Query 031871
Match_columns 151
No_of_seqs 386 out of 2487
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 06:31:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031871.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031871hhsearch_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 4.4E-30 9.5E-35 184.8 10.9 133 8-151 1-133 (135)
2 PF08523 MBF1: Multiprotein br 99.8 6.1E-21 1.3E-25 126.5 0.1 67 9-76 1-68 (71)
3 PRK06424 transcription factor; 99.6 4.8E-15 1E-19 110.8 10.4 63 89-151 82-144 (144)
4 PHA01976 helix-turn-helix prot 99.6 1.6E-15 3.4E-20 98.5 6.3 58 91-148 2-59 (67)
5 PRK08359 transcription factor; 99.5 3.5E-14 7.6E-19 109.1 9.4 63 87-149 81-143 (176)
6 TIGR03070 couple_hipB transcri 99.5 3.2E-14 6.8E-19 88.8 7.6 57 91-147 2-58 (58)
7 PF12844 HTH_19: Helix-turn-he 99.5 2E-14 4.3E-19 92.5 4.9 56 93-148 1-56 (64)
8 PF01381 HTH_3: Helix-turn-hel 99.5 2.8E-14 6E-19 89.1 4.9 53 96-148 1-53 (55)
9 COG1476 Predicted transcriptio 99.5 9.7E-14 2.1E-18 91.1 5.5 56 94-149 4-59 (68)
10 TIGR00270 conserved hypothetic 99.5 1.3E-13 2.8E-18 104.1 6.4 63 87-149 65-127 (154)
11 PRK09726 antitoxin HipB; Provi 99.4 5.5E-13 1.2E-17 91.5 7.9 60 89-148 10-69 (88)
12 PF13560 HTH_31: Helix-turn-he 99.4 1.7E-13 3.8E-18 88.4 5.1 58 91-148 1-59 (64)
13 PRK09706 transcriptional repre 99.4 6.4E-13 1.4E-17 97.6 6.9 59 90-148 4-62 (135)
14 PRK09943 DNA-binding transcrip 99.3 3.8E-12 8.2E-17 97.9 6.8 60 89-148 5-64 (185)
15 PRK13890 conjugal transfer pro 99.3 5.1E-12 1.1E-16 91.7 7.0 60 89-148 3-62 (120)
16 TIGR02607 antidote_HigA addict 99.3 8.6E-12 1.9E-16 82.9 6.7 58 91-148 4-62 (78)
17 TIGR02684 dnstrm_HI1420 probab 99.3 1.7E-11 3.7E-16 84.7 6.8 59 88-148 29-87 (89)
18 PRK08154 anaerobic benzoate ca 99.3 1.8E-11 4E-16 101.2 8.2 60 89-148 26-85 (309)
19 COG1813 Predicted transcriptio 99.3 1.5E-11 3.2E-16 93.4 6.8 65 86-150 74-138 (165)
20 PRK10072 putative transcriptio 99.2 6.6E-11 1.4E-15 82.9 6.7 54 93-147 35-88 (96)
21 TIGR02612 mob_myst_A mobile my 99.1 1.2E-10 2.7E-15 87.6 6.7 55 94-148 28-84 (150)
22 PF13443 HTH_26: Cro/C1-type H 99.1 7.5E-11 1.6E-15 75.4 4.4 55 95-149 1-56 (63)
23 PRK04140 hypothetical protein; 99.1 2.5E-10 5.4E-15 95.1 7.2 60 89-148 124-183 (317)
24 smart00530 HTH_XRE Helix-turn- 99.1 5.7E-10 1.2E-14 66.6 6.3 53 96-148 2-54 (56)
25 cd00093 HTH_XRE Helix-turn-hel 99.0 1.7E-09 3.7E-14 64.9 6.5 55 94-148 2-56 (58)
26 TIGR03830 CxxCG_CxxCG_HTH puta 99.0 1.5E-09 3.2E-14 78.2 6.2 58 90-148 64-121 (127)
27 PF13744 HTH_37: Helix-turn-he 99.0 1.7E-09 3.7E-14 72.9 6.0 60 89-148 16-76 (80)
28 COG3620 Predicted transcriptio 98.9 4.3E-09 9.3E-14 79.9 6.4 52 93-144 7-58 (187)
29 PHA00542 putative Cro-like pro 98.8 1.4E-08 2.9E-13 69.0 7.0 50 94-143 21-71 (82)
30 PRK10856 cytoskeletal protein 98.8 6.7E-09 1.5E-13 87.1 6.5 59 90-148 13-77 (331)
31 smart00352 POU Found in Pit-Oc 98.8 3E-08 6.4E-13 66.3 6.9 53 89-143 9-67 (75)
32 COG2944 Predicted transcriptio 98.7 2.9E-08 6.2E-13 70.3 5.8 45 92-136 45-89 (104)
33 PRK02866 cyanate hydratase; Va 98.7 8.6E-08 1.9E-12 71.8 7.9 59 90-148 4-62 (147)
34 PRK13355 bifunctional HTH-doma 98.7 4.3E-08 9.4E-13 85.9 7.1 59 90-148 2-65 (517)
35 COG1709 Predicted transcriptio 98.6 2.8E-08 6E-13 78.6 3.8 57 87-143 23-80 (241)
36 COG3093 VapI Plasmid maintenan 98.6 2.2E-07 4.8E-12 65.7 6.5 56 93-148 11-67 (104)
37 TIGR00673 cynS cyanate hydrata 98.5 3.7E-07 8.1E-12 68.6 7.5 56 92-147 9-64 (150)
38 COG3655 Predicted transcriptio 98.4 7.9E-07 1.7E-11 59.1 5.0 58 92-149 3-61 (73)
39 COG1396 HipB Predicted transcr 98.4 2.6E-06 5.7E-11 55.1 7.5 56 92-147 2-58 (120)
40 COG1395 Predicted transcriptio 98.3 1.4E-06 3.1E-11 72.2 6.1 57 92-148 126-182 (313)
41 PF07022 Phage_CI_repr: Bacter 98.3 3.8E-07 8.2E-12 59.3 1.6 53 95-148 2-56 (66)
42 PF13413 HTH_25: Helix-turn-he 98.2 7.3E-06 1.6E-10 52.9 6.2 54 95-148 1-60 (62)
43 PF08667 BetR: BetR domain; I 98.0 2.6E-05 5.7E-10 58.5 6.4 60 89-148 3-66 (147)
44 cd01392 HTH_LacI Helix-turn-he 97.9 4.3E-05 9.3E-10 46.6 5.3 40 109-148 2-44 (52)
45 COG5499 Predicted transcriptio 97.9 2.6E-05 5.6E-10 55.6 4.6 56 92-148 61-116 (120)
46 TIGR01321 TrpR trp operon repr 97.9 6.3E-05 1.4E-09 52.4 6.4 52 90-141 39-92 (94)
47 COG1426 Predicted transcriptio 97.8 3.2E-05 6.9E-10 63.8 5.5 58 91-148 3-66 (284)
48 PHA01083 hypothetical protein 97.8 4.1E-05 9E-10 57.3 4.9 54 95-148 6-61 (149)
49 PF08965 DUF1870: Domain of un 97.6 0.0002 4.4E-09 51.8 5.6 50 94-143 4-55 (118)
50 PF00356 LacI: Bacterial regul 97.6 0.00031 6.7E-09 42.7 5.6 40 106-145 1-43 (46)
51 COG4800 Predicted transcriptio 97.5 0.00036 7.7E-09 52.1 6.8 54 89-143 14-67 (170)
52 smart00354 HTH_LACI helix_turn 97.5 0.00032 6.9E-09 45.9 5.6 43 105-147 1-46 (70)
53 COG2522 Predicted transcriptio 97.4 0.00057 1.2E-08 49.6 6.0 43 88-131 6-49 (119)
54 COG5606 Uncharacterized conser 97.1 0.00091 2E-08 45.9 4.4 60 89-148 26-86 (91)
55 PF00157 Pou: Pou domain - N-t 97.1 0.0024 5.3E-08 42.7 6.2 53 89-143 9-67 (75)
56 TIGR03879 near_KaiC_dom probab 96.8 0.0052 1.1E-07 40.9 5.9 48 91-140 19-66 (73)
57 TIGR02147 Fsuc_second hypothet 96.8 0.0039 8.5E-08 51.2 6.3 46 104-149 27-73 (271)
58 COG3636 Predicted transcriptio 96.7 0.0067 1.4E-07 42.5 6.3 56 90-147 37-92 (100)
59 PF01710 HTH_Tnp_IS630: Transp 96.7 0.0065 1.4E-07 43.7 6.5 74 29-126 19-93 (119)
60 PF13693 HTH_35: Winged helix- 96.6 0.006 1.3E-07 41.1 5.0 52 94-148 5-56 (78)
61 PHA00675 hypothetical protein 96.5 0.0075 1.6E-07 40.5 5.2 39 91-129 26-64 (78)
62 PHA02591 hypothetical protein; 96.4 0.0075 1.6E-07 40.6 4.5 26 101-126 56-81 (83)
63 PF13384 HTH_23: Homeodomain-l 96.3 0.0077 1.7E-07 36.2 4.1 24 104-127 17-40 (50)
64 PRK10014 DNA-binding transcrip 96.3 0.011 2.4E-07 48.1 6.3 45 103-147 5-52 (342)
65 PF14549 P22_Cro: DNA-binding 96.3 0.0094 2E-07 38.2 4.4 40 102-145 8-47 (60)
66 COG3423 Nlp Predicted transcri 96.1 0.016 3.5E-07 38.9 5.1 51 96-149 13-63 (82)
67 TIGR02293 TAS_TIGR02293 putati 96.1 0.018 3.9E-07 42.3 5.7 48 95-142 27-74 (133)
68 PRK09492 treR trehalose repres 96.1 0.014 3E-07 47.0 5.6 44 104-147 4-50 (315)
69 PF13936 HTH_38: Helix-turn-he 96.1 0.011 2.5E-07 35.2 3.8 30 95-125 12-41 (44)
70 PF02796 HTH_7: Helix-turn-hel 96.1 0.015 3.2E-07 34.7 4.3 33 93-126 11-43 (45)
71 TIGR02844 spore_III_D sporulat 96.0 0.059 1.3E-06 36.5 7.6 49 95-144 11-60 (80)
72 PRK09526 lacI lac repressor; R 96.0 0.016 3.4E-07 47.3 5.6 45 103-147 4-51 (342)
73 PF13412 HTH_24: Winged helix- 96.0 0.026 5.7E-07 33.7 5.1 34 93-126 6-39 (48)
74 TIGR00721 tfx DNA-binding prot 95.9 0.016 3.5E-07 43.0 5.0 34 93-127 11-44 (137)
75 PF04814 HNF-1_N: Hepatocyte n 95.9 0.023 4.9E-07 44.0 5.7 54 89-142 116-169 (180)
76 PRK03975 tfx putative transcri 95.9 0.016 3.5E-07 43.2 4.7 45 102-147 19-66 (141)
77 PRK14987 gluconate operon tran 95.7 0.022 4.9E-07 46.3 5.2 44 104-147 5-51 (331)
78 KOG3802 Transcription factor O 95.5 0.032 6.9E-07 47.9 5.5 53 89-143 208-266 (398)
79 PF08535 KorB: KorB domain; I 95.4 0.014 3E-07 40.1 2.7 25 102-126 1-25 (93)
80 PF05225 HTH_psq: helix-turn-h 95.3 0.053 1.1E-06 32.6 4.7 39 90-129 3-41 (45)
81 COG1513 CynS Cyanate lyase [In 95.3 0.1 2.2E-06 38.6 7.1 59 89-147 6-64 (151)
82 smart00351 PAX Paired Box doma 95.2 0.055 1.2E-06 39.2 5.5 45 81-126 11-55 (125)
83 PF04545 Sigma70_r4: Sigma-70, 95.2 0.059 1.3E-06 32.5 4.7 32 95-126 11-42 (50)
84 PRK01381 Trp operon repressor; 95.1 0.05 1.1E-06 38.3 4.8 57 89-145 38-96 (99)
85 PF02001 DUF134: Protein of un 95.1 0.051 1.1E-06 38.7 4.9 37 100-143 53-89 (106)
86 COG4197 Uncharacterized protei 95.0 0.014 3.1E-07 40.5 1.6 39 106-144 14-52 (96)
87 PRK10344 DNA-binding transcrip 95.0 0.074 1.6E-06 36.8 5.1 51 96-149 13-63 (92)
88 cd00131 PAX Paired Box domain 94.9 0.076 1.6E-06 38.7 5.5 44 81-125 11-54 (128)
89 cd04762 HTH_MerR-trunc Helix-T 94.8 0.051 1.1E-06 31.5 3.7 24 105-128 1-24 (49)
90 PRK08558 adenine phosphoribosy 94.6 0.13 2.8E-06 41.4 6.5 50 93-144 14-63 (238)
91 PF07037 DUF1323: Putative tra 94.6 0.034 7.5E-07 40.3 2.8 23 105-127 1-23 (122)
92 COG1356 tfx Transcriptional re 94.5 0.033 7.2E-07 40.9 2.6 27 101-127 20-46 (143)
93 PF01371 Trp_repressor: Trp re 94.4 0.11 2.4E-06 35.7 5.0 38 89-126 32-71 (87)
94 PF06056 Terminase_5: Putative 94.4 0.054 1.2E-06 34.4 3.1 25 103-127 12-36 (58)
95 PF05269 Phage_CII: Bacterioph 94.3 0.0075 1.6E-07 41.8 -1.0 41 103-147 22-62 (91)
96 PF02376 CUT: CUT domain; Int 94.2 0.56 1.2E-05 32.1 8.2 58 89-146 11-75 (87)
97 COG2944 Predicted transcriptio 94.0 0.043 9.3E-07 39.0 2.3 26 31-56 60-85 (104)
98 PF04218 CENP-B_N: CENP-B N-te 93.8 0.064 1.4E-06 33.2 2.6 38 91-128 8-46 (53)
99 COG1342 Predicted DNA-binding 93.8 0.14 3E-06 35.8 4.5 28 99-126 44-71 (99)
100 cd04764 HTH_MlrA-like_sg1 Heli 93.8 0.19 4.1E-06 32.0 4.8 22 105-126 1-22 (67)
101 PF00325 Crp: Bacterial regula 93.7 0.085 1.8E-06 29.6 2.7 22 104-125 2-23 (32)
102 TIGR01764 excise DNA binding d 93.6 0.13 2.9E-06 29.9 3.6 27 105-131 2-28 (49)
103 cd04761 HTH_MerR-SF Helix-Turn 93.6 0.13 2.8E-06 30.3 3.6 24 105-128 1-24 (49)
104 PRK15418 transcriptional regul 93.5 0.14 3E-06 42.8 5.0 55 92-146 17-84 (318)
105 PF02954 HTH_8: Bacterial regu 93.5 0.16 3.4E-06 29.8 3.9 32 93-124 7-38 (42)
106 cd04763 HTH_MlrA-like Helix-Tu 93.5 0.49 1.1E-05 30.1 6.5 62 32-114 4-67 (68)
107 PRK13698 plasmid-partitioning 93.5 0.14 3E-06 43.1 4.8 40 89-128 160-200 (323)
108 PHA01976 helix-turn-helix prot 93.4 0.026 5.5E-07 35.9 0.3 29 29-57 16-44 (67)
109 cd00569 HTH_Hin_like Helix-tur 93.4 0.38 8.3E-06 25.1 5.2 23 102-124 19-41 (42)
110 PF12728 HTH_17: Helix-turn-he 93.4 0.14 3E-06 30.8 3.6 28 105-132 2-29 (51)
111 COG2390 DeoR Transcriptional r 93.3 0.16 3.5E-06 42.7 5.0 58 89-146 11-81 (321)
112 PF08279 HTH_11: HTH domain; 93.3 0.16 3.5E-06 30.9 3.9 31 95-125 5-36 (55)
113 PF13518 HTH_28: Helix-turn-he 93.3 0.21 4.5E-06 29.8 4.2 24 103-126 11-34 (52)
114 TIGR02531 yecD_yerC TrpR-relat 93.2 0.22 4.7E-06 34.2 4.7 27 101-127 47-73 (88)
115 PF00376 MerR: MerR family reg 93.2 0.13 2.8E-06 29.7 3.1 25 106-130 1-25 (38)
116 cd00131 PAX Paired Box domain 93.1 0.75 1.6E-05 33.4 7.7 76 29-126 34-125 (128)
117 PF01527 HTH_Tnp_1: Transposas 92.8 0.15 3.2E-06 33.0 3.2 39 88-126 7-45 (76)
118 PF10668 Phage_terminase: Phag 92.7 0.14 3.1E-06 32.8 3.0 25 103-127 21-45 (60)
119 PF01047 MarR: MarR family; I 92.7 0.28 6.1E-06 30.1 4.3 33 93-125 6-38 (59)
120 cd04774 HTH_YfmP Helix-Turn-He 92.7 0.31 6.7E-06 33.7 4.9 68 32-119 4-72 (96)
121 cd01104 HTH_MlrA-CarA Helix-Tu 92.7 0.65 1.4E-05 29.2 6.1 62 32-114 4-67 (68)
122 TIGR00180 parB_part ParB-like 92.6 0.42 9.2E-06 36.7 6.1 52 89-141 105-156 (187)
123 cd01104 HTH_MlrA-CarA Helix-Tu 92.6 0.15 3.2E-06 32.3 3.0 22 105-126 1-22 (68)
124 cd06171 Sigma70_r4 Sigma70, re 92.5 0.33 7.2E-06 28.1 4.3 29 98-126 20-48 (55)
125 COG2842 Uncharacterized ATPase 92.4 0.38 8.2E-06 40.1 5.9 58 89-147 4-62 (297)
126 PRK09413 IS2 repressor TnpA; R 92.3 0.46 1E-05 34.0 5.6 40 87-126 12-51 (121)
127 PF13613 HTH_Tnp_4: Helix-turn 92.3 0.13 2.9E-06 31.6 2.4 27 100-126 15-41 (53)
128 PF13411 MerR_1: MerR HTH fami 92.2 0.18 4E-06 31.9 3.1 23 105-127 1-23 (69)
129 cd04763 HTH_MlrA-like Helix-Tu 92.0 0.19 4.2E-06 32.0 3.0 22 105-126 1-22 (68)
130 PF04967 HTH_10: HTH DNA bindi 92.0 0.24 5.1E-06 30.9 3.2 24 103-126 22-45 (53)
131 KOG1168 Transcription factor A 91.9 0.11 2.4E-06 43.2 2.2 39 89-127 219-266 (385)
132 cd00092 HTH_CRP helix_turn_hel 91.9 0.45 9.8E-06 29.6 4.6 26 101-126 22-47 (67)
133 TIGR03070 couple_hipB transcri 91.8 0.061 1.3E-06 32.5 0.5 27 29-55 16-42 (58)
134 PF13411 MerR_1: MerR HTH fami 91.8 0.61 1.3E-05 29.4 5.2 63 32-114 4-66 (69)
135 cd04764 HTH_MlrA-like_sg1 Heli 91.6 0.76 1.6E-05 29.1 5.5 64 31-115 3-67 (67)
136 TIGR01610 phage_O_Nterm phage 91.6 0.58 1.2E-05 32.2 5.2 24 101-124 44-67 (95)
137 COG1191 FliA DNA-directed RNA 91.5 0.27 5.7E-06 40.0 4.0 34 93-126 201-234 (247)
138 PF01381 HTH_3: Helix-turn-hel 91.4 0.054 1.2E-06 32.9 -0.1 27 30-56 11-37 (55)
139 PF08281 Sigma70_r4_2: Sigma-7 91.4 0.54 1.2E-05 28.4 4.4 33 93-125 15-47 (54)
140 PRK09744 DNA-binding transcrip 91.3 0.61 1.3E-05 31.1 4.9 36 106-144 12-47 (75)
141 smart00422 HTH_MERR helix_turn 91.3 0.36 7.8E-06 30.5 3.8 22 105-126 1-22 (70)
142 TIGR03764 ICE_PFGI_1_parB inte 91.2 0.35 7.5E-06 39.6 4.4 42 103-144 135-181 (258)
143 PF12802 MarR_2: MarR family; 91.1 0.67 1.5E-05 28.5 4.8 33 93-125 8-42 (62)
144 smart00550 Zalpha Z-DNA-bindin 90.8 0.59 1.3E-05 30.2 4.4 29 96-124 12-42 (68)
145 PRK10072 putative transcriptio 90.7 0.23 5E-06 34.6 2.5 29 29-57 47-75 (96)
146 PF13542 HTH_Tnp_ISL3: Helix-t 90.6 1 2.2E-05 26.9 5.1 36 90-126 14-49 (52)
147 PRK04217 hypothetical protein; 90.4 0.52 1.1E-05 33.7 4.2 32 95-126 49-80 (110)
148 PF13545 HTH_Crp_2: Crp-like h 90.3 0.37 8.1E-06 31.0 3.2 23 103-125 27-49 (76)
149 PF01418 HTH_6: Helix-turn-hel 90.3 0.37 8E-06 31.8 3.1 44 91-134 20-64 (77)
150 PF04552 Sigma54_DBD: Sigma-54 90.1 0.084 1.8E-06 40.1 -0.1 46 102-147 47-92 (160)
151 smart00421 HTH_LUXR helix_turn 90.0 0.46 1E-05 28.1 3.2 25 102-126 16-40 (58)
152 PF13404 HTH_AsnC-type: AsnC-t 89.8 1.2 2.7E-05 26.1 4.8 30 94-123 7-36 (42)
153 PF14590 DUF4447: Domain of un 89.8 1.6 3.4E-05 32.4 6.3 42 93-134 9-50 (166)
154 PF09339 HTH_IclR: IclR helix- 89.5 0.41 8.9E-06 29.0 2.7 26 101-126 15-40 (52)
155 smart00419 HTH_CRP helix_turn_ 89.5 0.51 1.1E-05 27.3 3.0 24 103-126 7-30 (48)
156 PF13551 HTH_29: Winged helix- 89.5 1.2 2.7E-05 30.3 5.5 82 30-126 14-109 (112)
157 cd04780 HTH_MerR-like_sg5 Heli 89.4 1.8 4E-05 29.8 6.2 66 32-116 4-70 (95)
158 cd01105 HTH_GlnR-like Helix-Tu 89.2 0.66 1.4E-05 31.4 3.8 24 104-127 1-24 (88)
159 cd04773 HTH_TioE_rpt2 Second H 89.2 0.6 1.3E-05 32.8 3.7 23 105-127 1-23 (108)
160 PRK00118 putative DNA-binding 89.1 0.77 1.7E-05 32.5 4.2 33 94-126 23-55 (104)
161 COG3415 Transposase and inacti 89.1 1.1 2.3E-05 33.4 5.1 37 90-126 7-43 (138)
162 COG2973 TrpR Trp operon repres 88.9 1.5 3.3E-05 30.8 5.4 56 89-144 43-100 (103)
163 PRK04132 replication factor C 88.9 0.54 1.2E-05 44.4 4.2 43 107-149 420-462 (846)
164 smart00420 HTH_DEOR helix_turn 88.8 1.2 2.7E-05 25.9 4.5 25 101-125 11-35 (53)
165 PF13560 HTH_31: Helix-turn-he 88.7 0.15 3.2E-06 32.2 0.2 27 30-56 16-43 (64)
166 cd00592 HTH_MerR-like Helix-Tu 88.5 1.3 2.9E-05 30.1 5.0 22 105-126 1-22 (100)
167 PF02042 RWP-RK: RWP-RK domain 88.5 0.93 2E-05 28.2 3.7 31 96-126 7-37 (52)
168 cd01105 HTH_GlnR-like Helix-Tu 88.4 2.6 5.6E-05 28.4 6.4 65 31-115 4-69 (88)
169 PF00165 HTH_AraC: Bacterial r 88.4 0.76 1.7E-05 26.5 3.2 31 102-132 6-36 (42)
170 COG2512 Predicted membrane-ass 88.2 0.96 2.1E-05 36.9 4.8 40 86-125 191-231 (258)
171 PF07638 Sigma70_ECF: ECF sigm 88.1 0.82 1.8E-05 34.8 4.1 32 94-125 141-172 (185)
172 PF13022 HTH_Tnp_1_2: Helix-tu 88.1 0.49 1.1E-05 35.3 2.7 25 104-128 34-58 (142)
173 COG1522 Lrp Transcriptional re 88.0 1.4 3E-05 32.1 5.2 34 91-124 9-42 (154)
174 smart00422 HTH_MERR helix_turn 87.8 3.7 8E-05 25.7 6.5 63 32-115 4-68 (70)
175 cd01106 HTH_TipAL-Mta Helix-Tu 87.8 0.87 1.9E-05 31.5 3.8 23 105-127 1-23 (103)
176 cd04774 HTH_YfmP Helix-Turn-He 87.7 0.9 2E-05 31.3 3.8 23 105-127 1-23 (96)
177 cd04789 HTH_Cfa Helix-Turn-Hel 87.6 0.91 2E-05 31.5 3.8 23 105-127 2-24 (102)
178 cd04768 HTH_BmrR-like Helix-Tu 87.5 3.5 7.5E-05 28.2 6.6 20 32-51 4-23 (96)
179 PRK10458 DNA cytosine methylas 87.4 1.5 3.2E-05 38.8 5.8 45 100-144 25-78 (467)
180 PF08220 HTH_DeoR: DeoR-like h 87.4 1.4 2.9E-05 27.4 4.1 29 96-124 6-34 (57)
181 cd04768 HTH_BmrR-like Helix-Tu 87.4 0.95 2.1E-05 31.1 3.7 24 105-128 1-24 (96)
182 cd04788 HTH_NolA-AlbR Helix-Tu 87.3 1 2.2E-05 31.0 3.8 23 105-127 1-23 (96)
183 cd01107 HTH_BmrR Helix-Turn-He 87.2 0.95 2.1E-05 31.7 3.7 23 105-127 1-23 (108)
184 TIGR01636 phage_rinA phage tra 87.2 2.5 5.4E-05 30.8 6.1 35 104-145 100-134 (134)
185 cd04765 HTH_MlrA-like_sg2 Heli 87.2 0.7 1.5E-05 32.1 3.0 22 105-126 1-22 (99)
186 PF12840 HTH_20: Helix-turn-he 87.1 1.3 2.9E-05 27.6 4.0 29 96-124 16-44 (61)
187 TIGR02885 spore_sigF RNA polym 87.1 1 2.3E-05 35.2 4.3 28 100-127 195-222 (231)
188 PF05930 Phage_AlpA: Prophage 87.1 0.29 6.3E-06 29.8 0.9 28 105-132 4-31 (51)
189 PF13551 HTH_29: Winged helix- 86.8 0.93 2E-05 30.9 3.4 26 101-126 8-34 (112)
190 cd04766 HTH_HspR Helix-Turn-He 86.8 2.1 4.6E-05 28.9 5.2 64 32-115 5-69 (91)
191 PF13011 LZ_Tnp_IS481: leucine 86.7 1.5 3.2E-05 30.0 4.3 31 96-126 17-47 (85)
192 PRK09943 DNA-binding transcrip 86.7 0.24 5.3E-06 37.7 0.5 47 26-72 18-64 (185)
193 PRK09706 transcriptional repre 86.7 0.23 4.9E-06 36.1 0.3 29 30-58 20-48 (135)
194 PRK09726 antitoxin HipB; Provi 86.7 0.24 5.2E-06 33.5 0.4 44 27-70 24-67 (88)
195 PRK08154 anaerobic benzoate ca 86.6 0.38 8.3E-06 39.8 1.6 57 16-72 29-85 (309)
196 cd04775 HTH_Cfa-like Helix-Tur 86.5 1.1 2.5E-05 31.0 3.8 23 105-127 2-24 (102)
197 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 86.5 1.1 2.5E-05 27.6 3.3 34 95-128 11-44 (50)
198 cd04780 HTH_MerR-like_sg5 Heli 86.4 1.2 2.6E-05 30.7 3.7 24 105-128 1-24 (95)
199 PF09048 Cro: Cro; InterPro: 86.4 0.56 1.2E-05 29.9 1.9 33 96-130 6-38 (59)
200 cd04772 HTH_TioE_rpt1 First He 86.3 1.2 2.6E-05 30.8 3.8 24 105-128 1-24 (99)
201 cd04782 HTH_BltR Helix-Turn-He 86.1 1.2 2.7E-05 30.6 3.7 22 105-126 1-22 (97)
202 TIGR03697 NtcA_cyano global ni 86.1 1.7 3.8E-05 32.3 4.9 23 103-125 142-164 (193)
203 PF00292 PAX: 'Paired box' dom 86.0 2.2 4.8E-05 31.2 5.2 45 81-126 11-55 (125)
204 cd04766 HTH_HspR Helix-Turn-He 85.6 1.3 2.8E-05 30.0 3.6 23 105-127 2-24 (91)
205 PRK11512 DNA-binding transcrip 85.6 2.5 5.5E-05 30.7 5.4 32 93-124 43-74 (144)
206 cd01109 HTH_YyaN Helix-Turn-He 85.4 1.3 2.9E-05 31.1 3.7 24 105-128 1-24 (113)
207 smart00497 IENR1 Intron encode 85.4 1.4 3E-05 26.3 3.3 25 106-130 19-43 (53)
208 TIGR02044 CueR Cu(I)-responsiv 85.3 1.3 2.9E-05 31.8 3.7 24 105-128 1-24 (127)
209 cd04769 HTH_MerR2 Helix-Turn-H 85.1 1 2.2E-05 31.9 3.0 23 105-127 1-23 (116)
210 cd01279 HTH_HspR-like Helix-Tu 85.1 1.5 3.2E-05 30.3 3.7 22 105-126 2-23 (98)
211 PRK08215 sporulation sigma fac 85.1 1.6 3.5E-05 34.9 4.5 31 96-126 217-247 (258)
212 COG0789 SoxR Predicted transcr 85.0 1 2.3E-05 31.7 3.0 23 105-127 1-23 (124)
213 cd01282 HTH_MerR-like_sg3 Heli 84.9 1.5 3.2E-05 30.9 3.8 23 105-127 1-23 (112)
214 smart00345 HTH_GNTR helix_turn 84.9 2.3 5E-05 25.4 4.2 21 104-124 19-40 (60)
215 cd01107 HTH_BmrR Helix-Turn-He 84.9 5.3 0.00012 27.9 6.6 68 32-118 4-72 (108)
216 cd04781 HTH_MerR-like_sg6 Heli 84.8 1.5 3.2E-05 31.3 3.8 24 105-128 1-24 (120)
217 cd01111 HTH_MerD Helix-Turn-He 84.8 1.5 3.3E-05 30.8 3.8 24 105-128 1-24 (107)
218 PRK09391 fixK transcriptional 84.8 2.5 5.3E-05 33.1 5.4 22 103-124 178-199 (230)
219 PRK11891 aspartate carbamoyltr 84.8 1.2 2.7E-05 38.9 3.9 36 92-127 4-39 (429)
220 PF01978 TrmB: Sugar-specific 84.7 1.6 3.4E-05 27.7 3.5 34 93-126 11-44 (68)
221 PRK05572 sporulation sigma fac 84.6 1.7 3.7E-05 34.6 4.4 29 99-127 213-241 (252)
222 cd04784 HTH_CadR-PbrR Helix-Tu 84.5 1.1 2.4E-05 32.2 3.0 24 105-128 1-24 (127)
223 PF13730 HTH_36: Helix-turn-he 84.5 1.3 2.8E-05 26.8 2.9 21 106-126 27-47 (55)
224 PRK11161 fumarate/nitrate redu 84.3 2.1 4.5E-05 33.2 4.7 22 104-125 184-205 (235)
225 cd06170 LuxR_C_like C-terminal 84.3 1.5 3.3E-05 25.9 3.1 25 102-126 13-37 (57)
226 cd04783 HTH_MerR1 Helix-Turn-H 84.3 1.1 2.5E-05 32.1 3.0 24 105-128 1-24 (126)
227 COG1318 Predicted transcriptio 84.1 1.4 2.9E-05 34.1 3.4 33 98-130 55-87 (182)
228 cd04770 HTH_HMRTR Helix-Turn-H 84.1 1.2 2.6E-05 31.7 3.0 23 105-127 1-23 (123)
229 PRK11169 leucine-responsive tr 84.1 1.7 3.6E-05 32.7 3.9 31 93-123 17-47 (164)
230 cd01111 HTH_MerD Helix-Turn-He 83.9 4 8.7E-05 28.7 5.6 19 32-50 4-22 (107)
231 PRK00215 LexA repressor; Valid 83.9 2.3 5E-05 32.7 4.8 35 90-124 7-44 (205)
232 PRK12427 flagellar biosynthesi 83.9 1.8 4E-05 34.2 4.3 29 98-126 193-221 (231)
233 TIGR02850 spore_sigG RNA polym 83.8 2 4.3E-05 34.3 4.5 28 99-126 217-244 (254)
234 TIGR00122 birA_repr_reg BirA b 83.8 2.6 5.7E-05 26.8 4.3 25 101-125 10-34 (69)
235 TIGR03209 P21_Cbot clostridium 83.7 1.5 3.2E-05 31.4 3.4 30 93-122 112-141 (142)
236 PF00440 TetR_N: Bacterial reg 83.6 5.1 0.00011 23.5 5.2 32 95-126 7-38 (47)
237 cd04765 HTH_MlrA-like_sg2 Heli 83.5 4.5 9.8E-05 28.0 5.7 19 32-50 4-22 (99)
238 TIGR02392 rpoH_proteo alternat 83.5 2.1 4.5E-05 34.6 4.5 24 103-126 235-258 (270)
239 PF01022 HTH_5: Bacterial regu 83.4 2.5 5.3E-05 25.0 3.8 29 96-125 8-36 (47)
240 TIGR02043 ZntR Zn(II)-responsi 83.4 4.2 9E-05 29.5 5.7 21 31-51 4-24 (131)
241 TIGR02047 CadR-PbrR Cd(II)/Pb( 83.3 1.3 2.9E-05 31.9 3.0 24 105-128 1-24 (127)
242 PF07453 NUMOD1: NUMOD1 domain 83.2 1.6 3.4E-05 24.6 2.7 19 106-124 18-36 (37)
243 cd04767 HTH_HspR-like_MBC Heli 83.2 3.1 6.7E-05 30.1 4.9 71 31-122 4-75 (120)
244 cd01108 HTH_CueR Helix-Turn-He 83.2 1.9 4E-05 31.1 3.7 24 105-128 1-24 (127)
245 cd04788 HTH_NolA-AlbR Helix-Tu 83.1 9.3 0.0002 26.0 7.1 66 32-117 4-70 (96)
246 TIGR02607 antidote_HigA addict 83.0 0.49 1.1E-05 30.6 0.6 26 30-55 20-45 (78)
247 smart00351 PAX Paired Box doma 83.0 7 0.00015 28.1 6.7 21 30-50 35-55 (125)
248 cd04777 HTH_MerR-like_sg1 Heli 82.8 2 4.4E-05 29.8 3.7 23 105-127 1-23 (107)
249 PF12844 HTH_19: Helix-turn-he 82.6 0.34 7.4E-06 30.2 -0.3 29 28-56 12-40 (64)
250 TIGR02054 MerD mercuric resist 82.6 2.3 5E-05 30.7 4.0 25 104-128 3-27 (120)
251 PF00376 MerR: MerR family reg 82.6 1.1 2.4E-05 25.7 1.9 20 32-51 3-22 (38)
252 PF01710 HTH_Tnp_IS630: Transp 82.4 2.8 6E-05 29.9 4.4 37 89-126 4-40 (119)
253 cd01110 HTH_SoxR Helix-Turn-He 82.3 2.1 4.5E-05 31.5 3.7 23 105-127 2-24 (139)
254 PRK06759 RNA polymerase factor 82.3 2.7 5.8E-05 30.3 4.4 33 94-126 112-144 (154)
255 PRK13413 mpi multiple promoter 82.2 2.3 4.9E-05 32.7 4.1 32 95-127 164-195 (200)
256 PF01325 Fe_dep_repress: Iron 82.1 4.2 9.2E-05 25.6 4.7 36 90-125 7-43 (60)
257 TIGR02393 RpoD_Cterm RNA polym 82.0 2.6 5.6E-05 33.3 4.5 26 102-127 194-219 (238)
258 COG1974 LexA SOS-response tran 81.9 1.6 3.5E-05 34.4 3.2 48 98-146 6-53 (201)
259 cd04767 HTH_HspR-like_MBC Heli 81.9 2.2 4.9E-05 30.9 3.7 23 105-127 2-24 (120)
260 PRK06424 transcription factor; 81.8 0.5 1.1E-05 35.3 0.3 28 30-57 99-126 (144)
261 PRK09514 zntR zinc-responsive 81.8 4.4 9.6E-05 29.8 5.4 21 31-51 4-24 (140)
262 cd01279 HTH_HspR-like Helix-Tu 81.6 5.2 0.00011 27.5 5.4 66 31-116 4-70 (98)
263 cd04776 HTH_GnyR Helix-Turn-He 81.6 2.4 5.1E-05 30.3 3.7 23 105-127 1-23 (118)
264 smart00346 HTH_ICLR helix_turn 81.6 3.6 7.8E-05 27.1 4.5 22 103-124 19-40 (91)
265 PRK11179 DNA-binding transcrip 81.5 4.3 9.3E-05 30.0 5.3 31 93-123 12-42 (153)
266 TIGR02999 Sig-70_X6 RNA polyme 81.5 2.7 5.9E-05 31.2 4.2 33 93-125 139-171 (183)
267 PRK13918 CRP/FNR family transc 81.3 1.6 3.4E-05 33.0 2.9 23 103-125 148-170 (202)
268 COG3311 AlpA Predicted transcr 81.3 2.6 5.6E-05 27.8 3.5 30 105-134 14-43 (70)
269 cd04785 HTH_CadR-PbrR-like Hel 81.3 2.4 5.3E-05 30.4 3.8 24 105-128 1-24 (126)
270 cd04782 HTH_BltR Helix-Turn-He 81.3 6.7 0.00014 26.8 5.8 19 32-50 4-22 (97)
271 cd04787 HTH_HMRTR_unk Helix-Tu 81.2 2.5 5.3E-05 30.7 3.8 23 105-127 1-23 (133)
272 PF00196 GerE: Bacterial regul 81.2 1.7 3.6E-05 26.8 2.5 25 102-126 16-40 (58)
273 TIGR00270 conserved hypothetic 81.2 0.58 1.2E-05 35.3 0.4 41 28-68 82-122 (154)
274 PRK13832 plasmid partitioning 81.1 4.3 9.4E-05 36.3 5.9 50 89-140 104-153 (520)
275 PRK11753 DNA-binding transcrip 80.9 1.7 3.7E-05 32.9 3.0 23 104-126 168-190 (211)
276 PRK07037 extracytoplasmic-func 80.9 3 6.6E-05 30.3 4.3 29 96-124 117-145 (163)
277 PRK12423 LexA repressor; Provi 80.6 5.3 0.00011 31.0 5.7 35 89-123 8-45 (202)
278 TIGR02985 Sig70_bacteroi1 RNA 80.6 3.2 7E-05 29.6 4.3 29 98-126 123-151 (161)
279 TIGR02980 SigBFG RNA polymeras 80.6 3 6.4E-05 32.5 4.3 31 96-126 186-216 (227)
280 PRK13890 conjugal transfer pro 80.5 0.58 1.3E-05 33.7 0.2 28 30-57 20-47 (120)
281 smart00344 HTH_ASNC helix_turn 80.4 3.4 7.5E-05 28.2 4.2 29 96-124 9-37 (108)
282 PRK10227 DNA-binding transcrip 80.4 2.7 5.9E-05 30.8 3.8 24 105-128 1-24 (135)
283 TIGR01950 SoxR redox-sensitive 80.3 2.6 5.7E-05 31.2 3.7 23 105-127 2-24 (142)
284 smart00347 HTH_MARR helix_turn 80.2 5.8 0.00013 26.0 5.1 35 90-124 10-44 (101)
285 PF06322 Phage_NinH: Phage Nin 80.1 2.1 4.5E-05 27.6 2.6 23 106-128 18-40 (64)
286 PRK09514 zntR zinc-responsive 80.0 2.7 5.9E-05 30.9 3.7 24 105-128 2-25 (140)
287 cd00592 HTH_MerR-like Helix-Tu 80.0 7.6 0.00017 26.3 5.8 63 32-115 4-67 (100)
288 PRK11924 RNA polymerase sigma 79.9 3.1 6.8E-05 30.3 4.0 28 99-126 136-163 (179)
289 TIGR02043 ZntR Zn(II)-responsi 79.8 2.9 6.3E-05 30.3 3.8 23 105-127 2-24 (131)
290 cd04786 HTH_MerR-like_sg7 Heli 79.6 3 6.5E-05 30.4 3.8 24 105-128 1-24 (131)
291 PF06892 Phage_CP76: Phage reg 79.5 9.9 0.00021 28.8 6.7 54 89-144 7-62 (162)
292 PRK13749 transcriptional regul 79.1 3.2 7E-05 30.0 3.8 25 104-128 3-27 (121)
293 PRK12519 RNA polymerase sigma 79.1 2.9 6.4E-05 31.5 3.8 31 96-126 149-179 (194)
294 TIGR02051 MerR Hg(II)-responsi 79.1 2.2 4.7E-05 30.6 2.9 23 106-128 1-23 (124)
295 PRK06596 RNA polymerase factor 79.1 2.1 4.5E-05 35.0 3.1 24 103-126 247-270 (284)
296 TIGR02937 sigma70-ECF RNA poly 79.1 3.7 8E-05 28.5 4.1 28 99-126 121-148 (158)
297 PRK09652 RNA polymerase sigma 79.0 3.6 7.9E-05 30.1 4.2 28 99-126 139-166 (182)
298 COG2963 Transposase and inacti 79.0 5.5 0.00012 27.8 4.9 40 86-125 6-46 (116)
299 TIGR02337 HpaR homoprotocatech 79.0 5.3 0.00012 27.9 4.8 32 93-124 31-62 (118)
300 PRK09954 putative kinase; Prov 78.9 4.5 9.8E-05 33.7 5.2 33 94-126 7-39 (362)
301 TIGR02989 Sig-70_gvs1 RNA poly 78.9 4 8.6E-05 29.5 4.3 31 94-124 117-147 (159)
302 smart00530 HTH_XRE Helix-turn- 78.8 0.75 1.6E-05 26.0 0.3 26 30-55 12-37 (56)
303 TIGR02395 rpoN_sigma RNA polym 78.7 1.4 3E-05 38.5 2.0 42 103-144 317-358 (429)
304 PRK13752 putative transcriptio 78.6 2.3 4.9E-05 31.6 2.9 24 104-127 7-30 (144)
305 cd07377 WHTH_GntR Winged helix 78.6 8.4 0.00018 23.3 5.2 19 106-124 27-45 (66)
306 PRK06986 fliA flagellar biosyn 78.5 3.9 8.4E-05 32.1 4.4 33 94-126 190-222 (236)
307 PRK13869 plasmid-partitioning 78.3 3.8 8.2E-05 35.3 4.6 42 103-144 47-100 (405)
308 PRK08583 RNA polymerase sigma 78.1 4 8.6E-05 32.5 4.4 29 98-126 215-243 (257)
309 PRK12529 RNA polymerase sigma 78.0 3.9 8.5E-05 30.6 4.2 33 94-126 133-165 (178)
310 cd04773 HTH_TioE_rpt2 Second H 78.0 12 0.00026 26.1 6.4 19 32-50 4-22 (108)
311 PRK09047 RNA polymerase factor 77.9 3.9 8.4E-05 29.6 4.0 32 95-126 113-144 (161)
312 PRK07122 RNA polymerase sigma 77.8 4.1 8.9E-05 32.9 4.5 31 96-126 223-253 (264)
313 PRK07408 RNA polymerase sigma 77.6 4 8.7E-05 32.7 4.3 28 99-126 214-241 (256)
314 cd01109 HTH_YyaN Helix-Turn-He 77.6 14 0.00031 25.7 6.7 20 32-51 4-23 (113)
315 PRK09639 RNA polymerase sigma 77.5 4.7 0.0001 29.4 4.4 32 94-126 118-149 (166)
316 COG3620 Predicted transcriptio 77.4 1.1 2.4E-05 34.5 0.9 28 30-57 20-47 (187)
317 COG3413 Predicted DNA binding 77.2 2.7 5.9E-05 32.8 3.2 24 103-126 177-200 (215)
318 PF08822 DUF1804: Protein of u 77.2 6.1 0.00013 30.3 4.9 38 89-126 4-41 (165)
319 PRK01905 DNA-binding protein F 76.9 6 0.00013 26.1 4.3 34 93-126 39-72 (77)
320 PF00126 HTH_1: Bacterial regu 76.8 6.4 0.00014 24.3 4.3 31 106-147 15-45 (60)
321 cd04779 HTH_MerR-like_sg4 Heli 76.8 3.9 8.5E-05 30.0 3.7 23 105-127 1-23 (134)
322 PRK15320 transcriptional activ 76.7 2.6 5.6E-05 33.7 2.8 26 101-126 176-201 (251)
323 PRK10840 transcriptional regul 76.5 7.6 0.00016 29.5 5.4 49 102-150 163-215 (216)
324 TIGR03830 CxxCG_CxxCG_HTH puta 76.5 2.6 5.7E-05 29.7 2.7 26 30-55 80-105 (127)
325 PRK09642 RNA polymerase sigma 76.4 4.8 0.0001 29.2 4.1 32 94-125 112-143 (160)
326 PRK15002 redox-sensitivie tran 76.4 4.5 9.8E-05 30.4 4.0 29 100-128 7-35 (154)
327 PF13463 HTH_27: Winged helix 76.4 4.7 0.0001 25.0 3.6 30 96-125 9-39 (68)
328 TIGR02684 dnstrm_HI1420 probab 76.3 0.89 1.9E-05 31.2 0.2 30 33-62 48-77 (89)
329 PF10078 DUF2316: Uncharacteri 76.2 7 0.00015 27.0 4.6 37 92-128 11-47 (89)
330 PRK13749 transcriptional regul 76.1 11 0.00025 27.2 5.9 65 31-116 6-72 (121)
331 PRK09649 RNA polymerase sigma 75.9 4.6 0.0001 30.4 4.0 33 93-125 135-167 (185)
332 PRK09645 RNA polymerase sigma 75.9 5 0.00011 29.5 4.2 31 95-125 125-155 (173)
333 PRK12523 RNA polymerase sigma 75.8 5.2 0.00011 29.6 4.2 34 93-126 124-157 (172)
334 TIGR02044 CueR Cu(I)-responsiv 75.8 14 0.0003 26.5 6.3 20 32-51 4-23 (127)
335 TIGR02054 MerD mercuric resist 75.8 13 0.00029 26.7 6.2 21 31-51 6-26 (120)
336 TIGR02941 Sigma_B RNA polymera 75.7 5.3 0.00011 31.7 4.5 31 96-126 213-243 (255)
337 TIGR03001 Sig-70_gmx1 RNA poly 75.7 4.1 8.9E-05 32.6 3.9 54 94-147 167-221 (244)
338 PRK11050 manganese transport r 75.6 7.2 0.00016 28.9 4.9 36 90-125 36-72 (152)
339 cd04775 HTH_Cfa-like Helix-Tur 75.6 11 0.00025 25.9 5.6 66 32-117 5-70 (102)
340 PRK05911 RNA polymerase sigma 75.5 5 0.00011 32.2 4.3 30 97-126 214-243 (257)
341 PRK12537 RNA polymerase sigma 75.4 4.8 0.0001 30.1 4.0 31 96-126 141-171 (182)
342 smart00342 HTH_ARAC helix_turn 75.4 6.9 0.00015 24.5 4.3 23 104-126 1-23 (84)
343 TIGR02702 SufR_cyano iron-sulf 75.3 5.7 0.00012 30.7 4.5 29 96-124 7-35 (203)
344 PRK13919 putative RNA polymera 75.3 5.3 0.00011 29.8 4.2 32 95-126 142-173 (186)
345 TIGR02479 FliA_WhiG RNA polyme 75.2 5.6 0.00012 30.9 4.5 31 96-126 183-213 (224)
346 PRK09646 RNA polymerase sigma 75.2 12 0.00026 28.2 6.2 43 96-145 150-192 (194)
347 PRK00430 fis global DNA-bindin 75.1 6.3 0.00014 27.2 4.2 33 94-126 58-90 (95)
348 PF07900 DUF1670: Protein of u 75.1 6.3 0.00014 31.5 4.7 40 94-133 94-140 (220)
349 PF13309 HTH_22: HTH domain 75.1 2.9 6.2E-05 26.7 2.3 20 106-125 44-63 (64)
350 PRK05932 RNA polymerase factor 75.1 1.4 3.1E-05 38.7 1.1 42 103-144 342-383 (455)
351 PF13556 HTH_30: PucR C-termin 75.0 8.6 0.00019 23.8 4.5 37 102-149 10-46 (59)
352 TIGR03453 partition_RepA plasm 75.0 5.8 0.00013 33.7 4.8 43 103-145 32-86 (387)
353 PRK13509 transcriptional repre 74.9 7.3 0.00016 31.3 5.1 33 93-125 8-40 (251)
354 PF04703 FaeA: FaeA-like prote 74.6 5.7 0.00012 25.4 3.6 24 102-125 13-36 (62)
355 PRK12469 RNA polymerase factor 74.6 1.8 3.8E-05 38.5 1.6 44 103-146 368-411 (481)
356 cd04777 HTH_MerR-like_sg1 Heli 74.6 11 0.00024 26.1 5.4 20 32-51 4-23 (107)
357 TIGR02366 DHAK_reg probable di 74.5 7.6 0.00016 28.6 4.8 39 90-128 6-47 (176)
358 cd04776 HTH_GnyR Helix-Turn-He 74.5 16 0.00035 25.9 6.4 19 32-50 4-22 (118)
359 PRK11511 DNA-binding transcrip 74.5 16 0.00034 26.1 6.4 26 103-128 24-49 (127)
360 smart00418 HTH_ARSR helix_turn 74.4 7 0.00015 23.1 3.9 24 102-125 8-31 (66)
361 PRK15411 rcsA colanic acid cap 74.4 3.4 7.5E-05 32.0 3.0 25 102-126 150-174 (207)
362 PRK08301 sporulation sigma fac 74.4 6.3 0.00014 30.8 4.6 25 102-126 196-220 (234)
363 PRK07500 rpoH2 RNA polymerase 74.3 5.8 0.00013 32.5 4.5 24 103-126 244-267 (289)
364 PRK12511 RNA polymerase sigma 74.3 5.5 0.00012 30.1 4.1 31 96-126 119-149 (182)
365 cd01106 HTH_TipAL-Mta Helix-Tu 74.2 19 0.00042 24.6 6.6 66 32-117 4-70 (103)
366 TIGR02612 mob_myst_A mobile my 74.2 4.7 0.0001 30.3 3.6 43 28-70 38-82 (150)
367 PHA01082 putative transcriptio 74.2 2.4 5.2E-05 31.0 1.9 41 101-141 27-68 (133)
368 PRK12547 RNA polymerase sigma 74.1 6.1 0.00013 29.0 4.2 34 93-126 117-150 (164)
369 cd01392 HTH_LacI Helix-turn-he 74.0 2.7 5.8E-05 24.9 1.9 21 33-53 2-22 (52)
370 TIGR02984 Sig-70_plancto1 RNA 73.8 6.6 0.00014 29.1 4.4 31 96-126 148-178 (189)
371 TIGR02997 Sig70-cyanoRpoD RNA 73.7 6.1 0.00013 32.4 4.5 25 102-126 267-291 (298)
372 cd04790 HTH_Cfa-like_unk Helix 73.7 16 0.00034 27.8 6.4 20 31-50 4-23 (172)
373 PRK05602 RNA polymerase sigma 73.7 5.7 0.00012 29.7 4.1 29 98-126 138-166 (186)
374 TIGR02954 Sig70_famx3 RNA poly 73.6 5.8 0.00012 29.1 4.0 33 94-126 125-157 (169)
375 PRK12534 RNA polymerase sigma 73.5 5.8 0.00013 29.6 4.0 29 98-126 147-175 (187)
376 TIGR02952 Sig70_famx2 RNA poly 73.5 6.8 0.00015 28.5 4.3 31 95-125 129-159 (170)
377 PRK10411 DNA-binding transcrip 73.4 8.4 0.00018 30.8 5.1 32 94-125 8-39 (240)
378 PRK10219 DNA-binding transcrip 73.3 16 0.00035 24.9 6.0 26 103-128 20-45 (107)
379 PRK12516 RNA polymerase sigma 72.9 6.5 0.00014 29.8 4.2 33 94-126 122-154 (187)
380 PRK03573 transcriptional regul 72.8 12 0.00026 26.9 5.4 30 95-124 36-66 (144)
381 PRK14165 winged helix-turn-hel 72.7 4.4 9.5E-05 32.3 3.3 27 99-125 16-42 (217)
382 cd01108 HTH_CueR Helix-Turn-He 72.4 20 0.00043 25.6 6.5 20 32-51 4-23 (127)
383 PRK12527 RNA polymerase sigma 72.3 6.7 0.00014 28.5 4.0 33 94-126 111-143 (159)
384 PRK13777 transcriptional regul 72.2 10 0.00022 29.4 5.1 32 93-124 48-79 (185)
385 COG1309 AcrR Transcriptional r 72.2 4.6 0.0001 28.3 3.1 30 100-129 28-57 (201)
386 PRK12524 RNA polymerase sigma 72.1 6.9 0.00015 29.6 4.2 33 94-126 142-174 (196)
387 TIGR02047 CadR-PbrR Cd(II)/Pb( 72.1 23 0.00049 25.4 6.7 20 32-51 4-23 (127)
388 PRK12542 RNA polymerase sigma 72.1 6.8 0.00015 29.3 4.1 32 94-125 128-159 (185)
389 TIGR02959 SigZ RNA polymerase 72.1 7.3 0.00016 28.8 4.3 33 94-126 106-138 (170)
390 TIGR01889 Staph_reg_Sar staphy 72.0 12 0.00026 25.9 5.1 23 102-124 41-63 (109)
391 cd01110 HTH_SoxR Helix-Turn-He 71.9 12 0.00025 27.5 5.2 21 31-51 4-24 (139)
392 cd04778 HTH_MerR-like_sg2 Heli 71.9 32 0.00069 27.3 8.0 22 104-126 97-118 (219)
393 PRK12532 RNA polymerase sigma 71.8 6.3 0.00014 29.8 3.9 31 96-126 144-174 (195)
394 TIGR01884 cas_HTH CRISPR locus 71.7 11 0.00023 29.2 5.2 33 93-125 146-178 (203)
395 smart00342 HTH_ARAC helix_turn 71.7 10 0.00022 23.6 4.4 25 102-126 48-73 (84)
396 PF08280 HTH_Mga: M protein tr 71.6 8.2 0.00018 24.0 3.8 29 97-125 12-40 (59)
397 PRK12528 RNA polymerase sigma 71.6 7.7 0.00017 28.2 4.2 33 93-125 118-150 (161)
398 TIGR02983 SigE-fam_strep RNA p 71.6 6.6 0.00014 28.5 3.9 32 95-126 117-148 (162)
399 PRK12545 RNA polymerase sigma 71.6 6.6 0.00014 30.0 4.0 34 93-126 144-177 (201)
400 COG1595 RpoE DNA-directed RNA 71.6 7 0.00015 29.3 4.1 31 96-126 135-165 (182)
401 COG0789 SoxR Predicted transcr 71.3 22 0.00047 24.8 6.4 67 31-117 3-70 (124)
402 PF04760 IF2_N: Translation in 71.2 1.5 3.3E-05 26.8 0.3 42 104-145 3-53 (54)
403 PRK12530 RNA polymerase sigma 71.2 7.2 0.00016 29.5 4.1 34 93-126 139-172 (189)
404 PRK11302 DNA-binding transcrip 71.1 4.1 9E-05 32.6 2.9 32 103-134 33-64 (284)
405 PF09012 FeoC: FeoC like trans 71.0 6.1 0.00013 25.2 3.2 29 96-124 5-34 (69)
406 PRK11923 algU RNA polymerase s 71.0 7.3 0.00016 29.2 4.1 32 94-125 144-175 (193)
407 PRK09647 RNA polymerase sigma 70.7 7.6 0.00016 30.0 4.2 30 97-126 147-176 (203)
408 PRK06930 positive control sigm 70.5 8.1 0.00018 29.4 4.2 30 97-126 123-152 (170)
409 cd04769 HTH_MerR2 Helix-Turn-H 70.5 22 0.00048 25.0 6.2 19 32-50 4-22 (116)
410 cd04786 HTH_MerR-like_sg7 Heli 70.3 25 0.00053 25.6 6.6 19 32-50 4-22 (131)
411 cd04785 HTH_CadR-PbrR-like Hel 70.1 23 0.00051 25.2 6.4 20 32-51 4-23 (126)
412 TIGR02394 rpoS_proteo RNA poly 70.1 8.3 0.00018 31.3 4.5 43 102-148 240-282 (285)
413 cd00090 HTH_ARSR Arsenical Res 70.0 12 0.00025 22.7 4.3 21 105-125 21-41 (78)
414 TIGR03826 YvyF flagellar opero 70.0 13 0.00028 27.6 5.0 60 89-148 29-92 (137)
415 PRK09648 RNA polymerase sigma 69.9 8.5 0.00018 28.8 4.2 32 94-125 145-176 (189)
416 PRK06288 RNA polymerase sigma 69.8 8 0.00017 31.1 4.3 30 97-126 221-250 (268)
417 PRK09519 recA DNA recombinatio 69.6 11 0.00023 35.7 5.5 60 86-145 582-644 (790)
418 cd08316 Death_FAS_TNFRSF6 Deat 69.4 19 0.00041 25.1 5.5 38 91-128 6-44 (97)
419 PF11268 DUF3071: Protein of u 69.3 5.4 0.00012 30.6 3.0 31 96-126 61-91 (170)
420 TIGR02947 SigH_actino RNA poly 69.3 5.2 0.00011 30.2 2.9 29 98-126 141-169 (193)
421 COG1654 BirA Biotin operon rep 69.3 11 0.00024 25.3 4.2 20 105-124 20-39 (79)
422 PRK10046 dpiA two-component re 69.2 5.2 0.00011 30.8 3.0 22 104-125 177-198 (225)
423 COG4565 CitB Response regulato 69.0 13 0.00027 29.9 5.1 36 90-125 157-194 (224)
424 PRK12514 RNA polymerase sigma 68.8 8.5 0.00018 28.5 4.0 29 98-126 139-167 (179)
425 PRK12526 RNA polymerase sigma 68.8 8.8 0.00019 29.4 4.2 29 97-125 162-190 (206)
426 COG1321 TroR Mn-dependent tran 68.7 12 0.00026 28.1 4.7 36 90-125 9-45 (154)
427 PRK13752 putative transcriptio 68.6 22 0.00047 26.3 6.1 21 30-50 9-29 (144)
428 PRK12515 RNA polymerase sigma 68.6 8.9 0.00019 28.7 4.1 31 95-125 138-168 (189)
429 cd06571 Bac_DnaA_C C-terminal 68.5 8 0.00017 26.1 3.5 29 96-124 36-65 (90)
430 PRK11557 putative DNA-binding 68.5 4.9 0.00011 32.2 2.8 28 101-128 27-54 (278)
431 PRK05901 RNA polymerase sigma 68.5 8.7 0.00019 34.4 4.5 26 102-127 465-490 (509)
432 PRK08359 transcription factor; 68.4 1.8 3.9E-05 33.5 0.2 29 30-58 100-128 (176)
433 PRK14845 translation initiatio 68.4 6.8 0.00015 38.1 4.1 48 92-144 323-370 (1049)
434 PRK09641 RNA polymerase sigma 68.3 8.9 0.00019 28.4 4.0 29 98-126 146-174 (187)
435 PRK12520 RNA polymerase sigma 68.3 9.4 0.0002 28.7 4.2 31 95-125 138-168 (191)
436 PRK09480 slmA division inhibit 68.2 5.5 0.00012 29.5 2.8 28 103-130 29-56 (194)
437 PRK12525 RNA polymerase sigma 68.2 9.6 0.00021 28.1 4.1 30 96-125 126-155 (168)
438 PRK10402 DNA-binding transcrip 68.1 5 0.00011 31.1 2.7 21 104-124 169-189 (226)
439 PF04297 UPF0122: Putative hel 68.1 9.3 0.0002 26.9 3.8 47 94-144 23-69 (101)
440 PRK09483 response regulator; P 68.0 12 0.00026 27.7 4.7 43 102-144 161-207 (217)
441 PF01726 LexA_DNA_bind: LexA D 67.9 13 0.00029 23.7 4.2 35 90-124 9-46 (65)
442 PRK10227 DNA-binding transcrip 67.8 25 0.00054 25.7 6.2 20 32-51 4-23 (135)
443 PRK12543 RNA polymerase sigma 67.7 9.7 0.00021 28.3 4.1 33 94-126 123-155 (179)
444 cd01282 HTH_MerR-like_sg3 Heli 67.7 22 0.00049 24.8 5.8 20 32-51 4-23 (112)
445 PRK09651 RNA polymerase sigma 67.7 9.3 0.0002 28.3 4.0 31 95-125 126-156 (172)
446 PF06971 Put_DNA-bind_N: Putat 67.5 15 0.00032 22.5 4.1 31 93-123 15-47 (50)
447 PRK11361 acetoacetate metaboli 67.4 7.9 0.00017 33.0 4.0 33 93-125 419-451 (457)
448 PRK05803 sporulation sigma fac 67.3 11 0.00024 29.5 4.5 25 102-126 193-217 (233)
449 PRK12531 RNA polymerase sigma 67.2 9 0.0002 28.9 3.9 29 96-124 149-177 (194)
450 PRK11608 pspF phage shock prot 67.1 8.6 0.00019 32.0 4.0 34 93-126 288-321 (326)
451 PRK12540 RNA polymerase sigma 67.0 10 0.00022 28.6 4.1 31 96-126 119-149 (182)
452 TIGR02943 Sig70_famx1 RNA poly 66.9 10 0.00022 28.7 4.1 31 95-125 138-168 (188)
453 PRK15090 DNA-binding transcrip 66.9 10 0.00022 30.3 4.3 26 100-125 24-49 (257)
454 PRK09637 RNA polymerase sigma 66.9 10 0.00022 28.5 4.1 33 93-125 111-143 (181)
455 PF05732 RepL: Firmicute plasm 66.7 5.2 0.00011 30.4 2.4 20 105-124 76-95 (165)
456 TIGR03454 partition_RepB plasm 66.5 28 0.0006 29.4 7.0 39 101-139 174-212 (325)
457 PF07750 GcrA: GcrA cell cycle 66.5 6.9 0.00015 29.7 3.1 30 93-123 8-38 (162)
458 cd04784 HTH_CadR-PbrR Helix-Tu 66.5 30 0.00064 24.6 6.3 20 32-51 4-23 (127)
459 PRK10141 DNA-binding transcrip 66.4 12 0.00026 26.9 4.2 26 99-124 25-50 (117)
460 PRK07670 RNA polymerase sigma 66.4 11 0.00024 29.9 4.4 33 94-126 207-239 (251)
461 TIGR02846 spore_sigmaK RNA pol 66.3 12 0.00026 29.2 4.5 24 103-126 193-216 (227)
462 PRK12513 RNA polymerase sigma 66.2 5.4 0.00012 30.0 2.5 27 99-125 150-176 (194)
463 PRK12546 RNA polymerase sigma 66.2 10 0.00022 28.8 4.0 34 93-126 118-151 (188)
464 COG2771 CsgD DNA-binding HTH d 66.1 16 0.00035 22.0 4.3 27 100-126 15-41 (65)
465 TIGR02948 SigW_bacill RNA poly 66.1 9.9 0.00021 28.1 3.9 29 98-126 146-174 (187)
466 PRK12533 RNA polymerase sigma 66.0 9.5 0.00021 29.8 3.9 31 96-126 142-172 (216)
467 PRK10365 transcriptional regul 66.0 8.8 0.00019 32.5 4.0 33 93-125 407-439 (441)
468 PRK12536 RNA polymerase sigma 66.0 11 0.00024 28.1 4.1 28 98-125 139-166 (181)
469 PF12116 SpoIIID: Stage III sp 65.8 7.9 0.00017 26.3 2.9 47 97-143 12-59 (82)
470 PRK12512 RNA polymerase sigma 65.8 11 0.00024 28.0 4.1 30 96-125 139-168 (184)
471 PF05043 Mga: Mga helix-turn-h 65.7 7.8 0.00017 25.6 2.9 46 94-147 20-65 (87)
472 PF04552 Sigma54_DBD: Sigma-54 65.6 9.7 0.00021 28.9 3.7 92 30-132 51-154 (160)
473 PF12824 MRP-L20: Mitochondria 65.4 32 0.00069 26.2 6.5 51 88-142 86-138 (164)
474 TIGR02939 RpoE_Sigma70 RNA pol 65.2 9.8 0.00021 28.2 3.7 29 97-125 147-175 (190)
475 PRK09210 RNA polymerase sigma 65.2 11 0.00024 32.0 4.5 25 103-127 324-348 (367)
476 PRK12517 RNA polymerase sigma 65.1 11 0.00024 28.5 4.0 29 98-126 138-166 (188)
477 PRK09643 RNA polymerase sigma 65.1 11 0.00024 28.5 4.0 31 94-124 140-170 (192)
478 PRK12522 RNA polymerase sigma 65.0 11 0.00025 27.7 4.0 30 96-125 127-156 (173)
479 PRK06811 RNA polymerase factor 64.9 11 0.00025 28.2 4.1 29 98-126 141-169 (189)
480 TIGR02974 phageshock_pspF psp 64.9 11 0.00023 31.6 4.2 34 93-126 294-327 (329)
481 PRK15201 fimbriae regulatory p 64.8 20 0.00043 28.1 5.3 25 102-126 146-170 (198)
482 TIGR00637 ModE_repress ModE mo 64.7 16 0.00034 25.3 4.4 31 106-147 18-48 (99)
483 PRK15482 transcriptional regul 64.6 6.6 0.00014 31.7 2.8 34 101-134 31-64 (285)
484 PHA02535 P terminase ATPase su 64.6 13 0.00029 33.8 5.0 37 90-127 5-41 (581)
485 TIGR02835 spore_sigmaE RNA pol 64.4 13 0.00029 29.1 4.5 24 103-126 197-220 (234)
486 PRK11475 DNA-binding transcrip 64.3 8.2 0.00018 30.1 3.2 25 102-126 147-171 (207)
487 PRK09392 ftrB transcriptional 64.2 6.9 0.00015 30.3 2.8 22 104-125 173-194 (236)
488 PRK10430 DNA-binding transcrip 64.2 7.3 0.00016 30.2 2.9 25 102-126 176-200 (239)
489 COG5484 Uncharacterized conser 64.1 9.6 0.00021 31.3 3.6 27 102-128 17-43 (279)
490 PRK11337 DNA-binding transcrip 64.0 6.5 0.00014 31.8 2.7 34 102-135 44-77 (292)
491 PRK15043 transcriptional regul 64.0 18 0.00039 29.4 5.2 65 31-116 6-72 (243)
492 PHA03103 double-strand RNA-bin 63.9 12 0.00027 29.1 4.1 39 86-124 9-47 (183)
493 PF13443 HTH_26: Cro/C1-type H 63.8 1.6 3.4E-05 27.0 -0.8 25 29-53 11-35 (63)
494 PRK09415 RNA polymerase factor 63.8 12 0.00025 28.0 3.9 28 98-125 137-164 (179)
495 PF03333 PapB: Adhesin biosynt 63.7 8.7 0.00019 26.6 2.9 22 103-124 52-73 (91)
496 PRK15115 response regulator Gl 63.4 10 0.00022 32.4 3.8 34 93-126 400-433 (444)
497 PRK12541 RNA polymerase sigma 63.3 13 0.00028 26.9 4.0 32 94-125 118-149 (161)
498 COG2197 CitB Response regulato 63.3 8.1 0.00017 30.1 3.0 26 101-126 160-185 (211)
499 COG3355 Predicted transcriptio 63.1 15 0.00032 26.9 4.1 31 94-124 31-62 (126)
500 COG1737 RpiR Transcriptional r 63.1 5.9 0.00013 32.3 2.3 42 102-143 34-76 (281)
No 1
>KOG3398 consensus Transcription factor MBF1 [Transcription]
Probab=99.97 E-value=4.4e-30 Score=184.78 Aligned_cols=133 Identities=65% Similarity=0.904 Sum_probs=123.5
Q ss_pred CCCCCceeeccCCCCCccccCHHHHHHHHHcCCChhhHHhhhcCCCccCCCCcccccccccccchhhhHHHHHhhccCCc
Q 031871 8 TQDWEPVVIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDR 87 (151)
Q Consensus 8 ~~~w~~~~~~~~~~~~~~~~~~~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~ 87 (151)
++||+||++-++.++..+.++++++|+|+|+|+.|+|+++|.+|.++.+ +..+++++||++++.+.+ ..
T Consensus 1 ~~dw~~vt~~~~~~~s~~~k~~~~vnaa~r~g~~v~t~~k~~~g~nkq~--~~~~~t~klD~etE~~~~---------~~ 69 (135)
T KOG3398|consen 1 TSDWDPVTVLKKKAKAATLKDEKAVNAARRAGVDVETVKKFPAGLNKQH--PSTQSTAKLDRETEELGH---------DR 69 (135)
T ss_pred CCCcccceeeecccccccccCHHHHHHHHHhcchhhhhhhhcccccccC--Ccccchhhcccccccccc---------cc
Confidence 4899999644444588899999999999999999999999999999864 457889999999999999 99
Q ss_pred chHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCCCC
Q 031871 88 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRGKK 151 (151)
Q Consensus 88 ~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~e~~ 151 (151)
+...++..|.+.|..+||||+|||.+++..++.|..||+|+..|+..+|.+|.++|||.+++++
T Consensus 70 v~~~Vg~aIq~aR~~KgmsqkDLA~kInekpqVv~dyEsGrAIpNqqil~kmEraLgvKlrgk~ 133 (135)
T KOG3398|consen 70 VPLEVGKAIQQARAQKGMSQKDLAQKINEKPQVIQDYESGRAIPNQQILSKMERALGVKLRGKN 133 (135)
T ss_pred ccHHHHHHHHHHHHhccccHHHHHHHHccCchhhhhHhccccCchHHHHHHHHHHhceeccccc
Confidence 9999999999999999999999999999999999999999999999999999999999999875
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=99.80 E-value=6.1e-21 Score=126.48 Aligned_cols=67 Identities=51% Similarity=0.726 Sum_probs=0.0
Q ss_pred CCCCce-eeccCCCCCccccCHHHHHHHHHcCCChhhHHhhhcCCCccCCCCcccccccccccchhhhH
Q 031871 9 QDWEPV-VIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLAL 76 (151)
Q Consensus 9 ~~w~~~-~~~~~~~~~~~~~~~~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~~~~~~~~ 76 (151)
|||||| ||+|+.|+++++++++++|+|||+|..|+|.+||.+|+|+ +..+.+++++|||++++.++|
T Consensus 1 qDWd~vtvi~kk~p~~~~~r~~~avNaArR~G~~v~T~KK~~~g~Nk-~~~~~~~n~~KLD~etE~~~~ 68 (71)
T PF08523_consen 1 QDWDPVTVIGKKGPRAKVARSESAVNAARRSGAVVETEKKYGAGNNK-HQHGEGQNAAKLDRETEELKH 68 (71)
T ss_dssp ---------------------------------------------------------------------
T ss_pred CCCcccceecccCCCccccCCHHHHHHHHHcCCceEEEEeeeccccc-cCCCcccccccccccccccCC
Confidence 799999 9999999999999999999999999999999999999999 667789999999999999987
No 3
>PRK06424 transcription factor; Provisional
Probab=99.62 E-value=4.8e-15 Score=110.76 Aligned_cols=63 Identities=30% Similarity=0.452 Sum_probs=60.8
Q ss_pred hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCCCC
Q 031871 89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRGKK 151 (151)
Q Consensus 89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~e~~ 151 (151)
...|+.+|+.+|+++||||.+||+.+|+++++|++||+|+..|+.+.+.+|+++||+++.|+.
T Consensus 82 ~~~~g~~Ir~lRe~~GLSQ~eLA~~iGvs~stIskiE~G~~~Ps~~~l~kLa~~Lgvsl~e~~ 144 (144)
T PRK06424 82 VEDYAELVKNARERLSMSQADLAAKIFERKNVIASIERGDLLPDIKTARKLEKILGITLIEKA 144 (144)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCCCCC
Confidence 578999999999999999999999999999999999999999999999999999999999874
No 4
>PHA01976 helix-turn-helix protein
Probab=99.61 E-value=1.6e-15 Score=98.48 Aligned_cols=58 Identities=28% Similarity=0.509 Sum_probs=56.3
Q ss_pred HHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871 91 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 148 (151)
Q Consensus 91 ~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~ 148 (151)
.|+.+|+.+|..+|+||.+||+.+|+++++|++||+|...|+.+.+.+||++|||+++
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 5899999999999999999999999999999999999999999999999999999975
No 5
>PRK08359 transcription factor; Validated
Probab=99.54 E-value=3.5e-14 Score=109.13 Aligned_cols=63 Identities=17% Similarity=0.245 Sum_probs=60.5
Q ss_pred cchHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 031871 87 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG 149 (151)
Q Consensus 87 ~~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~e 149 (151)
.+.++|+++|+++|+.+||||.+||+.+|+++++|++||+|+..|+.+.+.+||++|+|++.+
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 557899999999999999999999999999999999999999999999999999999999875
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=99.54 E-value=3.2e-14 Score=88.84 Aligned_cols=57 Identities=26% Similarity=0.353 Sum_probs=54.9
Q ss_pred HHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 031871 91 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 147 (151)
Q Consensus 91 ~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l 147 (151)
.++.+|+.+|...||||.+||+.+|+++++|++||+|+..|+.+.+.+|+++|||++
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 478999999999999999999999999999999999999999999999999999985
No 7
>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=99.51 E-value=2e-14 Score=92.46 Aligned_cols=56 Identities=34% Similarity=0.484 Sum_probs=48.4
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 148 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~ 148 (151)
|++|+++|+.+|+||.+||+.+|+++++|++||+|+..|+...+.+||++|||+++
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 68999999999999999999999999999999999999999999999999999875
No 8
>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=99.50 E-value=2.8e-14 Score=89.07 Aligned_cols=53 Identities=34% Similarity=0.494 Sum_probs=49.0
Q ss_pred HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871 96 IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 148 (151)
Q Consensus 96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~ 148 (151)
|+++|+++||||.|||+.+|+++++|++||+|+..|+.+.+.+|+++|||+++
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 68899999999999999999999999999999999999999999999999864
No 9
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=99.47 E-value=9.7e-14 Score=91.07 Aligned_cols=56 Identities=29% Similarity=0.431 Sum_probs=53.6
Q ss_pred HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 031871 94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG 149 (151)
Q Consensus 94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~e 149 (151)
.+++++|.+.|+||.+||+.+|||++||..||+|+..|+.....+||+.|++++++
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 48999999999999999999999999999999999999999999999999998764
No 10
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=99.46 E-value=1.3e-13 Score=104.13 Aligned_cols=63 Identities=30% Similarity=0.469 Sum_probs=59.7
Q ss_pred cchHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 031871 87 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG 149 (151)
Q Consensus 87 ~~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~e 149 (151)
.+...|+.+|+.+|+++||||.+||+++|+++++|++||+|+..|+.+.+.+|+++||+++.+
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 446789999999999999999999999999999999999999999999999999999999864
No 11
>PRK09726 antitoxin HipB; Provisional
Probab=99.44 E-value=5.5e-13 Score=91.54 Aligned_cols=60 Identities=25% Similarity=0.361 Sum_probs=57.5
Q ss_pred hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871 89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 148 (151)
Q Consensus 89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~ 148 (151)
...++.+|+.+|..+|+||.+||+.+|+++++|++||+|...|+.+.+.+||++|||+++
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 468999999999999999999999999999999999999999999999999999999975
No 12
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=99.44 E-value=1.7e-13 Score=88.42 Aligned_cols=58 Identities=29% Similarity=0.461 Sum_probs=50.4
Q ss_pred HHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCC
Q 031871 91 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA-IPNQQILTKLERALGVKLR 148 (151)
Q Consensus 91 ~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~-~p~~~~l~kLa~~Lgv~l~ 148 (151)
.||..|+.+|+..||||.++|+.+|+|+++|++||+|+. .|+.+.+.+|+++||++.+
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=99.40 E-value=6.4e-13 Score=97.64 Aligned_cols=59 Identities=25% Similarity=0.294 Sum_probs=56.6
Q ss_pred HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871 90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 148 (151)
Q Consensus 90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~ 148 (151)
..|+.+|+.+|..+||||.+||+.+||++++|++||+|...|+.+.+.+||++|||+++
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 56899999999999999999999999999999999999999999999999999999865
No 14
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=99.32 E-value=3.8e-12 Score=97.90 Aligned_cols=60 Identities=25% Similarity=0.300 Sum_probs=57.4
Q ss_pred hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871 89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 148 (151)
Q Consensus 89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~ 148 (151)
.+.++.+|+.+|+++||||.+||+.+|+|+++|++||+|+..|+...+.+||++|||+++
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 456999999999999999999999999999999999999999999999999999999875
No 15
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=99.32 E-value=5.1e-12 Score=91.69 Aligned_cols=60 Identities=15% Similarity=0.295 Sum_probs=56.6
Q ss_pred hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871 89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 148 (151)
Q Consensus 89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~ 148 (151)
...|+.+|+++|.++||||.|||+.+|+|+++|++||+|+..|+.+++.+||++|||+++
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 357899999999999999999999999999999999999999999999999999999654
No 16
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=99.30 E-value=8.6e-12 Score=82.86 Aligned_cols=58 Identities=14% Similarity=0.163 Sum_probs=54.5
Q ss_pred HHHHHHH-HHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871 91 ELKKAIV-QARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 148 (151)
Q Consensus 91 ~~~~~Lk-~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~ 148 (151)
..+++|+ .+|++.|+||.+||+.+|+++++|++||+|...|+.+.+.+|+++|||+++
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 4578899 899999999999999999999999999999999999999999999999864
No 17
>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=99.26 E-value=1.7e-11 Score=84.71 Aligned_cols=59 Identities=27% Similarity=0.345 Sum_probs=55.0
Q ss_pred chHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871 88 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 148 (151)
Q Consensus 88 ~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~ 148 (151)
-...++.+|+.+|+++|||| ||+++||++++|++||+|+..|+.+.+.+||++||+++.
T Consensus 29 ~~~~~~~~l~~~r~~~glSq--LAe~~GIs~stLs~iE~g~~~Ps~~tL~kI~~aLgi~l~ 87 (89)
T TIGR02684 29 DPAYIAHALGYIARARGMTQ--LARKTGLSRESLYKALSGKGNPTFDTILKVTKALGLKLT 87 (89)
T ss_pred CHHHHHHHHHHHHHHCChHH--HHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHcCCcee
Confidence 34678999999999999995 999999999999999999999999999999999999874
No 18
>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed
Probab=99.26 E-value=1.8e-11 Score=101.23 Aligned_cols=60 Identities=23% Similarity=0.339 Sum_probs=57.7
Q ss_pred hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871 89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 148 (151)
Q Consensus 89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~ 148 (151)
...++++|+.+|+++||||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||+++
T Consensus 26 ~~~~g~rl~~~R~~~gltq~~lA~~~gvs~~~i~~~E~g~~~ps~~~l~~ia~~l~v~~~ 85 (309)
T PRK08154 26 LAALGERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCSLA 85 (309)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCCCHH
Confidence 467999999999999999999999999999999999999999999999999999999875
No 19
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=99.25 E-value=1.5e-11 Score=93.36 Aligned_cols=65 Identities=37% Similarity=0.546 Sum_probs=61.4
Q ss_pred CcchHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCCC
Q 031871 86 DRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRGK 150 (151)
Q Consensus 86 ~~~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~e~ 150 (151)
..+..+++++|+.+|+.+||||+|||++++++.+.|.+||+|+..|+...+.+|+++||+.+.++
T Consensus 74 ~elvedY~e~Ir~ARE~~G~SqedLA~ki~ek~svI~~iE~g~~~P~~~~akkLEk~LgIkL~e~ 138 (165)
T COG1813 74 PELVEDYGERIREAREKRGLSQEDLAAKLKEKVSVIRRIERGEATPNIKVAKKLEKLLGIKLVEK 138 (165)
T ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHhcccHHHHHHHHhcccCccHHHHHHHHHHhCceeeee
Confidence 35578999999999999999999999999999999999999999999999999999999998764
No 20
>PRK10072 putative transcriptional regulator; Provisional
Probab=99.18 E-value=6.6e-11 Score=82.87 Aligned_cols=54 Identities=22% Similarity=0.316 Sum_probs=50.1
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 147 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l 147 (151)
...|+.+|...||||.+||+.+|+|.++|++||+|++.|+...+ .|+++|++++
T Consensus 35 ~~eik~LR~~~glTQ~elA~~lGvS~~TVs~WE~G~r~P~~~~l-~Ll~~L~~~P 88 (96)
T PRK10072 35 FTEFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVKPSSAEL-KLMRLIQANP 88 (96)
T ss_pred hHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH-HHHHHHhhCH
Confidence 44599999999999999999999999999999999999999986 5999999886
No 21
>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=99.13 E-value=1.2e-10 Score=87.58 Aligned_cols=55 Identities=18% Similarity=0.194 Sum_probs=51.5
Q ss_pred HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCC--CCHHHHHHHHHHhCCCCC
Q 031871 94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAI--PNQQILTKLERALGVKLR 148 (151)
Q Consensus 94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~--p~~~~l~kLa~~Lgv~l~ 148 (151)
..|+.+|...||||.+||+++|||+++|++||+|+.. |+.+.+.+||++|||++.
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 6799999999999999999999999999999999864 899999999999999853
No 22
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=99.12 E-value=7.5e-11 Score=75.42 Aligned_cols=55 Identities=20% Similarity=0.291 Sum_probs=42.4
Q ss_pred HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCCCCCC
Q 031871 95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK-AIPNQQILTKLERALGVKLRG 149 (151)
Q Consensus 95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~-~~p~~~~l~kLa~~Lgv~l~e 149 (151)
+|+.+..++|+|+.+||+.+|++++++++|-+|+ ..|+.+.+.+||++|||++++
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 689999999999999998753
No 23
>PRK04140 hypothetical protein; Provisional
Probab=99.09 E-value=2.5e-10 Score=95.13 Aligned_cols=60 Identities=25% Similarity=0.313 Sum_probs=56.8
Q ss_pred hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871 89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 148 (151)
Q Consensus 89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~ 148 (151)
....+++|+.+|+++||||.+||+.+|+|+++|++||+|+..|+.+.+.+|+++||+++.
T Consensus 124 v~i~GerLk~lRe~~GlSq~eLA~~lGVSr~tIskyE~G~~~Ps~e~~~kLa~~Lgv~l~ 183 (317)
T PRK04140 124 VKIDGDVLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDVPLT 183 (317)
T ss_pred ehhhHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCChH
Confidence 356799999999999999999999999999999999999999999999999999999864
No 24
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=99.07 E-value=5.7e-10 Score=66.55 Aligned_cols=53 Identities=36% Similarity=0.543 Sum_probs=50.2
Q ss_pred HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871 96 IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 148 (151)
Q Consensus 96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~ 148 (151)
|+.+|...++|+.+||+.+|+++.+|++|++|...|+.+.+.+|+++||+++.
T Consensus 2 i~~~~~~~~~s~~~la~~~~i~~~~i~~~~~~~~~~~~~~~~~i~~~~~~~~~ 54 (56)
T smart00530 2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLD 54 (56)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCCChh
Confidence 67788999999999999999999999999999999999999999999999875
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=99.00 E-value=1.7e-09 Score=64.91 Aligned_cols=55 Identities=36% Similarity=0.529 Sum_probs=51.5
Q ss_pred HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871 94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 148 (151)
Q Consensus 94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~ 148 (151)
+.|+..|...|+|+.++|+.+|+++.+|++|++|...|+...+.+|++.||++++
T Consensus 2 ~~l~~~~~~~~~s~~~~a~~~~~~~~~v~~~~~g~~~~~~~~~~~i~~~~~~~~~ 56 (58)
T cd00093 2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLD 56 (58)
T ss_pred hHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCChh
Confidence 4578888999999999999999999999999999999999999999999999875
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=98.96 E-value=1.5e-09 Score=78.24 Aligned_cols=58 Identities=26% Similarity=0.324 Sum_probs=52.2
Q ss_pred HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871 90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 148 (151)
Q Consensus 90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~ 148 (151)
...+..|+.+|...|+||.+||+.+|+++++|++||+|+..|+.. +.+|++.|+++++
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 456778999999999999999999999999999999999988865 6788899998875
No 27
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=98.96 E-value=1.7e-09 Score=72.94 Aligned_cols=60 Identities=27% Similarity=0.349 Sum_probs=49.4
Q ss_pred hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCCCCC
Q 031871 89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK-AIPNQQILTKLERALGVKLR 148 (151)
Q Consensus 89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~-~~p~~~~l~kLa~~Lgv~l~ 148 (151)
...+...|.++|+++||||.|+|+.+|++++.|+++|+|+ ..++.+.|.+++..||..++
T Consensus 16 k~~l~~~i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L~~~l~aLG~~v~ 76 (80)
T PF13744_consen 16 KAQLMAAIRELREERGLTQAELAERLGISQPRVSRLENGKIDDFSLDTLLRYLEALGGRVE 76 (80)
T ss_dssp HHHHHHHHHHHHHCCT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHHHHHHHHHTTEEEE
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHHHHHHHHHcCCeEE
Confidence 5677888999999999999999999999999999999987 67899999999999997653
No 28
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=98.89 E-value=4.3e-09 Score=79.88 Aligned_cols=52 Identities=23% Similarity=0.319 Sum_probs=49.1
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALG 144 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lg 144 (151)
.+-|++.|++.|+||++||++.|+|+++|.++|.|+..|....+.+|.++|.
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 5669999999999999999999999999999999999999999999999874
No 29
>PHA00542 putative Cro-like protein
Probab=98.84 E-value=1.4e-08 Score=69.02 Aligned_cols=50 Identities=22% Similarity=0.245 Sum_probs=45.4
Q ss_pred HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHh
Q 031871 94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK-AIPNQQILTKLERAL 143 (151)
Q Consensus 94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~-~~p~~~~l~kLa~~L 143 (151)
.++..++...|+||.+||+.+||++++|++||+|. ..|+.+.+.+|++++
T Consensus 21 ~~l~~~l~~~glTq~elA~~lgIs~~tIsr~e~g~~~~p~~~~l~ki~~~~ 71 (82)
T PHA00542 21 DELVCALIRAGWSQEQIADATDVSQPTICRIYSGRHKDPRYSVVEKLRHLV 71 (82)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHH
Confidence 35667788899999999999999999999999999 479999999999876
No 30
>PRK10856 cytoskeletal protein RodZ; Provisional
Probab=98.83 E-value=6.7e-09 Score=87.11 Aligned_cols=59 Identities=20% Similarity=0.213 Sum_probs=54.0
Q ss_pred HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCH------HHHHHHHHHhCCCCC
Q 031871 90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQ------QILTKLERALGVKLR 148 (151)
Q Consensus 90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~------~~l~kLa~~Lgv~l~ 148 (151)
+.+|.+|+++|+++||||.+||+++++++++|++||+|+..+.. ..+..+|++|||+.+
T Consensus 13 ~~~G~~Lr~aRe~~GlSq~~vA~~l~l~~~~I~~iE~g~~~~~~~~tf~RGyir~yA~~lgv~~~ 77 (331)
T PRK10856 13 LTTGERLRQAREQLGLTQQAVAERLCLKVSTVRDIEEDKAPADLASTFLRGYIRSYARLVHIPEE 77 (331)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHCCCCCCChhHHHHHHHHHHHHHHHCcCHH
Confidence 46899999999999999999999999999999999999987766 458899999999865
No 31
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=98.78 E-value=3e-08 Score=66.26 Aligned_cols=53 Identities=19% Similarity=0.178 Sum_probs=44.7
Q ss_pred hHHHHHHHHHHHhcCCcCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q 031871 89 PSELKKAIVQARNDKKLTQSQLAQLIN------EKPQVIQEYESGKAIPNQQILTKLERAL 143 (151)
Q Consensus 89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lg------is~s~Is~~E~G~~~p~~~~l~kLa~~L 143 (151)
.+.|+.+|+..|...|+||.|||+.+| +|+++|++||+|. .+...+.+|--+|
T Consensus 9 le~~~~~lk~~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es~~--ls~~n~~kl~p~l 67 (75)
T smart00352 9 LEAFAKTFKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEALQ--LSFKNMCKLKPLL 67 (75)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHhcC--ccHHHHHHHHHHH
Confidence 467999999999999999999999999 5999999999986 4666666654433
No 32
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=98.72 E-value=2.9e-08 Score=70.28 Aligned_cols=45 Identities=20% Similarity=0.338 Sum_probs=40.8
Q ss_pred HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH
Q 031871 92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQIL 136 (151)
Q Consensus 92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l 136 (151)
-+..|+.+|+..||||.+||..+|+|.+||++||+|+..|+-.-+
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 366799999999999999999999999999999999999976543
No 33
>PRK02866 cyanate hydratase; Validated
Probab=98.69 E-value=8.6e-08 Score=71.80 Aligned_cols=59 Identities=22% Similarity=0.254 Sum_probs=55.5
Q ss_pred HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871 90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 148 (151)
Q Consensus 90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~ 148 (151)
..+.+.|..+|.++|+|++++|+.+|+|..++..++.|...++.+.+.+|+++||++.+
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 46788999999999999999999999999999999999999999999999999998743
No 34
>PRK13355 bifunctional HTH-domain containing protein/aminotransferase; Provisional
Probab=98.68 E-value=4.3e-08 Score=85.92 Aligned_cols=59 Identities=27% Similarity=0.361 Sum_probs=55.3
Q ss_pred HHHHHHHHHHHhcCCcCHHHHHHHh-----CCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871 90 SELKKAIVQARNDKKLTQSQLAQLI-----NEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 148 (151)
Q Consensus 90 ~~~~~~Lk~~R~~~glTQ~eLA~~l-----gis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~ 148 (151)
+.|+++|+.+|+++|+||.+||+.+ |+++++|++||+|+..|+.+.+.+|+++|||+++
T Consensus 2 ~~~~~rL~~~r~~~g~tq~~la~~~~~~g~~vs~~~is~~e~g~~~p~~~~l~~la~~l~v~~~ 65 (517)
T PRK13355 2 TTFAERLKQAMKARGLKQEDLVHAAEARGVKLGKSHISQYVSGKTGPRRDVLPFLAAILGVSED 65 (517)
T ss_pred chHHHHHHHHHHHCCCCHHHHHHHHHhccCCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCcCHH
Confidence 3678999999999999999999996 6999999999999999999999999999999975
No 35
>COG1709 Predicted transcriptional regulator [Transcription]
Probab=98.63 E-value=2.8e-08 Score=78.57 Aligned_cols=57 Identities=26% Similarity=0.424 Sum_probs=52.1
Q ss_pred cchHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCC-CCHHHHHHHHHHh
Q 031871 87 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAI-PNQQILTKLERAL 143 (151)
Q Consensus 87 ~~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~-p~~~~l~kLa~~L 143 (151)
.+.++.|+.|++||+..+.||.+||+.+|+|++.||.||.|++. |....+.++-++|
T Consensus 23 vlS~~pge~lrKWR~~F~vSQ~elA~~l~vSpSVISDYE~GRRk~Pg~~~vkk~V~AL 80 (241)
T COG1709 23 VLSEDPGETLRKWREIFNVSQTELARELGVSPSVISDYESGRRKSPGIAFVKKFVEAL 80 (241)
T ss_pred EecCChhHHHHHHHHHhCccHHHHHHHhCCCcceeehhhccCccCccHHHHHHHHHHH
Confidence 34678899999999999999999999999999999999999988 9999888887765
No 36
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=98.56 E-value=2.2e-07 Score=65.67 Aligned_cols=56 Identities=18% Similarity=0.275 Sum_probs=49.6
Q ss_pred HHHHHHH-HhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871 93 KKAIVQA-RNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 148 (151)
Q Consensus 93 ~~~Lk~~-R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~ 148 (151)
|+.|++- .+..|+||.+||+.+||++.+|+++-+|++.++.+++.+|+++||.+++
T Consensus 11 GEiL~eeflep~glt~~~lA~~lgV~r~~is~ling~~~iT~dmAlrL~k~fGtspe 67 (104)
T COG3093 11 GEILREEFLEPLGLTQTELAEALGVTRNTISELINGRRAITADMALRLAKVFGTSPE 67 (104)
T ss_pred hHHHHHHHhccccCCHHHHHHHhCCCHHHHHHHHcCCcCCCHHHHHHHHHHhCCCHH
Confidence 5556543 5556999999999999999999999999999999999999999998864
No 37
>TIGR00673 cynS cyanate hydratase. Alternate names include cyanate lyase, cyanase and cyanate hydrolase.
Probab=98.54 E-value=3.7e-07 Score=68.56 Aligned_cols=56 Identities=16% Similarity=0.174 Sum_probs=53.9
Q ss_pred HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 031871 92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 147 (151)
Q Consensus 92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l 147 (151)
+.+.|..+|.++|||++++|+.+|+|...+..++.|...++.+.+.+|+++||++-
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 78899999999999999999999999999999999999999999999999999864
No 38
>COG3655 Predicted transcriptional regulator [Transcription]
Probab=98.37 E-value=7.9e-07 Score=59.14 Aligned_cols=58 Identities=19% Similarity=0.232 Sum_probs=51.7
Q ss_pred HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCC-CCHHHHHHHHHHhCCCCCC
Q 031871 92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAI-PNQQILTKLERALGVKLRG 149 (151)
Q Consensus 92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~-p~~~~l~kLa~~Lgv~l~e 149 (151)
+..++..++.+++++..|||+.+|+|.++++.+.+|+.. ++.++|.+||++|+|.+.+
T Consensus 3 i~~~l~~~l~~r~~~~~eLa~~igis~~~ls~l~~gk~k~I~~~tL~~iC~~LeCqpgD 61 (73)
T COG3655 3 IAVRLDVMLADRKISLKELAEAIGISEANLSKLKTGKVKAIRLSTLEKICKALECQPGD 61 (73)
T ss_pred chHhHHHHHHHHhhhHHHHHHHHcccHHHHHHHHcCCcceeeHHHHHHHHHHcCCChhh
Confidence 345678888899999999999999999999999999854 6999999999999998753
No 39
>COG1396 HipB Predicted transcriptional regulators [Transcription]
Probab=98.37 E-value=2.6e-06 Score=55.06 Aligned_cols=56 Identities=30% Similarity=0.520 Sum_probs=52.6
Q ss_pred HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCC
Q 031871 92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA-IPNQQILTKLERALGVKL 147 (151)
Q Consensus 92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~-~p~~~~l~kLa~~Lgv~l 147 (151)
++.+++.+|...|+||.++|..+|++..+++.||+|.. .|....+..++..|+++.
T Consensus 2 ~~~~~~~~r~~~~~s~~~~a~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~ 58 (120)
T COG1396 2 IGERLKELRKKKGLSQEELAERLGVSRSTISRIERGRSESPSLELLARLAAALGVSL 58 (120)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCCHHHHHHHHHHHCCCH
Confidence 57899999999999999999999999999999999999 899999999999988754
No 40
>COG1395 Predicted transcriptional regulator [Transcription]
Probab=98.30 E-value=1.4e-06 Score=72.20 Aligned_cols=57 Identities=19% Similarity=0.330 Sum_probs=54.2
Q ss_pred HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871 92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 148 (151)
Q Consensus 92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~ 148 (151)
-|+.|++.|+++|+|..+||..+|+|+.+|++||+|...|+.+.+.+|.+.||.++-
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 488999999999999999999999999999999999999999999999999998764
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=98.26 E-value=3.8e-07 Score=59.35 Aligned_cols=53 Identities=19% Similarity=0.332 Sum_probs=37.5
Q ss_pred HHHHHHhcCCcC-HHHHHHHhCCCHHHHH-HHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871 95 AIVQARNDKKLT-QSQLAQLINEKPQVIQ-EYESGKAIPNQQILTKLERALGVKLR 148 (151)
Q Consensus 95 ~Lk~~R~~~glT-Q~eLA~~lgis~s~Is-~~E~G~~~p~~~~l~kLa~~Lgv~l~ 148 (151)
+|+++++..|.+ +.+||+.+|||+++|+ .|......| .+.+.+|+..+||+++
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 456666666665 5699999999999999 898877766 9999999999999874
No 42
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=98.18 E-value=7.3e-06 Score=52.86 Aligned_cols=54 Identities=24% Similarity=0.374 Sum_probs=40.3
Q ss_pred HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCC--CCCCH----HHHHHHHHHhCCCCC
Q 031871 95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK--AIPNQ----QILTKLERALGVKLR 148 (151)
Q Consensus 95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~--~~p~~----~~l~kLa~~Lgv~l~ 148 (151)
+|+..|+.+|+|..|+|..++|+.++|..+|+|. ..|.. ..+.++|++||++.+
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 4899999999999999999999999999999996 44543 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=97.96 E-value=2.6e-05 Score=58.48 Aligned_cols=60 Identities=15% Similarity=0.211 Sum_probs=54.7
Q ss_pred hHHHHHHHHHHHhcCCcCH----HHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871 89 PSELKKAIVQARNDKKLTQ----SQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 148 (151)
Q Consensus 89 ~~~~~~~Lk~~R~~~glTQ----~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~ 148 (151)
...+.++|+.+...+|+.+ .+||+.+|+|+++.++-.+|+..++...+.+|++.||++++
T Consensus 3 ~~~~~erV~~Ll~~~Gi~kr~~~s~LA~iL~Is~ssa~RKL~G~~~ftl~EI~~Ia~~fgvS~d 66 (147)
T PF08667_consen 3 DQAIAERVRELLDRKGIPKRKHASELADILGISYSSAYRKLNGKSPFTLEEIKKIAKHFGVSPD 66 (147)
T ss_pred hHHHHHHHHHHHHHcCCcchhhHHHHHHHHCCCHHHHHHHhcCCCCCCHHHHHHHHHHhCcCHH
Confidence 3568899999999999766 56999999999999999999999999999999999999975
No 44
>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=97.87 E-value=4.3e-05 Score=46.57 Aligned_cols=40 Identities=13% Similarity=0.185 Sum_probs=33.1
Q ss_pred HHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCC
Q 031871 109 QLAQLINEKPQVIQEYESGKAIPNQQI---LTKLERALGVKLR 148 (151)
Q Consensus 109 eLA~~lgis~s~Is~~E~G~~~p~~~~---l~kLa~~Lgv~l~ 148 (151)
+||+.+|+|+++|++|++|...++... +.++++.||+.++
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~~vs~~~~~~i~~~~~~l~~~~~ 44 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKPRVSEETRERVLAAAEELGYRPN 44 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHHHhCCCCC
Confidence 799999999999999999997766554 5558888888654
No 45
>COG5499 Predicted transcription regulator containing HTH domain [Transcription]
Probab=97.86 E-value=2.6e-05 Score=55.61 Aligned_cols=56 Identities=20% Similarity=0.225 Sum_probs=51.2
Q ss_pred HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871 92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 148 (151)
Q Consensus 92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~ 148 (151)
=-+.|+.++...|+|+.+||..+| |.+.+|++.+|++..+.+++.+|.+.||++.+
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 356789999999999999999998 77889999999999999999999999999864
No 46
>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=97.85 E-value=6.3e-05 Score=52.45 Aligned_cols=52 Identities=12% Similarity=0.113 Sum_probs=40.6
Q ss_pred HHHHHHHHHHH--hcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHH
Q 031871 90 SELKKAIVQAR--NDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLER 141 (151)
Q Consensus 90 ~~~~~~Lk~~R--~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~ 141 (151)
..+..|++-.+ ...++||.|+|+.+|||.+||++++++-...+++.-.-|.+
T Consensus 39 ~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn~lk~~~~~~~~~l~~ 92 (94)
T TIGR01321 39 EDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRGSNNLKTMDPNFKQFLRK 92 (94)
T ss_pred HHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHHhhcccCCHHHHHHHHh
Confidence 45666666665 35789999999999999999999999988666665555543
No 47
>COG1426 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]
Probab=97.83 E-value=3.2e-05 Score=63.77 Aligned_cols=58 Identities=21% Similarity=0.357 Sum_probs=50.9
Q ss_pred HHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCC--CCC----HHHHHHHHHHhCCCCC
Q 031871 91 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA--IPN----QQILTKLERALGVKLR 148 (151)
Q Consensus 91 ~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~--~p~----~~~l~kLa~~Lgv~l~ 148 (151)
.+|++||+.|+++|||+.|+|.+++|..++|..+|.|.- .|. ...+...|++||++.+
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 332 3467889999998865
No 48
>PHA01083 hypothetical protein
Probab=97.78 E-value=4.1e-05 Score=57.26 Aligned_cols=54 Identities=17% Similarity=0.242 Sum_probs=45.3
Q ss_pred HHHHHHhcCCc-CHHHHHHHhCCCHHHHHHHHcC-CCCCCHHHHHHHHHHhCCCCC
Q 031871 95 AIVQARNDKKL-TQSQLAQLINEKPQVIQEYESG-KAIPNQQILTKLERALGVKLR 148 (151)
Q Consensus 95 ~Lk~~R~~~gl-TQ~eLA~~lgis~s~Is~~E~G-~~~p~~~~l~kLa~~Lgv~l~ 148 (151)
.|....+.+++ +-.+||+.+||+++.|++|.+| ++.++.+.+..||+.+|+++.
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 34444555554 4569999999999999999999 999999999999999999864
No 49
>PF08965 DUF1870: Domain of unknown function (DUF1870); InterPro: IPR015060 This family consist of hypothetical bacterial proteins. ; PDB: 1S4K_A.
Probab=97.56 E-value=0.0002 Score=51.78 Aligned_cols=50 Identities=18% Similarity=0.172 Sum_probs=38.3
Q ss_pred HHHHHHHhcCCcCHHHHHHHhC--CCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q 031871 94 KAIVQARNDKKLTQSQLAQLIN--EKPQVIQEYESGKAIPNQQILTKLERAL 143 (151)
Q Consensus 94 ~~Lk~~R~~~glTQ~eLA~~lg--is~s~Is~~E~G~~~p~~~~l~kLa~~L 143 (151)
-.|+.+|...+||+.|.|..++ ++..+..+||+|++.++.+++..|....
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 4589999999999999999999 9999999999999999999888776543
No 50
>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=97.56 E-value=0.00031 Score=42.69 Aligned_cols=40 Identities=13% Similarity=0.189 Sum_probs=32.7
Q ss_pred CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH---HHHhCC
Q 031871 106 TQSQLAQLINEKPQVIQEYESGKAIPNQQILTKL---ERALGV 145 (151)
Q Consensus 106 TQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kL---a~~Lgv 145 (151)
|.+|+|+.+|+|.+|||++.+|...++.+...+| ++.||-
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~~~~vs~~tr~rI~~~a~~lgY 43 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNGPPRVSEETRERILEAAEELGY 43 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTTCSSSTHHHHHHHHHHHHHHTB
T ss_pred CHHHHHHHHCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHCC
Confidence 6789999999999999999999988887766555 445553
No 51
>COG4800 Predicted transcriptional regulator with an HTH domain [Transcription]
Probab=97.55 E-value=0.00036 Score=52.05 Aligned_cols=54 Identities=17% Similarity=0.242 Sum_probs=49.8
Q ss_pred hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q 031871 89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERAL 143 (151)
Q Consensus 89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~L 143 (151)
.+.|+..|+.+..++|||..|||++.|+..+++.++.+| +.|..+++.+|-+.+
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 468999999999999999999999999999999999999 789999999887765
No 52
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=97.51 E-value=0.00032 Score=45.86 Aligned_cols=43 Identities=14% Similarity=0.139 Sum_probs=34.9
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESGKAIPNQQI---LTKLERALGVKL 147 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~---l~kLa~~Lgv~l 147 (151)
+|+.|+|+.+|+|.++|+++.+|....+.+. +.++++.+|..+
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln~~~~v~~~t~~~i~~~~~~~gy~~ 46 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLNGNGRVSEETREKVLAAMEELGYIP 46 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCCC
Confidence 4789999999999999999999987776554 555677777654
No 53
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=97.37 E-value=0.00057 Score=49.62 Aligned_cols=43 Identities=21% Similarity=0.349 Sum_probs=34.4
Q ss_pred chHHHHHHHH-HHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCC
Q 031871 88 VPSELKKAIV-QARNDKKLTQSQLAQLINEKPQVIQEYESGKAIP 131 (151)
Q Consensus 88 ~~~~~~~~Lk-~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p 131 (151)
+-+.+...|. .++.+ |+||.++|+.+|+|++.||+|-+|++.+
T Consensus 6 vlPaiRa~lA~~L~ee-G~Sq~~iA~LLGltqaAVS~Yls~krg~ 49 (119)
T COG2522 6 VLPAIRALLAKELIEE-GLSQYRIAKLLGLTQAAVSQYLSGKRGS 49 (119)
T ss_pred HHHHHHHHHHHHHHHc-CCcHHHHHHHhCCCHHHHHHHHccCCch
Confidence 3345555554 44555 9999999999999999999999999874
No 54
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=97.11 E-value=0.00091 Score=45.90 Aligned_cols=60 Identities=23% Similarity=0.237 Sum_probs=52.7
Q ss_pred hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCC
Q 031871 89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA-IPNQQILTKLERALGVKLR 148 (151)
Q Consensus 89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~-~p~~~~l~kLa~~Lgv~l~ 148 (151)
...+...|..+.+..+|+|+++|+.+||+++.+|.+-+|+. ..+.+.|.-+....|..++
T Consensus 26 r~~l~~~i~~~i~q~~l~Q~qiae~lgV~qprvS~l~~gk~~~fs~dkLvtml~~~g~ei~ 86 (91)
T COG5606 26 RSALMMAIKQWIEQAALSQAQIAELLGVTQPRVSDLARGKIQDFSIDKLVTMLARAGQEID 86 (91)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHhcchhHhhHHHHHHHHHHcCCccc
Confidence 56788889999999999999999999999999999999994 4688888888888887654
No 55
>PF00157 Pou: Pou domain - N-terminal to homeobox domain; InterPro: IPR000327 POU proteins are eukaryotic transcription factors containing a bipartite DNA binding domain referred to as the POU domain. The acronym POU (pronounced 'pow') is derived from the names of three mammalian transcription factors, the pituitary-specific Pit-1, the octamer-binding proteins Oct-1 and Oct-2, and the neural Unc-86 from Caenorhabditis elegans. POU domain genes have been identified in diverse organisms including nematodes, flies, amphibians, fish and mammals but have not been yet identified in plants and fungi. The various members of the POU family have a wide variety of functions, all of which are related to the function of the neuroendocrine system [] and the development of an organism []. Some other genes are also regulated, including those for immunoglobulin light and heavy chains (Oct-2) [, ], and trophic hormone genes, such as those for prolactin and growth hormone (Pit-1). The POU domain is a bipartite domain composed of two subunits separated by a non-conserved region of 15-55 aa. The N-terminal subunit is known as the POU-specific (POUs) domain (IPR000327 from INTERPRO), while the C-terminal subunit is a homeobox domain (IPR007103 from INTERPRO). 3D structures of complexes including both POU subdomains bound to DNA are available. Both subdomains contain the structural motif 'helix-turn-helix', which directly associates with the two components of bipartite DNA binding sites, and both are required for high affinity sequence-specific DNA-binding. The domain may also be involved in protein-protein interactions []. The subdomains are connected by a flexible linker [, , ]. In proteins a POU-specific domain is always accompanied by a homeodomain. Despite of the lack of sequence homology, 3D structure of POUs is similar to 3D structure of bacteriophage lambda repressor and other members of HTH_3 family [, ]. This entry represents the POU-specific subunit of the POU domain.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3D1N_O 1AU7_A 3L1P_A 2XSD_C 1O4X_A 1HF0_B 1GT0_C 1POU_A 1CQT_B 1E3O_C ....
Probab=97.08 E-value=0.0024 Score=42.72 Aligned_cols=53 Identities=19% Similarity=0.160 Sum_probs=41.7
Q ss_pred hHHHHHHHHHHHhcCCcCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q 031871 89 PSELKKAIVQARNDKKLTQSQLAQLIN------EKPQVIQEYESGKAIPNQQILTKLERAL 143 (151)
Q Consensus 89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lg------is~s~Is~~E~G~~~p~~~~l~kLa~~L 143 (151)
...|+..++..|...|+||.+++..+| .|+++|+++|+= ..+...+.+|--.|
T Consensus 9 le~Fa~~fk~rRi~LG~TQ~dVg~al~~~~G~~~SQttI~RFE~L--~LS~kn~~klkP~L 67 (75)
T PF00157_consen 9 LEQFAKEFKQRRIKLGYTQADVGAALGRLYGKEFSQTTICRFEAL--QLSFKNMCKLKPLL 67 (75)
T ss_dssp HHHHHHHHHHHHHHTT--HHHHHHHHHHHHSSGGSHHHHHHHHTT--TSCHHHHHHHHHHH
T ss_pred HHHHHHHHHHhhhhcccCHHHHhHHHHHhcCccccchhhhhhHhc--ccCHHHHHHHHHHH
Confidence 467999999999999999999998876 489999999984 46777777665443
No 56
>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=96.81 E-value=0.0052 Score=40.95 Aligned_cols=48 Identities=23% Similarity=0.245 Sum_probs=36.3
Q ss_pred HHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHH
Q 031871 91 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLE 140 (151)
Q Consensus 91 ~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa 140 (151)
.....+...|...|+|+.|+|+.+|+|.++|..+.+.. +....+.+++
T Consensus 19 ~~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~--~~~~~~~~~~ 66 (73)
T TIGR03879 19 LAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKGE--TKAGGLVKLA 66 (73)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcC--cccchHHHHH
Confidence 33444444477799999999999999999999999953 4555566665
No 57
>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=96.78 E-value=0.0039 Score=51.15 Aligned_cols=46 Identities=15% Similarity=0.241 Sum_probs=42.9
Q ss_pred CcCHHHHHHHhCCCH-HHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 031871 104 KLTQSQLAQLINEKP-QVIQEYESGKAIPNQQILTKLERALGVKLRG 149 (151)
Q Consensus 104 glTQ~eLA~~lgis~-s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~e 149 (151)
.+|-.+||+.+|++. ++++.+.+|++.++...+.+++++||++..|
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 9999999999999999999999999987654
No 58
>COG3636 Predicted transcriptional regulator [Transcription]
Probab=96.75 E-value=0.0067 Score=42.48 Aligned_cols=56 Identities=16% Similarity=0.194 Sum_probs=47.3
Q ss_pred HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 031871 90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 147 (151)
Q Consensus 90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l 147 (151)
..+...+...-..+||| ++|++.|+++..+.+-.+...+|+.+++.++.++||+.+
T Consensus 37 a~i~~alg~var~~GMs--qvA~~aGlsRe~LYkaLS~~GNPtf~Til~V~kAlG~rl 92 (100)
T COG3636 37 ALIAAALGVVARSRGMS--QVARKAGLSREGLYKALSPGGNPTFDTILAVLKALGLRL 92 (100)
T ss_pred HHHHHHHHHHHHhcCHH--HHHHHhCccHHHHHHHhCCCCCCcHHHHHHHHHHcCcee
Confidence 44555555555667876 589999999999999999999999999999999999865
No 59
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=96.73 E-value=0.0065 Score=43.67 Aligned_cols=74 Identities=19% Similarity=0.234 Sum_probs=47.7
Q ss_pred HHHHHHHHHcCCChhhHHhhhcCCCccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHH-HhcCCcCH
Q 031871 29 EKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQA-RNDKKLTQ 107 (151)
Q Consensus 29 ~~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~-R~~~glTQ 107 (151)
.+..++|++.||+..|+.+|-.-.......+..+.-.++|. .. |+.+ -....+|+
T Consensus 19 ~s~~eaa~~F~VS~~Tv~~W~k~~~~G~~~~k~r~~~Kid~--------------------~~----L~~~v~~~pd~tl 74 (119)
T PF01710_consen 19 KSIREAAKRFGVSRNTVYRWLKRKETGDLEPKPRGRKKIDR--------------------DE----LKALVEENPDATL 74 (119)
T ss_pred chHHHHHHHhCcHHHHHHHHHHhcccccccccccccccccH--------------------HH----HHHHHHHCCCcCH
Confidence 46788999999999999999762111100010111113321 11 2222 34678999
Q ss_pred HHHHHHhCCCHHHHHHHHc
Q 031871 108 SQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 108 ~eLA~~lgis~s~Is~~E~ 126 (151)
.|+|+.+|||+++|.....
T Consensus 75 ~Ela~~l~Vs~~ti~~~Lk 93 (119)
T PF01710_consen 75 RELAERLGVSPSTIWRALK 93 (119)
T ss_pred HHHHHHcCCCHHHHHHHHH
Confidence 9999999999999998864
No 60
>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A.
Probab=96.57 E-value=0.006 Score=41.13 Aligned_cols=52 Identities=15% Similarity=0.095 Sum_probs=38.4
Q ss_pred HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871 94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 148 (151)
Q Consensus 94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~ 148 (151)
..|+.....+|+|..+||+..|++.++++.... .|....-..||++|||++.
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 346666778999999999999999999998754 4556667789999999875
No 61
>PHA00675 hypothetical protein
Probab=96.52 E-value=0.0075 Score=40.46 Aligned_cols=39 Identities=10% Similarity=0.049 Sum_probs=34.0
Q ss_pred HHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCC
Q 031871 91 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA 129 (151)
Q Consensus 91 ~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~ 129 (151)
.--+.|+.+++..|.|+.+||..+|+|+++|+.|-+|++
T Consensus 26 ~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~~gk~ 64 (78)
T PHA00675 26 AEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICRYER 64 (78)
T ss_pred HHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHHccch
Confidence 345568888878899999999999999999999999874
No 62
>PHA02591 hypothetical protein; Provisional
Probab=96.38 E-value=0.0075 Score=40.63 Aligned_cols=26 Identities=19% Similarity=0.325 Sum_probs=23.5
Q ss_pred hcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 101 NDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 101 ~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
.+.|+||.++|+.+|+++.+|++|-.
T Consensus 56 ~eqGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 56 ARKGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 45799999999999999999999864
No 63
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=96.34 E-value=0.0077 Score=36.23 Aligned_cols=24 Identities=4% Similarity=0.097 Sum_probs=19.2
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHcC
Q 031871 104 KLTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 104 glTQ~eLA~~lgis~s~Is~~E~G 127 (151)
|+|+.++|+.+|+|++||.+|-+-
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 999999999999999999999763
No 64
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=96.31 E-value=0.011 Score=48.11 Aligned_cols=45 Identities=20% Similarity=0.127 Sum_probs=37.9
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH---HHHhCCCC
Q 031871 103 KKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKL---ERALGVKL 147 (151)
Q Consensus 103 ~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kL---a~~Lgv~l 147 (151)
+..|.+|+|+++|||++|||++.||+..++.++..++ ++.||..+
T Consensus 5 ~~~Ti~dIA~~agVS~~TVSr~Ln~~~~vs~~tr~~V~~~a~elgY~p 52 (342)
T PRK10014 5 KKITIHDVALAAGVSVSTVSLVLSGKGRISTATGERVNQAIEELGFVR 52 (342)
T ss_pred CCCcHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCCc
Confidence 3579999999999999999999999988887776655 77777654
No 65
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=96.27 E-value=0.0094 Score=38.19 Aligned_cols=40 Identities=20% Similarity=0.242 Sum_probs=28.9
Q ss_pred cCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Q 031871 102 DKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV 145 (151)
Q Consensus 102 ~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv 145 (151)
..| ++..||+.+|||+++|+.| +. .++......|..+-+=
T Consensus 8 ~~G-~~~~lAkalGVs~~aVs~W--~~-~IP~~ra~~Ie~~T~G 47 (60)
T PF14549_consen 8 YFG-GQSKLAKALGVSPQAVSQW--GE-RIPAERAYQIEKLTNG 47 (60)
T ss_dssp HHS-SHHHHHHHHTS-HHHHHHH--HT-S--HHHHHHHHHHTTT
T ss_pred HHC-CHHHHHHHHCCCHHHHHHh--cC-ccCHHHHHHHHHHhCC
Confidence 345 8999999999999999999 33 3566677777776553
No 66
>COG3423 Nlp Predicted transcriptional regulator [Transcription]
Probab=96.13 E-value=0.016 Score=38.88 Aligned_cols=51 Identities=18% Similarity=0.199 Sum_probs=40.9
Q ss_pred HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 031871 96 IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG 149 (151)
Q Consensus 96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~e 149 (151)
|....+.+|+|...|+.+.|+|++|+.....- .-|..+ .-||++|||++.|
T Consensus 13 I~A~Lkk~G~Sl~~LS~~agls~~tL~n~L~r-p~pkgE--riIA~algv~P~e 63 (82)
T COG3423 13 IIAALKKKGTSLAALSREAGLSSSTLANALDR-PWPKGE--RIIADALGVPPEE 63 (82)
T ss_pred HHHHHHHccccHHHHHHHcCCCHHHHHHHHcC-CCchHH--HHHHHHhCCCHHH
Confidence 45556678999999999999999999998773 335554 4589999999865
No 67
>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=96.10 E-value=0.018 Score=42.26 Aligned_cols=48 Identities=8% Similarity=0.063 Sum_probs=37.7
Q ss_pred HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHH
Q 031871 95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERA 142 (151)
Q Consensus 95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~ 142 (151)
.+..+....|+|++++|..+|++++|++++-++...++.+.-.++.+.
T Consensus 27 ~~~~l~~~l~ls~~el~~~lgis~~Tl~R~~~~~~~Ls~~~serl~~l 74 (133)
T TIGR02293 27 ALDRLAHLLAIGKAEIFKATGIPKATLQRRKMAHQRLSSEESDRLARV 74 (133)
T ss_pred HHHHHHHHHCCCHHHHHHHHCCCHHHHHHHhhcCCCCCHHHHHHHHHH
Confidence 345556778999999999999999999999987767776655555443
No 68
>PRK09492 treR trehalose repressor; Provisional
Probab=96.08 E-value=0.014 Score=47.02 Aligned_cols=44 Identities=14% Similarity=0.136 Sum_probs=36.1
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHH---HHHHhCCCC
Q 031871 104 KLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTK---LERALGVKL 147 (151)
Q Consensus 104 glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~k---La~~Lgv~l 147 (151)
.+|.+|+|+.+|||.+|||++.||...++.++..+ .++.||-.+
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 47999999999999999999999987777766555 466777544
No 69
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=96.07 E-value=0.011 Score=35.18 Aligned_cols=30 Identities=7% Similarity=0.124 Sum_probs=20.4
Q ss_pred HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
.|..++ ..|+|+.++|+.+|++++||+++-
T Consensus 12 ~I~~l~-~~G~s~~~IA~~lg~s~sTV~rel 41 (44)
T PF13936_consen 12 QIEALL-EQGMSIREIAKRLGRSRSTVSREL 41 (44)
T ss_dssp HHHHHH-CS---HHHHHHHTT--HHHHHHHH
T ss_pred HHHHHH-HcCCCHHHHHHHHCcCcHHHHHHH
Confidence 355554 689999999999999999999864
No 70
>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=96.05 E-value=0.015 Score=34.74 Aligned_cols=33 Identities=9% Similarity=0.172 Sum_probs=23.6
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
.+.+.+++. .|+|..++|+.+|||++||.+|.+
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 459999999999999999999875
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=96.05 E-value=0.059 Score=36.45 Aligned_cols=49 Identities=10% Similarity=0.087 Sum_probs=39.7
Q ss_pred HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhC
Q 031871 95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK-AIPNQQILTKLERALG 144 (151)
Q Consensus 95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~-~~p~~~~l~kLa~~Lg 144 (151)
.+..++. ..+|..++|+.+|+|.+||++..++. ..++.++..++-++..
T Consensus 11 I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L~~~~~~Vs~~Tr~rV~~aa~ 60 (80)
T TIGR02844 11 IGKYIVE-TKATVRETAKVFGVSKSTVHKDVTERLPEINPELAEEVKEVLD 60 (80)
T ss_pred HHHHHHH-CCCCHHHHHHHhCCCHHHHHHHhcCCCCCCCHHHHHHHHHHHc
Confidence 3444555 78899999999999999999999986 6788888877776654
No 72
>PRK09526 lacI lac repressor; Reviewed
Probab=96.00 E-value=0.016 Score=47.29 Aligned_cols=45 Identities=11% Similarity=-0.011 Sum_probs=35.6
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH---HHHHHHhCCCC
Q 031871 103 KKLTQSQLAQLINEKPQVIQEYESGKAIPNQQIL---TKLERALGVKL 147 (151)
Q Consensus 103 ~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l---~kLa~~Lgv~l 147 (151)
+..|.+|+|+++|||.+|||++.||...++.++. .++++.||-.+
T Consensus 4 ~~~ti~dIA~~aGVS~~TVSrvLn~~~~vs~~tr~rV~~~a~elgY~p 51 (342)
T PRK09526 4 KPVTLYDVARYAGVSYQTVSRVLNQASHVSAKTREKVEAAMAELNYVP 51 (342)
T ss_pred CCCcHHHHHHHhCCCHHHHHHHhcCCCCCCHHHHHHHHHHHHHHCCCc
Confidence 3469999999999999999999999877766654 45566666544
No 73
>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=95.96 E-value=0.026 Score=33.68 Aligned_cols=34 Identities=21% Similarity=0.371 Sum_probs=26.8
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
.+-|..+...-++|+.|+|+.+|+|.++++++-+
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 4456777888889999999999999999998743
No 74
>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=95.95 E-value=0.016 Score=43.02 Aligned_cols=34 Identities=18% Similarity=0.329 Sum_probs=28.3
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcC
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G 127 (151)
...+-.+| ..|+||+|+|+.+|+|+++|+.+|+.
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 33444555 59999999999999999999999985
No 75
>PF04814 HNF-1_N: Hepatocyte nuclear factor 1 (HNF-1), N terminus; InterPro: IPR006899 This domain consists of the N terminus of homeobox-containing transcription factor HNF-1. This region contains a dimerisation sequence [] and an acidic region that may be involved in transcription activation. Mutations and the common Ala/Val 98 polymorphism in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3) [].; GO: 0045893 positive regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2GYP_B 1IC8_B 2H8R_B 1G2Y_D 1F93_H 1G39_D 1G2Z_B 1JB6_B.
Probab=95.91 E-value=0.023 Score=44.03 Aligned_cols=54 Identities=15% Similarity=0.115 Sum_probs=37.7
Q ss_pred hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHH
Q 031871 89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERA 142 (151)
Q Consensus 89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~ 142 (151)
...+.+.||.+...++++|.++++.+||++++||.|.+-....+...-..|-.-
T Consensus 116 ~~~VkeeIK~fl~~h~IsQ~~V~q~TGisQS~lSq~L~kGt~Mk~qKR~alY~W 169 (180)
T PF04814_consen 116 PWRVKEEIKAFLQQHNISQREVVQVTGISQSHLSQHLNKGTPMKEQKRRALYRW 169 (180)
T ss_dssp HHHHHHHHHHHHHHCT--CHHHHHHHT--HHHHHHHHCTB----HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHcCCcHHHHHHHhhhhHHHHHHHHHcCCCccHHHHHHHHHH
Confidence 467899999999999999999999999999999999875555565554444443
No 76
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=95.87 E-value=0.016 Score=43.21 Aligned_cols=45 Identities=16% Similarity=0.283 Sum_probs=33.8
Q ss_pred cCCcCHHHHHHHhCCCHHHHHHHHcCCCC-C--CHHHHHHHHHHhCCCC
Q 031871 102 DKKLTQSQLAQLINEKPQVIQEYESGKAI-P--NQQILTKLERALGVKL 147 (151)
Q Consensus 102 ~~glTQ~eLA~~lgis~s~Is~~E~G~~~-p--~~~~l~kLa~~Lgv~l 147 (151)
..|+||+|+|+.+|+|+++|+.+|++-.. . ...++ +++++|+-++
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 59999999999999999999999996321 1 12333 6677776554
No 77
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=95.67 E-value=0.022 Score=46.30 Aligned_cols=44 Identities=7% Similarity=0.045 Sum_probs=35.6
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH---HHHHHHhCCCC
Q 031871 104 KLTQSQLAQLINEKPQVIQEYESGKAIPNQQIL---TKLERALGVKL 147 (151)
Q Consensus 104 glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l---~kLa~~Lgv~l 147 (151)
..|.+|+|+.+|||.+|||++.||....+.++- .++++.||-.+
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 469999999999999999999999877776654 45566777544
No 78
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=95.46 E-value=0.032 Score=47.93 Aligned_cols=53 Identities=19% Similarity=0.187 Sum_probs=43.8
Q ss_pred hHHHHHHHHHHHhcCCcCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q 031871 89 PSELKKAIVQARNDKKLTQSQLAQLIN------EKPQVIQEYESGKAIPNQQILTKLERAL 143 (151)
Q Consensus 89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lg------is~s~Is~~E~G~~~p~~~~l~kLa~~L 143 (151)
-+.|++.+|+.|...|+||.|+...+| .|++||+++|. -.++..++-||--.|
T Consensus 208 LEqFAK~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEA--LqLSFKNMCKLKPLL 266 (398)
T KOG3802|consen 208 LEQFAKTFKQRRIKLGFTQADVGLALGALYGNVFSQTTICRFEA--LQLSFKNMCKLKPLL 266 (398)
T ss_pred HHHHHHHHHhheeccccchhHHHHHHHhhhCcccchhhhhHhHh--hccCHHHHhhhHHHH
Confidence 478999999999999999999999998 59999999998 346666666654333
No 79
>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=95.44 E-value=0.014 Score=40.06 Aligned_cols=25 Identities=12% Similarity=0.145 Sum_probs=18.9
Q ss_pred cCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 102 DKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 102 ~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
+.||||.|+|+++|.|+++|+++..
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 4799999999999999999999865
No 80
>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=95.34 E-value=0.053 Score=32.57 Aligned_cols=39 Identities=23% Similarity=0.314 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCC
Q 031871 90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA 129 (151)
Q Consensus 90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~ 129 (151)
+.+...|..++... +|+.+.|+..||+++||.+.-+|..
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 46777888888555 9999999999999999999988864
No 81
>COG1513 CynS Cyanate lyase [Inorganic ion transport and metabolism]
Probab=95.34 E-value=0.1 Score=38.56 Aligned_cols=59 Identities=19% Similarity=0.160 Sum_probs=54.7
Q ss_pred hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 031871 89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 147 (151)
Q Consensus 89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l 147 (151)
...+.+.|-...+.+|+|-.||++.+|.+...+...--|....+.+.+.++++.||++-
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 46788889999999999999999999999999999999999999999999999999763
No 82
>smart00351 PAX Paired Box domain.
Probab=95.23 E-value=0.055 Score=39.21 Aligned_cols=45 Identities=9% Similarity=0.246 Sum_probs=36.2
Q ss_pred hhccCCcchHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 81 LYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 81 ~~~~~~~~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
.|++...+..++..+|-.+-. .|+|+.++|+.+|||+++|.+|-+
T Consensus 11 ~~~~~~~~s~~~R~riv~~~~-~G~s~~~iA~~~gvs~~tV~kwi~ 55 (125)
T smart00351 11 VFVNGRPLPDEERQRIVELAQ-NGVRPCDISRQLCVSHGCVSKILG 55 (125)
T ss_pred eecCCCCCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHH
Confidence 455666677777777776654 799999999999999999999843
No 83
>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=95.16 E-value=0.059 Score=32.46 Aligned_cols=32 Identities=13% Similarity=0.194 Sum_probs=26.1
Q ss_pred HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
.+-.+|-..++|+.|+|+.+|+|.++|+++++
T Consensus 11 ~vi~~~y~~~~t~~eIa~~lg~s~~~V~~~~~ 42 (50)
T PF04545_consen 11 EVIRLRYFEGLTLEEIAERLGISRSTVRRILK 42 (50)
T ss_dssp HHHHHHHTST-SHHHHHHHHTSCHHHHHHHHH
T ss_pred HHHHHHhcCCCCHHHHHHHHCCcHHHHHHHHH
Confidence 34455558899999999999999999999875
No 84
>PRK01381 Trp operon repressor; Provisional
Probab=95.14 E-value=0.05 Score=38.29 Aligned_cols=57 Identities=14% Similarity=0.080 Sum_probs=43.5
Q ss_pred hHHHHHHHHHHHh--cCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Q 031871 89 PSELKKAIVQARN--DKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV 145 (151)
Q Consensus 89 ~~~~~~~Lk~~R~--~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv 145 (151)
...++.|++-.+. ..++||.|+|+.+|+|.+||++--+--...+.+....|...|.-
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 4667888877764 44599999999999999999997765555567777777766653
No 85
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=95.14 E-value=0.051 Score=38.68 Aligned_cols=37 Identities=19% Similarity=0.171 Sum_probs=29.0
Q ss_pred HhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q 031871 100 RNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERAL 143 (151)
Q Consensus 100 R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~L 143 (151)
-...||||.|-|+.+|||++|+.++-.. --.|||++|
T Consensus 53 ~D~egl~QeeaA~~MgVSR~T~~ril~~-------ARkKiA~AL 89 (106)
T PF02001_consen 53 VDYEGLSQEEAAERMGVSRPTFQRILES-------ARKKIADAL 89 (106)
T ss_pred HHHcCCCHHHHHHHcCCcHHHHHHHHHH-------HHHHHHHHH
Confidence 3457999999999999999999998762 235666554
No 86
>COG4197 Uncharacterized protein conserved in bacteria, prophage-related [Function unknown]
Probab=94.98 E-value=0.014 Score=40.49 Aligned_cols=39 Identities=23% Similarity=0.358 Sum_probs=36.3
Q ss_pred CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 031871 106 TQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALG 144 (151)
Q Consensus 106 TQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lg 144 (151)
.|..||..+|+++++|++|-+|.+....+....|+++.+
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 588999999999999999999999999888889998887
No 87
>PRK10344 DNA-binding transcriptional regulator Nlp; Provisional
Probab=94.96 E-value=0.074 Score=36.79 Aligned_cols=51 Identities=14% Similarity=0.118 Sum_probs=39.9
Q ss_pred HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 031871 96 IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG 149 (151)
Q Consensus 96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~e 149 (151)
|+.....+|+|..+|+...|++.+|+..-... ..|.-+ ..||++|||.+.+
T Consensus 13 I~AaL~KrG~sLa~lsr~~Gls~~TL~nAL~r-p~PKgE--riIA~aLGv~P~e 63 (92)
T PRK10344 13 IIAGLRKKGTSMAAESRRNGLSSSTLANALSR-PWPKGE--MIIAKALGTDPWV 63 (92)
T ss_pred HHHHHHHcCCcHHHHHHHcCCChHHHHHHHcC-CCchHH--HHHHHHHCcCHHH
Confidence 45555668999999999999999999887663 234444 5699999998764
No 88
>cd00131 PAX Paired Box domain
Probab=94.92 E-value=0.076 Score=38.73 Aligned_cols=44 Identities=7% Similarity=0.283 Sum_probs=36.5
Q ss_pred hhccCCcchHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 81 LYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 81 ~~~~~~~~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
.|.|...+..++..+|-.+-. .|+|+.++|+.+|||+++|.+|-
T Consensus 11 ~~~m~~~lS~d~R~rIv~~~~-~G~s~~~iA~~~~Vs~~tV~r~i 54 (128)
T cd00131 11 VFVNGRPLPDSIRQRIVELAQ-SGIRPCDISRQLRVSHGCVSKIL 54 (128)
T ss_pred cccCCCcCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHH
Confidence 456667777778888876654 79999999999999999999993
No 89
>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=94.84 E-value=0.051 Score=31.53 Aligned_cols=24 Identities=21% Similarity=0.411 Sum_probs=21.2
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESGK 128 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G~ 128 (151)
+|..|+|+.+||++++|.+|++-.
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~g 24 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKEG 24 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcC
Confidence 578999999999999999998643
No 90
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=94.57 E-value=0.13 Score=41.39 Aligned_cols=50 Identities=16% Similarity=0.355 Sum_probs=39.3
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALG 144 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lg 144 (151)
-..|+.++.. +|-+||++.+|++.+.+++|-+|+..|+.+....|.+-|.
T Consensus 14 v~~lr~lk~~--~ty~el~~~~g~p~~~l~RYv~g~~~P~~~~a~~~~~~l~ 63 (238)
T PRK08558 14 VRVLRSLKKT--YTYEELSSITGLPESVLNRYVNGHVLPSVERAREIVEKLG 63 (238)
T ss_pred HHHHHHHhcc--cCHHHHHHHHCCCHHHHHHHHcCCcCCCHHHHHHHHHHHH
Confidence 4445555443 5999999999999999999999999999886666655443
No 91
>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=94.56 E-value=0.034 Score=40.32 Aligned_cols=23 Identities=26% Similarity=0.351 Sum_probs=21.2
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G 127 (151)
||.+|||+.+|++++||++|-+-
T Consensus 1 MT~eELA~~tG~srQTINrWvRk 23 (122)
T PF07037_consen 1 MTPEELAELTGYSRQTINRWVRK 23 (122)
T ss_pred CCHHHHHHHhCccHHHHHHHHHh
Confidence 79999999999999999999664
No 92
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=94.45 E-value=0.033 Score=40.92 Aligned_cols=27 Identities=26% Similarity=0.412 Sum_probs=24.8
Q ss_pred hcCCcCHHHHHHHhCCCHHHHHHHHcC
Q 031871 101 NDKKLTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 101 ~~~glTQ~eLA~~lgis~s~Is~~E~G 127 (151)
.++|+||+++|+.+|.++..||.+|+.
T Consensus 20 RekG~tQ~eIA~~L~TTraNvSaIEkr 46 (143)
T COG1356 20 REKGLTQSEIARILKTTRANVSAIEKR 46 (143)
T ss_pred hhccccHHHHHHHHccchhhHHHHHHH
Confidence 468999999999999999999999984
No 93
>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=94.44 E-value=0.11 Score=35.71 Aligned_cols=38 Identities=13% Similarity=0.058 Sum_probs=31.5
Q ss_pred hHHHHHHHHHHH--hcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 89 PSELKKAIVQAR--NDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 89 ~~~~~~~Lk~~R--~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
...++.|++-++ ...|+||.++|+.+|+|..||++.-+
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 367788887775 45799999999999999999998643
No 94
>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=94.37 E-value=0.054 Score=34.35 Aligned_cols=25 Identities=4% Similarity=0.157 Sum_probs=23.1
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHcC
Q 031871 103 KKLTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 103 ~glTQ~eLA~~lgis~s~Is~~E~G 127 (151)
.|+++.++|+.+|++.+||..|-.-
T Consensus 12 ~G~~~~eIA~~Lg~~~~TV~~W~~r 36 (58)
T PF06056_consen 12 QGWSIKEIAEELGVPRSTVYSWKDR 36 (58)
T ss_pred cCCCHHHHHHHHCCChHHHHHHHHh
Confidence 6999999999999999999999763
No 95
>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=94.30 E-value=0.0075 Score=41.83 Aligned_cols=41 Identities=15% Similarity=0.220 Sum_probs=31.5
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 031871 103 KKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 147 (151)
Q Consensus 103 ~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l 147 (151)
..++|..+|+.+|++.++||+|-.+ -...+..|..+|+..+
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 3478999999999999999999654 2355666666776654
No 96
>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=94.24 E-value=0.56 Score=32.08 Aligned_cols=58 Identities=12% Similarity=0.130 Sum_probs=41.2
Q ss_pred hHHHHHHHHHHHhcCCcCHHHHHHH-hCCCHHHHHHHHcCCCCCCHH------HHHHHHHHhCCC
Q 031871 89 PSELKKAIVQARNDKKLTQSQLAQL-INEKPQVIQEYESGKAIPNQQ------ILTKLERALGVK 146 (151)
Q Consensus 89 ~~~~~~~Lk~~R~~~glTQ~eLA~~-lgis~s~Is~~E~G~~~p~~~------~l~kLa~~Lgv~ 146 (151)
...+..+|++.....+++|+.||+. +|.|+.+++.+.+--..-+.- ...++-..|..+
T Consensus 11 T~~I~~~ik~~L~~~~IsQ~~Fa~~vL~rsqgtlsdlL~~PKpW~~L~~~gre~y~RM~nWL~~~ 75 (87)
T PF02376_consen 11 TKEIARRIKEWLKRNNISQRVFAKKVLNRSQGTLSDLLRKPKPWNKLKPKGREPYIRMYNWLSLP 75 (87)
T ss_dssp HHHHHHHHHHHHHHTT--HHHHHHHTTSS-HHHHHHHHHSCCTTCHHHHHHHHHHHHHHHHHCST
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHhccChhHHHHHhCCCCCHHHcCccccHHHHHHHHHhcCC
Confidence 4678999999999999999999998 499999999999854333322 245555555543
No 97
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=93.99 E-value=0.043 Score=38.95 Aligned_cols=26 Identities=35% Similarity=0.377 Sum_probs=22.6
Q ss_pred HHHHHHHcCCChhhHHhhhcCCCccC
Q 031871 31 VVNAARRAGADIETVRKSHAGTNKAA 56 (151)
Q Consensus 31 ~~~~a~r~g~~v~t~~k~~~g~~~~~ 56 (151)
+-.-|++.|++++|+++||.|..+|.
T Consensus 60 Q~vFA~~L~vs~~Tv~~WEqGr~kPs 85 (104)
T COG2944 60 QPVFARYLGVSVSTVRKWEQGRKKPS 85 (104)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCcCCC
Confidence 34578999999999999999999873
No 98
>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=93.83 E-value=0.064 Score=33.25 Aligned_cols=38 Identities=11% Similarity=0.140 Sum_probs=26.2
Q ss_pred HHHHHHHHH-HhcCCcCHHHHHHHhCCCHHHHHHHHcCC
Q 031871 91 ELKKAIVQA-RNDKKLTQSQLAQLINEKPQVIQEYESGK 128 (151)
Q Consensus 91 ~~~~~Lk~~-R~~~glTQ~eLA~~lgis~s~Is~~E~G~ 128 (151)
.+.+.+.-+ +.+.|.++.++|+..||+.+||+.|.+.+
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 344445444 45778899999999999999999997753
No 99
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=93.78 E-value=0.14 Score=35.84 Aligned_cols=28 Identities=18% Similarity=0.054 Sum_probs=24.6
Q ss_pred HHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 99 ARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 99 ~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
+....||+|.|.|.++|||++|+.+..+
T Consensus 44 LvD~~~l~QeeAA~rMgISr~Tfwr~l~ 71 (99)
T COG1342 44 LVDYEGLTQEEAALRMGISRQTFWRLLT 71 (99)
T ss_pred HHhHhhccHHHHHHHhcccHHHHHHHHH
Confidence 3456899999999999999999998765
No 100
>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=93.75 E-value=0.19 Score=31.95 Aligned_cols=22 Identities=27% Similarity=0.567 Sum_probs=20.3
Q ss_pred cCHHHHHHHhCCCHHHHHHHHc
Q 031871 105 LTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~ 126 (151)
+|..|+|+.+||++++|..||+
T Consensus 1 ~~i~evA~~~gvs~~tlR~~~~ 22 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEK 22 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4778999999999999999986
No 101
>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=93.72 E-value=0.085 Score=29.60 Aligned_cols=22 Identities=9% Similarity=0.228 Sum_probs=17.2
Q ss_pred CcCHHHHHHHhCCCHHHHHHHH
Q 031871 104 KLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 104 glTQ~eLA~~lgis~s~Is~~E 125 (151)
.||+.|+|+.+|+++.+||+.-
T Consensus 2 ~mtr~diA~~lG~t~ETVSR~l 23 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVSRIL 23 (32)
T ss_dssp E--HHHHHHHHTS-HHHHHHHH
T ss_pred CcCHHHHHHHhCCcHHHHHHHH
Confidence 4799999999999999999874
No 102
>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=93.57 E-value=0.13 Score=29.90 Aligned_cols=27 Identities=15% Similarity=0.235 Sum_probs=23.1
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcCCCCC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESGKAIP 131 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G~~~p 131 (151)
||..|+|+.+|+++++|.+|.+....|
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g~i~ 28 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEGELP 28 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcCCCC
Confidence 688999999999999999998655444
No 103
>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=93.57 E-value=0.13 Score=30.32 Aligned_cols=24 Identities=29% Similarity=0.385 Sum_probs=21.1
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESGK 128 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G~ 128 (151)
+|..|+|+.+|+++++|..|++-.
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHCC
Confidence 578899999999999999997644
No 104
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=93.55 E-value=0.14 Score=42.80 Aligned_cols=55 Identities=15% Similarity=0.117 Sum_probs=40.2
Q ss_pred HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc-----CCC--------CCCHHHHHHHHHHhCCC
Q 031871 92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES-----GKA--------IPNQQILTKLERALGVK 146 (151)
Q Consensus 92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~-----G~~--------~p~~~~l~kLa~~Lgv~ 146 (151)
+--++..+--..||||.|+|+++|+|+++|+++.. |-. ....+.-.+|.+.||+.
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 44556666777899999999999999999999843 422 11344556777788754
No 105
>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=93.54 E-value=0.16 Score=29.80 Aligned_cols=32 Identities=22% Similarity=0.114 Sum_probs=25.7
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEY 124 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~ 124 (151)
...|.......+.++.+.|+.+||+++++.+-
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 45577888889999999999999999999864
No 106
>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=93.51 E-value=0.49 Score=30.12 Aligned_cols=62 Identities=16% Similarity=0.145 Sum_probs=38.8
Q ss_pred HHHHHHcCCChhhHHhhhc--CCCccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHH
Q 031871 32 VNAARRAGADIETVRKSHA--GTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQ 109 (151)
Q Consensus 32 ~~~a~r~g~~v~t~~k~~~--g~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~e 109 (151)
-++|++.|++..|++.|+. |-..|..+.. .-+....+ ....-..|+.++. .|+|.++
T Consensus 4 ~e~A~~~gVs~~tlr~ye~~~gl~~~~r~~~--g~R~yt~~------------------di~~l~~i~~l~~-~g~~l~~ 62 (68)
T cd04763 4 GEVALLTGIKPHVLRAWEREFGLLKPQRSDG--GHRLFNDA------------------DIDRILEIKRWID-NGVQVSK 62 (68)
T ss_pred HHHHHHHCcCHHHHHHHHHhcCCCCCCcCCC--CCcccCHH------------------HHHHHHHHHHHHH-cCCCHHH
Confidence 4689999999999999975 4433322111 11111111 1223445777777 9999999
Q ss_pred HHHHh
Q 031871 110 LAQLI 114 (151)
Q Consensus 110 LA~~l 114 (151)
+++.+
T Consensus 63 i~~~l 67 (68)
T cd04763 63 VKKLL 67 (68)
T ss_pred HHHHh
Confidence 98765
No 107
>PRK13698 plasmid-partitioning protein; Provisional
Probab=93.46 E-value=0.14 Score=43.12 Aligned_cols=40 Identities=18% Similarity=0.036 Sum_probs=33.5
Q ss_pred hHHHHHHH-HHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCC
Q 031871 89 PSELKKAI-VQARNDKKLTQSQLAQLINEKPQVIQEYESGK 128 (151)
Q Consensus 89 ~~~~~~~L-k~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~ 128 (151)
..+.+... +.+....|+||++||+.+|+|+++|++..+=-
T Consensus 160 ~iE~A~ay~~~L~~~~~~tQeeLA~~lG~SRs~Vsn~Lrla 200 (323)
T PRK13698 160 AYERGLRYASRLQNEFAGNISALADAENISRKIITRCINTA 200 (323)
T ss_pred HHHHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 45667766 66778999999999999999999999987743
No 108
>PHA01976 helix-turn-helix protein
Probab=93.45 E-value=0.026 Score=35.85 Aligned_cols=29 Identities=17% Similarity=0.093 Sum_probs=24.7
Q ss_pred HHHHHHHHHcCCChhhHHhhhcCCCccCC
Q 031871 29 EKVVNAARRAGADIETVRKSHAGTNKAAS 57 (151)
Q Consensus 29 ~~~~~~a~r~g~~v~t~~k~~~g~~~~~~ 57 (151)
-+..+.|++.|++.+++.+||+|...|..
T Consensus 16 lt~~~lA~~~gvs~~~v~~~e~g~~~p~~ 44 (67)
T PHA01976 16 WSAPELSRRAGVRHSLIYDFEADKRLPNL 44 (67)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCH
Confidence 45678999999999999999999876543
No 109
>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=93.40 E-value=0.38 Score=25.09 Aligned_cols=23 Identities=9% Similarity=0.186 Sum_probs=20.8
Q ss_pred cCCcCHHHHHHHhCCCHHHHHHH
Q 031871 102 DKKLTQSQLAQLINEKPQVIQEY 124 (151)
Q Consensus 102 ~~glTQ~eLA~~lgis~s~Is~~ 124 (151)
..+++..++|+.+|+++++|.+|
T Consensus 19 ~~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 19 AAGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHh
Confidence 36789999999999999999987
No 110
>PF12728 HTH_17: Helix-turn-helix domain
Probab=93.37 E-value=0.14 Score=30.78 Aligned_cols=28 Identities=21% Similarity=0.297 Sum_probs=23.6
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESGKAIPN 132 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G~~~p~ 132 (151)
||.+|+|+.+|||.++|.+|-+....|.
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 6889999999999999999986555443
No 111
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=93.32 E-value=0.16 Score=42.74 Aligned_cols=58 Identities=17% Similarity=0.165 Sum_probs=44.7
Q ss_pred hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc-----CCC--------CCCHHHHHHHHHHhCCC
Q 031871 89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES-----GKA--------IPNQQILTKLERALGVK 146 (151)
Q Consensus 89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~-----G~~--------~p~~~~l~kLa~~Lgv~ 146 (151)
......++..+.-..||||.|+|+++|+|+.+|+++.. |-. ....+.-.+|.+.||++
T Consensus 11 ~~~l~~~~A~lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I~i~~~~~~~~~Le~~L~~~fgL~ 81 (321)
T COG2390 11 EERLLARAAWLYYVEGLTQSEIAERLGISRATVSRLLAKAREEGIVKISINSPVEGCLELEQQLKERFGLK 81 (321)
T ss_pred HHHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEEEeCCCCcchHHHHHHHHHhcCCC
Confidence 35667788888889999999999999999999999843 321 12344567788888875
No 112
>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=93.31 E-value=0.16 Score=30.89 Aligned_cols=31 Identities=16% Similarity=0.171 Sum_probs=23.2
Q ss_pred HHHHHHhcCC-cCHHHHHHHhCCCHHHHHHHH
Q 031871 95 AIVQARNDKK-LTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 95 ~Lk~~R~~~g-lTQ~eLA~~lgis~s~Is~~E 125 (151)
-|..+....+ +|..+||+.+|||+.||.+.-
T Consensus 5 il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i 36 (55)
T PF08279_consen 5 ILKLLLESKEPITAKELAEELGVSRRTIRRDI 36 (55)
T ss_dssp HHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHH
T ss_pred HHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHH
Confidence 3455544444 999999999999999998864
No 113
>PF13518 HTH_28: Helix-turn-helix domain
Probab=93.26 E-value=0.21 Score=29.79 Aligned_cols=24 Identities=4% Similarity=0.059 Sum_probs=21.7
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 103 KKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 103 ~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
.|.|..++|+.+|||+++|.+|.+
T Consensus 11 ~g~s~~~~a~~~gis~~tv~~w~~ 34 (52)
T PF13518_consen 11 EGESVREIAREFGISRSTVYRWIK 34 (52)
T ss_pred cCCCHHHHHHHHCCCHhHHHHHHH
Confidence 477999999999999999999964
No 114
>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=93.21 E-value=0.22 Score=34.25 Aligned_cols=27 Identities=11% Similarity=0.025 Sum_probs=24.7
Q ss_pred hcCCcCHHHHHHHhCCCHHHHHHHHcC
Q 031871 101 NDKKLTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 101 ~~~glTQ~eLA~~lgis~s~Is~~E~G 127 (151)
...|+|+.++|+.+|+|++||.++-+|
T Consensus 47 l~~G~S~~eIA~~LgISrsTIyRi~R~ 73 (88)
T TIGR02531 47 LKQGKTYSDIEAETGASTATISRVKRC 73 (88)
T ss_pred HHCCCCHHHHHHHHCcCHHHHHHHHHh
Confidence 457899999999999999999999885
No 115
>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=93.19 E-value=0.13 Score=29.74 Aligned_cols=25 Identities=24% Similarity=0.473 Sum_probs=20.4
Q ss_pred CHHHHHHHhCCCHHHHHHHHcCCCC
Q 031871 106 TQSQLAQLINEKPQVIQEYESGKAI 130 (151)
Q Consensus 106 TQ~eLA~~lgis~s~Is~~E~G~~~ 130 (151)
|..|+|+.+|||..+|..||+-.-.
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 4679999999999999999986543
No 116
>cd00131 PAX Paired Box domain
Probab=93.13 E-value=0.75 Score=33.43 Aligned_cols=76 Identities=11% Similarity=0.097 Sum_probs=45.5
Q ss_pred HHHHHHHHHcCCChhhHHhhhc-----CCCccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHH-HHHHHhc
Q 031871 29 EKVVNAARRAGADIETVRKSHA-----GTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKA-IVQARND 102 (151)
Q Consensus 29 ~~~~~~a~r~g~~v~t~~k~~~-----g~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~-Lk~~R~~ 102 (151)
.+.-..|++.|++..|+.+|-. |...|.+.+ +..-.++. ...... +...+..
T Consensus 34 ~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~g-g~rpr~~~---------------------~~~~~~i~~~v~~~ 91 (128)
T cd00131 34 IRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIG-GSKPRVAT---------------------PEVVKKIEIYKQEN 91 (128)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCC-CCCCCcCC---------------------HHHHHHHHHHHHHC
Confidence 3556689999999999999854 444332111 11111111 111111 2235677
Q ss_pred CCcCHHHHHHHh---CC-------CHHHHHHHHc
Q 031871 103 KKLTQSQLAQLI---NE-------KPQVIQEYES 126 (151)
Q Consensus 103 ~glTQ~eLA~~l---gi-------s~s~Is~~E~ 126 (151)
-.+|+.||++.+ |+ |.++|+++..
T Consensus 92 p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~ 125 (128)
T cd00131 92 PGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILR 125 (128)
T ss_pred CCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHH
Confidence 789999999886 55 8888888754
No 117
>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=92.79 E-value=0.15 Score=32.98 Aligned_cols=39 Identities=15% Similarity=0.196 Sum_probs=28.8
Q ss_pred chHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 88 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 88 ~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
...+|-..+-......|.|..++|+..||++++|.+|.+
T Consensus 7 ys~e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 7 YSPEFKLQAVREYLESGESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp --HHHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHCCCceEeeecccccccccccHHHH
Confidence 345555555555566799999999999999999999965
No 118
>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=92.72 E-value=0.14 Score=32.78 Aligned_cols=25 Identities=16% Similarity=0.315 Sum_probs=22.2
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHcC
Q 031871 103 KKLTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 103 ~glTQ~eLA~~lgis~s~Is~~E~G 127 (151)
-+++..|+|+.+|||.++|+.|-+-
T Consensus 21 g~i~lkdIA~~Lgvs~~tIr~WK~~ 45 (60)
T PF10668_consen 21 GKIKLKDIAEKLGVSESTIRKWKSR 45 (60)
T ss_pred CCccHHHHHHHHCCCHHHHHHHhhh
Confidence 3689999999999999999999653
No 119
>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=92.69 E-value=0.28 Score=30.10 Aligned_cols=33 Identities=15% Similarity=0.136 Sum_probs=27.1
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
...|..+...-++|+.+||+.+++++++++++-
T Consensus 6 ~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i 38 (59)
T PF01047_consen 6 FRILRILYENGGITQSELAEKLGISRSTVTRII 38 (59)
T ss_dssp HHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHH
Confidence 345667778889999999999999999999874
No 120
>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=92.66 E-value=0.31 Score=33.70 Aligned_cols=68 Identities=13% Similarity=0.100 Sum_probs=41.8
Q ss_pred HHHHHHcCCChhhHHhhhcCC-CccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHHH
Q 031871 32 VNAARRAGADIETVRKSHAGT-NKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQL 110 (151)
Q Consensus 32 ~~~a~r~g~~v~t~~k~~~g~-~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~eL 110 (151)
-+.|++.|++..|++.|+.-. ..|... ...-+..+. ..-..-..|..++...|++.+++
T Consensus 4 ~e~a~~~gvs~~tLR~ye~~Gll~p~r~--~~g~R~Y~~------------------~dv~~l~~I~~L~~~~G~~l~ei 63 (96)
T cd04774 4 DEVAKRLGLTKRTLKYYEEIGLVSPERS--EGRYRLYSE------------------EDLKRLERILRLREVLGFSLQEV 63 (96)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCCcC--CCCCEEECH------------------HHHHHHHHHHHHHHHcCCCHHHH
Confidence 468999999999999998632 221110 000001111 11234556778888889999999
Q ss_pred HHHhCCCHH
Q 031871 111 AQLINEKPQ 119 (151)
Q Consensus 111 A~~lgis~s 119 (151)
...+.....
T Consensus 64 ~~~l~~~~~ 72 (96)
T cd04774 64 THFLERPLE 72 (96)
T ss_pred HHHHhcccc
Confidence 887766554
No 121
>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=92.65 E-value=0.65 Score=29.23 Aligned_cols=62 Identities=19% Similarity=0.131 Sum_probs=36.7
Q ss_pred HHHHHHcCCChhhHHhhhc--CCCccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHH
Q 031871 32 VNAARRAGADIETVRKSHA--GTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQ 109 (151)
Q Consensus 32 ~~~a~r~g~~v~t~~k~~~--g~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~e 109 (151)
-+.|++.|++.+|+++|+. |...|..++ ..-+. +.. + ...--..|+.++. .|+|.++
T Consensus 4 ~eva~~~gvs~~tlr~w~~~~g~~~~~r~~--~~~r~-------yt~---------~--~v~~l~~i~~l~~-~g~~l~~ 62 (68)
T cd01104 4 GAVARLTGVSPDTLRAWERRYGLPAPQRTD--GGHRL-------YSE---------A--DVARLRLIRRLTS-EGVRISQ 62 (68)
T ss_pred HHHHHHHCcCHHHHHHHHHhCCCCCCCcCC--CCCee-------cCH---------H--HHHHHHHHHHHHH-CCCCHHH
Confidence 4689999999999999996 322221110 00011 111 0 1223455667776 8999999
Q ss_pred HHHHh
Q 031871 110 LAQLI 114 (151)
Q Consensus 110 LA~~l 114 (151)
+.+.+
T Consensus 63 i~~~~ 67 (68)
T cd01104 63 AAALA 67 (68)
T ss_pred HHHHh
Confidence 88754
No 122
>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=92.60 E-value=0.42 Score=36.68 Aligned_cols=52 Identities=19% Similarity=0.139 Sum_probs=39.7
Q ss_pred hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHH
Q 031871 89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLER 141 (151)
Q Consensus 89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~ 141 (151)
..+.+..++++....|+|+.++|+.+|+|+++|+++..=-. .+.+.+..+..
T Consensus 105 ~~e~a~~~~~l~~~~g~s~~~iA~~lg~s~~~V~r~l~l~~-lp~~v~~~~~~ 156 (187)
T TIGR00180 105 PIEEAQAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLRLLK-LPSEIQSAIPE 156 (187)
T ss_pred HHHHHHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHHHHc-CCHHHHHHHHh
Confidence 35567777777777899999999999999999999877433 55555555554
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=92.55 E-value=0.15 Score=32.29 Aligned_cols=22 Identities=23% Similarity=0.437 Sum_probs=20.5
Q ss_pred cCHHHHHHHhCCCHHHHHHHHc
Q 031871 105 LTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~ 126 (151)
+|..|+|+.+||++++|..|++
T Consensus 1 ~s~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4788999999999999999997
No 124
>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=92.49 E-value=0.33 Score=28.10 Aligned_cols=29 Identities=10% Similarity=0.184 Sum_probs=24.6
Q ss_pred HHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 98 QARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 98 ~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
.++-..|+|+.++|+.+|++.++|.++..
T Consensus 20 ~~~~~~~~~~~~ia~~~~~s~~~i~~~~~ 48 (55)
T cd06171 20 LLRFGEGLSYEEIAEILGISRSTVRQRLH 48 (55)
T ss_pred HHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34445899999999999999999998864
No 125
>COG2842 Uncharacterized ATPase, putative transposase [General function prediction only]
Probab=92.43 E-value=0.38 Score=40.10 Aligned_cols=58 Identities=17% Similarity=0.057 Sum_probs=47.1
Q ss_pred hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCC-HHHHHHHHHHhCCCC
Q 031871 89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPN-QQILTKLERALGVKL 147 (151)
Q Consensus 89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~-~~~l~kLa~~Lgv~l 147 (151)
....-+.++++-+..+|+|..+|..+|+++.+|+.+.+| ..++ ..+-.+|+..|+.+.
T Consensus 4 n~~~~k~~k~f~e~~~~~q~~~a~gi~~~~~~vsk~L~g-~~g~~~~~~a~ia~~le~~~ 62 (297)
T COG2842 4 NFIEIKKLKEFAEFSGMCQKYLARGIGTSAPALSKYLNG-YKGDYATNEAKIAAFLEKKG 62 (297)
T ss_pred hHHHHHHHHHHHHhhhhhHHHHHHHhccCchhHHHHhcC-cCchHHHHHHHHHHHHcCCC
Confidence 355678899999999999999999999999999999998 4443 445667777776543
No 126
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=92.31 E-value=0.46 Score=34.00 Aligned_cols=40 Identities=23% Similarity=0.166 Sum_probs=32.2
Q ss_pred cchHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 87 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 87 ~~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
....+|-..+-......|.|..++|+.+||++++|++|-+
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 3455666666666677899999999999999999999954
No 127
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=92.27 E-value=0.13 Score=31.60 Aligned_cols=27 Identities=15% Similarity=-0.012 Sum_probs=23.4
Q ss_pred HhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 100 RNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 100 R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
+-..|.++.+||...|||++++++|-+
T Consensus 15 ~LR~~~~~~~La~~FgIs~stvsri~~ 41 (53)
T PF13613_consen 15 YLRLNLTFQDLAYRFGISQSTVSRIFH 41 (53)
T ss_pred HHHcCCcHhHHhhheeecHHHHHHHHH
Confidence 344688999999999999999999854
No 128
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=92.22 E-value=0.18 Score=31.91 Aligned_cols=23 Identities=26% Similarity=0.483 Sum_probs=20.8
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G 127 (151)
+|..|+|+.+|+|+++|..||+-
T Consensus 1 yti~eva~~~gvs~~tlr~y~~~ 23 (69)
T PF13411_consen 1 YTIKEVAKLLGVSPSTLRYYERE 23 (69)
T ss_dssp EEHHHHHHHTTTTHHHHHHHHHT
T ss_pred CcHHHHHHHHCcCHHHHHHHHHh
Confidence 47889999999999999999874
No 129
>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=91.98 E-value=0.19 Score=32.04 Aligned_cols=22 Identities=32% Similarity=0.510 Sum_probs=20.2
Q ss_pred cCHHHHHHHhCCCHHHHHHHHc
Q 031871 105 LTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~ 126 (151)
++..|+|+.+||++++|..||.
T Consensus 1 ~~i~e~A~~~gVs~~tlr~ye~ 22 (68)
T cd04763 1 YTIGEVALLTGIKPHVLRAWER 22 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4678999999999999999986
No 130
>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=91.96 E-value=0.24 Score=30.93 Aligned_cols=24 Identities=17% Similarity=0.254 Sum_probs=21.1
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 103 KKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 103 ~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
++.|..|||+.+|||+++++...+
T Consensus 22 R~~tl~elA~~lgis~st~~~~LR 45 (53)
T PF04967_consen 22 RRITLEELAEELGISKSTVSEHLR 45 (53)
T ss_pred CcCCHHHHHHHhCCCHHHHHHHHH
Confidence 578999999999999999997643
No 131
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=91.92 E-value=0.11 Score=43.25 Aligned_cols=39 Identities=18% Similarity=0.188 Sum_probs=34.7
Q ss_pred hHHHHHHHHHHHhcCCcCHHHHHHHh---------CCCHHHHHHHHcC
Q 031871 89 PSELKKAIVQARNDKKLTQSQLAQLI---------NEKPQVIQEYESG 127 (151)
Q Consensus 89 ~~~~~~~Lk~~R~~~glTQ~eLA~~l---------gis~s~Is~~E~G 127 (151)
-+.|++++++.|...|.||.|+...+ .+|++||-++|+=
T Consensus 219 LEaFAErFKQRRIKLGVTQADVG~ALAnLKiPGVGsLSQSTICRFESL 266 (385)
T KOG1168|consen 219 LEAFAERFKQRRIKLGVTQADVGKALANLKIPGVGSLSQSTICRFESL 266 (385)
T ss_pred HHHHHHHHHhhhhhhcccHHHHHHHHHhCcCCCcccccccceeeeeee
Confidence 47899999999999999999999876 2689999999974
No 132
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=91.88 E-value=0.45 Score=29.59 Aligned_cols=26 Identities=12% Similarity=0.161 Sum_probs=21.8
Q ss_pred hcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 101 NDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 101 ~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
....+|+.+||+.+|+++++++++-+
T Consensus 22 ~~~~~s~~ela~~~g~s~~tv~r~l~ 47 (67)
T cd00092 22 VQLPLTRQEIADYLGLTRETVSRTLK 47 (67)
T ss_pred ccCCcCHHHHHHHHCCCHHHHHHHHH
Confidence 34569999999999999999988643
No 133
>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=91.80 E-value=0.061 Score=32.50 Aligned_cols=27 Identities=19% Similarity=0.254 Sum_probs=23.2
Q ss_pred HHHHHHHHHcCCChhhHHhhhcCCCcc
Q 031871 29 EKVVNAARRAGADIETVRKSHAGTNKA 55 (151)
Q Consensus 29 ~~~~~~a~r~g~~v~t~~k~~~g~~~~ 55 (151)
-+..+.|.+.|++.+++.+|+.|...|
T Consensus 16 ltq~~lA~~~gvs~~~vs~~e~g~~~~ 42 (58)
T TIGR03070 16 LTQADLADLAGVGLRFIRDVENGKPTV 42 (58)
T ss_pred CCHHHHHHHhCCCHHHHHHHHCCCCCC
Confidence 356789999999999999999998654
No 134
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=91.78 E-value=0.61 Score=29.44 Aligned_cols=63 Identities=16% Similarity=0.183 Sum_probs=38.8
Q ss_pred HHHHHHcCCChhhHHhhhcCCCccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHHHH
Q 031871 32 VNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLA 111 (151)
Q Consensus 32 ~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~eLA 111 (151)
-+.|+..|++.+|++.|+.-..-+.... ...-...+.+ ....-..|+.++. .|+|..++.
T Consensus 4 ~eva~~~gvs~~tlr~y~~~gll~~~~~-~~g~r~y~~~------------------dv~~l~~i~~l~~-~G~sl~~I~ 63 (69)
T PF13411_consen 4 KEVAKLLGVSPSTLRYYEREGLLPPPRD-ENGYRYYSEE------------------DVERLREIKELRK-QGMSLEEIK 63 (69)
T ss_dssp HHHHHHTTTTHHHHHHHHHTTSSTTBES-TTSSEEE-HH------------------HHHHHHHHHHHHH-TTTHHHHHH
T ss_pred HHHHHHHCcCHHHHHHHHHhcCcccccc-cCceeeccHH------------------HHHHHHHHHHHHH-CcCCHHHHH
Confidence 4689999999999999997433211100 0000111111 1334566788888 999999998
Q ss_pred HHh
Q 031871 112 QLI 114 (151)
Q Consensus 112 ~~l 114 (151)
+.+
T Consensus 64 ~~l 66 (69)
T PF13411_consen 64 KLL 66 (69)
T ss_dssp HHH
T ss_pred HHH
Confidence 765
No 135
>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=91.62 E-value=0.76 Score=29.08 Aligned_cols=64 Identities=17% Similarity=0.176 Sum_probs=38.5
Q ss_pred HHHHHHHcCCChhhHHhhhc-CCCccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHH
Q 031871 31 VVNAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQ 109 (151)
Q Consensus 31 ~~~~a~r~g~~v~t~~k~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~e 109 (151)
.-+.|+..|++..|++.|+. |.-.+..+ . ..-+..+. . .-..-..|+.++. .|+|.++
T Consensus 3 i~evA~~~gvs~~tlR~~~~~g~l~~~~~-~-~g~R~y~~----------------~--~l~~l~~i~~l~~-~g~~l~~ 61 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKEFNLYIPRT-E-NGRRYYTD----------------E--DIELLKKIKTLLE-KGLSIKE 61 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHhcCCCCCCC-C-CCceeeCH----------------H--HHHHHHHHHHHHH-CCCCHHH
Confidence 34689999999999999986 43321110 0 00011111 1 1223455777777 8999999
Q ss_pred HHHHhC
Q 031871 110 LAQLIN 115 (151)
Q Consensus 110 LA~~lg 115 (151)
+.+.++
T Consensus 62 i~~~l~ 67 (67)
T cd04764 62 IKEILN 67 (67)
T ss_pred HHHHhC
Confidence 987653
No 136
>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=91.60 E-value=0.58 Score=32.18 Aligned_cols=24 Identities=13% Similarity=0.250 Sum_probs=21.9
Q ss_pred hcCCcCHHHHHHHhCCCHHHHHHH
Q 031871 101 NDKKLTQSQLAQLINEKPQVIQEY 124 (151)
Q Consensus 101 ~~~glTQ~eLA~~lgis~s~Is~~ 124 (151)
....+||.|||+.+|+++.++++.
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~ 67 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDA 67 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHH
Confidence 577899999999999999999984
No 137
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=91.51 E-value=0.27 Score=39.97 Aligned_cols=34 Identities=18% Similarity=0.333 Sum_probs=29.2
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
-+.+-.+|-..++||+|+|+.+|||++.||++++
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 3445567777899999999999999999999987
No 138
>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=91.39 E-value=0.054 Score=32.89 Aligned_cols=27 Identities=15% Similarity=0.256 Sum_probs=21.7
Q ss_pred HHHHHHHHcCCChhhHHhhhcCCCccC
Q 031871 30 KVVNAARRAGADIETVRKSHAGTNKAA 56 (151)
Q Consensus 30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~ 56 (151)
+.-+.|++.|++..|+.+|+.|...|.
T Consensus 11 s~~~la~~~gis~~~i~~~~~g~~~~~ 37 (55)
T PF01381_consen 11 SQKELAEKLGISRSTISRIENGKRNPS 37 (55)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSSTSB
T ss_pred CHHHHHHHhCCCcchhHHHhcCCCCCC
Confidence 557899999999999999999976653
No 139
>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=91.38 E-value=0.54 Score=28.39 Aligned_cols=33 Identities=9% Similarity=0.209 Sum_probs=23.8
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
...+-.++-..|+|..|+|+.+|+|.++|..+-
T Consensus 15 ~r~i~~l~~~~g~s~~eIa~~l~~s~~~v~~~l 47 (54)
T PF08281_consen 15 QREIFLLRYFQGMSYAEIAEILGISESTVKRRL 47 (54)
T ss_dssp HHHHHHHHHTS---HHHHHHHCTS-HHHHHHHH
T ss_pred HHHHHHHHHHHCcCHHHHHHHHCcCHHHHHHHH
Confidence 445566777899999999999999999998764
No 140
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=91.35 E-value=0.61 Score=31.11 Aligned_cols=36 Identities=19% Similarity=0.413 Sum_probs=27.3
Q ss_pred CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 031871 106 TQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALG 144 (151)
Q Consensus 106 TQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lg 144 (151)
+...+|+.+|||+++|++| |+..|. ..+.+|..+-+
T Consensus 12 s~~kvA~aLGIs~~AVsQW--Ge~VPe-~rA~~ie~~T~ 47 (75)
T PRK09744 12 SKTKLANAAGVRLASVAAW--GELVPE-GRAMRLQEASG 47 (75)
T ss_pred cHHHHHHHHCCCHHHHHHH--hccCcH-HHHHHHHHHhC
Confidence 6788999999999999999 766554 34556665544
No 141
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=91.32 E-value=0.36 Score=30.51 Aligned_cols=22 Identities=23% Similarity=0.345 Sum_probs=19.9
Q ss_pred cCHHHHHHHhCCCHHHHHHHHc
Q 031871 105 LTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~ 126 (151)
+|..|+|+.+||++++|..|++
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999965
No 142
>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=91.20 E-value=0.35 Score=39.56 Aligned_cols=42 Identities=21% Similarity=0.218 Sum_probs=30.9
Q ss_pred CCcCHHHHHHHhCC-----CHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 031871 103 KKLTQSQLAQLINE-----KPQVIQEYESGKAIPNQQILTKLERALG 144 (151)
Q Consensus 103 ~glTQ~eLA~~lgi-----s~s~Is~~E~G~~~p~~~~l~kLa~~Lg 144 (151)
.++||.+||+++|- |+++|+++.+=-..+...+...|+.-+|
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 9999999987544455555555544443
No 143
>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=91.07 E-value=0.67 Score=28.48 Aligned_cols=33 Identities=18% Similarity=0.216 Sum_probs=25.4
Q ss_pred HHHHHHHHhcCC--cCHHHHHHHhCCCHHHHHHHH
Q 031871 93 KKAIVQARNDKK--LTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 93 ~~~Lk~~R~~~g--lTQ~eLA~~lgis~s~Is~~E 125 (151)
...|..+...-+ +|+.+||+.++++++++++.-
T Consensus 8 ~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v 42 (62)
T PF12802_consen 8 FRVLMALARHPGEELTQSELAERLGISKSTVSRIV 42 (62)
T ss_dssp HHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHH
Confidence 344556666666 999999999999999999864
No 144
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=90.82 E-value=0.59 Score=30.18 Aligned_cols=29 Identities=17% Similarity=0.103 Sum_probs=22.9
Q ss_pred HHHHHhcCC--cCHHHHHHHhCCCHHHHHHH
Q 031871 96 IVQARNDKK--LTQSQLAQLINEKPQVIQEY 124 (151)
Q Consensus 96 Lk~~R~~~g--lTQ~eLA~~lgis~s~Is~~ 124 (151)
|..++..-+ +|+.|||+.+|++.+++++.
T Consensus 12 L~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~ 42 (68)
T smart00550 12 LEFLENSGDETSTALQLAKNLGLPKKEVNRV 42 (68)
T ss_pred HHHHHHCCCCCcCHHHHHHHHCCCHHHHHHH
Confidence 344444444 99999999999999999886
No 145
>PRK10072 putative transcriptional regulator; Provisional
Probab=90.71 E-value=0.23 Score=34.62 Aligned_cols=29 Identities=24% Similarity=0.266 Sum_probs=25.1
Q ss_pred HHHHHHHHHcCCChhhHHhhhcCCCccCC
Q 031871 29 EKVVNAARRAGADIETVRKSHAGTNKAAS 57 (151)
Q Consensus 29 ~~~~~~a~r~g~~v~t~~k~~~g~~~~~~ 57 (151)
-++.+.|+..|++..|+.+|+.|...|..
T Consensus 47 lTQ~elA~~lGvS~~TVs~WE~G~r~P~~ 75 (96)
T PRK10072 47 LKIDDFARVLGVSVAMVKEWESRRVKPSS 75 (96)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCH
Confidence 35678999999999999999999988643
No 146
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=90.61 E-value=1 Score=26.94 Aligned_cols=36 Identities=8% Similarity=0.096 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
..+...|-.+.... .|++++|+.+|+|.++|.++-+
T Consensus 14 ~~~~~~i~~~~~~~-~s~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 14 KRLEQYILKLLRES-RSFKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred HHHHHHHHHHHhhc-CCHHHHHHHHCCCHHHHHHHHH
Confidence 34444454444444 7999999999999999998854
No 147
>PRK04217 hypothetical protein; Provisional
Probab=90.40 E-value=0.52 Score=33.70 Aligned_cols=32 Identities=9% Similarity=0.055 Sum_probs=27.6
Q ss_pred HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
.+-.++...|+|++|+|+.+|+|.+||.++..
T Consensus 49 eai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~ 80 (110)
T PRK04217 49 EALRLVDYEGLTQEEAGKRMGVSRGTVWRALT 80 (110)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 44466777899999999999999999999866
No 148
>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=90.33 E-value=0.37 Score=30.96 Aligned_cols=23 Identities=17% Similarity=0.287 Sum_probs=20.7
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHH
Q 031871 103 KKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 103 ~glTQ~eLA~~lgis~s~Is~~E 125 (151)
..+||.+||..+|+|+.++++.-
T Consensus 27 ~~lt~~~iA~~~g~sr~tv~r~l 49 (76)
T PF13545_consen 27 LPLTQEEIADMLGVSRETVSRIL 49 (76)
T ss_dssp EESSHHHHHHHHTSCHHHHHHHH
T ss_pred ecCCHHHHHHHHCCCHHHHHHHH
Confidence 56899999999999999999874
No 149
>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=90.29 E-value=0.37 Score=31.79 Aligned_cols=44 Identities=14% Similarity=0.175 Sum_probs=28.3
Q ss_pred HHHHHHH-HHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHH
Q 031871 91 ELKKAIV-QARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQ 134 (151)
Q Consensus 91 ~~~~~Lk-~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~ 134 (151)
.+++.|- ....-..+|..+||+.+|+|+++|.++-+.-..-...
T Consensus 20 ~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~kkLG~~gf~ 64 (77)
T PF01418_consen 20 KIADYILENPDEIAFMSISELAEKAGVSPSTIVRFCKKLGFSGFK 64 (77)
T ss_dssp HHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHHHHCTTTCHH
T ss_pred HHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHHHHhCCCCHH
Confidence 3444443 3455678999999999999999999987754444433
No 150
>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=90.06 E-value=0.084 Score=40.13 Aligned_cols=46 Identities=15% Similarity=0.120 Sum_probs=1.6
Q ss_pred cCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 031871 102 DKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 147 (151)
Q Consensus 102 ~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l 147 (151)
..-||++|+|+.+|++.+|||+.-+|+..-+..-+.-|...|...+
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 3458999999999999999999999997666665667776666554
No 151
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=89.96 E-value=0.46 Score=28.08 Aligned_cols=25 Identities=16% Similarity=0.226 Sum_probs=22.6
Q ss_pred cCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 102 DKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 102 ~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
..|+|..++|+.+|+|+++|..+-.
T Consensus 16 ~~g~s~~eia~~l~is~~tv~~~~~ 40 (58)
T smart00421 16 AEGLTNKEIAERLGISEKTVKTHLS 40 (58)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4789999999999999999998755
No 152
>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=89.83 E-value=1.2 Score=26.15 Aligned_cols=30 Identities=13% Similarity=0.224 Sum_probs=22.5
Q ss_pred HHHHHHHhcCCcCHHHHHHHhCCCHHHHHH
Q 031871 94 KAIVQARNDKKLTQSQLAQLINEKPQVIQE 123 (151)
Q Consensus 94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~ 123 (151)
.-|..+...-..+..++|+.+|+|.+++.+
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 446677777889999999999999998865
No 153
>PF14590 DUF4447: Domain of unknown function (DUF4447); PDB: 2OX6_B.
Probab=89.82 E-value=1.6 Score=32.36 Aligned_cols=42 Identities=21% Similarity=0.198 Sum_probs=32.0
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHH
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQ 134 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~ 134 (151)
+-.|+-+|...|+|..++|+..+.|..-+-.||.|+...+.-
T Consensus 9 aie~~ylr~slgl~~aqv~~l~k~se~dv~aweage~~~~~l 50 (166)
T PF14590_consen 9 AIEIKYLRLSLGLTTAQVAELTKASEADVLAWEAGEKPAPGL 50 (166)
T ss_dssp HHHHHHHHHHTT--HHHHHHHHTS-HHHHHHHHTTSS---HH
T ss_pred HHHHHHHHHHcCCCHHHHHHhhccCHHHhhhhhccCCcCchH
Confidence 345788999999999999999999999999999999765543
No 154
>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=89.54 E-value=0.41 Score=29.03 Aligned_cols=26 Identities=15% Similarity=0.195 Sum_probs=21.2
Q ss_pred hcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 101 NDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 101 ~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
...++|..|+|+.+|++++++.++-+
T Consensus 15 ~~~~~t~~eia~~~gl~~stv~r~L~ 40 (52)
T PF09339_consen 15 SGGPLTLSEIARALGLPKSTVHRLLQ 40 (52)
T ss_dssp TBSCEEHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34458999999999999999998853
No 155
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=89.45 E-value=0.51 Score=27.34 Aligned_cols=24 Identities=17% Similarity=0.259 Sum_probs=20.7
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 103 KKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 103 ~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
..+|+.++|+.+|+++++++++-+
T Consensus 7 ~~~s~~~la~~l~~s~~tv~~~l~ 30 (48)
T smart00419 7 LPLTRQEIAELLGLTRETVSRTLK 30 (48)
T ss_pred eccCHHHHHHHHCCCHHHHHHHHH
Confidence 468999999999999999988643
No 156
>PF13551 HTH_29: Winged helix-turn helix
Probab=89.45 E-value=1.2 Score=30.26 Aligned_cols=82 Identities=16% Similarity=0.211 Sum_probs=45.1
Q ss_pred HHHHHHHHcCCChhhHHhhhcCCCccCCCCcccccccccccchhhhHHHHHhhccCCc-chHHHHHHHHHHHhcC-----
Q 031871 30 KVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDR-VPSELKKAIVQARNDK----- 103 (151)
Q Consensus 30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~-~~~~~~~~Lk~~R~~~----- 103 (151)
+...+|+..|++..|+.+|-.-....-.+ . -+++....-.+ .. +.+..-..|.++....
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~---~---l~~~~~~~g~~---------~~~l~~~~~~~l~~~~~~~p~~g~ 78 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREGGIE---G---LLPRKPRGGRP---------RKRLSEEQRAQLIELLRENPPEGR 78 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHcccHH---H---HHhccccCCCC---------CCCCCHHHHHHHHHHHHHCCCCCC
Confidence 36789999999999998887643321000 0 00000000000 11 2333333444444332
Q ss_pred -CcCHHHHHHHh-------CCCHHHHHHHHc
Q 031871 104 -KLTQSQLAQLI-------NEKPQVIQEYES 126 (151)
Q Consensus 104 -glTQ~eLA~~l-------gis~s~Is~~E~ 126 (151)
.+|..+|++.+ .+|.++|.+|..
T Consensus 79 ~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 79 SRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 48888998855 678888888754
No 157
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=89.37 E-value=1.8 Score=29.76 Aligned_cols=66 Identities=15% Similarity=0.207 Sum_probs=40.9
Q ss_pred HHHHHHcCCChhhHHhhhcCCC-ccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHHH
Q 031871 32 VNAARRAGADIETVRKSHAGTN-KAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQL 110 (151)
Q Consensus 32 ~~~a~r~g~~v~t~~k~~~g~~-~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~eL 110 (151)
-+.|++.|+++.|++-|+.-.. .|... ...+-...+.+ .-..-..|+.++...|++..++
T Consensus 4 ~eva~~~gvs~~tlR~Ye~~GLl~p~~r-~~~g~r~Y~~~------------------dv~~l~~I~~L~~~~G~~l~~I 64 (95)
T cd04780 4 SELSKRSGVSVATIKYYLREGLLPEGRR-LAPNQAEYSEA------------------HVERLRLIRALQQEGGLPISQI 64 (95)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCCcC-CCCCCeecCHH------------------HHHHHHHHHHHHHHcCCCHHHH
Confidence 4689999999999999997333 22111 00111111111 1233555677777789999999
Q ss_pred HHHhCC
Q 031871 111 AQLINE 116 (151)
Q Consensus 111 A~~lgi 116 (151)
++.+..
T Consensus 65 ~~~l~~ 70 (95)
T cd04780 65 KEVLDA 70 (95)
T ss_pred HHHHHh
Confidence 988764
No 158
>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=89.25 E-value=0.66 Score=31.38 Aligned_cols=24 Identities=13% Similarity=0.315 Sum_probs=21.5
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHcC
Q 031871 104 KLTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 104 glTQ~eLA~~lgis~s~Is~~E~G 127 (151)
++|..|+|+.+||+.++|..||+-
T Consensus 1 ~~ti~evA~~~gvs~~tLR~ye~~ 24 (88)
T cd01105 1 VIGIGEVSKLTGVSPRQLRYWEEK 24 (88)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHC
Confidence 468899999999999999999863
No 159
>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=89.24 E-value=0.6 Score=32.82 Aligned_cols=23 Identities=26% Similarity=0.541 Sum_probs=21.0
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G 127 (151)
||..|+|+.+|||+.||..||.-
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~ 23 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEKE 23 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 57899999999999999999874
No 160
>PRK00118 putative DNA-binding protein; Validated
Probab=89.10 E-value=0.77 Score=32.50 Aligned_cols=33 Identities=9% Similarity=0.090 Sum_probs=27.3
Q ss_pred HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
..+-.++-..|+|..++|+.+|+|+++|.++-.
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 334466677899999999999999999998854
No 161
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=89.05 E-value=1.1 Score=33.38 Aligned_cols=37 Identities=14% Similarity=0.207 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
.++..++-..-...|+|..++|+.+|+|.+|+.+|-+
T Consensus 7 ~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~ 43 (138)
T COG3415 7 NDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVR 43 (138)
T ss_pred HHHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHH
Confidence 3445555555667899999999999999999998843
No 162
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=88.94 E-value=1.5 Score=30.82 Aligned_cols=56 Identities=16% Similarity=0.124 Sum_probs=38.6
Q ss_pred hHHHHHHHHHHH--hcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 031871 89 PSELKKAIVQAR--NDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALG 144 (151)
Q Consensus 89 ~~~~~~~Lk~~R--~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lg 144 (151)
.+.++.|++-.+ .+..+||.|++..+|+|-.+|.+=-|.-...+.+...-|.+.|.
T Consensus 43 Real~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITRGSN~LK~~~~~~k~~L~~~l~ 100 (103)
T COG2973 43 REALGTRVRIVEELLRGELSQREIAQKLGVSIATITRGSNSLKTADPEFKQWLEKVLL 100 (103)
T ss_pred HHHHHHHHHHHHHHHhccccHHHHHHHhCcchhhhccchhhhccCCHHHHHHHHHHhc
Confidence 466777776654 45689999999999999999887433333345555555555543
No 163
>PRK04132 replication factor C small subunit; Provisional
Probab=88.91 E-value=0.54 Score=44.39 Aligned_cols=43 Identities=28% Similarity=0.461 Sum_probs=40.1
Q ss_pred HHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 031871 107 QSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG 149 (151)
Q Consensus 107 Q~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~e 149 (151)
.+++|++.|+....+-.|-+|++.|+.....+||++||+++++
T Consensus 420 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 462 (846)
T PRK04132 420 RKEIAEKTGIRADRILEYIKGKRKPSLKNYIKIAKALGINLEK 462 (846)
T ss_pred HHHHHHHhCCcHHHHHHHHhcCCCccHHHHHHHHHHhcccHHH
Confidence 5689999999999999999999999999999999999998753
No 164
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=88.80 E-value=1.2 Score=25.93 Aligned_cols=25 Identities=20% Similarity=0.264 Sum_probs=21.5
Q ss_pred hcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 101 NDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 101 ~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
...++|..++|+.+++++++++++-
T Consensus 11 ~~~~~s~~~l~~~l~~s~~tv~~~l 35 (53)
T smart00420 11 QQGKVSVEELAELLGVSEMTIRRDL 35 (53)
T ss_pred HcCCcCHHHHHHHHCCCHHHHHHHH
Confidence 3467999999999999999998764
No 165
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=88.65 E-value=0.15 Score=32.21 Aligned_cols=27 Identities=22% Similarity=0.329 Sum_probs=21.4
Q ss_pred HHHHHHHHcCCChhhHHhhhcCCC-ccC
Q 031871 30 KVVNAARRAGADIETVRKSHAGTN-KAA 56 (151)
Q Consensus 30 ~~~~~a~r~g~~v~t~~k~~~g~~-~~~ 56 (151)
+.-..|.+.|++.+++.+||.|.. .|.
T Consensus 16 s~~~lA~~~g~s~s~v~~iE~G~~~~p~ 43 (64)
T PF13560_consen 16 SQAQLADRLGVSQSTVSRIERGRRPRPS 43 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSSSS-B
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCCCCCC
Confidence 567899999999999999999988 353
No 166
>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=88.49 E-value=1.3 Score=30.12 Aligned_cols=22 Identities=23% Similarity=0.406 Sum_probs=20.1
Q ss_pred cCHHHHHHHhCCCHHHHHHHHc
Q 031871 105 LTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~ 126 (151)
+|..|+|+.+|+++++|..|++
T Consensus 1 ~~~~eva~~~gi~~~tlr~~~~ 22 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYEE 22 (100)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999976
No 167
>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=88.46 E-value=0.93 Score=28.19 Aligned_cols=31 Identities=6% Similarity=-0.010 Sum_probs=25.3
Q ss_pred HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 96 IVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
+.+++.-..+++.|.|+.+||+.+++-+.-+
T Consensus 7 ~~~L~~~fhlp~~eAA~~Lgv~~T~LKr~CR 37 (52)
T PF02042_consen 7 LEDLSQYFHLPIKEAAKELGVSVTTLKRRCR 37 (52)
T ss_pred HHHHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence 5667778899999999999999888776543
No 168
>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=88.44 E-value=2.6 Score=28.43 Aligned_cols=65 Identities=14% Similarity=0.112 Sum_probs=39.0
Q ss_pred HHHHHHHcCCChhhHHhhhc-CCCccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHH
Q 031871 31 VVNAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQ 109 (151)
Q Consensus 31 ~~~~a~r~g~~v~t~~k~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~e 109 (151)
.-+.|++.|++..|++.|+. |-..|..... ..-+.-+. + .-..-..|+.+|. .|+|.++
T Consensus 4 i~evA~~~gvs~~tLR~ye~~Gll~p~r~~~-~g~R~Ys~--~----------------dv~~l~~I~~Lr~-~G~sl~~ 63 (88)
T cd01105 4 IGEVSKLTGVSPRQLRYWEEKGLIKSIRSDG-GGQRKYSL--A----------------DVDRLLVIKELLD-EGFTLAA 63 (88)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCCCCccCC-CCceecCH--H----------------HHHHHHHHHHHHH-CCCCHHH
Confidence 34689999999999999976 3332211110 01111111 1 1223455777776 8999999
Q ss_pred HHHHhC
Q 031871 110 LAQLIN 115 (151)
Q Consensus 110 LA~~lg 115 (151)
+++.+.
T Consensus 64 i~~~l~ 69 (88)
T cd01105 64 AVEKLR 69 (88)
T ss_pred HHHHHH
Confidence 888775
No 169
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=88.35 E-value=0.76 Score=26.47 Aligned_cols=31 Identities=16% Similarity=0.126 Sum_probs=21.0
Q ss_pred cCCcCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q 031871 102 DKKLTQSQLAQLINEKPQVIQEYESGKAIPN 132 (151)
Q Consensus 102 ~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~ 132 (151)
..++|..|+|..+|+|++++.+.-+-....+
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~~~g~t 36 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRLFKKETGMT 36 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHHHHHHTSS-
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHHCcC
Confidence 3568999999999999999999876443333
No 170
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=88.22 E-value=0.96 Score=36.93 Aligned_cols=40 Identities=13% Similarity=0.141 Sum_probs=34.9
Q ss_pred CcchHHHHHHHHHHHhcCC-cCHHHHHHHhCCCHHHHHHHH
Q 031871 86 DRVPSELKKAIVQARNDKK-LTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 86 ~~~~~~~~~~Lk~~R~~~g-lTQ~eLA~~lgis~s~Is~~E 125 (151)
..+.++-.+.|.-++..-| ++|+||.+++|.|+++++++-
T Consensus 191 ~~L~~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L 231 (258)
T COG2512 191 YDLNEDEKEILDLIRERGGRITQAELRRALGLSKTTVSRIL 231 (258)
T ss_pred CCCCHHHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHH
Confidence 3456777888999999999 999999999999999999864
No 171
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=88.07 E-value=0.82 Score=34.84 Aligned_cols=32 Identities=13% Similarity=0.199 Sum_probs=26.8
Q ss_pred HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
.++-.+|.-.|+|..|+|+.+|||+.||.+..
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 44555677789999999999999999998754
No 172
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=88.06 E-value=0.49 Score=35.32 Aligned_cols=25 Identities=12% Similarity=0.252 Sum_probs=19.7
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHcCC
Q 031871 104 KLTQSQLAQLINEKPQVIQEYESGK 128 (151)
Q Consensus 104 glTQ~eLA~~lgis~s~Is~~E~G~ 128 (151)
..|+.++|+.+||+++++.+|-+..
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 173
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=88.04 E-value=1.4 Score=32.06 Aligned_cols=34 Identities=12% Similarity=0.273 Sum_probs=27.8
Q ss_pred HHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871 91 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEY 124 (151)
Q Consensus 91 ~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~ 124 (151)
.-.+.|+.+.....+++.+||+++|+|++++.+-
T Consensus 9 ~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~R 42 (154)
T COG1522 9 IDRRILRLLQEDARISNAELAERVGLSPSTVLRR 42 (154)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHH
Confidence 3345577788888899999999999999988764
No 174
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=87.82 E-value=3.7 Score=25.69 Aligned_cols=63 Identities=16% Similarity=0.201 Sum_probs=36.7
Q ss_pred HHHHHHcCCChhhHHhhhc-CCCccC-CCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHH
Q 031871 32 VNAARRAGADIETVRKSHA-GTNKAA-SSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQ 109 (151)
Q Consensus 32 ~~~a~r~g~~v~t~~k~~~-g~~~~~-~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~e 109 (151)
-+.|++.|++.+|++.|+. |-..|. .... .-.. +.. . ....-..+..+|. .|++.++
T Consensus 4 ~eva~~~gvs~~tlr~~~~~gli~~~~~~~~--g~r~-------y~~---------~--dl~~l~~i~~lr~-~g~~~~~ 62 (70)
T smart00422 4 GEVAKLAGVSVRTLRYYERIGLLPPPIRTEG--GYRL-------YSD---------E--DLERLRFIKRLKE-LGFSLEE 62 (70)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCCccCCC--CCEe-------cCH---------H--HHHHHHHHHHHHH-cCCCHHH
Confidence 4689999999999999976 222221 0100 0011 111 0 1223455666665 8888888
Q ss_pred HHHHhC
Q 031871 110 LAQLIN 115 (151)
Q Consensus 110 LA~~lg 115 (151)
++..+.
T Consensus 63 i~~~l~ 68 (70)
T smart00422 63 IKELLE 68 (70)
T ss_pred HHHHHh
Confidence 887664
No 175
>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=87.79 E-value=0.87 Score=31.51 Aligned_cols=23 Identities=17% Similarity=0.263 Sum_probs=20.6
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G 127 (151)
+|..|+|+.+||++++|..||+-
T Consensus 1 ~ti~eva~~~gvs~~tlR~ye~~ 23 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYDEI 23 (103)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 57889999999999999999763
No 176
>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=87.69 E-value=0.9 Score=31.32 Aligned_cols=23 Identities=13% Similarity=0.211 Sum_probs=20.7
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G 127 (151)
++..++|+.+|+++++|..||+-
T Consensus 1 ~~I~e~a~~~gvs~~tLR~ye~~ 23 (96)
T cd04774 1 YKVDEVAKRLGLTKRTLKYYEEI 23 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 57789999999999999999874
No 177
>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=87.60 E-value=0.91 Score=31.54 Aligned_cols=23 Identities=26% Similarity=0.182 Sum_probs=21.2
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G 127 (151)
++..|+|+.+|||++||..||+-
T Consensus 2 ~~i~eva~~~gvs~~tlR~ye~~ 24 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEKL 24 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 68899999999999999999874
No 178
>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=87.46 E-value=3.5 Score=28.22 Aligned_cols=20 Identities=30% Similarity=0.260 Sum_probs=17.8
Q ss_pred HHHHHHcCCChhhHHhhhcC
Q 031871 32 VNAARRAGADIETVRKSHAG 51 (151)
Q Consensus 32 ~~~a~r~g~~v~t~~k~~~g 51 (151)
-+.|++.|+++.|++-|+.-
T Consensus 4 ~eva~~~gvs~~tLRyye~~ 23 (96)
T cd04768 4 GEFAKLAGVSIRTLRHYDDI 23 (96)
T ss_pred HHHHHHHCcCHHHHHHHHHC
Confidence 46899999999999999974
No 179
>PRK10458 DNA cytosine methylase; Provisional
Probab=87.43 E-value=1.5 Score=38.79 Aligned_cols=45 Identities=16% Similarity=0.181 Sum_probs=34.4
Q ss_pred HhcCCcCHHHHHHHhC------CCHHHHHHHHcCCCCC---CHHHHHHHHHHhC
Q 031871 100 RNDKKLTQSQLAQLIN------EKPQVIQEYESGKAIP---NQQILTKLERALG 144 (151)
Q Consensus 100 R~~~glTQ~eLA~~lg------is~s~Is~~E~G~~~p---~~~~l~kLa~~Lg 144 (151)
|...+++|++||+.+| .+..+|.+||+|+..+ +...+..|-..+.
T Consensus 25 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 78 (467)
T PRK10458 25 KLLEIYDVKTLAAQLNGVGENHWSRAILKRWLAGKSAWHRLSEAEFAHLQTLLP 78 (467)
T ss_pred HHHHhcCHHHHHHHHhhcccCccCHHHHHHHHcCCCCCCCccHHHHHHHHHhcc
Confidence 4445789999999997 7889999999999743 4455566665553
No 180
>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=87.41 E-value=1.4 Score=27.44 Aligned_cols=29 Identities=14% Similarity=0.168 Sum_probs=24.4
Q ss_pred HHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871 96 IVQARNDKKLTQSQLAQLINEKPQVIQEY 124 (151)
Q Consensus 96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~ 124 (151)
+..+.....+|..+||+.+|||..||.+-
T Consensus 6 l~~l~~~~~~s~~ela~~~~VS~~TiRRD 34 (57)
T PF08220_consen 6 LELLKEKGKVSVKELAEEFGVSEMTIRRD 34 (57)
T ss_pred HHHHHHcCCEEHHHHHHHHCcCHHHHHHH
Confidence 45566677899999999999999999874
No 181
>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=87.36 E-value=0.95 Score=31.06 Aligned_cols=24 Identities=21% Similarity=0.326 Sum_probs=21.4
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESGK 128 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G~ 128 (151)
+|..|+|+.+|||+.||.-||+-.
T Consensus 1 ~ti~eva~~~gvs~~tLRyye~~G 24 (96)
T cd04768 1 LTIGEFAKLAGVSIRTLRHYDDIG 24 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCC
Confidence 478899999999999999999743
No 182
>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=87.26 E-value=1 Score=30.96 Aligned_cols=23 Identities=13% Similarity=0.180 Sum_probs=20.9
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G 127 (151)
|+..|+|+.+|+|..+|..||+-
T Consensus 1 m~i~eva~~~gvs~~tlR~ye~~ 23 (96)
T cd04788 1 WKIGELARRTGLSVRTLHHYDHI 23 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 57889999999999999999863
No 183
>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=87.24 E-value=0.95 Score=31.72 Aligned_cols=23 Identities=22% Similarity=0.300 Sum_probs=20.9
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G 127 (151)
++..|+|+.+|||++||.-||+-
T Consensus 1 ~~i~eva~~~gis~~tlR~ye~~ 23 (108)
T cd01107 1 FTIGEFAKLSNLSIKALRYYDKI 23 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc
Confidence 57889999999999999999874
No 184
>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=87.19 E-value=2.5 Score=30.81 Aligned_cols=35 Identities=23% Similarity=0.264 Sum_probs=30.6
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Q 031871 104 KLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV 145 (151)
Q Consensus 104 glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv 145 (151)
.+|..++|..+|+|++++.++.+ ..+.+||..||.
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 36999999999999999999876 668889988873
No 185
>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=87.16 E-value=0.7 Score=32.10 Aligned_cols=22 Identities=18% Similarity=0.534 Sum_probs=20.1
Q ss_pred cCHHHHHHHhCCCHHHHHHHHc
Q 031871 105 LTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~ 126 (151)
+|..|+|+.+|||+++|..||+
T Consensus 1 yti~EvA~~~gVs~~tLR~ye~ 22 (99)
T cd04765 1 FSIGEVAEILGLPPHVLRYWET 22 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4778999999999999999975
No 186
>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=87.13 E-value=1.3 Score=27.57 Aligned_cols=29 Identities=14% Similarity=0.126 Sum_probs=23.6
Q ss_pred HHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871 96 IVQARNDKKLTQSQLAQLINEKPQVIQEY 124 (151)
Q Consensus 96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~ 124 (151)
|+.+....++|..+||+.+|+++++++.-
T Consensus 16 l~~L~~~~~~t~~ela~~l~~~~~t~s~h 44 (61)
T PF12840_consen 16 LRLLASNGPMTVSELAEELGISQSTVSYH 44 (61)
T ss_dssp HHHHHHCSTBEHHHHHHHHTS-HHHHHHH
T ss_pred HHHHhcCCCCCHHHHHHHHCCCHHHHHHH
Confidence 44456889999999999999999998863
No 187
>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=87.10 E-value=1 Score=35.19 Aligned_cols=28 Identities=21% Similarity=0.242 Sum_probs=24.8
Q ss_pred HhcCCcCHHHHHHHhCCCHHHHHHHHcC
Q 031871 100 RNDKKLTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 100 R~~~glTQ~eLA~~lgis~s~Is~~E~G 127 (151)
|-..|+|++++|+.+|+|+.+|+++++.
T Consensus 195 ~~~~~~t~~eIA~~lgis~~~V~~~~~~ 222 (231)
T TIGR02885 195 RYFKDKTQTEVANMLGISQVQVSRLEKK 222 (231)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 4457999999999999999999999873
No 188
>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=87.08 E-value=0.29 Score=29.78 Aligned_cols=28 Identities=18% Similarity=0.268 Sum_probs=20.4
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESGKAIPN 132 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G~~~p~ 132 (151)
++.+|+++.+|+|++++.++.+....|.
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 5788999999999999999988555553
No 189
>PF13551 HTH_29: Winged helix-turn helix
Probab=86.76 E-value=0.93 Score=30.91 Aligned_cols=26 Identities=8% Similarity=0.142 Sum_probs=22.1
Q ss_pred hcCCc-CHHHHHHHhCCCHHHHHHHHc
Q 031871 101 NDKKL-TQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 101 ~~~gl-TQ~eLA~~lgis~s~Is~~E~ 126 (151)
...|+ |..++|+.+|+|++||.+|-+
T Consensus 8 ~~~g~~~~~~ia~~lg~s~~Tv~r~~~ 34 (112)
T PF13551_consen 8 LAEGVSTIAEIARRLGISRRTVYRWLK 34 (112)
T ss_pred HHcCCCcHHHHHHHHCcCHHHHHHHHH
Confidence 45678 599999999999999999843
No 190
>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=86.76 E-value=2.1 Score=28.89 Aligned_cols=64 Identities=14% Similarity=0.105 Sum_probs=40.4
Q ss_pred HHHHHHcCCChhhHHhhhcC-CCccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHHH
Q 031871 32 VNAARRAGADIETVRKSHAG-TNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQL 110 (151)
Q Consensus 32 ~~~a~r~g~~v~t~~k~~~g-~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~eL 110 (151)
-+.|...|+++.|++.|+.- -..|..+. ..-.. +.. ..-.....|+.++...|++.+++
T Consensus 5 ~e~A~~~gvs~~tLr~ye~~Gli~p~r~~--~g~R~-------y~~-----------~dv~~l~~i~~L~~d~g~~l~~i 64 (91)
T cd04766 5 SVAAELSGMHPQTLRLYERLGLLSPSRTD--GGTRR-------YSE-----------RDIERLRRIQRLTQELGVNLAGV 64 (91)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCcCCCcCC--CCCee-------ECH-----------HHHHHHHHHHHHHHHcCCCHHHH
Confidence 46899999999999999863 22221110 00111 111 11234566777888899999999
Q ss_pred HHHhC
Q 031871 111 AQLIN 115 (151)
Q Consensus 111 A~~lg 115 (151)
+..+.
T Consensus 65 ~~~l~ 69 (91)
T cd04766 65 KRILE 69 (91)
T ss_pred HHHHH
Confidence 88875
No 191
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=86.69 E-value=1.5 Score=30.01 Aligned_cols=31 Identities=6% Similarity=0.064 Sum_probs=25.5
Q ss_pred HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 96 IVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
|-..-.+.|++..++|+..|||..|..+|..
T Consensus 17 lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~ 47 (85)
T PF13011_consen 17 LVRRVVEQGWPVAHAAAEFGVSRRTAYKWLA 47 (85)
T ss_pred HHHHHHHcCCcHHHHHHHhCCCHHHHHHHHH
Confidence 3344456899999999999999999999954
No 192
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=86.69 E-value=0.24 Score=37.72 Aligned_cols=47 Identities=11% Similarity=-0.000 Sum_probs=35.8
Q ss_pred ccCHHHHHHHHHcCCChhhHHhhhcCCCccCCCCcccccccccccch
Q 031871 26 KKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTE 72 (151)
Q Consensus 26 ~~~~~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~~~~ 72 (151)
.++-++.+.|+++|++.+|+.+||.|...|....+.+.+..|+...+
T Consensus 18 ~~glt~~elA~~~gis~~~is~~E~g~~~p~~~~l~~ia~~l~v~~~ 64 (185)
T PRK09943 18 QQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLS 64 (185)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHH
Confidence 34446678999999999999999999988766555566666665544
No 193
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=86.68 E-value=0.23 Score=36.11 Aligned_cols=29 Identities=3% Similarity=0.023 Sum_probs=24.6
Q ss_pred HHHHHHHHcCCChhhHHhhhcCCCccCCC
Q 031871 30 KVVNAARRAGADIETVRKSHAGTNKAASS 58 (151)
Q Consensus 30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~~~ 58 (151)
++...|.+.|++.+|+.+|+.|...|..+
T Consensus 20 tq~~lA~~~gvs~~~is~~E~g~~~p~~~ 48 (135)
T PRK09706 20 SQRSLAKAVKVSHVSISQWERDETEPTGK 48 (135)
T ss_pred CHHHHHHHhCCCHHHHHHHHcCCCCCCHH
Confidence 56789999999999999999998776443
No 194
>PRK09726 antitoxin HipB; Provisional
Probab=86.68 E-value=0.24 Score=33.48 Aligned_cols=44 Identities=9% Similarity=0.072 Sum_probs=31.6
Q ss_pred cCHHHHHHHHHcCCChhhHHhhhcCCCccCCCCccccccccccc
Q 031871 27 KDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDED 70 (151)
Q Consensus 27 ~~~~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~~ 70 (151)
++-+.-++|++.|++.+|+.+|+.|...|..+.+.+.+..++..
T Consensus 24 ~gltq~elA~~~gvs~~tis~~e~g~~~ps~~~l~~ia~~lgv~ 67 (88)
T PRK09726 24 NGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELS 67 (88)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHcCCC
Confidence 34467789999999999999999998765444444444444443
No 195
>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed
Probab=86.64 E-value=0.38 Score=39.79 Aligned_cols=57 Identities=9% Similarity=0.075 Sum_probs=39.4
Q ss_pred eccCCCCCccccCHHHHHHHHHcCCChhhHHhhhcCCCccCCCCcccccccccccch
Q 031871 16 IKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTE 72 (151)
Q Consensus 16 ~~~~~~~~~~~~~~~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~~~~ 72 (151)
+|.+-...+..++-++...|.+.|++.+++.+||.|...|....+.+.+..|+.+.+
T Consensus 29 ~g~rl~~~R~~~gltq~~lA~~~gvs~~~i~~~E~g~~~ps~~~l~~ia~~l~v~~~ 85 (309)
T PRK08154 29 LGERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCSLA 85 (309)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCCCHH
Confidence 444433334445556788999999999999999999988765555555555555433
No 196
>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=86.52 E-value=1.1 Score=31.03 Aligned_cols=23 Identities=22% Similarity=0.198 Sum_probs=21.1
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G 127 (151)
+|..|+|+.+|||++||..||+-
T Consensus 2 ~~i~eva~~~gvs~~tLR~ye~~ 24 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYESI 24 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 67899999999999999999874
No 197
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=86.50 E-value=1.1 Score=27.56 Aligned_cols=34 Identities=12% Similarity=0.234 Sum_probs=25.0
Q ss_pred HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCC
Q 031871 95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK 128 (151)
Q Consensus 95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~ 128 (151)
.--..+.+.|++..++|+.+|-|+..|.+|.+.-
T Consensus 11 aqid~m~qlG~s~~~isr~i~RSr~~Ir~yl~dP 44 (50)
T PF11427_consen 11 AQIDVMHQLGMSLREISRRIGRSRTCIRRYLKDP 44 (50)
T ss_dssp HHHHHHHHTT--HHHHHHHHT--HHHHHHHHHSC
T ss_pred HHHHHHHHhchhHHHHHHHhCccHHHHHHHhcCh
Confidence 3345677899999999999999999999998753
No 198
>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=86.37 E-value=1.2 Score=30.70 Aligned_cols=24 Identities=17% Similarity=0.146 Sum_probs=21.4
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESGK 128 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G~ 128 (151)
|+..|||+.+|++.++|..||+-.
T Consensus 1 m~I~eva~~~gvs~~tlR~Ye~~G 24 (95)
T cd04780 1 MRMSELSKRSGVSVATIKYYLREG 24 (95)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCC
Confidence 578899999999999999999744
No 199
>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=86.36 E-value=0.56 Score=29.94 Aligned_cols=33 Identities=9% Similarity=0.082 Sum_probs=23.8
Q ss_pred HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCC
Q 031871 96 IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAI 130 (151)
Q Consensus 96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~ 130 (151)
|.++-.+.| |.+.|+.+||+++.|++-.+-.+.
T Consensus 6 L~eyv~~~G--Q~kaA~~lGV~Q~AIsKAlr~gR~ 38 (59)
T PF09048_consen 6 LAEYVKEHG--QAKAARALGVTQSAISKALRAGRN 38 (59)
T ss_dssp HHHHHHHHH--HHHHHHHHTS-HHHHHHHHHCT-E
T ss_pred HHHHHHHhC--hHHHHHHcCCcHHHHHHHHHcCCc
Confidence 334444555 999999999999999998775553
No 200
>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=86.27 E-value=1.2 Score=30.81 Aligned_cols=24 Identities=33% Similarity=0.446 Sum_probs=20.9
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESGK 128 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G~ 128 (151)
++..|+|+.+|||.+||..||+-.
T Consensus 1 y~i~e~A~~~gvs~~tlR~Ye~~G 24 (99)
T cd04772 1 YRTVDLARAIGLSPQTVRNYESLG 24 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcC
Confidence 367899999999999999999743
No 201
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=86.07 E-value=1.2 Score=30.56 Aligned_cols=22 Identities=23% Similarity=0.403 Sum_probs=20.2
Q ss_pred cCHHHHHHHhCCCHHHHHHHHc
Q 031871 105 LTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~ 126 (151)
+|..|+|+.+|||..+|..||+
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~ 22 (97)
T cd04782 1 FTTGEFAKLCGISKQTLFHYDK 22 (97)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4788999999999999999986
No 202
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=86.07 E-value=1.7 Score=32.32 Aligned_cols=23 Identities=17% Similarity=0.247 Sum_probs=20.5
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHH
Q 031871 103 KKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 103 ~glTQ~eLA~~lgis~s~Is~~E 125 (151)
..+||.|||..+|+++.+|++.-
T Consensus 142 ~~~t~~~iA~~lG~tretvsR~l 164 (193)
T TIGR03697 142 LRLSHQAIAEAIGSTRVTITRLL 164 (193)
T ss_pred CCCCHHHHHHHhCCcHHHHHHHH
Confidence 45899999999999999999863
No 203
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=86.03 E-value=2.2 Score=31.21 Aligned_cols=45 Identities=13% Similarity=0.324 Sum_probs=33.9
Q ss_pred hhccCCcchHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 81 LYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 81 ~~~~~~~~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
.|+++..+..++..+|-++-. .|+...++|+.+.||.+.|++|.+
T Consensus 11 ~~~nGrPLp~~~R~rIvela~-~G~rp~~Isr~l~Vs~gcVsKIl~ 55 (125)
T PF00292_consen 11 VFINGRPLPNELRQRIVELAK-EGVRPCDISRQLRVSHGCVSKILS 55 (125)
T ss_dssp EEETTSSS-HHHHHHHHHHHH-TT--HHHHHHHHT--HHHHHHHHH
T ss_pred eeeCCccCcHHHHHHHHHHhh-hcCCHHHHHHHHccchhHHHHHHH
Confidence 477778888899888888775 599999999999999999999843
No 204
>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=85.63 E-value=1.3 Score=29.98 Aligned_cols=23 Identities=30% Similarity=0.313 Sum_probs=20.8
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G 127 (151)
+|..++|+.+|||+++|..||.-
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye~~ 24 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYERL 24 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHC
Confidence 57889999999999999999863
No 205
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=85.58 E-value=2.5 Score=30.68 Aligned_cols=32 Identities=13% Similarity=0.173 Sum_probs=26.1
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEY 124 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~ 124 (151)
...|..+...-++||.+||+.++++++++++.
T Consensus 43 ~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~ 74 (144)
T PRK11512 43 FKVLCSIRCAACITPVELKKVLSVDLGALTRM 74 (144)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHH
Confidence 34455555667899999999999999999886
No 206
>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=85.43 E-value=1.3 Score=31.08 Aligned_cols=24 Identities=17% Similarity=0.220 Sum_probs=21.1
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESGK 128 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G~ 128 (151)
+|..|+|+.+|||++||..||+-.
T Consensus 1 ~~i~e~a~~~gvs~~tlr~ye~~g 24 (113)
T cd01109 1 YTIKEVAEKTGLSADTLRYYEKEG 24 (113)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCC
Confidence 578899999999999999998743
No 207
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=85.38 E-value=1.4 Score=26.33 Aligned_cols=25 Identities=12% Similarity=0.123 Sum_probs=22.4
Q ss_pred CHHHHHHHhCCCHHHHHHHHcCCCC
Q 031871 106 TQSQLAQLINEKPQVIQEYESGKAI 130 (151)
Q Consensus 106 TQ~eLA~~lgis~s~Is~~E~G~~~ 130 (151)
|+.|.|+.+|+++++|++.-+|...
T Consensus 19 S~~eAa~~lg~~~~~I~~~~~~~~~ 43 (53)
T smart00497 19 SIREAAKYLGISHSSISKYLNTGKK 43 (53)
T ss_pred CHHHHHHHhCCCHHHHHHHHhCCCc
Confidence 7889999999999999999998643
No 208
>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=85.25 E-value=1.3 Score=31.82 Aligned_cols=24 Identities=25% Similarity=0.376 Sum_probs=21.6
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESGK 128 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G~ 128 (151)
|+..|+|+.+|||..||.-||+-.
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe~~G 24 (127)
T TIGR02044 1 MNIGQVAKLTGLSSKMIRYYEEKG 24 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCC
Confidence 678999999999999999999744
No 209
>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=85.10 E-value=1 Score=31.91 Aligned_cols=23 Identities=26% Similarity=0.274 Sum_probs=21.1
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G 127 (151)
||..|+|+.+|||+.||.-||.-
T Consensus 1 ~~ige~a~~~gvs~~tLryYe~~ 23 (116)
T cd04769 1 MYIGELAQQTGVTIKAIRLYEEK 23 (116)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 67899999999999999999974
No 210
>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=85.08 E-value=1.5 Score=30.31 Aligned_cols=22 Identities=27% Similarity=0.454 Sum_probs=20.3
Q ss_pred cCHHHHHHHhCCCHHHHHHHHc
Q 031871 105 LTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~ 126 (151)
+|..++|+.+|||+++|..||+
T Consensus 2 ~~i~eva~~~gVs~~tLR~ye~ 23 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVYDR 23 (98)
T ss_pred cCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999976
No 211
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=85.06 E-value=1.6 Score=34.91 Aligned_cols=31 Identities=23% Similarity=0.181 Sum_probs=26.0
Q ss_pred HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 96 IVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
+-.+|-..|+|+.|+|+.+|+|+++|+++++
T Consensus 217 vi~~~~~~~~t~~eIA~~lgis~~~V~~~~~ 247 (258)
T PRK08215 217 ILNLRFFQGKTQMEVAEEIGISQAQVSRLEK 247 (258)
T ss_pred HHHHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3334555799999999999999999999987
No 212
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=85.00 E-value=1 Score=31.65 Aligned_cols=23 Identities=22% Similarity=0.300 Sum_probs=20.8
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G 127 (151)
+|..++|+.+|||..||.-||+-
T Consensus 1 ~~I~eva~~~gvs~~tLRyYE~~ 23 (124)
T COG0789 1 YTIGEVAKLTGVSVRTLRFYERK 23 (124)
T ss_pred CcHHHHHHHhCCCHHHHHHHHHc
Confidence 57889999999999999999873
No 213
>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=84.94 E-value=1.5 Score=30.94 Aligned_cols=23 Identities=17% Similarity=0.229 Sum_probs=20.9
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G 127 (151)
|+..|+|+.+|+|.+||..||+-
T Consensus 1 m~i~eva~~~gvs~~tlR~Ye~~ 23 (112)
T cd01282 1 MRIGELAARTGVSVRSLRYYEEQ 23 (112)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHC
Confidence 57889999999999999999873
No 214
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=84.89 E-value=2.3 Score=25.38 Aligned_cols=21 Identities=24% Similarity=0.366 Sum_probs=18.6
Q ss_pred Cc-CHHHHHHHhCCCHHHHHHH
Q 031871 104 KL-TQSQLAQLINEKPQVIQEY 124 (151)
Q Consensus 104 gl-TQ~eLA~~lgis~s~Is~~ 124 (151)
.+ |+.+||+.+|+|++++.+.
T Consensus 19 ~l~s~~~la~~~~vs~~tv~~~ 40 (60)
T smart00345 19 KLPSERELAAQLGVSRTTVREA 40 (60)
T ss_pred cCcCHHHHHHHHCCCHHHHHHH
Confidence 46 8999999999999998875
No 215
>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=84.86 E-value=5.3 Score=27.86 Aligned_cols=68 Identities=13% Similarity=0.100 Sum_probs=38.1
Q ss_pred HHHHHHcCCChhhHHhhhcCCC-ccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHHH
Q 031871 32 VNAARRAGADIETVRKSHAGTN-KAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQL 110 (151)
Q Consensus 32 ~~~a~r~g~~v~t~~k~~~g~~-~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~eL 110 (151)
-+.|++.|++++|++-|+.-.. .|........-+.-+.. .-..-..|+.+|. .|++.+++
T Consensus 4 ~eva~~~gis~~tlR~ye~~GLi~p~~~~~~ngyR~Y~~~------------------~i~~l~~I~~lr~-~G~sl~~i 64 (108)
T cd01107 4 GEFAKLSNLSIKALRYYDKIGLLKPAYVDPDTGYRYYSAE------------------QLERLNRIKYLRD-LGFPLEEI 64 (108)
T ss_pred HHHHHHHCcCHHHHHHHHHcCCCCCCcCCCCCCccccCHH------------------HHHHHHHHHHHHH-cCCCHHHH
Confidence 4689999999999999997422 22110000000111110 1122344555554 88999998
Q ss_pred HHHhCCCH
Q 031871 111 AQLINEKP 118 (151)
Q Consensus 111 A~~lgis~ 118 (151)
...+....
T Consensus 65 ~~l~~~~~ 72 (108)
T cd01107 65 KEILDADN 72 (108)
T ss_pred HHHHhcCC
Confidence 88776544
No 216
>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=84.83 E-value=1.5 Score=31.28 Aligned_cols=24 Identities=17% Similarity=0.220 Sum_probs=21.6
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESGK 128 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G~ 128 (151)
||..|+|+.+|||..+|.-||+-.
T Consensus 1 m~IgevA~~~gvs~~tlRyYe~~G 24 (120)
T cd04781 1 LDIAEVARQSGLPASTLRYYEEKG 24 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCC
Confidence 578999999999999999999743
No 217
>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=84.82 E-value=1.5 Score=30.80 Aligned_cols=24 Identities=21% Similarity=0.192 Sum_probs=21.1
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESGK 128 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G~ 128 (151)
+|..|+|+.+|||..||..||+-.
T Consensus 1 y~Ige~A~~~gvs~~tlR~ye~~G 24 (107)
T cd01111 1 YSISQLALDAGVSVHIVRDYLLRG 24 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCC
Confidence 477899999999999999998743
No 218
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=84.81 E-value=2.5 Score=33.09 Aligned_cols=22 Identities=5% Similarity=0.169 Sum_probs=19.7
Q ss_pred CCcCHHHHHHHhCCCHHHHHHH
Q 031871 103 KKLTQSQLAQLINEKPQVIQEY 124 (151)
Q Consensus 103 ~glTQ~eLA~~lgis~s~Is~~ 124 (151)
..+||.+||..+|+++.++++.
T Consensus 178 i~lt~~~IA~~lGisretlsR~ 199 (230)
T PRK09391 178 LPMSRRDIADYLGLTIETVSRA 199 (230)
T ss_pred ecCCHHHHHHHHCCCHHHHHHH
Confidence 3489999999999999999985
No 219
>PRK11891 aspartate carbamoyltransferase; Provisional
Probab=84.76 E-value=1.2 Score=38.88 Aligned_cols=36 Identities=11% Similarity=0.118 Sum_probs=32.0
Q ss_pred HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcC
Q 031871 92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G 127 (151)
-.+-|++++.+.|||..+||+++|++..++.+|.--
T Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~wl~p 39 (429)
T PRK11891 4 QQAFLRDAMRRLNMTREAFANRIGVSRRALDTWLLP 39 (429)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHhCCcHHhHHhhcCC
Confidence 356689999999999999999999999999999653
No 220
>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=84.74 E-value=1.6 Score=27.68 Aligned_cols=34 Identities=9% Similarity=0.057 Sum_probs=27.4
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
.+.+..+....++|..++|+.+|++++++++.-+
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 4445556677889999999999999999988643
No 221
>PRK05572 sporulation sigma factor SigF; Validated
Probab=84.63 E-value=1.7 Score=34.64 Aligned_cols=29 Identities=24% Similarity=0.180 Sum_probs=25.3
Q ss_pred HHhcCCcCHHHHHHHhCCCHHHHHHHHcC
Q 031871 99 ARNDKKLTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 99 ~R~~~glTQ~eLA~~lgis~s~Is~~E~G 127 (151)
++-..|+|++++|+.+|+|+++|+++++.
T Consensus 213 l~~~~~~s~~eIA~~lgis~~~V~~~~~r 241 (252)
T PRK05572 213 LRYFKDKTQSEVAKRLGISQVQVSRLEKK 241 (252)
T ss_pred HHHhCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 45567999999999999999999999873
No 222
>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=84.54 E-value=1.1 Score=32.18 Aligned_cols=24 Identities=21% Similarity=0.253 Sum_probs=21.3
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESGK 128 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G~ 128 (151)
|+..|+|+.+|+|+.||.-||+-.
T Consensus 1 m~IgevA~~~gvs~~tLRyYe~~G 24 (127)
T cd04784 1 MKIGELAKKTGCSVETIRYYEKEG 24 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCC
Confidence 578899999999999999998743
No 223
>PF13730 HTH_36: Helix-turn-helix domain
Probab=84.53 E-value=1.3 Score=26.80 Aligned_cols=21 Identities=19% Similarity=0.188 Sum_probs=19.0
Q ss_pred CHHHHHHHhCCCHHHHHHHHc
Q 031871 106 TQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 106 TQ~eLA~~lgis~s~Is~~E~ 126 (151)
|++.||+.+|+|+.||.++-+
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~ 47 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIK 47 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 899999999999999998743
No 224
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=84.33 E-value=2.1 Score=33.21 Aligned_cols=22 Identities=9% Similarity=0.220 Sum_probs=20.0
Q ss_pred CcCHHHHHHHhCCCHHHHHHHH
Q 031871 104 KLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 104 glTQ~eLA~~lgis~s~Is~~E 125 (151)
.+||++||..+|+++.++++.-
T Consensus 184 ~lt~~~iA~~lG~sr~tvsR~l 205 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETISRLL 205 (235)
T ss_pred cccHHHHHHHhCCcHHHHHHHH
Confidence 4899999999999999999964
No 225
>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=84.27 E-value=1.5 Score=25.89 Aligned_cols=25 Identities=8% Similarity=0.169 Sum_probs=22.2
Q ss_pred cCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 102 DKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 102 ~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
..|+|..++|+.+|+|+++|..+-.
T Consensus 13 ~~~~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 13 AEGKTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3689999999999999999998754
No 226
>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=84.25 E-value=1.1 Score=32.11 Aligned_cols=24 Identities=25% Similarity=0.304 Sum_probs=21.3
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESGK 128 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G~ 128 (151)
|+..|+|+.+|+|+.||..||+-.
T Consensus 1 m~I~e~a~~~gvs~~tlR~Ye~~G 24 (126)
T cd04783 1 LTIGELAKAAGVNVETIRYYQRRG 24 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCC
Confidence 578899999999999999998743
No 227
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=84.13 E-value=1.4 Score=34.14 Aligned_cols=33 Identities=21% Similarity=0.301 Sum_probs=29.9
Q ss_pred HHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCC
Q 031871 98 QARNDKKLTQSQLAQLINEKPQVIQEYESGKAI 130 (151)
Q Consensus 98 ~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~ 130 (151)
-+|...|+|..++|+.+|.+.+||.++-+|...
T Consensus 55 ~arekag~Ti~EIAeelG~TeqTir~hlkgetk 87 (182)
T COG1318 55 LAREKAGMTISEIAEELGRTEQTVRNHLKGETK 87 (182)
T ss_pred HHHHHccCcHHHHHHHhCCCHHHHHHHHhcchh
Confidence 356899999999999999999999999998754
No 228
>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=84.10 E-value=1.2 Score=31.68 Aligned_cols=23 Identities=26% Similarity=0.372 Sum_probs=20.9
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G 127 (151)
||..|+|+.+|||+.+|.-||+-
T Consensus 1 ~~I~eva~~~gvs~~tLRyYe~~ 23 (123)
T cd04770 1 MKIGELAKAAGVSPDTIRYYERI 23 (123)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 57899999999999999999873
No 229
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=84.10 E-value=1.7 Score=32.66 Aligned_cols=31 Identities=13% Similarity=0.324 Sum_probs=26.4
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHH
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQE 123 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~ 123 (151)
.+-|..+...-.+|..+||+++|+|++++.+
T Consensus 17 ~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~ 47 (164)
T PRK11169 17 RNILNELQKDGRISNVELSKRVGLSPTPCLE 47 (164)
T ss_pred HHHHHHhccCCCCCHHHHHHHHCcCHHHHHH
Confidence 4556778888899999999999999988765
No 230
>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=83.94 E-value=4 Score=28.66 Aligned_cols=19 Identities=26% Similarity=0.256 Sum_probs=17.3
Q ss_pred HHHHHHcCCChhhHHhhhc
Q 031871 32 VNAARRAGADIETVRKSHA 50 (151)
Q Consensus 32 ~~~a~r~g~~v~t~~k~~~ 50 (151)
-+.|++.|+++.|++-|+.
T Consensus 4 ge~A~~~gvs~~tlR~ye~ 22 (107)
T cd01111 4 SQLALDAGVSVHIVRDYLL 22 (107)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 4689999999999999986
No 231
>PRK00215 LexA repressor; Validated
Probab=83.90 E-value=2.3 Score=32.75 Aligned_cols=35 Identities=14% Similarity=0.210 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHh--cCCcCHHHHHHHhCC-CHHHHHHH
Q 031871 90 SELKKAIVQARN--DKKLTQSQLAQLINE-KPQVIQEY 124 (151)
Q Consensus 90 ~~~~~~Lk~~R~--~~glTQ~eLA~~lgi-s~s~Is~~ 124 (151)
..+-..|.+.+. ...+|+.|||+.+|+ ++++++++
T Consensus 7 ~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~ 44 (205)
T PRK00215 7 QEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEH 44 (205)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHH
Confidence 345555665443 445699999999999 99999998
No 232
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=83.87 E-value=1.8 Score=34.23 Aligned_cols=29 Identities=7% Similarity=0.155 Sum_probs=25.2
Q ss_pred HHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 98 QARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 98 ~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
.+|-..|+|++++|+.+|+|++.|+++++
T Consensus 193 ~l~~~~~~t~~EIA~~lgis~~~V~q~~~ 221 (231)
T PRK12427 193 HLYYQHEMSLKEIALVLDLTEARICQLNK 221 (231)
T ss_pred HHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34456799999999999999999999876
No 233
>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=83.83 E-value=2 Score=34.30 Aligned_cols=28 Identities=21% Similarity=0.125 Sum_probs=24.8
Q ss_pred HHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 99 ARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 99 ~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
+|-..|+|++++|+.+|+|+.+|+++++
T Consensus 217 ~~~~~~~t~~eIA~~lgis~~~V~~~~~ 244 (254)
T TIGR02850 217 MRFFEGKTQMEVAEEIGISQAQVSRLEK 244 (254)
T ss_pred HHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3445799999999999999999999986
No 234
>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=83.82 E-value=2.6 Score=26.78 Aligned_cols=25 Identities=8% Similarity=0.194 Sum_probs=20.8
Q ss_pred hcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 101 NDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 101 ~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
.+..++..+||+.+|+|+++|.+.-
T Consensus 10 ~~~~~~~~eLa~~l~vS~~tv~~~l 34 (69)
T TIGR00122 10 ADNPFSGEKLGEALGMSRTAVNKHI 34 (69)
T ss_pred HcCCcCHHHHHHHHCCCHHHHHHHH
Confidence 3445889999999999999988763
No 235
>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=83.73 E-value=1.5 Score=31.42 Aligned_cols=30 Identities=13% Similarity=0.199 Sum_probs=24.7
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHH
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQ 122 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is 122 (151)
.+.+-.++-..|+|.+|+|+.+|+|.+||.
T Consensus 112 ~r~v~~l~~~~~~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 112 QKKIIYMKFFEDMKEIDIAKKLHISRQSVY 141 (142)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHhhc
Confidence 444555677789999999999999999985
No 236
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=83.58 E-value=5.1 Score=23.51 Aligned_cols=32 Identities=6% Similarity=0.102 Sum_probs=25.8
Q ss_pred HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
.+-..+--.++|..++|+++|++++++.++-.
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 34445566789999999999999999998743
No 237
>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=83.48 E-value=4.5 Score=27.98 Aligned_cols=19 Identities=16% Similarity=0.029 Sum_probs=17.1
Q ss_pred HHHHHHcCCChhhHHhhhc
Q 031871 32 VNAARRAGADIETVRKSHA 50 (151)
Q Consensus 32 ~~~a~r~g~~v~t~~k~~~ 50 (151)
-+.|+..|++.+|++.|+.
T Consensus 4 ~EvA~~~gVs~~tLR~ye~ 22 (99)
T cd04765 4 GEVAEILGLPPHVLRYWET 22 (99)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 4689999999999999974
No 238
>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=83.46 E-value=2.1 Score=34.63 Aligned_cols=24 Identities=29% Similarity=0.307 Sum_probs=22.6
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 103 KKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 103 ~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
.++|++|+|+.+|||+.+|+++++
T Consensus 235 ~~~t~~eIA~~lgvS~~~V~q~~~ 258 (270)
T TIGR02392 235 DKLTLQELAAEYGVSAERIRQIEK 258 (270)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHH
Confidence 489999999999999999999986
No 239
>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=83.41 E-value=2.5 Score=25.01 Aligned_cols=29 Identities=17% Similarity=0.125 Sum_probs=22.3
Q ss_pred HHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 96 IVQARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
|..+.. ..++..|||+.+|+++++|++.-
T Consensus 8 l~~L~~-~~~~~~el~~~l~~s~~~vs~hL 36 (47)
T PF01022_consen 8 LKLLSE-GPLTVSELAEELGLSQSTVSHHL 36 (47)
T ss_dssp HHHHTT-SSEEHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHh-CCCchhhHHHhccccchHHHHHH
Confidence 334444 77999999999999999999863
No 240
>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=83.35 E-value=4.2 Score=29.49 Aligned_cols=21 Identities=19% Similarity=0.235 Sum_probs=18.2
Q ss_pred HHHHHHHcCCChhhHHhhhcC
Q 031871 31 VVNAARRAGADIETVRKSHAG 51 (151)
Q Consensus 31 ~~~~a~r~g~~v~t~~k~~~g 51 (151)
.-+.|++.|+++.|++-|+.-
T Consensus 4 I~e~a~~~gvs~~tlR~Ye~~ 24 (131)
T TIGR02043 4 IGELAKLCGVTSDTLRFYEKN 24 (131)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 346899999999999999973
No 241
>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=83.25 E-value=1.3 Score=31.93 Aligned_cols=24 Identities=25% Similarity=0.266 Sum_probs=21.3
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESGK 128 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G~ 128 (151)
|+..|+|+.+|||..||..||+-.
T Consensus 1 m~I~e~a~~~gvs~~tlR~Ye~~G 24 (127)
T TIGR02047 1 MKIGELAQKTGVSVETIRFYEKQG 24 (127)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHCC
Confidence 578899999999999999998743
No 242
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [].
Probab=83.24 E-value=1.6 Score=24.57 Aligned_cols=19 Identities=16% Similarity=0.295 Sum_probs=17.5
Q ss_pred CHHHHHHHhCCCHHHHHHH
Q 031871 106 TQSQLAQLINEKPQVIQEY 124 (151)
Q Consensus 106 TQ~eLA~~lgis~s~Is~~ 124 (151)
|+.|.|+.+|+++++|+++
T Consensus 18 Si~eAa~~l~i~~~~I~~~ 36 (37)
T PF07453_consen 18 SIREAARYLGISHSTISKY 36 (37)
T ss_pred CHHHHHHHhCCCHHHHHHh
Confidence 7889999999999999875
No 243
>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=83.21 E-value=3.1 Score=30.15 Aligned_cols=71 Identities=21% Similarity=0.138 Sum_probs=44.6
Q ss_pred HHHHHHHcCCChhhHHhhhc-CCCccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHH
Q 031871 31 VVNAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQ 109 (151)
Q Consensus 31 ~~~~a~r~g~~v~t~~k~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~e 109 (151)
.-+.|++.|++..|++.|+. |-..|.. ..-..+ +. .....--+.|+.++.+.|++.++
T Consensus 4 I~eVA~~~GVs~~TLR~wE~~GLl~p~r----~~G~R~------Ys-----------~~dv~rL~~I~~L~~e~G~~l~e 62 (120)
T cd04767 4 IGVVAELLNIHPETLRIWERHGLIKPAR----RNGQRL------YS-----------NNDLKRLRFIKKLINEKGLNIAG 62 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCCCcC----CCCcEE------EC-----------HHHHHHHHHHHHHHHHcCCCHHH
Confidence 34689999999999999986 3332211 000000 11 11233456788888889999999
Q ss_pred HHHHhCCCHHHHH
Q 031871 110 LAQLINEKPQVIQ 122 (151)
Q Consensus 110 LA~~lgis~s~Is 122 (151)
+...+..-+...+
T Consensus 63 I~~~L~l~~~~~~ 75 (120)
T cd04767 63 VKQILSMYPCWSI 75 (120)
T ss_pred HHHHHHhCccccc
Confidence 9988766544333
No 244
>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=83.17 E-value=1.9 Score=31.10 Aligned_cols=24 Identities=21% Similarity=0.272 Sum_probs=21.4
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESGK 128 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G~ 128 (151)
||..|+|+.+|||+.||.-||+-.
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe~~G 24 (127)
T cd01108 1 MNIGEAAKLTGLSAKMIRYYEEIG 24 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCC
Confidence 578999999999999999998743
No 245
>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=83.13 E-value=9.3 Score=26.04 Aligned_cols=66 Identities=14% Similarity=0.160 Sum_probs=38.6
Q ss_pred HHHHHHcCCChhhHHhhhcC-CCccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHHH
Q 031871 32 VNAARRAGADIETVRKSHAG-TNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQL 110 (151)
Q Consensus 32 ~~~a~r~g~~v~t~~k~~~g-~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~eL 110 (151)
-+.|++.|+++.|++-|+.- --.|.... ...-+.-+. + .-..-..|+.+|. .|++.+++
T Consensus 4 ~eva~~~gvs~~tlR~ye~~Gll~p~~r~-~~gyR~Y~~--~----------------~l~~l~~I~~lr~-~G~~l~eI 63 (96)
T cd04788 4 GELARRTGLSVRTLHHYDHIGLLSPSQRT-EGGHRLYDR--A----------------DIRRLHQIIALRR-LGFSLREI 63 (96)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCCccC-CCCceeeCH--H----------------HHHHHHHHHHHHH-cCCCHHHH
Confidence 46899999999999999973 22221110 000111111 1 1122444666654 69999999
Q ss_pred HHHhCCC
Q 031871 111 AQLINEK 117 (151)
Q Consensus 111 A~~lgis 117 (151)
...+...
T Consensus 64 ~~~l~~~ 70 (96)
T cd04788 64 GRALDGP 70 (96)
T ss_pred HHHHhCC
Confidence 9988654
No 246
>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=83.05 E-value=0.49 Score=30.59 Aligned_cols=26 Identities=15% Similarity=0.201 Sum_probs=22.9
Q ss_pred HHHHHHHHcCCChhhHHhhhcCCCcc
Q 031871 30 KVVNAARRAGADIETVRKSHAGTNKA 55 (151)
Q Consensus 30 ~~~~~a~r~g~~v~t~~k~~~g~~~~ 55 (151)
+..+.|++.|++..|+.+|++|...+
T Consensus 20 t~~~lA~~~gis~~tis~~~~g~~~~ 45 (78)
T TIGR02607 20 SIRALAKALGVSRSTLSRIVNGRRGI 45 (78)
T ss_pred CHHHHHHHhCCCHHHHHHHHcCCCCC
Confidence 45689999999999999999998764
No 247
>smart00351 PAX Paired Box domain.
Probab=83.01 E-value=7 Score=28.07 Aligned_cols=21 Identities=14% Similarity=0.109 Sum_probs=17.8
Q ss_pred HHHHHHHHcCCChhhHHhhhc
Q 031871 30 KVVNAARRAGADIETVRKSHA 50 (151)
Q Consensus 30 ~~~~~a~r~g~~v~t~~k~~~ 50 (151)
+.-..|++.|++..|+.+|-.
T Consensus 35 s~~~iA~~~gvs~~tV~kwi~ 55 (125)
T smart00351 35 RPCDISRQLCVSHGCVSKILG 55 (125)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 456789999999999998854
No 248
>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=82.76 E-value=2 Score=29.84 Aligned_cols=23 Identities=13% Similarity=0.141 Sum_probs=20.9
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G 127 (151)
|+..|+|+.+|+|..||.-||+-
T Consensus 1 m~Ige~a~~~gvs~~tlRyYe~~ 23 (107)
T cd04777 1 MKIGKFAKKNNITIDTVRHYIDL 23 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 57889999999999999999873
No 249
>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=82.60 E-value=0.34 Score=30.22 Aligned_cols=29 Identities=21% Similarity=0.256 Sum_probs=21.3
Q ss_pred CHHHHHHHHHcCCChhhHHhhhcCCCccC
Q 031871 28 DEKVVNAARRAGADIETVRKSHAGTNKAA 56 (151)
Q Consensus 28 ~~~~~~~a~r~g~~v~t~~k~~~g~~~~~ 56 (151)
+-++-..|...|++.+++.+|++|...|.
T Consensus 12 ~lt~~~~a~~~~i~~~~i~~~e~g~~~~~ 40 (64)
T PF12844_consen 12 GLTQKDLAEKLGISRSTISKIENGKRKPS 40 (64)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHTTSS--B
T ss_pred CCCHHHHHHHHCcCHHHHHHHHCCCcCCC
Confidence 34677889999999999999999987653
No 250
>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=82.57 E-value=2.3 Score=30.70 Aligned_cols=25 Identities=24% Similarity=0.224 Sum_probs=22.6
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHcCC
Q 031871 104 KLTQSQLAQLINEKPQVIQEYESGK 128 (151)
Q Consensus 104 glTQ~eLA~~lgis~s~Is~~E~G~ 128 (151)
.+|..|||+.+|+|..||.-||+-.
T Consensus 3 ~~tI~elA~~~gvs~~tlR~Ye~~G 27 (120)
T TIGR02054 3 AYTISRLAEDAGVSVHVVRDYLLRG 27 (120)
T ss_pred CCcHHHHHHHHCcCHHHHHHHHHCC
Confidence 5899999999999999999998743
No 251
>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=82.55 E-value=1.1 Score=25.74 Aligned_cols=20 Identities=20% Similarity=0.142 Sum_probs=16.7
Q ss_pred HHHHHHcCCChhhHHhhhcC
Q 031871 32 VNAARRAGADIETVRKSHAG 51 (151)
Q Consensus 32 ~~~a~r~g~~v~t~~k~~~g 51 (151)
-+.|+..|+++.|++.|+.-
T Consensus 3 ~e~A~~~gvs~~tlR~ye~~ 22 (38)
T PF00376_consen 3 GEVAKLLGVSPRTLRYYERE 22 (38)
T ss_dssp HHHHHHHTS-HHHHHHHHHT
T ss_pred HHHHHHHCCCHHHHHHHHHC
Confidence 36799999999999999974
No 252
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=82.36 E-value=2.8 Score=29.87 Aligned_cols=37 Identities=5% Similarity=0.102 Sum_probs=30.2
Q ss_pred hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
..+|.+++-...+. |.|..++|...+||.+||.+|.+
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 35667777666555 78999999999999999999955
No 253
>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=82.29 E-value=2.1 Score=31.53 Aligned_cols=23 Identities=17% Similarity=0.219 Sum_probs=21.3
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G 127 (151)
||..|+|+.+||+.+||.-||+-
T Consensus 2 ~~I~EvA~~~Gvs~~tLRyYE~~ 24 (139)
T cd01110 2 LSVGEVAKRSGVAVSALHFYEQK 24 (139)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 78899999999999999999873
No 254
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=82.29 E-value=2.7 Score=30.26 Aligned_cols=33 Identities=15% Similarity=-0.089 Sum_probs=26.7
Q ss_pred HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
..+-.++-..|+|.+|+|+.+|+|.++|..+-.
T Consensus 112 r~ii~l~~~~~~s~~EIA~~l~is~~tV~~~~~ 144 (154)
T PRK06759 112 KYIIFERFFVGKTMGEIALETEMTYYQVRWIYR 144 (154)
T ss_pred HHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 344445667899999999999999999988754
No 255
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=82.22 E-value=2.3 Score=32.73 Aligned_cols=32 Identities=16% Similarity=0.229 Sum_probs=25.9
Q ss_pred HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcC
Q 031871 95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G 127 (151)
.+..++ ..|+|..++|+.+|||++|+.++-+.
T Consensus 164 ~i~~~~-~~g~s~~~iak~lgis~~Tv~r~~k~ 195 (200)
T PRK13413 164 KIKKLL-DKGTSKSEIARKLGVSRTTLARFLKT 195 (200)
T ss_pred HHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 344443 46899999999999999999999763
No 256
>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=82.14 E-value=4.2 Score=25.59 Aligned_cols=36 Identities=17% Similarity=0.267 Sum_probs=25.2
Q ss_pred HHHHHHHHHHH-hcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 90 SELKKAIVQAR-NDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 90 ~~~~~~Lk~~R-~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
+++-+.|-.+. .....+..+||+.+|+|+++++..-
T Consensus 7 e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml 43 (60)
T PF01325_consen 7 EDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEML 43 (60)
T ss_dssp HHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHH
Confidence 33444444443 4566899999999999999998763
No 257
>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=82.03 E-value=2.6 Score=33.28 Aligned_cols=26 Identities=19% Similarity=0.221 Sum_probs=23.8
Q ss_pred cCCcCHHHHHHHhCCCHHHHHHHHcC
Q 031871 102 DKKLTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 102 ~~glTQ~eLA~~lgis~s~Is~~E~G 127 (151)
..++|++++|+.+|+|+.+|++++..
T Consensus 194 ~~~~t~~EIA~~lgis~~~V~q~~~~ 219 (238)
T TIGR02393 194 GRPHTLEEVGKEFNVTRERIRQIESK 219 (238)
T ss_pred CCCccHHHHHHHHCCCHHHHHHHHHH
Confidence 57899999999999999999999873
No 258
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=81.93 E-value=1.6 Score=34.35 Aligned_cols=48 Identities=15% Similarity=0.115 Sum_probs=42.7
Q ss_pred HHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Q 031871 98 QARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVK 146 (151)
Q Consensus 98 ~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~ 146 (151)
+.+++.+.++.++++..|+++ ++..|.++-..++...+....++|+.+
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 366777889999999999999 999999999999999999999988764
No 259
>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=81.91 E-value=2.2 Score=30.89 Aligned_cols=23 Identities=22% Similarity=0.414 Sum_probs=20.9
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G 127 (151)
++..++|+.+||++++|..||+-
T Consensus 2 ysI~eVA~~~GVs~~TLR~wE~~ 24 (120)
T cd04767 2 YPIGVVAELLNIHPETLRIWERH 24 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 67899999999999999999863
No 260
>PRK06424 transcription factor; Provisional
Probab=81.83 E-value=0.5 Score=35.34 Aligned_cols=28 Identities=7% Similarity=-0.033 Sum_probs=23.8
Q ss_pred HHHHHHHHcCCChhhHHhhhcCCCccCC
Q 031871 30 KVVNAARRAGADIETVRKSHAGTNKAAS 57 (151)
Q Consensus 30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~~ 57 (151)
++.++|.+.|++.+++.+||+|...|..
T Consensus 99 SQ~eLA~~iGvs~stIskiE~G~~~Ps~ 126 (144)
T PRK06424 99 SQADLAAKIFERKNVIASIERGDLLPDI 126 (144)
T ss_pred CHHHHHHHhCCCHHHHHHHHCCCCCCCH
Confidence 4558899999999999999999987643
No 261
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=81.80 E-value=4.4 Score=29.75 Aligned_cols=21 Identities=19% Similarity=0.113 Sum_probs=18.2
Q ss_pred HHHHHHHcCCChhhHHhhhcC
Q 031871 31 VVNAARRAGADIETVRKSHAG 51 (151)
Q Consensus 31 ~~~~a~r~g~~v~t~~k~~~g 51 (151)
.-+.|++.|+++.|+|-|+.-
T Consensus 4 I~e~a~~~gvs~~tlR~Ye~~ 24 (140)
T PRK09514 4 IGELAKLAEVTPDTLRFYEKQ 24 (140)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 346899999999999999973
No 262
>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=81.65 E-value=5.2 Score=27.50 Aligned_cols=66 Identities=18% Similarity=0.207 Sum_probs=40.7
Q ss_pred HHHHHHHcCCChhhHHhhhc-CCCccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHH
Q 031871 31 VVNAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQ 109 (151)
Q Consensus 31 ~~~~a~r~g~~v~t~~k~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~e 109 (151)
.-+.|++.|++.+|++.|+. |-..|..+. ..-.. +.. ..-..-..|+.++...|++.++
T Consensus 4 i~eva~~~gVs~~tLR~ye~~Gli~p~r~~--~g~R~-------Ys~-----------~dv~~l~~I~~L~~~~G~~l~~ 63 (98)
T cd01279 4 ISVAAELLGIHPQTLRVYDRLGLVSPARTN--GGGRR-------YSN-----------NDLELLRQVQRLSQDEGFNLAG 63 (98)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCCCCcCC--CCCee-------ECH-----------HHHHHHHHHHHHHHHCCCCHHH
Confidence 34689999999999999976 222211000 00000 111 1223456677788889999999
Q ss_pred HHHHhCC
Q 031871 110 LAQLINE 116 (151)
Q Consensus 110 LA~~lgi 116 (151)
+...+..
T Consensus 64 i~~~l~l 70 (98)
T cd01279 64 IKRIIEL 70 (98)
T ss_pred HHHHHHh
Confidence 9988754
No 263
>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=81.63 E-value=2.4 Score=30.31 Aligned_cols=23 Identities=30% Similarity=0.455 Sum_probs=20.7
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G 127 (151)
++..|+|+.+|||..||.-||+-
T Consensus 1 ~~Igeva~~~gvs~~tlRyYe~~ 23 (118)
T cd04776 1 YTISELAREFDVTPRTLRFYEDK 23 (118)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 46789999999999999999873
No 264
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=81.55 E-value=3.6 Score=27.06 Aligned_cols=22 Identities=18% Similarity=0.188 Sum_probs=20.4
Q ss_pred CCcCHHHHHHHhCCCHHHHHHH
Q 031871 103 KKLTQSQLAQLINEKPQVIQEY 124 (151)
Q Consensus 103 ~glTQ~eLA~~lgis~s~Is~~ 124 (151)
.++|..|+|+.+|+++++++++
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~ 40 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRL 40 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHH
Confidence 4799999999999999999887
No 265
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=81.52 E-value=4.3 Score=29.99 Aligned_cols=31 Identities=13% Similarity=0.214 Sum_probs=25.9
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHH
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQE 123 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~ 123 (151)
..-|..+...-..|..+||+.+|+|++++.+
T Consensus 12 ~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~ 42 (153)
T PRK11179 12 RGILEALMENARTPYAELAKQFGVSPGTIHV 42 (153)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHH
Confidence 4446777778889999999999999988765
No 266
>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=81.52 E-value=2.7 Score=31.23 Aligned_cols=33 Identities=18% Similarity=0.211 Sum_probs=26.9
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
...+-.++...|+|.+|+|+.+|+|.++|...-
T Consensus 139 ~r~v~~l~~~~g~s~~EIA~~lgis~~tVk~~l 171 (183)
T TIGR02999 139 QAEVVELRFFAGLTVEEIAELLGVSVRTVERDW 171 (183)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 344555677789999999999999999998754
No 267
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=81.30 E-value=1.6 Score=32.95 Aligned_cols=23 Identities=13% Similarity=0.130 Sum_probs=20.3
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHH
Q 031871 103 KKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 103 ~glTQ~eLA~~lgis~s~Is~~E 125 (151)
..+||.+||..+|+++.+|++..
T Consensus 148 ~~~t~~~iA~~lG~tretvsR~l 170 (202)
T PRK13918 148 IYATHDELAAAVGSVRETVTKVI 170 (202)
T ss_pred ecCCHHHHHHHhCccHHHHHHHH
Confidence 35799999999999999999863
No 268
>COG3311 AlpA Predicted transcriptional regulator [Transcription]
Probab=81.29 E-value=2.6 Score=27.80 Aligned_cols=30 Identities=20% Similarity=0.213 Sum_probs=25.6
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcCCCCCCHH
Q 031871 105 LTQSQLAQLINEKPQVIQEYESGKAIPNQQ 134 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G~~~p~~~ 134 (151)
+...|+++.+|+|+++|.++.+....|..-
T Consensus 14 lrl~ev~~~~GlSrstiYr~i~~~~FPkpv 43 (70)
T COG3311 14 LRLPEVAQLTGLSRSTIYRLIKDGTFPKPV 43 (70)
T ss_pred hhHHHHHHHHCccHHHHHHHHccCCCCCCe
Confidence 456799999999999999999988777653
No 269
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=81.29 E-value=2.4 Score=30.44 Aligned_cols=24 Identities=29% Similarity=0.290 Sum_probs=21.3
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESGK 128 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G~ 128 (151)
||..|+|+.+|||..+|..||+-.
T Consensus 1 ~~I~e~a~~~gvs~~tlR~Ye~~G 24 (126)
T cd04785 1 LSIGELARRTGVNVETIRYYESIG 24 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCC
Confidence 578899999999999999998743
No 270
>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=81.25 E-value=6.7 Score=26.84 Aligned_cols=19 Identities=16% Similarity=0.079 Sum_probs=17.2
Q ss_pred HHHHHHcCCChhhHHhhhc
Q 031871 32 VNAARRAGADIETVRKSHA 50 (151)
Q Consensus 32 ~~~a~r~g~~v~t~~k~~~ 50 (151)
-+.|++.|++..|++-|+.
T Consensus 4 ~eva~~~gvs~~tlR~ye~ 22 (97)
T cd04782 4 GEFAKLCGISKQTLFHYDK 22 (97)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 4689999999999999986
No 271
>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=81.25 E-value=2.5 Score=30.72 Aligned_cols=23 Identities=17% Similarity=0.278 Sum_probs=20.8
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G 127 (151)
|+..|+|+.+|||..||.-||+-
T Consensus 1 m~IgE~A~~~gvs~~TLRyYE~~ 23 (133)
T cd04787 1 MKVKELANAAGVTPDTVRFYTRI 23 (133)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 57889999999999999999863
No 272
>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=81.22 E-value=1.7 Score=26.77 Aligned_cols=25 Identities=4% Similarity=0.207 Sum_probs=20.9
Q ss_pred cCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 102 DKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 102 ~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
..|++..++|+.+|+|+.+|..+-+
T Consensus 16 ~~G~~~~eIA~~l~is~~tV~~~~~ 40 (58)
T PF00196_consen 16 AQGMSNKEIAEELGISEKTVKSHRR 40 (58)
T ss_dssp HTTS-HHHHHHHHTSHHHHHHHHHH
T ss_pred HhcCCcchhHHhcCcchhhHHHHHH
Confidence 4699999999999999999987643
No 273
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=81.21 E-value=0.58 Score=35.33 Aligned_cols=41 Identities=7% Similarity=0.008 Sum_probs=29.0
Q ss_pred CHHHHHHHHHcCCChhhHHhhhcCCCccCCCCccccccccc
Q 031871 28 DEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLD 68 (151)
Q Consensus 28 ~~~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~ 68 (151)
+-++-+.|.+.|++.+++.+||+|...|..+...+....|+
T Consensus 82 glSqeeLA~~lgvs~s~IsriE~G~~~Ps~~~l~kLa~~Lg 122 (154)
T TIGR00270 82 GWSQEQLAKKIQEKESLIKKIENAEIEPEPKVVEKLEKLLK 122 (154)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhC
Confidence 33556789999999999999999998765443333333333
No 274
>PRK13832 plasmid partitioning protein; Provisional
Probab=81.14 E-value=4.3 Score=36.35 Aligned_cols=50 Identities=16% Similarity=0.114 Sum_probs=36.5
Q ss_pred hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHH
Q 031871 89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLE 140 (151)
Q Consensus 89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa 140 (151)
..+-...++++. +.|+|+.++|+.+|+|+++|+++-. -.......+..++
T Consensus 104 PiEea~AfkrLi-e~G~T~EeIA~~lG~S~~~V~rlll-LA~L~P~lLdal~ 153 (520)
T PRK13832 104 PVDQWRAIERLV-ALGWTEEAIAVALALPVRQIRKLRL-LANVLPAMLDHMA 153 (520)
T ss_pred HHHHHHHHHHHH-hcCCCHHHHHHHHCCCHHHHHHHHH-HcCCCHHHHHHHH
Confidence 355677777777 7999999999999999999998644 2234444444443
No 275
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=80.91 E-value=1.7 Score=32.93 Aligned_cols=23 Identities=9% Similarity=0.309 Sum_probs=20.6
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHc
Q 031871 104 KLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 104 glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
.+||++||..+|+++.+++++-+
T Consensus 168 ~~t~~~lA~~lG~tr~tvsR~l~ 190 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGRVLK 190 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Confidence 58999999999999999999743
No 276
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=80.89 E-value=3 Score=30.34 Aligned_cols=29 Identities=14% Similarity=0.141 Sum_probs=24.6
Q ss_pred HHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871 96 IVQARNDKKLTQSQLAQLINEKPQVIQEY 124 (151)
Q Consensus 96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~ 124 (151)
+-.++--.|+|.+|+|+.+|+|.++|...
T Consensus 117 v~~l~~~~~~s~~EIA~~lgis~~tV~~~ 145 (163)
T PRK07037 117 AFEMYRLHGETQKDIARELGVSPTLVNFM 145 (163)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHHHHH
Confidence 44455667999999999999999999986
No 277
>PRK12423 LexA repressor; Provisional
Probab=80.59 E-value=5.3 Score=30.99 Aligned_cols=35 Identities=11% Similarity=0.116 Sum_probs=28.7
Q ss_pred hHHHHHHHHHHHhcCCc--CHHHHHHHhC-CCHHHHHH
Q 031871 89 PSELKKAIVQARNDKKL--TQSQLAQLIN-EKPQVIQE 123 (151)
Q Consensus 89 ~~~~~~~Lk~~R~~~gl--TQ~eLA~~lg-is~s~Is~ 123 (151)
...+-..|+....+.|+ |..|||+.+| .|++++++
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 35677788888788888 9999999999 58988764
No 278
>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=80.59 E-value=3.2 Score=29.63 Aligned_cols=29 Identities=7% Similarity=-0.044 Sum_probs=24.5
Q ss_pred HHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 98 QARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 98 ~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
.++-..|+|..|+|+.+|+|+++|.....
T Consensus 123 ~l~~~~~~~~~eIA~~lgis~~tv~~~~~ 151 (161)
T TIGR02985 123 ILSRFEGKSYKEIAEELGISVKTVEYHIS 151 (161)
T ss_pred HHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34556799999999999999999988654
No 279
>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=80.57 E-value=3 Score=32.46 Aligned_cols=31 Identities=19% Similarity=0.127 Sum_probs=25.8
Q ss_pred HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 96 IVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
+-.++-..|+|++|+|+.+|+|+++|..+..
T Consensus 186 vl~l~y~~~~s~~eIA~~lgis~~~v~~~~~ 216 (227)
T TIGR02980 186 ILLLRFFEDKTQSEIAERLGISQMHVSRLLR 216 (227)
T ss_pred HHHHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3334556799999999999999999999865
No 280
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=80.52 E-value=0.58 Score=33.70 Aligned_cols=28 Identities=14% Similarity=0.236 Sum_probs=23.6
Q ss_pred HHHHHHHHcCCChhhHHhhhcCCCccCC
Q 031871 30 KVVNAARRAGADIETVRKSHAGTNKAAS 57 (151)
Q Consensus 30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~~ 57 (151)
+.-+.|+++|++.+++.+|+.|...|..
T Consensus 20 sq~eLA~~~Gis~~~is~iE~g~~~ps~ 47 (120)
T PRK13890 20 TKKELSERSGVSISFLSDLTTGKANPSL 47 (120)
T ss_pred CHHHHHHHHCcCHHHHHHHHcCCCCCCH
Confidence 4567999999999999999999876533
No 281
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=80.37 E-value=3.4 Score=28.24 Aligned_cols=29 Identities=14% Similarity=0.392 Sum_probs=23.2
Q ss_pred HHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871 96 IVQARNDKKLTQSQLAQLINEKPQVIQEY 124 (151)
Q Consensus 96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~ 124 (151)
|..+.....+|..+||+.+|++++++.+.
T Consensus 9 l~~L~~~~~~~~~~la~~l~~s~~tv~~~ 37 (108)
T smart00344 9 LEELQKDARISLAELAKKVGLSPSTVHNR 37 (108)
T ss_pred HHHHHHhCCCCHHHHHHHHCcCHHHHHHH
Confidence 44444556799999999999999998764
No 282
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=80.36 E-value=2.7 Score=30.81 Aligned_cols=24 Identities=21% Similarity=0.322 Sum_probs=21.5
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESGK 128 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G~ 128 (151)
|+..|||+.+|+|..||.-||+-.
T Consensus 1 m~Ige~a~~~gvs~~tlRyYE~~G 24 (135)
T PRK10227 1 MNISDVAKITGLTSKAIRFYEEKG 24 (135)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCC
Confidence 678899999999999999998744
No 283
>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=80.31 E-value=2.6 Score=31.18 Aligned_cols=23 Identities=30% Similarity=0.294 Sum_probs=21.2
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G 127 (151)
||..|+|+.+|+|+.||.-||+-
T Consensus 2 ~~IgevA~~~Gvs~~tLRyYE~~ 24 (142)
T TIGR01950 2 LTVGELAKRSGVAVSALHFYESK 24 (142)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 68899999999999999999873
No 284
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=80.17 E-value=5.8 Score=26.00 Aligned_cols=35 Identities=14% Similarity=0.158 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871 90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEY 124 (151)
Q Consensus 90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~ 124 (151)
..-...|..+....++++.++|+.+++++++|++.
T Consensus 10 ~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~ 44 (101)
T smart00347 10 PTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRV 44 (101)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHH
Confidence 34444556666666899999999999999988875
No 285
>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=80.15 E-value=2.1 Score=27.61 Aligned_cols=23 Identities=17% Similarity=0.388 Sum_probs=20.7
Q ss_pred CHHHHHHHhCCCHHHHHHHHcCC
Q 031871 106 TQSQLAQLINEKPQVIQEYESGK 128 (151)
Q Consensus 106 TQ~eLA~~lgis~s~Is~~E~G~ 128 (151)
.|.|+|+.+++++.||.+|-...
T Consensus 18 nqtEvaR~l~c~R~TVrKY~~D~ 40 (64)
T PF06322_consen 18 NQTEVARRLGCNRATVRKYSRDK 40 (64)
T ss_pred cHHHHHHHhcccHHHHHHHhccc
Confidence 79999999999999999997643
No 286
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=80.03 E-value=2.7 Score=30.90 Aligned_cols=24 Identities=25% Similarity=0.397 Sum_probs=21.6
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESGK 128 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G~ 128 (151)
++..|+|+.+|||+.||..||+-.
T Consensus 2 ~~I~e~a~~~gvs~~tlR~Ye~~G 25 (140)
T PRK09514 2 YRIGELAKLAEVTPDTLRFYEKQG 25 (140)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHCC
Confidence 678999999999999999998743
No 287
>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=79.97 E-value=7.6 Score=26.28 Aligned_cols=63 Identities=17% Similarity=0.163 Sum_probs=37.5
Q ss_pred HHHHHHcCCChhhHHhhhcCCCc-cCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHHH
Q 031871 32 VNAARRAGADIETVRKSHAGTNK-AASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQL 110 (151)
Q Consensus 32 ~~~a~r~g~~v~t~~k~~~g~~~-~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~eL 110 (151)
-+.|++.|++..|++.|+.-..- |..+. + .-.. +.. -....-..++.+|. .|++.+++
T Consensus 4 ~eva~~~gi~~~tlr~~~~~Gll~~~~~~-~-g~r~-------y~~-----------~dv~~l~~i~~l~~-~g~~~~~i 62 (100)
T cd00592 4 GEVAKLLGVSVRTLRYYEEKGLLPPERSE-N-GYRL-------YSE-----------EDLERLRLIRRLRE-LGLSLKEI 62 (100)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCcCCCcCC-C-CCcc-------cCH-----------HHHHHHHHHHHHHH-cCCCHHHH
Confidence 46899999999999999863222 11110 0 0000 111 11234556667777 89999998
Q ss_pred HHHhC
Q 031871 111 AQLIN 115 (151)
Q Consensus 111 A~~lg 115 (151)
+..+.
T Consensus 63 ~~~l~ 67 (100)
T cd00592 63 RELLD 67 (100)
T ss_pred HHHHh
Confidence 87663
No 288
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=79.87 E-value=3.1 Score=30.33 Aligned_cols=28 Identities=11% Similarity=0.147 Sum_probs=24.2
Q ss_pred HHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 99 ARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 99 ~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
++...|+|+.++|+.+|+|+++|..+..
T Consensus 136 l~~~~~~~~~eIA~~lgis~~tv~~~~~ 163 (179)
T PRK11924 136 LRYVEGLSYREIAEILGVPVGTVKSRLR 163 (179)
T ss_pred HHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4445799999999999999999998765
No 289
>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=79.82 E-value=2.9 Score=30.31 Aligned_cols=23 Identities=22% Similarity=0.367 Sum_probs=21.2
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G 127 (151)
++..|+|+.+|||+.||..||+-
T Consensus 2 ~~I~e~a~~~gvs~~tlR~Ye~~ 24 (131)
T TIGR02043 2 FQIGELAKLCGVTSDTLRFYEKN 24 (131)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 67899999999999999999874
No 290
>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=79.61 E-value=3 Score=30.41 Aligned_cols=24 Identities=21% Similarity=0.220 Sum_probs=21.3
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESGK 128 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G~ 128 (151)
|+..|+|+.+|||..||.-||+-.
T Consensus 1 m~Ige~a~~~gvs~~tLRyYE~~G 24 (131)
T cd04786 1 MKIGELAKRSGMAASRIRFYEAEG 24 (131)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCC
Confidence 578899999999999999998743
No 291
>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=79.54 E-value=9.9 Score=28.82 Aligned_cols=54 Identities=15% Similarity=0.180 Sum_probs=43.1
Q ss_pred hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCC--CCCCHHHHHHHHHHhC
Q 031871 89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK--AIPNQQILTKLERALG 144 (151)
Q Consensus 89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~--~~p~~~~l~kLa~~Lg 144 (151)
.+.|-..++......+ .++||..+|++++++.+--|.. ..++...+..|.++-|
T Consensus 7 ~~~~~~Ac~~fa~~h~--~~~lA~~lGm~~~~LrNKLNP~q~H~Lt~~el~~i~~~Tg 62 (162)
T PF06892_consen 7 QPHFDEACRAFAKNHN--MAALAERLGMNPQTLRNKLNPEQPHKLTVDELIAITDATG 62 (162)
T ss_pred hHHHHHHHHHHHHhcC--HHHHHHHhCCCHHHHHHHcCCCCCCCCCHHHHHHHHHHhC
Confidence 3567788888888887 4799999999999999988866 3457888888877654
No 292
>PRK13749 transcriptional regulator MerD; Provisional
Probab=79.11 E-value=3.2 Score=30.03 Aligned_cols=25 Identities=20% Similarity=0.182 Sum_probs=22.1
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHcCC
Q 031871 104 KLTQSQLAQLINEKPQVIQEYESGK 128 (151)
Q Consensus 104 glTQ~eLA~~lgis~s~Is~~E~G~ 128 (151)
.+|..|||+.+|+|..+|.-||.-.
T Consensus 3 ~~tIgelA~~~gvS~~tiR~YE~~G 27 (121)
T PRK13749 3 AYTVSRLALDAGVSVHIVRDYLLRG 27 (121)
T ss_pred CCcHHHHHHHHCCCHHHHHHHHHCC
Confidence 4789999999999999999998643
No 293
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=79.08 E-value=2.9 Score=31.46 Aligned_cols=31 Identities=13% Similarity=0.179 Sum_probs=25.6
Q ss_pred HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 96 IVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
+-.++...|+|++|+|+.+|+|.++|..+..
T Consensus 149 v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ 179 (194)
T PRK12519 149 VLELAYYEGLSQSEIAKRLGIPLGTVKARAR 179 (194)
T ss_pred hhhhhhhcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 3344556799999999999999999998764
No 294
>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=79.07 E-value=2.2 Score=30.65 Aligned_cols=23 Identities=26% Similarity=0.286 Sum_probs=20.0
Q ss_pred CHHHHHHHhCCCHHHHHHHHcCC
Q 031871 106 TQSQLAQLINEKPQVIQEYESGK 128 (151)
Q Consensus 106 TQ~eLA~~lgis~s~Is~~E~G~ 128 (151)
|..|||+.+|||+.||..||+-.
T Consensus 1 ~I~e~a~~~gvs~~tlR~Ye~~G 23 (124)
T TIGR02051 1 TIGELAKAAGVNVETIRYYERKG 23 (124)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCC
Confidence 46799999999999999998743
No 295
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=79.06 E-value=2.1 Score=35.01 Aligned_cols=24 Identities=21% Similarity=0.210 Sum_probs=22.7
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 103 KKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 103 ~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
.++|+.++|+.+|+|+.+|+++++
T Consensus 247 ~~~Tl~EIA~~lgvS~~rVrqi~~ 270 (284)
T PRK06596 247 DKSTLQELAAEYGVSAERVRQIEK 270 (284)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHH
Confidence 489999999999999999999987
No 296
>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=79.05 E-value=3.7 Score=28.52 Aligned_cols=28 Identities=11% Similarity=0.143 Sum_probs=23.8
Q ss_pred HHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 99 ARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 99 ~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
+.-..|+|..++|+.+|+|+++|.++.+
T Consensus 121 ~~~~~g~s~~eIA~~l~~s~~~v~~~~~ 148 (158)
T TIGR02937 121 LRYLEGLSYKEIAEILGISVGTVKRRLK 148 (158)
T ss_pred hHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3435799999999999999999998765
No 297
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=79.02 E-value=3.6 Score=30.07 Aligned_cols=28 Identities=11% Similarity=0.113 Sum_probs=23.9
Q ss_pred HHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 99 ARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 99 ~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
++...|+|.+++|+.+|+|.++|..+..
T Consensus 139 l~~~~~~s~~eIA~~lgis~~tV~~~l~ 166 (182)
T PRK09652 139 LREIEGLSYEEIAEIMGCPIGTVRSRIF 166 (182)
T ss_pred HHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4456799999999999999999987654
No 298
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=79.00 E-value=5.5 Score=27.81 Aligned_cols=40 Identities=15% Similarity=0.100 Sum_probs=34.0
Q ss_pred CcchHHHHHHHHHHHhcCCcCHHHHHHHhCC-CHHHHHHHH
Q 031871 86 DRVPSELKKAIVQARNDKKLTQSQLAQLINE-KPQVIQEYE 125 (151)
Q Consensus 86 ~~~~~~~~~~Lk~~R~~~glTQ~eLA~~lgi-s~s~Is~~E 125 (151)
.....+|-..+-++..+.|.|..++|+..|| +.+.+.+|-
T Consensus 6 r~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~ 46 (116)
T COG2963 6 KKYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKWR 46 (116)
T ss_pred ccCCHHHHHHHHHHHHhcCccHHHHHHHhCCCChHHHHHHH
Confidence 3456788888888889999999999999996 999998763
No 299
>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=79.00 E-value=5.3 Score=27.88 Aligned_cols=32 Identities=9% Similarity=-0.019 Sum_probs=26.6
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEY 124 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~ 124 (151)
...|..+....++|+.+||+.+|++++++++.
T Consensus 31 ~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~ 62 (118)
T TIGR02337 31 WRILRILAEQGSMEFTQLANQACILRPSLTGI 62 (118)
T ss_pred HHHHHHHHHcCCcCHHHHHHHhCCCchhHHHH
Confidence 34566666778999999999999999998875
No 300
>PRK09954 putative kinase; Provisional
Probab=78.90 E-value=4.5 Score=33.71 Aligned_cols=33 Identities=9% Similarity=0.169 Sum_probs=27.6
Q ss_pred HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
+.|+.+++...+|+.+||+.+|+|+++|.+.-+
T Consensus 7 ~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~ 39 (362)
T PRK09954 7 EILAILRRNPLIQQNEIADILQISRSRVAAHIM 39 (362)
T ss_pred HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 456777777889999999999999999887644
No 301
>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=78.86 E-value=4 Score=29.47 Aligned_cols=31 Identities=13% Similarity=0.294 Sum_probs=25.1
Q ss_pred HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871 94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEY 124 (151)
Q Consensus 94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~ 124 (151)
..+-.++...|++.+|+|+.+|+|.++|...
T Consensus 117 r~v~~l~~~~g~~~~eIA~~l~is~~tv~~~ 147 (159)
T TIGR02989 117 RELLQLRYQRGVSLTALAEQLGRTVNAVYKA 147 (159)
T ss_pred HHHHHHHHhcCCCHHHHHHHhCCCHHHHHHH
Confidence 3344456678999999999999999999864
No 302
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=78.84 E-value=0.75 Score=26.02 Aligned_cols=26 Identities=19% Similarity=0.275 Sum_probs=21.5
Q ss_pred HHHHHHHHcCCChhhHHhhhcCCCcc
Q 031871 30 KVVNAARRAGADIETVRKSHAGTNKA 55 (151)
Q Consensus 30 ~~~~~a~r~g~~v~t~~k~~~g~~~~ 55 (151)
+....|+..|++..++.+|+.|...+
T Consensus 12 s~~~la~~~~i~~~~i~~~~~~~~~~ 37 (56)
T smart00530 12 TQEELAEKLGVSRSTLSRIENGKRKP 37 (56)
T ss_pred CHHHHHHHhCCCHHHHHHHHCCCCCC
Confidence 34578899999999999999987643
No 303
>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=78.71 E-value=1.4 Score=38.51 Aligned_cols=42 Identities=17% Similarity=0.153 Sum_probs=31.9
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 031871 103 KKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALG 144 (151)
Q Consensus 103 ~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lg 144 (151)
+=||++++|+.+|++.||||+.-+|+..-+..-+.-|-.+|.
T Consensus 317 kPLtlkdiA~~lglheSTVSRav~~Kyi~tp~Gi~~lk~FFs 358 (429)
T TIGR02395 317 KPLTLREVAEELGLHESTISRAINNKYLQTPRGVFELKYFFS 358 (429)
T ss_pred cCCcHHHHHHHhCCCccchhhhhcCceEecCCceEEHHHhcC
Confidence 348999999999999999999999986544443444444444
No 304
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=78.64 E-value=2.3 Score=31.60 Aligned_cols=24 Identities=21% Similarity=0.241 Sum_probs=22.0
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHcC
Q 031871 104 KLTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 104 glTQ~eLA~~lgis~s~Is~~E~G 127 (151)
.+|..+||+.+|||..||.-||+-
T Consensus 7 ~~~IgevAk~~Gvs~~TLRyYE~~ 30 (144)
T PRK13752 7 NLTIGVFAKAAGVNVETIRFYQRK 30 (144)
T ss_pred cccHHHHHHHHCcCHHHHHHHHHC
Confidence 489999999999999999999873
No 305
>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=78.59 E-value=8.4 Score=23.31 Aligned_cols=19 Identities=16% Similarity=0.291 Sum_probs=17.0
Q ss_pred CHHHHHHHhCCCHHHHHHH
Q 031871 106 TQSQLAQLINEKPQVIQEY 124 (151)
Q Consensus 106 TQ~eLA~~lgis~s~Is~~ 124 (151)
|..+||+.+|+|++++++.
T Consensus 27 ~~~~la~~~~is~~~v~~~ 45 (66)
T cd07377 27 SERELAEELGVSRTTVREA 45 (66)
T ss_pred CHHHHHHHHCCCHHHHHHH
Confidence 4999999999999998875
No 306
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=78.49 E-value=3.9 Score=32.13 Aligned_cols=33 Identities=6% Similarity=0.203 Sum_probs=27.2
Q ss_pred HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
..+-.++-..|+|.+|+|+.+|+|.++|.....
T Consensus 190 r~vl~l~~~~g~s~~EIA~~lgis~~tV~~~~~ 222 (236)
T PRK06986 190 QLVLSLYYQEELNLKEIGAVLGVSESRVSQIHS 222 (236)
T ss_pred HHHHHhHhccCCCHHHHHHHHCCCHHHHHHHHH
Confidence 334445667899999999999999999998765
No 307
>PRK13869 plasmid-partitioning protein RepA; Provisional
Probab=78.27 E-value=3.8 Score=35.32 Aligned_cols=42 Identities=14% Similarity=0.305 Sum_probs=34.0
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHc------------CCCCCCHHHHHHHHHHhC
Q 031871 103 KKLTQSQLAQLINEKPQVIQEYES------------GKAIPNQQILTKLERALG 144 (151)
Q Consensus 103 ~glTQ~eLA~~lgis~s~Is~~E~------------G~~~p~~~~l~kLa~~Lg 144 (151)
+.+|..|+|+.+||+.+||..|+. |++..+.+.+..|.+.|+
T Consensus 47 r~ft~~e~A~~lgvs~~tlr~~~~~g~~~~~~~~~~grR~yt~~di~~lr~~l~ 100 (405)
T PRK13869 47 RKFTSGEAARLMKISDSTLRKMTLAGEGPQPELASNGRRFYTLGQINEIRQMLA 100 (405)
T ss_pred CCCCHHHHHHHhCcCHHHHHHHHHcCCCCCCccCCCCceeecHHHHHHHHHHHH
Confidence 468999999999999999999943 444456777888888776
No 308
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=78.11 E-value=4 Score=32.51 Aligned_cols=29 Identities=10% Similarity=0.110 Sum_probs=25.2
Q ss_pred HHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 98 QARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 98 ~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
.++-..|+|++|+|+.+|+|..+|..+..
T Consensus 215 ~l~~~~g~s~~eIA~~l~is~~tV~~~~~ 243 (257)
T PRK08583 215 QCTFIENLSQKETGERLGISQMHVSRLQR 243 (257)
T ss_pred HHHHhCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34556899999999999999999999875
No 309
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=78.03 E-value=3.9 Score=30.56 Aligned_cols=33 Identities=15% Similarity=0.191 Sum_probs=26.4
Q ss_pred HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
..+-.++...|+|.+|+|+.+|+|.++|...-.
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 334455667899999999999999999987643
No 310
>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=77.98 E-value=12 Score=26.11 Aligned_cols=19 Identities=21% Similarity=0.106 Sum_probs=17.4
Q ss_pred HHHHHHcCCChhhHHhhhc
Q 031871 32 VNAARRAGADIETVRKSHA 50 (151)
Q Consensus 32 ~~~a~r~g~~v~t~~k~~~ 50 (151)
-+.|++.|+++.|++.|+.
T Consensus 4 ~eva~~~gvs~~tlR~ye~ 22 (108)
T cd04773 4 GELAHLLGVPPSTLRHWEK 22 (108)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 4689999999999999987
No 311
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=77.94 E-value=3.9 Score=29.58 Aligned_cols=32 Identities=9% Similarity=-0.007 Sum_probs=25.7
Q ss_pred HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
.+-.++...|+|.+|+|+.+|+|.++|...-.
T Consensus 113 ~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ 144 (161)
T PRK09047 113 EAFLLRYWEDMDVAETAAAMGCSEGSVKTHCS 144 (161)
T ss_pred HHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHH
Confidence 33445566799999999999999999987644
No 312
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=77.85 E-value=4.1 Score=32.92 Aligned_cols=31 Identities=16% Similarity=0.187 Sum_probs=25.9
Q ss_pred HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 96 IVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
+-.+|-..|+|++++|+.+|+|..+|.+++.
T Consensus 223 vl~l~y~~~~t~~EIA~~lgis~~~V~~~~~ 253 (264)
T PRK07122 223 VLVLRFFESMTQTQIAERVGISQMHVSRLLA 253 (264)
T ss_pred HHHHHhcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3344556799999999999999999999876
No 313
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=77.62 E-value=4 Score=32.73 Aligned_cols=28 Identities=18% Similarity=0.100 Sum_probs=24.5
Q ss_pred HHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 99 ARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 99 ~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
+|-..|+|++++|+.+|+|.++|+++..
T Consensus 214 l~y~~~~s~~eIA~~lgvs~~~V~~~~~ 241 (256)
T PRK07408 214 FVFLHDLTQKEAAERLGISPVTVSRRVK 241 (256)
T ss_pred HHHHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3445699999999999999999999876
No 314
>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=77.56 E-value=14 Score=25.75 Aligned_cols=20 Identities=20% Similarity=0.292 Sum_probs=17.7
Q ss_pred HHHHHHcCCChhhHHhhhcC
Q 031871 32 VNAARRAGADIETVRKSHAG 51 (151)
Q Consensus 32 ~~~a~r~g~~v~t~~k~~~g 51 (151)
-+.|++.|+++.|++.|+.-
T Consensus 4 ~e~a~~~gvs~~tlr~ye~~ 23 (113)
T cd01109 4 KEVAEKTGLSADTLRYYEKE 23 (113)
T ss_pred HHHHHHHCcCHHHHHHHHHC
Confidence 46899999999999999963
No 315
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=77.52 E-value=4.7 Score=29.37 Aligned_cols=32 Identities=9% Similarity=0.149 Sum_probs=26.1
Q ss_pred HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
..+-.++. .|+|.+++|+.+|+|.++|.....
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 999999999999999999988653
No 316
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=77.45 E-value=1.1 Score=34.51 Aligned_cols=28 Identities=25% Similarity=0.281 Sum_probs=24.3
Q ss_pred HHHHHHHHcCCChhhHHhhhcCCCccCC
Q 031871 30 KVVNAARRAGADIETVRKSHAGTNKAAS 57 (151)
Q Consensus 30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~~ 57 (151)
++-++|+++|++-..+.+.|+|..-|.-
T Consensus 20 tQ~dLA~~aGVSQ~~IArlE~G~vdPrl 47 (187)
T COG3620 20 TQKDLARRAGVSQPYIARLEAGKVDPRL 47 (187)
T ss_pred CHHHHHHHcCccHHHHHHHhcCCCCccH
Confidence 5678999999999999999999887643
No 317
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=77.22 E-value=2.7 Score=32.79 Aligned_cols=24 Identities=13% Similarity=0.207 Sum_probs=21.4
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 103 KKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 103 ~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
+..+.+|||+.+|||+++++...+
T Consensus 177 R~~~l~dLA~~lGISkst~~ehLR 200 (215)
T COG3413 177 RRVSLKDLAKELGISKSTLSEHLR 200 (215)
T ss_pred ccCCHHHHHHHhCCCHHHHHHHHH
Confidence 567999999999999999998765
No 318
>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=77.21 E-value=6.1 Score=30.27 Aligned_cols=38 Identities=18% Similarity=0.190 Sum_probs=33.2
Q ss_pred hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
..+....+|.+-...++|....|..+|||..|+.+|-.
T Consensus 4 ~~e~R~~~R~~YV~~~~sLe~aA~~~gVs~~TarrWK~ 41 (165)
T PF08822_consen 4 PQETRDAVRRAYVFDRLSLEQAAAKCGVSYATARRWKR 41 (165)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 35567778888888899999999999999999999965
No 319
>PRK01905 DNA-binding protein Fis; Provisional
Probab=76.91 E-value=6 Score=26.07 Aligned_cols=34 Identities=12% Similarity=0.039 Sum_probs=27.9
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
...|.......+-++.+.|+.+|++++++.+.-+
T Consensus 39 ~~~i~~aL~~~~gn~s~aAr~LGIsrstL~rklk 72 (77)
T PRK01905 39 KPLLEVVMEQAGGNQSLAAEYLGINRNTLRKKLQ 72 (77)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4457777778888999999999999999887654
No 320
>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=76.83 E-value=6.4 Score=24.30 Aligned_cols=31 Identities=26% Similarity=0.369 Sum_probs=25.1
Q ss_pred CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 031871 106 TQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 147 (151)
Q Consensus 106 TQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l 147 (151)
|....|+.+|+|+++|++. +..|.+.||+++
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 7788999999999999974 567777787765
No 321
>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=76.80 E-value=3.9 Score=30.03 Aligned_cols=23 Identities=26% Similarity=0.258 Sum_probs=20.6
Q ss_pred cCHHHHHHHhCCCHHHHHHHHcC
Q 031871 105 LTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E~G 127 (151)
++..++|+.+|||+.||..||+-
T Consensus 1 y~I~e~a~~~gvs~~TLR~Ye~~ 23 (134)
T cd04779 1 YRIGQLAHLAGVSKRTIDYYTNL 23 (134)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 47789999999999999999863
No 322
>PRK15320 transcriptional activator SprB; Provisional
Probab=76.72 E-value=2.6 Score=33.70 Aligned_cols=26 Identities=12% Similarity=0.107 Sum_probs=23.2
Q ss_pred hcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 101 NDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 101 ~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
...|+|++|+|+.+++|.+||+.+-+
T Consensus 176 LAkG~SNKEIAekL~LS~KTVSTYKn 201 (251)
T PRK15320 176 LSSGHPAIELAKKFGLGTKTVSIYRK 201 (251)
T ss_pred HHcCCCHHHHHHHhccchhhHHHHHH
Confidence 35799999999999999999998854
No 323
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=76.52 E-value=7.6 Score=29.47 Aligned_cols=49 Identities=12% Similarity=0.182 Sum_probs=31.8
Q ss_pred cCCcCHHHHHHHhCCCHHHHHHHHcCC----CCCCHHHHHHHHHHhCCCCCCC
Q 031871 102 DKKLTQSQLAQLINEKPQVIQEYESGK----AIPNQQILTKLERALGVKLRGK 150 (151)
Q Consensus 102 ~~glTQ~eLA~~lgis~s~Is~~E~G~----~~p~~~~l~kLa~~Lgv~l~e~ 150 (151)
..|+|.+|+|+.+++|..||..+-+.- ..-+...+..++.-.-+++-+|
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 379999999999999999998876421 2234444444443334444444
No 324
>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=76.46 E-value=2.6 Score=29.67 Aligned_cols=26 Identities=15% Similarity=0.244 Sum_probs=22.8
Q ss_pred HHHHHHHHcCCChhhHHhhhcCCCcc
Q 031871 30 KVVNAARRAGADIETVRKSHAGTNKA 55 (151)
Q Consensus 30 ~~~~~a~r~g~~v~t~~k~~~g~~~~ 55 (151)
++-.+|++.|++..|+.+|++|...|
T Consensus 80 tq~~lA~~lg~~~~tis~~e~g~~~p 105 (127)
T TIGR03830 80 SQREAAELLGGGVNAFSRYERGEVRP 105 (127)
T ss_pred CHHHHHHHhCCCHHHHHHHHCCCCCC
Confidence 45679999999999999999998765
No 325
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=76.39 E-value=4.8 Score=29.25 Aligned_cols=32 Identities=9% Similarity=0.035 Sum_probs=25.9
Q ss_pred HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
..+-.++...|+|.+|+|+.+|+|.++|...-
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 34445667789999999999999999997653
No 326
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=76.37 E-value=4.5 Score=30.42 Aligned_cols=29 Identities=24% Similarity=0.210 Sum_probs=24.5
Q ss_pred HhcCCcCHHHHHHHhCCCHHHHHHHHcCC
Q 031871 100 RNDKKLTQSQLAQLINEKPQVIQEYESGK 128 (151)
Q Consensus 100 R~~~glTQ~eLA~~lgis~s~Is~~E~G~ 128 (151)
|...=||..|+|+.+|+|..||..||+-.
T Consensus 7 ~~~~~~~IgevAk~~gvs~~TlRyYE~~G 35 (154)
T PRK15002 7 RIKALLTPGEVAKRSGVAVSALHFYESKG 35 (154)
T ss_pred hhcccccHHHHHHHHCcCHHHHHHHHHCC
Confidence 44455899999999999999999999743
No 327
>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=76.36 E-value=4.7 Score=24.99 Aligned_cols=30 Identities=20% Similarity=0.226 Sum_probs=21.4
Q ss_pred HHHHH-hcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 96 IVQAR-NDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 96 Lk~~R-~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
|..+. ....+++.+||+.++++++++++.-
T Consensus 9 L~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i 39 (68)
T PF13463_consen 9 LRALAHSDGPMTQSDLAERLGISKSTVSRII 39 (68)
T ss_dssp HHHHT--TS-BEHHHHHHHTT--HHHHHHHH
T ss_pred HHHHHccCCCcCHHHHHHHHCcCHHHHHHHH
Confidence 44454 6778999999999999999999864
No 328
>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=76.34 E-value=0.89 Score=31.18 Aligned_cols=30 Identities=20% Similarity=0.282 Sum_probs=24.0
Q ss_pred HHHHHcCCChhhHHhhhcCCCccCCCCccc
Q 031871 33 NAARRAGADIETVRKSHAGTNKAASSSTSL 62 (151)
Q Consensus 33 ~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~ 62 (151)
..|.++|++.+|+.+|+.|...|..+.+.+
T Consensus 48 qLAe~~GIs~stLs~iE~g~~~Ps~~tL~k 77 (89)
T TIGR02684 48 QLARKTGLSRESLYKALSGKGNPTFDTILK 77 (89)
T ss_pred HHHHHHCCCHHHHHHHHcCCCCCCHHHHHH
Confidence 399999999999999999987765443333
No 329
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=76.23 E-value=7 Score=26.96 Aligned_cols=37 Identities=14% Similarity=0.153 Sum_probs=31.9
Q ss_pred HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCC
Q 031871 92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK 128 (151)
Q Consensus 92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~ 128 (151)
-...|+.-.+..|+|.+++|..+|+|...|.++.+=+
T Consensus 11 T~~ELq~nf~~~~ls~~~ia~dL~~s~~~le~vL~l~ 47 (89)
T PF10078_consen 11 TRQELQANFELSGLSLEQIAADLGTSPEHLEQVLNLK 47 (89)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC
Confidence 4556777788899999999999999999999998744
No 330
>PRK13749 transcriptional regulator MerD; Provisional
Probab=76.09 E-value=11 Score=27.19 Aligned_cols=65 Identities=17% Similarity=0.108 Sum_probs=38.0
Q ss_pred HHHHHHHcCCChhhHHhhhcCCCccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHH--hcCCcCHH
Q 031871 31 VVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQAR--NDKKLTQS 108 (151)
Q Consensus 31 ~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R--~~~glTQ~ 108 (151)
.-+.|+++|+++.|+|-|+.-..-|.. .+ +.... ......--.+|+.++ ...||+..
T Consensus 6 IgelA~~~gvS~~tiR~YE~~GLl~p~---~r-------~~~gy-----------R~Y~~~~l~rL~~I~~~r~~G~sL~ 64 (121)
T PRK13749 6 VSRLALDAGVSVHIVRDYLLRGLLRPV---AC-------TTGGY-----------GLFDDAALQRLCFVRAAFEAGIGLD 64 (121)
T ss_pred HHHHHHHHCCCHHHHHHHHHCCCCCCC---Cc-------CCCCC-----------ccCCHHHHHHHHHHHHHHHcCCCHH
Confidence 457899999999999999963332111 01 10000 011222333444443 46799999
Q ss_pred HHHHHhCC
Q 031871 109 QLAQLINE 116 (151)
Q Consensus 109 eLA~~lgi 116 (151)
++.+.+..
T Consensus 65 eI~~ll~l 72 (121)
T PRK13749 65 ALARLCRA 72 (121)
T ss_pred HHHHHHhh
Confidence 99887765
No 331
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=75.92 E-value=4.6 Score=30.44 Aligned_cols=33 Identities=9% Similarity=-0.006 Sum_probs=27.2
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
...+-.++.-.|+|.+|+|+.+|+|.++|...-
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 444555677789999999999999999998764
No 332
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=75.89 E-value=5 Score=29.53 Aligned_cols=31 Identities=10% Similarity=0.073 Sum_probs=25.3
Q ss_pred HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
.+-.++.-.|+|.+|+|+.+|+|.++|...-
T Consensus 125 ~vl~L~~~~g~s~~EIA~~lgis~~tV~~~l 155 (173)
T PRK09645 125 AVLVRSYYRGWSTAQIAADLGIPEGTVKSRL 155 (173)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence 3445666789999999999999999997653
No 333
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=75.84 E-value=5.2 Score=29.59 Aligned_cols=34 Identities=9% Similarity=0.167 Sum_probs=27.1
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
...+-.++.-.|+|.+|+|+.+|+|.++|.....
T Consensus 124 ~r~v~~L~~~~g~s~~EIA~~lgis~~tV~~~l~ 157 (172)
T PRK12523 124 ARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLA 157 (172)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3344455667899999999999999999987653
No 334
>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=75.78 E-value=14 Score=26.45 Aligned_cols=20 Identities=15% Similarity=0.149 Sum_probs=17.7
Q ss_pred HHHHHHcCCChhhHHhhhcC
Q 031871 32 VNAARRAGADIETVRKSHAG 51 (151)
Q Consensus 32 ~~~a~r~g~~v~t~~k~~~g 51 (151)
-+.|++.|+++.|++-|+.-
T Consensus 4 ~e~a~~~gvs~~tlRyYe~~ 23 (127)
T TIGR02044 4 GQVAKLTGLSSKMIRYYEEK 23 (127)
T ss_pred HHHHHHHCcCHHHHHHHHHC
Confidence 46899999999999999974
No 335
>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=75.78 E-value=13 Score=26.73 Aligned_cols=21 Identities=24% Similarity=0.309 Sum_probs=18.5
Q ss_pred HHHHHHHcCCChhhHHhhhcC
Q 031871 31 VVNAARRAGADIETVRKSHAG 51 (151)
Q Consensus 31 ~~~~a~r~g~~v~t~~k~~~g 51 (151)
.-+.|+++|+++.|+|-|+.-
T Consensus 6 I~elA~~~gvs~~tlR~Ye~~ 26 (120)
T TIGR02054 6 ISRLAEDAGVSVHVVRDYLLR 26 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999974
No 336
>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=75.74 E-value=5.3 Score=31.75 Aligned_cols=31 Identities=10% Similarity=0.233 Sum_probs=26.3
Q ss_pred HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 96 IVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
+-.++-..|+|.+|+|+.+|+|.++|..+..
T Consensus 213 ii~l~~~~g~s~~eIA~~lgis~~~V~~~~~ 243 (255)
T TIGR02941 213 IIHCTFEENLSQKETGERLGISQMHVSRLQR 243 (255)
T ss_pred HHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 4445567899999999999999999998765
No 337
>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=75.72 E-value=4.1 Score=32.62 Aligned_cols=54 Identities=6% Similarity=0.139 Sum_probs=37.2
Q ss_pred HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH-cCCCCCCHHHHHHHHHHhCCCC
Q 031871 94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE-SGKAIPNQQILTKLERALGVKL 147 (151)
Q Consensus 94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E-~G~~~p~~~~l~kLa~~Lgv~l 147 (151)
..+-.++...|+|.+|+|+.+|+|.++|...- ++........-..++.-|++..
T Consensus 167 R~v~~L~~~eg~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~~~~~~~~~~~ 221 (244)
T TIGR03001 167 RHLLRLHFVDGLSMDRIGAMYQVHRSTVSRWVAQARERLLERTRRRLAERLKLSS 221 (244)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCc
Confidence 33444566689999999999999999987754 3444445555555666666443
No 338
>PRK11050 manganese transport regulator MntR; Provisional
Probab=75.56 E-value=7.2 Score=28.93 Aligned_cols=36 Identities=8% Similarity=0.054 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHh-cCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 90 SELKKAIVQARN-DKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 90 ~~~~~~Lk~~R~-~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
..+...|..+.. .-++++.+||+.+++++++|+++-
T Consensus 36 e~~l~~I~~~l~~~~~~t~~eLA~~l~is~stVsr~l 72 (152)
T PRK11050 36 EDYVELIADLIAEVGEARQVDIAARLGVSQPTVAKML 72 (152)
T ss_pred HHHHHHHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHH
Confidence 344455554443 357899999999999999999874
No 339
>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=75.55 E-value=11 Score=25.91 Aligned_cols=66 Identities=15% Similarity=0.063 Sum_probs=38.1
Q ss_pred HHHHHHcCCChhhHHhhhcCCCccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHHHH
Q 031871 32 VNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLA 111 (151)
Q Consensus 32 ~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~eLA 111 (151)
-+.|++.|+++.|++-|+.--.-|...... .-+. +.. . .-..-..|+.+|. .|+|.++++
T Consensus 5 ~eva~~~gvs~~tLR~ye~~Gll~~~r~~~-g~R~-------Y~~---------~--dl~~l~~I~~l~~-~G~~l~ei~ 64 (102)
T cd04775 5 GQMSRKFGVSRSTLLYYESIGLIPSARSEA-NYRL-------YSE---------A--DLSRLEKIVFLQA-GGLPLEEIA 64 (102)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCCCCCC-CCee-------eCH---------H--HHHHHHHHHHHHH-CCCCHHHHH
Confidence 468999999999999999732222110000 0000 111 0 1233455666654 699999999
Q ss_pred HHhCCC
Q 031871 112 QLINEK 117 (151)
Q Consensus 112 ~~lgis 117 (151)
..+...
T Consensus 65 ~~~~~~ 70 (102)
T cd04775 65 GCLAQP 70 (102)
T ss_pred HHHcCC
Confidence 877543
No 340
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=75.46 E-value=5 Score=32.21 Aligned_cols=30 Identities=7% Similarity=0.162 Sum_probs=25.6
Q ss_pred HHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 97 VQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 97 k~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
-.+|-..++|++|+|+.+|+|.++|..++.
T Consensus 214 i~l~y~e~~t~~EIA~~lgis~~~V~~~~~ 243 (257)
T PRK05911 214 MALYYYEELVLKEIGKILGVSESRVSQIHS 243 (257)
T ss_pred HHHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 334445799999999999999999999876
No 341
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=75.42 E-value=4.8 Score=30.11 Aligned_cols=31 Identities=6% Similarity=0.101 Sum_probs=25.6
Q ss_pred HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 96 IVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
+-.++...|+|.+|+|+.+|+|.++|..+-.
T Consensus 141 i~~l~~~~~~s~~eIA~~lgis~~tV~~~l~ 171 (182)
T PRK12537 141 CILHAYVDGCSHAEIAQRLGAPLGTVKAWIK 171 (182)
T ss_pred HHHHHHHcCCCHHHHHHHHCCChhhHHHHHH
Confidence 3445567899999999999999999988654
No 342
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=75.40 E-value=6.9 Score=24.48 Aligned_cols=23 Identities=26% Similarity=0.332 Sum_probs=18.8
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHc
Q 031871 104 KLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 104 glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
.+|..+||+.+|++..++.++-+
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~ 23 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFK 23 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Confidence 36788899999999988888765
No 343
>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=75.27 E-value=5.7 Score=30.69 Aligned_cols=29 Identities=17% Similarity=0.241 Sum_probs=24.2
Q ss_pred HHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871 96 IVQARNDKKLTQSQLAQLINEKPQVIQEY 124 (151)
Q Consensus 96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~ 124 (151)
|..+...-++|+.+||+.+|+++++|++.
T Consensus 7 L~~L~~~~~~t~~eLA~~lgis~~tV~~~ 35 (203)
T TIGR02702 7 LSYLLKQGQATAAALAEALAISPQAVRRH 35 (203)
T ss_pred HHHHHHcCCCCHHHHHHHHCcCHHHHHHH
Confidence 44555567799999999999999999876
No 344
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=75.27 E-value=5.3 Score=29.76 Aligned_cols=32 Identities=13% Similarity=0.140 Sum_probs=26.1
Q ss_pred HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
.+-.++...|+|.+|+|+.+|+|.++|.....
T Consensus 142 ~vl~l~~~~~~s~~eIA~~lgis~~~V~~~l~ 173 (186)
T PRK13919 142 RVIEVLYYQGYTHREAAQLLGLPLGTLKTRAR 173 (186)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34445667899999999999999999987654
No 345
>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=75.21 E-value=5.6 Score=30.92 Aligned_cols=31 Identities=6% Similarity=0.184 Sum_probs=25.6
Q ss_pred HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 96 IVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
+-.++-..|+|++|+|+.+|+|..+|.....
T Consensus 183 il~l~y~~~~s~~eIA~~lgis~~tV~~~~~ 213 (224)
T TIGR02479 183 VLSLYYYEELNLKEIGEVLGLTESRVSQIHS 213 (224)
T ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 3334556899999999999999999988764
No 346
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=75.17 E-value=12 Score=28.24 Aligned_cols=43 Identities=21% Similarity=0.170 Sum_probs=31.1
Q ss_pred HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Q 031871 96 IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV 145 (151)
Q Consensus 96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv 145 (151)
+-.++...|+|.+|+|+.+|+|.++|..... .-+.+|...|++
T Consensus 150 vl~l~~~~~~s~~EIA~~Lgis~~tVk~~l~-------ra~~~Lr~~l~~ 192 (194)
T PRK09646 150 SVTLAYYGGLTYREVAERLAVPLGTVKTRMR-------DGLIRLRDCLGV 192 (194)
T ss_pred HHHHHHHcCCCHHHHHHHhCCChHhHHHHHH-------HHHHHHHHHhcc
Confidence 3345667899999999999999999977653 234455555544
No 347
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=75.15 E-value=6.3 Score=27.25 Aligned_cols=33 Identities=6% Similarity=0.008 Sum_probs=27.3
Q ss_pred HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
..|..+....+..+.+.|+.+||+++++.+.-+
T Consensus 58 ~~i~~aL~~~~gn~s~AAr~LGIsRsTL~rKLk 90 (95)
T PRK00430 58 PLLDMVMQYTRGNQTRAALMLGINRGTLRKKLK 90 (95)
T ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 356777777888999999999999999877644
No 348
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=75.14 E-value=6.3 Score=31.54 Aligned_cols=40 Identities=30% Similarity=0.459 Sum_probs=27.7
Q ss_pred HHHHHHHhcCC-cCHHHHHHHhCCCHHHHHHH------HcCCCCCCH
Q 031871 94 KAIVQARNDKK-LTQSQLAQLINEKPQVIQEY------ESGKAIPNQ 133 (151)
Q Consensus 94 ~~Lk~~R~~~g-lTQ~eLA~~lgis~s~Is~~------E~G~~~p~~ 133 (151)
+.+.++..+-| |||.|||-.+|+|++||++. |+|...|+.
T Consensus 94 Rl~~EAy~QgglLT~~Dla~LL~~S~~TI~~~i~~yq~e~g~vvPtr 140 (220)
T PF07900_consen 94 RLTNEAYDQGGLLTQEDLAMLLGISPRTISKDIKEYQKEHGVVVPTR 140 (220)
T ss_pred HHHHHHHHcCCcccHHHHHHHHCCCHHHHHHHHHHHHHHcCceeccC
Confidence 33344444433 79999999999999999886 335555544
No 349
>PF13309 HTH_22: HTH domain
Probab=75.08 E-value=2.9 Score=26.72 Aligned_cols=20 Identities=10% Similarity=0.130 Sum_probs=18.1
Q ss_pred CHHHHHHHhCCCHHHHHHHH
Q 031871 106 TQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 106 TQ~eLA~~lgis~s~Is~~E 125 (151)
+-..+|+.+|||+.||.+|.
T Consensus 44 av~~vA~~L~iS~~TVY~YL 63 (64)
T PF13309_consen 44 AVEYVAEKLGISRATVYRYL 63 (64)
T ss_pred HHHHHHHHHCCCHHHHHHHc
Confidence 67789999999999999885
No 350
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=75.06 E-value=1.4 Score=38.71 Aligned_cols=42 Identities=14% Similarity=0.178 Sum_probs=31.6
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 031871 103 KKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALG 144 (151)
Q Consensus 103 ~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lg 144 (151)
+-||++++|+.+|++.||||+.-+|+..-+..-+.-|-.+|.
T Consensus 342 kPLtlkdvAe~lglheSTVSRav~~Kyv~tp~Gi~~lk~FFs 383 (455)
T PRK05932 342 KPLVLKDIAEELGMHESTISRATTNKYMATPRGIFELKYFFS 383 (455)
T ss_pred cCccHHHHHHHhCCCccchhhhhcCceeecCCceEEHHHhcc
Confidence 358999999999999999999999986544433344444443
No 351
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=74.97 E-value=8.6 Score=23.82 Aligned_cols=37 Identities=22% Similarity=0.309 Sum_probs=26.9
Q ss_pred cCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 031871 102 DKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG 149 (151)
Q Consensus 102 ~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~e 149 (151)
+.+.+..+.|+.+++.+.|+.. .+.+|.+.+|+++++
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 4567899999999999999864 467888888888764
No 352
>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=74.95 E-value=5.8 Score=33.69 Aligned_cols=43 Identities=16% Similarity=0.261 Sum_probs=32.8
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHcCC------------CCCCHHHHHHHHHHhCC
Q 031871 103 KKLTQSQLAQLINEKPQVIQEYESGK------------AIPNQQILTKLERALGV 145 (151)
Q Consensus 103 ~glTQ~eLA~~lgis~s~Is~~E~G~------------~~p~~~~l~kLa~~Lgv 145 (151)
.-+|..|+|+.+|++++||..||.-. +..+.+.+..|...+..
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 45899999999999999999997533 33456677777766654
No 353
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=74.88 E-value=7.3 Score=31.25 Aligned_cols=33 Identities=6% Similarity=-0.032 Sum_probs=26.4
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
...+..+++...+++.|||+.+|+|..||.+..
T Consensus 8 ~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL 40 (251)
T PRK13509 8 QILLELLAQLGFVTVEKVIERLGISPATARRDI 40 (251)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHH
Confidence 344555666777999999999999999998763
No 354
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=74.60 E-value=5.7 Score=25.42 Aligned_cols=24 Identities=13% Similarity=0.123 Sum_probs=19.0
Q ss_pred cCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 102 DKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 102 ~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
...+|-.|+|+.+|+|..++..|.
T Consensus 13 ~~p~~T~eiA~~~gls~~~aR~yL 36 (62)
T PF04703_consen 13 NGPLKTREIADALGLSIYQARYYL 36 (62)
T ss_dssp TS-EEHHHHHHHHTS-HHHHHHHH
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHH
Confidence 678999999999999988877763
No 355
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=74.60 E-value=1.8 Score=38.48 Aligned_cols=44 Identities=14% Similarity=0.112 Sum_probs=34.1
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Q 031871 103 KKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVK 146 (151)
Q Consensus 103 ~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~ 146 (151)
+=||.+++|+.+|++.||||+.-+|+..-++.-+..|-.+|.-.
T Consensus 368 kPLtlkdVAe~lglHeSTVSRa~~~KY~~tp~GifeLK~FFs~~ 411 (481)
T PRK12469 368 KPLVLRDVAEELGLHESTISRATGNKYMATPRGTFEFKHFFPRK 411 (481)
T ss_pred cCCcHHHHHHHhCCCcchhhHHhcCceeecCCceEeHHHhhccc
Confidence 45899999999999999999999999765555455555555433
No 356
>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=74.57 E-value=11 Score=26.07 Aligned_cols=20 Identities=25% Similarity=0.192 Sum_probs=17.6
Q ss_pred HHHHHHcCCChhhHHhhhcC
Q 031871 32 VNAARRAGADIETVRKSHAG 51 (151)
Q Consensus 32 ~~~a~r~g~~v~t~~k~~~g 51 (151)
-+.|+++|+++.|++-|+.-
T Consensus 4 ge~a~~~gvs~~tlRyYe~~ 23 (107)
T cd04777 4 GKFAKKNNITIDTVRHYIDL 23 (107)
T ss_pred HHHHHHHCcCHHHHHHHHHC
Confidence 35799999999999999973
No 357
>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=74.49 E-value=7.6 Score=28.58 Aligned_cols=39 Identities=13% Similarity=0.104 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHhcCC---cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871 90 SELKKAIVQARNDKK---LTQSQLAQLINEKPQVIQEYESGK 128 (151)
Q Consensus 90 ~~~~~~Lk~~R~~~g---lTQ~eLA~~lgis~s~Is~~E~G~ 128 (151)
..+.+.+.++..++| +|.+|+++++||+++|...+-..+
T Consensus 6 ~~I~~a~~~Ll~~k~~~~ITV~~I~~~AgvsR~TFY~hF~dK 47 (176)
T TIGR02366 6 KKIAKAFKDLMEVQAFSKISVSDIMSTAQIRRQTFYNHFQDK 47 (176)
T ss_pred HHHHHHHHHHHHHCCCccCCHHHHHHHhCCCHHHHHHHCCCH
Confidence 445666666666654 799999999999999998876554
No 358
>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=74.48 E-value=16 Score=25.92 Aligned_cols=19 Identities=21% Similarity=0.104 Sum_probs=17.1
Q ss_pred HHHHHHcCCChhhHHhhhc
Q 031871 32 VNAARRAGADIETVRKSHA 50 (151)
Q Consensus 32 ~~~a~r~g~~v~t~~k~~~ 50 (151)
-+.|+..|+++.|++-|+.
T Consensus 4 geva~~~gvs~~tlRyYe~ 22 (118)
T cd04776 4 SELAREFDVTPRTLRFYED 22 (118)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 3689999999999999986
No 359
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=74.46 E-value=16 Score=26.07 Aligned_cols=26 Identities=8% Similarity=0.005 Sum_probs=22.9
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHcCC
Q 031871 103 KKLTQSQLAQLINEKPQVIQEYESGK 128 (151)
Q Consensus 103 ~glTQ~eLA~~lgis~s~Is~~E~G~ 128 (151)
..+|..+||+.+|+|+.++.++-+..
T Consensus 24 ~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 24 SPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 35999999999999999999987654
No 360
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=74.42 E-value=7 Score=23.13 Aligned_cols=24 Identities=13% Similarity=0.234 Sum_probs=20.4
Q ss_pred cCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 102 DKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 102 ~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
...+|..++++.+|++++++++.-
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l 31 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHL 31 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHH
Confidence 456899999999999999988763
No 361
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=74.41 E-value=3.4 Score=31.98 Aligned_cols=25 Identities=12% Similarity=0.114 Sum_probs=22.5
Q ss_pred cCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 102 DKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 102 ~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
..|+|.+|+|+++|+|..||..+-+
T Consensus 150 a~G~snkeIA~~L~iS~~TVk~h~~ 174 (207)
T PRK15411 150 MAGQGTIQISDQMNIKAKTVSSHKG 174 (207)
T ss_pred HcCCCHHHHHHHcCCCHHHHHHHHH
Confidence 4699999999999999999998754
No 362
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=74.36 E-value=6.3 Score=30.80 Aligned_cols=25 Identities=20% Similarity=0.310 Sum_probs=22.6
Q ss_pred cCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 102 DKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 102 ~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
..|+|.+|+|+.+|+|.++|.....
T Consensus 196 ~eg~s~~EIA~~lgis~~tVk~~~~ 220 (234)
T PRK08301 196 GEEKTQKEVADMLGISQSYISRLEK 220 (234)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 5799999999999999999988754
No 363
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=74.34 E-value=5.8 Score=32.53 Aligned_cols=24 Identities=13% Similarity=0.176 Sum_probs=22.9
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 103 KKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 103 ~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
.|+|++|+|+.+|+|+.+|.+++.
T Consensus 244 ~~~t~~EIa~~lgvs~~~V~q~~~ 267 (289)
T PRK07500 244 DGATLEALGEELGISKERVRQIEA 267 (289)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Confidence 689999999999999999999987
No 364
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=74.31 E-value=5.5 Score=30.11 Aligned_cols=31 Identities=6% Similarity=-0.022 Sum_probs=25.5
Q ss_pred HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 96 IVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
+-.++...|+|.+|+|+.+|+|.++|...-.
T Consensus 119 v~~L~~~eg~s~~EIA~~lgis~~tV~~~l~ 149 (182)
T PRK12511 119 ALHLVAIEGLSYQEAAAVLGIPIGTLMSRIG 149 (182)
T ss_pred HHHHHHHcCCCHHHHHHHhCcCHHHHHHHHH
Confidence 4445566799999999999999999988643
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=74.25 E-value=19 Score=24.61 Aligned_cols=66 Identities=12% Similarity=0.136 Sum_probs=37.5
Q ss_pred HHHHHHcCCChhhHHhhhcC-CCccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHHH
Q 031871 32 VNAARRAGADIETVRKSHAG-TNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQL 110 (151)
Q Consensus 32 ~~~a~r~g~~v~t~~k~~~g-~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~eL 110 (151)
-+.|+..|++..|++.|+.- -..|.... ...-+. +.+ . .-..-..|..+|. .|++.+++
T Consensus 4 ~eva~~~gvs~~tlR~ye~~Gll~~~~~~-~~g~R~-------y~~---------~--di~~l~~i~~lr~-~g~~l~~i 63 (103)
T cd01106 4 GEVAKLTGVSVRTLHYYDEIGLLKPSRRT-ENGYRL-------YTE---------E--DLERLQQILFLKE-LGFSLKEI 63 (103)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCCccC-CCCcee-------eCH---------H--HHHHHHHHHHHHH-cCCCHHHH
Confidence 46899999999999999863 22221100 001111 111 0 1122344555665 69999999
Q ss_pred HHHhCCC
Q 031871 111 AQLINEK 117 (151)
Q Consensus 111 A~~lgis 117 (151)
.+.+...
T Consensus 64 ~~~~~~~ 70 (103)
T cd01106 64 KELLKDP 70 (103)
T ss_pred HHHHHcC
Confidence 8887655
No 366
>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=74.23 E-value=4.7 Score=30.27 Aligned_cols=43 Identities=14% Similarity=0.061 Sum_probs=29.5
Q ss_pred CHHHHHHHHHcCCChhhHHhhhcCCCcc--CCCCccccccccccc
Q 031871 28 DEKVVNAARRAGADIETVRKSHAGTNKA--ASSSTSLNTRKLDED 70 (151)
Q Consensus 28 ~~~~~~~a~r~g~~v~t~~k~~~g~~~~--~~~~~~~~~~kl~~~ 70 (151)
+=+..+.|.+.|++..++.+||.|...+ ....+.+.+..|+..
T Consensus 38 GmTq~eLAerlGVS~~tIs~iE~G~~~~~psl~~L~kIA~aLgv~ 82 (150)
T TIGR02612 38 GMSGAQLAGRLGVTPQRVEALEKSELSGTVTLKTLRAAAEALDCT 82 (150)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHcCCCCCCCCHHHHHHHHHHcCCC
Confidence 3456789999999999999999998653 222333444444443
No 367
>PHA01082 putative transcription regulator
Probab=74.19 E-value=2.4 Score=31.01 Aligned_cols=41 Identities=17% Similarity=0.302 Sum_probs=33.8
Q ss_pred hcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCH-HHHHHHHH
Q 031871 101 NDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQ-QILTKLER 141 (151)
Q Consensus 101 ~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~-~~l~kLa~ 141 (151)
-+.|+|..|-|+.+--|..+|.+|-.|+..|+. ..|.++-.
T Consensus 27 feCgLsveeaa~LCfKsVrtVk~WD~G~~IPPeCkRLMr~~~ 68 (133)
T PHA01082 27 FECGLSVEEAAKLCFKTVSEVKQWDAGEKIPPICKRLMRWHS 68 (133)
T ss_pred hccCccHHHHHHHHHHhHHHHhhccCCCcCChHHHHHHHHhc
Confidence 368999999999999999999999999987764 34555544
No 368
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=74.14 E-value=6.1 Score=29.00 Aligned_cols=34 Identities=9% Similarity=0.043 Sum_probs=26.8
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
...+-.++...|+|.+|+|+.+|+|..+|...-.
T Consensus 117 ~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ 150 (164)
T PRK12547 117 QREAIILIGASGFSYEDAAAICGCAVGTIKSRVS 150 (164)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 3344455667899999999999999999987644
No 369
>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=73.99 E-value=2.7 Score=24.85 Aligned_cols=21 Identities=33% Similarity=0.502 Sum_probs=18.5
Q ss_pred HHHHHcCCChhhHHhhhcCCC
Q 031871 33 NAARRAGADIETVRKSHAGTN 53 (151)
Q Consensus 33 ~~a~r~g~~v~t~~k~~~g~~ 53 (151)
+.|++.|++.+|+.+|..|..
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 368999999999999998864
No 370
>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=73.84 E-value=6.6 Score=29.10 Aligned_cols=31 Identities=10% Similarity=0.159 Sum_probs=25.1
Q ss_pred HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 96 IVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
+-.++.-.|+|++++|+.+|+|.++|.....
T Consensus 148 vi~l~~~~g~s~~eIA~~lgis~~~v~~~l~ 178 (189)
T TIGR02984 148 VILLRHLEGLSFAEVAERMDRSEGAVSMLWV 178 (189)
T ss_pred HHHHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3345556899999999999999999987643
No 371
>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=73.71 E-value=6.1 Score=32.37 Aligned_cols=25 Identities=16% Similarity=0.322 Sum_probs=23.2
Q ss_pred cCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 102 DKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 102 ~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
..++|.+|+|+.+|+|+.+|..++.
T Consensus 267 ~~~~Tl~EIa~~lgiS~erVrq~~~ 291 (298)
T TIGR02997 267 GEPLTLAEIGRRLNLSRERVRQIEA 291 (298)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 4789999999999999999999986
No 372
>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=73.69 E-value=16 Score=27.82 Aligned_cols=20 Identities=20% Similarity=0.160 Sum_probs=17.8
Q ss_pred HHHHHHHcCCChhhHHhhhc
Q 031871 31 VVNAARRAGADIETVRKSHA 50 (151)
Q Consensus 31 ~~~~a~r~g~~v~t~~k~~~ 50 (151)
.-+.|++.|+++.|++-|+.
T Consensus 4 I~evA~~~gvs~~tLRyYe~ 23 (172)
T cd04790 4 ISQLARQFGLSRSTLLYYER 23 (172)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 34689999999999999997
No 373
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=73.69 E-value=5.7 Score=29.67 Aligned_cols=29 Identities=7% Similarity=0.097 Sum_probs=25.0
Q ss_pred HHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 98 QARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 98 ~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
.++.-.|+|..|+|+.+|+|..+|.....
T Consensus 138 ~l~~~~g~s~~EIA~~lgis~~tV~~~l~ 166 (186)
T PRK05602 138 VLQYYQGLSNIEAAAVMDISVDALESLLA 166 (186)
T ss_pred hHHHhcCCCHHHHHHHhCcCHHHHHHHHH
Confidence 35566899999999999999999998764
No 374
>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=73.61 E-value=5.8 Score=29.13 Aligned_cols=33 Identities=18% Similarity=0.332 Sum_probs=26.0
Q ss_pred HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
..+-.++-..|+|.+|+|+.+|+|.++|...-.
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 344445566799999999999999999887543
No 375
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=73.49 E-value=5.8 Score=29.61 Aligned_cols=29 Identities=10% Similarity=0.080 Sum_probs=24.5
Q ss_pred HHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 98 QARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 98 ~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
.++-..|+|.+|+|+.+|+|.++|.....
T Consensus 147 ~l~~~~g~s~~eIA~~lgis~~~v~~~l~ 175 (187)
T PRK12534 147 RTAFFEGITYEELAARTDTPIGTVKSWIR 175 (187)
T ss_pred HHHHHcCCCHHHHHHHhCCChhHHHHHHH
Confidence 34556899999999999999999988654
No 376
>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=73.47 E-value=6.8 Score=28.47 Aligned_cols=31 Identities=10% Similarity=0.305 Sum_probs=25.1
Q ss_pred HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
.+-.++--.|+|..|+|+.+|+|.++|...-
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 3444566689999999999999999987753
No 377
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=73.36 E-value=8.4 Score=30.77 Aligned_cols=32 Identities=22% Similarity=0.185 Sum_probs=26.0
Q ss_pred HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
..+..+.+...+++.|||+.+|+|..||.+..
T Consensus 8 ~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL 39 (240)
T PRK10411 8 AIVDLLLNHTSLTTEALAEQLNVSKETIRRDL 39 (240)
T ss_pred HHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHH
Confidence 34555667788999999999999999988763
No 378
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=73.33 E-value=16 Score=24.87 Aligned_cols=26 Identities=12% Similarity=-0.042 Sum_probs=22.3
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHcCC
Q 031871 103 KKLTQSQLAQLINEKPQVIQEYESGK 128 (151)
Q Consensus 103 ~glTQ~eLA~~lgis~s~Is~~E~G~ 128 (151)
..+|..+||+.+|+|+.++.+.-+..
T Consensus 20 ~~~~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 20 QPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 45999999999999999999886643
No 379
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=72.89 E-value=6.5 Score=29.81 Aligned_cols=33 Identities=6% Similarity=0.038 Sum_probs=26.6
Q ss_pred HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
..+-.++...|+|.+|+|+.+|+|.++|...-.
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 334456677899999999999999999987643
No 380
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=72.75 E-value=12 Score=26.94 Aligned_cols=30 Identities=17% Similarity=0.121 Sum_probs=23.7
Q ss_pred HHHHHHhc-CCcCHHHHHHHhCCCHHHHHHH
Q 031871 95 AIVQARND-KKLTQSQLAQLINEKPQVIQEY 124 (151)
Q Consensus 95 ~Lk~~R~~-~glTQ~eLA~~lgis~s~Is~~ 124 (151)
.|..+... -++||.+||+.++++++++++.
T Consensus 36 vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~ 66 (144)
T PRK03573 36 TLHNIHQLPPEQSQIQLAKAIGIEQPSLVRT 66 (144)
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCChhhHHHH
Confidence 45555443 4689999999999999999876
No 381
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=72.72 E-value=4.4 Score=32.27 Aligned_cols=27 Identities=15% Similarity=0.186 Sum_probs=22.4
Q ss_pred HHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 99 ARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 99 ~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
+...-++|+.+||+.+|+|++++++.-
T Consensus 16 l~~~~~IS~~eLA~~L~iS~~Tvsr~L 42 (217)
T PRK14165 16 VNNTVKISSSEFANHTGTSSKTAARIL 42 (217)
T ss_pred cCCCCCcCHHHHHHHHCcCHHHHHHHH
Confidence 334457999999999999999999873
No 382
>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=72.44 E-value=20 Score=25.64 Aligned_cols=20 Identities=20% Similarity=0.150 Sum_probs=17.7
Q ss_pred HHHHHHcCCChhhHHhhhcC
Q 031871 32 VNAARRAGADIETVRKSHAG 51 (151)
Q Consensus 32 ~~~a~r~g~~v~t~~k~~~g 51 (151)
-+.|++.|+++.|++-|+.-
T Consensus 4 ~e~a~~~gvs~~tlRyYe~~ 23 (127)
T cd01108 4 GEAAKLTGLSAKMIRYYEEI 23 (127)
T ss_pred HHHHHHHCcCHHHHHHHHHC
Confidence 46899999999999999974
No 383
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=72.29 E-value=6.7 Score=28.48 Aligned_cols=33 Identities=12% Similarity=0.163 Sum_probs=26.5
Q ss_pred HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
..+-.++.-.|+|.+|+|+.+|+|.++|...-.
T Consensus 111 r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~ 143 (159)
T PRK12527 111 RDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIV 143 (159)
T ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 344455677899999999999999999987543
No 384
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=72.23 E-value=10 Score=29.40 Aligned_cols=32 Identities=13% Similarity=0.028 Sum_probs=26.2
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEY 124 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~ 124 (151)
...|..+....++||.+||+.+++++++++++
T Consensus 48 ~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~ 79 (185)
T PRK13777 48 HHILWIAYHLKGASISEIAKFGVMHVSTAFNF 79 (185)
T ss_pred HHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHH
Confidence 34566677778999999999999999888774
No 385
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=72.17 E-value=4.6 Score=28.29 Aligned_cols=30 Identities=10% Similarity=0.030 Sum_probs=26.1
Q ss_pred HhcCCcCHHHHHHHhCCCHHHHHHHHcCCC
Q 031871 100 RNDKKLTQSQLAQLINEKPQVIQEYESGKA 129 (151)
Q Consensus 100 R~~~glTQ~eLA~~lgis~s~Is~~E~G~~ 129 (151)
+--.++|..++|+++|++++++.++-.++-
T Consensus 28 ~G~~~~t~~~Ia~~agvs~~~~Y~~f~~K~ 57 (201)
T COG1309 28 KGYAATTVDEIAKAAGVSKGTLYRHFPSKE 57 (201)
T ss_pred cCcCCCCHHHHHHHhCCCcchhHHHcCCHH
Confidence 555678999999999999999999987764
No 386
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=72.09 E-value=6.9 Score=29.63 Aligned_cols=33 Identities=12% Similarity=0.276 Sum_probs=27.2
Q ss_pred HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
..+-.++...|++.+|+|+.+|+|.++|...-.
T Consensus 142 r~i~~L~~~~g~s~~eIA~~lgis~~tV~~~l~ 174 (196)
T PRK12524 142 RQAVVLRHIEGLSNPEIAEVMEIGVEAVESLTA 174 (196)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 345556667899999999999999999988754
No 387
>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=23 Score=25.43 Aligned_cols=20 Identities=25% Similarity=0.361 Sum_probs=17.6
Q ss_pred HHHHHHcCCChhhHHhhhcC
Q 031871 32 VNAARRAGADIETVRKSHAG 51 (151)
Q Consensus 32 ~~~a~r~g~~v~t~~k~~~g 51 (151)
-+.|++.|+++.|++-|+.-
T Consensus 4 ~e~a~~~gvs~~tlR~Ye~~ 23 (127)
T TIGR02047 4 GELAQKTGVSVETIRFYEKQ 23 (127)
T ss_pred HHHHHHHCcCHHHHHHHHHC
Confidence 46899999999999999973
No 388
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=72.08 E-value=6.8 Score=29.31 Aligned_cols=32 Identities=6% Similarity=0.105 Sum_probs=25.8
Q ss_pred HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
..+-.++.-.|+|.+|+|+.+|+|.++|...-
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 33444666789999999999999999998753
No 389
>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=72.06 E-value=7.3 Score=28.85 Aligned_cols=33 Identities=9% Similarity=0.098 Sum_probs=26.5
Q ss_pred HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
..+-.++...|+|.+|+|+.+|+|..+|.....
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 344446677899999999999999999977643
No 390
>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=71.98 E-value=12 Score=25.89 Aligned_cols=23 Identities=22% Similarity=0.228 Sum_probs=20.6
Q ss_pred cCCcCHHHHHHHhCCCHHHHHHH
Q 031871 102 DKKLTQSQLAQLINEKPQVIQEY 124 (151)
Q Consensus 102 ~~glTQ~eLA~~lgis~s~Is~~ 124 (151)
..++|+.+||+.+++++++|++.
T Consensus 41 ~~~~t~~eL~~~l~~~~stvs~~ 63 (109)
T TIGR01889 41 EGKLTLKEIIKEILIKQSALVKI 63 (109)
T ss_pred CCcCcHHHHHHHHCCCHHHHHHH
Confidence 35699999999999999999876
No 391
>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=71.95 E-value=12 Score=27.48 Aligned_cols=21 Identities=19% Similarity=0.297 Sum_probs=18.3
Q ss_pred HHHHHHHcCCChhhHHhhhcC
Q 031871 31 VVNAARRAGADIETVRKSHAG 51 (151)
Q Consensus 31 ~~~~a~r~g~~v~t~~k~~~g 51 (151)
.-+.|++.|+++.|++-|+.-
T Consensus 4 I~EvA~~~Gvs~~tLRyYE~~ 24 (139)
T cd01110 4 VGEVAKRSGVAVSALHFYEQK 24 (139)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 356899999999999999863
No 392
>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=71.86 E-value=32 Score=27.28 Aligned_cols=22 Identities=5% Similarity=0.048 Sum_probs=19.6
Q ss_pred CcCHHHHHHHhCCCHHHHHHHHc
Q 031871 104 KLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 104 glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
.||..||++.+| +++.+.+||.
T Consensus 97 ~~t~~eL~~~~G-~~~~l~~l~~ 118 (219)
T cd04778 97 TALLAELQSEFG-DERALARAVA 118 (219)
T ss_pred ccCHHHHHHHHC-CHHHHHHHHH
Confidence 578899999999 9999999976
No 393
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=71.79 E-value=6.3 Score=29.76 Aligned_cols=31 Identities=3% Similarity=0.055 Sum_probs=25.3
Q ss_pred HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 96 IVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
+-.++...|+|.+|+|+.+|+|..+|...-.
T Consensus 144 i~~L~~~~g~s~~EIA~~lgis~~tVk~~l~ 174 (195)
T PRK12532 144 VFTLKEILGFSSDEIQQMCGISTSNYHTIMH 174 (195)
T ss_pred HhhhHHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3345667899999999999999999987543
No 394
>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=71.73 E-value=11 Score=29.18 Aligned_cols=33 Identities=9% Similarity=0.102 Sum_probs=25.7
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
...|..+....++++.++|+.+|+|++++++.-
T Consensus 146 ~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L 178 (203)
T TIGR01884 146 LKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHL 178 (203)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHH
Confidence 344555555567899999999999999998764
No 395
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=71.67 E-value=10 Score=23.62 Aligned_cols=25 Identities=12% Similarity=0.110 Sum_probs=21.5
Q ss_pred cCCcCHHHHHHHhCC-CHHHHHHHHc
Q 031871 102 DKKLTQSQLAQLINE-KPQVIQEYES 126 (151)
Q Consensus 102 ~~glTQ~eLA~~lgi-s~s~Is~~E~ 126 (151)
...++..++|..+|+ +++++++.-+
T Consensus 48 ~~~~~~~~ia~~~g~~s~~~f~r~Fk 73 (84)
T smart00342 48 DTDLSVTEIALRVGFSSQSYFSRAFK 73 (84)
T ss_pred cCCCCHHHHHHHhCCCChHHHHHHHH
Confidence 337999999999999 9999988754
No 396
>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=71.64 E-value=8.2 Score=23.97 Aligned_cols=29 Identities=21% Similarity=0.152 Sum_probs=22.5
Q ss_pred HHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 97 VQARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 97 k~~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
..+-....++..+||+.+|+|..+|..+-
T Consensus 12 ~~L~~~~~~~~~ela~~l~~S~rti~~~i 40 (59)
T PF08280_consen 12 ELLLKNKWITLKELAKKLNISERTIKNDI 40 (59)
T ss_dssp HHHHHHTSBBHHHHHHHCTS-HHHHHHHH
T ss_pred HHHHcCCCCcHHHHHHHHCCCHHHHHHHH
Confidence 33444677899999999999999998764
No 397
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=71.64 E-value=7.7 Score=28.20 Aligned_cols=33 Identities=12% Similarity=0.081 Sum_probs=26.6
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
...+-.++.-.|+|.+|+|+.+|+|.++|...-
T Consensus 118 ~r~v~~L~~~~g~s~~EIA~~l~is~~tV~~~l 150 (161)
T PRK12528 118 VKRAFLLAQVDGLGYGEIATELGISLATVKRYL 150 (161)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 344555667789999999999999999997753
No 398
>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=71.62 E-value=6.6 Score=28.47 Aligned_cols=32 Identities=22% Similarity=0.255 Sum_probs=25.7
Q ss_pred HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
.+-.++-..|+|.+|+|+.+|+|.++|...-.
T Consensus 117 ~i~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ 148 (162)
T TIGR02983 117 AVVVLRYYEDLSEAQVAEALGISVGTVKSRLS 148 (162)
T ss_pred HHhhhHHHhcCCHHHHHHHhCCCHHHHHHHHH
Confidence 34445557799999999999999999987654
No 399
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=71.59 E-value=6.6 Score=30.02 Aligned_cols=34 Identities=3% Similarity=-0.083 Sum_probs=27.1
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
...+-.++...|+|.+|+|+.+|+|.++|...-.
T Consensus 144 ~r~v~~L~~~eg~s~~EIA~~lgis~~tVk~~l~ 177 (201)
T PRK12545 144 IGRVFMMREFLDFEIDDICTELTLTANHCSVLLY 177 (201)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3444456677899999999999999999987543
No 400
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=71.56 E-value=7 Score=29.25 Aligned_cols=31 Identities=10% Similarity=0.100 Sum_probs=26.0
Q ss_pred HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 96 IVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
+-.++.-.|+|+.|+|+.+|++.++|.....
T Consensus 135 ~~~l~~~~gls~~EIA~~l~i~~~tVks~l~ 165 (182)
T COG1595 135 AFLLRYLEGLSYEEIAEILGISVGTVKSRLH 165 (182)
T ss_pred HhhhHhhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3445677899999999999999999988754
No 401
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=71.29 E-value=22 Score=24.75 Aligned_cols=67 Identities=15% Similarity=0.198 Sum_probs=38.3
Q ss_pred HHHHHHHcCCChhhHHhhhc-CCCccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHH
Q 031871 31 VVNAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQ 109 (151)
Q Consensus 31 ~~~~a~r~g~~v~t~~k~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~e 109 (151)
.-+.|+++|+++.|++-|+. |--.|..... +--++-.+. ....-..|+.+| ..|++.++
T Consensus 3 I~eva~~~gvs~~tLRyYE~~GLl~p~~~~~--~gyR~Ys~~-----------------dl~~l~~I~~~r-~~G~~L~~ 62 (124)
T COG0789 3 IGEVAKLTGVSVRTLRFYERKGLLSPERRDE--GGYRYYTPE-----------------DLELLQIIKTLR-ELGFSLAE 62 (124)
T ss_pred HHHHHHHhCCCHHHHHHHHHcCCCCCcccCC--CCceecCHH-----------------HHHHHHHHHHHH-HcCCCHHH
Confidence 34689999999999999997 3333322110 011111111 122333455555 67888888
Q ss_pred HHHHhCCC
Q 031871 110 LAQLINEK 117 (151)
Q Consensus 110 LA~~lgis 117 (151)
+-+.+...
T Consensus 63 I~~~l~~~ 70 (124)
T COG0789 63 IKELLDLL 70 (124)
T ss_pred HHHHHhcc
Confidence 88877543
No 402
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=71.21 E-value=1.5 Score=26.75 Aligned_cols=42 Identities=19% Similarity=0.198 Sum_probs=28.1
Q ss_pred CcCHHHHHHHhCCCHHHHHHHH---cCCC------CCCHHHHHHHHHHhCC
Q 031871 104 KLTQSQLAQLINEKPQVIQEYE---SGKA------IPNQQILTKLERALGV 145 (151)
Q Consensus 104 glTQ~eLA~~lgis~s~Is~~E---~G~~------~p~~~~l~kLa~~Lgv 145 (151)
.++..|||+.+|++...|-+.. .|.. .++.+.+..|++.||+
T Consensus 3 ~i~V~elAk~l~v~~~~ii~~l~~~~Gi~~~~~~~~ld~e~~~~i~~~~~~ 53 (54)
T PF04760_consen 3 KIRVSELAKELGVPSKEIIKKLFKELGIMVKSINSSLDEEEAELIAEEFGV 53 (54)
T ss_dssp EE-TTHHHHHHSSSHHHHHHHH-HHHTS---SSSS-EETTGGGHHHHHH--
T ss_pred ceEHHHHHHHHCcCHHHHHHHHHHhCCcCcCCCCCcCCHHHHHHHHHHhCc
Confidence 4677899999999987666654 4543 3456778888888875
No 403
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=71.20 E-value=7.2 Score=29.48 Aligned_cols=34 Identities=12% Similarity=0.097 Sum_probs=26.4
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
...+-.++...|+|.+|+|+.+|+|.++|...-.
T Consensus 139 ~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~ 172 (189)
T PRK12530 139 QARVFMMREYLELSSEQICQECDISTSNLHVLLY 172 (189)
T ss_pred HHHHHhHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3344445666799999999999999999977643
No 404
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=71.08 E-value=4.1 Score=32.61 Aligned_cols=32 Identities=9% Similarity=0.094 Sum_probs=25.8
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHH
Q 031871 103 KKLTQSQLAQLINEKPQVIQEYESGKAIPNQQ 134 (151)
Q Consensus 103 ~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~ 134 (151)
..+|..+||+++|+|++||.++-+--..-...
T Consensus 33 ~~~si~~lA~~~~vS~aTv~Rf~kklG~~gf~ 64 (284)
T PRK11302 33 IHSSIATLAKMANVSEPTVNRFCRSLDTKGFP 64 (284)
T ss_pred HhcCHHHHHHHhCCCHHHHHHHHHHcCCCCHH
Confidence 56899999999999999999997754444433
No 405
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=71.04 E-value=6.1 Score=25.22 Aligned_cols=29 Identities=17% Similarity=0.358 Sum_probs=20.3
Q ss_pred HHH-HHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871 96 IVQ-ARNDKKLTQSQLAQLINEKPQVIQEY 124 (151)
Q Consensus 96 Lk~-~R~~~glTQ~eLA~~lgis~s~Is~~ 124 (151)
|++ ++....+|..|||..+++++++|..+
T Consensus 5 i~~~l~~~~~~S~~eLa~~~~~s~~~ve~m 34 (69)
T PF09012_consen 5 IRDYLRERGRVSLAELAREFGISPEAVEAM 34 (69)
T ss_dssp HHHHHHHS-SEEHHHHHHHTT--HHHHHHH
T ss_pred HHHHHHHcCCcCHHHHHHHHCcCHHHHHHH
Confidence 444 56667799999999999999877653
No 406
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=70.96 E-value=7.3 Score=29.23 Aligned_cols=32 Identities=9% Similarity=0.135 Sum_probs=26.1
Q ss_pred HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
..+-.++.-.|+|++|+|+.+|+|..+|...-
T Consensus 144 r~v~~l~~~~g~s~~eIA~~lgis~~tv~~~l 175 (193)
T PRK11923 144 RTALTLREFDGLSYEDIASVMQCPVGTVRSRI 175 (193)
T ss_pred hHHHhhHHhcCCCHHHHHHHHCCCHHHHHHHH
Confidence 34555666789999999999999999987754
No 407
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=70.68 E-value=7.6 Score=29.95 Aligned_cols=30 Identities=13% Similarity=0.088 Sum_probs=25.1
Q ss_pred HHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 97 VQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 97 k~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
-.++...|++.+|+|+.+|+|..+|...-.
T Consensus 147 ~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~ 176 (203)
T PRK09647 147 VVLCDIEGLSYEEIAATLGVKLGTVRSRIH 176 (203)
T ss_pred HHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 345567899999999999999999987654
No 408
>PRK06930 positive control sigma-like factor; Validated
Probab=70.55 E-value=8.1 Score=29.39 Aligned_cols=30 Identities=20% Similarity=0.204 Sum_probs=25.4
Q ss_pred HHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 97 VQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 97 k~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
-.++...|+|..|+|+.+|+|.++|..+..
T Consensus 123 ~~L~~~eg~s~~EIA~~lgiS~~tVk~~l~ 152 (170)
T PRK06930 123 YLMHRGYGLSYSEIADYLNIKKSTVQSMIE 152 (170)
T ss_pred HHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 334567899999999999999999998765
No 409
>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=70.49 E-value=22 Score=24.97 Aligned_cols=19 Identities=21% Similarity=0.337 Sum_probs=17.3
Q ss_pred HHHHHHcCCChhhHHhhhc
Q 031871 32 VNAARRAGADIETVRKSHA 50 (151)
Q Consensus 32 ~~~a~r~g~~v~t~~k~~~ 50 (151)
-+.|++.|+++.|++-|+.
T Consensus 4 ge~a~~~gvs~~tLryYe~ 22 (116)
T cd04769 4 GELAQQTGVTIKAIRLYEE 22 (116)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 4689999999999999997
No 410
>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=70.33 E-value=25 Score=25.56 Aligned_cols=19 Identities=26% Similarity=0.309 Sum_probs=17.2
Q ss_pred HHHHHHcCCChhhHHhhhc
Q 031871 32 VNAARRAGADIETVRKSHA 50 (151)
Q Consensus 32 ~~~a~r~g~~v~t~~k~~~ 50 (151)
-+.|+++|+++.|++-|+.
T Consensus 4 ge~a~~~gvs~~tLRyYE~ 22 (131)
T cd04786 4 GELAKRSGMAASRIRFYEA 22 (131)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 4689999999999999986
No 411
>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=70.08 E-value=23 Score=25.24 Aligned_cols=20 Identities=35% Similarity=0.463 Sum_probs=17.7
Q ss_pred HHHHHHcCCChhhHHhhhcC
Q 031871 32 VNAARRAGADIETVRKSHAG 51 (151)
Q Consensus 32 ~~~a~r~g~~v~t~~k~~~g 51 (151)
-+.|++.|+++.|++-|+.-
T Consensus 4 ~e~a~~~gvs~~tlR~Ye~~ 23 (126)
T cd04785 4 GELARRTGVNVETIRYYESI 23 (126)
T ss_pred HHHHHHHCcCHHHHHHHHHC
Confidence 46899999999999999973
No 412
>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=70.07 E-value=8.3 Score=31.33 Aligned_cols=43 Identities=12% Similarity=0.112 Sum_probs=32.3
Q ss_pred cCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871 102 DKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 148 (151)
Q Consensus 102 ~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~ 148 (151)
..|+|++|+|+.+|+|.++|..+..- ....|.+.-...+++++
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 78999999999999999999998763 23444444455666554
No 413
>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=70.03 E-value=12 Score=22.72 Aligned_cols=21 Identities=24% Similarity=0.224 Sum_probs=19.0
Q ss_pred cCHHHHHHHhCCCHHHHHHHH
Q 031871 105 LTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~E 125 (151)
++..++|+.+|++.++++++-
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l 41 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHL 41 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHH
Confidence 999999999999999987764
No 414
>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=70.02 E-value=13 Score=27.61 Aligned_cols=60 Identities=15% Similarity=0.140 Sum_probs=41.7
Q ss_pred hHHHHHHHHHHHhcCC--cCHHHHHHHhCCCHHHHHHHHcCCCC-C-CHHHHHHHHHHhCCCCC
Q 031871 89 PSELKKAIVQARNDKK--LTQSQLAQLINEKPQVIQEYESGKAI-P-NQQILTKLERALGVKLR 148 (151)
Q Consensus 89 ~~~~~~~Lk~~R~~~g--lTQ~eLA~~lgis~s~Is~~E~G~~~-p-~~~~l~kLa~~Lgv~l~ 148 (151)
...|...-..+|+.-+ .|..++++.+||+...|.+|-+..+. + ....+.--++-.|.++.
T Consensus 29 e~~f~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~IreGRL~~~~~~nl~~~CE~CG~~I~ 92 (137)
T TIGR03826 29 EREFEKVYKFLRKHENRQATVSEIVEETGVSEKLILKFIREGRLQLKHFPNLGYPCERCGTSIR 92 (137)
T ss_pred HHHHHHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCCeeccCCCCCcCcccccCCcCC
Confidence 3456666666788877 99999999999999999999875432 2 22344455555555544
No 415
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=69.87 E-value=8.5 Score=28.81 Aligned_cols=32 Identities=16% Similarity=0.249 Sum_probs=25.8
Q ss_pred HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
..+-.++--.|+|.+|+|+.+|+|.++|...-
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 44445556679999999999999999998764
No 416
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=69.84 E-value=8 Score=31.08 Aligned_cols=30 Identities=10% Similarity=0.164 Sum_probs=25.0
Q ss_pred HHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 97 VQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 97 k~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
-.+|-..|+|++++|+.+|+|.++|.....
T Consensus 221 l~l~~~~~~s~~eIA~~lgis~~tV~~~~~ 250 (268)
T PRK06288 221 LILYYYEDLTLKEIGKVLGVTESRISQLHT 250 (268)
T ss_pred HHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 334556799999999999999999998764
No 417
>PRK09519 recA DNA recombination protein RecA; Reviewed
Probab=69.56 E-value=11 Score=35.68 Aligned_cols=60 Identities=15% Similarity=0.198 Sum_probs=45.7
Q ss_pred CcchHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHH-HHHHc--CCCCCCHHHHHHHHHHhCC
Q 031871 86 DRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVI-QEYES--GKAIPNQQILTKLERALGV 145 (151)
Q Consensus 86 ~~~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~I-s~~E~--G~~~p~~~~l~kLa~~Lgv 145 (151)
..++.++...++.++.+.|+|+.|+|..+|+..... +-|.. +++.++.+.+.++|.+|+-
T Consensus 582 ~~~p~e~~~~v~~~~~~~g~t~~~~~~~~g~a~g~~~~~~~~~~~~~~~sR~r~~~~a~~l~~ 644 (790)
T PRK09519 582 TYLAAEMTDAVLNYLDERGVTAQEAAAMIGVASGDPRGGMKQVLGASRLRRDRVQALADALDD 644 (790)
T ss_pred ccCCHHHHHHHHHHHHhcCCCHHHHHHHhccccCccchhhhcccccccccHHHHHHHHHHhCC
Confidence 344567778888889999999999999999976322 12222 5567899999999999873
No 418
>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=69.37 E-value=19 Score=25.06 Aligned_cols=38 Identities=16% Similarity=0.142 Sum_probs=30.8
Q ss_pred HHHHHHHHHHhcCCcC-HHHHHHHhCCCHHHHHHHHcCC
Q 031871 91 ELKKAIVQARNDKKLT-QSQLAQLINEKPQVIQEYESGK 128 (151)
Q Consensus 91 ~~~~~Lk~~R~~~glT-Q~eLA~~lgis~s~Is~~E~G~ 128 (151)
+++..|..++...++. -++||+++|+|...|..+|...
T Consensus 6 dl~~~l~~Ia~~~~~~~wK~faR~lglse~~Id~I~~~~ 44 (97)
T cd08316 6 DLSKHIPDIADVMTLKDVKKFVRKSGLSEPKIDEIKLDN 44 (97)
T ss_pred cHHHhhHHHHHHcCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence 4566677777777765 5789999999999999999755
No 419
>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=69.33 E-value=5.4 Score=30.64 Aligned_cols=31 Identities=13% Similarity=0.176 Sum_probs=26.3
Q ss_pred HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 96 IVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
--+.|...|.|..|+|+..|++...|.+||-
T Consensus 61 eIQarIRaGas~eeVA~~~G~~~~rV~rfa~ 91 (170)
T PF11268_consen 61 EIQARIRAGASAEEVAEEAGVPVERVRRFAG 91 (170)
T ss_pred HHHHHHHCCCCHHHHHHHhCCCHHHhhhccc
Confidence 3455666799999999999999999999864
No 420
>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=69.28 E-value=5.2 Score=30.16 Aligned_cols=29 Identities=3% Similarity=0.053 Sum_probs=24.5
Q ss_pred HHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 98 QARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 98 ~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
.++...|+|.+|+|+.+|+|.++|...-.
T Consensus 141 ~L~~~~g~s~~EIA~~lgis~~tVk~~l~ 169 (193)
T TIGR02947 141 YLADVEGFAYKEIAEIMGTPIGTVMSRLH 169 (193)
T ss_pred eehhhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34566799999999999999999988654
No 421
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=69.27 E-value=11 Score=25.29 Aligned_cols=20 Identities=10% Similarity=0.144 Sum_probs=18.3
Q ss_pred cCHHHHHHHhCCCHHHHHHH
Q 031871 105 LTQSQLAQLINEKPQVIQEY 124 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~ 124 (151)
.|..+||+.+|+|+++|.+-
T Consensus 20 ~SGe~La~~LgiSRtaVwK~ 39 (79)
T COG1654 20 VSGEKLAEELGISRTAVWKH 39 (79)
T ss_pred ccHHHHHHHHCccHHHHHHH
Confidence 89999999999999998764
No 422
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=69.15 E-value=5.2 Score=30.83 Aligned_cols=22 Identities=18% Similarity=0.209 Sum_probs=20.4
Q ss_pred CcCHHHHHHHhCCCHHHHHHHH
Q 031871 104 KLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 104 glTQ~eLA~~lgis~s~Is~~E 125 (151)
|+|.+|+|+.+|+|+.||..+-
T Consensus 177 g~s~~eIa~~l~iS~~Tv~~~~ 198 (225)
T PRK10046 177 QHTAETVAQALTISRTTARRYL 198 (225)
T ss_pred CcCHHHHHHHhCccHHHHHHHH
Confidence 7999999999999999998874
No 423
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=68.98 E-value=13 Score=29.91 Aligned_cols=36 Identities=22% Similarity=0.249 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHh--cCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 90 SELKKAIVQARN--DKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 90 ~~~~~~Lk~~R~--~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
..--..|.++-+ ...+|-.++|+.+|+|+.|+.+|.
T Consensus 157 ~~Tl~~i~~~~~~~~~~~Taeela~~~giSRvTaRRYL 194 (224)
T COG4565 157 ELTLQKVREALKEPDQELTAEELAQALGISRVTARRYL 194 (224)
T ss_pred HHHHHHHHHHHhCcCCccCHHHHHHHhCccHHHHHHHH
Confidence 333444555544 578999999999999999999984
No 424
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=68.82 E-value=8.5 Score=28.49 Aligned_cols=29 Identities=10% Similarity=0.087 Sum_probs=23.8
Q ss_pred HHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 98 QARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 98 ~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
.++-..|+|.+|+|+.+|+|..+|.....
T Consensus 139 ~l~~~~g~s~~eIA~~lgis~~tV~~~l~ 167 (179)
T PRK12514 139 RRAYLEGLSYKELAERHDVPLNTMRTWLR 167 (179)
T ss_pred HHHHHcCCCHHHHHHHHCCChHHHHHHHH
Confidence 34456899999999999999999977543
No 425
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=68.80 E-value=8.8 Score=29.43 Aligned_cols=29 Identities=28% Similarity=0.229 Sum_probs=24.1
Q ss_pred HHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 97 VQARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 97 k~~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
-.++...|+|.+|+|+.+|+|.++|....
T Consensus 162 l~l~~~~g~s~~EIA~~lgis~~tV~~~l 190 (206)
T PRK12526 162 VKGVYFQELSQEQLAQQLNVPLGTVKSRL 190 (206)
T ss_pred HHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 34456679999999999999999997654
No 426
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=68.70 E-value=12 Score=28.10 Aligned_cols=36 Identities=14% Similarity=0.240 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHhcCC-cCHHHHHHHhCCCHHHHHHHH
Q 031871 90 SELKKAIVQARNDKK-LTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 90 ~~~~~~Lk~~R~~~g-lTQ~eLA~~lgis~s~Is~~E 125 (151)
++..+.|..+-...| ....++|+.++|++++++...
T Consensus 9 edYL~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml 45 (154)
T COG1321 9 EDYLETIYELLEEKGFARTKDIAERLKVSPPSVTEML 45 (154)
T ss_pred HHHHHHHHHHHhccCcccHHHHHHHhCCCcHHHHHHH
Confidence 455566665544444 789999999999999997663
No 427
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=68.64 E-value=22 Score=26.28 Aligned_cols=21 Identities=29% Similarity=0.376 Sum_probs=18.5
Q ss_pred HHHHHHHHcCCChhhHHhhhc
Q 031871 30 KVVNAARRAGADIETVRKSHA 50 (151)
Q Consensus 30 ~~~~~a~r~g~~v~t~~k~~~ 50 (151)
+.-+.|+++|+++.|+|-|+.
T Consensus 9 ~IgevAk~~Gvs~~TLRyYE~ 29 (144)
T PRK13752 9 TIGVFAKAAGVNVETIRFYQR 29 (144)
T ss_pred cHHHHHHHHCcCHHHHHHHHH
Confidence 345789999999999999996
No 428
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=68.62 E-value=8.9 Score=28.74 Aligned_cols=31 Identities=3% Similarity=0.105 Sum_probs=25.2
Q ss_pred HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
.+-.++...|+|..|+|+.+|+|.++|...-
T Consensus 138 ~vl~l~~~~~~s~~eIA~~lgis~~tV~~~l 168 (189)
T PRK12515 138 EIIDLVYYHEKSVEEVGEIVGIPESTVKTRM 168 (189)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence 3444566789999999999999999997654
No 429
>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=68.51 E-value=8 Score=26.06 Aligned_cols=29 Identities=10% Similarity=0.157 Sum_probs=24.3
Q ss_pred HHHHHhcCCcCHHHHHHHhC-CCHHHHHHH
Q 031871 96 IVQARNDKKLTQSQLAQLIN-EKPQVIQEY 124 (151)
Q Consensus 96 Lk~~R~~~glTQ~eLA~~lg-is~s~Is~~ 124 (151)
+.-++...|+|..++|+.+| .+.++|+.-
T Consensus 36 ~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a 65 (90)
T cd06571 36 MYLARELTGLSLPEIGRAFGGRDHSTVLHA 65 (90)
T ss_pred HHHHHHHhCCCHHHHHHHhCCCCHhHHHHH
Confidence 34567778999999999999 999998764
No 430
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=68.47 E-value=4.9 Score=32.20 Aligned_cols=28 Identities=14% Similarity=0.217 Sum_probs=23.7
Q ss_pred hcCCcCHHHHHHHhCCCHHHHHHHHcCC
Q 031871 101 NDKKLTQSQLAQLINEKPQVIQEYESGK 128 (151)
Q Consensus 101 ~~~glTQ~eLA~~lgis~s~Is~~E~G~ 128 (151)
.-..+|..+||+++|+|++||.++-+--
T Consensus 27 ~v~~~si~elA~~~~vS~aTv~Rf~kkl 54 (278)
T PRK11557 27 TARHLSSQQLANEAGVSQSSVVKFAQKL 54 (278)
T ss_pred HHHhcCHHHHHHHhCCCHHHHHHHHHHc
Confidence 3456999999999999999999997643
No 431
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=68.47 E-value=8.7 Score=34.41 Aligned_cols=26 Identities=19% Similarity=0.229 Sum_probs=23.5
Q ss_pred cCCcCHHHHHHHhCCCHHHHHHHHcC
Q 031871 102 DKKLTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 102 ~~glTQ~eLA~~lgis~s~Is~~E~G 127 (151)
..++|+.++|+.+|||+..|+++|+.
T Consensus 465 ~e~~TL~EIa~~lGVSrERVRQIe~k 490 (509)
T PRK05901 465 GQPKTLDEIGQVYGVTRERIRQIESK 490 (509)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 35799999999999999999999973
No 432
>PRK08359 transcription factor; Validated
Probab=68.44 E-value=1.8 Score=33.46 Aligned_cols=29 Identities=10% Similarity=0.234 Sum_probs=24.6
Q ss_pred HHHHHHHHcCCChhhHHhhhcCCCccCCC
Q 031871 30 KVVNAARRAGADIETVRKSHAGTNKAASS 58 (151)
Q Consensus 30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~~~ 58 (151)
++-++|...|++.+|+++||.|...|..+
T Consensus 100 SQeeLA~~lgvs~stI~~iE~G~~~Ps~~ 128 (176)
T PRK08359 100 SYEELSHEVGLSVNDLRRIAHGEYEPTIK 128 (176)
T ss_pred CHHHHHHHhCCCHHHHHHHHCCCcCCCHH
Confidence 45678899999999999999999876544
No 433
>PRK14845 translation initiation factor IF-2; Provisional
Probab=68.39 E-value=6.8 Score=38.08 Aligned_cols=48 Identities=19% Similarity=0.326 Sum_probs=41.3
Q ss_pred HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 031871 92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALG 144 (151)
Q Consensus 92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lg 144 (151)
+...|+++|...++||.|+.. .+++++.||+ ...|+.+.+..+..+|.
T Consensus 323 i~~el~~lr~~~~lt~~e~~~----~~~~Y~~~e~-~~~~s~~~l~~~l~~~~ 370 (1049)
T PRK14845 323 INEELKRLRLLFGFTRNELSS----NIPFYSKYES-EEAPSYEILMEILNSIE 370 (1049)
T ss_pred cHHHHHHHHHhcCcchhhccc----cchhhhhhhc-ccCCCHHHHHHHHHHHH
Confidence 455688899999999999876 7899999999 88899999988877765
No 434
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=68.35 E-value=8.9 Score=28.38 Aligned_cols=29 Identities=3% Similarity=0.108 Sum_probs=24.1
Q ss_pred HHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 98 QARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 98 ~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
.++-..|++.+++|+.+|+|.++|.....
T Consensus 146 ~l~~~~~~s~~eIA~~lgis~~~v~~~l~ 174 (187)
T PRK09641 146 VLKYIEDLSLKEISEILDLPVGTVKTRIH 174 (187)
T ss_pred hhHHhhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34456799999999999999999987644
No 435
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=68.28 E-value=9.4 Score=28.68 Aligned_cols=31 Identities=10% Similarity=0.005 Sum_probs=25.3
Q ss_pred HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
.+-.++.-.|+|.+|+|+.+|+|.++|...-
T Consensus 138 ~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l 168 (191)
T PRK12520 138 RVFMMREWLELETEEICQELQITATNAWVLL 168 (191)
T ss_pred HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 3444566679999999999999999998754
No 436
>PRK09480 slmA division inhibitor protein; Provisional
Probab=68.19 E-value=5.5 Score=29.55 Aligned_cols=28 Identities=18% Similarity=0.196 Sum_probs=25.2
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHcCCCC
Q 031871 103 KKLTQSQLAQLINEKPQVIQEYESGKAI 130 (151)
Q Consensus 103 ~glTQ~eLA~~lgis~s~Is~~E~G~~~ 130 (151)
.+.|..++|+++|||++++..+-.++..
T Consensus 29 ~~~ti~~Ia~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 29 ERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred CccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence 6899999999999999999999887754
No 437
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=68.17 E-value=9.6 Score=28.06 Aligned_cols=30 Identities=13% Similarity=0.134 Sum_probs=24.7
Q ss_pred HHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 96 IVQARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
+-.++--.|+|.+|+|+.+|+|.++|...-
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 334556789999999999999999998754
No 438
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=68.10 E-value=5 Score=31.13 Aligned_cols=21 Identities=10% Similarity=0.025 Sum_probs=19.1
Q ss_pred CcCHHHHHHHhCCCHHHHHHH
Q 031871 104 KLTQSQLAQLINEKPQVIQEY 124 (151)
Q Consensus 104 glTQ~eLA~~lgis~s~Is~~ 124 (151)
.+||.+||..+|+++.+|++.
T Consensus 169 ~~t~~~lA~~lG~sretvsR~ 189 (226)
T PRK10402 169 HEKHTQAAEYLGVSYRHLLYV 189 (226)
T ss_pred cchHHHHHHHHCCcHHHHHHH
Confidence 369999999999999999985
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=68.08 E-value=9.3 Score=26.91 Aligned_cols=47 Identities=19% Similarity=0.309 Sum_probs=28.1
Q ss_pred HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 031871 94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALG 144 (151)
Q Consensus 94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lg 144 (151)
..+-.+--.-.+|..|+|+.+|||++.|+..-+- ....+..+...||
T Consensus 23 ~~~l~lyy~eDlSlsEIAe~~~iSRqaV~d~ikr----~~~~L~~yE~kL~ 69 (101)
T PF04297_consen 23 REILELYYEEDLSLSEIAEELGISRQAVYDSIKR----AEKKLEEYEEKLG 69 (101)
T ss_dssp HHHHHHHCTS---HHHHHHHCTS-HHHHHHHHHH----HHHHHHHHHHHH-
T ss_pred HHHHHHHHccCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHHHHh
Confidence 3344455667899999999999999999987652 2244444444444
No 440
>PRK09483 response regulator; Provisional
Probab=67.96 E-value=12 Score=27.70 Aligned_cols=43 Identities=23% Similarity=0.352 Sum_probs=30.3
Q ss_pred cCCcCHHHHHHHhCCCHHHHHHHHcC---C-CCCCHHHHHHHHHHhC
Q 031871 102 DKKLTQSQLAQLINEKPQVIQEYESG---K-AIPNQQILTKLERALG 144 (151)
Q Consensus 102 ~~glTQ~eLA~~lgis~s~Is~~E~G---~-~~p~~~~l~kLa~~Lg 144 (151)
..|+|.+++|+.+++|.+||..+-+. + ..-+...+..+|.-.|
T Consensus 161 ~~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~v~~~~~l~~~a~~~~ 207 (217)
T PRK09483 161 TKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDVELTHLAIRHG 207 (217)
T ss_pred HCCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHcC
Confidence 57999999999999999999887542 1 2234555555555444
No 441
>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=67.88 E-value=13 Score=23.73 Aligned_cols=35 Identities=17% Similarity=0.200 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHhcCCc--CHHHHHHHhCCC-HHHHHHH
Q 031871 90 SELKKAIVQARNDKKL--TQSQLAQLINEK-PQVIQEY 124 (151)
Q Consensus 90 ~~~~~~Lk~~R~~~gl--TQ~eLA~~lgis-~s~Is~~ 124 (151)
..+-..|++...+.|+ |..|+|+.+|++ +++|...
T Consensus 9 ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~ 46 (65)
T PF01726_consen 9 KEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRH 46 (65)
T ss_dssp HHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHH
Confidence 4566677777777776 678999999997 8877765
No 442
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=67.76 E-value=25 Score=25.65 Aligned_cols=20 Identities=15% Similarity=0.200 Sum_probs=17.8
Q ss_pred HHHHHHcCCChhhHHhhhcC
Q 031871 32 VNAARRAGADIETVRKSHAG 51 (151)
Q Consensus 32 ~~~a~r~g~~v~t~~k~~~g 51 (151)
-+.|+++|+++.|+|-||.-
T Consensus 4 ge~a~~~gvs~~tlRyYE~~ 23 (135)
T PRK10227 4 SDVAKITGLTSKAIRFYEEK 23 (135)
T ss_pred HHHHHHHCcCHHHHHHHHHC
Confidence 46899999999999999974
No 443
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=67.73 E-value=9.7 Score=28.34 Aligned_cols=33 Identities=15% Similarity=0.211 Sum_probs=26.3
Q ss_pred HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
..+-.++.-.|+|.+|+|+.+|+|.++|...-.
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 345555677899999999999999999877543
No 444
>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=67.68 E-value=22 Score=24.83 Aligned_cols=20 Identities=20% Similarity=0.295 Sum_probs=17.7
Q ss_pred HHHHHHcCCChhhHHhhhcC
Q 031871 32 VNAARRAGADIETVRKSHAG 51 (151)
Q Consensus 32 ~~~a~r~g~~v~t~~k~~~g 51 (151)
-+.|++.|+++.|++-|+.-
T Consensus 4 ~eva~~~gvs~~tlR~Ye~~ 23 (112)
T cd01282 4 GELAARTGVSVRSLRYYEEQ 23 (112)
T ss_pred HHHHHHHCCCHHHHHHHHHC
Confidence 46899999999999999973
No 445
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=67.66 E-value=9.3 Score=28.29 Aligned_cols=31 Identities=16% Similarity=0.173 Sum_probs=25.7
Q ss_pred HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
.+-.++.-.|+|.+|+|+.+|+|.++|...-
T Consensus 126 ~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l 156 (172)
T PRK09651 126 EAFLLSQLDGLTYSEIAHKLGVSVSSVKKYV 156 (172)
T ss_pred HHhhhhhccCCCHHHHHHHhCCCHHHHHHHH
Confidence 4444667789999999999999999998754
No 446
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=67.48 E-value=15 Score=22.53 Aligned_cols=31 Identities=13% Similarity=0.324 Sum_probs=20.6
Q ss_pred HHHHHHHHh--cCCcCHHHHHHHhCCCHHHHHH
Q 031871 93 KKAIVQARN--DKKLTQSQLAQLINEKPQVIQE 123 (151)
Q Consensus 93 ~~~Lk~~R~--~~glTQ~eLA~~lgis~s~Is~ 123 (151)
-..|+.+.. ...+|-.+||+.+|+++..|.+
T Consensus 15 ~r~L~~l~~~G~~~vSS~~La~~~gi~~~qVRK 47 (50)
T PF06971_consen 15 LRYLEQLKEEGVERVSSQELAEALGITPAQVRK 47 (50)
T ss_dssp HHHHHHHHHTT-SEE-HHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHHHcCCeeECHHHHHHHHCCCHHHhcc
Confidence 344444443 3467999999999999998865
No 447
>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional
Probab=67.37 E-value=7.9 Score=33.04 Aligned_cols=33 Identities=9% Similarity=0.135 Sum_probs=27.9
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
...|..+..+.+..+.+.|+.+|||++|+.+-.
T Consensus 419 ~~~i~~al~~~~gn~~~aA~~LGisr~tL~rkl 451 (457)
T PRK11361 419 KRIIMEVLEQQEGNRTRTALMLGISRRALMYKL 451 (457)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHH
Confidence 446777778888899999999999999998754
No 448
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=67.26 E-value=11 Score=29.51 Aligned_cols=25 Identities=20% Similarity=0.270 Sum_probs=22.4
Q ss_pred cCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 102 DKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 102 ~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
..|+|++++|+.+|+|.++|.+...
T Consensus 193 ~e~~S~~EIA~~lgis~~tV~~~~~ 217 (233)
T PRK05803 193 GKEKTQREIAKALGISRSYVSRIEK 217 (233)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 4689999999999999999988864
No 449
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=67.22 E-value=9 Score=28.95 Aligned_cols=29 Identities=17% Similarity=0.249 Sum_probs=23.8
Q ss_pred HHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871 96 IVQARNDKKLTQSQLAQLINEKPQVIQEY 124 (151)
Q Consensus 96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~ 124 (151)
+-.++-..|+|.+|+|+.+|+|.++|...
T Consensus 149 v~~l~~~eg~s~~EIA~~lgis~~tVk~r 177 (194)
T PRK12531 149 VLQAVYLEELPHQQVAEMFDIPLGTVKSR 177 (194)
T ss_pred HHHHHHHcCCCHHHHHHHhCcCHHHHHHH
Confidence 44455668999999999999999999654
No 450
>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional
Probab=67.05 E-value=8.6 Score=32.00 Aligned_cols=34 Identities=15% Similarity=0.215 Sum_probs=28.5
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
...|..+..+.+..+.+.|+.+|||++|+.+..+
T Consensus 288 r~~I~~aL~~~~gn~~~aA~~LGIsR~tLyrklk 321 (326)
T PRK11608 288 KELLQRSLQQAKFNQKRAAELLGLTYHQLRALLK 321 (326)
T ss_pred HHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence 3447777778888999999999999999988754
No 451
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=66.99 E-value=10 Score=28.62 Aligned_cols=31 Identities=6% Similarity=-0.022 Sum_probs=25.3
Q ss_pred HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 96 IVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
+-.++...|+|.+|+|+.+|+|.++|...-.
T Consensus 119 v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~ 149 (182)
T PRK12540 119 ALILVGASGFSYEDAAAICGCAVGTIKSRVN 149 (182)
T ss_pred HhhHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3344567899999999999999999987644
No 452
>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=66.94 E-value=10 Score=28.66 Aligned_cols=31 Identities=6% Similarity=0.029 Sum_probs=25.1
Q ss_pred HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
.+-.++...|+|.+|+|+.+|+|.++|...-
T Consensus 138 ~v~~l~~~~g~s~~EIA~~lgis~~tvk~rl 168 (188)
T TIGR02943 138 RVFMMREVLGFESDEICQELEISTSNCHVLL 168 (188)
T ss_pred HHHHHHHHhCCCHHHHHHHhCCCHHHHHHHH
Confidence 3444566679999999999999999997654
No 453
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=66.91 E-value=10 Score=30.27 Aligned_cols=26 Identities=8% Similarity=0.230 Sum_probs=22.3
Q ss_pred HhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 100 RNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 100 R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
.....+|..|||+.+|++++++.++-
T Consensus 24 ~~~~~l~l~eia~~lgl~kstv~Rll 49 (257)
T PRK15090 24 GEEREIGITELSQRVMMSKSTVYRFL 49 (257)
T ss_pred hcCCCCCHHHHHHHHCcCHHHHHHHH
Confidence 34457999999999999999999873
No 454
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=66.90 E-value=10 Score=28.51 Aligned_cols=33 Identities=9% Similarity=0.030 Sum_probs=25.9
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
...+-.++.-.|++..|+|+.+|+|.++|...-
T Consensus 111 ~r~i~~l~~~~g~~~~EIA~~lgis~~tV~~~l 143 (181)
T PRK09637 111 YAEALRLTELEGLSQKEIAEKLGLSLSGAKSRV 143 (181)
T ss_pred HHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHH
Confidence 334444566789999999999999999996654
No 455
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=66.67 E-value=5.2 Score=30.42 Aligned_cols=20 Identities=15% Similarity=0.200 Sum_probs=18.6
Q ss_pred cCHHHHHHHhCCCHHHHHHH
Q 031871 105 LTQSQLAQLINEKPQVIQEY 124 (151)
Q Consensus 105 lTQ~eLA~~lgis~s~Is~~ 124 (151)
+||++||+.+|+|.+||++.
T Consensus 76 ~t~~~ia~~l~iS~~Tv~r~ 95 (165)
T PF05732_consen 76 ATQKEIAEKLGISKPTVSRA 95 (165)
T ss_pred eeHHHHHHHhCCCHHHHHHH
Confidence 69999999999999999875
No 456
>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=66.54 E-value=28 Score=29.41 Aligned_cols=39 Identities=5% Similarity=0.135 Sum_probs=29.1
Q ss_pred hcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH
Q 031871 101 NDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKL 139 (151)
Q Consensus 101 ~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kL 139 (151)
.+.|+++.++|+.+|+++++|+++.+=-..++.+.+..|
T Consensus 174 ~~~G~~~~~ia~~Lg~~ks~vSr~lsl~~~lP~~li~~i 212 (325)
T TIGR03454 174 EDRGFDRDTIMAALSVDKTELSRMISVARRIPEELIEAI 212 (325)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHhCCHHHHHHh
Confidence 468999999999999999999999773222334444444
No 457
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=66.52 E-value=6.9 Score=29.70 Aligned_cols=30 Identities=13% Similarity=0.171 Sum_probs=23.6
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhC-CCHHHHHH
Q 031871 93 KKAIVQARNDKKLTQSQLAQLIN-EKPQVIQE 123 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lg-is~s~Is~ 123 (151)
-+.|+++- ..|+|-.|+|+.|| +|++.|..
T Consensus 8 ~~~L~~lw-~~G~SasqIA~~lg~vsRnAViG 38 (162)
T PF07750_consen 8 VERLRKLW-AEGLSASQIARQLGGVSRNAVIG 38 (162)
T ss_pred HHHHHHHH-HcCCCHHHHHHHhCCcchhhhhh
Confidence 34566665 56999999999999 99987654
No 458
>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=66.47 E-value=30 Score=24.63 Aligned_cols=20 Identities=25% Similarity=0.411 Sum_probs=17.8
Q ss_pred HHHHHHcCCChhhHHhhhcC
Q 031871 32 VNAARRAGADIETVRKSHAG 51 (151)
Q Consensus 32 ~~~a~r~g~~v~t~~k~~~g 51 (151)
-+.|++.|+++.|++-|+.-
T Consensus 4 gevA~~~gvs~~tLRyYe~~ 23 (127)
T cd04784 4 GELAKKTGCSVETIRYYEKE 23 (127)
T ss_pred HHHHHHHCcCHHHHHHHHHC
Confidence 46899999999999999973
No 459
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=66.40 E-value=12 Score=26.85 Aligned_cols=26 Identities=15% Similarity=0.238 Sum_probs=21.6
Q ss_pred HHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871 99 ARNDKKLTQSQLAQLINEKPQVIQEY 124 (151)
Q Consensus 99 ~R~~~glTQ~eLA~~lgis~s~Is~~ 124 (151)
+.....++..+||+.+|+++++|++-
T Consensus 25 L~~~~~~~v~ela~~l~lsqstvS~H 50 (117)
T PRK10141 25 LRESGELCVCDLCTALDQSQPKISRH 50 (117)
T ss_pred HHHcCCcCHHHHHHHHCcCHHHHHHH
Confidence 33445689999999999999999975
No 460
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=66.38 E-value=11 Score=29.90 Aligned_cols=33 Identities=18% Similarity=0.301 Sum_probs=26.7
Q ss_pred HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
..+-.+|-..|+|.+|+|+.+|+|..+|.....
T Consensus 207 r~vl~l~~~~~~s~~EIA~~lgis~~tV~~~~~ 239 (251)
T PRK07670 207 QLVISLFYKEELTLTEIGQVLNLSTSRISQIHS 239 (251)
T ss_pred HHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 334445667899999999999999999988764
No 461
>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=66.30 E-value=12 Score=29.24 Aligned_cols=24 Identities=17% Similarity=0.349 Sum_probs=21.8
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 103 KKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 103 ~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
.|+|.+|+|+.+|+|+++|..+.+
T Consensus 193 e~~S~~EIAe~lgis~~tV~~~~~ 216 (227)
T TIGR02846 193 RRKTQREIAKILGISRSYVSRIEK 216 (227)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHH
Confidence 789999999999999999988754
No 462
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=66.25 E-value=5.4 Score=30.03 Aligned_cols=27 Identities=15% Similarity=0.224 Sum_probs=22.7
Q ss_pred HHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 99 ARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 99 ~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
++.-.|+|..|+|+.+|+|.++|....
T Consensus 150 l~~~~g~s~~EIA~~lgis~~tV~~~l 176 (194)
T PRK12513 150 LREHGDLELEEIAELTGVPEETVKSRL 176 (194)
T ss_pred eehccCCCHHHHHHHHCCCHHHHHHHH
Confidence 344579999999999999999997654
No 463
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=66.23 E-value=10 Score=28.84 Aligned_cols=34 Identities=3% Similarity=0.068 Sum_probs=26.8
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
...+-.++...|+|..|+|+.+|+|..+|...-.
T Consensus 118 ~r~v~~L~~~~g~s~~EIA~~LgiS~~tVk~~l~ 151 (188)
T PRK12546 118 QREALILVGASGFSYEEAAEMCGVAVGTVKSRAN 151 (188)
T ss_pred HhHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3344456667899999999999999999987643
No 464
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=66.10 E-value=16 Score=22.01 Aligned_cols=27 Identities=4% Similarity=0.103 Sum_probs=23.0
Q ss_pred HhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 100 RNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 100 R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
....|.+..++|..+++|..||.....
T Consensus 15 l~~~G~s~~eia~~l~is~~tV~~h~~ 41 (65)
T COG2771 15 LVAQGKSNKEIARILGISEETVKTHLR 41 (65)
T ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 445689999999999999999987654
No 465
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=66.08 E-value=9.9 Score=28.13 Aligned_cols=29 Identities=3% Similarity=0.117 Sum_probs=24.4
Q ss_pred HHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 98 QARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 98 ~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
.++...|+|.+|+|+.+|+|..+|.....
T Consensus 146 ~l~~~~g~s~~eIA~~lgis~~~v~~~l~ 174 (187)
T TIGR02948 146 VLKYMEDLSLKEISEILDLPVGTVKTRIH 174 (187)
T ss_pred hhHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 44556799999999999999999987653
No 466
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=66.01 E-value=9.5 Score=29.85 Aligned_cols=31 Identities=6% Similarity=0.134 Sum_probs=24.9
Q ss_pred HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 96 IVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
+-.++...|+|.+|+|+.+|+|.++|...-.
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 3344556799999999999999999977644
No 467
>PRK10365 transcriptional regulatory protein ZraR; Provisional
Probab=66.00 E-value=8.8 Score=32.53 Aligned_cols=33 Identities=12% Similarity=0.104 Sum_probs=27.7
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
...|.+...+.+..+.+.|+.+|||++|+.+--
T Consensus 407 ~~~i~~~l~~~~gn~~~aa~~Lgisr~tl~rk~ 439 (441)
T PRK10365 407 KEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439 (441)
T ss_pred HHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHh
Confidence 345777778888899999999999999998743
No 468
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=65.97 E-value=11 Score=28.07 Aligned_cols=28 Identities=14% Similarity=0.004 Sum_probs=24.1
Q ss_pred HHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 98 QARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 98 ~~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
.++...|+|.+|+|+.+|+|.++|...-
T Consensus 139 ~l~~~~g~s~~EIA~~l~is~~tV~~~l 166 (181)
T PRK12536 139 VHVKLEGLSVAETAQLTGLSESAVKVGI 166 (181)
T ss_pred HHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 4456789999999999999999998764
No 469
>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=65.83 E-value=7.9 Score=26.27 Aligned_cols=47 Identities=13% Similarity=0.159 Sum_probs=27.7
Q ss_pred HHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHh
Q 031871 97 VQARNDKKLTQSQLAQLINEKPQVIQEYESGK-AIPNQQILTKLERAL 143 (151)
Q Consensus 97 k~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~-~~p~~~~l~kLa~~L 143 (151)
.....+.+.|..+.|...|||.|||.+=...+ ..++.+.....-.+|
T Consensus 12 ~~yIi~~~aTVR~~Ak~FGvSKSTVHkDvteRL~~in~~La~eV~~vL 59 (82)
T PF12116_consen 12 ANYIIETKATVRQAAKVFGVSKSTVHKDVTERLPKINPELAREVRKVL 59 (82)
T ss_dssp HHHHHHH---HHHHHHHHTS-HHHHHHHHTTHHHHH-HHHHHHHHHHH
T ss_pred HHHHHHcccHHHHHHHHHCCcHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence 33444557899999999999999999876633 223455555544444
No 470
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=65.82 E-value=11 Score=28.02 Aligned_cols=30 Identities=10% Similarity=0.037 Sum_probs=24.3
Q ss_pred HHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 96 IVQARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
+-.++-..|+|..|+|+.+|+|..+|...-
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 471
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 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 []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=65.69 E-value=7.8 Score=25.57 Aligned_cols=46 Identities=17% Similarity=0.165 Sum_probs=29.8
Q ss_pred HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 031871 94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 147 (151)
Q Consensus 94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l 147 (151)
.-+..+-.....|..+||+.+++|.+|+.+.-+ .+.+..+.+|+.+
T Consensus 20 ~ll~~ll~~~~~s~~~la~~~~iS~sti~~~i~--------~l~~~l~~~~l~i 65 (87)
T PF05043_consen 20 QLLKLLLNNEYVSIEDLAEELFISRSTIYRDIK--------KLNKYLKKYGLKI 65 (87)
T ss_dssp HHHHHHHH-SEEEHHHHHHHHT--HHHHHHHHH--------HHHHHHHCCT-EE
T ss_pred HHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHH--------HHHHHHHHcCeEE
Confidence 334555678899999999999999999998643 3444444555554
No 472
>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=65.63 E-value=9.7 Score=28.86 Aligned_cols=92 Identities=16% Similarity=0.237 Sum_probs=24.4
Q ss_pred HHHHHHHHcCCChhhHHhhhcCCCccCCCCcccccccccccchhhhHHHHHhhccC--Cc-chHHHHHHHHHHHh----c
Q 031871 30 KVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTD--DR-VPSELKKAIVQARN----D 102 (151)
Q Consensus 30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~--~~-~~~~~~~~Lk~~R~----~ 102 (151)
..-+.|...|+.++|+.+--.|+--....... . +...|+.-.... .. ....+-..|+++-. .
T Consensus 51 t~~~iA~~lgl~~STVSRav~~Ky~~t~~Gi~----p-------lk~fF~~~~~~~~~~~~S~~~ik~~i~~lI~~Ed~~ 119 (160)
T PF04552_consen 51 TMKDIADELGLHESTVSRAVKNKYIQTPRGIF----P-------LKDFFSRSVSSGSGEEFSSEAIKARIKELIEEEDKK 119 (160)
T ss_dssp ---------------------------------------------S-----SS--SS-SS---TTH-HHHHHHHTTS-TT
T ss_pred CHHHHHHHhCCCHhHHHHHHcCceeecCCeee----e-------HHHhccccccCCCCcccHHHHHHHHHHHHHHhcCCC
Confidence 44557889999999999877765421111000 0 000011100000 00 12334556666644 3
Q ss_pred CCcCHHHHHHHh-----CCCHHHHHHHHcCCCCCC
Q 031871 103 KKLTQSQLAQLI-----NEKPQVIQEYESGKAIPN 132 (151)
Q Consensus 103 ~glTQ~eLA~~l-----gis~s~Is~~E~G~~~p~ 132 (151)
+-+|-.+|++.+ .|++.||.+|=..-..|+
T Consensus 120 ~PlSD~~i~~~L~~~gi~isRRTVaKYR~~L~Ip~ 154 (160)
T PF04552_consen 120 KPLSDQEIAELLKEEGIKISRRTVAKYREELGIPS 154 (160)
T ss_dssp S---HHHHHHHHTTTTS---HHHHHHHHHHHT-S-
T ss_pred CCCCHHHHHHHHHHcCCCccHHHHHHHHHHcCCCC
Confidence 679999999999 789999999865444443
No 473
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=65.38 E-value=32 Score=26.20 Aligned_cols=51 Identities=20% Similarity=0.234 Sum_probs=37.7
Q ss_pred chHHHHHHHHHHHhcC--CcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHH
Q 031871 88 VPSELKKAIVQARNDK--KLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERA 142 (151)
Q Consensus 88 ~~~~~~~~Lk~~R~~~--glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~ 142 (151)
+..+--..|++||.+- .||...||++.|||+-.|+-+- .++.+....+...
T Consensus 86 Lt~e~i~Eir~LR~~DP~~wTr~~LAkkF~~S~~fV~~v~----~~~~e~~~~~~~~ 138 (164)
T PF12824_consen 86 LTPEDIQEIRRLRAEDPEKWTRKKLAKKFNCSPLFVSMVA----PAPKEKKKEMEAR 138 (164)
T ss_pred CCHHHHHHHHHHHHcCchHhhHHHHHHHhCCCHHHHHHhc----CCCHHHHHHHHHH
Confidence 4566677899999874 7999999999999999999874 2344444444433
No 474
>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=65.23 E-value=9.8 Score=28.23 Aligned_cols=29 Identities=10% Similarity=0.193 Sum_probs=24.0
Q ss_pred HHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 97 VQARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 97 k~~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
-.++...|+|..|+|+.+|++..+|...-
T Consensus 147 ~~l~~~~~~s~~EIA~~lgis~~tv~~~l 175 (190)
T TIGR02939 147 ITLRELEGLSYEDIARIMDCPVGTVRSRI 175 (190)
T ss_pred hhhhhhcCCCHHHHHHHHCcCHHHHHHHH
Confidence 33555689999999999999999997754
No 475
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=65.21 E-value=11 Score=31.97 Aligned_cols=25 Identities=12% Similarity=0.235 Sum_probs=22.7
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHcC
Q 031871 103 KKLTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 103 ~glTQ~eLA~~lgis~s~Is~~E~G 127 (151)
.++|+.++|+.+|+|+..|+++|..
T Consensus 324 ~~~tl~EIa~~lgvs~erVrQi~~~ 348 (367)
T PRK09210 324 RTRTLEEVGKVFGVTRERIRQIEAK 348 (367)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHH
Confidence 4589999999999999999999873
No 476
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=65.10 E-value=11 Score=28.53 Aligned_cols=29 Identities=3% Similarity=0.029 Sum_probs=24.3
Q ss_pred HHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 98 QARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 98 ~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
.++...|++.+|+|+.+|+|.++|...-.
T Consensus 138 ~l~~~~g~s~~EIA~~lgis~~tV~~~l~ 166 (188)
T PRK12517 138 LLQVIGGFSGEEIAEILDLNKNTVMTRLF 166 (188)
T ss_pred HHHHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 35666799999999999999999987643
No 477
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=65.09 E-value=11 Score=28.54 Aligned_cols=31 Identities=10% Similarity=0.158 Sum_probs=25.6
Q ss_pred HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871 94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEY 124 (151)
Q Consensus 94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~ 124 (151)
..+-.++...|+|.+|+|+.+|+|.++|..-
T Consensus 140 r~i~~l~~~~g~s~~EIA~~lg~s~~tV~~r 170 (192)
T PRK09643 140 RAALVAVDMQGYSVADAARMLGVAEGTVKSR 170 (192)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHH
Confidence 4455667778999999999999999998654
No 478
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=65.00 E-value=11 Score=27.70 Aligned_cols=30 Identities=3% Similarity=0.068 Sum_probs=24.3
Q ss_pred HHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 96 IVQARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
+-.++-..|+|.+|+|+.+|+|..+|...-
T Consensus 127 i~~l~~~~~~s~~EIA~~lgis~~tV~~~l 156 (173)
T PRK12522 127 VLVLYYYEQYSYKEMSEILNIPIGTVKYRL 156 (173)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 333556689999999999999999987753
No 479
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=64.94 E-value=11 Score=28.24 Aligned_cols=29 Identities=14% Similarity=-0.011 Sum_probs=23.7
Q ss_pred HHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 98 QARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 98 ~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
.++-..|+|.+|+|+.+|+|.++|...-.
T Consensus 141 ~l~~~~g~s~~EIAe~lgis~~~V~~~l~ 169 (189)
T PRK06811 141 IRRYLLGEKIEEIAKKLGLTRSAIDNRLS 169 (189)
T ss_pred HHHHHccCCHHHHHHHHCCCHHHHHHHHH
Confidence 34445799999999999999999987643
No 480
>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=64.93 E-value=11 Score=31.57 Aligned_cols=34 Identities=15% Similarity=0.165 Sum_probs=29.0
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
...|.......+..+.+.|+.+|||++++.+..+
T Consensus 294 ~~~I~~aL~~~~gn~~~aA~~LGisr~tL~rklk 327 (329)
T TIGR02974 294 IELLQQALAEAQFNQRKAAELLGLTYHQLRGLLR 327 (329)
T ss_pred HHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence 5567778888899999999999999999987643
No 481
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=64.76 E-value=20 Score=28.13 Aligned_cols=25 Identities=12% Similarity=0.104 Sum_probs=22.1
Q ss_pred cCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 102 DKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 102 ~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
..|+|.+|+|+.+++|++||..+-+
T Consensus 146 AqGkTnKEIAe~L~IS~rTVkth~s 170 (198)
T PRK15201 146 ASGYHLSETAALLSLSEEQTKSLRR 170 (198)
T ss_pred HCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 4699999999999999999988754
No 482
>TIGR00637 ModE_repress ModE molybdate transport repressor domain. ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.
Probab=64.66 E-value=16 Score=25.29 Aligned_cols=31 Identities=19% Similarity=0.170 Sum_probs=23.3
Q ss_pred CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 031871 106 TQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 147 (151)
Q Consensus 106 TQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l 147 (151)
|....|+.+|+|++++++- +..|.+.||+++
T Consensus 18 Sis~AA~~L~iS~stvs~~-----------I~~LE~~lg~~L 48 (99)
T TIGR00637 18 SISQAAKDAGISYKSAWDY-----------IRAMNNLSGEPL 48 (99)
T ss_pred CHHHHHHHHCCCHHHHHHH-----------HHHHHHHhCCCe
Confidence 6778899999999999874 455566666554
No 483
>PRK15482 transcriptional regulator MurR; Provisional
Probab=64.59 E-value=6.6 Score=31.72 Aligned_cols=34 Identities=9% Similarity=0.128 Sum_probs=26.5
Q ss_pred hcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHH
Q 031871 101 NDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQ 134 (151)
Q Consensus 101 ~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~ 134 (151)
.-..+|..+||+++|+|++||.++-+--..-...
T Consensus 31 ~v~~~si~elA~~~~vS~aTv~Rf~kkLGf~Gf~ 64 (285)
T PRK15482 31 ELKSVSSRKMAKQLGISQSSIVKFAQKLGAQGFT 64 (285)
T ss_pred HHHhcCHHHHHHHhCCCHHHHHHHHHHhCCCCHH
Confidence 3357899999999999999999997744444433
No 484
>PHA02535 P terminase ATPase subunit; Provisional
Probab=64.56 E-value=13 Score=33.80 Aligned_cols=37 Identities=14% Similarity=0.188 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcC
Q 031871 90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESG 127 (151)
Q Consensus 90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G 127 (151)
.+|....+.+-.+ |+|..++|+.+|+++++|..|-.-
T Consensus 5 ~EfK~~Av~Ly~~-G~sv~eIA~~LGv~~~Tl~~W~kr 41 (581)
T PHA02535 5 DDVRRAAKFLYWQ-GWTVAEIAEELGLKSRTIYSWKER 41 (581)
T ss_pred HHHHHHHHHHHHc-CCCHHHHHHHhCCChhHHHHHhcc
Confidence 3455555555555 999999999999999999999653
No 485
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=64.41 E-value=13 Score=29.11 Aligned_cols=24 Identities=21% Similarity=0.306 Sum_probs=21.7
Q ss_pred CCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 103 KKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 103 ~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
.|+|.+|+|+.+|+|.++|.....
T Consensus 197 eg~s~~EIA~~Lgis~~tV~~~l~ 220 (234)
T TIGR02835 197 TEKTQKEVADMLGISQSYISRLEK 220 (234)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Confidence 689999999999999999987753
No 486
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=64.34 E-value=8.2 Score=30.08 Aligned_cols=25 Identities=12% Similarity=0.222 Sum_probs=21.7
Q ss_pred cCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 102 DKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 102 ~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
..|+|.+|+|+.+++|..||..+-.
T Consensus 147 ~~G~snkeIA~~L~iS~~TV~~h~~ 171 (207)
T PRK11475 147 SRGYSMPQIAEQLERNIKTIRAHKF 171 (207)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3699999999999999999887643
No 487
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=64.18 E-value=6.9 Score=30.29 Aligned_cols=22 Identities=14% Similarity=0.175 Sum_probs=19.5
Q ss_pred CcCHHHHHHHhCCCHHHHHHHH
Q 031871 104 KLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 104 glTQ~eLA~~lgis~s~Is~~E 125 (151)
.+|++++|..+|+++.+|+++-
T Consensus 173 ~~t~~~iA~~lG~tretvsR~l 194 (236)
T PRK09392 173 PYEKRVLASYLGMTPENLSRAF 194 (236)
T ss_pred eCCHHHHHHHhCCChhHHHHHH
Confidence 4678999999999999999964
No 488
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=64.16 E-value=7.3 Score=30.22 Aligned_cols=25 Identities=20% Similarity=0.283 Sum_probs=22.6
Q ss_pred cCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 102 DKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 102 ~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
..|+|.+++|+.+|+|+.||..+-+
T Consensus 176 ~~g~s~~eIA~~l~iS~~Tv~~~~~ 200 (239)
T PRK10430 176 DYEFSTDELANAVNISRVSCRKYLI 200 (239)
T ss_pred CCCcCHHHHHHHhCchHHHHHHHHH
Confidence 4899999999999999999998754
No 489
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=64.12 E-value=9.6 Score=31.32 Aligned_cols=27 Identities=15% Similarity=0.313 Sum_probs=23.8
Q ss_pred cCCcCHHHHHHHhCCCHHHHHHHHcCC
Q 031871 102 DKKLTQSQLAQLINEKPQVIQEYESGK 128 (151)
Q Consensus 102 ~~glTQ~eLA~~lgis~s~Is~~E~G~ 128 (151)
..||...++|+++|||+.+|..|-+-.
T Consensus 17 l~gmk~~dIAeklGvspntiksWKrr~ 43 (279)
T COG5484 17 LKGMKLKDIAEKLGVSPNTIKSWKRRD 43 (279)
T ss_pred HhhccHHHHHHHhCCChHHHHHHHHhc
Confidence 357999999999999999999997744
No 490
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=64.03 E-value=6.5 Score=31.79 Aligned_cols=34 Identities=6% Similarity=0.053 Sum_probs=26.8
Q ss_pred cCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH
Q 031871 102 DKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQI 135 (151)
Q Consensus 102 ~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~ 135 (151)
-..+|..+||+.+|+|++||.++-+--..-....
T Consensus 44 v~~~si~~lA~~~~vS~aTi~Rf~kkLGf~gf~e 77 (292)
T PRK11337 44 SEATALKDIAEALAVSEAMIVKVAKKLGFSGFRN 77 (292)
T ss_pred HHhcCHHHHHHHhCCChHHHHHHHHHcCCCCHHH
Confidence 3568999999999999999999987554444433
No 491
>PRK15043 transcriptional regulator MirA; Provisional
Probab=63.98 E-value=18 Score=29.38 Aligned_cols=65 Identities=15% Similarity=0.180 Sum_probs=39.3
Q ss_pred HHHHHHHcCCChhhHHhhhc--CCCccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHH
Q 031871 31 VVNAARRAGADIETVRKSHA--GTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQS 108 (151)
Q Consensus 31 ~~~~a~r~g~~v~t~~k~~~--g~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~ 108 (151)
.-+.|++.|++..|++.|+. |--.|..+.. .-+.-++ ++ -.--..|+.++ ..|++..
T Consensus 6 IgeVA~~~GVs~~TLR~wErr~GLL~P~Rt~~--G~R~Ys~--~d----------------v~rL~~I~~l~-~~G~~i~ 64 (243)
T PRK15043 6 IGEVALLCDINPVTLRAWQRRYGLLKPQRTDG--GHRLFND--AD----------------IDRIREIKRWI-DNGVQVS 64 (243)
T ss_pred HHHHHHHHCcCHHHHHHHHHhcCCCCCccCCC--CCEEECH--HH----------------HHHHHHHHHHH-HcCCCHH
Confidence 34689999999999999983 8776533211 1111111 11 12234455665 5789988
Q ss_pred HHHHHhCC
Q 031871 109 QLAQLINE 116 (151)
Q Consensus 109 eLA~~lgi 116 (151)
++...+.-
T Consensus 65 eIk~ll~~ 72 (243)
T PRK15043 65 KVKMLLSN 72 (243)
T ss_pred HHHHHHhc
Confidence 88877653
No 492
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=63.92 E-value=12 Score=29.08 Aligned_cols=39 Identities=10% Similarity=0.121 Sum_probs=31.2
Q ss_pred CcchHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871 86 DRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEY 124 (151)
Q Consensus 86 ~~~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~ 124 (151)
.....-+-+.+..++...+.|-.++|+++|++.+.|++.
T Consensus 9 ~~~~~lv~~~~~~l~~~~~~~a~~i~~~l~~~k~~vNr~ 47 (183)
T PHA03103 9 VDIYELVKKEVKNLGLGEGITAIEISRKLNIEKSEVNKQ 47 (183)
T ss_pred HHHHHHHHHHHHHhccCCCccHHHHHHHhCCCHHHHHHH
Confidence 333455666677788888899999999999999988875
No 493
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=63.82 E-value=1.6 Score=27.03 Aligned_cols=25 Identities=20% Similarity=0.246 Sum_probs=18.4
Q ss_pred HHHHHHHHHcCCChhhHHhhhcCCC
Q 031871 29 EKVVNAARRAGADIETVRKSHAGTN 53 (151)
Q Consensus 29 ~~~~~~a~r~g~~v~t~~k~~~g~~ 53 (151)
-+....|+++|++.+|+.+|-.|..
T Consensus 11 it~~~La~~~gis~~tl~~~~~~~~ 35 (63)
T PF13443_consen 11 ITQKDLARKTGISRSTLSRILNGKP 35 (63)
T ss_dssp --HHHHHHHHT--HHHHHHHHTTT-
T ss_pred CCHHHHHHHHCcCHHHHHHHHhccc
Confidence 3567899999999999999999873
No 494
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=63.81 E-value=12 Score=27.96 Aligned_cols=28 Identities=7% Similarity=0.062 Sum_probs=23.5
Q ss_pred HHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 98 QARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 98 ~~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
.++.-.|+|..|+|+.+|+|.++|...-
T Consensus 137 ~l~~~~g~s~~EIA~~l~is~~tv~~~l 164 (179)
T PRK09415 137 YLFYYEELSIKEIAEVTGVNENTVKTRL 164 (179)
T ss_pred HhHHhcCCCHHHHHHHHCCCHHHHHHHH
Confidence 3455679999999999999999998754
No 495
>PF03333 PapB: Adhesin biosynthesis transcription regulatory protein; InterPro: IPR004356 P pili, or fimbriae, are ~68A in diameter and 1 micron in length, the bulk of which is a fibre composed of the main structural protein PapA []. At its tip, the pilus is terminated by a fibrillum consisting of repeating units of the PapE protein. This, in turn, is topped by the adhesins, PapF and PapG, both of which are needed for receptor binding. The tip fibrillum is anchored to the main PapA fibre by the PapK pilus-adaptor protein. PapH, an outer membrane protein, then anchors the entire rod in the bacterial envelope []. A cytoplasmic chaperone (PapD) assists in assembling the monomers of the macromolecule in the membrane. All of the functional pap genes are arranged in a cluster (operon) on the Escherichia coli genome. It is believed that selective pressure exerted by the host's urinal and intestinal tract isoreceptors forced the spread of this operon to other strains via lateral transfer []. PapB, encoded within the cluster, acts as a transcriptional regulator of the functional pap genes and is located in the bacterial cytoplasm []. Its mechanism involves differential binding to separate sites in the cluster, suggesting that this protein is both an activator and repressor of pilus-adhesion transcription. The protein shares similarity with other E. coli fimbrial- adhesion transcription regulators, such as AfaA, DaaA and FanB. ; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 3M8J_A.
Probab=63.66 E-value=8.7 Score=26.57 Aligned_cols=22 Identities=5% Similarity=0.039 Sum_probs=15.2
Q ss_pred CCcCHHHHHHHhCCCHHHHHHH
Q 031871 103 KKLTQSQLAQLINEKPQVIQEY 124 (151)
Q Consensus 103 ~glTQ~eLA~~lgis~s~Is~~ 124 (151)
.|+++++.+++-||++++++.=
T Consensus 52 ~G~srkeac~~~gV~~syfs~~ 73 (91)
T PF03333_consen 52 DGLSRKEACERHGVNQSYFSRA 73 (91)
T ss_dssp T---HHHHHHHTT--HHHHHHH
T ss_pred cCCcHHHHHHHhCCCHHHHHHH
Confidence 5999999999999999998864
No 496
>PRK15115 response regulator GlrR; Provisional
Probab=63.35 E-value=10 Score=32.40 Aligned_cols=34 Identities=9% Similarity=-0.034 Sum_probs=27.9
Q ss_pred HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
...|.++..+.+..+.+.|+.+|||++|+.+-.+
T Consensus 400 ~~~i~~al~~~~gn~~~aA~~Lgisr~tL~rkl~ 433 (444)
T PRK15115 400 LNYLRKLLQITKGNVTHAARMAGRNRTEFYKLLS 433 (444)
T ss_pred HHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence 3456777777888999999999999999987654
No 497
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=63.30 E-value=13 Score=26.95 Aligned_cols=32 Identities=6% Similarity=0.086 Sum_probs=25.7
Q ss_pred HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871 94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 125 (151)
Q Consensus 94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E 125 (151)
..+-.++...|+|..++|+.+|+|..+|...-
T Consensus 118 r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l 149 (161)
T PRK12541 118 RNVLLLRDYYGFSYKEIAEMTGLSLAKVKIEL 149 (161)
T ss_pred HHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHH
Confidence 33445566789999999999999999987653
No 498
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=63.27 E-value=8.1 Score=30.11 Aligned_cols=26 Identities=15% Similarity=0.212 Sum_probs=22.7
Q ss_pred hcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871 101 NDKKLTQSQLAQLINEKPQVIQEYES 126 (151)
Q Consensus 101 ~~~glTQ~eLA~~lgis~s~Is~~E~ 126 (151)
...|+|-+|+|+++++|..||..+-+
T Consensus 160 la~G~snkeIA~~L~iS~~TVk~h~~ 185 (211)
T COG2197 160 LAEGLSNKEIAEELNLSEKTVKTHVS 185 (211)
T ss_pred HHCCCCHHHHHHHHCCCHhHHHHHHH
Confidence 35799999999999999999987754
No 499
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=63.13 E-value=15 Score=26.95 Aligned_cols=31 Identities=16% Similarity=0.229 Sum_probs=25.5
Q ss_pred HHHHHHH-hcCCcCHHHHHHHhCCCHHHHHHH
Q 031871 94 KAIVQAR-NDKKLTQSQLAQLINEKPQVIQEY 124 (151)
Q Consensus 94 ~~Lk~~R-~~~glTQ~eLA~~lgis~s~Is~~ 124 (151)
+.+..+. ....+|-.+||+.++.+++|+++-
T Consensus 31 ~v~~~LL~~~~~~tvdelae~lnr~rStv~rs 62 (126)
T COG3355 31 EVYKALLEENGPLTVDELAEILNRSRSTVYRS 62 (126)
T ss_pred HHHHHHHhhcCCcCHHHHHHHHCccHHHHHHH
Confidence 3445555 678899999999999999999875
No 500
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=63.11 E-value=5.9 Score=32.25 Aligned_cols=42 Identities=14% Similarity=0.184 Sum_probs=28.8
Q ss_pred cCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCH-HHHHHHHHHh
Q 031871 102 DKKLTQSQLAQLINEKPQVIQEYESGKAIPNQ-QILTKLERAL 143 (151)
Q Consensus 102 ~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~-~~l~kLa~~L 143 (151)
-..+|..|||+.+|||++||.++-+--..-.. +.-..|++.|
T Consensus 34 ~~~~si~elA~~a~VS~aTv~Rf~~kLGf~Gf~efk~~l~~~l 76 (281)
T COG1737 34 VALLSIAELAERAGVSPATVVRFARKLGFEGFSEFKLALAQEL 76 (281)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHHHcCCCCHHHHHHHHHHHH
Confidence 34589999999999999999999774433322 2233444444
Done!