 Identities=19% Similarity=0.160 Sum_probs=54.2
Q ss_pred hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 032366 80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 138 (142)
Q Consensus 80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl 138 (142)
...+.+.|-...+.+|+|-.+|++.+|.+...+....-|....+.+.+.++++.||.+-
T Consensus 6 i~~l~~~ll~~Kk~kgLsfaDl~~~lG~~ev~vaa~~ygqa~~~~~ear~v~e~L~L~~ 64 (151)
T COG1513 6 ILDLADALLLAKKKKGLSFADLADGLGLAEVFVAAALYGQAALPADEARAVGEALDLDE 64 (151)
T ss_pred HHHHHHHHHHHHHhcCCcHHHHHhhcCccHHHHHHHHHhhccCCHHHHHHHHHHhCCCH
Confidence 45678888889999999999999999999999999999999999999999999999764
No 97
>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=94.94 E-value=0.29 Score=33.00 Aligned_cols=42 Identities=12% Similarity=0.173 Sum_probs=33.6
Q ss_pred chHHHHHHHHHHHHhCCCCHHHHHHHh-CCCHHHHHHHHcCCC
Q 032366 79 VPSELKKAIVQARNDKKLTQSQLAQLI-NEKPQVIQEYESGKA 120 (142)
Q Consensus 79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~l-gis~stIs~~E~G~~ 120 (142)
....+...|+..+...+++|+.||+.+ |.|+.+++.+.+.-.
T Consensus 10 dT~~I~~~ik~~L~~~~IsQ~~Fa~~vL~rsqgtlsdlL~~PK 52 (87)
T PF02376_consen 10 DTKEIARRIKEWLKRNNISQRVFAKKVLNRSQGTLSDLLRKPK 52 (87)
T ss_dssp -HHHHHHHHHHHHHHTT--HHHHHHHTTSS-HHHHHHHHHSCC
T ss_pred CHHHHHHHHHHHHHHcCCCHHHHHHHHhccChhHHHHHhCCCC
Confidence 345789999999999999999999976 999999999998443
No 98
>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=94.89 E-value=0.073 Score=33.20 Aligned_cols=25 Identities=4% Similarity=0.117 Sum_probs=23.5
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 93 DKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 93 ~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
..|+++.++|+.+|++.+||..|-.
T Consensus 11 ~~G~~~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 11 LQGWSIKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred HcCCCHHHHHHHHCCChHHHHHHHH
Confidence 3699999999999999999999986
No 99
>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=94.86 E-value=0.078 Score=30.60 Aligned_cols=32 Identities=22% Similarity=0.114 Sum_probs=26.2
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHH
Q 032366 84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEY 115 (142)
Q Consensus 84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~ 115 (142)
...|.......+.++.+.|+.+|||++++.+-
T Consensus 7 ~~~i~~aL~~~~gn~~~aA~~Lgisr~tL~~k 38 (42)
T PF02954_consen 7 KQLIRQALERCGGNVSKAARLLGISRRTLYRK 38 (42)
T ss_dssp HHHHHHHHHHTTT-HHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHH
Confidence 35678888999999999999999999999864
No 100
>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=94.74 E-value=0.19 Score=25.98 Aligned_cols=23 Identities=9% Similarity=0.186 Sum_probs=21.1
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHH
Q 032366 93 DKKLTQSQLAQLINEKPQVIQEY 115 (142)
Q Consensus 93 ~~glTQ~eLA~~lgis~stIs~~ 115 (142)
..+++..++|+.+|++.++|.+|
T Consensus 19 ~~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 19 AAGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHh
Confidence 46889999999999999999987
No 101
>PF12728 HTH_17: Helix-turn-helix domain
Probab=94.73 E-value=0.054 Score=32.13 Aligned_cols=28 Identities=21% Similarity=0.297 Sum_probs=23.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q 032366 96 LTQSQLAQLINEKPQVIQEYESGKAIPN 123 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~G~~~p~ 123 (142)
||..|+|+.+|||.++|.+|.+....|.
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g~i~~ 29 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQGKIPP 29 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCCCe
Confidence 6889999999999999999987555543
No 102
>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=94.65 E-value=0.0054 Score=41.84 Aligned_cols=41 Identities=15% Similarity=0.220 Sum_probs=31.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 032366 94 KKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 138 (142)
Q Consensus 94 ~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl 138 (142)
..++|..+|+.+|++.++|++|-.+ -...+..|+.+|+..+
T Consensus 22 A~~gq~~vA~~~Gv~eStISR~k~~----~~~~~a~lLa~L~~~v 62 (91)
T PF05269_consen 22 ASVGQKKVAEAMGVDESTISRWKND----FIEKMAMLLAALELGV 62 (91)
T ss_dssp HHHHHHHHHHHHTSSTTTHHHHHHH----HHHHHHHHHHHTTTTH
T ss_pred HHHhhHHHHHHhCCCHHHHHHHHhh----HHHHHHHHHHHHHhcc
Confidence 4468999999999999999999654 2355666666666654
No 103
>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=94.65 E-value=0.062 Score=30.86 Aligned_cols=27 Identities=15% Similarity=0.235 Sum_probs=23.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCC
Q 032366 96 LTQSQLAQLINEKPQVIQEYESGKAIP 122 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~G~~~p 122 (142)
||..|+|+.+|+|+++|.+|.+....|
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g~i~ 28 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEGELP 28 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcCCCC
Confidence 688999999999999999999754444
No 104
>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=94.62 E-value=0.035 Score=39.62 Aligned_cols=23 Identities=26% Similarity=0.351 Sum_probs=21.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Q 032366 96 LTQSQLAQLINEKPQVIQEYESG 118 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~G 118 (142)
||.+|||+.+|++++||++|-+-
T Consensus 1 MT~eELA~~tG~srQTINrWvRk 23 (122)
T PF07037_consen 1 MTPEELAELTGYSRQTINRWVRK 23 (122)
T ss_pred CCHHHHHHHhCccHHHHHHHHHh
Confidence 79999999999999999999863
No 105
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=94.62 E-value=0.032 Score=40.34 Aligned_cols=28 Identities=25% Similarity=0.372 Sum_probs=25.1
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 032366 91 RNDKKLTQSQLAQLINEKPQVIQEYESG 118 (142)
Q Consensus 91 R~~~glTQ~eLA~~lgis~stIs~~E~G 118 (142)
..++|+||+++|+.+|.++..||.+|+.
T Consensus 19 lRekG~tQ~eIA~~L~TTraNvSaIEkr 46 (143)
T COG1356 19 LREKGLTQSEIARILKTTRANVSAIEKR 46 (143)
T ss_pred hhhccccHHHHHHHHccchhhHHHHHHH
Confidence 3468999999999999999999999963
No 106
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=94.58 E-value=0.033 Score=47.02 Aligned_cols=49 Identities=18% Similarity=0.160 Sum_probs=39.9
Q ss_pred hHHHHHHHHHHHHhCCCCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHH
Q 032366 80 PSELKKAIVQARNDKKLTQSQLAQLIN------EKPQVIQEYESGKAIPNQQILTKL 130 (142)
Q Consensus 80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lg------is~stIs~~E~G~~~p~~~~l~kL 130 (142)
.+.|++.+|..|..+|+||.|+.-.+| .|++||.++|.= ..+..++-||
T Consensus 208 LEqFAK~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEAL--qLSFKNMCKL 262 (398)
T KOG3802|consen 208 LEQFAKTFKQRRIKLGFTQADVGLALGALYGNVFSQTTICRFEAL--QLSFKNMCKL 262 (398)
T ss_pred HHHHHHHHHhheeccccchhHHHHHHHhhhCcccchhhhhHhHhh--ccCHHHHhhh
Confidence 456999999999999999999999998 699999999963 3445544444
No 107
>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=94.53 E-value=0.051 Score=33.15 Aligned_cols=38 Identities=11% Similarity=0.140 Sum_probs=26.8
Q ss_pred HHHHHHHHH-HHhCCCCHHHHHHHhCCCHHHHHHHHcCC
Q 032366 82 ELKKAIVQA-RNDKKLTQSQLAQLINEKPQVIQEYESGK 119 (142)
Q Consensus 82 ~~g~~Lk~~-R~~~glTQ~eLA~~lgis~stIs~~E~G~ 119 (142)
++.+.+.-+ +.+.|.++.++|+..||+.+||+.|.+.+
T Consensus 8 Tl~eK~~iI~~~e~g~s~~~ia~~fgv~~sTv~~I~K~k 46 (53)
T PF04218_consen 8 TLEEKLEIIKRLEEGESKRDIAREFGVSRSTVSTILKNK 46 (53)
T ss_dssp -HHHHHHHHHHHHCTT-HHHHHHHHT--CCHHHHHHHCH
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHhH
Confidence 345555443 56789999999999999999999998653
No 108
>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=94.43 E-value=0.14 Score=34.55 Aligned_cols=38 Identities=13% Similarity=0.058 Sum_probs=31.1
Q ss_pred hHHHHHHHHHHH--HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 80 PSELKKAIVQAR--NDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 80 ~~~~g~~Lk~~R--~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
...+..|++-++ ...|+||.++|+.+|+|..||++.-+
T Consensus 32 ~~~l~~R~~va~~lL~~g~syreIa~~tgvS~aTItRvsr 71 (87)
T PF01371_consen 32 LEALAQRWQVAKELLDEGKSYREIAEETGVSIATITRVSR 71 (87)
T ss_dssp HHHHHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 345777877654 55899999999999999999998754
No 109
>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=94.42 E-value=0.054 Score=34.51 Aligned_cols=40 Identities=18% Similarity=0.230 Sum_probs=29.8
Q ss_pred cchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 78 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.+..+|-..+-.....-|.|..++|+..||++++|.+|.+
T Consensus 6 ~ys~e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 6 RYSPEFKLQAVREYLESGESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp ---HHHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHCCCceEeeecccccccccccHHHH
Confidence 3455666666555566799999999999999999999985
No 110
>PRK13698 plasmid-partitioning protein; Provisional
Probab=94.31 E-value=0.091 Score=43.51 Aligned_cols=43 Identities=16% Similarity=0.044 Sum_probs=34.8
Q ss_pred chHHHHHHH-HHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCC
Q 032366 79 VPSELKKAI-VQARNDKKLTQSQLAQLINEKPQVIQEYESGKAI 121 (142)
Q Consensus 79 ~~~~~g~~L-k~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~ 121 (142)
-..+.+... +.+....|+||++||+.+|+|+++|++..+=-..
T Consensus 159 s~iE~A~ay~~~L~~~~~~tQeeLA~~lG~SRs~Vsn~Lrla~L 202 (323)
T PRK13698 159 SAYERGLRYASRLQNEFAGNISALADAENISRKIITRCINTAKL 202 (323)
T ss_pred CHHHHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHcC
Confidence 344567766 5677889999999999999999999999875443
No 111
>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=94.30 E-value=0.081 Score=30.71 Aligned_cols=23 Identities=30% Similarity=0.417 Sum_probs=20.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Q 032366 96 LTQSQLAQLINEKPQVIQEYESG 118 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~G 118 (142)
||..|+|+.+||++++|..|++-
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~~~ 23 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERI 23 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHC
Confidence 57889999999999999999863
No 112
>PF13518 HTH_28: Helix-turn-helix domain
Probab=94.20 E-value=0.12 Score=30.38 Aligned_cols=24 Identities=4% Similarity=0.059 Sum_probs=22.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 94 KKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 94 ~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.|.|..++|+.+|||+++|.+|.+
T Consensus 11 ~g~s~~~~a~~~gis~~tv~~w~~ 34 (52)
T PF13518_consen 11 EGESVREIAREFGISRSTVYRWIK 34 (52)
T ss_pred cCCCHHHHHHHHCCCHhHHHHHHH
Confidence 477999999999999999999975
No 113
>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=94.19 E-value=0.15 Score=31.94 Aligned_cols=22 Identities=27% Similarity=0.567 Sum_probs=20.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
+|..|+|+.+|||++||..||.
T Consensus 1 ~~i~evA~~~gvs~~tlR~~~~ 22 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEK 22 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5778999999999999999986
No 114
>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=94.18 E-value=0.064 Score=29.61 Aligned_cols=23 Identities=9% Similarity=0.219 Sum_probs=17.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHc
Q 032366 95 KLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 95 glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.||+.|+|+.+|+++.||++...
T Consensus 2 ~mtr~diA~~lG~t~ETVSR~l~ 24 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVSRILK 24 (32)
T ss_dssp E--HHHHHHHHTS-HHHHHHHHH
T ss_pred CcCHHHHHHHhCCcHHHHHHHHH
Confidence 47999999999999999998753
No 115
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=93.99 E-value=0.046 Score=38.16 Aligned_cols=24 Identities=38% Similarity=0.414 Sum_probs=21.2
Q ss_pred HHHHHHcCCChhHHHhhhcCCCCC
Q 032366 32 VNAARRAGADIETVRKSHAGTNKA 55 (142)
Q Consensus 32 ~~~a~r~G~~v~t~kk~~~g~~~~ 55 (142)
=.-|+..|++++|+++||.|..+|
T Consensus 61 ~vFA~~L~vs~~Tv~~WEqGr~kP 84 (104)
T COG2944 61 PVFARYLGVSVSTVRKWEQGRKKP 84 (104)
T ss_pred HHHHHHHCCCHHHHHHHHcCCcCC
Confidence 346889999999999999999985
No 116
>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=93.79 E-value=0.11 Score=31.16 Aligned_cols=32 Identities=16% Similarity=0.167 Sum_probs=24.1
Q ss_pred HHHHHHHhCC-CCHHHHHHHhCCCHHHHHHHHc
Q 032366 86 AIVQARNDKK-LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 86 ~Lk~~R~~~g-lTQ~eLA~~lgis~stIs~~E~ 117 (142)
.|..+....+ +|..+||+.+|||+.||.+..+
T Consensus 5 il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~ 37 (55)
T PF08279_consen 5 ILKLLLESKEPITAKELAEELGVSRRTIRRDIK 37 (55)
T ss_dssp HHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHH
Confidence 3455545554 9999999999999999998753
No 117
>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=93.78 E-value=0.25 Score=31.03 Aligned_cols=61 Identities=16% Similarity=0.151 Sum_probs=38.1
Q ss_pred HHHHHcCCChhHHHhhhc--CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHh
Q 032366 33 NAARRAGADIETVRKSHA--GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLI 105 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~--g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~l 105 (142)
+.|++.|++..|++.|+. |-..+.... ..-..+..++ ...-..|+.++. .|+|..++++.+
T Consensus 5 e~A~~~gVs~~tlr~ye~~~gl~~~~r~~--~g~R~yt~~d---------i~~l~~i~~l~~-~g~~l~~i~~~l 67 (68)
T cd04763 5 EVALLTGIKPHVLRAWEREFGLLKPQRSD--GGHRLFNDAD---------IDRILEIKRWID-NGVQVSKVKKLL 67 (68)
T ss_pred HHHHHHCcCHHHHHHHHHhcCCCCCCcCC--CCCcccCHHH---------HHHHHHHHHHHH-cCCCHHHHHHHh
Confidence 589999999999999974 544332211 1112222211 123345677776 999999998765
No 118
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=93.69 E-value=0.14 Score=42.02 Aligned_cols=55 Identities=15% Similarity=0.108 Sum_probs=40.7
Q ss_pred HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc-----CC--------CCCCHHHHHHHHHHhCCC
Q 032366 83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES-----GK--------AIPNQQILTKLERALGVK 137 (142)
Q Consensus 83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~-----G~--------~~p~~~~l~kLa~~Lgvs 137 (142)
+--++..+=-..||||.|+|+++|+|+++|+++.. |- .....+.-.+|.+.||+.
T Consensus 17 l~~~vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~I~I~~~~~~~~~Le~~L~~~fgLk 84 (318)
T PRK15418 17 LVARIAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQINSRFEGCLELENALRQHFSLQ 84 (318)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEEEEEeCCCccHHHHHHHHHHHhCCC
Confidence 33455666667899999999999999999999974 32 112345667788888864
No 119
>PF13551 HTH_29: Winged helix-turn helix
Probab=93.69 E-value=0.46 Score=31.98 Aligned_cols=80 Identities=16% Similarity=0.231 Sum_probs=49.0
Q ss_pred HHHHHHHcCCChhHHHhhhcCCCCCCCCCCCcccccchh-hhccccCCc-chHHHHHHHHHHHHhC------CCCHHHHH
Q 032366 31 VVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDE-DTENLAHDR-VPSELKKAIVQARNDK------KLTQSQLA 102 (142)
Q Consensus 31 ~~~~a~r~G~~v~t~kk~~~g~~~~~~~~~~~~~~kl~~-~~~~~~~~~-~~~~~g~~Lk~~R~~~------glTQ~eLA 102 (142)
.-..|+..|++..|+.+|-.--... + +..+.. ....-.+.. +.++.-..|.++..+. .+|..+|+
T Consensus 15 ~~~ia~~lg~s~~Tv~r~~~~~~~~-----G--~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~ 87 (112)
T PF13551_consen 15 IAEIARRLGISRRTVYRWLKRYREG-----G--IEGLLPRKPRGGRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELA 87 (112)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHcc-----c--HHHHHhccccCCCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHH
Confidence 5678999999999999887642220 0 111111 111112222 4555555666665553 48899999
Q ss_pred HHh-------CCCHHHHHHHHc
Q 032366 103 QLI-------NEKPQVIQEYES 117 (142)
Q Consensus 103 ~~l-------gis~stIs~~E~ 117 (142)
+.+ .+|.+||.+|..
T Consensus 88 ~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 88 EWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred HHHHHhccCccCCHHHHHHHHH
Confidence 865 689999998864
No 120
>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=93.66 E-value=0.096 Score=29.82 Aligned_cols=25 Identities=24% Similarity=0.473 Sum_probs=20.1
Q ss_pred CHHHHHHHhCCCHHHHHHHHcCCCC
Q 032366 97 TQSQLAQLINEKPQVIQEYESGKAI 121 (142)
Q Consensus 97 TQ~eLA~~lgis~stIs~~E~G~~~ 121 (142)
|..|+|+.+|||..||..||.-.-.
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 4578999999999999999985443
No 121
>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=93.66 E-value=0.28 Score=37.05 Aligned_cols=53 Identities=19% Similarity=0.130 Sum_probs=40.2
Q ss_pred chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHH
Q 032366 79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLER 132 (142)
Q Consensus 79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~ 132 (142)
...+.+..+++++...|+|+.++|+.+|+|.++|+++..=-. .+.+.+..+..
T Consensus 104 t~~e~a~~~~~l~~~~g~s~~~iA~~lg~s~~~V~r~l~l~~-lp~~v~~~~~~ 156 (187)
T TIGR00180 104 SPIEEAQAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLRLLK-LPSEIQSAIPE 156 (187)
T ss_pred CHHHHHHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHHHHc-CCHHHHHHHHh
Confidence 344566677777777899999999999999999999987433 45566655554
No 122
>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=93.65 E-value=0.12 Score=32.17 Aligned_cols=22 Identities=23% Similarity=0.437 Sum_probs=20.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
+|..|+|+.+||+++||..|++
T Consensus 1 ~s~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999997
No 123
>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=93.43 E-value=0.45 Score=29.49 Aligned_cols=61 Identities=21% Similarity=0.183 Sum_probs=35.5
Q ss_pred HHHHHcCCChhHHHhhhc--CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHh
Q 032366 33 NAARRAGADIETVRKSHA--GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLI 105 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~--g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~l 105 (142)
+.|++.|++..|+++|+. |...+... ...-..+..+ ....-..|+.++. .|+|..++.+.+
T Consensus 5 eva~~~gvs~~tlr~w~~~~g~~~~~r~--~~~~r~yt~~---------~v~~l~~i~~l~~-~g~~l~~i~~~~ 67 (68)
T cd01104 5 AVARLTGVSPDTLRAWERRYGLPAPQRT--DGGHRLYSEA---------DVARLRLIRRLTS-EGVRISQAAALA 67 (68)
T ss_pred HHHHHHCcCHHHHHHHHHhCCCCCCCcC--CCCCeecCHH---------HHHHHHHHHHHHH-CCCCHHHHHHHh
Confidence 579999999999999996 33221110 0011111111 1113345566665 899999888754
No 124
>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=93.38 E-value=0.11 Score=32.85 Aligned_cols=24 Identities=17% Similarity=0.343 Sum_probs=21.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHcC
Q 032366 95 KLTQSQLAQLINEKPQVIQEYESG 118 (142)
Q Consensus 95 glTQ~eLA~~lgis~stIs~~E~G 118 (142)
+++..++|+.+|||.+||+.|-+-
T Consensus 22 ~i~lkdIA~~Lgvs~~tIr~WK~~ 45 (60)
T PF10668_consen 22 KIKLKDIAEKLGVSESTIRKWKSR 45 (60)
T ss_pred CccHHHHHHHHCCCHHHHHHHhhh
Confidence 589999999999999999999763
No 125
>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=93.29 E-value=0.25 Score=28.23 Aligned_cols=29 Identities=10% Similarity=0.184 Sum_probs=24.8
Q ss_pred HHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 89 QARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 89 ~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.++-..|+|+.++|+.+|++.++|.++..
T Consensus 20 ~~~~~~~~~~~~ia~~~~~s~~~i~~~~~ 48 (55)
T cd06171 20 LLRFGEGLSYEEIAEILGISRSTVRQRLH 48 (55)
T ss_pred HHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 44445899999999999999999999864
No 126
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=93.29 E-value=0.18 Score=41.66 Aligned_cols=57 Identities=18% Similarity=0.171 Sum_probs=44.1
Q ss_pred HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc-----CC--------CCCCHHHHHHHHHHhCCC
Q 032366 81 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES-----GK--------AIPNQQILTKLERALGVK 137 (142)
Q Consensus 81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~-----G~--------~~p~~~~l~kLa~~Lgvs 137 (142)
..+..++..+.-..||||.|+|+++|||+.+|+++.. |- .....+.-.+|.+.||++
T Consensus 12 ~~l~~~~A~lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I~i~~~~~~~~~Le~~L~~~fgL~ 81 (321)
T COG2390 12 ERLLARAAWLYYVEGLTQSEIAERLGISRATVSRLLAKAREEGIVKISINSPVEGCLELEQQLKERFGLK 81 (321)
T ss_pred HHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEEEeCCCCcchHHHHHHHHHhcCCC
Confidence 3456677778888999999999999999999999874 21 122455667888888876
No 127
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=93.25 E-value=0.27 Score=34.67 Aligned_cols=40 Identities=23% Similarity=0.166 Sum_probs=32.9
Q ss_pred cchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 78 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
....+|-..+-....+.|.|..++|+.+|||+++|++|-+
T Consensus 12 ~ys~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r 51 (121)
T PRK09413 12 RRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRK 51 (121)
T ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 4556676666666677899999999999999999999965
No 128
>PRK04217 hypothetical protein; Provisional
Probab=93.25 E-value=0.31 Score=34.29 Aligned_cols=32 Identities=9% Similarity=0.055 Sum_probs=27.9
Q ss_pred HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.+-.++...|+|++++|+.+|+|.+||.++..
T Consensus 49 eai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~ 80 (110)
T PRK04217 49 EALRLVDYEGLTQEEAGKRMGVSRGTVWRALT 80 (110)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 44566777899999999999999999999875
No 129
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=93.23 E-value=0.11 Score=35.71 Aligned_cols=28 Identities=18% Similarity=0.054 Sum_probs=24.7
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 90 ARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 90 ~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+..-.||+|.|.|.++|||++|+.+..+
T Consensus 44 LvD~~~l~QeeAA~rMgISr~Tfwr~l~ 71 (99)
T COG1342 44 LVDYEGLTQEEAALRMGISRQTFWRLLT 71 (99)
T ss_pred HHhHhhccHHHHHHHhcccHHHHHHHHH
Confidence 4456899999999999999999999875
No 130
>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=93.20 E-value=0.34 Score=30.24 Aligned_cols=62 Identities=18% Similarity=0.199 Sum_probs=37.9
Q ss_pred HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhC
Q 032366 33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLIN 106 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lg 106 (142)
+.|+..|++..|++.|+. |.... +...+ .-..++.++ ...-..|+.++. .|+|.+++...++
T Consensus 5 evA~~~gvs~~tlR~~~~~g~l~~-~~~~~-g~R~y~~~~---------l~~l~~i~~l~~-~g~~l~~i~~~l~ 67 (67)
T cd04764 5 EVSEIIGVKPHTLRYYEKEFNLYI-PRTEN-GRRYYTDED---------IELLKKIKTLLE-KGLSIKEIKEILN 67 (67)
T ss_pred HHHHHHCcCHHHHHHHHHhcCCCC-CCCCC-CceeeCHHH---------HHHHHHHHHHHH-CCCCHHHHHHHhC
Confidence 578999999999999985 44431 11111 112222111 123455677777 8999999987663
No 131
>smart00351 PAX Paired Box domain.
Probab=93.09 E-value=0.34 Score=34.44 Aligned_cols=38 Identities=11% Similarity=0.236 Sum_probs=30.5
Q ss_pred chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+..++..+|-.+-. .|+|+.++|+.+|||++||++|.+
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 45556666665544 799999999999999999999964
No 132
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=93.02 E-value=0.38 Score=28.39 Aligned_cols=38 Identities=8% Similarity=0.119 Sum_probs=29.2
Q ss_pred chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+...+...|-.+.... .|.+++|+.+|+|.+||.++-+
T Consensus 12 ~T~~~~~~i~~~~~~~-~s~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 12 ITKRLEQYILKLLRES-RSFKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred HHHHHHHHHHHHHhhc-CCHHHHHHHHCCCHHHHHHHHH
Confidence 4444555665555555 7999999999999999999864
No 133
>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=92.98 E-value=0.33 Score=29.75 Aligned_cols=24 Identities=13% Similarity=0.192 Sum_probs=21.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 94 KKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 94 ~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
..+|+.+||+.+|+|+++++++.+
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~ 47 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLK 47 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHH
Confidence 459999999999999999988754
No 134
>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=92.90 E-value=0.29 Score=29.18 Aligned_cols=34 Identities=9% Similarity=0.181 Sum_probs=24.3
Q ss_pred HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
-.+.+-.++-..|+|..|+|+.+|+|.++|..+-
T Consensus 14 ~~r~i~~l~~~~g~s~~eIa~~l~~s~~~v~~~l 47 (54)
T PF08281_consen 14 RQREIFLLRYFQGMSYAEIAEILGISESTVKRRL 47 (54)
T ss_dssp HHHHHHHHHHTS---HHHHHHHCTS-HHHHHHHH
T ss_pred HHHHHHHHHHHHCcCHHHHHHHHCcCHHHHHHHH
Confidence 3445566777889999999999999999998764
No 135
>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=92.84 E-value=0.026 Score=42.19 Aligned_cols=46 Identities=15% Similarity=0.120 Sum_probs=1.8
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 032366 93 DKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 138 (142)
Q Consensus 93 ~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl 138 (142)
..-||++++|+.+|++.||||+.-+|+..-++.-+.-|..+|...+
T Consensus 47 l~PLt~~~iA~~lgl~~STVSRav~~Ky~~t~~Gi~plk~fF~~~~ 92 (160)
T PF04552_consen 47 LKPLTMKDIADELGLHESTVSRAVKNKYIQTPRGIFPLKDFFSRSV 92 (160)
T ss_dssp --------------------------------------S-----SS
T ss_pred CcCCCHHHHHHHhCCCHhHHHHHHcCceeecCCeeeeHHHhccccc
Confidence 3458999999999999999999999998777766777777776654
No 136
>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=92.79 E-value=0.3 Score=29.51 Aligned_cols=34 Identities=15% Similarity=0.133 Sum_probs=27.9
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
...|..+...-++|+.+||+.+++++++++++-+
T Consensus 6 ~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~ 39 (59)
T PF01047_consen 6 FRILRILYENGGITQSELAEKLGISRSTVTRIIK 39 (59)
T ss_dssp HHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHH
Confidence 3456777888999999999999999999998753
No 137
>COG2842 Uncharacterized ATPase, putative transposase [General function prediction only]
Probab=92.78 E-value=0.36 Score=39.54 Aligned_cols=60 Identities=17% Similarity=0.042 Sum_probs=47.2
Q ss_pred chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 032366 79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 138 (142)
Q Consensus 79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl 138 (142)
.....-+.+++.-+-.+++|+.+|..+|+|+.+|+.+.+|...-...+-.+|+.+|+-+.
T Consensus 3 ~n~~~~k~~k~f~e~~~~~q~~~a~gi~~~~~~vsk~L~g~~g~~~~~~a~ia~~le~~~ 62 (297)
T COG2842 3 INFIEIKKLKEFAEFSGMCQKYLARGIGTSAPALSKYLNGYKGDYATNEAKIAAFLEKKG 62 (297)
T ss_pred hhHHHHHHHHHHHHhhhhhHHHHHHHhccCchhHHHHhcCcCchHHHHHHHHHHHHcCCC
Confidence 345567889999999999999999999999999999999833223455667777776543
No 138
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=92.73 E-value=0.12 Score=32.24 Aligned_cols=22 Identities=27% Similarity=0.517 Sum_probs=20.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
+|..|+|+.+|||+++|..||+
T Consensus 1 yti~eva~~~gvs~~tlr~y~~ 22 (69)
T PF13411_consen 1 YTIKEVAKLLGVSPSTLRYYER 22 (69)
T ss_dssp EEHHHHHHHTTTTHHHHHHHHH
T ss_pred CcHHHHHHHHCcCHHHHHHHHH
Confidence 4678999999999999999996
No 139
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=92.70 E-value=0.13 Score=31.08 Aligned_cols=28 Identities=14% Similarity=-0.020 Sum_probs=24.3
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 90 ARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 90 ~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.+-+.|+++.+||...|||++|+++|-+
T Consensus 14 ~~LR~~~~~~~La~~FgIs~stvsri~~ 41 (53)
T PF13613_consen 14 MYLRLNLTFQDLAYRFGISQSTVSRIFH 41 (53)
T ss_pred HHHHcCCcHhHHhhheeecHHHHHHHHH
Confidence 3455789999999999999999999864
No 140
>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=92.62 E-value=0.15 Score=32.02 Aligned_cols=22 Identities=32% Similarity=0.510 Sum_probs=20.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
++..|+|+.+||++++|..||.
T Consensus 1 ~~i~e~A~~~gVs~~tlr~ye~ 22 (68)
T cd04763 1 YTIGEVALLTGIKPHVLRAWER 22 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4678999999999999999985
No 141
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=92.62 E-value=0.19 Score=40.11 Aligned_cols=34 Identities=18% Similarity=0.333 Sum_probs=28.7
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
-+.|-.+|-..++||+++|+.+|||++.|+++++
T Consensus 201 Ek~Vl~l~y~eelt~kEI~~~LgISes~VSql~k 234 (247)
T COG1191 201 EKLVLVLRYKEELTQKEIAEVLGISESRVSRLHK 234 (247)
T ss_pred HHHHHHHHHHhccCHHHHHHHhCccHHHHHHHHH
Confidence 3445556677799999999999999999999985
No 142
>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=92.59 E-value=0.19 Score=30.88 Aligned_cols=24 Identities=17% Similarity=0.254 Sum_probs=21.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 94 KKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 94 ~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
++.|..+||+.+|||++|++...+
T Consensus 22 R~~tl~elA~~lgis~st~~~~LR 45 (53)
T PF04967_consen 22 RRITLEELAEELGISKSTVSEHLR 45 (53)
T ss_pred CcCCHHHHHHHhCCCHHHHHHHHH
Confidence 568999999999999999998654
No 143
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=92.54 E-value=0.57 Score=29.12 Aligned_cols=62 Identities=18% Similarity=0.242 Sum_probs=38.4
Q ss_pred HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhC
Q 032366 33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLIN 106 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lg 106 (142)
+.|+..|++.+|++.|+. |...+.. ....-..++.+ ....-..|+.++. .|+|..++.+.+.
T Consensus 5 eva~~~gvs~~tlr~y~~~gll~~~~--~~~g~r~y~~~---------dv~~l~~i~~l~~-~G~sl~~I~~~l~ 67 (69)
T PF13411_consen 5 EVAKLLGVSPSTLRYYEREGLLPPPR--DENGYRYYSEE---------DVERLREIKELRK-QGMSLEEIKKLLK 67 (69)
T ss_dssp HHHHHTTTTHHHHHHHHHTTSSTTBE--STTSSEEE-HH---------HHHHHHHHHHHHH-TTTHHHHHHHHH-
T ss_pred HHHHHHCcCHHHHHHHHHhcCccccc--ccCceeeccHH---------HHHHHHHHHHHHH-CcCCHHHHHHHHc
Confidence 579999999999999987 3332211 01111222222 1224556777777 9999999887763
No 144
>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=92.43 E-value=0.28 Score=33.24 Aligned_cols=25 Identities=12% Similarity=0.205 Sum_probs=22.2
Q ss_pred HhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 92 NDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 92 ~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
....+||.|||+.+|+++.+|++..
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L 68 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAI 68 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHH
Confidence 5678999999999999999999843
No 145
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=92.41 E-value=0.24 Score=30.84 Aligned_cols=22 Identities=23% Similarity=0.345 Sum_probs=20.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
+|..++|+.+|||+++|..|+.
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999975
No 146
>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=92.39 E-value=0.6 Score=31.70 Aligned_cols=67 Identities=15% Similarity=0.193 Sum_probs=42.0
Q ss_pred HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHH
Q 032366 33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQ 110 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~s 110 (142)
..|++.|++..|++.|+. |-..+... .-.-..++.. ....-..|..++...|++..++...+.....
T Consensus 5 e~a~~~gvs~~tLR~ye~~Gll~p~r~--~~g~R~Y~~~---------dv~~l~~I~~L~~~~G~~l~ei~~~l~~~~~ 72 (96)
T cd04774 5 EVAKRLGLTKRTLKYYEEIGLVSPERS--EGRYRLYSEE---------DLKRLERILRLREVLGFSLQEVTHFLERPLE 72 (96)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCcC--CCCCEEECHH---------HHHHHHHHHHHHHHcCCCHHHHHHHHhcccc
Confidence 578999999999999986 33322111 1111222221 1224556777788789999999888766544
No 147
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=92.32 E-value=0.61 Score=27.08 Aligned_cols=25 Identities=16% Similarity=0.226 Sum_probs=23.0
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 93 DKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 93 ~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
..|+|..++|+.+|+|+++|..+..
T Consensus 16 ~~g~s~~eia~~l~is~~tv~~~~~ 40 (58)
T smart00421 16 AEGLTNKEIAERLGISEKTVKTHLS 40 (58)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 5799999999999999999998865
No 148
>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=92.17 E-value=0.27 Score=39.54 Aligned_cols=42 Identities=21% Similarity=0.218 Sum_probs=31.3
Q ss_pred CCCCHHHHHHHhCC-----CHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 032366 94 KKLTQSQLAQLINE-----KPQVIQEYESGKAIPNQQILTKLERALG 135 (142)
Q Consensus 94 ~glTQ~eLA~~lgi-----s~stIs~~E~G~~~p~~~~l~kLa~~Lg 135 (142)
.++||.+||+++|- |+++|+++..=-....+.+...|+.-+|
T Consensus 135 ~~ltq~ela~~lgk~g~~isrs~Isn~lrll~~L~~~i~~~l~~glG 181 (258)
T TIGR03764 135 ESLSQRELARRLSADGYPISQSHISRMGDTVEYLYPAIPNLLYSGLG 181 (258)
T ss_pred CCCCHHHHHHHhcccCCCCCHHHHHHHHHHHHhChHHHHHHHHccCC
Confidence 68999999999976 9999999987544455555555554443
No 149
>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=91.99 E-value=0.45 Score=27.57 Aligned_cols=30 Identities=13% Similarity=0.224 Sum_probs=22.8
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHH
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQE 114 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~ 114 (142)
..|..+......+..+||+.+|+|.++|.+
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 446677778889999999999999999875
No 150
>PF14590 DUF4447: Domain of unknown function (DUF4447); PDB: 2OX6_B.
Probab=91.92 E-value=1 Score=32.82 Aligned_cols=40 Identities=23% Similarity=0.224 Sum_probs=31.1
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCH
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQ 124 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~ 124 (142)
-.|+.+|...|+|..++++..+.|..-|-.||.|....+.
T Consensus 10 ie~~ylr~slgl~~aqv~~l~k~se~dv~aweage~~~~~ 49 (166)
T PF14590_consen 10 IEIKYLRLSLGLTTAQVAELTKASEADVLAWEAGEKPAPG 49 (166)
T ss_dssp HHHHHHHHHTT--HHHHHHHHTS-HHHHHHHHTTSS---H
T ss_pred HHHHHHHHHcCCCHHHHHHhhccCHHHhhhhhccCCcCch
Confidence 3478899999999999999999999999999999876553
No 151
>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=91.72 E-value=0.35 Score=34.24 Aligned_cols=22 Identities=23% Similarity=0.305 Sum_probs=20.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
|+..|||+.+|||..||.-||+
T Consensus 1 m~IgevA~~~gvs~~tLRyYe~ 22 (127)
T cd04784 1 MKIGELAKKTGCSVETIRYYEK 22 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999996
No 152
>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=91.70 E-value=0.46 Score=28.78 Aligned_cols=34 Identities=18% Similarity=0.211 Sum_probs=26.2
Q ss_pred HHHHHHHHHhCC--CCHHHHHHHhCCCHHHHHHHHc
Q 032366 84 KKAIVQARNDKK--LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 84 g~~Lk~~R~~~g--lTQ~eLA~~lgis~stIs~~E~ 117 (142)
...|..+...-+ +|+.+||+.++++++++++..+
T Consensus 8 ~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~ 43 (62)
T PF12802_consen 8 FRVLMALARHPGEELTQSELAERLGISKSTVSRIVK 43 (62)
T ss_dssp HHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 345566666666 9999999999999999998753
No 153
>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=91.66 E-value=0.57 Score=27.44 Aligned_cols=21 Identities=33% Similarity=0.510 Sum_probs=18.5
Q ss_pred HHHHcCCChhHHHhhhcCCCC
Q 032366 34 AARRAGADIETVRKSHAGTNK 54 (142)
Q Consensus 34 ~a~r~G~~v~t~kk~~~g~~~ 54 (142)
.|++.|++.+|+.+|+.|...
T Consensus 3 lA~~~gvs~~tvs~~l~g~~~ 23 (52)
T cd01392 3 IARAAGVSVATVSRVLNGKPR 23 (52)
T ss_pred HHHHHCcCHHHHHHHHcCCCC
Confidence 689999999999999988753
No 154
>smart00351 PAX Paired Box domain.
Probab=91.65 E-value=0.86 Score=32.35 Aligned_cols=74 Identities=9% Similarity=0.132 Sum_probs=44.4
Q ss_pred HHHHHHHHcCCChhHHHhhhc-----CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHH-HHHhCCCCHHHHHH
Q 032366 30 KVVNAARRAGADIETVRKSHA-----GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQ-ARNDKKLTQSQLAQ 103 (142)
Q Consensus 30 ~~~~~a~r~G~~v~t~kk~~~-----g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~-~R~~~glTQ~eLA~ 103 (142)
+.-..|++.|++..|+.+|-. |...+.+.. +....+ ........|.. ....-.+|..+|++
T Consensus 35 s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~g-g~rp~~------------~~~~~~~~I~~~~~~~p~~t~~el~~ 101 (125)
T smart00351 35 RPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIG-GSKPKV------------ATPKVVKKIADYKQENPGIFAWEIRD 101 (125)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCC-CCCCCc------------cCHHHHHHHHHHHHHCCCCCHHHHHH
Confidence 455689999999999999854 544432111 111111 22223333443 45666899999988
Q ss_pred HhC-----C-----CHHHHHHHH
Q 032366 104 LIN-----E-----KPQVIQEYE 116 (142)
Q Consensus 104 ~lg-----i-----s~stIs~~E 116 (142)
.+. + |.+||.+|.
T Consensus 102 ~L~~~gv~~~~~~Ps~sti~~~l 124 (125)
T smart00351 102 RLLSEGVCDKDNVPSVSSINRIL 124 (125)
T ss_pred HHHHcCCCcCCCCCChhhHHHhh
Confidence 772 2 677777664
No 155
>cd00131 PAX Paired Box domain
Probab=91.35 E-value=0.72 Score=33.00 Aligned_cols=39 Identities=8% Similarity=0.267 Sum_probs=30.7
Q ss_pred cchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 78 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.+..++..+|-.+- +.|+|+.++|+.+|||++||.+|-+
T Consensus 17 ~lS~d~R~rIv~~~-~~G~s~~~iA~~~~Vs~~tV~r~i~ 55 (128)
T cd00131 17 PLPDSIRQRIVELA-QSGIRPCDISRQLRVSHGCVSKILN 55 (128)
T ss_pred cCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34455666666554 4799999999999999999999953
No 156
>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=91.30 E-value=0.27 Score=31.15 Aligned_cols=24 Identities=17% Similarity=0.277 Sum_probs=21.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 94 KKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 94 ~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
..+|+.+||..+|+|+.++++..+
T Consensus 27 ~~lt~~~iA~~~g~sr~tv~r~l~ 50 (76)
T PF13545_consen 27 LPLTQEEIADMLGVSRETVSRILK 50 (76)
T ss_dssp EESSHHHHHHHHTSCHHHHHHHHH
T ss_pred ecCCHHHHHHHHCCCHHHHHHHHH
Confidence 468999999999999999998753
No 157
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=91.29 E-value=0.52 Score=29.93 Aligned_cols=29 Identities=17% Similarity=0.039 Sum_probs=23.1
Q ss_pred HHHHHhCC--CCHHHHHHHhCCCHHHHHHHH
Q 032366 88 VQARNDKK--LTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 88 k~~R~~~g--lTQ~eLA~~lgis~stIs~~E 116 (142)
..++..-+ +|+.+||+.+|++.+++++..
T Consensus 13 ~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L 43 (68)
T smart00550 13 EFLENSGDETSTALQLAKNLGLPKKEVNRVL 43 (68)
T ss_pred HHHHHCCCCCcCHHHHHHHHCCCHHHHHHHH
Confidence 34444435 999999999999999998874
No 158
>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=91.26 E-value=0.34 Score=31.43 Aligned_cols=42 Identities=14% Similarity=0.192 Sum_probs=27.9
Q ss_pred HHHHHHH-HHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q 032366 82 ELKKAIV-QARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPN 123 (142)
Q Consensus 82 ~~g~~Lk-~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~ 123 (142)
.+.+.|. ....-..+|..+||+.+|+|+++|.++.+.-..-+
T Consensus 20 ~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~kkLG~~g 62 (77)
T PF01418_consen 20 KIADYILENPDEIAFMSISELAEKAGVSPSTIVRFCKKLGFSG 62 (77)
T ss_dssp HHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHHHHCTTTC
T ss_pred HHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHHHHhCCCC
Confidence 3455553 34566789999999999999999999987433333
No 159
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=91.22 E-value=0.75 Score=30.20 Aligned_cols=36 Identities=19% Similarity=0.421 Sum_probs=27.2
Q ss_pred CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 032366 97 TQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALG 135 (142)
Q Consensus 97 TQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lg 135 (142)
+...+|+.+|||+++|++| |+.+| ...+.+|..+-+
T Consensus 12 s~~kvA~aLGIs~~AVsQW--Ge~VP-e~rA~~ie~~T~ 47 (75)
T PRK09744 12 SKTKLANAAGVRLASVAAW--GELVP-EGRAMRLQEASG 47 (75)
T ss_pred cHHHHHHHHCCCHHHHHHH--hccCc-HHHHHHHHHHhC
Confidence 6778999999999999999 77665 344455655544
No 160
>PRK00118 putative DNA-binding protein; Validated
Probab=91.07 E-value=0.53 Score=32.78 Aligned_cols=33 Identities=9% Similarity=0.090 Sum_probs=27.7
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+.+-.++...|+|..++|+.+|+|++||.++..
T Consensus 23 Revl~L~y~eg~S~~EIAe~lGIS~~TV~r~L~ 55 (104)
T PRK00118 23 RNYMELYYLDDYSLGEIAEEFNVSRQAVYDNIK 55 (104)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 334466677899999999999999999999864
No 161
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=90.80 E-value=0.68 Score=33.85 Aligned_cols=36 Identities=14% Similarity=0.205 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 82 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 82 ~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
++..++-..-...|+|..++|+++|+|.+||.+|.+
T Consensus 8 ~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~ 43 (138)
T COG3415 8 DLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVR 43 (138)
T ss_pred HHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHH
Confidence 344555556667899999999999999999999975
No 162
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=90.68 E-value=0.37 Score=27.54 Aligned_cols=24 Identities=17% Similarity=0.259 Sum_probs=20.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 94 KKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 94 ~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
..+|+.++|+.+|+|+++++++.+
T Consensus 7 ~~~s~~~la~~l~~s~~tv~~~l~ 30 (48)
T smart00419 7 LPLTRQEIAELLGLTRETVSRTLK 30 (48)
T ss_pred eccCHHHHHHHHCCCHHHHHHHHH
Confidence 458999999999999999988654
No 163
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=90.68 E-value=0.99 Score=27.37 Aligned_cols=35 Identities=11% Similarity=0.242 Sum_probs=26.1
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK 119 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~ 119 (142)
+..-..+.+.|++..++|+.+|-|+..|.+|.++-
T Consensus 10 qaqid~m~qlG~s~~~isr~i~RSr~~Ir~yl~dP 44 (50)
T PF11427_consen 10 QAQIDVMHQLGMSLREISRRIGRSRTCIRRYLKDP 44 (50)
T ss_dssp HHHHHHHHHTT--HHHHHHHHT--HHHHHHHHHSC
T ss_pred HHHHHHHHHhchhHHHHHHHhCccHHHHHHHhcCh
Confidence 33446788999999999999999999999998753
No 164
>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=90.51 E-value=0.48 Score=31.57 Aligned_cols=23 Identities=13% Similarity=0.345 Sum_probs=21.2
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHc
Q 032366 95 KLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 95 glTQ~eLA~~lgis~stIs~~E~ 117 (142)
++|..++|+.+|||.+||..||+
T Consensus 1 ~~ti~evA~~~gvs~~tLR~ye~ 23 (88)
T cd01105 1 VIGIGEVSKLTGVSPRQLRYWEE 23 (88)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHH
Confidence 47889999999999999999986
No 165
>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=90.31 E-value=0.46 Score=32.86 Aligned_cols=22 Identities=27% Similarity=0.578 Sum_probs=20.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
||..++|+.+|||++||..||.
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~ 22 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEK 22 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999996
No 166
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=90.31 E-value=0.56 Score=35.20 Aligned_cols=32 Identities=13% Similarity=0.199 Sum_probs=26.5
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
.++-.+|.-.|+|..|+|+.+|||+.||.+..
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 34445677789999999999999999998754
No 167
>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=90.24 E-value=0.09 Score=31.58 Aligned_cols=28 Identities=18% Similarity=0.268 Sum_probs=20.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q 032366 96 LTQSQLAQLINEKPQVIQEYESGKAIPN 123 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~G~~~p~ 123 (142)
++.+|+++.+|+|++||.++.+....|.
T Consensus 4 l~~~ev~~~~g~s~~ti~~~~k~g~FP~ 31 (51)
T PF05930_consen 4 LRIKEVAELLGVSRSTIYRLIKDGKFPK 31 (51)
T ss_dssp E-HHHHHHHHSS-HHHHHHHHHHHH---
T ss_pred ccHHHHHHHHCCCHHHHHHHHhcccCCC
Confidence 5678999999999999999998555553
No 168
>PF13551 HTH_29: Winged helix-turn helix
Probab=90.17 E-value=0.5 Score=31.79 Aligned_cols=27 Identities=7% Similarity=0.110 Sum_probs=23.2
Q ss_pred HHhCCC-CHHHHHHHhCCCHHHHHHHHc
Q 032366 91 RNDKKL-TQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 91 R~~~gl-TQ~eLA~~lgis~stIs~~E~ 117 (142)
....|+ |..++|+.+|+|++||++|.+
T Consensus 7 l~~~g~~~~~~ia~~lg~s~~Tv~r~~~ 34 (112)
T PF13551_consen 7 LLAEGVSTIAEIARRLGISRRTVYRWLK 34 (112)
T ss_pred HHHcCCCcHHHHHHHHCcCHHHHHHHHH
Confidence 345688 599999999999999999874
No 169
>PRK10072 putative transcriptional regulator; Provisional
Probab=90.07 E-value=0.29 Score=33.56 Aligned_cols=27 Identities=22% Similarity=0.245 Sum_probs=23.8
Q ss_pred HHHHHHHHHcCCChhHHHhhhcCCCCC
Q 032366 29 EKVVNAARRAGADIETVRKSHAGTNKA 55 (142)
Q Consensus 29 ~~~~~~a~r~G~~v~t~kk~~~g~~~~ 55 (142)
-++.+.|+..|++..|+.+|+.|...|
T Consensus 47 lTQ~elA~~lGvS~~TVs~WE~G~r~P 73 (96)
T PRK10072 47 LKIDDFARVLGVSVAMVKEWESRRVKP 73 (96)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCC
Confidence 356789999999999999999999874
No 170
>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=90.06 E-value=1.7 Score=29.39 Aligned_cols=65 Identities=17% Similarity=0.248 Sum_probs=40.8
Q ss_pred HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCC
Q 032366 33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINE 107 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgi 107 (142)
+.|++.|+++.|++-|+. |-..|.... ..+-..++.+ ....-..|+.++...|++..++++.+..
T Consensus 5 eva~~~gvs~~tlR~Ye~~GLl~p~~r~-~~g~r~Y~~~---------dv~~l~~I~~L~~~~G~~l~~I~~~l~~ 70 (95)
T cd04780 5 ELSKRSGVSVATIKYYLREGLLPEGRRL-APNQAEYSEA---------HVERLRLIRALQQEGGLPISQIKEVLDA 70 (95)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCcCC-CCCCeecCHH---------HHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 478999999999999998 444321111 1111222221 1124455666777789999999988764
No 171
>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=90.05 E-value=0.94 Score=30.39 Aligned_cols=22 Identities=23% Similarity=0.406 Sum_probs=20.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
+|..|+|+.+||++++|..|++
T Consensus 1 ~~~~eva~~~gi~~~tlr~~~~ 22 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYEE 22 (100)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5778999999999999999986
No 172
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=90.03 E-value=0.16 Score=41.56 Aligned_cols=38 Identities=18% Similarity=0.221 Sum_probs=33.8
Q ss_pred hHHHHHHHHHHHHhCCCCHHHHHHHhC---------CCHHHHHHHHc
Q 032366 80 PSELKKAIVQARNDKKLTQSQLAQLIN---------EKPQVIQEYES 117 (142)
Q Consensus 80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lg---------is~stIs~~E~ 117 (142)
.+.|+++.++.|..+|.||.|+.+.+- +|++||-++|+
T Consensus 219 LEaFAErFKQRRIKLGVTQADVG~ALAnLKiPGVGsLSQSTICRFES 265 (385)
T KOG1168|consen 219 LEAFAERFKQRRIKLGVTQADVGKALANLKIPGVGSLSQSTICRFES 265 (385)
T ss_pred HHHHHHHHHhhhhhhcccHHHHHHHHHhCcCCCcccccccceeeeee
Confidence 456999999999999999999998772 68999999996
No 173
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=89.91 E-value=0.33 Score=35.65 Aligned_cols=25 Identities=12% Similarity=0.252 Sum_probs=19.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHcCC
Q 032366 95 KLTQSQLAQLINEKPQVIQEYESGK 119 (142)
Q Consensus 95 glTQ~eLA~~lgis~stIs~~E~G~ 119 (142)
..|+.++|+.+||+++|+.+|-+..
T Consensus 34 r~T~~eiAee~Gis~~tLYrWr~~~ 58 (142)
T PF13022_consen 34 RRTQAEIAEEVGISRSTLYRWRQQN 58 (142)
T ss_dssp -S-HHHHHHHHTS-HHHHHHHHHH-
T ss_pred cchHHHHHHHhCCCHHHHHHHHhcC
Confidence 4799999999999999999998654
No 174
>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=89.81 E-value=0.87 Score=27.85 Aligned_cols=31 Identities=6% Similarity=-0.010 Sum_probs=26.8
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 87 IVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+.+++.-..+++.+.|+.+||+.+++.+..+
T Consensus 7 ~~~L~~~fhlp~~eAA~~Lgv~~T~LKr~CR 37 (52)
T PF02042_consen 7 LEDLSQYFHLPIKEAAKELGVSVTTLKRRCR 37 (52)
T ss_pred HHHHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence 5677888899999999999999998887765
No 175
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=89.77 E-value=1 Score=25.86 Aligned_cols=26 Identities=19% Similarity=0.247 Sum_probs=22.2
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 91 RNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 91 R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
....++|..++++.+++++++++++.
T Consensus 10 ~~~~~~s~~~l~~~l~~s~~tv~~~l 35 (53)
T smart00420 10 AQQGKVSVEELAELLGVSEMTIRRDL 35 (53)
T ss_pred HHcCCcCHHHHHHHHCCCHHHHHHHH
Confidence 33467999999999999999998865
No 176
>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=89.52 E-value=2.1 Score=28.39 Aligned_cols=63 Identities=14% Similarity=0.119 Sum_probs=38.3
Q ss_pred HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhC
Q 032366 33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLIN 106 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lg 106 (142)
+.|++.|++..|++.|+. |-..+..... -.-..+..++ -..-..|+.+|. .|+|.+++.+.+.
T Consensus 6 evA~~~gvs~~tLR~ye~~Gll~p~r~~~-~g~R~Ys~~d---------v~~l~~I~~Lr~-~G~sl~~i~~~l~ 69 (88)
T cd01105 6 EVSKLTGVSPRQLRYWEEKGLIKSIRSDG-GGQRKYSLAD---------VDRLLVIKELLD-EGFTLAAAVEKLR 69 (88)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCccCC-CCceecCHHH---------HHHHHHHHHHHH-CCCCHHHHHHHHH
Confidence 589999999999999976 4433211110 0112222211 123455666766 8999999888775
No 177
>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=89.50 E-value=2 Score=28.55 Aligned_cols=63 Identities=17% Similarity=0.210 Sum_probs=40.3
Q ss_pred HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhC
Q 032366 33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLIN 106 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lg 106 (142)
..|...|+++.|++.|+. |-..|.... ..-..++.. .-..-..|+.++.+.|++..++...+.
T Consensus 6 e~A~~~gvs~~tLr~ye~~Gli~p~r~~--~g~R~y~~~---------dv~~l~~i~~L~~d~g~~l~~i~~~l~ 69 (91)
T cd04766 6 VAAELSGMHPQTLRLYERLGLLSPSRTD--GGTRRYSER---------DIERLRRIQRLTQELGVNLAGVKRILE 69 (91)
T ss_pred HHHHHHCcCHHHHHHHHHCCCcCCCcCC--CCCeeECHH---------HHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 479999999999999986 333321110 111112211 122456677778889999999988876
No 178
>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=89.48 E-value=0.6 Score=31.81 Aligned_cols=22 Identities=18% Similarity=0.342 Sum_probs=20.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
+|..|+|+.+|||++||..||+
T Consensus 1 ~ti~eva~~~gvs~~tlR~ye~ 22 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYDE 22 (103)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999986
No 179
>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=89.33 E-value=0.34 Score=28.93 Aligned_cols=25 Identities=16% Similarity=0.191 Sum_probs=20.8
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 93 DKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 93 ~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
..++|..|||+.+|++++++.++.+
T Consensus 16 ~~~~t~~eia~~~gl~~stv~r~L~ 40 (52)
T PF09339_consen 16 GGPLTLSEIARALGLPKSTVHRLLQ 40 (52)
T ss_dssp BSCEEHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3458999999999999999999864
No 180
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=89.20 E-value=0.88 Score=36.55 Aligned_cols=41 Identities=12% Similarity=0.136 Sum_probs=35.7
Q ss_pred CcchHHHHHHHHHHHHhCC-CCHHHHHHHhCCCHHHHHHHHc
Q 032366 77 DRVPSELKKAIVQARNDKK-LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 77 ~~~~~~~g~~Lk~~R~~~g-lTQ~eLA~~lgis~stIs~~E~ 117 (142)
..+..+..+.|..++..-| ++|+||.+.+|.|++|++++.+
T Consensus 191 ~~L~~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~ 232 (258)
T COG2512 191 YDLNEDEKEILDLIRERGGRITQAELRRALGLSKTTVSRILR 232 (258)
T ss_pred CCCCHHHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHH
Confidence 4567778888999999998 9999999999999999998753
No 181
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=89.08 E-value=0.64 Score=32.25 Aligned_cols=22 Identities=23% Similarity=0.330 Sum_probs=20.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
+|..++|+.+|||..||.-||.
T Consensus 1 ~~I~eva~~~gvs~~tLRyYE~ 22 (124)
T COG0789 1 YTIGEVAKLTGVSVRTLRFYER 22 (124)
T ss_pred CcHHHHHHHhCCCHHHHHHHHH
Confidence 5778999999999999999996
No 182
>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=89.01 E-value=0.66 Score=32.00 Aligned_cols=22 Identities=23% Similarity=0.382 Sum_probs=20.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
++..++|+.+|||++||.-||+
T Consensus 1 ~~i~eva~~~gis~~tlR~ye~ 22 (108)
T cd01107 1 FTIGEFAKLSNLSIKALRYYDK 22 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5778999999999999999997
No 183
>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=88.83 E-value=0.72 Score=31.56 Aligned_cols=22 Identities=27% Similarity=0.256 Sum_probs=20.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
++..|+|+.+|||++||..||+
T Consensus 2 ~~i~eva~~~gvs~~tlR~ye~ 23 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEK 23 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 6889999999999999999996
No 184
>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=88.82 E-value=0.71 Score=31.19 Aligned_cols=23 Identities=22% Similarity=0.356 Sum_probs=20.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Q 032366 96 LTQSQLAQLINEKPQVIQEYESG 118 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~G 118 (142)
+|..|+|+.+|||++||.-||+-
T Consensus 1 ~ti~eva~~~gvs~~tLRyye~~ 23 (96)
T cd04768 1 LTIGEFAKLAGVSIRTLRHYDDI 23 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 47889999999999999999973
No 185
>PRK04132 replication factor C small subunit; Provisional
Probab=88.77 E-value=0.67 Score=43.06 Aligned_cols=43 Identities=28% Similarity=0.461 Sum_probs=40.1
Q ss_pred HHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 032366 98 QSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG 140 (142)
Q Consensus 98 Q~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~e 140 (142)
.+++|++.||...-+-.|..|++.|+.....+||++||+.++.
T Consensus 420 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 462 (846)
T PRK04132 420 RKEIAEKTGIRADRILEYIKGKRKPSLKNYIKIAKALGINLEK 462 (846)
T ss_pred HHHHHHHhCCcHHHHHHHHhcCCCccHHHHHHHHHHhcccHHH
Confidence 5689999999999999999999999999999999999998763
No 186
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=88.77 E-value=0.86 Score=32.63 Aligned_cols=33 Identities=12% Similarity=0.322 Sum_probs=27.5
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
.+.|+.+......++.+||+.+|+|++++.+.-
T Consensus 11 ~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri 43 (154)
T COG1522 11 RRILRLLQEDARISNAELAERVGLSPSTVLRRI 43 (154)
T ss_pred HHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHH
Confidence 455677888888999999999999999987643
No 187
>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=88.75 E-value=0.74 Score=31.24 Aligned_cols=22 Identities=14% Similarity=0.288 Sum_probs=20.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
++..++|+.+|+|.+||..||+
T Consensus 1 ~~I~e~a~~~gvs~~tLR~ye~ 22 (96)
T cd04774 1 YKVDEVAKRLGLTKRTLKYYEE 22 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5778999999999999999996
No 188
>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=88.69 E-value=0.72 Score=32.17 Aligned_cols=22 Identities=27% Similarity=0.303 Sum_probs=20.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
||..++|+.+|||..||.-||.
T Consensus 1 ~~ige~a~~~gvs~~tLryYe~ 22 (116)
T cd04769 1 MYIGELAQQTGVTIKAIRLYEE 22 (116)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999997
No 189
>COG3311 AlpA Predicted transcriptional regulator [Transcription]
Probab=88.65 E-value=0.43 Score=30.99 Aligned_cols=31 Identities=19% Similarity=0.184 Sum_probs=26.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH
Q 032366 96 LTQSQLAQLINEKPQVIQEYESGKAIPNQQI 126 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~G~~~p~~~~ 126 (142)
|...|++..+|+|+++|.++.+....|.+..
T Consensus 14 lrl~ev~~~~GlSrstiYr~i~~~~FPkpvk 44 (70)
T COG3311 14 LRLPEVAQLTGLSRSTIYRLIKDGTFPKPVK 44 (70)
T ss_pred hhHHHHHHHHCccHHHHHHHHccCCCCCCee
Confidence 4567899999999999999999888776543
No 190
>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=88.63 E-value=0.97 Score=27.64 Aligned_cols=31 Identities=13% Similarity=0.118 Sum_probs=25.2
Q ss_pred HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
.+..+.....+|-.+||+.+|||..||.+-.
T Consensus 5 Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl 35 (57)
T PF08220_consen 5 ILELLKEKGKVSVKELAEEFGVSEMTIRRDL 35 (57)
T ss_pred HHHHHHHcCCEEHHHHHHHHCcCHHHHHHHH
Confidence 3455666777899999999999999998754
No 191
>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=88.55 E-value=0.9 Score=35.00 Aligned_cols=28 Identities=21% Similarity=0.242 Sum_probs=24.7
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 032366 91 RNDKKLTQSQLAQLINEKPQVIQEYESG 118 (142)
Q Consensus 91 R~~~glTQ~eLA~~lgis~stIs~~E~G 118 (142)
|--.|+|+.++|+.+|+|+.+|+++++.
T Consensus 195 ~~~~~~t~~eIA~~lgis~~~V~~~~~~ 222 (231)
T TIGR02885 195 RYFKDKTQTEVANMLGISQVQVSRLEKK 222 (231)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 4457999999999999999999999863
No 192
>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=88.54 E-value=0.53 Score=32.17 Aligned_cols=22 Identities=18% Similarity=0.534 Sum_probs=20.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
+|..|+|+.+|||.+||..||.
T Consensus 1 yti~EvA~~~gVs~~tLR~ye~ 22 (99)
T cd04765 1 FSIGEVAEILGLPPHVLRYWET 22 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4778999999999999999985
No 193
>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=88.54 E-value=0.79 Score=30.97 Aligned_cols=22 Identities=14% Similarity=0.256 Sum_probs=20.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
|+..++|+.+|+|..||..||+
T Consensus 1 m~i~eva~~~gvs~~tlR~ye~ 22 (96)
T cd04788 1 WKIGELARRTGLSVRTLHHYDH 22 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999996
No 194
>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=88.50 E-value=1.1 Score=26.58 Aligned_cols=21 Identities=33% Similarity=0.439 Sum_probs=18.1
Q ss_pred HHHHHcCCChhHHHhhhcCCC
Q 032366 33 NAARRAGADIETVRKSHAGTN 53 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~g~~ 53 (142)
.-|+++|+++.|+.+...|..
T Consensus 4 dIA~~agvS~~TVSr~ln~~~ 24 (46)
T PF00356_consen 4 DIAREAGVSKSTVSRVLNGPP 24 (46)
T ss_dssp HHHHHHTSSHHHHHHHHTTCS
T ss_pred HHHHHHCcCHHHHHHHHhCCC
Confidence 468999999999999987763
No 195
>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=88.43 E-value=0.79 Score=31.21 Aligned_cols=22 Identities=36% Similarity=0.569 Sum_probs=20.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
++..|+|+.+|||.+||..||+
T Consensus 1 y~i~e~A~~~gvs~~tlR~Ye~ 22 (99)
T cd04772 1 YRTVDLARAIGLSPQTVRNYES 22 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 3678999999999999999996
No 196
>PHA01976 helix-turn-helix protein
Probab=88.29 E-value=0.42 Score=29.59 Aligned_cols=26 Identities=19% Similarity=0.131 Sum_probs=22.6
Q ss_pred HHHHHHHHHcCCChhHHHhhhcCCCC
Q 032366 29 EKVVNAARRAGADIETVRKSHAGTNK 54 (142)
Q Consensus 29 ~~~~~~a~r~G~~v~t~kk~~~g~~~ 54 (142)
-++-..|.+.|++.+|+.+||.|...
T Consensus 16 lt~~~lA~~~gvs~~~v~~~e~g~~~ 41 (67)
T PHA01976 16 WSAPELSRRAGVRHSLIYDFEADKRL 41 (67)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 35667899999999999999999875
No 197
>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=88.25 E-value=0.5 Score=27.87 Aligned_cols=25 Identities=20% Similarity=0.310 Sum_probs=22.0
Q ss_pred HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366 30 KVVNAARRAGADIETVRKSHAGTNK 54 (142)
Q Consensus 30 ~~~~~a~r~G~~v~t~kk~~~g~~~ 54 (142)
++-..|.+.|++.+|+.+|+.|...
T Consensus 17 tq~~lA~~~gvs~~~vs~~e~g~~~ 41 (58)
T TIGR03070 17 TQADLADLAGVGLRFIRDVENGKPT 41 (58)
T ss_pred CHHHHHHHhCCCHHHHHHHHCCCCC
Confidence 4567899999999999999999864
No 198
>PRK10458 DNA cytosine methylase; Provisional
Probab=88.20 E-value=1.7 Score=37.76 Aligned_cols=46 Identities=15% Similarity=0.177 Sum_probs=35.0
Q ss_pred HHHhCCCCHHHHHHHhC------CCHHHHHHHHcCCCCC---CHHHHHHHHHHhC
Q 032366 90 ARNDKKLTQSQLAQLIN------EKPQVIQEYESGKAIP---NQQILTKLERALG 135 (142)
Q Consensus 90 ~R~~~glTQ~eLA~~lg------is~stIs~~E~G~~~p---~~~~l~kLa~~Lg 135 (142)
.|...+++|++||+.++ .+..+|.+||+|+..| +...+..|-..+.
T Consensus 24 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 78 (467)
T PRK10458 24 EKLLEIYDVKTLAAQLNGVGENHWSRAILKRWLAGKSAWHRLSEAEFAHLQTLLP 78 (467)
T ss_pred HHHHHhcCHHHHHHHHhhcccCccCHHHHHHHHcCCCCCCCccHHHHHHHHHhcc
Confidence 34556789999999997 7899999999998744 4455556665553
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=88.19 E-value=0.83 Score=30.91 Aligned_cols=22 Identities=23% Similarity=0.403 Sum_probs=20.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
+|..|+|+.+|||..||..||+
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~ 22 (97)
T cd04782 1 FTTGEFAKLCGISKQTLFHYDK 22 (97)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5778999999999999999986
No 200
>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=88.11 E-value=0.85 Score=31.16 Aligned_cols=22 Identities=23% Similarity=0.274 Sum_probs=20.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
+|..|+|+.+|||++||..||+
T Consensus 2 ~~i~eva~~~gvs~~tLR~ye~ 23 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYES 23 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 6889999999999999999996
No 201
>PRK11891 aspartate carbamoyltransferase; Provisional
Probab=88.07 E-value=0.87 Score=39.17 Aligned_cols=35 Identities=11% Similarity=0.136 Sum_probs=32.3
Q ss_pred HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
-.+.|+.++.+.|||..+||+++|++..++.+|.-
T Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~wl~ 38 (429)
T PRK11891 4 QQAFLRDAMRRLNMTREAFANRIGVSRRALDTWLL 38 (429)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHhCCcHHhHHhhcC
Confidence 45678999999999999999999999999999985
No 202
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=87.89 E-value=0.87 Score=26.79 Aligned_cols=25 Identities=12% Similarity=0.123 Sum_probs=22.4
Q ss_pred CHHHHHHHhCCCHHHHHHHHcCCCC
Q 032366 97 TQSQLAQLINEKPQVIQEYESGKAI 121 (142)
Q Consensus 97 TQ~eLA~~lgis~stIs~~E~G~~~ 121 (142)
|+.+.|+.+|++.++|++..+|...
T Consensus 19 S~~eAa~~lg~~~~~I~~~~~~~~~ 43 (53)
T smart00497 19 SIREAAKYLGISHSSISKYLNTGKK 43 (53)
T ss_pred CHHHHHHHhCCCHHHHHHHHhCCCc
Confidence 7889999999999999999998643
No 203
>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=87.73 E-value=0.94 Score=30.70 Aligned_cols=22 Identities=18% Similarity=0.188 Sum_probs=20.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
|+..+||+.+|+|.++|..||+
T Consensus 1 m~I~eva~~~gvs~~tlR~Ye~ 22 (95)
T cd04780 1 MRMSELSKRSGVSVATIKYYLR 22 (95)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999997
No 204
>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=87.71 E-value=3.1 Score=28.58 Aligned_cols=67 Identities=15% Similarity=0.173 Sum_probs=38.2
Q ss_pred HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCCCH
Q 032366 33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKP 109 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~ 109 (142)
+.|++.|++++|++-|+. |-..|......-+-..++..+ ...-..|+.+|. .|++..++...+....
T Consensus 5 eva~~~gis~~tlR~ye~~GLi~p~~~~~~ngyR~Y~~~~---------i~~l~~I~~lr~-~G~sl~~i~~l~~~~~ 72 (108)
T cd01107 5 EFAKLSNLSIKALRYYDKIGLLKPAYVDPDTGYRYYSAEQ---------LERLNRIKYLRD-LGFPLEEIKEILDADN 72 (108)
T ss_pred HHHHHHCcCHHHHHHHHHcCCCCCCcCCCCCCccccCHHH---------HHHHHHHHHHHH-cCCCHHHHHHHHhcCC
Confidence 478999999999999997 333321110001111222111 112234555544 8999999888776544
No 205
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=87.69 E-value=4 Score=25.13 Aligned_cols=63 Identities=16% Similarity=0.233 Sum_probs=35.9
Q ss_pred HHHHHHcCCChhHHHhhhc-CCCCCC-CCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhC
Q 032366 32 VNAARRAGADIETVRKSHA-GTNKAA-SSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLIN 106 (142)
Q Consensus 32 ~~~a~r~G~~v~t~kk~~~-g~~~~~-~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lg 106 (142)
-+.|++.|++..|++.|+. |-..+. ....+ -..+..+ ....-..+..+|. .|++..+++..+.
T Consensus 4 ~eva~~~gvs~~tlr~~~~~gli~~~~~~~~g--~r~y~~~---------dl~~l~~i~~lr~-~g~~~~~i~~~l~ 68 (70)
T smart00422 4 GEVAKLAGVSVRTLRYYERIGLLPPPIRTEGG--YRLYSDE---------DLERLRFIKRLKE-LGFSLEEIKELLE 68 (70)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCCccCCCC--CEecCHH---------HHHHHHHHHHHHH-cCCCHHHHHHHHh
Confidence 3578999999999999976 333321 01000 0111111 1123445566665 8888888877664
No 206
>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=87.42 E-value=2.9 Score=28.51 Aligned_cols=63 Identities=17% Similarity=0.060 Sum_probs=36.5
Q ss_pred HHHHHcCCChhHHHhhhc--CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhC
Q 032366 33 NAARRAGADIETVRKSHA--GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLIN 106 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~--g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lg 106 (142)
+.|+..|++.+|++.|+. |...+.... .+-..+..++ -..-..|+.+....|++..++.+.++
T Consensus 5 EvA~~~gVs~~tLR~ye~~~gli~p~r~~--~g~R~Yt~~d---------i~~l~~I~~llr~~G~~l~~i~~~l~ 69 (99)
T cd04765 5 EVAEILGLPPHVLRYWETEFPQLKPVKRA--GGRRYYRPKD---------VELLLLIKHLLYEKGYTIEGAKQALK 69 (99)
T ss_pred HHHHHHCcCHHHHHHHHHHcCCCCCcCCC--CCCeeeCHHH---------HHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence 579999999999999974 444322211 1112222111 11223344444568899988888665
No 207
>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=87.34 E-value=1.5 Score=32.11 Aligned_cols=24 Identities=17% Similarity=0.242 Sum_probs=21.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 94 KKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 94 ~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
..+||.|||..+|+++.+|++..+
T Consensus 142 ~~~t~~~iA~~lG~tretvsR~l~ 165 (193)
T TIGR03697 142 LRLSHQAIAEAIGSTRVTITRLLG 165 (193)
T ss_pred CCCCHHHHHHHhCCcHHHHHHHHH
Confidence 348999999999999999999653
No 208
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=87.30 E-value=0.97 Score=25.59 Aligned_cols=27 Identities=19% Similarity=0.212 Sum_probs=20.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 032366 94 KKLTQSQLAQLINEKPQVIQEYESGKA 120 (142)
Q Consensus 94 ~glTQ~eLA~~lgis~stIs~~E~G~~ 120 (142)
.+++..++|..+|+|++++.+..+-..
T Consensus 7 ~~~~l~~iA~~~g~S~~~f~r~Fk~~~ 33 (42)
T PF00165_consen 7 QKLTLEDIAEQAGFSPSYFSRLFKKET 33 (42)
T ss_dssp SS--HHHHHHHHTS-HHHHHHHHHHHT
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 468999999999999999999876443
No 209
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=87.30 E-value=1.7 Score=25.65 Aligned_cols=22 Identities=23% Similarity=0.308 Sum_probs=19.1
Q ss_pred CC-CHHHHHHHhCCCHHHHHHHH
Q 032366 95 KL-TQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 95 gl-TQ~eLA~~lgis~stIs~~E 116 (142)
.+ |+.+||+.+|+|+++|.+..
T Consensus 19 ~l~s~~~la~~~~vs~~tv~~~l 41 (60)
T smart00345 19 KLPSERELAAQLGVSRTTVREAL 41 (60)
T ss_pred cCcCHHHHHHHHCCCHHHHHHHH
Confidence 35 89999999999999998754
No 210
>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=87.25 E-value=0.97 Score=30.09 Aligned_cols=22 Identities=32% Similarity=0.394 Sum_probs=20.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
+|..++|+.+|||++||..||.
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye~ 23 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYER 23 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999996
No 211
>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=87.23 E-value=1.1 Score=27.96 Aligned_cols=34 Identities=9% Similarity=0.057 Sum_probs=27.6
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.+.+..+...-.+|..++|+.+|+++++++++.+
T Consensus 11 ~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~ 44 (68)
T PF01978_consen 11 AKVYLALLKNGPATAEEIAEELGISRSTVYRALK 44 (68)
T ss_dssp HHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3445556678889999999999999999988753
No 212
>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=87.19 E-value=1 Score=31.22 Aligned_cols=22 Identities=18% Similarity=0.268 Sum_probs=20.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
+|..++|+.+|||++||..||+
T Consensus 1 ~~i~e~a~~~gvs~~tlr~ye~ 22 (113)
T cd01109 1 YTIKEVAEKTGLSADTLRYYEK 22 (113)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999996
No 213
>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=87.18 E-value=1 Score=32.42 Aligned_cols=22 Identities=23% Similarity=0.268 Sum_probs=20.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
|+..|||+.+|||..||.-||+
T Consensus 1 m~Ige~a~~~gvs~~tLRyYE~ 22 (131)
T cd04786 1 MKIGELAKRSGMAASRIRFYEA 22 (131)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999996
No 214
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=87.16 E-value=1.9 Score=30.88 Aligned_cols=36 Identities=11% Similarity=0.123 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 81 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
..-...|..+...-++||.+||+.++++++++++..
T Consensus 40 ~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l 75 (144)
T PRK11512 40 AAQFKVLCSIRCAACITPVELKKVLSVDLGALTRML 75 (144)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHH
Confidence 333444555556678999999999999999998764
No 215
>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=87.12 E-value=0.96 Score=26.37 Aligned_cols=25 Identities=8% Similarity=0.169 Sum_probs=22.7
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 93 DKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 93 ~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
..|+|..++|+.+|+|.++|..+-.
T Consensus 13 ~~~~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 13 AEGKTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4789999999999999999998864
No 216
>PRK15043 transcriptional regulator MirA; Provisional
Probab=87.09 E-value=0.94 Score=36.15 Aligned_cols=23 Identities=17% Similarity=0.326 Sum_probs=21.1
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHc
Q 032366 95 KLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 95 glTQ~eLA~~lgis~stIs~~E~ 117 (142)
-+|..++|+.+|||+.||..||+
T Consensus 3 ~ytIgeVA~~~GVs~~TLR~wEr 25 (243)
T PRK15043 3 LYTIGEVALLCDINPVTLRAWQR 25 (243)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHH
Confidence 37899999999999999999983
No 217
>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=87.04 E-value=1.1 Score=30.52 Aligned_cols=22 Identities=27% Similarity=0.454 Sum_probs=20.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
+|..++|+.+|||+++|..||+
T Consensus 2 ~~i~eva~~~gVs~~tLR~ye~ 23 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVYDR 23 (98)
T ss_pred cCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999986
No 218
>PF13730 HTH_36: Helix-turn-helix domain
Probab=87.03 E-value=0.83 Score=27.20 Aligned_cols=21 Identities=19% Similarity=0.188 Sum_probs=19.3
Q ss_pred CHHHHHHHhCCCHHHHHHHHc
Q 032366 97 TQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 97 TQ~eLA~~lgis~stIs~~E~ 117 (142)
|++.||+.+|+|+.||.++.+
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~ 47 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIK 47 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 899999999999999998754
No 219
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=86.99 E-value=2.9 Score=28.13 Aligned_cols=32 Identities=6% Similarity=0.056 Sum_probs=26.6
Q ss_pred HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.|-..-.+.|++..++|+..|||..|..+|..
T Consensus 16 ~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~ 47 (85)
T PF13011_consen 16 RLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLA 47 (85)
T ss_pred HHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHH
Confidence 34444557899999999999999999999974
No 220
>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=86.99 E-value=1.1 Score=31.66 Aligned_cols=30 Identities=13% Similarity=0.199 Sum_probs=24.7
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHH
Q 032366 84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQ 113 (142)
Q Consensus 84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs 113 (142)
.+.+-.++.-.|+|.+|+|+.+|+|.+||.
T Consensus 112 ~r~v~~l~~~~~~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 112 QKKIIYMKFFEDMKEIDIAKKLHISRQSVY 141 (142)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHhhc
Confidence 344555667789999999999999999985
No 221
>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=86.96 E-value=1.2 Score=27.38 Aligned_cols=30 Identities=13% Similarity=0.113 Sum_probs=24.1
Q ss_pred HHHHHHHhCCCCHHHHHHHhCCCHHHHHHH
Q 032366 86 AIVQARNDKKLTQSQLAQLINEKPQVIQEY 115 (142)
Q Consensus 86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~ 115 (142)
.|+.+....++|..+||+.+|+++++++.-
T Consensus 15 Il~~L~~~~~~t~~ela~~l~~~~~t~s~h 44 (61)
T PF12840_consen 15 ILRLLASNGPMTVSELAEELGISQSTVSYH 44 (61)
T ss_dssp HHHHHHHCSTBEHHHHHHHHTS-HHHHHHH
T ss_pred HHHHHhcCCCCCHHHHHHHHCCCHHHHHHH
Confidence 344556888999999999999999998864
No 222
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=86.91 E-value=2.4 Score=26.84 Aligned_cols=50 Identities=22% Similarity=0.348 Sum_probs=34.8
Q ss_pred HHHHHHcCCChhHHHhhhcCCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHh
Q 032366 32 VNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLI 105 (142)
Q Consensus 32 ~~~a~r~G~~v~t~kk~~~g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~l 105 (142)
-+.|+++|++..|+.++..|... +.++..++|.+.-.+.|+.....+..+
T Consensus 4 ~~iA~~~gvS~~TVSr~ln~~~~------------------------v~~~t~~~i~~~~~~~gy~~~~~~~~~ 53 (70)
T smart00354 4 KDVARLAGVSKATVSRVLNGNGR------------------------VSEETREKVLAAMEELGYIPNRVARSL 53 (70)
T ss_pred HHHHHHHCCCHHHHHHHHCCCCC------------------------CCHHHHHHHHHHHHHhCCCCCHHHHHH
Confidence 35799999999999998876543 234466667777777777655555443
No 223
>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=86.90 E-value=1.1 Score=31.13 Aligned_cols=22 Identities=18% Similarity=0.255 Sum_probs=20.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
|+..|+|+.+|||.+||..||+
T Consensus 1 m~i~eva~~~gvs~~tlR~Ye~ 22 (112)
T cd01282 1 MRIGELAARTGVSVRSLRYYEE 22 (112)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 5788999999999999999996
No 224
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=86.80 E-value=1.3 Score=33.50 Aligned_cols=32 Identities=16% Similarity=0.221 Sum_probs=26.4
Q ss_pred HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 032366 86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESG 118 (142)
Q Consensus 86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G 118 (142)
.+..+ ...|+|..++|+.+|||++||.+|.+.
T Consensus 164 ~i~~~-~~~g~s~~~iak~lgis~~Tv~r~~k~ 195 (200)
T PRK13413 164 KIKKL-LDKGTSKSEIARKLGVSRTTLARFLKT 195 (200)
T ss_pred HHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 44444 356999999999999999999999864
No 225
>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=86.76 E-value=3.1 Score=29.66 Aligned_cols=68 Identities=21% Similarity=0.111 Sum_probs=43.3
Q ss_pred HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHH
Q 032366 33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQV 111 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~st 111 (142)
..|++.|++..|++-|+. |-..+... ..-+.++. .....-+.|+.++.+.|++..++...+..-+.-
T Consensus 6 eVA~~~GVs~~TLR~wE~~GLl~p~r~---~G~R~Ys~---------~dv~rL~~I~~L~~e~G~~l~eI~~~L~l~~~~ 73 (120)
T cd04767 6 VVAELLNIHPETLRIWERHGLIKPARR---NGQRLYSN---------NDLKRLRFIKKLINEKGLNIAGVKQILSMYPCW 73 (120)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCcCC---CCcEEECH---------HHHHHHHHHHHHHHHcCCCHHHHHHHHHhCccc
Confidence 478899999999999976 44432110 11111111 122345667888888999999999887654333
Q ss_pred H
Q 032366 112 I 112 (142)
Q Consensus 112 I 112 (142)
.
T Consensus 74 ~ 74 (120)
T cd04767 74 S 74 (120)
T ss_pred c
Confidence 3
No 226
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=86.69 E-value=1.3 Score=34.83 Aligned_cols=29 Identities=21% Similarity=0.126 Sum_probs=25.0
Q ss_pred HHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 89 QARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 89 ~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.+|--.|+|+.++|+.+|+|+++|+++++
T Consensus 219 ~~~~~~~~t~~eIA~~lgis~~~V~~~~~ 247 (258)
T PRK08215 219 NLRFFQGKTQMEVAEEIGISQAQVSRLEK 247 (258)
T ss_pred HHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 33445699999999999999999999975
No 227
>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=86.51 E-value=1.2 Score=30.86 Aligned_cols=22 Identities=23% Similarity=0.241 Sum_probs=20.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
+|..|+|+.+|||..||..||+
T Consensus 1 y~Ige~A~~~gvs~~tlR~ye~ 22 (107)
T cd01111 1 YSISQLALDAGVSVHIVRDYLL 22 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4778999999999999999996
No 228
>PRK05572 sporulation sigma factor SigF; Validated
Probab=86.40 E-value=1.4 Score=34.59 Aligned_cols=30 Identities=23% Similarity=0.155 Sum_probs=25.4
Q ss_pred HHHHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 032366 89 QARNDKKLTQSQLAQLINEKPQVIQEYESG 118 (142)
Q Consensus 89 ~~R~~~glTQ~eLA~~lgis~stIs~~E~G 118 (142)
.++-..|+|++++|+.+|+|+++|+++++.
T Consensus 212 ~l~~~~~~s~~eIA~~lgis~~~V~~~~~r 241 (252)
T PRK05572 212 YLRYFKDKTQSEVAKRLGISQVQVSRLEKK 241 (252)
T ss_pred HHHHhCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 334457999999999999999999999863
No 229
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=86.23 E-value=1.1 Score=33.12 Aligned_cols=31 Identities=13% Similarity=0.324 Sum_probs=26.3
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHH
Q 032366 84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQE 114 (142)
Q Consensus 84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~ 114 (142)
.+.|..+...-.+|..+||+.+|+|++++.+
T Consensus 17 ~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~ 47 (164)
T PRK11169 17 RNILNELQKDGRISNVELSKRVGLSPTPCLE 47 (164)
T ss_pred HHHHHHhccCCCCCHHHHHHHHCcCHHHHHH
Confidence 3456777888899999999999999998765
No 230
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=86.22 E-value=0.9 Score=35.19 Aligned_cols=48 Identities=15% Similarity=0.115 Sum_probs=43.2
Q ss_pred HHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Q 032366 89 QARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVK 137 (142)
Q Consensus 89 ~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvs 137 (142)
+.+++.+.++.++++..|+++ ++..|.++-..++...+....++|+.+
T Consensus 6 rrq~el~~~~~~~~~~~g~~p-s~~e~~~~~~~~s~~~~~~~l~~L~~~ 53 (201)
T COG1974 6 RRQKELLDFIRSLIKETGYPP-SIREIGDALGLASPSAIHSHLKALERK 53 (201)
T ss_pred HHHHHHHHHHHHHHHHhCCCc-cHHHHHHhhCCCChHHHHHHHHHHhcC
Confidence 467788899999999999999 999999999999999999999988764
No 231
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=86.20 E-value=2.4 Score=29.38 Aligned_cols=55 Identities=16% Similarity=0.137 Sum_probs=36.7
Q ss_pred hHHHHHHHHHH--HHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q 032366 80 PSELKKAIVQA--RNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERAL 134 (142)
Q Consensus 80 ~~~~g~~Lk~~--R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~L 134 (142)
...++.|++-. ..+..+||.|++..+|+|-.+|.+=-|.-...+++.-.-|.+.|
T Consensus 43 Real~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITRGSN~LK~~~~~~k~~L~~~l 99 (103)
T COG2973 43 REALGTRVRIVEELLRGELSQREIAQKLGVSIATITRGSNSLKTADPEFKQWLEKVL 99 (103)
T ss_pred HHHHHHHHHHHHHHHhccccHHHHHHHhCcchhhhccchhhhccCCHHHHHHHHHHh
Confidence 34567666544 45568999999999999988887744333333555555555544
No 232
>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=86.19 E-value=1.2 Score=31.58 Aligned_cols=22 Identities=27% Similarity=0.443 Sum_probs=20.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
|+..|+|+.+|||..||.-||.
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe~ 22 (127)
T TIGR02044 1 MNIGQVAKLTGLSSKMIRYYEE 22 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999997
No 233
>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=86.10 E-value=2.1 Score=26.82 Aligned_cols=27 Identities=7% Similarity=0.155 Sum_probs=22.2
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 91 RNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 91 R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
..+..++..+||+.+|+|+++|++.-+
T Consensus 9 L~~~~~~~~eLa~~l~vS~~tv~~~l~ 35 (69)
T TIGR00122 9 LADNPFSGEKLGEALGMSRTAVNKHIQ 35 (69)
T ss_pred HHcCCcCHHHHHHHHCCCHHHHHHHHH
Confidence 345568899999999999999988653
No 234
>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=86.03 E-value=1.7 Score=30.48 Aligned_cols=37 Identities=5% Similarity=0.102 Sum_probs=30.4
Q ss_pred hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+.+|.+++-...+. |.|..++|...+||.+||.+|.+
T Consensus 4 S~DlR~rVl~~~~~-g~s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 4 SLDLRQRVLAYIEK-GKSIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred CHHHHHHHHHHHHc-cchHHHHHHHhCcHHHHHHHHHH
Confidence 34577777665554 88999999999999999999965
No 235
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=85.98 E-value=1.2 Score=33.92 Aligned_cols=33 Identities=21% Similarity=0.301 Sum_probs=30.2
Q ss_pred HHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCC
Q 032366 89 QARNDKKLTQSQLAQLINEKPQVIQEYESGKAI 121 (142)
Q Consensus 89 ~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~ 121 (142)
-+|...|+|..++|+.+|.+.+||.++..|...
T Consensus 55 ~arekag~Ti~EIAeelG~TeqTir~hlkgetk 87 (182)
T COG1318 55 LAREKAGMTISEIAEELGRTEQTVRNHLKGETK 87 (182)
T ss_pred HHHHHccCcHHHHHHHhCCCHHHHHHHHhcchh
Confidence 457999999999999999999999999998764
No 236
>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=85.93 E-value=6.5 Score=26.40 Aligned_cols=65 Identities=15% Similarity=0.235 Sum_probs=38.5
Q ss_pred HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCCC
Q 032366 33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEK 108 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis 108 (142)
+.|++.|+++.|++-|+. |-..|.... .-.-..++.+ ....-..|+.+|. .|++.+++...++..
T Consensus 5 eva~~~gvs~~tlR~ye~~Gll~p~~r~-~~gyR~Y~~~---------~l~~l~~I~~lr~-~G~~l~eI~~~l~~~ 70 (96)
T cd04788 5 ELARRTGLSVRTLHHYDHIGLLSPSQRT-EGGHRLYDRA---------DIRRLHQIIALRR-LGFSLREIGRALDGP 70 (96)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCccC-CCCceeeCHH---------HHHHHHHHHHHHH-cCCCHHHHHHHHhCC
Confidence 479999999999999997 333321110 0111222211 1113344556654 799999999988654
No 237
>PRK00215 LexA repressor; Validated
Probab=85.93 E-value=1.8 Score=32.78 Aligned_cols=35 Identities=14% Similarity=0.182 Sum_probs=26.4
Q ss_pred HHHHHHHHHHH--hCCCCHHHHHHHhCC-CHHHHHHHH
Q 032366 82 ELKKAIVQARN--DKKLTQSQLAQLINE-KPQVIQEYE 116 (142)
Q Consensus 82 ~~g~~Lk~~R~--~~glTQ~eLA~~lgi-s~stIs~~E 116 (142)
.+-..|.+.+. ...+|+.|||+.+|+ ++++++++.
T Consensus 8 ~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l 45 (205)
T PRK00215 8 EILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHL 45 (205)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHH
Confidence 34555665444 445699999999999 999999983
No 238
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=85.88 E-value=1.6 Score=34.08 Aligned_cols=29 Identities=7% Similarity=0.155 Sum_probs=24.9
Q ss_pred HHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 89 QARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 89 ~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.+|-..|+|++++|+.+|+|.+.|+++++
T Consensus 193 ~l~~~~~~t~~EIA~~lgis~~~V~q~~~ 221 (231)
T PRK12427 193 HLYYQHEMSLKEIALVLDLTEARICQLNK 221 (231)
T ss_pred HHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34445699999999999999999999875
No 239
>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=85.84 E-value=1.3 Score=31.06 Aligned_cols=22 Identities=18% Similarity=0.273 Sum_probs=20.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
||..|+|+.+|||..||.-||+
T Consensus 1 m~IgevA~~~gvs~~tlRyYe~ 22 (120)
T cd04781 1 LDIAEVARQSGLPASTLRYYEE 22 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5789999999999999999997
No 240
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=85.68 E-value=1.9 Score=30.64 Aligned_cols=33 Identities=15% Similarity=-0.089 Sum_probs=26.6
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+.+-.++--.|+|..|+|+.+|+|.++|..+..
T Consensus 112 r~ii~l~~~~~~s~~EIA~~l~is~~tV~~~~~ 144 (154)
T PRK06759 112 KYIIFERFFVGKTMGEIALETEMTYYQVRWIYR 144 (154)
T ss_pred HHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 334445566799999999999999999998753
No 241
>PF13309 HTH_22: HTH domain
Probab=85.67 E-value=2.5 Score=26.60 Aligned_cols=21 Identities=10% Similarity=0.121 Sum_probs=18.5
Q ss_pred CHHHHHHHhCCCHHHHHHHHc
Q 032366 97 TQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 97 TQ~eLA~~lgis~stIs~~E~ 117 (142)
+-..+|+.+|||+.||.+|.+
T Consensus 44 av~~vA~~L~iS~~TVY~YLr 64 (64)
T PF13309_consen 44 AVEYVAEKLGISRATVYRYLR 64 (64)
T ss_pred HHHHHHHHHCCCHHHHHHHcC
Confidence 677899999999999999853
No 242
>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=85.64 E-value=0.27 Score=42.14 Aligned_cols=42 Identities=14% Similarity=0.112 Sum_probs=34.2
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Q 032366 95 KLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV 136 (142)
Q Consensus 95 glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgv 136 (142)
=||++++|+.+|++.||||+.-+|+..-++.-+.-|-.+|.-
T Consensus 318 PLtlkdiA~~lglheSTVSRav~~Kyi~tp~Gi~~lk~FFs~ 359 (429)
T TIGR02395 318 PLTLREVAEELGLHESTISRAINNKYLQTPRGVFELKYFFSR 359 (429)
T ss_pred CCcHHHHHHHhCCCccchhhhhcCceEecCCceEEHHHhcCC
Confidence 489999999999999999999999976665555566666654
No 243
>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=85.56 E-value=3.9 Score=29.28 Aligned_cols=35 Identities=23% Similarity=0.264 Sum_probs=30.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Q 032366 95 KLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV 136 (142)
Q Consensus 95 glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgv 136 (142)
.+|..++|..+|+|.+++.++.+ ..+.+||..||.
T Consensus 100 ~~t~~~Ia~~l~iS~~t~~r~r~-------~~l~kla~~lG~ 134 (134)
T TIGR01636 100 PLTLVGLAQQLFISKSTAYRLRN-------HIIEAVAEELGM 134 (134)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHH-------HHHHHHHHHhCc
Confidence 36999999999999999999864 568888888873
No 244
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=85.55 E-value=1.4 Score=34.67 Aligned_cols=55 Identities=5% Similarity=0.137 Sum_probs=38.5
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc-CCCCCCHHHHHHHHHHhCCCCC
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES-GKAIPNQQILTKLERALGVKLR 139 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~-G~~~p~~~~l~kLa~~Lgvsl~ 139 (142)
+.+-.++.-.|+|.+|+|+.+|||.+||..... +........-..++.-|++...
T Consensus 167 R~v~~L~~~eg~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~~~~~~~~~~~~ 222 (244)
T TIGR03001 167 RHLLRLHFVDGLSMDRIGAMYQVHRSTVSRWVAQARERLLERTRRRLAERLKLSSP 222 (244)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcc
Confidence 334445566899999999999999999987764 4444455555666666665443
No 245
>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=85.53 E-value=4.9 Score=27.19 Aligned_cols=64 Identities=19% Similarity=0.220 Sum_probs=39.9
Q ss_pred HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCC
Q 032366 33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINE 107 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgi 107 (142)
+.|++.|++..|++.|+. |-..|... ...-..++. .....-..|+.++...|++..++...+..
T Consensus 6 eva~~~gVs~~tLR~ye~~Gli~p~r~--~~g~R~Ys~---------~dv~~l~~I~~L~~~~G~~l~~i~~~l~l 70 (98)
T cd01279 6 VAAELLGIHPQTLRVYDRLGLVSPART--NGGGRRYSN---------NDLELLRQVQRLSQDEGFNLAGIKRIIEL 70 (98)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCcC--CCCCeeECH---------HHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 578999999999999976 32222110 001111111 11224556777788899999999988755
No 246
>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=85.43 E-value=0.97 Score=31.94 Aligned_cols=22 Identities=27% Similarity=0.363 Sum_probs=20.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
|+..|+|+.+|||..||..||.
T Consensus 1 m~I~e~a~~~gvs~~tlR~Ye~ 22 (126)
T cd04783 1 LTIGELAKAAGVNVETIRYYQR 22 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999996
No 247
>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=85.39 E-value=1.9 Score=31.62 Aligned_cols=32 Identities=19% Similarity=0.202 Sum_probs=26.5
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
+.+-.++.-.|+|.+|+|+.+|+|.+||....
T Consensus 140 r~v~~l~~~~g~s~~EIA~~lgis~~tVk~~l 171 (183)
T TIGR02999 140 AEVVELRFFAGLTVEEIAELLGVSVRTVERDW 171 (183)
T ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 34455567789999999999999999998765
No 248
>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=85.27 E-value=0.94 Score=27.46 Aligned_cols=26 Identities=4% Similarity=0.161 Sum_probs=21.8
Q ss_pred HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 92 NDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 92 ~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
...|++..++|+.+|+|+.||..+-+
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 45799999999999999999988753
No 249
>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=85.22 E-value=1.7 Score=34.17 Aligned_cols=28 Identities=21% Similarity=0.125 Sum_probs=24.4
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 90 ARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 90 ~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+|--.|+|++++|+.+|+|+.+|+++++
T Consensus 217 ~~~~~~~t~~eIA~~lgis~~~V~~~~~ 244 (254)
T TIGR02850 217 MRFFEGKTQMEVAEEIGISQAQVSRLEK 244 (254)
T ss_pred HHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3444699999999999999999999985
No 250
>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=85.21 E-value=4.2 Score=23.49 Aligned_cols=32 Identities=6% Similarity=0.102 Sum_probs=25.7
Q ss_pred HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.+-..+--.++|..++|+++|+|++++.++-.
T Consensus 7 ~l~~~~G~~~~s~~~Ia~~~gvs~~~~y~~f~ 38 (47)
T PF00440_consen 7 ELFAEKGYEAVSIRDIARRAGVSKGSFYRYFP 38 (47)
T ss_dssp HHHHHHHTTTSSHHHHHHHHTSCHHHHHHHCS
T ss_pred HHHHHhCHHhCCHHHHHHHHccchhhHHHHcC
Confidence 34445556789999999999999999998754
No 251
>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=85.19 E-value=1.6 Score=34.72 Aligned_cols=24 Identities=29% Similarity=0.307 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 94 KKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 94 ~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.++|++++|+.+|||+.+|+++++
T Consensus 235 ~~~t~~eIA~~lgvS~~~V~q~~~ 258 (270)
T TIGR02392 235 DKLTLQELAAEYGVSAERIRQIEK 258 (270)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHH
Confidence 379999999999999999999985
No 252
>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=85.19 E-value=1.2 Score=31.50 Aligned_cols=22 Identities=23% Similarity=0.382 Sum_probs=20.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
||..|+|+.+|||..||.-||+
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe~ 22 (127)
T cd01108 1 MNIGEAAKLTGLSAKMIRYYEE 22 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999996
No 253
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=84.83 E-value=2.1 Score=30.68 Aligned_cols=30 Identities=13% Similarity=0.107 Sum_probs=25.0
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 87 IVQARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
+-.++--.|+|.+|+|+.+|+|.++|....
T Consensus 117 v~~l~~~~~~s~~EIA~~lgis~~tV~~~l 146 (163)
T PRK07037 117 AFEMYRLHGETQKDIARELGVSPTLVNFMI 146 (163)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 334556679999999999999999999863
No 254
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [].
Probab=84.77 E-value=1.3 Score=24.52 Aligned_cols=19 Identities=16% Similarity=0.295 Sum_probs=17.5
Q ss_pred CHHHHHHHhCCCHHHHHHH
Q 032366 97 TQSQLAQLINEKPQVIQEY 115 (142)
Q Consensus 97 TQ~eLA~~lgis~stIs~~ 115 (142)
|..+.|+.+|+++++|+++
T Consensus 18 Si~eAa~~l~i~~~~I~~~ 36 (37)
T PF07453_consen 18 SIREAARYLGISHSTISKY 36 (37)
T ss_pred CHHHHHHHhCCCHHHHHHh
Confidence 7889999999999999876
No 255
>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=84.72 E-value=2.2 Score=30.04 Aligned_cols=29 Identities=7% Similarity=-0.044 Sum_probs=24.6
Q ss_pred HHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 89 QARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 89 ~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.++--.|+|..|+|+.+|+|+++|.....
T Consensus 123 ~l~~~~~~~~~eIA~~lgis~~tv~~~~~ 151 (161)
T TIGR02985 123 ILSRFEGKSYKEIAEELGISVKTVEYHIS 151 (161)
T ss_pred HHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34556799999999999999999988753
No 256
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=84.65 E-value=0.45 Score=41.46 Aligned_cols=44 Identities=14% Similarity=0.118 Sum_probs=36.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 032366 95 KLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 138 (142)
Q Consensus 95 glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl 138 (142)
=|+.+++|+.+|++.||||+.-+++..-++.-+..|-.+|.-.+
T Consensus 369 PLtlkdVAe~lglHeSTVSRa~~~KY~~tp~GifeLK~FFs~~v 412 (481)
T PRK12469 369 PLVLRDVAEELGLHESTISRATGNKYMATPRGTFEFKHFFPRKL 412 (481)
T ss_pred CCcHHHHHHHhCCCcchhhHHhcCceeecCCceEeHHHhhcccc
Confidence 58999999999999999999999998777666666767776444
No 257
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=84.51 E-value=2.9 Score=31.29 Aligned_cols=49 Identities=14% Similarity=0.207 Sum_probs=32.1
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHcC---C-CCCCHHHHHHHHHHhCCCCCCC
Q 032366 93 DKKLTQSQLAQLINEKPQVIQEYESG---K-AIPNQQILTKLERALGVKLRGK 141 (142)
Q Consensus 93 ~~glTQ~eLA~~lgis~stIs~~E~G---~-~~p~~~~l~kLa~~Lgvsl~e~ 141 (142)
..|+|.+|+|+.+++|..||..+-+. + ...+...+..++.-.-.++-+|
T Consensus 163 ~~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~v~~~~~l~~~~~~~~~~~~~~ 215 (216)
T PRK10840 163 AEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLNYLSSVTLSPADK 215 (216)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhcCCcccC
Confidence 47999999999999999999888742 1 2224333434443334454444
No 258
>PRK09526 lacI lac repressor; Reviewed
Probab=84.41 E-value=2.1 Score=34.19 Aligned_cols=50 Identities=20% Similarity=0.294 Sum_probs=33.3
Q ss_pred HHHHHHHcCCChhHHHhhhcCCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHH
Q 032366 31 VVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQL 104 (142)
Q Consensus 31 ~~~~a~r~G~~v~t~kk~~~g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~ 104 (142)
--.-|+++|++++|+.+..+|... +.++..++|.+.-+++|+.....|+.
T Consensus 8 i~dIA~~aGVS~~TVSrvLn~~~~------------------------vs~~tr~rV~~~a~elgY~pn~~a~~ 57 (342)
T PRK09526 8 LYDVARYAGVSYQTVSRVLNQASH------------------------VSAKTREKVEAAMAELNYVPNRVAQQ 57 (342)
T ss_pred HHHHHHHhCCCHHHHHHHhcCCCC------------------------CCHHHHHHHHHHHHHHCCCcCHHHHH
Confidence 346799999999999999876432 33445555666666666655555543
No 259
>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=84.41 E-value=1.7 Score=29.80 Aligned_cols=22 Identities=14% Similarity=0.214 Sum_probs=20.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
|+..+||+.+|+|..||.-||+
T Consensus 1 m~Ige~a~~~gvs~~tlRyYe~ 22 (107)
T cd04777 1 MKIGKFAKKNNITIDTVRHYID 22 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999996
No 260
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=84.25 E-value=2 Score=30.85 Aligned_cols=28 Identities=11% Similarity=0.147 Sum_probs=24.2
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 90 ARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 90 ~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
++...|+++.++|+.+|+|+++|..+..
T Consensus 136 l~~~~~~~~~eIA~~lgis~~tv~~~~~ 163 (179)
T PRK11924 136 LRYVEGLSYREIAEILGVPVGTVKSRLR 163 (179)
T ss_pred HHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3445799999999999999999998864
No 261
>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=84.20 E-value=1.9 Score=33.48 Aligned_cols=25 Identities=20% Similarity=0.244 Sum_probs=23.2
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 93 DKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 93 ~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
..++|++++|+.+|+|.++|++++.
T Consensus 194 ~~~~t~~EIA~~lgis~~~V~q~~~ 218 (238)
T TIGR02393 194 GRPHTLEEVGKEFNVTRERIRQIES 218 (238)
T ss_pred CCCccHHHHHHHHCCCHHHHHHHHH
Confidence 4689999999999999999999986
No 262
>PRK13832 plasmid partitioning protein; Provisional
Probab=84.19 E-value=3.2 Score=36.56 Aligned_cols=49 Identities=14% Similarity=0.049 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHH
Q 032366 81 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLE 131 (142)
Q Consensus 81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa 131 (142)
.+..+.++.+. +.|+|+.++|+.+|+|+++|+++-.= ...++.++..++
T Consensus 105 iEea~AfkrLi-e~G~T~EeIA~~lG~S~~~V~rlllL-A~L~P~lLdal~ 153 (520)
T PRK13832 105 VDQWRAIERLV-ALGWTEEAIAVALALPVRQIRKLRLL-ANVLPAMLDHMA 153 (520)
T ss_pred HHHHHHHHHHH-hcCCCHHHHHHHHCCCHHHHHHHHHH-cCCCHHHHHHHH
Confidence 34566677776 79999999999999999999996542 123445554443
No 263
>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=84.16 E-value=0.93 Score=26.77 Aligned_cols=25 Identities=16% Similarity=0.258 Sum_probs=20.3
Q ss_pred HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366 30 KVVNAARRAGADIETVRKSHAGTNK 54 (142)
Q Consensus 30 ~~~~~a~r~G~~v~t~kk~~~g~~~ 54 (142)
++-..|.+.|++..|+.+|+.|...
T Consensus 11 s~~~la~~~gis~~~i~~~~~g~~~ 35 (55)
T PF01381_consen 11 SQKELAEKLGISRSTISRIENGKRN 35 (55)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSST
T ss_pred CHHHHHHHhCCCcchhHHHhcCCCC
Confidence 4567899999999999999999665
No 264
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=84.14 E-value=0.49 Score=40.89 Aligned_cols=43 Identities=12% Similarity=0.139 Sum_probs=34.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Q 032366 95 KLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVK 137 (142)
Q Consensus 95 glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvs 137 (142)
=||++++|+.+|++.||||+.-+|+..-++.-+.-|-.+|.-.
T Consensus 343 PLtlkdvAe~lglheSTVSRav~~Kyv~tp~Gi~~lk~FFs~~ 385 (455)
T PRK05932 343 PLVLKDIAEELGMHESTISRATTNKYMATPRGIFELKYFFSSA 385 (455)
T ss_pred CccHHHHHHHhCCCccchhhhhcCceeecCCceEEHHHhcccc
Confidence 4899999999999999999999999766555555555555433
No 265
>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=84.13 E-value=1.7 Score=31.00 Aligned_cols=22 Identities=23% Similarity=0.454 Sum_probs=20.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
++..++|+.+||+++||..||+
T Consensus 2 ysI~eVA~~~GVs~~TLR~wE~ 23 (120)
T cd04767 2 YPIGVVAELLNIHPETLRIWER 23 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 6789999999999999999986
No 266
>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=84.11 E-value=1.9 Score=30.60 Aligned_cols=23 Identities=26% Similarity=0.274 Sum_probs=21.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHc
Q 032366 95 KLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 95 glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.+|..|||+.+|+|..||.-||+
T Consensus 3 ~~tI~elA~~~gvs~~tlR~Ye~ 25 (120)
T TIGR02054 3 AYTISRLAEDAGVSVHVVRDYLL 25 (120)
T ss_pred CCcHHHHHHHHCcCHHHHHHHHH
Confidence 58999999999999999999996
No 267
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=83.89 E-value=2.3 Score=32.46 Aligned_cols=22 Identities=9% Similarity=0.220 Sum_probs=20.2
Q ss_pred CCCHHHHHHHhCCCHHHHHHHH
Q 032366 95 KLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 95 glTQ~eLA~~lgis~stIs~~E 116 (142)
.+||++||..+|+++.+|++..
T Consensus 184 ~lt~~~iA~~lG~sr~tvsR~l 205 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETISRLL 205 (235)
T ss_pred cccHHHHHHHhCCcHHHHHHHH
Confidence 4899999999999999999965
No 268
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=83.88 E-value=2.2 Score=34.04 Aligned_cols=50 Identities=18% Similarity=0.244 Sum_probs=32.8
Q ss_pred HHHHHHHcCCChhHHHhhhcCCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHH
Q 032366 31 VVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQL 104 (142)
Q Consensus 31 ~~~~a~r~G~~v~t~kk~~~g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~ 104 (142)
--.-|+++|++++|+.+..+|... +.++..+++.++-+++|+.....|+.
T Consensus 8 i~dIA~~agVS~~TVSrvLn~~~~------------------------vs~~tr~rV~~~a~elgY~pn~~a~~ 57 (331)
T PRK14987 8 LQDVADRVGVTKMTVSRFLRNPEQ------------------------VSVALRGKIAAALDELGYIPNRAPDI 57 (331)
T ss_pred HHHHHHHhCCCHHHhhhhhCCCCC------------------------CCHHHHHHHHHHHHHhCCCccHHHHH
Confidence 346899999999999998865432 23345555666666666655555543
No 269
>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=83.78 E-value=2.2 Score=32.63 Aligned_cols=31 Identities=19% Similarity=0.127 Sum_probs=25.6
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 87 IVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+-.++-..|+|++++|+.+|+|+++|..+..
T Consensus 186 vl~l~y~~~~s~~eIA~~lgis~~~v~~~~~ 216 (227)
T TIGR02980 186 ILLLRFFEDKTQSEIAERLGISQMHVSRLLR 216 (227)
T ss_pred HHHHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3334455799999999999999999999865
No 270
>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=83.75 E-value=1.7 Score=31.40 Aligned_cols=22 Identities=18% Similarity=0.246 Sum_probs=20.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
||..|+|+.+|||.+||.-||+
T Consensus 2 ~~I~EvA~~~Gvs~~tLRyYE~ 23 (139)
T cd01110 2 LSVGEVAKRSGVAVSALHFYEQ 23 (139)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 6889999999999999999996
No 271
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=83.70 E-value=2.2 Score=32.83 Aligned_cols=23 Identities=4% Similarity=0.121 Sum_probs=20.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHH
Q 032366 94 KKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 94 ~glTQ~eLA~~lgis~stIs~~E 116 (142)
..+||++||..+|+++.++++..
T Consensus 178 i~lt~~~IA~~lGisretlsR~L 200 (230)
T PRK09391 178 LPMSRRDIADYLGLTIETVSRAL 200 (230)
T ss_pred ecCCHHHHHHHHCCCHHHHHHHH
Confidence 34899999999999999999854
No 272
>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=83.70 E-value=1.8 Score=25.23 Aligned_cols=26 Identities=19% Similarity=0.170 Sum_probs=21.2
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 91 RNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 91 R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
.....++..||++.+|+++++|++..
T Consensus 11 L~~~~~~~~el~~~l~~s~~~vs~hL 36 (47)
T PF01022_consen 11 LSEGPLTVSELAEELGLSQSTVSHHL 36 (47)
T ss_dssp HTTSSEEHHHHHHHHTS-HHHHHHHH
T ss_pred HHhCCCchhhHHHhccccchHHHHHH
Confidence 33477899999999999999999864
No 273
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=83.54 E-value=2.3 Score=30.95 Aligned_cols=31 Identities=13% Similarity=0.214 Sum_probs=25.9
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHH
Q 032366 84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQE 114 (142)
Q Consensus 84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~ 114 (142)
.+.|..+...-..|..+||+.+|+|++++.+
T Consensus 12 ~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~ 42 (153)
T PRK11179 12 RGILEALMENARTPYAELAKQFGVSPGTIHV 42 (153)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHH
Confidence 3445777777889999999999999998865
No 274
>PRK01905 DNA-binding protein Fis; Provisional
Probab=83.54 E-value=3.2 Score=26.95 Aligned_cols=34 Identities=12% Similarity=0.039 Sum_probs=28.7
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
...|.......+-++.+.|+.+||+++++.+.-+
T Consensus 39 ~~~i~~aL~~~~gn~s~aAr~LGIsrstL~rklk 72 (77)
T PRK01905 39 KPLLEVVMEQAGGNQSLAAEYLGINRNTLRKKLQ 72 (77)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3457788888899999999999999999887654
No 275
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=83.52 E-value=1.2 Score=33.09 Aligned_cols=23 Identities=13% Similarity=0.130 Sum_probs=20.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHH
Q 032366 94 KKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 94 ~glTQ~eLA~~lgis~stIs~~E 116 (142)
.-+||.+||..+|+++.+|++..
T Consensus 148 ~~~t~~~iA~~lG~tretvsR~l 170 (202)
T PRK13918 148 IYATHDELAAAVGSVRETVTKVI 170 (202)
T ss_pred ecCCHHHHHHHhCccHHHHHHHH
Confidence 35799999999999999999865
No 276
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=83.43 E-value=3 Score=28.36 Aligned_cols=33 Identities=6% Similarity=0.008 Sum_probs=28.3
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
..|.......+..+.+.|+.+|||++++.+..+
T Consensus 58 ~~i~~aL~~~~gn~s~AAr~LGIsRsTL~rKLk 90 (95)
T PRK00430 58 PLLDMVMQYTRGNQTRAALMLGINRGTLRKKLK 90 (95)
T ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 457778888899999999999999999887654
No 277
>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=83.40 E-value=1.1 Score=28.08 Aligned_cols=32 Identities=9% Similarity=0.114 Sum_probs=23.7
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 032366 87 IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA 120 (142)
Q Consensus 87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~ 120 (142)
|.+.-.+.| |.+.|+.+||+++.|++-.+-.+
T Consensus 6 L~eyv~~~G--Q~kaA~~lGV~Q~AIsKAlr~gR 37 (59)
T PF09048_consen 6 LAEYVKEHG--QAKAARALGVTQSAISKALRAGR 37 (59)
T ss_dssp HHHHHHHHH--HHHHHHHHTS-HHHHHHHHHCT-
T ss_pred HHHHHHHhC--hHHHHHHcCCcHHHHHHHHHcCC
Confidence 344555566 99999999999999999887443
No 278
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=83.38 E-value=2.9 Score=27.07 Aligned_cols=23 Identities=17% Similarity=0.140 Sum_probs=20.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHH
Q 032366 94 KKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 94 ~glTQ~eLA~~lgis~stIs~~E 116 (142)
.++|..++|+.+|+++++++++.
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 279
>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=83.36 E-value=1.9 Score=30.49 Aligned_cols=22 Identities=32% Similarity=0.401 Sum_probs=20.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
||..++|+.+|||..||..||+
T Consensus 1 ~~I~e~a~~~gvs~~tlR~Ye~ 22 (126)
T cd04785 1 LSIGELARRTGVNVETIRYYES 22 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999996
No 280
>PHA01082 putative transcription regulator
Probab=83.31 E-value=0.94 Score=32.55 Aligned_cols=40 Identities=18% Similarity=0.282 Sum_probs=33.5
Q ss_pred HhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH-HHHHH
Q 032366 92 NDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQI-LTKLE 131 (142)
Q Consensus 92 ~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~-l~kLa 131 (142)
-+.|+|.+|-|+.|--|..+|.+|-.|+..|+.-. +.++-
T Consensus 27 feCgLsveeaa~LCfKsVrtVk~WD~G~~IPPeCkRLMr~~ 67 (133)
T PHA01082 27 FECGLSVEEAAKLCFKTVSEVKQWDAGEKIPPICKRLMRWH 67 (133)
T ss_pred hccCccHHHHHHHHHHhHHHHhhccCCCcCChHHHHHHHHh
Confidence 47899999999999999999999999999887542 44443
No 281
>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=83.28 E-value=6 Score=27.47 Aligned_cols=63 Identities=24% Similarity=0.308 Sum_probs=37.0
Q ss_pred HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCC
Q 032366 33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINE 107 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgi 107 (142)
+.|++.|+++.|++-|+. |-..|.... + +-+.++..+ ...-..|+.+|. .|++.+++...+..
T Consensus 5 e~a~~~gvs~~tLryYe~~GLi~p~~~~-~-~yR~Y~~~d---------~~~l~~I~~lr~-~G~sl~eI~~~l~~ 68 (116)
T cd04769 5 ELAQQTGVTIKAIRLYEEKGLLPSPKRS-G-NYRVYDAQH---------VECLRFIKEARQ-LGFTLAELKAIFAG 68 (116)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCCCC-C-CceeeCHHH---------HHHHHHHHHHHH-cCCCHHHHHHHHhc
Confidence 478999999999999997 444421111 1 222222211 113334555544 88998888876643
No 282
>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=83.23 E-value=2.7 Score=29.90 Aligned_cols=32 Identities=13% Similarity=0.256 Sum_probs=25.5
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
..+-.++.-.|++.+++|+.+|+|.++|....
T Consensus 117 r~v~~l~~~~g~~~~eIA~~l~is~~tv~~~l 148 (159)
T TIGR02989 117 RELLQLRYQRGVSLTALAEQLGRTVNAVYKAL 148 (159)
T ss_pred HHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHH
Confidence 33444466689999999999999999998653
No 283
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=83.08 E-value=2.8 Score=28.25 Aligned_cols=30 Identities=13% Similarity=0.358 Sum_probs=24.0
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 87 IVQARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
|..+...-.+|..+||+.+|+|++++.+..
T Consensus 9 l~~L~~~~~~~~~~la~~l~~s~~tv~~~l 38 (108)
T smart00344 9 LEELQKDARISLAELAKKVGLSPSTVHNRV 38 (108)
T ss_pred HHHHHHhCCCCHHHHHHHHCcCHHHHHHHH
Confidence 445555567999999999999999997654
No 284
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=83.04 E-value=2.6 Score=30.01 Aligned_cols=31 Identities=10% Similarity=-0.007 Sum_probs=25.4
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 87 IVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+-.++.-.|+|.+|+|+.+|+|.++|.....
T Consensus 114 v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ 144 (161)
T PRK09047 114 AFLLRYWEDMDVAETAAAMGCSEGSVKTHCS 144 (161)
T ss_pred HHHHHHHhcCCHHHHHHHHCCCHHHHHHHHH
Confidence 3344556799999999999999999988754
No 285
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=83.04 E-value=2.7 Score=30.98 Aligned_cols=33 Identities=15% Similarity=0.191 Sum_probs=26.6
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+.+-.++.-.|+|.+|+|+.+|+|.+||.....
T Consensus 133 R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~ 165 (178)
T PRK12529 133 KQAFLMATLDGMKQKDIAQALDIALPTVKKYIH 165 (178)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 334455666899999999999999999987653
No 286
>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=83.02 E-value=2 Score=30.14 Aligned_cols=22 Identities=32% Similarity=0.492 Sum_probs=20.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
++..++|+.+|||..||.-||+
T Consensus 1 ~~Igeva~~~gvs~~tlRyYe~ 22 (118)
T cd04776 1 YTISELAREFDVTPRTLRFYED 22 (118)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4678999999999999999996
No 287
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=83.01 E-value=1.3 Score=33.01 Aligned_cols=23 Identities=9% Similarity=0.309 Sum_probs=20.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHc
Q 032366 95 KLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 95 glTQ~eLA~~lgis~stIs~~E~ 117 (142)
-+||++||..+|+++.+|+++.+
T Consensus 168 ~~t~~~lA~~lG~tr~tvsR~l~ 190 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGRVLK 190 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Confidence 58999999999999999999764
No 288
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=82.84 E-value=2.7 Score=30.28 Aligned_cols=29 Identities=10% Similarity=0.109 Sum_probs=24.3
Q ss_pred HHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 89 QARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 89 ~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.++.-.|+|.+++|+.+|+|.++|..+..
T Consensus 138 ~l~~~~~~s~~eIA~~lgis~~tV~~~l~ 166 (182)
T PRK09652 138 TLREIEGLSYEEIAEIMGCPIGTVRSRIF 166 (182)
T ss_pred HHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34455799999999999999999987754
No 289
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=82.83 E-value=2 Score=31.82 Aligned_cols=29 Identities=14% Similarity=0.135 Sum_probs=24.7
Q ss_pred HHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 89 QARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 89 ~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.++.-.|+|++|+|+.+|+|.++|..+..
T Consensus 151 ~l~~~~g~s~~EIA~~lgis~~tV~~~l~ 179 (194)
T PRK12519 151 ELAYYEGLSQSEIAKRLGIPLGTVKARAR 179 (194)
T ss_pred hhhhhcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 34555799999999999999999998764
No 290
>PF09571 RE_XcyI: XcyI restriction endonuclease; InterPro: IPR019071 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents the restriction endonuclease XcyI, which recognises and cleaves the double-stranded sequence C^CCGGG. ; GO: 0000287 magnesium ion binding, 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=82.83 E-value=0.8 Score=37.41 Aligned_cols=65 Identities=15% Similarity=-0.002 Sum_probs=49.8
Q ss_pred hccccCCcchHHHHHHHHHHHHhCCCCHHHHHHH-hCCCHHHHHHHH-cCCCCCC-HHHHHHHHHHhC
Q 032366 71 TENLAHDRVPSELKKAIVQARNDKKLTQSQLAQL-INEKPQVIQEYE-SGKAIPN-QQILTKLERALG 135 (142)
Q Consensus 71 ~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~-lgis~stIs~~E-~G~~~p~-~~~l~kLa~~Lg 135 (142)
...|+++.+.+.....+-..|.-.|+||++|... .|.+..-+..+| +|...+. ...+.-||.+|+
T Consensus 61 ev~F~vP~vL~~nPrligYYRLL~g~SQK~~yr~~~gl~~g~f~~mE~kG~~~~~~~~~i~dLc~~~~ 128 (318)
T PF09571_consen 61 EVVFAVPYVLEANPRLIGYYRLLLGYSQKSFYRMNKGLGFGKFKSMESKGKIPKAQEPDIQDLCVAFN 128 (318)
T ss_pred eEEeechHHHhhCcHHHHHHHHHHcccHHHhcccccCccccchhhhhhcCCccccccccHHHHHHHHH
Confidence 4567777888888899999999999999999986 677777788999 5665543 334666776664
No 291
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=82.79 E-value=3.9 Score=28.12 Aligned_cols=40 Identities=15% Similarity=0.081 Sum_probs=34.6
Q ss_pred cchHHHHHHHHHHHHhCCCCHHHHHHHhCC-CHHHHHHHHc
Q 032366 78 RVPSELKKAIVQARNDKKLTQSQLAQLINE-KPQVIQEYES 117 (142)
Q Consensus 78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgi-s~stIs~~E~ 117 (142)
....+|-..+-.+..+-|.|..++|+..|| +.+++.+|-.
T Consensus 7 ~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~ 47 (116)
T COG2963 7 KYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKWRI 47 (116)
T ss_pred cCCHHHHHHHHHHHHhcCccHHHHHHHhCCCChHHHHHHHH
Confidence 466778888888999999999999999996 9999997754
No 292
>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=82.75 E-value=2.1 Score=29.88 Aligned_cols=22 Identities=27% Similarity=0.457 Sum_probs=20.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
||..|+|+.+|||..||.-||+
T Consensus 1 ~~I~eva~~~gvs~~tLRyYe~ 22 (123)
T cd04770 1 MKIGELAKAAGVSPDTIRYYER 22 (123)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999996
No 293
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=82.69 E-value=4.8 Score=26.00 Aligned_cols=37 Identities=14% Similarity=0.126 Sum_probs=27.8
Q ss_pred hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
...-...|..+....++++.++|+.+++++++|++..
T Consensus 9 ~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l 45 (101)
T smart00347 9 TPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVL 45 (101)
T ss_pred CHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHH
Confidence 3334445566666667999999999999999888764
No 294
>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=82.67 E-value=2.1 Score=30.55 Aligned_cols=22 Identities=18% Similarity=0.359 Sum_probs=20.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
|+..|||+.+|||..||.-||+
T Consensus 1 m~IgE~A~~~gvs~~TLRyYE~ 22 (133)
T cd04787 1 MKVKELANAAGVTPDTVRFYTR 22 (133)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999996
No 295
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=82.54 E-value=2.4 Score=33.98 Aligned_cols=21 Identities=29% Similarity=0.411 Sum_probs=18.1
Q ss_pred HHHHHcCCChhHHHhhhcCCC
Q 032366 33 NAARRAGADIETVRKSHAGTN 53 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~g~~ 53 (142)
.-|+++|++++|+.+..+|..
T Consensus 6 dIA~~aGVS~~TVSrvLn~~~ 26 (343)
T PRK10727 6 DVARLAGVSVATVSRVINNSP 26 (343)
T ss_pred HHHHHhCCCHHHHHHHhCCCC
Confidence 469999999999999987653
No 296
>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=82.46 E-value=1.2 Score=25.27 Aligned_cols=19 Identities=21% Similarity=0.207 Sum_probs=15.9
Q ss_pred HHHHHcCCChhHHHhhhcC
Q 032366 33 NAARRAGADIETVRKSHAG 51 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~g 51 (142)
+.|+.+|+++.|++.|+.-
T Consensus 4 e~A~~~gvs~~tlR~ye~~ 22 (38)
T PF00376_consen 4 EVAKLLGVSPRTLRYYERE 22 (38)
T ss_dssp HHHHHHTS-HHHHHHHHHT
T ss_pred HHHHHHCCCHHHHHHHHHC
Confidence 4789999999999999973
No 297
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=82.45 E-value=2.5 Score=32.66 Aligned_cols=33 Identities=6% Similarity=0.203 Sum_probs=26.7
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+.+-.++-..|+|.+|+|+.+|+|.++|..+..
T Consensus 190 r~vl~l~~~~g~s~~EIA~~lgis~~tV~~~~~ 222 (236)
T PRK06986 190 QLVLSLYYQEELNLKEIGAVLGVSESRVSQIHS 222 (236)
T ss_pred HHHHHhHhccCCCHHHHHHHHCCCHHHHHHHHH
Confidence 333444556799999999999999999998864
No 298
>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=82.25 E-value=2.9 Score=28.65 Aligned_cols=27 Identities=11% Similarity=0.163 Sum_probs=23.5
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 91 RNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 91 R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.--.|+|..++|+.+|+|+++|.++.+
T Consensus 122 ~~~~g~s~~eIA~~l~~s~~~v~~~~~ 148 (158)
T TIGR02937 122 RYLEGLSYKEIAEILGISVGTVKRRLK 148 (158)
T ss_pred HHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 334699999999999999999998864
No 299
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=82.23 E-value=3 Score=33.00 Aligned_cols=20 Identities=30% Similarity=0.303 Sum_probs=17.1
Q ss_pred HHHHHcCCChhHHHhhhcCC
Q 032366 33 NAARRAGADIETVRKSHAGT 52 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~g~ 52 (142)
.-|+++|++++|+.+..+|.
T Consensus 3 dIA~~agVS~~TVSrvLn~~ 22 (327)
T PRK10423 3 DVARLAGVSTSTVSHVINKD 22 (327)
T ss_pred hHHHHhCCcHHHHHHHhCCC
Confidence 35899999999999998754
No 300
>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=82.22 E-value=1.9 Score=30.60 Aligned_cols=22 Identities=27% Similarity=0.321 Sum_probs=20.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
|+..++|+.+|||..||..||+
T Consensus 1 m~I~e~a~~~gvs~~tlR~Ye~ 22 (127)
T TIGR02047 1 MKIGELAQKTGVSVETIRFYEK 22 (127)
T ss_pred CcHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999996
No 301
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=82.18 E-value=2.1 Score=30.93 Aligned_cols=22 Identities=27% Similarity=0.465 Sum_probs=20.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
++..|+|+.+|||..||..||+
T Consensus 2 ~~I~e~a~~~gvs~~tlR~Ye~ 23 (140)
T PRK09514 2 YRIGELAKLAEVTPDTLRFYEK 23 (140)
T ss_pred CcHHHHHHHHCcCHHHHHHHHH
Confidence 6789999999999999999997
No 302
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=82.18 E-value=2 Score=30.98 Aligned_cols=22 Identities=23% Similarity=0.385 Sum_probs=20.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
|+..|||+.+|+|..||.-||+
T Consensus 1 m~Ige~a~~~gvs~~tlRyYE~ 22 (135)
T PRK10227 1 MNISDVAKITGLTSKAIRFYEE 22 (135)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999997
No 303
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=82.17 E-value=3 Score=29.95 Aligned_cols=32 Identities=9% Similarity=0.149 Sum_probs=26.4
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+.+-.++. .|+|.+++|+.+|+|.++|.....
T Consensus 118 r~il~l~~-~g~s~~eIA~~lgis~~tV~~~i~ 149 (166)
T PRK09639 118 RTVLLLRF-SGYSYKEIAEALGIKESSVGTTLA 149 (166)
T ss_pred HHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34445566 999999999999999999998763
No 304
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=82.08 E-value=2.8 Score=32.81 Aligned_cols=29 Identities=10% Similarity=0.110 Sum_probs=25.0
Q ss_pred HHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 89 QARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 89 ~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.++--.|+|++|+|+.+|+|..+|..+..
T Consensus 215 ~l~~~~g~s~~eIA~~l~is~~tV~~~~~ 243 (257)
T PRK08583 215 QCTFIENLSQKETGERLGISQMHVSRLQR 243 (257)
T ss_pred HHHHhCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34456799999999999999999999874
No 305
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=81.94 E-value=3.1 Score=29.77 Aligned_cols=32 Identities=9% Similarity=0.035 Sum_probs=25.9
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
+.+-.++.-.|+|.+|+|+.+|+|.++|....
T Consensus 112 r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l 143 (160)
T PRK09642 112 RDVVLAHYLEEKSYQEIALQEKIEVKTVEMKL 143 (160)
T ss_pred HHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHH
Confidence 33445566789999999999999999997654
No 306
>PRK09954 putative kinase; Provisional
Probab=81.90 E-value=3.3 Score=33.99 Aligned_cols=33 Identities=9% Similarity=0.169 Sum_probs=28.0
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+.|+.+++...+|+.+||+.+|+|+++|.+..+
T Consensus 7 ~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~ 39 (362)
T PRK09954 7 EILAILRRNPLIQQNEIADILQISRSRVAAHIM 39 (362)
T ss_pred HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 456777777789999999999999999988765
No 307
>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=81.87 E-value=4.2 Score=30.63 Aligned_cols=37 Identities=16% Similarity=0.127 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 81 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.+....++.+-.--++|....|..+|||..|+.+|-.
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 4566777888788899999999999999999999986
No 308
>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=81.78 E-value=2.3 Score=31.00 Aligned_cols=22 Identities=32% Similarity=0.324 Sum_probs=20.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
|+..|+|+.+|||..||.-||+
T Consensus 2 ~~IgevA~~~Gvs~~tLRyYE~ 23 (142)
T TIGR01950 2 LTVGELAKRSGVAVSALHFYES 23 (142)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 6889999999999999999996
No 309
>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=81.74 E-value=2.9 Score=26.47 Aligned_cols=24 Identities=17% Similarity=0.311 Sum_probs=21.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCC
Q 032366 96 LTQSQLAQLINEKPQVIQEYESGK 119 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~G~ 119 (142)
=+|.|+|+.+++++.||.+|-...
T Consensus 17 GnqtEvaR~l~c~R~TVrKY~~D~ 40 (64)
T PF06322_consen 17 GNQTEVARRLGCNRATVRKYSRDK 40 (64)
T ss_pred CcHHHHHHHhcccHHHHHHHhccc
Confidence 379999999999999999998654
No 310
>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=81.64 E-value=2.4 Score=30.23 Aligned_cols=22 Identities=23% Similarity=0.377 Sum_probs=20.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
++..|+|+.+|||..||..||.
T Consensus 2 ~~I~e~a~~~gvs~~tlR~Ye~ 23 (131)
T TIGR02043 2 FQIGELAKLCGVTSDTLRFYEK 23 (131)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 6789999999999999999996
No 311
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 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 (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=81.63 E-value=0.95 Score=33.73 Aligned_cols=49 Identities=10% Similarity=0.158 Sum_probs=32.3
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc-CCCCCCHHHHHHHHHHhCCCCC
Q 032366 90 ARNDKKLTQSQLAQLINEKPQVIQEYES-GKAIPNQQILTKLERALGVKLR 139 (142)
Q Consensus 90 ~R~~~glTQ~eLA~~lgis~stIs~~E~-G~~~p~~~~l~kLa~~Lgvsl~ 139 (142)
++.-.|+|.+|+|+.+|+|.++|..... ++... ...+...+...|+.++
T Consensus 142 L~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~L-r~~l~~~~~~~~~~~~ 191 (193)
T TIGR02947 142 LADVEGFAYKEIAEIMGTPIGTVMSRLHRGRKQL-RKQLVDVAGERGFGPR 191 (193)
T ss_pred ehhhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH-HHHHHHHHhccccccc
Confidence 4556799999999999999999988764 32222 1223344444555554
No 312
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=81.49 E-value=2 Score=32.84 Aligned_cols=26 Identities=12% Similarity=0.064 Sum_probs=23.3
Q ss_pred HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 92 NDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 92 ~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
...|+|.+|+|+++++|..||..+-+
T Consensus 149 la~G~snkeIA~~L~iS~~TVk~h~~ 174 (207)
T PRK15411 149 WMAGQGTIQISDQMNIKAKTVSSHKG 174 (207)
T ss_pred HHcCCCHHHHHHHcCCCHHHHHHHHH
Confidence 45799999999999999999998864
No 313
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=81.45 E-value=7.8 Score=28.66 Aligned_cols=64 Identities=14% Similarity=0.215 Sum_probs=37.0
Q ss_pred HHHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCC
Q 032366 32 VNAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINE 107 (142)
Q Consensus 32 ~~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgi 107 (142)
=+.|++.|+++.|++-|+. |-..+... .+ .-+.++.++ ...-..|+.+ ...|||..++.+.+..
T Consensus 15 gevAk~~gvs~~TlRyYE~~GLi~~~r~-~~-g~R~Y~~~~---------i~~L~~I~~l-r~lG~sL~eIk~ll~~ 79 (154)
T PRK15002 15 GEVAKRSGVAVSALHFYESKGLITSIRN-SG-NQRRYKRDV---------LRYVAIIKIA-QRIGIPLATIGEAFGV 79 (154)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCccC-CC-CCEEECHHH---------HHHHHHHHHH-HHcCCCHHHHHHHHHH
Confidence 3579999999999999997 44443111 11 112222211 1112223333 4589999999987753
No 314
>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=81.35 E-value=1.6 Score=32.66 Aligned_cols=90 Identities=14% Similarity=0.199 Sum_probs=24.3
Q ss_pred HHHHHcCCChhHHHhhhcCCCCCCCCCCCcccccchhhhccccCCc-chHHHHHHHHHHHH----hCCCCHHHHHHHh--
Q 032366 33 NAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLAHDR-VPSELKKAIVQARN----DKKLTQSQLAQLI-- 105 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~g~~~~~~~~~~~~~~kl~~~~~~~~~~~-~~~~~g~~Lk~~R~----~~glTQ~eLA~~l-- 105 (142)
..|...|++++|+.+--.|+--.++.+.-+--..+......-.... ....+-..|+++-. .+-+|-.+|++.+
T Consensus 54 ~iA~~lgl~~STVSRav~~Ky~~t~~Gi~plk~fF~~~~~~~~~~~~S~~~ik~~i~~lI~~Ed~~~PlSD~~i~~~L~~ 133 (160)
T PF04552_consen 54 DIADELGLHESTVSRAVKNKYIQTPRGIFPLKDFFSRSVSSGSGEEFSSEAIKARIKELIEEEDKKKPLSDQEIAELLKE 133 (160)
T ss_dssp -------------------------------S-----SS--SS-SS---TTH-HHHHHHHTTS-TTS---HHHHHHHHTT
T ss_pred HHHHHhCCCHhHHHHHHcCceeecCCeeeeHHHhccccccCCCCcccHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHH
Confidence 4688999999999998877664333332232233332211111111 11224445555543 4689999999999
Q ss_pred ---CCCHHHHHHHHcCCCCC
Q 032366 106 ---NEKPQVIQEYESGKAIP 122 (142)
Q Consensus 106 ---gis~stIs~~E~G~~~p 122 (142)
.||+.||.+|=..-..|
T Consensus 134 ~gi~isRRTVaKYR~~L~Ip 153 (160)
T PF04552_consen 134 EGIKISRRTVAKYREELGIP 153 (160)
T ss_dssp TTS---HHHHHHHHHHHT-S
T ss_pred cCCCccHHHHHHHHHHcCCC
Confidence 78999999986543344
No 315
>TIGR02366 DHAK_reg probable dihydroxyacetone kinase regulator. The seed alignment for this family was built from a set of closely related uncharacterized proteins associated with operons for the type of bacterial dihydroxyacetone kinase that transfers PEP-derived phosphate from a phosphoprotein, as in phosphotransferase system transport, rather than from ATP. Members have a TetR transcriptional regulator domain (pfam00440) at the N-terminus and sequence homology throughout.
Probab=81.33 E-value=4.3 Score=29.47 Aligned_cols=38 Identities=13% Similarity=0.106 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHhCC---CCHHHHHHHhCCCHHHHHHHHcCC
Q 032366 82 ELKKAIVQARNDKK---LTQSQLAQLINEKPQVIQEYESGK 119 (142)
Q Consensus 82 ~~g~~Lk~~R~~~g---lTQ~eLA~~lgis~stIs~~E~G~ 119 (142)
.+.+.+.++..++| +|.+++++++|||++|+.++-..+
T Consensus 7 ~I~~a~~~Ll~~k~~~~ITV~~I~~~AgvsR~TFY~hF~dK 47 (176)
T TIGR02366 7 KIAKAFKDLMEVQAFSKISVSDIMSTAQIRRQTFYNHFQDK 47 (176)
T ss_pred HHHHHHHHHHHHCCCccCCHHHHHHHhCCCHHHHHHHCCCH
Confidence 46666677777765 689999999999999999887655
No 316
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=81.32 E-value=1.6 Score=26.94 Aligned_cols=25 Identities=24% Similarity=0.292 Sum_probs=20.8
Q ss_pred HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366 30 KVVNAARRAGADIETVRKSHAGTNK 54 (142)
Q Consensus 30 ~~~~~a~r~G~~v~t~kk~~~g~~~ 54 (142)
++-..|.+.|++.+|+.+||.|...
T Consensus 16 s~~~lA~~~g~s~s~v~~iE~G~~~ 40 (64)
T PF13560_consen 16 SQAQLADRLGVSQSTVSRIERGRRP 40 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSSS
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCCC
Confidence 5667899999999999999999884
No 317
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=81.28 E-value=3.5 Score=30.05 Aligned_cols=32 Identities=9% Similarity=0.170 Sum_probs=26.5
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
+.+-.++.-.|+|.+|+|+.+|+|.++|....
T Consensus 125 r~v~~L~~~~g~s~~EIA~~lgis~~tV~~~l 156 (172)
T PRK12523 125 RAAFLYNRLDGMGHAEIAERLGVSVSRVRQYL 156 (172)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 34445566789999999999999999998875
No 318
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=81.20 E-value=3.1 Score=32.82 Aligned_cols=27 Identities=19% Similarity=0.132 Sum_probs=23.8
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 91 RNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 91 R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+--.|+|++++|+.+|+|.++|+++..
T Consensus 215 ~y~~~~s~~eIA~~lgvs~~~V~~~~~ 241 (256)
T PRK07408 215 VFLHDLTQKEAAERLGISPVTVSRRVK 241 (256)
T ss_pred HHHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 344699999999999999999999875
No 319
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=81.06 E-value=1.7 Score=34.97 Aligned_cols=24 Identities=21% Similarity=0.210 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 94 KKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 94 ~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.++|+.++|+.+|||+.+|+++++
T Consensus 247 ~~~Tl~EIA~~lgvS~~rVrqi~~ 270 (284)
T PRK06596 247 DKSTLQELAAEYGVSAERVRQIEK 270 (284)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHH
Confidence 379999999999999999999986
No 320
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=81.06 E-value=3.5 Score=29.91 Aligned_cols=31 Identities=10% Similarity=0.073 Sum_probs=25.3
Q ss_pred HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
.+-.++.-.|+|.+|+|+.+|+|.++|....
T Consensus 125 ~vl~L~~~~g~s~~EIA~~lgis~~tV~~~l 155 (173)
T PRK09645 125 AVLVRSYYRGWSTAQIAADLGIPEGTVKSRL 155 (173)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence 3444566679999999999999999997654
No 321
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=80.99 E-value=3.3 Score=30.51 Aligned_cols=31 Identities=6% Similarity=0.101 Sum_probs=25.5
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 87 IVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+-.++.-.|+|.+|+|+.+|+|.++|..+..
T Consensus 141 i~~l~~~~~~s~~eIA~~lgis~~tV~~~l~ 171 (182)
T PRK12537 141 CILHAYVDGCSHAEIAQRLGAPLGTVKAWIK 171 (182)
T ss_pred HHHHHHHcCCCHHHHHHHHCCChhhHHHHHH
Confidence 3444566899999999999999999988753
No 322
>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=80.97 E-value=6.2 Score=26.55 Aligned_cols=64 Identities=13% Similarity=0.119 Sum_probs=36.1
Q ss_pred HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCC
Q 032366 33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINE 107 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgi 107 (142)
+.|++.|++..|++-|+. |-..|..... -.-+.++.++ ..--..|+.+ ...|++..++...+..
T Consensus 5 eva~~~gvs~~tlR~ye~~Gll~p~~~~~-~gyR~Y~~~~---------~~~l~~I~~l-r~~G~~l~eI~~~l~~ 69 (97)
T cd04782 5 EFAKLCGISKQTLFHYDKIGLFKPEIVKE-NGYRYYTLEQ---------FEQLDIILLL-KELGISLKEIKDYLDN 69 (97)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCccCC-CCCccCCHHH---------HHHHHHHHHH-HHcCCCHHHHHHHHhc
Confidence 579999999999999986 4444321110 1111111111 1122334444 4478999998887754
No 323
>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=80.94 E-value=1.8 Score=30.58 Aligned_cols=21 Identities=29% Similarity=0.347 Sum_probs=19.2
Q ss_pred CHHHHHHHhCCCHHHHHHHHc
Q 032366 97 TQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 97 TQ~eLA~~lgis~stIs~~E~ 117 (142)
|..+||+.+|||+.||..||.
T Consensus 1 ~I~e~a~~~gvs~~tlR~Ye~ 21 (124)
T TIGR02051 1 TIGELAKAAGVNVETIRYYER 21 (124)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 457999999999999999996
No 324
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=80.89 E-value=3 Score=33.15 Aligned_cols=29 Identities=17% Similarity=0.143 Sum_probs=24.7
Q ss_pred HHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 89 QARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 89 ~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.++--.|+|+.++|+.+|+|.++|.+++.
T Consensus 225 ~l~y~~~~t~~EIA~~lgis~~~V~~~~~ 253 (264)
T PRK07122 225 VLRFFESMTQTQIAERVGISQMHVSRLLA 253 (264)
T ss_pred HHHhcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34445699999999999999999999875
No 325
>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=80.84 E-value=9.5 Score=25.38 Aligned_cols=62 Identities=19% Similarity=0.225 Sum_probs=36.3
Q ss_pred HHHHHcCCChhHHHhhhcC-CCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhC
Q 032366 33 NAARRAGADIETVRKSHAG-TNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLIN 106 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~g-~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lg 106 (142)
+.|++.|++..|++.|+.- -..+.... ..-..++.+ ....-..++.++. .|++..+++..+.
T Consensus 5 eva~~~gi~~~tlr~~~~~Gll~~~~~~--~g~r~y~~~---------dv~~l~~i~~l~~-~g~~~~~i~~~l~ 67 (100)
T cd00592 5 EVAKLLGVSVRTLRYYEEKGLLPPERSE--NGYRLYSEE---------DLERLRLIRRLRE-LGLSLKEIRELLD 67 (100)
T ss_pred HHHHHHCcCHHHHHHHHHCCCcCCCcCC--CCCcccCHH---------HHHHHHHHHHHHH-cCCCHHHHHHHHh
Confidence 5788999999999999862 22211110 111111111 1124455666666 8888888887664
No 326
>PRK13749 transcriptional regulator MerD; Provisional
Probab=80.80 E-value=2.8 Score=29.89 Aligned_cols=23 Identities=22% Similarity=0.228 Sum_probs=21.4
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHc
Q 032366 95 KLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 95 glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.||..|||+++|+|..||.-||.
T Consensus 3 ~~tIgelA~~~gvS~~tiR~YE~ 25 (121)
T PRK13749 3 AYTVSRLALDAGVSVHIVRDYLL 25 (121)
T ss_pred CCcHHHHHHHHCCCHHHHHHHHH
Confidence 47899999999999999999986
No 327
>PRK15320 transcriptional activator SprB; Provisional
Probab=80.75 E-value=2 Score=33.76 Aligned_cols=27 Identities=11% Similarity=0.076 Sum_probs=23.9
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 91 RNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 91 R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
....|+|++|+|+.+++|.+||+.+-+
T Consensus 175 LLAkG~SNKEIAekL~LS~KTVSTYKn 201 (251)
T PRK15320 175 LLSSGHPAIELAKKFGLGTKTVSIYRK 201 (251)
T ss_pred HHHcCCCHHHHHHHhccchhhHHHHHH
Confidence 346799999999999999999998864
No 328
>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=80.62 E-value=7.5 Score=23.16 Aligned_cols=20 Identities=15% Similarity=0.230 Sum_probs=17.6
Q ss_pred CHHHHHHHhCCCHHHHHHHH
Q 032366 97 TQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 97 TQ~eLA~~lgis~stIs~~E 116 (142)
|..+||+.+|+|++++++..
T Consensus 27 ~~~~la~~~~is~~~v~~~l 46 (66)
T cd07377 27 SERELAEELGVSRTTVREAL 46 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHH
Confidence 49999999999999988754
No 329
>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=80.57 E-value=9.9 Score=26.10 Aligned_cols=63 Identities=17% Similarity=0.136 Sum_probs=35.2
Q ss_pred HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhC
Q 032366 33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLIN 106 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lg 106 (142)
+.|++.|+++.|++.|+. |-..+.... .-.-..++.+ .-..-..|+.+| ..|++..++...+.
T Consensus 5 eva~~~gvs~~tlR~ye~~Gll~p~~~~-~~g~R~Y~~~---------dl~~l~~I~~lr-~~G~~l~~I~~~l~ 68 (108)
T cd04773 5 ELAHLLGVPPSTLRHWEKEGLLSPDREP-ETGYRVYDPS---------DVRDARLIHLLR-RGGYLLEQIATVVE 68 (108)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCcCC-CCCceeeCHH---------HHHHHHHHHHHH-HCCCCHHHHHHHHH
Confidence 578999999999999987 333321110 0011111111 111334455554 47889888877664
No 330
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=80.56 E-value=3.3 Score=30.73 Aligned_cols=33 Identities=9% Similarity=-0.006 Sum_probs=27.1
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
.+.+-.++.-.|+|.+|+|+.+|+|.++|....
T Consensus 135 ~r~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l 167 (185)
T PRK09649 135 QREALLLTQLLGLSYADAAAVCGCPVGTIRSRV 167 (185)
T ss_pred HhHHhhhHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 344455667789999999999999999998765
No 331
>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=80.55 E-value=2.6 Score=31.56 Aligned_cols=22 Identities=36% Similarity=0.357 Sum_probs=20.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
+|..|||+.+|||++||..||.
T Consensus 2 ~~I~evA~~~gvs~~tLRyYe~ 23 (172)
T cd04790 2 LTISQLARQFGLSRSTLLYYER 23 (172)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 6889999999999999999996
No 332
>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=80.28 E-value=4.3 Score=25.14 Aligned_cols=34 Identities=18% Similarity=0.255 Sum_probs=24.0
Q ss_pred HHHHHHHHH-HhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 83 LKKAIVQAR-NDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 83 ~g~~Lk~~R-~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
+-+.|-.+. .....+..+||+.+|+|+++++...
T Consensus 9 YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml 43 (60)
T PF01325_consen 9 YLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEML 43 (60)
T ss_dssp HHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHH
Confidence 334444443 4456789999999999999998764
No 333
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=80.28 E-value=3.8 Score=30.09 Aligned_cols=31 Identities=13% Similarity=0.150 Sum_probs=25.5
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 87 IVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+-.++.-.|+|.+|+|+.+|+|.++|.....
T Consensus 143 vl~l~~~~~~s~~eIA~~lgis~~~V~~~l~ 173 (186)
T PRK13919 143 VIEVLYYQGYTHREAAQLLGLPLGTLKTRAR 173 (186)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3344566899999999999999999987754
No 334
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=80.01 E-value=3.1 Score=30.81 Aligned_cols=27 Identities=26% Similarity=0.252 Sum_probs=23.8
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 91 RNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 91 R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+...=|+..|+|+.+|||..||..||+
T Consensus 7 ~~~~~~~IgevAk~~gvs~~TlRyYE~ 33 (154)
T PRK15002 7 RIKALLTPGEVAKRSGVAVSALHFYES 33 (154)
T ss_pred hhcccccHHHHHHHHCcCHHHHHHHHH
Confidence 444558999999999999999999996
No 335
>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=79.94 E-value=12 Score=25.82 Aligned_cols=63 Identities=16% Similarity=0.138 Sum_probs=35.1
Q ss_pred HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhC
Q 032366 33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLIN 106 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lg 106 (142)
+.|++.|+++.|++-|+. |-..|....+ -.-+.++.++- ..-..|+. ....|++..++.+.+.
T Consensus 5 e~A~~~gvs~~tlR~ye~~GLl~p~~r~~-~g~R~Y~~~~l---------~~l~~I~~-lr~~G~~l~~I~~~l~ 68 (107)
T cd01111 5 QLALDAGVSVHIVRDYLLRGLLHPVARTE-GGYGLFDDCAL---------QRLRFVRA-AFEAGIGLDELARLCR 68 (107)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCCcCC-CCCeecCHHHH---------HHHHHHHH-HHHcCCCHHHHHHHHH
Confidence 579999999999999986 5444321111 11222222111 11222333 3456999888887664
No 336
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=79.80 E-value=2.1 Score=32.86 Aligned_cols=24 Identities=13% Similarity=0.207 Sum_probs=21.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 94 KKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 94 ~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+..+.++||+.+|||++|++...+
T Consensus 177 R~~~l~dLA~~lGISkst~~ehLR 200 (215)
T COG3413 177 RRVSLKDLAKELGISKSTLSEHLR 200 (215)
T ss_pred ccCCHHHHHHHhCCCHHHHHHHHH
Confidence 467999999999999999998764
No 337
>PRK12423 LexA repressor; Provisional
Probab=79.80 E-value=5 Score=30.58 Aligned_cols=35 Identities=11% Similarity=0.116 Sum_probs=28.9
Q ss_pred hHHHHHHHHHHHHhCCC--CHHHHHHHhC-CCHHHHHH
Q 032366 80 PSELKKAIVQARNDKKL--TQSQLAQLIN-EKPQVIQE 114 (142)
Q Consensus 80 ~~~~g~~Lk~~R~~~gl--TQ~eLA~~lg-is~stIs~ 114 (142)
..++-..|+....+.|+ |..|||+.+| .|++++++
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 44577788888888888 9999999999 48988764
No 338
>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=79.80 E-value=5 Score=27.55 Aligned_cols=34 Identities=9% Similarity=-0.061 Sum_probs=27.5
Q ss_pred HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
-...|..+....++|+.+||+.++++++++++..
T Consensus 30 q~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l 63 (118)
T TIGR02337 30 QWRILRILAEQGSMEFTQLANQACILRPSLTGIL 63 (118)
T ss_pred HHHHHHHHHHcCCcCHHHHHHHhCCCchhHHHHH
Confidence 3445666667788999999999999999988764
No 339
>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=79.71 E-value=6.2 Score=27.80 Aligned_cols=65 Identities=20% Similarity=0.268 Sum_probs=36.5
Q ss_pred HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCCC
Q 032366 33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEK 108 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis 108 (142)
+.|++.|+++.|++-|+. |-..+..... -.-..++.++ -.--..|+.+ ...|+|..++.+.+...
T Consensus 4 e~a~~~gvs~~tlR~Ye~~GLl~~~~r~~-~g~R~Y~~~~---------l~~l~~I~~l-~~~G~sl~eI~~~l~~~ 69 (124)
T TIGR02051 4 ELAKAAGVNVETIRYYERKGLLPEPDRPE-GGYRRYPEET---------VKRLRFIKRA-QELGFSLEEIGGLLGLV 69 (124)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCccCC-CCCEeECHHH---------HHHHHHHHHH-HHCCCCHHHHHHHHhcc
Confidence 478999999999999986 4433211100 0111111110 0111333443 56899999999988653
No 340
>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=79.67 E-value=4.1 Score=32.26 Aligned_cols=21 Identities=29% Similarity=0.278 Sum_probs=18.3
Q ss_pred HHHHHHcCCChhHHHhhhcCC
Q 032366 32 VNAARRAGADIETVRKSHAGT 52 (142)
Q Consensus 32 ~~~a~r~G~~v~t~kk~~~g~ 52 (142)
-.-|+++|++++|+.+..+|.
T Consensus 5 ~dIA~~agVS~sTVSr~Ln~~ 25 (311)
T TIGR02405 5 KDIARLAGVGKSTVSRVLNNE 25 (311)
T ss_pred HHHHHHhCCCHHHHHHHhCCC
Confidence 457999999999999999764
No 341
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=79.67 E-value=4.2 Score=29.42 Aligned_cols=33 Identities=9% Similarity=0.029 Sum_probs=26.4
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+.+-.++...|+|.+|+|+.+|+|..+|.....
T Consensus 118 r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ 150 (164)
T PRK12547 118 REAIILIGASGFSYEDAAAICGCAVGTIKSRVS 150 (164)
T ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 334445566899999999999999999987653
No 342
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=79.63 E-value=3.8 Score=30.49 Aligned_cols=31 Identities=6% Similarity=-0.022 Sum_probs=25.5
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 87 IVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+-.++.-.|+|.+|+|+.+|+|.++|.....
T Consensus 119 v~~L~~~eg~s~~EIA~~lgis~~tV~~~l~ 149 (182)
T PRK12511 119 ALHLVAIEGLSYQEAAAVLGIPIGTLMSRIG 149 (182)
T ss_pred HHHHHHHcCCCHHHHHHHhCcCHHHHHHHHH
Confidence 3444566799999999999999999988753
No 343
>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=79.63 E-value=11 Score=25.86 Aligned_cols=63 Identities=16% Similarity=0.226 Sum_probs=35.2
Q ss_pred HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhC
Q 032366 33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLIN 106 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lg 106 (142)
+.|++.|+++.|++-|+. |-..+.... .-.-+.++.+ . ...-..|..+| ..|+|.+++...+.
T Consensus 5 e~a~~~gvs~~tlr~ye~~gll~~~~r~-~~gyR~Y~~~-------~--l~~l~~I~~lr-~~G~sL~eI~~~l~ 68 (113)
T cd01109 5 EVAEKTGLSADTLRYYEKEGLLPPVKRD-ENGIRDFTEE-------D--LEWLEFIKCLR-NTGMSIKDIKEYAE 68 (113)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCCcC-CCCCccCCHH-------H--HHHHHHHHHHH-HcCCCHHHHHHHHH
Confidence 578999999999999987 333211110 0011111111 1 11223445554 47999999887664
No 344
>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=79.46 E-value=4.5 Score=32.34 Aligned_cols=43 Identities=12% Similarity=0.112 Sum_probs=32.3
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366 93 DKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 139 (142)
Q Consensus 93 ~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~ 139 (142)
..|+|++|+|+.+|+|.++|..+..- ....|.+.-...+++++
T Consensus 240 ~e~~s~~EIA~~Lgis~~tVk~~l~r----AlkkLr~~l~~~~~~~~ 282 (285)
T TIGR02394 240 YEPATLEEVAAEVGLTRERVRQIQVE----ALKKLRRILERDGVDRE 282 (285)
T ss_pred CCCccHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHHHhhhhhh
Confidence 67899999999999999999998753 23445455455666554
No 345
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=79.41 E-value=2.1 Score=31.21 Aligned_cols=23 Identities=22% Similarity=0.267 Sum_probs=21.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHc
Q 032366 95 KLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 95 glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.+|..+||+.+|||..||.-||+
T Consensus 7 ~~~IgevAk~~Gvs~~TLRyYE~ 29 (144)
T PRK13752 7 NLTIGVFAKAAGVNVETIRFYQR 29 (144)
T ss_pred cccHHHHHHHHCcCHHHHHHHHH
Confidence 48999999999999999999996
No 346
>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=79.39 E-value=3.9 Score=32.02 Aligned_cols=32 Identities=9% Similarity=0.237 Sum_probs=26.4
Q ss_pred HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.+-.++-..|+|..|+|+.+|+|.++|..+..
T Consensus 212 ~ii~l~~~~g~s~~eIA~~lgis~~~V~~~~~ 243 (255)
T TIGR02941 212 SIIHCTFEENLSQKETGERLGISQMHVSRLQR 243 (255)
T ss_pred HHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34445556899999999999999999998864
No 347
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=79.34 E-value=3.9 Score=32.30 Aligned_cols=29 Identities=7% Similarity=0.149 Sum_probs=24.9
Q ss_pred HHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 89 QARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 89 ~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.+|--.++|++|+|+.+|+|.++|++++.
T Consensus 215 ~l~y~e~~t~~EIA~~lgis~~~V~~~~~ 243 (257)
T PRK05911 215 ALYYYEELVLKEIGKILGVSESRVSQIHS 243 (257)
T ss_pred HHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 33445799999999999999999999975
No 348
>cd08316 Death_FAS_TNFRSF6 Death domain of FAS or TNF receptor superfamily member 6. Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in sign
Probab=79.33 E-value=8.2 Score=26.45 Aligned_cols=39 Identities=15% Similarity=0.141 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHhCCCC-HHHHHHHhCCCHHHHHHHHcCCC
Q 032366 82 ELKKAIVQARNDKKLT-QSQLAQLINEKPQVIQEYESGKA 120 (142)
Q Consensus 82 ~~g~~Lk~~R~~~glT-Q~eLA~~lgis~stIs~~E~G~~ 120 (142)
++...|..++...++. -++||+.+|+|...|..+|....
T Consensus 6 dl~~~l~~Ia~~~~~~~wK~faR~lglse~~Id~I~~~~~ 45 (97)
T cd08316 6 DLSKHIPDIADVMTLKDVKKFVRKSGLSEPKIDEIKLDNP 45 (97)
T ss_pred cHHHhhHHHHHHcCHHHHHHHHHHcCCCHHHHHHHHHcCC
Confidence 4667777888888875 67899999999999999997653
No 349
>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=79.33 E-value=3.7 Score=32.55 Aligned_cols=20 Identities=35% Similarity=0.569 Sum_probs=17.6
Q ss_pred HHHHHcCCChhHHHhhhcCC
Q 032366 33 NAARRAGADIETVRKSHAGT 52 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~g~ 52 (142)
.-|+++|++++|+.+..+|.
T Consensus 6 dIA~~agvS~~TVSrvLn~~ 25 (329)
T TIGR01481 6 DVAREAGVSMATVSRVVNGN 25 (329)
T ss_pred HHHHHhCCCHHHHHHHhCCC
Confidence 46999999999999998764
No 350
>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=79.30 E-value=3.9 Score=29.57 Aligned_cols=33 Identities=18% Similarity=0.332 Sum_probs=26.0
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
..|-.++.-.|+|.+++|+.+|+|.++|.....
T Consensus 125 r~i~~l~~~~g~s~~eiA~~lgis~~tv~~~l~ 157 (169)
T TIGR02954 125 QTAIILRYYHDLTIKEIAEVMNKPEGTVKTYLH 157 (169)
T ss_pred hHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 334445556799999999999999999987653
No 351
>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=79.29 E-value=4.1 Score=31.18 Aligned_cols=30 Identities=7% Similarity=0.155 Sum_probs=24.9
Q ss_pred HHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 88 VQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 88 k~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
-.++-..|+|.+++|+.+|+|..+|..+..
T Consensus 184 l~l~y~~~~s~~eIA~~lgis~~tV~~~~~ 213 (224)
T TIGR02479 184 LSLYYYEELNLKEIGEVLGLTESRVSQIHS 213 (224)
T ss_pred HHHHHhCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 334456799999999999999999998764
No 352
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=79.29 E-value=7 Score=23.83 Aligned_cols=37 Identities=22% Similarity=0.309 Sum_probs=26.2
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 032366 93 DKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG 140 (142)
Q Consensus 93 ~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~e 140 (142)
+.+.+..+.|+.++|.++||.. .+.+|.+.+|+++++
T Consensus 10 ~~~~n~~~tA~~L~iHrNTl~y-----------Rl~ki~~l~g~dl~~ 46 (59)
T PF13556_consen 10 ENNGNISKTARALHIHRNTLRY-----------RLKKIEELLGLDLDD 46 (59)
T ss_dssp HTTT-HHHHHHHHTS-HHHHHH-----------HHHHHHHHHS--TTS
T ss_pred HcCCCHHHHHHHHCCCHHHHHH-----------HHHHHHHHHCcCCCC
Confidence 4678999999999999999864 366777777777764
No 353
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=79.17 E-value=6.5 Score=26.67 Aligned_cols=36 Identities=11% Similarity=0.127 Sum_probs=31.3
Q ss_pred HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 032366 83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESG 118 (142)
Q Consensus 83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G 118 (142)
-...|+.-....|+|-.++|..+|+|...|.++.+=
T Consensus 11 T~~ELq~nf~~~~ls~~~ia~dL~~s~~~le~vL~l 46 (89)
T PF10078_consen 11 TRQELQANFELSGLSLEQIAADLGTSPEHLEQVLNL 46 (89)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 345677788889999999999999999999999873
No 354
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=79.17 E-value=4 Score=30.02 Aligned_cols=29 Identities=10% Similarity=0.080 Sum_probs=24.6
Q ss_pred HHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 89 QARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 89 ~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.++-..|+|.+|+|+.+|+|.++|.....
T Consensus 147 ~l~~~~g~s~~eIA~~lgis~~~v~~~l~ 175 (187)
T PRK12534 147 RTAFFEGITYEELAARTDTPIGTVKSWIR 175 (187)
T ss_pred HHHHHcCCCHHHHHHHhCCChhHHHHHHH
Confidence 34456799999999999999999988764
No 355
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=79.15 E-value=4 Score=31.43 Aligned_cols=25 Identities=20% Similarity=0.310 Sum_probs=22.5
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 93 DKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 93 ~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
..|+|.+|+|+.+|+|.+||.....
T Consensus 196 ~eg~s~~EIA~~lgis~~tVk~~~~ 220 (234)
T PRK08301 196 GEEKTQKEVADMLGISQSYISRLEK 220 (234)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4699999999999999999988754
No 356
>PRK13869 plasmid-partitioning protein RepA; Provisional
Probab=79.14 E-value=3.4 Score=34.98 Aligned_cols=43 Identities=14% Similarity=0.273 Sum_probs=34.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHc------------CCCCCCHHHHHHHHHHhCC
Q 032366 94 KKLTQSQLAQLINEKPQVIQEYES------------GKAIPNQQILTKLERALGV 136 (142)
Q Consensus 94 ~glTQ~eLA~~lgis~stIs~~E~------------G~~~p~~~~l~kLa~~Lgv 136 (142)
+-+|..|+|+.|||+.+||..|+. |++..+.+.+..|.+.|+-
T Consensus 47 r~ft~~e~A~~lgvs~~tlr~~~~~g~~~~~~~~~~grR~yt~~di~~lr~~l~~ 101 (405)
T PRK13869 47 RKFTSGEAARLMKISDSTLRKMTLAGEGPQPELASNGRRFYTLGQINEIRQMLAG 101 (405)
T ss_pred CCCCHHHHHHHhCcCHHHHHHHHHcCCCCCCccCCCCceeecHHHHHHHHHHHHh
Confidence 468999999999999999999954 3444567778888887763
No 357
>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=79.11 E-value=3.2 Score=29.99 Aligned_cols=22 Identities=27% Similarity=0.336 Sum_probs=20.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
++..++|+.+|||+.||..||.
T Consensus 1 y~I~e~a~~~gvs~~TLR~Ye~ 22 (134)
T cd04779 1 YRIGQLAHLAGVSKRTIDYYTN 22 (134)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4778999999999999999996
No 358
>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=79.07 E-value=5 Score=33.53 Aligned_cols=43 Identities=16% Similarity=0.290 Sum_probs=32.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHcC------------CCCCCHHHHHHHHHHhCC
Q 032366 94 KKLTQSQLAQLINEKPQVIQEYESG------------KAIPNQQILTKLERALGV 136 (142)
Q Consensus 94 ~glTQ~eLA~~lgis~stIs~~E~G------------~~~p~~~~l~kLa~~Lgv 136 (142)
+-+|..|+|+.+||+.+||..||.- .+..+.+.+..|...+..
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 4589999999999999999999752 233456677777766654
No 359
>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=79.06 E-value=16 Score=24.39 Aligned_cols=65 Identities=20% Similarity=0.216 Sum_probs=37.5
Q ss_pred HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCCC
Q 032366 33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEK 108 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis 108 (142)
..|++.|+++.|++-|+. |-..|.... .-.-+.++..+- .--..|+.+| ..|++.+++.+.+...
T Consensus 5 eva~~~gvs~~tLRyye~~Gll~p~~~~-~~gyR~Y~~~~l---------~~l~~I~~lr-~~G~~l~~I~~~l~~~ 70 (96)
T cd04768 5 EFAKLAGVSIRTLRHYDDIGLFKPAKIA-ENGYRYYSYAQL---------YQLQFILFLR-ELGFSLAEIKELLDTE 70 (96)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCccC-CCCeeeCCHHHH---------HHHHHHHHHH-HcCCCHHHHHHHHhcC
Confidence 478999999999999997 333322111 111122222111 1223344444 4799999998888654
No 360
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=79.01 E-value=4.2 Score=30.34 Aligned_cols=33 Identities=6% Similarity=0.038 Sum_probs=26.5
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+.+-.++.-.|+|.+|+|+.+|+|.++|.....
T Consensus 122 r~i~~L~~~~g~s~~EIA~~Lgis~~tVk~~l~ 154 (187)
T PRK12516 122 REAIILVGASGFAYEEAAEICGCAVGTIKSRVN 154 (187)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 334455666899999999999999999987653
No 361
>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=78.99 E-value=4.6 Score=29.47 Aligned_cols=33 Identities=9% Similarity=0.098 Sum_probs=26.7
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
..+-.++...|++.+|+|+.+|+|..+|.....
T Consensus 106 r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ 138 (170)
T TIGR02959 106 REAIRLTELEGLSQQEIAEKLGLSLSGAKSRVQ 138 (170)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 334445667899999999999999999987753
No 362
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 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 a limited number of Gram-positive bacterial lineages.
Probab=78.90 E-value=4.7 Score=28.90 Aligned_cols=31 Identities=10% Similarity=0.305 Sum_probs=25.2
Q ss_pred HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
.+-.++--.|+|..|+|+.+|+|.++|...-
T Consensus 129 ~vl~l~~~~g~s~~eIA~~l~is~~tv~~~l 159 (170)
T TIGR02952 129 HVIALRFGQNLPIAEVARILGKTEGAVKILQ 159 (170)
T ss_pred HHHHHHHhcCCCHHHHHHHHCCCHHHHHHHH
Confidence 3444555679999999999999999998764
No 363
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=78.88 E-value=4 Score=29.20 Aligned_cols=32 Identities=22% Similarity=0.255 Sum_probs=25.8
Q ss_pred HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.+-.++--.|+|.+|+|+.+|+|.++|.....
T Consensus 117 ~i~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ 148 (162)
T TIGR02983 117 AVVVLRYYEDLSEAQVAEALGISVGTVKSRLS 148 (162)
T ss_pred HHhhhHHHhcCCHHHHHHHhCCCHHHHHHHHH
Confidence 34444556799999999999999999988753
No 364
>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=78.77 E-value=4.7 Score=29.44 Aligned_cols=30 Identities=10% Similarity=0.175 Sum_probs=24.8
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 87 IVQARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
+-.++.-.|+|.+++|+.+|+|.++|....
T Consensus 148 vi~l~~~~g~s~~eIA~~lgis~~~v~~~l 177 (189)
T TIGR02984 148 VILLRHLEGLSFAEVAERMDRSEGAVSMLW 177 (189)
T ss_pred HHHHHHhcCCCHHHHHHHHCcCHHHHHHHH
Confidence 334455689999999999999999998865
No 365
>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=78.72 E-value=13 Score=25.06 Aligned_cols=65 Identities=15% Similarity=0.244 Sum_probs=37.1
Q ss_pred HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCCC
Q 032366 33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEK 108 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis 108 (142)
+.|...|++..|++.|+. |-..+.... ..+-..++.+ . ...-..|..+|. .|++..++.+.+...
T Consensus 5 eva~~~gvs~~tlR~ye~~Gll~~~~~~-~~g~R~y~~~-------d--i~~l~~i~~lr~-~g~~l~~i~~~~~~~ 70 (103)
T cd01106 5 EVAKLTGVSVRTLHYYDEIGLLKPSRRT-ENGYRLYTEE-------D--LERLQQILFLKE-LGFSLKEIKELLKDP 70 (103)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCccC-CCCceeeCHH-------H--HHHHHHHHHHHH-cCCCHHHHHHHHHcC
Confidence 478899999999999976 333321111 0111112211 1 112334455554 699999988887655
No 366
>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=78.57 E-value=4.2 Score=32.25 Aligned_cols=21 Identities=24% Similarity=0.238 Sum_probs=18.2
Q ss_pred HHHHHcCCChhHHHhhhcCCC
Q 032366 33 NAARRAGADIETVRKSHAGTN 53 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~g~~ 53 (142)
.-|+++|++++|+.+..+|..
T Consensus 4 dIA~~aGVS~~TVSrvLn~~~ 24 (327)
T TIGR02417 4 DIAKLAGVSKTTASYVINGKA 24 (327)
T ss_pred HHHHHhCCCHHHHHHHHcCCC
Confidence 468999999999999997754
No 367
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=78.54 E-value=4.2 Score=33.25 Aligned_cols=50 Identities=20% Similarity=0.300 Sum_probs=37.7
Q ss_pred HHHHHcCCChhHHHhhhcCCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhC
Q 032366 33 NAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLIN 106 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lg 106 (142)
.-|+++|+++.|+.+..+|... +..+..+++.+.-++.|+.....|+.+-
T Consensus 5 DVA~~AGVS~sTVSrvln~~~~------------------------Vs~eTr~kV~~a~~elgY~pN~~Ar~L~ 54 (333)
T COG1609 5 DVAKLAGVSKATVSRVLNGSPY------------------------VSEETREKVLAAIKELGYRPNAVARSLR 54 (333)
T ss_pred HHHHHhCCCHHHHHHHHcCCCC------------------------CCHHHHHHHHHHHHHHCCCCCHHHHHHH
Confidence 4689999999999998876553 4455677777777777877666666554
No 368
>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional
Probab=78.49 E-value=3.8 Score=33.55 Aligned_cols=33 Identities=12% Similarity=0.189 Sum_probs=28.9
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
..|.......+.++.+.|+.+|||++|+++..+
T Consensus 289 ~~I~~aL~~~~gn~~~aA~~LGIsR~tLyrklk 321 (326)
T PRK11608 289 ELLQRSLQQAKFNQKRAAELLGLTYHQLRALLK 321 (326)
T ss_pred HHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence 447778888899999999999999999998765
No 369
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=78.45 E-value=4.2 Score=29.93 Aligned_cols=29 Identities=7% Similarity=0.097 Sum_probs=25.0
Q ss_pred HHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 89 QARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 89 ~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.++.-.|+|..|+|+.+|+|..+|.....
T Consensus 138 ~l~~~~g~s~~EIA~~lgis~~tV~~~l~ 166 (186)
T PRK05602 138 VLQYYQGLSNIEAAAVMDISVDALESLLA 166 (186)
T ss_pred hHHHhcCCCHHHHHHHhCcCHHHHHHHHH
Confidence 34556799999999999999999998864
No 370
>PRK09492 treR trehalose repressor; Provisional
Probab=78.43 E-value=4.4 Score=31.86 Aligned_cols=22 Identities=23% Similarity=0.293 Sum_probs=18.6
Q ss_pred HHHHHHHcCCChhHHHhhhcCC
Q 032366 31 VVNAARRAGADIETVRKSHAGT 52 (142)
Q Consensus 31 ~~~~a~r~G~~v~t~kk~~~g~ 52 (142)
.-.-|+++|++++|+.+..+|.
T Consensus 7 i~dIA~~agVS~~TVSrvLn~~ 28 (315)
T PRK09492 7 IKDIARLSGVGKSTVSRVLNNE 28 (315)
T ss_pred HHHHHHHhCCCHHHHhHHhCCC
Confidence 3467999999999999998764
No 371
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=78.40 E-value=4.5 Score=29.79 Aligned_cols=32 Identities=6% Similarity=0.105 Sum_probs=26.0
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
+.+-.++.-.|+|.+|+|+.+|+|.++|....
T Consensus 128 r~i~~l~~~~g~s~~EIA~~lgis~~tVk~~l 159 (185)
T PRK12542 128 RQVFKYKVFYNLTYQEISSVMGITEANVRKQF 159 (185)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 33444566689999999999999999998764
No 372
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=78.20 E-value=5.1 Score=28.69 Aligned_cols=32 Identities=13% Similarity=0.101 Sum_probs=26.2
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
+.+-.++.-.|+|.+|+|+.+|+|.+||....
T Consensus 119 r~v~~L~~~~g~s~~EIA~~l~is~~tV~~~l 150 (161)
T PRK12528 119 KRAFLLAQVDGLGYGEIATELGISLATVKRYL 150 (161)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 34445566789999999999999999998764
No 373
>PRK13749 transcriptional regulator MerD; Provisional
Probab=78.20 E-value=13 Score=26.39 Aligned_cols=63 Identities=16% Similarity=0.143 Sum_probs=39.0
Q ss_pred HHHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHH--HhCCCCHHHHHHHhCC
Q 032366 32 VNAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQAR--NDKKLTQSQLAQLINE 107 (142)
Q Consensus 32 ~~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R--~~~glTQ~eLA~~lgi 107 (142)
-..|+++|+++.|++-|+. |-..+.... .-+-+ .+...--.+|+.++ ...||+..++.+.+..
T Consensus 7 gelA~~~gvS~~tiR~YE~~GLl~p~~r~-~~gyR------------~Y~~~~l~rL~~I~~~r~~G~sL~eI~~ll~l 72 (121)
T PRK13749 7 SRLALDAGVSVHIVRDYLLRGLLRPVACT-TGGYG------------LFDDAALQRLCFVRAAFEAGIGLDALARLCRA 72 (121)
T ss_pred HHHHHHHCCCHHHHHHHHHCCCCCCCCcC-CCCCc------------cCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhh
Confidence 3579999999999999987 433321110 01111 22333444555554 4789999999887765
No 374
>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=78.13 E-value=12 Score=27.01 Aligned_cols=62 Identities=18% Similarity=0.205 Sum_probs=36.7
Q ss_pred HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhC
Q 032366 33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLIN 106 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lg 106 (142)
+.|++.|+++.|++-|+. |-..+... .-+-+.++.+ ....-..|+.+| ..|+|.+++.+.+.
T Consensus 6 EvA~~~Gvs~~tLRyYE~~GLl~p~r~--~~g~R~Y~~~---------dl~~l~~I~~lr-~~G~sl~eI~~~l~ 68 (139)
T cd01110 6 EVAKRSGVAVSALHFYEQKGLIASWRN--AGNQRRYPRD---------VLRRIAFIKVAQ-RLGLSLAEIAEALA 68 (139)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCcC--CCCCeEECHH---------HHHHHHHHHHHH-HcCCCHHHHHHHHH
Confidence 579999999999999987 44432111 1111222221 111334455554 57999999888764
No 375
>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=78.10 E-value=11 Score=26.30 Aligned_cols=62 Identities=16% Similarity=0.185 Sum_probs=35.5
Q ss_pred HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCC
Q 032366 33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINE 107 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgi 107 (142)
..|++.|+++.|++-|+. |-..|... + +-+-++.+ ....-..|+.+| ..|+|..++.+.+..
T Consensus 5 eva~~~gvs~~tlRyYe~~GLl~p~r~--~-gyR~Y~~~---------~l~~l~~I~~lr-~~G~~L~~I~~~l~~ 67 (118)
T cd04776 5 ELAREFDVTPRTLRFYEDKGLLSPERR--G-QTRVYSRR---------DRARLKLILRGK-RLGFSLEEIRELLDL 67 (118)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCcCC--C-CccccCHH---------HHHHHHHHHHHH-HCCCCHHHHHHHHHh
Confidence 478999999999999986 44442111 0 11111111 111223344444 479999888877653
No 376
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=78.08 E-value=4.7 Score=30.09 Aligned_cols=32 Identities=13% Similarity=0.257 Sum_probs=26.7
Q ss_pred HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.+-.++.-.|++.+++|+.+|+|.++|.....
T Consensus 143 ~i~~L~~~~g~s~~eIA~~lgis~~tV~~~l~ 174 (196)
T PRK12524 143 QAVVLRHIEGLSNPEIAEVMEIGVEAVESLTA 174 (196)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34455666899999999999999999998764
No 377
>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=78.05 E-value=4.1 Score=32.87 Aligned_cols=25 Identities=16% Similarity=0.322 Sum_probs=23.0
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 93 DKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 93 ~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
..++|.+|+|+.+|+|+.+|.+++.
T Consensus 267 ~~~~Tl~EIa~~lgiS~erVrq~~~ 291 (298)
T TIGR02997 267 GEPLTLAEIGRRLNLSRERVRQIEA 291 (298)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 4689999999999999999999985
No 378
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 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, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=78.05 E-value=5.6 Score=24.16 Aligned_cols=31 Identities=26% Similarity=0.369 Sum_probs=24.5
Q ss_pred CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 032366 97 TQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 138 (142)
Q Consensus 97 TQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl 138 (142)
|....|+.+|+|+++|++. +..|.+.||+++
T Consensus 15 s~~~AA~~l~is~~~vs~~-----------i~~LE~~lg~~L 45 (60)
T PF00126_consen 15 SISAAAEELGISQSAVSRQ-----------IKQLEEELGVPL 45 (60)
T ss_dssp SHHHHHHHCTSSHHHHHHH-----------HHHHHHHHTS-S
T ss_pred CHHHHHHHhhccchHHHHH-----------HHHHHHHhCCeE
Confidence 7788999999999999874 556777777765
No 379
>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=78.01 E-value=4.9 Score=24.60 Aligned_cols=31 Identities=19% Similarity=0.182 Sum_probs=24.2
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 87 IVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
|..+-....++..+||+.+|+|..+|.++.+
T Consensus 11 l~~L~~~~~~~~~ela~~l~~S~rti~~~i~ 41 (59)
T PF08280_consen 11 LELLLKNKWITLKELAKKLNISERTIKNDIN 41 (59)
T ss_dssp HHHHHHHTSBBHHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHcCCCCcHHHHHHHHCCCHHHHHHHHH
Confidence 3444457789999999999999999988754
No 380
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=77.98 E-value=5.1 Score=31.55 Aligned_cols=29 Identities=31% Similarity=0.338 Sum_probs=22.4
Q ss_pred HHHHHhC-CCCHHHHHHHhCCCHHHHHHHH
Q 032366 88 VQARNDK-KLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 88 k~~R~~~-glTQ~eLA~~lgis~stIs~~E 116 (142)
.++..+- =|||.|||-.+|+|+.||++..
T Consensus 97 ~EAy~QgglLT~~Dla~LL~~S~~TI~~~i 126 (220)
T PF07900_consen 97 NEAYDQGGLLTQEDLAMLLGISPRTISKDI 126 (220)
T ss_pred HHHHHcCCcccHHHHHHHHCCCHHHHHHHH
Confidence 3443333 3799999999999999998764
No 381
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=77.84 E-value=4.3 Score=30.16 Aligned_cols=31 Identities=3% Similarity=0.055 Sum_probs=25.4
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 87 IVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+-.++.-.|+|..|+|+.+|+|..+|.....
T Consensus 144 i~~L~~~~g~s~~EIA~~lgis~~tVk~~l~ 174 (195)
T PRK12532 144 VFTLKEILGFSSDEIQQMCGISTSNYHTIMH 174 (195)
T ss_pred HhhhHHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3345666799999999999999999987653
No 382
>PF07471 Phage_Nu1: Phage DNA packaging protein Nu1; InterPro: IPR010906 This entry is represented by the Bacteriophage lambda, Nu1, terminase small subunit. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Terminase, the DNA packaging enzyme of bacteriophage lambda, is a heteromultimer composed of subunits Nu1 and A. The smaller Nu1 terminase subunit has a low-affinity ATPase stimulated by non-specific DNA [].; PDB: 1J9I_A.
Probab=77.77 E-value=1.3 Score=33.24 Aligned_cols=23 Identities=17% Similarity=0.465 Sum_probs=18.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHc
Q 032366 95 KLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 95 glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.++.++||+.+|||..||.+|..
T Consensus 2 ~vnk~~lA~i~gvS~~ti~~W~~ 24 (164)
T PF07471_consen 2 KVNKKELAEIFGVSERTIDKWQR 24 (164)
T ss_dssp EEEHHHHHHHTT--HHHHHHHTT
T ss_pred CCCHHHHHHHHCCCHHHHHHHHH
Confidence 36789999999999999999985
No 383
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=77.68 E-value=4.9 Score=30.53 Aligned_cols=30 Identities=13% Similarity=0.088 Sum_probs=25.1
Q ss_pred HHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 88 VQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 88 k~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
-.++.-.|++.+|+|+.+|+|..+|.....
T Consensus 147 ~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~ 176 (203)
T PRK09647 147 VVLCDIEGLSYEEIAATLGVKLGTVRSRIH 176 (203)
T ss_pred HHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 345556899999999999999999988754
No 384
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=77.67 E-value=13 Score=25.52 Aligned_cols=65 Identities=17% Similarity=0.221 Sum_probs=39.0
Q ss_pred HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCCC
Q 032366 33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEK 108 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis 108 (142)
+.|.++|+++.|++=|+. |-..|..... -.-+.+...+ ...-..|+.+| ..|++.+++-+.+...
T Consensus 5 eva~~~gvs~~tLRyYE~~GLl~p~~~~~-~gyR~Ys~~d---------l~~l~~I~~~r-~~G~~L~~I~~~l~~~ 70 (124)
T COG0789 5 EVAKLTGVSVRTLRFYERKGLLSPERRDE-GGYRYYTPED---------LELLQIIKTLR-ELGFSLAEIKELLDLL 70 (124)
T ss_pred HHHHHhCCCHHHHHHHHHcCCCCCcccCC-CCceecCHHH---------HHHHHHHHHHH-HcCCCHHHHHHHHhcc
Confidence 578999999999999998 4444321111 1122222221 12334455444 7899999888877653
No 385
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=77.58 E-value=4.5 Score=30.46 Aligned_cols=33 Identities=3% Similarity=-0.065 Sum_probs=26.6
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+.+-.++.-.|+|.+|+|+.+|+|.++|.....
T Consensus 145 r~v~~L~~~eg~s~~EIA~~lgis~~tVk~~l~ 177 (201)
T PRK12545 145 GRVFMMREFLDFEIDDICTELTLTANHCSVLLY 177 (201)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 344455667899999999999999999987653
No 386
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=77.53 E-value=5 Score=28.68 Aligned_cols=33 Identities=12% Similarity=0.163 Sum_probs=26.6
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
..+-.++.-.|+|.+|+|+.+|+|.++|.....
T Consensus 111 r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~ 143 (159)
T PRK12527 111 RDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIV 143 (159)
T ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 344455667899999999999999999987653
No 387
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=77.53 E-value=4.9 Score=29.91 Aligned_cols=33 Identities=12% Similarity=0.085 Sum_probs=26.1
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+.+-.++.-.|+|.+|+|+.+|+|.+||.....
T Consensus 140 R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~ 172 (189)
T PRK12530 140 ARVFMMREYLELSSEQICQECDISTSNLHVLLY 172 (189)
T ss_pred HHHHhHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 334445556799999999999999999987653
No 388
>PRK09726 antitoxin HipB; Provisional
Probab=77.45 E-value=2.2 Score=28.21 Aligned_cols=27 Identities=11% Similarity=0.144 Sum_probs=23.0
Q ss_pred CHHHHHHHHHcCCChhHHHhhhcCCCC
Q 032366 28 DEKVVNAARRAGADIETVRKSHAGTNK 54 (142)
Q Consensus 28 ~~~~~~~a~r~G~~v~t~kk~~~g~~~ 54 (142)
+-++-..|++.|++..|+.+|+.|...
T Consensus 25 gltq~elA~~~gvs~~tis~~e~g~~~ 51 (88)
T PRK09726 25 GWTQSELAKKIGIKQATISNFENNPDN 51 (88)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHCCCCC
Confidence 345678999999999999999998754
No 389
>PRK06930 positive control sigma-like factor; Validated
Probab=77.38 E-value=5.3 Score=29.91 Aligned_cols=31 Identities=19% Similarity=0.231 Sum_probs=26.0
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 87 IVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+-.++...|+|..++|+.+|+|.++|..+..
T Consensus 122 V~~L~~~eg~s~~EIA~~lgiS~~tVk~~l~ 152 (170)
T PRK06930 122 VYLMHRGYGLSYSEIADYLNIKKSTVQSMIE 152 (170)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3344567899999999999999999998864
No 390
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=77.31 E-value=7.9 Score=23.09 Aligned_cols=29 Identities=3% Similarity=0.071 Sum_probs=24.6
Q ss_pred HHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 89 QARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 89 ~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
..+...|.+..++|..+++|..||.....
T Consensus 13 ~~l~~~G~s~~eia~~l~is~~tV~~h~~ 41 (65)
T COG2771 13 LRLVAQGKSNKEIARILGISEETVKTHLR 41 (65)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34566789999999999999999988764
No 391
>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=77.22 E-value=15 Score=24.93 Aligned_cols=64 Identities=19% Similarity=0.176 Sum_probs=37.9
Q ss_pred HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCCC
Q 032366 33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEK 108 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis 108 (142)
+.|++.|+++.|++-|+. |-..+ ....+ .-..++.+ .-..-..|+.+| +.|++.++++..+...
T Consensus 6 eva~~~gvs~~tLR~ye~~Gll~~-~r~~~-g~R~Y~~~---------dl~~l~~I~~l~-~~G~~l~ei~~~~~~~ 70 (102)
T cd04775 6 QMSRKFGVSRSTLLYYESIGLIPS-ARSEA-NYRLYSEA---------DLSRLEKIVFLQ-AGGLPLEEIAGCLAQP 70 (102)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCC-CCCCC-CCeeeCHH---------HHHHHHHHHHHH-HCCCCHHHHHHHHcCC
Confidence 478999999999999997 33321 11111 11122211 112344556664 4699999999877643
No 392
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=77.21 E-value=5.4 Score=31.53 Aligned_cols=33 Identities=6% Similarity=-0.038 Sum_probs=26.0
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
..+..++....++..|||+.+|+|..||.+..+
T Consensus 9 ~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~ 41 (251)
T PRK13509 9 ILLELLAQLGFVTVEKVIERLGISPATARRDIN 41 (251)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 334555666679999999999999999987654
No 393
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=77.06 E-value=6.7 Score=30.93 Aligned_cols=38 Identities=21% Similarity=0.232 Sum_probs=28.6
Q ss_pred hHHHHHHHHHHHH--hCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 80 PSELKKAIVQARN--DKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 80 ~~~~g~~Lk~~R~--~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
...--+.|.++-+ ...+|-.++|+.+|+|+.|+.+|..
T Consensus 156 ~~~Tl~~i~~~~~~~~~~~Taeela~~~giSRvTaRRYLe 195 (224)
T COG4565 156 DELTLQKVREALKEPDQELTAEELAQALGISRVTARRYLE 195 (224)
T ss_pred CHHHHHHHHHHHhCcCCccCHHHHHHHhCccHHHHHHHHH
Confidence 3333445555544 5789999999999999999999863
No 394
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=77.04 E-value=4.6 Score=32.56 Aligned_cols=24 Identities=13% Similarity=0.176 Sum_probs=22.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 94 KKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 94 ~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.|+|++|+|+.+|+|+.+|.+++.
T Consensus 244 ~~~t~~EIa~~lgvs~~~V~q~~~ 267 (289)
T PRK07500 244 DGATLEALGEELGISKERVRQIEA 267 (289)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Confidence 589999999999999999999985
No 395
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=76.99 E-value=3.2 Score=31.83 Aligned_cols=27 Identities=15% Similarity=0.177 Sum_probs=23.8
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 91 RNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 91 R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
....|+|.+|+|+++++|..||..+-+
T Consensus 159 lla~G~snkeIA~~L~iS~~TVk~h~~ 185 (211)
T COG2197 159 LLAEGLSNKEIAEELNLSEKTVKTHVS 185 (211)
T ss_pred HHHCCCCHHHHHHHHCCCHhHHHHHHH
Confidence 456799999999999999999988764
No 396
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=76.93 E-value=5.5 Score=23.23 Aligned_cols=25 Identities=12% Similarity=0.226 Sum_probs=21.2
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 93 DKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 93 ~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
...+|..++++.+|+|++++++..+
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~ 32 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLK 32 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHH
Confidence 5568999999999999999887653
No 397
>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=76.89 E-value=5.2 Score=30.42 Aligned_cols=30 Identities=17% Similarity=0.202 Sum_probs=24.8
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 87 IVQARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
|..+...-++|+.+||+.+|+++++|++..
T Consensus 7 L~~L~~~~~~t~~eLA~~lgis~~tV~~~L 36 (203)
T TIGR02702 7 LSYLLKQGQATAAALAEALAISPQAVRRHL 36 (203)
T ss_pred HHHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence 445556677999999999999999998764
No 398
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=76.88 E-value=2 Score=30.57 Aligned_cols=25 Identities=4% Similarity=0.008 Sum_probs=22.4
Q ss_pred HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366 30 KVVNAARRAGADIETVRKSHAGTNK 54 (142)
Q Consensus 30 ~~~~~a~r~G~~v~t~kk~~~g~~~ 54 (142)
++-..|.+.|++.+|+.+|+.|...
T Consensus 20 tq~~lA~~~gvs~~~is~~E~g~~~ 44 (135)
T PRK09706 20 SQRSLAKAVKVSHVSISQWERDETE 44 (135)
T ss_pred CHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 5677899999999999999999875
No 399
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=76.86 E-value=2.7 Score=31.89 Aligned_cols=23 Identities=17% Similarity=0.203 Sum_probs=21.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHc
Q 032366 95 KLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 95 glTQ~eLA~~lgis~stIs~~E~ 117 (142)
|+|.+|+|+.+|+|+.||..+-.
T Consensus 177 g~s~~eIa~~l~iS~~Tv~~~~~ 199 (225)
T PRK10046 177 QHTAETVAQALTISRTTARRYLE 199 (225)
T ss_pred CcCHHHHHHHhCccHHHHHHHHH
Confidence 69999999999999999998863
No 400
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=76.71 E-value=4.8 Score=29.66 Aligned_cols=30 Identities=10% Similarity=0.112 Sum_probs=25.2
Q ss_pred HHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 88 VQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 88 k~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
-.++.-.|+|+.|+|+.+|||.+||.....
T Consensus 136 ~~l~~~~gls~~EIA~~l~i~~~tVks~l~ 165 (182)
T COG1595 136 FLLRYLEGLSYEEIAEILGISVGTVKSRLH 165 (182)
T ss_pred hhhHhhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 344566799999999999999999988764
No 401
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=76.63 E-value=6.5 Score=30.90 Aligned_cols=33 Identities=21% Similarity=0.189 Sum_probs=26.7
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
..+..+.+...+++.+||+.+|+|..||.+..+
T Consensus 8 ~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~ 40 (240)
T PRK10411 8 AIVDLLLNHTSLTTEALAEQLNVSKETIRRDLN 40 (240)
T ss_pred HHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHH
Confidence 345556677789999999999999999987654
No 402
>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=76.59 E-value=9.4 Score=27.33 Aligned_cols=63 Identities=19% Similarity=0.242 Sum_probs=36.2
Q ss_pred HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhC
Q 032366 33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLIN 106 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lg 106 (142)
+.|+++|+++.|++-|+. |-..|.... .-.-+.++.. ....-..|+.+ +..|+|..++.+.+.
T Consensus 5 e~a~~~gvs~~tLRyYE~~GLl~p~~r~-~~gyR~Y~~~---------~v~~l~~I~~l-r~~GfsL~eI~~ll~ 68 (131)
T cd04786 5 ELAKRSGMAASRIRFYEAEGLLSSVERS-ANGYRDYPPE---------TVWVLEIISSA-QQAGFSLDEIRQLLP 68 (131)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCCcC-CCCCeecCHH---------HHHHHHHHHHH-HHcCCCHHHHHHHHh
Confidence 478999999999999986 444421110 0111112211 11123334444 448999999888775
No 403
>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF. Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH
Probab=76.57 E-value=4.9 Score=33.05 Aligned_cols=34 Identities=15% Similarity=0.165 Sum_probs=29.5
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
...|.....+.+..+.+.|+.+|||++|+++..+
T Consensus 294 ~~~I~~aL~~~~gn~~~aA~~LGisr~tL~rklk 327 (329)
T TIGR02974 294 IELLQQALAEAQFNQRKAAELLGLTYHQLRGLLR 327 (329)
T ss_pred HHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence 4567788888999999999999999999988753
No 404
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=76.38 E-value=5.4 Score=31.77 Aligned_cols=24 Identities=25% Similarity=0.347 Sum_probs=19.6
Q ss_pred HHHHHHHHcCCChhHHHhhhcCCC
Q 032366 30 KVVNAARRAGADIETVRKSHAGTN 53 (142)
Q Consensus 30 ~~~~~a~r~G~~v~t~kk~~~g~~ 53 (142)
+--.-|+++|+++.|+.+..+|+.
T Consensus 8 Ti~dIA~~agVS~~TVSr~Ln~~~ 31 (342)
T PRK10014 8 TIHDVALAAGVSVSTVSLVLSGKG 31 (342)
T ss_pred cHHHHHHHhCCCHHHHHHHHCCCC
Confidence 445689999999999999987543
No 405
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=76.31 E-value=5.4 Score=29.48 Aligned_cols=33 Identities=9% Similarity=0.103 Sum_probs=26.5
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+.+-.++.-.|+|++|+|+.+|+|..+|...-.
T Consensus 144 r~v~~l~~~~g~s~~eIA~~lgis~~tv~~~l~ 176 (193)
T PRK11923 144 RTALTLREFDGLSYEDIASVMQCPVGTVRSRIF 176 (193)
T ss_pred hHHHhhHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 334455667899999999999999999987653
No 406
>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional
Probab=76.04 E-value=4.9 Score=33.77 Aligned_cols=34 Identities=9% Similarity=0.134 Sum_probs=28.9
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
...|.....+.+.++.+.|+.+|||++|+++..+
T Consensus 419 ~~~i~~al~~~~gn~~~aA~~LGisr~tL~rkl~ 452 (457)
T PRK11361 419 KRIIMEVLEQQEGNRTRTALMLGISRRALMYKLQ 452 (457)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4467778888889999999999999999988653
No 407
>PRK11050 manganese transport regulator MntR; Provisional
Probab=76.03 E-value=8 Score=28.22 Aligned_cols=34 Identities=9% Similarity=0.029 Sum_probs=25.7
Q ss_pred HHHHHHHHHH-hCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 83 LKKAIVQARN-DKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 83 ~g~~Lk~~R~-~~glTQ~eLA~~lgis~stIs~~E 116 (142)
+-..|..+.. .-++++.+||+.+++++++|+++.
T Consensus 38 ~l~~I~~~l~~~~~~t~~eLA~~l~is~stVsr~l 72 (152)
T PRK11050 38 YVELIADLIAEVGEARQVDIAARLGVSQPTVAKML 72 (152)
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHH
Confidence 3344544443 356899999999999999999876
No 408
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=75.96 E-value=6.8 Score=24.11 Aligned_cols=22 Identities=27% Similarity=0.356 Sum_probs=17.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 032366 96 LTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~ 117 (142)
+|..+||+.+|+|..++.++-+
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~ 23 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFK 23 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHH
Confidence 6778888888888888888775
No 409
>PRK09483 response regulator; Provisional
Probab=75.95 E-value=6.5 Score=28.73 Aligned_cols=44 Identities=23% Similarity=0.323 Sum_probs=30.8
Q ss_pred HhCCCCHHHHHHHhCCCHHHHHHHHcC---C-CCCCHHHHHHHHHHhC
Q 032366 92 NDKKLTQSQLAQLINEKPQVIQEYESG---K-AIPNQQILTKLERALG 135 (142)
Q Consensus 92 ~~~glTQ~eLA~~lgis~stIs~~E~G---~-~~p~~~~l~kLa~~Lg 135 (142)
...|+|.+++|+.+++|.+||..+-+. + ...+...+..+|.-.|
T Consensus 160 ~~~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~v~~~~~l~~~a~~~~ 207 (217)
T PRK09483 160 ITKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDVELTHLAIRHG 207 (217)
T ss_pred HHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHcC
Confidence 468999999999999999999887642 1 2234444555554444
No 410
>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=75.93 E-value=13 Score=26.79 Aligned_cols=62 Identities=19% Similarity=0.232 Sum_probs=37.2
Q ss_pred HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhC
Q 032366 33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLIN 106 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lg 106 (142)
..|+..|+++.|++-|+. |-.+|.... ..-+.++.+ ....-..|+.+| ..|+|..++.+.+.
T Consensus 5 e~a~~~gvs~~TLR~Ye~~GLl~p~r~~--~g~R~Y~~~---------~l~~l~~I~~lr-~~G~sL~eI~~~l~ 67 (134)
T cd04779 5 QLAHLAGVSKRTIDYYTNLGLLTPERSD--SNYRYYDET---------ALDRLQLIEHLK-GQRLSLAEIKDQLE 67 (134)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCccCC--CCCeeECHH---------HHHHHHHHHHHH-HCCCCHHHHHHHHH
Confidence 478999999999999986 444432111 011111111 112344556664 68999999888764
No 411
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=75.82 E-value=5.4 Score=32.00 Aligned_cols=20 Identities=30% Similarity=0.513 Sum_probs=17.6
Q ss_pred HHHHHcCCChhHHHhhhcCC
Q 032366 33 NAARRAGADIETVRKSHAGT 52 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~g~ 52 (142)
.-|+++|++++|+.+..+|.
T Consensus 6 dIA~~aGVS~~TVSrvLn~~ 25 (346)
T PRK10401 6 DVARQAGVSVATVSRVLNNS 25 (346)
T ss_pred HHHHHhCCCHHHHHHHHCCC
Confidence 57999999999999998764
No 412
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=75.75 E-value=6.4 Score=28.55 Aligned_cols=30 Identities=13% Similarity=0.134 Sum_probs=24.8
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 87 IVQARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
+-.++--.|+|.+|+|+.+|+|.++|....
T Consensus 126 v~~L~~~eg~s~~EIA~~l~is~~tV~~~l 155 (168)
T PRK12525 126 AFLMSQLEGLTYVEIGERLGVSLSRIHQYM 155 (168)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 334456679999999999999999998764
No 413
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=75.70 E-value=6.3 Score=29.06 Aligned_cols=32 Identities=16% Similarity=0.249 Sum_probs=25.5
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
+.+-.++--.|+|.+|+|+.+|+|.++|....
T Consensus 145 r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l 176 (189)
T PRK09648 145 REILILRVVVGLSAEETAEAVGSTPGAVRVAQ 176 (189)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 33444455579999999999999999998765
No 414
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=75.69 E-value=6.2 Score=29.15 Aligned_cols=31 Identities=3% Similarity=0.105 Sum_probs=25.5
Q ss_pred HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
.+-.++.-.|+|..++|+.+|+|.++|....
T Consensus 138 ~vl~l~~~~~~s~~eIA~~lgis~~tV~~~l 168 (189)
T PRK12515 138 EIIDLVYYHEKSVEEVGEIVGIPESTVKTRM 168 (189)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence 3344566689999999999999999997765
No 415
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=75.65 E-value=6.1 Score=31.24 Aligned_cols=30 Identities=10% Similarity=0.164 Sum_probs=24.9
Q ss_pred HHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 88 VQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 88 k~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
-.++-..|+|++++|+.+|+|.++|..+..
T Consensus 221 l~l~~~~~~s~~eIA~~lgis~~tV~~~~~ 250 (268)
T PRK06288 221 LILYYYEDLTLKEIGKVLGVTESRISQLHT 250 (268)
T ss_pred HHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 334556799999999999999999998763
No 416
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=75.55 E-value=6.1 Score=29.25 Aligned_cols=32 Identities=9% Similarity=-0.015 Sum_probs=25.7
Q ss_pred HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.+-.++.-.|+|.+|+|+.+|+|.++|.....
T Consensus 138 ~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ 169 (191)
T PRK12520 138 RVFMMREWLELETEEICQELQITATNAWVLLY 169 (191)
T ss_pred HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34445556799999999999999999987653
No 417
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=75.54 E-value=6.1 Score=29.85 Aligned_cols=28 Identities=25% Similarity=0.197 Sum_probs=23.6
Q ss_pred HHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 89 QARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 89 ~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
.++.-.|+|.+++|+.+|+|.++|....
T Consensus 163 ~l~~~~g~s~~EIA~~lgis~~tV~~~l 190 (206)
T PRK12526 163 KGVYFQELSQEQLAQQLNVPLGTVKSRL 190 (206)
T ss_pred HHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 3455679999999999999999997764
No 418
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=75.47 E-value=7 Score=27.73 Aligned_cols=32 Identities=16% Similarity=0.067 Sum_probs=24.7
Q ss_pred HHHHHHHHh-CCCCHHHHHHHhCCCHHHHHHHH
Q 032366 85 KAIVQARND-KKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 85 ~~Lk~~R~~-~glTQ~eLA~~lgis~stIs~~E 116 (142)
..|..+... -++||.+||+.+++++++|++..
T Consensus 35 ~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v 67 (144)
T PRK03573 35 VTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTL 67 (144)
T ss_pred HHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHH
Confidence 345555443 46899999999999999998764
No 419
>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=75.45 E-value=15 Score=25.98 Aligned_cols=65 Identities=17% Similarity=0.194 Sum_probs=35.9
Q ss_pred HHHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCC
Q 032366 32 VNAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINE 107 (142)
Q Consensus 32 ~~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgi 107 (142)
-+.|+++|+++.|++-|+. |-..|.... .-.-+-++.++ -.--..|+.+| ..|++..++...+..
T Consensus 7 ~elA~~~gvs~~tlR~Ye~~GLL~p~~r~-~~gyR~Y~~~~---------l~rL~~I~~lr-~~G~~L~eI~~ll~~ 72 (120)
T TIGR02054 7 SRLAEDAGVSVHVVRDYLLRGLLHPVRRT-TSGYGIFDDAS---------LQRLRFVRAAF-EAGIGLGELARLCRA 72 (120)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCCccC-CCCCeeCCHHH---------HHHHHHHHHHH-HcCCCHHHHHHHHHh
Confidence 3579999999999999997 333321110 01111111110 01222333333 489999999887653
No 420
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=75.42 E-value=6.1 Score=29.41 Aligned_cols=30 Identities=13% Similarity=0.011 Sum_probs=25.0
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 87 IVQARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
+-.++.-.|+|.+|+|+.+|+|.++|....
T Consensus 150 vl~l~~~~~~s~~EIA~~Lgis~~tVk~~l 179 (194)
T PRK09646 150 SVTLAYYGGLTYREVAERLAVPLGTVKTRM 179 (194)
T ss_pred HHHHHHHcCCCHHHHHHHhCCChHhHHHHH
Confidence 334556689999999999999999998775
No 421
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=75.24 E-value=4.8 Score=31.02 Aligned_cols=26 Identities=12% Similarity=0.064 Sum_probs=23.0
Q ss_pred HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 92 NDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 92 ~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
...|+|.+|+|+.+++|++||..+-+
T Consensus 145 LAqGkTnKEIAe~L~IS~rTVkth~s 170 (198)
T PRK15201 145 IASGYHLSETAALLSLSEEQTKSLRR 170 (198)
T ss_pred HHCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 35699999999999999999988764
No 422
>PF06892 Phage_CP76: Phage regulatory protein CII (CP76); InterPro: IPR009679 This entry is represented by Bacteriophage 186, CII. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage regulatory protein CII (CP76) sequences which are thought to be DNA binding proteins which are involved in the establishment of lysogeny [].
Probab=75.15 E-value=17 Score=27.06 Aligned_cols=53 Identities=15% Similarity=0.189 Sum_probs=40.3
Q ss_pred HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC--CCCHHHHHHHHHHhC
Q 032366 81 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA--IPNQQILTKLERALG 135 (142)
Q Consensus 81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~--~p~~~~l~kLa~~Lg 135 (142)
+.|-+.++......+ .++||..+|++++++.+-.|... .++...+..|.++-|
T Consensus 8 ~~~~~Ac~~fa~~h~--~~~lA~~lGm~~~~LrNKLNP~q~H~Lt~~el~~i~~~Tg 62 (162)
T PF06892_consen 8 PHFDEACRAFAKNHN--MAALAERLGMNPQTLRNKLNPEQPHKLTVDELIAITDATG 62 (162)
T ss_pred HHHHHHHHHHHHhcC--HHHHHHHhCCCHHHHHHHcCCCCCCCCCHHHHHHHHHHhC
Confidence 346677777777776 57899999999999999998653 346777777766654
No 423
>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=75.10 E-value=19 Score=25.36 Aligned_cols=63 Identities=17% Similarity=0.203 Sum_probs=36.2
Q ss_pred HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhC
Q 032366 33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLIN 106 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lg 106 (142)
+.|++.|+++.|++-|+. |-..|.... .-.-+.++.++ ...-..|+.+| ..|+|.+++.+.+.
T Consensus 5 e~a~~~gvs~~tlRyYe~~GLl~p~~r~-~~gyR~Y~~~~---------l~~l~~I~~lr-~~G~sL~eI~~~l~ 68 (127)
T TIGR02044 5 QVAKLTGLSSKMIRYYEEKGLIPPPLRS-EGGYRTYTQQH---------LDELRLISRAR-QVGFSLEECKELLN 68 (127)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCCcC-CCCCeecCHHH---------HHHHHHHHHHH-HCCCCHHHHHHHHH
Confidence 478999999999999997 333321110 11112222111 11223344444 68999999988775
No 424
>PRK10365 transcriptional regulatory protein ZraR; Provisional
Probab=75.09 E-value=5.9 Score=33.08 Aligned_cols=33 Identities=12% Similarity=0.104 Sum_probs=28.3
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
...|.+...+.+..+.+.|+.+|||++|+++-.
T Consensus 407 ~~~i~~~l~~~~gn~~~aa~~Lgisr~tl~rk~ 439 (441)
T PRK10365 407 KEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439 (441)
T ss_pred HHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHh
Confidence 345778888889999999999999999998754
No 425
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=75.08 E-value=4.6 Score=25.43 Aligned_cols=25 Identities=12% Similarity=0.121 Sum_probs=20.0
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 93 DKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 93 ~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
...+|-.|+|+.+|+|..++..|..
T Consensus 13 ~~p~~T~eiA~~~gls~~~aR~yL~ 37 (62)
T PF04703_consen 13 NGPLKTREIADALGLSIYQARYYLE 37 (62)
T ss_dssp TS-EEHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 5779999999999999998887753
No 426
>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=75.06 E-value=16 Score=25.89 Aligned_cols=63 Identities=19% Similarity=0.297 Sum_probs=36.7
Q ss_pred HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhC
Q 032366 33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLIN 106 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lg 106 (142)
+.|++.|+++.|++-|+. |-..|.... .-.-+.++.++ ...-..|+.+| ..|+|..++.+.+.
T Consensus 6 e~a~~~gvs~~tlR~Ye~~GLl~p~~r~-~~gyR~Y~~~~---------l~~l~~I~~lr-~~G~sl~eI~~~l~ 69 (131)
T TIGR02043 6 ELAKLCGVTSDTLRFYEKNGLIKPAGRT-DSGYRLYTDED---------QKRLRFILKAK-ELGFTLDEIKELLS 69 (131)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCCcC-CCCceecCHHH---------HHHHHHHHHHH-HcCCCHHHHHHHHH
Confidence 478999999999999997 333321110 11111222111 11233455554 58999999988775
No 427
>PRK15115 response regulator GlrR; Provisional
Probab=74.99 E-value=4.9 Score=33.73 Aligned_cols=33 Identities=9% Similarity=-0.014 Sum_probs=28.7
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
..|.+...+.+..+.+.|+.+|||++|+++-.+
T Consensus 401 ~~i~~al~~~~gn~~~aA~~Lgisr~tL~rkl~ 433 (444)
T PRK15115 401 NYLRKLLQITKGNVTHAARMAGRNRTEFYKLLS 433 (444)
T ss_pred HHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence 457777888889999999999999999988765
No 428
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=74.91 E-value=6.5 Score=28.68 Aligned_cols=28 Identities=11% Similarity=0.093 Sum_probs=23.5
Q ss_pred HHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 89 QARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 89 ~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
.++--.|+|.+++|+.+|+|..+|....
T Consensus 139 ~l~~~~g~s~~eIA~~lgis~~tV~~~l 166 (179)
T PRK12514 139 RRAYLEGLSYKELAERHDVPLNTMRTWL 166 (179)
T ss_pred HHHHHcCCCHHHHHHHHCCChHHHHHHH
Confidence 3344579999999999999999998765
No 429
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=74.85 E-value=6.1 Score=28.83 Aligned_cols=29 Identities=3% Similarity=0.108 Sum_probs=24.1
Q ss_pred HHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 89 QARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 89 ~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.++.-.|++.+++|+.+|+|.++|.....
T Consensus 146 ~l~~~~~~s~~eIA~~lgis~~~v~~~l~ 174 (187)
T PRK09641 146 VLKYIEDLSLKEISEILDLPVGTVKTRIH 174 (187)
T ss_pred hhHHhhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34455799999999999999999988753
No 430
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=74.81 E-value=5.3 Score=29.18 Aligned_cols=57 Identities=16% Similarity=0.165 Sum_probs=39.9
Q ss_pred HHHHHHHHHHhCC--CCHHHHHHHhCCCHHHHHHHHc-CCCCC-CHHHHHHHHHHhCCCCC
Q 032366 83 LKKAIVQARNDKK--LTQSQLAQLINEKPQVIQEYES-GKAIP-NQQILTKLERALGVKLR 139 (142)
Q Consensus 83 ~g~~Lk~~R~~~g--lTQ~eLA~~lgis~stIs~~E~-G~~~p-~~~~l~kLa~~Lgvsl~ 139 (142)
|...-..+|+.-+ .|..++++.+|||...|.+|.+ |+-.. ....+.--|+.-|.+++
T Consensus 32 f~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~IreGRL~~~~~~nl~~~CE~CG~~I~ 92 (137)
T TIGR03826 32 FEKVYKFLRKHENRQATVSEIVEETGVSEKLILKFIREGRLQLKHFPNLGYPCERCGTSIR 92 (137)
T ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCCeeccCCCCCcCcccccCCcCC
Confidence 4444456677777 8999999999999999999997 44322 23345555666665554
No 431
>PRK03341 arginine repressor; Provisional
Probab=74.77 E-value=6.1 Score=29.74 Aligned_cols=35 Identities=17% Similarity=0.171 Sum_probs=25.9
Q ss_pred HHHHHHHHHHhC-CCCHHHHHHHh-----CCCHHHHHHHHc
Q 032366 83 LKKAIVQARNDK-KLTQSQLAQLI-----NEKPQVIQEYES 117 (142)
Q Consensus 83 ~g~~Lk~~R~~~-glTQ~eLA~~l-----gis~stIs~~E~ 117 (142)
-.+.|+++..+. =.||.||++.+ ++|++||++-.+
T Consensus 16 R~~~I~~li~~~~i~tQ~eL~~~L~~~Gi~vTQaTiSRDl~ 56 (168)
T PRK03341 16 RQARIVAILSRQSVRSQAELAALLADEGIEVTQATLSRDLD 56 (168)
T ss_pred HHHHHHHHHHHCCCccHHHHHHHHHHcCCcccHHHHHHHHH
Confidence 344455554444 45899999999 999999999653
No 432
>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=74.77 E-value=17 Score=25.56 Aligned_cols=64 Identities=22% Similarity=0.278 Sum_probs=36.7
Q ss_pred HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCC
Q 032366 33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINE 107 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgi 107 (142)
+.|.+.|+++.|++-|+. |-..+.... .-.-+.++.++ -..-..|+.+ ...|+|..++.+.+..
T Consensus 5 e~a~~~gvs~~tlR~Ye~~Gll~~~~r~-~~g~R~Y~~~~---------l~~l~~I~~l-r~~G~sL~eI~~~l~~ 69 (126)
T cd04785 5 ELARRTGVNVETIRYYESIGLLPEPART-AGGYRLYGAAH---------VERLRFIRRA-RDLGFSLEEIRALLAL 69 (126)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCCcC-CCCccccCHHH---------HHHHHHHHHH-HHCCCCHHHHHHHHhh
Confidence 478899999999999997 443321110 01111122111 1123334444 3689999999887754
No 433
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=74.73 E-value=6.7 Score=28.81 Aligned_cols=28 Identities=14% Similarity=0.004 Sum_probs=24.1
Q ss_pred HHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 89 QARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 89 ~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
.++.-.|+|.+|+|+.+|+|.++|....
T Consensus 139 ~l~~~~g~s~~EIA~~l~is~~tV~~~l 166 (181)
T PRK12536 139 VHVKLEGLSVAETAQLTGLSESAVKVGI 166 (181)
T ss_pred HHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 3455689999999999999999998875
No 434
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=74.73 E-value=6.9 Score=28.69 Aligned_cols=33 Identities=15% Similarity=0.211 Sum_probs=26.2
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+.+-.++.-.|+|.+|+|+.+|+|.++|.....
T Consensus 123 r~i~~l~~~e~~s~~EIA~~lgis~~tV~~~l~ 155 (179)
T PRK12543 123 RQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIH 155 (179)
T ss_pred HHHHHHHHHccCCHHHHHHHHCCCHHHHHHHHH
Confidence 334455666899999999999999999887653
No 435
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=74.68 E-value=9.5 Score=24.05 Aligned_cols=36 Identities=17% Similarity=0.169 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHhCCC--CHHHHHHHhCCC-HHHHHHHH
Q 032366 81 SELKKAIVQARNDKKL--TQSQLAQLINEK-PQVIQEYE 116 (142)
Q Consensus 81 ~~~g~~Lk~~R~~~gl--TQ~eLA~~lgis-~stIs~~E 116 (142)
..+-..|.+...+.|+ |..|||+.+|++ .++|.++.
T Consensus 9 ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L 47 (65)
T PF01726_consen 9 KEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHL 47 (65)
T ss_dssp HHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHH
Confidence 3466677777777777 678999999996 88887654
No 436
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=74.60 E-value=2.3 Score=29.41 Aligned_cols=30 Identities=10% Similarity=0.030 Sum_probs=25.1
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 032366 91 RNDKKLTQSQLAQLINEKPQVIQEYESGKA 120 (142)
Q Consensus 91 R~~~glTQ~eLA~~lgis~stIs~~E~G~~ 120 (142)
+--.++|..++|+.+||+++++.++-.++.
T Consensus 28 ~G~~~~t~~~Ia~~agvs~~~~Y~~f~~K~ 57 (201)
T COG1309 28 KGYAATTVDEIAKAAGVSKGTLYRHFPSKE 57 (201)
T ss_pred cCcCCCCHHHHHHHhCCCcchhHHHcCCHH
Confidence 344567899999999999999999987764
No 437
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=74.60 E-value=5.7 Score=24.21 Aligned_cols=31 Identities=19% Similarity=0.220 Sum_probs=21.8
Q ss_pred HHHHH-HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 87 IVQAR-NDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 87 Lk~~R-~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
|..+. ....+++.+||+.++++++++++..+
T Consensus 9 L~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~ 40 (68)
T PF13463_consen 9 LRALAHSDGPMTQSDLAERLGISKSTVSRIIK 40 (68)
T ss_dssp HHHHT--TS-BEHHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHccCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 44444 67789999999999999999998753
No 438
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=74.38 E-value=6.6 Score=29.14 Aligned_cols=31 Identities=6% Similarity=-0.022 Sum_probs=25.3
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 87 IVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+-.++.-.|+|..|+|+.+|+|.++|.....
T Consensus 119 v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~ 149 (182)
T PRK12540 119 ALILVGASGFSYEDAAAICGCAVGTIKSRVN 149 (182)
T ss_pred HhhHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3344556899999999999999999988753
No 439
>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=74.32 E-value=3.1 Score=28.86 Aligned_cols=44 Identities=18% Similarity=0.279 Sum_probs=26.8
Q ss_pred HHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 032366 88 VQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALG 135 (142)
Q Consensus 88 k~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lg 135 (142)
-.+--.-++|-.|+|+.+|||+++|+...+- ....+..+.+.||
T Consensus 26 l~lyy~eDlSlsEIAe~~~iSRqaV~d~ikr----~~~~L~~yE~kL~ 69 (101)
T PF04297_consen 26 LELYYEEDLSLSEIAEELGISRQAVYDSIKR----AEKKLEEYEEKLG 69 (101)
T ss_dssp HHHHCTS---HHHHHHHCTS-HHHHHHHHHH----HHHHHHHHHHHH-
T ss_pred HHHHHccCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHHHHh
Confidence 3344556899999999999999999988753 2244444444444
No 440
>TIGR01818 ntrC nitrogen regulation protein NR(I). This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc.
Probab=74.30 E-value=5.9 Score=33.38 Aligned_cols=32 Identities=9% Similarity=0.030 Sum_probs=27.8
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
..|.......+..+.+.|+.+|||++|+++..
T Consensus 429 ~~i~~al~~~~gn~~~aA~~Lgisr~tL~rkl 460 (463)
T TIGR01818 429 PLLEAALQHTRGHKQEAAALLGWGRNTLTRKL 460 (463)
T ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 35777888889999999999999999998764
No 441
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=74.24 E-value=11 Score=22.44 Aligned_cols=23 Identities=22% Similarity=0.198 Sum_probs=20.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHc
Q 032366 95 KLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 95 glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+++..++++.+|++.++++++.+
T Consensus 20 ~~~~~ei~~~~~i~~~~i~~~l~ 42 (78)
T cd00090 20 PLTVSELAERLGLSQSTVSRHLK 42 (78)
T ss_pred CcCHHHHHHHHCcCHhHHHHHHH
Confidence 49999999999999999877653
No 442
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=74.16 E-value=6.7 Score=31.03 Aligned_cols=21 Identities=29% Similarity=0.245 Sum_probs=18.2
Q ss_pred HHHHHcCCChhHHHhhhcCCC
Q 032366 33 NAARRAGADIETVRKSHAGTN 53 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~g~~ 53 (142)
.-|+++|++++|+.+..+|..
T Consensus 5 dIA~~aGVS~~TVSrvLn~~~ 25 (328)
T PRK11303 5 EIARLAGVSRTTASYVINGKA 25 (328)
T ss_pred HHHHHhCCCHHHHHHHHcCCC
Confidence 469999999999999987754
No 443
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=74.12 E-value=6.5 Score=29.26 Aligned_cols=29 Identities=17% Similarity=0.249 Sum_probs=23.9
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHH
Q 032366 87 IVQARNDKKLTQSQLAQLINEKPQVIQEY 115 (142)
Q Consensus 87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~ 115 (142)
+-.++--.|+|.+|+|+.+|+|.++|...
T Consensus 149 v~~l~~~eg~s~~EIA~~lgis~~tVk~r 177 (194)
T PRK12531 149 VLQAVYLEELPHQQVAEMFDIPLGTVKSR 177 (194)
T ss_pred HHHHHHHcCCCHHHHHHHhCcCHHHHHHH
Confidence 44445668999999999999999999654
No 444
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=74.06 E-value=18 Score=24.23 Aligned_cols=26 Identities=12% Similarity=-0.042 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 032366 94 KKLTQSQLAQLINEKPQVIQEYESGK 119 (142)
Q Consensus 94 ~glTQ~eLA~~lgis~stIs~~E~G~ 119 (142)
..++..+||+.+|+|+.++.+.-+-.
T Consensus 20 ~~~~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 20 QPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 35899999999999999999988643
No 445
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=74.03 E-value=9 Score=29.10 Aligned_cols=33 Identities=9% Similarity=0.121 Sum_probs=25.5
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
..|..+...-++++.++|+.+|+|++++++..+
T Consensus 147 ~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~ 179 (203)
T TIGR01884 147 KVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLR 179 (203)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 444555444578999999999999999987653
No 446
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=73.92 E-value=8.9 Score=29.22 Aligned_cols=37 Identities=11% Similarity=-0.000 Sum_probs=28.3
Q ss_pred chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHH
Q 032366 79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEY 115 (142)
Q Consensus 79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~ 115 (142)
+...-...|..+....++||.+||+.++++++|++++
T Consensus 43 Lt~~q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~ 79 (185)
T PRK13777 43 LNINEHHILWIAYHLKGASISEIAKFGVMHVSTAFNF 79 (185)
T ss_pred CCHHHHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHH
Confidence 3333445566677778999999999999999888774
No 447
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=73.82 E-value=6.8 Score=29.01 Aligned_cols=31 Identities=10% Similarity=0.058 Sum_probs=25.2
Q ss_pred HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
.+-.++.-.|++..|+|..+|+|.++|....
T Consensus 113 ~i~~l~~~~g~~~~EIA~~lgis~~tV~~~l 143 (181)
T PRK09637 113 EALRLTELEGLSQKEIAEKLGLSLSGAKSRV 143 (181)
T ss_pred HHHHHHHhcCCCHHHHHHHhCCCHHHHHHHH
Confidence 3444556689999999999999999997765
No 448
>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=73.81 E-value=9.9 Score=25.93 Aligned_cols=25 Identities=20% Similarity=0.175 Sum_probs=21.4
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 93 DKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 93 ~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
..++|+.+||+.+++++++|++..+
T Consensus 41 ~~~~t~~eL~~~l~~~~stvs~~i~ 65 (109)
T TIGR01889 41 EGKLTLKEIIKEILIKQSALVKIIK 65 (109)
T ss_pred CCcCcHHHHHHHHCCCHHHHHHHHH
Confidence 3569999999999999999987653
No 449
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=73.76 E-value=4 Score=27.01 Aligned_cols=21 Identities=10% Similarity=0.094 Sum_probs=19.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHH
Q 032366 96 LTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E 116 (142)
.|..+||+.+|+|+.+|.+..
T Consensus 20 ~SGe~La~~LgiSRtaVwK~I 40 (79)
T COG1654 20 VSGEKLAEELGISRTAVWKHI 40 (79)
T ss_pred ccHHHHHHHHCccHHHHHHHH
Confidence 899999999999999998754
No 450
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=73.61 E-value=4.9 Score=30.83 Aligned_cols=26 Identities=12% Similarity=0.185 Sum_probs=22.7
Q ss_pred HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 92 NDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 92 ~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
...|+|.+++|+.+++|..||..+-.
T Consensus 146 l~~G~snkeIA~~L~iS~~TV~~h~~ 171 (207)
T PRK11475 146 MSRGYSMPQIAEQLERNIKTIRAHKF 171 (207)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34699999999999999999988764
No 451
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=73.57 E-value=6.5 Score=29.41 Aligned_cols=33 Identities=3% Similarity=0.055 Sum_probs=26.5
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+.+-.++.-.|+|..|+|+.+|+|..+|.....
T Consensus 119 r~v~~L~~~~g~s~~EIA~~LgiS~~tVk~~l~ 151 (188)
T PRK12546 119 REALILVGASGFSYEEAAEMCGVAVGTVKSRAN 151 (188)
T ss_pred hHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 344455666899999999999999999987653
No 452
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=73.54 E-value=7.1 Score=31.12 Aligned_cols=20 Identities=35% Similarity=0.421 Sum_probs=17.5
Q ss_pred HHHHHcCCChhHHHhhhcCC
Q 032366 33 NAARRAGADIETVRKSHAGT 52 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~g~ 52 (142)
.-|+++|++++|+++..+|.
T Consensus 6 dIA~~agVS~~TVSrvLn~~ 25 (341)
T PRK10703 6 DVAKRAGVSTTTVSHVINKT 25 (341)
T ss_pred HHHHHhCCCHHHHHHHHcCC
Confidence 57899999999999998764
No 453
>PRK09480 slmA division inhibitor protein; Provisional
Probab=73.47 E-value=3.2 Score=30.32 Aligned_cols=27 Identities=19% Similarity=0.233 Sum_probs=24.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 032366 94 KKLTQSQLAQLINEKPQVIQEYESGKA 120 (142)
Q Consensus 94 ~glTQ~eLA~~lgis~stIs~~E~G~~ 120 (142)
.+.|..++|+.+|||++++..+-.++.
T Consensus 29 ~~~ti~~Ia~~agvs~gt~Y~~F~~K~ 55 (194)
T PRK09480 29 ERITTAKLAARVGVSEAALYRHFPSKA 55 (194)
T ss_pred CccCHHHHHHHhCCCHhHHHHHCCCHH
Confidence 589999999999999999999988765
No 454
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=73.43 E-value=6.2 Score=30.40 Aligned_cols=31 Identities=6% Similarity=0.134 Sum_probs=24.9
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 87 IVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+-.++.-.|+|.+|+|+.+|||.++|.....
T Consensus 142 v~~L~y~eg~s~~EIAe~LgiS~~tVk~~L~ 172 (216)
T PRK12533 142 VLVLRELEDMSYREIAAIADVPVGTVMSRLA 172 (216)
T ss_pred HhhhHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3334455799999999999999999987654
No 455
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=73.31 E-value=3.6 Score=32.45 Aligned_cols=37 Identities=11% Similarity=0.216 Sum_probs=27.6
Q ss_pred HHHHHHHH-HHhCCCCHHHHHHHhCCCHHHHHHHHcCC
Q 032366 83 LKKAIVQA-RNDKKLTQSQLAQLINEKPQVIQEYESGK 119 (142)
Q Consensus 83 ~g~~Lk~~-R~~~glTQ~eLA~~lgis~stIs~~E~G~ 119 (142)
+.+.|.+- -.-..+|..+||+++|+|++||.++.+--
T Consensus 21 Ia~yil~n~~~v~~~si~~lA~~~~vS~aTv~Rf~kkl 58 (284)
T PRK11302 21 VAEVILASPQTAIHSSIATLAKMANVSEPTVNRFCRSL 58 (284)
T ss_pred HHHHHHhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHHc
Confidence 44444333 23356899999999999999999999733
No 456
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=73.24 E-value=6.5 Score=28.66 Aligned_cols=29 Identities=3% Similarity=0.117 Sum_probs=24.4
Q ss_pred HHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 89 QARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 89 ~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.++.-.|+|.+|+|+.+|+|.++|.....
T Consensus 146 ~l~~~~g~s~~eIA~~lgis~~~v~~~l~ 174 (187)
T TIGR02948 146 VLKYMEDLSLKEISEILDLPVGTVKTRIH 174 (187)
T ss_pred hhHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 44556799999999999999999988753
No 457
>cd08804 Death_ank2 Death domain of Ankyrin-2. Death Domain (DD) of Ankyrin-2 (ANK-2) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with "Ankyrin-B syndrome", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other
Probab=73.15 E-value=12 Score=24.74 Aligned_cols=33 Identities=9% Similarity=0.131 Sum_probs=27.9
Q ss_pred HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 032366 86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESG 118 (142)
Q Consensus 86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G 118 (142)
+|..+....|..-++||+.+|+|...|.+++..
T Consensus 6 ~l~~ia~~LG~dWk~LAr~Lg~se~dI~~i~~~ 38 (84)
T cd08804 6 RLAVIADHLGFSWTELARELDFTEEQIHQIRIE 38 (84)
T ss_pred HHHHHHHHHhhhHHHHHHHcCCCHHHHHHHHHH
Confidence 456667777888889999999999999999876
No 458
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=73.10 E-value=19 Score=25.96 Aligned_cols=64 Identities=17% Similarity=0.156 Sum_probs=37.5
Q ss_pred HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCC
Q 032366 33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINE 107 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgi 107 (142)
+.|++.|+++.|++-|+. |-..|.... .-.-+.++.++ ...-..|+.+| ..|+|.+++.+.+..
T Consensus 6 e~a~~~gvs~~tlR~Ye~~GLl~p~~r~-~~gyR~Y~~~~---------l~~l~~I~~lr-~~G~sL~eI~~~l~~ 70 (140)
T PRK09514 6 ELAKLAEVTPDTLRFYEKQGLMDPEVRT-EGGYRLYTEQD---------LQRLRFIRRAK-QLGFTLEEIRELLSI 70 (140)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCcccC-CCCCeeeCHHH---------HHHHHHHHHHH-HcCCCHHHHHHHHHh
Confidence 578999999999999987 444421111 01112222211 11233444444 479999999988854
No 459
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 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.
Probab=72.94 E-value=7.7 Score=28.85 Aligned_cols=30 Identities=7% Similarity=0.037 Sum_probs=24.8
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 87 IVQARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
+-.++.-.|+|.+|+|+.+|+|.++|....
T Consensus 139 v~~l~~~~g~s~~EIA~~lgis~~tvk~rl 168 (188)
T TIGR02943 139 VFMMREVLGFESDEICQELEISTSNCHVLL 168 (188)
T ss_pred HHHHHHHhCCCHHHHHHHhCCCHHHHHHHH
Confidence 444556679999999999999999997764
No 460
>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=72.92 E-value=22 Score=24.75 Aligned_cols=64 Identities=14% Similarity=0.213 Sum_probs=38.1
Q ss_pred HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCCC
Q 032366 33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEK 108 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis 108 (142)
+.|++.|+++.|++-|+. |-..|... .+ +-+.++..+. ..-..|+.+ ...|+|.+++.+.++..
T Consensus 5 evA~~~gvs~~tlRyYe~~GLl~p~~~-~~-gyR~Y~~~~l---------~~l~~I~~l-r~~G~~L~eI~~~l~~~ 69 (120)
T cd04781 5 EVARQSGLPASTLRYYEEKGLIASIGR-RG-LRRQYDPQVL---------DRLALIALG-RAAGFSLDEIQAMLSHD 69 (120)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCcC-CC-CceecCHHHH---------HHHHHHHHH-HHcCCCHHHHHHHHhcc
Confidence 478999999999999997 44443211 11 2222222111 112234444 44799999999988754
No 461
>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=72.89 E-value=19 Score=26.06 Aligned_cols=62 Identities=15% Similarity=0.244 Sum_probs=36.8
Q ss_pred HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhC
Q 032366 33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLIN 106 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lg 106 (142)
+.|++.|+++.|++-|+. |-..+... .+ +-+.++.+ ....-..|+.+ ...|+|.+++...+.
T Consensus 6 evA~~~Gvs~~tLRyYE~~GLl~~~r~-~~-g~R~Y~~~---------di~~l~~I~~l-r~~G~sL~eI~~~l~ 68 (142)
T TIGR01950 6 ELAKRSGVAVSALHFYESKGLITSIRN-SG-NQRRYKRD---------VLRRVAVIKAA-QRVGIPLATIGEALA 68 (142)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCccC-CC-CCEEECHH---------HHHHHHHHHHH-HHcCCCHHHHHHHHH
Confidence 478999999999999997 44442111 11 11222211 11123345555 447999999888774
No 462
>PHA02535 P terminase ATPase subunit; Provisional
Probab=72.88 E-value=7.2 Score=34.92 Aligned_cols=38 Identities=13% Similarity=0.177 Sum_probs=29.8
Q ss_pred hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 032366 80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESG 118 (142)
Q Consensus 80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G 118 (142)
..++......+-.+ |+|..++|+.+||+++||.+|-.-
T Consensus 4 t~EfK~~Av~Ly~~-G~sv~eIA~~LGv~~~Tl~~W~kr 41 (581)
T PHA02535 4 DDDVRRAAKFLYWQ-GWTVAEIAEELGLKSRTIYSWKER 41 (581)
T ss_pred CHHHHHHHHHHHHc-CCCHHHHHHHhCCChhHHHHHhcc
Confidence 34455555555555 999999999999999999999863
No 463
>PRK15435 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional
Probab=72.86 E-value=19 Score=30.11 Aligned_cols=37 Identities=14% Similarity=0.153 Sum_probs=28.5
Q ss_pred HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC
Q 032366 83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK 119 (142)
Q Consensus 83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~ 119 (142)
+.+.+..+.....+|..+||+.+|+|+.++.++-+..
T Consensus 87 i~~a~~~I~~~~~lsl~eLA~~lG~S~~~L~R~Fkk~ 123 (353)
T PRK15435 87 ITHACRLLEQETPVTLEALADQVAMSPFHLHRLFKAT 123 (353)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 4444444444567999999999999999999998754
No 464
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=72.86 E-value=7.5 Score=28.94 Aligned_cols=28 Identities=4% Similarity=0.049 Sum_probs=24.0
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 90 ARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 90 ~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
++.-.|++.+|+|+.+|+|.++|.....
T Consensus 139 l~~~~g~s~~EIA~~lgis~~tV~~~l~ 166 (188)
T PRK12517 139 LQVIGGFSGEEIAEILDLNKNTVMTRLF 166 (188)
T ss_pred HHHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4556799999999999999999987653
No 465
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=72.85 E-value=7.8 Score=28.39 Aligned_cols=30 Identities=10% Similarity=0.037 Sum_probs=24.5
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 87 IVQARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
|-.++--.|+|..|+|+.+|+|..+|....
T Consensus 139 v~~l~~~~g~s~~eIA~~l~is~~tV~~~l 168 (184)
T PRK12512 139 VVQSISVEGASIKETAAKLSMSEGAVRVAL 168 (184)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 334455579999999999999999998764
No 466
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=72.83 E-value=10 Score=23.31 Aligned_cols=26 Identities=12% Similarity=0.110 Sum_probs=22.2
Q ss_pred HhCCCCHHHHHHHhCC-CHHHHHHHHc
Q 032366 92 NDKKLTQSQLAQLINE-KPQVIQEYES 117 (142)
Q Consensus 92 ~~~glTQ~eLA~~lgi-s~stIs~~E~ 117 (142)
....++..++|..+|+ |++++++.-+
T Consensus 47 ~~~~~~~~~ia~~~g~~s~~~f~r~Fk 73 (84)
T smart00342 47 RDTDLSVTEIALRVGFSSQSYFSRAFK 73 (84)
T ss_pred HcCCCCHHHHHHHhCCCChHHHHHHHH
Confidence 3447999999999999 9999988764
No 467
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=72.71 E-value=6.5 Score=28.66 Aligned_cols=31 Identities=16% Similarity=0.173 Sum_probs=25.3
Q ss_pred HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
.+-.++.-.|+|.+|+|+.+|+|.++|....
T Consensus 126 ~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l 156 (172)
T PRK09651 126 EAFLLSQLDGLTYSEIAHKLGVSVSSVKKYV 156 (172)
T ss_pred HHhhhhhccCCCHHHHHHHhCCCHHHHHHHH
Confidence 3334556679999999999999999998765
No 468
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=72.63 E-value=8 Score=28.64 Aligned_cols=29 Identities=14% Similarity=-0.011 Sum_probs=23.9
Q ss_pred HHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 89 QARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 89 ~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.++--.|+|.+|+|+.+|+|.++|.....
T Consensus 141 ~l~~~~g~s~~EIAe~lgis~~~V~~~l~ 169 (189)
T PRK06811 141 IRRYLLGEKIEEIAKKLGLTRSAIDNRLS 169 (189)
T ss_pred HHHHHccCCHHHHHHHHCCCHHHHHHHHH
Confidence 33445799999999999999999988653
No 469
>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=72.61 E-value=5 Score=31.35 Aligned_cols=23 Identities=13% Similarity=0.244 Sum_probs=21.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Q 032366 96 LTQSQLAQLINEKPQVIQEYESG 118 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~G 118 (142)
++..|||+.+|+|.++|..||+-
T Consensus 2 y~i~elA~~~Gvs~~tIR~Ye~~ 24 (219)
T cd04778 2 YRIDDLARAAGTTVRNVRAYQDR 24 (219)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 67899999999999999999973
No 470
>TIGR03454 partition_RepB plasmid partitioning protein RepB. Members of this family are the RepB protein involved in replicon partitioning. RepB is found, in general, as part of a repABC operon in plasmids and small chromosomes, separate from the main chromosome, in various bacteria. This model describes a rather narrow clade of proteins; it should be noted that additional homologs scoring below the trusted cutoff have very similar functions, although they may be named differently.
Probab=72.40 E-value=8.1 Score=32.08 Aligned_cols=40 Identities=5% Similarity=0.113 Sum_probs=29.6
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH
Q 032366 91 RNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKL 130 (142)
Q Consensus 91 R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kL 130 (142)
..+.|+++.++|+.+|+++++|+++.+=-...+.+++..|
T Consensus 173 L~~~G~~~~~ia~~Lg~~ks~vSr~lsl~~~lP~~li~~i 212 (325)
T TIGR03454 173 LEDRGFDRDTIMAALSVDKTELSRMISVARRIPEELIEAI 212 (325)
T ss_pred HHHcCCCHHHHHHHHCCCHHHHHHHHHHHHhCCHHHHHHh
Confidence 3568999999999999999999999873222234444444
No 471
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=72.25 E-value=7.7 Score=30.30 Aligned_cols=33 Identities=18% Similarity=0.301 Sum_probs=26.5
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+.+-.++--.|+|.+++|+.+|+|..+|.....
T Consensus 207 r~vl~l~~~~~~s~~EIA~~lgis~~tV~~~~~ 239 (251)
T PRK07670 207 QLVISLFYKEELTLTEIGQVLNLSTSRISQIHS 239 (251)
T ss_pred HHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 334445566799999999999999999988763
No 472
>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR. At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR.
Probab=72.23 E-value=7 Score=34.46 Aligned_cols=34 Identities=9% Similarity=-0.078 Sum_probs=29.4
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.+.|.....+.+..+.+.|+.+|||++|+++..+
T Consensus 492 r~~I~~aL~~~~Gn~~~aA~~LGIsRtTL~Rklk 525 (526)
T TIGR02329 492 ALAVRAALERFGGDRDAAAKALGISRTTLWRRLK 525 (526)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 3457888888999999999999999999998753
No 473
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=72.20 E-value=7.8 Score=28.12 Aligned_cols=28 Identities=4% Similarity=0.014 Sum_probs=23.6
Q ss_pred HHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 89 QARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 89 ~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
.++--.|+|.+|+|+.+|+|..+|....
T Consensus 129 ~l~~~~~~s~~EIA~~lgis~~tV~~~l 156 (173)
T PRK12522 129 VLYYYEQYSYKEMSEILNIPIGTVKYRL 156 (173)
T ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 3455579999999999999999998764
No 474
>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=72.08 E-value=25 Score=24.83 Aligned_cols=64 Identities=19% Similarity=0.223 Sum_probs=36.5
Q ss_pred HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCC
Q 032366 33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINE 107 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgi 107 (142)
+.|++.|+++.|++-|+. |-..+.... .-.-+.++.+ ...--..|+.+ ...|+|..++.+.+..
T Consensus 5 e~a~~~gvs~~tlR~Ye~~GLl~~~~r~-~~gyR~Y~~~---------~l~~l~~I~~l-r~lG~sL~eI~~~l~~ 69 (127)
T TIGR02047 5 ELAQKTGVSVETIRFYEKQGLLPPPART-DNNYRVYTVG---------HVERLAFIRNC-RTLDMSLAEIRQLLRY 69 (127)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCCcC-CCCCCcCCHH---------HHHHHHHHHHH-HHcCCCHHHHHHHHHh
Confidence 478999999999999987 444321110 0111111111 11123334444 4589999999987753
No 475
>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator. Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).
Probab=72.02 E-value=6.4 Score=33.06 Aligned_cols=33 Identities=12% Similarity=0.098 Sum_probs=28.2
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
..|.....+.+..+.+.|+.+|||++|+++-.+
T Consensus 408 ~~i~~al~~~~gn~~~aA~~Lgisr~tl~rkl~ 440 (445)
T TIGR02915 408 EAVRKAIARVDGNIARAAELLGITRPTLYDLMK 440 (445)
T ss_pred HHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence 457777888899999999999999999987643
No 476
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=71.99 E-value=7.7 Score=28.91 Aligned_cols=32 Identities=9% Similarity=0.122 Sum_probs=25.9
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
+.+-.++.-.|+|.+|+|+.+|+|.++|..-.
T Consensus 140 r~i~~l~~~~g~s~~EIA~~lg~s~~tV~~rl 171 (192)
T PRK09643 140 RAALVAVDMQGYSVADAARMLGVAEGTVKSRC 171 (192)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence 44445667789999999999999999997654
No 477
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=71.97 E-value=7.8 Score=29.88 Aligned_cols=24 Identities=21% Similarity=0.279 Sum_probs=21.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 94 KKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 94 ~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.|+|.+++|+.+|+|.++|.+...
T Consensus 194 e~~S~~EIA~~lgis~~tV~~~~~ 217 (233)
T PRK05803 194 KEKTQREIAKALGISRSYVSRIEK 217 (233)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHH
Confidence 678999999999999999988864
No 478
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=71.95 E-value=5.4 Score=30.30 Aligned_cols=25 Identities=28% Similarity=0.347 Sum_probs=22.7
Q ss_pred HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366 30 KVVNAARRAGADIETVRKSHAGTNK 54 (142)
Q Consensus 30 ~~~~~a~r~G~~v~t~kk~~~g~~~ 54 (142)
++-..|+++|++-..+.+.|+|...
T Consensus 20 tQ~dLA~~aGVSQ~~IArlE~G~vd 44 (187)
T COG3620 20 TQKDLARRAGVSQPYIARLEAGKVD 44 (187)
T ss_pred CHHHHHHHcCccHHHHHHHhcCCCC
Confidence 4567999999999999999999987
No 479
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=71.94 E-value=20 Score=26.09 Aligned_cols=64 Identities=19% Similarity=0.228 Sum_probs=36.4
Q ss_pred HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCC
Q 032366 33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINE 107 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgi 107 (142)
+.|++.|+++.|+|=|+. |-..+..... -.-+-++.. .-..-..|+.+| ..|+|.+++.+.+..
T Consensus 12 evAk~~Gvs~~TLRyYE~~GLl~p~~r~~-~gyR~Y~~~---------~l~rl~~I~~lr-~~G~sL~eI~~ll~~ 76 (144)
T PRK13752 12 VFAKAAGVNVETIRFYQRKGLLPEPDKPY-GSIRRYGEA---------DVTRVRFVKSAQ-RLGFSLDEIAELLRL 76 (144)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCccCC-CCCeecCHH---------HHHHHHHHHHHH-HcCCCHHHHHHHHhc
Confidence 578999999999999996 4333211100 001111111 111223344444 689999999887753
No 480
>PF11268 DUF3071: Protein of unknown function (DUF3071); InterPro: IPR021421 Some members in this family of proteins are annotated as DNA-binding proteins however this cannot be confirmed. Currently no function is known.
Probab=71.93 E-value=5.4 Score=30.17 Aligned_cols=31 Identities=13% Similarity=0.176 Sum_probs=26.9
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 87 IVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
--+.|...|.|..|+|+..|++.+.|.+|+.
T Consensus 61 eIQarIRaGas~eeVA~~~G~~~~rV~rfa~ 91 (170)
T PF11268_consen 61 EIQARIRAGASAEEVAEEAGVPVERVRRFAG 91 (170)
T ss_pred HHHHHHHCCCCHHHHHHHhCCCHHHhhhccc
Confidence 3466778899999999999999999999873
No 481
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=71.91 E-value=6.6 Score=31.74 Aligned_cols=31 Identities=13% Similarity=0.266 Sum_probs=25.6
Q ss_pred HHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC
Q 032366 89 QARNDKKLTQSQLAQLINEKPQVIQEYESGK 119 (142)
Q Consensus 89 ~~R~~~glTQ~eLA~~lgis~stIs~~E~G~ 119 (142)
.-.-..||...++|+++|||+.||..|-+-.
T Consensus 13 kk~yl~gmk~~dIAeklGvspntiksWKrr~ 43 (279)
T COG5484 13 KKDYLKGMKLKDIAEKLGVSPNTIKSWKRRD 43 (279)
T ss_pred HHHHHhhccHHHHHHHhCCChHHHHHHHHhc
Confidence 3334467999999999999999999998743
No 482
>PHA00542 putative Cro-like protein
Probab=71.81 E-value=2.4 Score=27.82 Aligned_cols=25 Identities=16% Similarity=0.149 Sum_probs=22.0
Q ss_pred HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366 30 KVVNAARRAGADIETVRKSHAGTNK 54 (142)
Q Consensus 30 ~~~~~a~r~G~~v~t~kk~~~g~~~ 54 (142)
++-..|+..|++-.|+.+|+.|...
T Consensus 33 Tq~elA~~lgIs~~tIsr~e~g~~~ 57 (82)
T PHA00542 33 SQEQIADATDVSQPTICRIYSGRHK 57 (82)
T ss_pred CHHHHHHHHCcCHHHHHHHHcCCCC
Confidence 5567899999999999999999864
No 483
>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=71.78 E-value=11 Score=25.59 Aligned_cols=62 Identities=15% Similarity=0.170 Sum_probs=35.7
Q ss_pred HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCC
Q 032366 33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINE 107 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgi 107 (142)
+.|+++|+++.|++=|+. |-..|... .+ -..++.. ....-..|+.+| ..|+|.+++.+.+..
T Consensus 5 e~a~~~gvs~~tlRyYe~~GLl~p~~~-~g--~r~Y~~~---------~~~~l~~I~~lr-~~G~sL~eI~~~l~~ 67 (107)
T cd04777 5 KFAKKNNITIDTVRHYIDLGLLIPEKK-GG--QYFFDEK---------CQDDLEFILELK-GLGFSLIEIQKIFSY 67 (107)
T ss_pred HHHHHHCcCHHHHHHHHHCCCcCCccC-CC--ccccCHH---------HHHHHHHHHHHH-HCCCCHHHHHHHHHh
Confidence 478999999999999997 44442110 00 0111111 111233344444 479999999987753
No 484
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=71.75 E-value=7.6 Score=28.51 Aligned_cols=28 Identities=7% Similarity=0.062 Sum_probs=23.5
Q ss_pred HHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 89 QARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 89 ~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
.++.-.|+|..|+|+.+|+|.++|...-
T Consensus 137 ~l~~~~g~s~~EIA~~l~is~~tv~~~l 164 (179)
T PRK09415 137 YLFYYEELSIKEIAEVTGVNENTVKTRL 164 (179)
T ss_pred HhHHhcCCCHHHHHHHHCCCHHHHHHHH
Confidence 3445579999999999999999998765
No 485
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=71.69 E-value=8.3 Score=29.67 Aligned_cols=24 Identities=17% Similarity=0.349 Sum_probs=21.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 94 KKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 94 ~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.|+|.+|+|+.+|+|.++|..+.+
T Consensus 193 e~~S~~EIAe~lgis~~tV~~~~~ 216 (227)
T TIGR02846 193 RRKTQREIAKILGISRSYVSRIEK 216 (227)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHH
Confidence 689999999999999999988753
No 486
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=71.68 E-value=4.1 Score=31.94 Aligned_cols=26 Identities=15% Similarity=0.189 Sum_probs=22.0
Q ss_pred HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 92 NDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 92 ~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
..-++|+.+||+.+++|+++++++.+
T Consensus 18 ~~~~IS~~eLA~~L~iS~~Tvsr~Lk 43 (217)
T PRK14165 18 NTVKISSSEFANHTGTSSKTAARILK 43 (217)
T ss_pred CCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 33468999999999999999988753
No 487
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. 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 RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=71.65 E-value=6.7 Score=28.67 Aligned_cols=28 Identities=11% Similarity=0.163 Sum_probs=23.7
Q ss_pred HHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 89 QARNDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 89 ~~R~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
.++.-.|+|..|+|+.+|+|..+|....
T Consensus 148 ~l~~~~~~s~~EIA~~lgis~~tv~~~l 175 (190)
T TIGR02939 148 TLRELEGLSYEDIARIMDCPVGTVRSRI 175 (190)
T ss_pred hhhhhcCCCHHHHHHHHCcCHHHHHHHH
Confidence 3455679999999999999999998765
No 488
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=71.63 E-value=2.8 Score=36.25 Aligned_cols=43 Identities=19% Similarity=0.162 Sum_probs=33.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 032366 96 LTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 138 (142)
Q Consensus 96 lTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl 138 (142)
|+.+++|+.+|++.|||++.-+++..-++.-+..|-.+|-..+
T Consensus 331 L~LrdvA~~i~~HESTISRai~nKy~~tprG~feLK~FFs~~i 373 (444)
T COG1508 331 LVLRDVADEIGMHESTISRAITNKYLATPRGLFELKYFFSSSL 373 (444)
T ss_pred ccHHHHHHHhCccHHHHHHHHhcccccCCcceeeHHHHHHHhc
Confidence 8999999999999999999999997666555555555554433
No 489
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=71.63 E-value=4.1 Score=31.14 Aligned_cols=25 Identities=20% Similarity=0.283 Sum_probs=22.9
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 93 DKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 93 ~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
..|+|.+++|+.+++|..||..+-+
T Consensus 176 ~~g~s~~eIA~~l~iS~~Tv~~~~~ 200 (239)
T PRK10430 176 DYEFSTDELANAVNISRVSCRKYLI 200 (239)
T ss_pred CCCcCHHHHHHHhCchHHHHHHHHH
Confidence 4899999999999999999998865
No 490
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=71.43 E-value=3.6 Score=30.50 Aligned_cols=25 Identities=12% Similarity=0.195 Sum_probs=21.8
Q ss_pred HhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366 92 NDKKLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 92 ~~~glTQ~eLA~~lgis~stIs~~E 116 (142)
.-.|+|..|+|+.+|+|.++|....
T Consensus 152 ~~~g~s~~EIA~~lgis~~tV~~~l 176 (194)
T PRK12513 152 EHGDLELEEIAELTGVPEETVKSRL 176 (194)
T ss_pred hccCCCHHHHHHHHCCCHHHHHHHH
Confidence 3469999999999999999998764
No 491
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=71.43 E-value=4.1 Score=32.12 Aligned_cols=35 Identities=14% Similarity=0.251 Sum_probs=27.0
Q ss_pred HHHHHHH-HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 83 LKKAIVQ-ARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 83 ~g~~Lk~-~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
+.+.|.. .-.-..+|..+||+++|+|++||.++.+
T Consensus 17 ia~yil~n~~~v~~~si~elA~~~~vS~aTv~Rf~k 52 (278)
T PRK11557 17 LADYLLLQPDTARHLSSQQLANEAGVSQSSVVKFAQ 52 (278)
T ss_pred HHHHHHhCHHHHHhcCHHHHHHHhCCCHHHHHHHHH
Confidence 4444433 2344569999999999999999999987
No 492
>PRK13866 plasmid partitioning protein RepB; Provisional
Probab=71.40 E-value=6.5 Score=32.87 Aligned_cols=42 Identities=7% Similarity=0.086 Sum_probs=31.6
Q ss_pred HHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH
Q 032366 89 QARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKL 130 (142)
Q Consensus 89 ~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kL 130 (142)
....+.|+++.++++.+|++.++|+++..=-...+.+++..|
T Consensus 173 ~~L~~~g~~~~~i~~aL~~~~s~vS~~l~v~~~lP~~li~~i 214 (336)
T PRK13866 173 LRLEDAGFDRATIIAALSTDKADLSRYITVARGIPLNLATQI 214 (336)
T ss_pred HHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHhCCHHHHHhh
Confidence 345778999999999999999999999763333344555544
No 493
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=71.17 E-value=7.2 Score=34.36 Aligned_cols=25 Identities=20% Similarity=0.236 Sum_probs=22.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHcC
Q 032366 94 KKLTQSQLAQLINEKPQVIQEYESG 118 (142)
Q Consensus 94 ~glTQ~eLA~~lgis~stIs~~E~G 118 (142)
.++|+.++|+.+|||+..|+++|+.
T Consensus 466 e~~TL~EIa~~lGVSrERVRQIe~k 490 (509)
T PRK05901 466 QPKTLDEIGQVYGVTRERIRQIESK 490 (509)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4699999999999999999999963
No 494
>PRK10923 glnG nitrogen regulation protein NR(I); Provisional
Probab=71.14 E-value=7 Score=33.10 Aligned_cols=33 Identities=9% Similarity=0.059 Sum_probs=28.3
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
..|.......+..+.+.|+.+|||++|+++-.+
T Consensus 432 ~~i~~aL~~~~gn~~~aA~~Lgisr~tL~rkl~ 464 (469)
T PRK10923 432 TLLTTALRHTQGHKQEAARLLGWGRNTLTRKLK 464 (469)
T ss_pred HHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence 357777888899999999999999999987654
No 495
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=70.97 E-value=4.1 Score=31.13 Aligned_cols=22 Identities=9% Similarity=-0.019 Sum_probs=19.5
Q ss_pred CCCHHHHHHHhCCCHHHHHHHH
Q 032366 95 KLTQSQLAQLINEKPQVIQEYE 116 (142)
Q Consensus 95 glTQ~eLA~~lgis~stIs~~E 116 (142)
.+||.+||..+|+++.+|++..
T Consensus 169 ~~t~~~lA~~lG~sretvsR~L 190 (226)
T PRK10402 169 HEKHTQAAEYLGVSYRHLLYVL 190 (226)
T ss_pred cchHHHHHHHHCCcHHHHHHHH
Confidence 3689999999999999999854
No 496
>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=70.96 E-value=24 Score=25.02 Aligned_cols=64 Identities=19% Similarity=0.224 Sum_probs=37.3
Q ss_pred HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCC
Q 032366 33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINE 107 (142)
Q Consensus 33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgi 107 (142)
+.|++.|+++.|++-|+. |-.+|.... .-.-+.++.++ ...-..|+.+| ..|+|.+++.+.+..
T Consensus 5 E~A~~~gvs~~TLRyYE~~GLl~p~r~~-~~gyR~Y~~~~---------~~~l~~I~~lr-~~G~sL~eI~~~l~~ 69 (133)
T cd04787 5 ELANAAGVTPDTVRFYTRIGLLRPTRDP-VNGYRLYSEKD---------LSRLRFILSAR-QLGFSLKDIKEILSH 69 (133)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCcCC-CCCeeeCCHHH---------HHHHHHHHHHH-HcCCCHHHHHHHHhh
Confidence 478999999999999986 444421110 01111222211 11234445554 589999999887764
No 497
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=70.91 E-value=14 Score=25.93 Aligned_cols=25 Identities=8% Similarity=0.004 Sum_probs=22.5
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHcCC
Q 032366 95 KLTQSQLAQLINEKPQVIQEYESGK 119 (142)
Q Consensus 95 glTQ~eLA~~lgis~stIs~~E~G~ 119 (142)
.+|..+||+.+|+|+.++.++-+..
T Consensus 25 ~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 25 PLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 5999999999999999999998744
No 498
>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent 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. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [].; PDB: 2L0K_A.
Probab=70.90 E-value=6.6 Score=26.19 Aligned_cols=49 Identities=14% Similarity=0.170 Sum_probs=29.6
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhC
Q 032366 87 IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA-IPNQQILTKLERALG 135 (142)
Q Consensus 87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~-~p~~~~l~kLa~~Lg 135 (142)
+.....+.+.|-.+.|+..|||.|||.+=...+- ..+++....+-.+|.
T Consensus 11 i~~yIi~~~aTVR~~Ak~FGvSKSTVHkDvteRL~~in~~La~eV~~vL~ 60 (82)
T PF12116_consen 11 IANYIIETKATVRQAAKVFGVSKSTVHKDVTERLPKINPELAREVRKVLD 60 (82)
T ss_dssp HHHHHHHH---HHHHHHHHTS-HHHHHHHHTTHHHHH-HHHHHHHHHHHH
T ss_pred HHHHHHHcccHHHHHHHHHCCcHHHHHHHHHHHHHhcCHHHHHHHHHHHH
Confidence 3444556688999999999999999998765431 235555555555543
No 499
>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=70.78 E-value=8.3 Score=25.56 Aligned_cols=31 Identities=10% Similarity=0.125 Sum_probs=25.6
Q ss_pred HHHHHHhCCCCHHHHHHHhC-CCHHHHHHHHc
Q 032366 87 IVQARNDKKLTQSQLAQLIN-EKPQVIQEYES 117 (142)
Q Consensus 87 Lk~~R~~~glTQ~eLA~~lg-is~stIs~~E~ 117 (142)
+.-++...|+|..++|+.+| .+.+||+.-.+
T Consensus 36 ~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~ 67 (90)
T cd06571 36 MYLARELTGLSLPEIGRAFGGRDHSTVLHAVR 67 (90)
T ss_pred HHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHH
Confidence 34567778999999999999 99999887543
No 500
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=70.69 E-value=8.6 Score=29.65 Aligned_cols=24 Identities=4% Similarity=0.001 Sum_probs=21.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366 94 KKLTQSQLAQLINEKPQVIQEYES 117 (142)
Q Consensus 94 ~glTQ~eLA~~lgis~stIs~~E~ 117 (142)
.|+|.+|+|+.+++|..||..+-+
T Consensus 169 ~G~s~~eIA~~L~iS~~TVk~~~~ 192 (216)
T PRK10100 169 IGASNNEIARSLFISENTVKTHLY 192 (216)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHH
Confidence 399999999999999999998864
Done!